JBPC Publications – 2019 and Prior

Top 25 Journals

Proc Natl Acad Sci U S A (56), ISME J (33), PLoS One (31), Appl Environ Microbiol (29), Environ Microbiol (26), Mol Biol Evol (24), Front Microbiol (21), Nucleic Acids Res (18), J Bacteriol (17), Biol Bull (17), Microbiome (15), Science (14), J Biol Chem (14), J Mol Biol (13), Nature (11), BMC Genomics (11), bioRxiv (10), J Eukaryot Microbiol (10), Genetics (10), mSystems (9), Hydrobiologia (9), European Journal of Protistology (9), MBio (8), Limnology and Oceanography (8), Gene (8)

Years

2019 (42) | 2018 (32) | 2017 (37) | 2016 (49) | 2015 (58) | 2014 (68) | 2013 (42) | 2012 (47) | 2011 (42) | 2010 (34) | 2009 (46) | 2008 (41) | 2007 (54) | 2006 (36) | 2005 (48) | 2004 (27) | 2003 (44) | 2002 (56) | 2001 (41) | 2000 (44) | 1999 (31) | 1998 (31) | 1997 (22) | 1996 (27)

2019

Antosca, K. M., Chernikova, D. A., Price, C. E., Ruoff, K. L., Li, K., Guill, M. F., Sontag, N. R., Morrison, H. G., Hao, S., Drumm, M. L., MacKenzie, T. A., Dorman, D. B., Feenan, L. M., Williams, M. A., Dessaint, J., Yuan, I. H., Aldrich, B. J., Moulton, L. A., Ting, L., Martinez-Del Campo, A., Stewart, E. J., Karagas, M. R., O’Toole, G. A., & Madan, J. C. (2019). “Altered Stool Microbiota of Infants with Cystic Fibrosis Shows a Reduction in Genera Associated with Immune Programming from Birth.” J Bacteriol, 201(16). doi:10.1128/JB.00274-1.

Arkhipova, I. R., & Yushenova, I. A. (2019). “Giant Transposons in Eukaryotes: Is Bigger Better?” Genome Biol Evol, 11(3), 906-918. doi:10.1093/gbe/evz04.

Bhatnagar, S., Cowley, E. S., Kopf, S. H., Castro, S. P., Kearney, S., Dawson, S. C., Hanselmann, K., & Ruff, S. E. (2019). “Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom.” bioRxiv, 604504. doi:10.1101/60450.

Blommaert, J., Riss, S., Hecox-Lea, B., Mark Welch, D. B., & Stelzer, C. P. (2019). “Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex.” BMC Genomics, 20(1), 466. doi:10.1186/s12864-019-5859-.

Bock, M. J., Jarvis, G. C., Corey, E. L., Stone, E. E., & Gribble, K. E. (2019). “Maternal age alters offspring lifespan, fitness, and lifespan extension under caloric restriction.” Sci Rep, 9(1), 3138. doi:10.1038/s41598-019-40011-.

Bono, L. M., Orton, R. J., Peredo, E. L., Morrison, H. G., Sistrom, M., Simmons, S., & Turner, P. E. (2019). “Spatiotemporal dynamics of RNA virus diversity in a phyllosphere microbial community.” bioRxiv, 772475. doi:10.1101/77247.

Cavicchioli, R., Ripple, W. J., Timmis, K. N., Azam, F., Bakken, L. R., Baylis, M., Behrenfeld, M. J., Boetius, A., Boyd, P. W., Classen, A. T., Crowther, T. W., Danovaro, R., Foreman, C. M., Huisman, J., Hutchins, D. A., Jansson, J. K., Karl, D. M., Koskella, B., Mark Welch, D. B., Martiny, J. B. H., Moran, M. A., Orphan, V. J., Reay, D. S., Remais, J. V., Rich, V. I., Singh, B. K., Stein, L. Y., Stewart, F. J., Sullivan, M. B., van Oppen, M. J. H., Weaver, S. C., Webb, E. A., & Webster, N. S. (2019). “Scientists’ warning to humanity: microorganisms and climate change.” Nat Rev Microbiol, 17(9), 569-586. doi:10.1038/s41579-019-0222-.

Coker, M. O., Hoen, A. G., Dade, E., Lundgren, S., Li, Z., Wong, A. D., Zens, M. S., Palys, T. J., Morrison, H. G., Sogin, M. L., Baker, E. R., Karagas, M. R., & Madan, J. C. (2019). “Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study.” BJOG, 0(0), 0. doi:10.1111/1471-0528.1579.

Cramm, M. A., Chakraborty, A., Li, C., Ruff, S. E., Jorgensen, B. B., & Hubert, C. R. J. (2019). “Freezing Tolerance of Thermophilic Bacterial Endospores in Marine Sediments.” Front Microbiol, 10, 945. doi:10.3389/fmicb.2019.0094.

Delmont, T. O., Kiefl, E., Kilinc, O., Esen, O. C., Uysal, I., Rappe, M. S., Giovannoni, S., & Eren, A. M. (2019). “Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade.” Elife, 8(ARTN e46497). doi:10.7554/eLife.4649.

Dobay, A., Haas, C., Fucile, G., Downey, N., Morrison, H. G., Kratzer, A., & Arora, N. (2019). “Microbiome-based body fluid identification of samples exposed to indoor conditions.” Forensic Sci Int Genet, 40, 105-113. doi:10.1016/j.fsigen.2019.02.01.

Ecklu-Mensah, G., Sackey, S. T., Morrison, H. G., Sogin, M. L., Murphy, L. G., & Reznikoff, W. S. (2019). “Assessment of bacterial diversity in western Accra, Ghana, drinking water samples.” Journal of Water, Sanitation and Hygiene for Development. doi:10.2166/washdev.2019.12.

Edsinger, E., Pnini, R., Ono, N., Yanagisawa, R., Dever, K., & Miller, J. (2019). “Social tolerance in Octopus laqueus – a maximal entropy model.” bioRxiv, 526905. doi:10.1101/52690.

Fiore-Donno, A. M., Richter-Heitmann, T., Degrune, F., Dumack, K., Regan, K., Mahran, S., Boeddinghaus, R., Rillig, M., Friedrich, M. W., Kandeler, E., & Bonkowski, M. (2019). “Environmental selection and spatiotemporal structure of a major group of soil protists (Rhizaria: Cercozoa) in a temperate grassland.” bioRxiv, 531970. doi:10.1101/53197.

Funikov, S. Y., Rezvykh, A. P., Kulikova, D. A., Zelentsova, E. S., Chuvakova, L. N., Tyukmaeva, V. I., Arkhipova, I. R., & Evgen’ev, M. B. (2019). “Insulator proteins contribute to expression of gene loci repositioned into heterochromatin in the course of Drosophila evolution.” bioRxiv, 802371. doi:10.1101/80237.

Goldmann, K., Boeddinghaus, R. S., Klemmer, S., Regan, K. M., Heintz-Buschart, A., Fischer, M., Prati, D., Piepho, H. P., Berner, D., Marhan, S., Kandeler, E., Buscot, F., & Wubet, T. (2019). “Unraveling spatiotemporal variability of arbuscular mycorrhizal fungi in a temperate grassland plot.” Environ Microbiol, 0(0). doi:10.1111/1462-2920.1465.

Gurdebeke, P. R., Mertens, K. N., Pospelova, V., Matsuoka, K., Li, Z., Gribble, K. E., Gu, H., Bogus, K., Vrielinck, H., & Louwye, S. (2019). “Taxonomic revision, phylogeny, and cyst wall composition of the dinoflagellate cyst genus Votadinium Reid (Dinophyceae, Peridiniales, Protoperidiniaceae).” Palynology, 1-26. doi:10.1080/01916122.2019.158062.

Han, M., Dsouza, M., Zhou, C., Li, H., Zhang, J., Chen, C., Yao, Q., Zhong, C., Zhou, H., Gilbert, J. A., Wang, Z., & Ning, K. (2019). “Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake.” Genomics Proteomics Bioinformatics, 17(1), 76-90. doi:10.1016/j.gpb.2018.04.00.

Hubbard, C. J., Li, B., McMinn, R., Brock, M. T., Maignien, L., Ewers, B. E., Kliebenstein, D., & Weinig, C. (2019). “The effect of rhizosphere microbes outweighs host plant genetics in reducing insect herbivory.” Mol Ecol, 28(7), 1801-1811. doi:10.1111/mec.1498.

Ivashkin, E., Melnikova, V., Kurtova, A., Brun, N. R., Obukhova, A., Khabarova, M. Y., Yakusheff, A., Adameyko, I., Gribble, K. E., & Voronezhskaya, E. E. (2019). “Transglutaminase Activity Determines Nuclear Localization of Serotonin Immunoreactivity in the Early Embryos of Invertebrates and Vertebrates.” ACS Chem Neurosci, 10(8), 3888-3899. doi:10.1021/acschemneuro.9b0034.

Lutz, H. L., Ramirez-Puebla, S. T., Abbo, L., Durand, A., Schlundt, C., Gottel, N. R., Sjaarda, A. K., Hanlon, R. T., Gilbert, J. A., & Mark Welch, J. L. (2019). “A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis.” mSystems, 4(4). doi:10.1128/mSystems.00177-1.

Mark Welch, J. L., Dewhirst, F. E., & Borisy, G. G. (2019). “Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis.” Annu Rev Microbiol, 73, 335-358. doi:10.1146/annurev-micro-090817-06250.

McKay, L. J., Dlakic, M., Fields, M. W., Delmont, T. O., Eren, A. M., Jay, Z. J., Klingelsmith, K. B., Rusch, D. B., & Inskeep, W. P. (2019). “Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota.” Nat Microbiol, 4(4), 614-622. doi:10.1038/s41564-019-0362-.

Mincer, T. J., Zettler, E. R., & Amaral-Zettler, L. A. (2019). “Biofilms on Plastic Debris and Their Influence on Marine Nutrient Cycling, Productivity, and Hazardous Chemical Mobility.” In H. Takada & H. K. Karapanagioti (Ed.), Hazardous Chemicals Associated with Plastics in the Marine Environment (pp. 221-233): Cham: Springer International Publishing.

Nedoluzhko, A. V., Sharko, F. S., Lê, B. M., Tsygankova, S. V., Boulygina, E. S., Rastorguev, S. M., Sokolov, A. S., Rodriguez, F., Mazur, A. M., Polilov, A. A., Benton, R., Evgen’ev, M. B., Arkhipova, I. R., Prokhortchouk, E. B., & Skryabin, K. G. (2019). “A draft genome sequence of the miniature parasitoid wasp, Megaphragma amalphitanum.” bioRxiv, 579052. doi:10.1101/57905.

Nissimov, J. I., Talmy, D., Haramaty, L., Fredricks, H. F., Zelzion, E., Knowles, B., Eren, A. M., Vandzura, R., Laber, C. P., Schieler, B. M., Johns, C. T., More, K. D., Coolen, M. J. L., Follows, M. J., Bhattacharya, D., Van Mooy, B. A. S., & Bidle, K. D. (2019). “Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology.” Environ Microbiol, 21(6), 2182-2197. doi:10.1111/1462-2920.1463.

Peramba, K. B., & Edsinger, E. (2019). “Imaging the neuromuscular systems of cephalopod arms and suckers.” Paper presented at the Annual Meeting of the Society for Integrative and Comparative Biology, Tampa, FL.

Peramba, K. B., Nash, C., Walters, D., Hackworth, L., Schumm, M., Pineda, O., & Edsinger, E. (2019). “Squid Monday: Characterizing population structure in Doryteuthis pealeii.” Paper presented at the Annual Meeting of the Society for Integrative and Comparative Biology, Tampa, FL.

Perez Castro, S., Cleland, E. E., Wagner, R., Sawad, R. A., & Lipson, D. A. (2019). “Soil microbial responses to drought and exotic plants shift carbon metabolism.” ISME J, 13(7), 1776-1787. doi:10.1038/s41396-019-0389-.

Puritty, C. E., Esch, E. H., Castro, S. P., Ryan, E. M., Lipson, D. A., & Cleland, E. E. (2019). “Drought in Southern California coastal sage scrub reduces herbaceous biomass of exotic species more than native species, but exotic growth recovers quickly when drought ends.” Plant Ecology, 220(2), 151-169. doi:10.1007/s11258-019-00912-.

Reveillaud, J., Bordenstein, S. R., Cruaud, C., Shaiber, A., Esen, O. C., Weill, M., Makoundou, P., Lolans, K., Watson, A. R., Rakotoarivony, I., Bordenstein, S. R., & Eren, A. M. (2019). “The Wolbachia mobilome in Culex pipiens includes a putative plasmid.” Nat Commun, 10(1), 1051. doi:10.1038/s41467-019-08973-.

Richter, N., Longo, W. M., George, S., Shipunova, A., Huang, Y., & Amaral-Zettler, L. (2019). “Phylogenetic diversity in freshwater-dwelling Isochrysidales haptophytes with implications for alkenone production.” Geobiology, 17(3), 272-280. doi:10.1111/gbi.1233.

Rossetti, B. J., Wilbert, S. A., Mark Welch, J. L., Borisy, G. G., & Nagy, J. G. (2019). “Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs.” bioRxiv, 674. doi:10.1093/bioinformatics/btz67.

Ruff, S. E. (2019). “Microbial communities and metabolisms at hydrocarbon seeps.” In A. Teske & V. Carvalho (Ed.), Marine Hydrocarbon Seeps – Microbiology and Biogeochemistry of a Global Marine Habitat (pp. 280): Springer.

Ruff, S. E., Felden, J., Gruber-Vodicka, H. R., Marcon, Y., Knittel, K., Ramette, A., & Boetius, A. (2019). “In situ development of a methanotrophic microbiome in deep-sea sediments.” ISME J, 13(1), 197-213. doi:10.1038/s41396-018-0263-.

Sevillano, M., Dai, Z., Calus, S., Bautista-de los Santos, Q. M., Eren, A. M., van der Wielen, P. W. J. J., Ijaz, U. Z., & Pinto, A. J. (2019). “Disinfectant residuals in drinking water systems select for mycobacterial populations with intrinsic antimicrobial resistance.” bioRxiv, 675561. doi:10.1101/67556.

Shaiber, A., & Eren, A. M. (2019). “Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories.” MBio, 10(3), e00725-00719. doi:10.1128/mBio.00725-1.

Theroux, S., Huang, Y. S., Toney, J. L., Andersen, R., Nyren, P., Bohn, R., Salacup, J., Murphy, L., & Amaral-Zettler, L. (2019). “Successional blooms of alkenone-producing haptophytes in Lake George, North Dakota: Implications for continental paleoclimate reconstructions.” Limnology and Oceanography, 0(0), 11311. doi:10.1002/lno.1131.

Trigodet, F., Larche, N., Morrison, H. G., Jebbar, M., Thierry, D., & Maignien, L. (2019). “Electroactive Bacteria Associated With Stainless Steel Ennoblement in Seawater.” Front Microbiol, 10, 170. doi:10.3389/fmicb.2019.0017.

Trigodet, F., Larché, N., Morrison, H. G., Maignien, L., & Thierry, D. (2019). “Influence of dissolved oxygen content on the bacteria‐induced ennoblement of stainless steels in seawater and its consequence on the localized corrosion risk.” Materials and Corrosion, 0(0). doi:10.1002/maco.20191122.

Watterson, W. J., Tanyeri, M., Watson, A. R., Cham, C. M., Shan, Y., Chang, E. B., Eren, A. M., & Tay, S. (2019). “High-throughput isolation and sorting of gut microbes reduce biases of traditional cultivation strategies.” bioRxiv, 759969. doi:10.1101/75996.

Yeoman, C. J., Brutscher, L. M., Esen, O. C., Ibaoglu, F., Fowler, C., Eren, A. M., Wanner, K., & Weaver, D. K. (2019). “Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus).” PeerJ, 7, e7548. doi:10.7717/peerj.754.

2018

Abrams, J. M., Arkhipova, I. R., Belfort, M., Boeke, J. D., Joan Curcio, M., Faulkner, G. J., Goodier, J. L., Lehmann, R., & Levin, H. L. (2018). “Meeting report: mobile genetic elements and genome plasticity 2018.” Mob DNA, 9(ARTN 21), 21. doi:10.1186/s13100-018-0126-.

Amaral-Zettler, L. A., Schmidt, V., & Smith, K. F. (2018). “Microbial Community and Potential Pathogen Shifts Along an Ornamental Fish Supply Chain.” Microorganisms, 6(3). doi:10.3390/microorganisms603009.

Arkhipova, I. R. (2018). “Neutral Theory, Transposable Elements, and Eukaryotic Genome Evolution.” Mol Biol Evol, 35(6), 1332-1337. doi:10.1093/molbev/msy08.

Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., Eloe-Fadrosh, E. A., Tringe, S. G., Ivanova, N. N., Copeland, A., Clum, A., Becraft, E. D., Malmstrom, R. R., Birren, B., Podar, M., Bork, P., Weinstock, G. M., Garrity, G. M., Dodsworth, J. A., Yooseph, S., Sutton, G., Glockner, F. O., Gilbert, J. A., Nelson, W. C., Hallam, S. J., Jungbluth, S. P., Ettema, T. J. G., Tighe, S., Konstantinidis, K. T., Liu, W. T., Baker, B. J., Rattei, T., Eisen, J. A., Hedlund, B., McMahon, K. D., Fierer, N., Knight, R., Finn, R., Cochrane, G., Karsch-Mizrachi, I., Tyson, G. W., Rinke, C., Genome Standards, C., Lapidus, A., Meyer, F., Yilmaz, P., Parks, D. H., Eren, A. M., Schriml, L., Banfield, J. F., Hugenholtz, P., & Woyke, T. (2018). “Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.” Nat Biotechnol, 36(2), 196. doi:10.1038/nbt0218-196.

Burnett, K., Edsinger, E., & Albrecht, D. R. (2018). “Rapid and gentle hydrogel encapsulation of living organisms enables long-term microscopy over multiple hours.” Commun Biol, 1(1), 73. doi:10.1038/s42003-018-0079-.

Chafee, M., Fernandez-Guerra, A., Buttigieg, P. L., Gerdts, G., Eren, A. M., Teeling, H., & Amann, R. I. (2018). “Recurrent patterns of microdiversity in a temperate coastal marine environment.” ISME J, 12(1), 237-252. doi:10.1038/ismej.2017.16.

Chernikova, D. A., Madan, J. C., Housman, M. L., Zain-Ul-Abideen, M., Lundgren, S. N., Morrison, H. G., Sogin, M. L., Williams, S. M., Moore, J. H., Karagas, M. R., & Hoen, A. G. (2018). “The premature infant gut microbiome during the first 6 weeks of life differs based on gestational maturity at birth.” Pediatr Res, 84(1), 71-79. doi:10.1038/s41390-018-0022-.

Crognale, S., Venturi, S., Tassi, F., Rossetti, S., Rashed, H., Cabassi, J., Capecchiacci, F., Nisi, B., Vaselli, O., Morrison, H. G., Sogin, M. L., & Fazi, S. (2018). “Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of the Solfatara Crater (Campi Flegrei, southern Italy).” FEMS Microbiol Ecol, 94(12), fiy190-fiy190. doi:10.1093/femsec/fiy19.

Delmont, T. O., & Eren, A. M. (2018). “Linking pangenomes and metagenomes: the Prochlorococcus metapangenome.” PeerJ, 6(ARTN e4320), e4320. doi:10.7717/peerj.432.

Delmont, T. O., Quince, C., Shaiber, A., Esen, O. C., Lee, S. T., Rappe, M. S., McLellan, S. L., Lucker, S., & Eren, A. M. (2018). “Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.” Nat Microbiol, 3(7), 804-813. doi:10.1038/s41564-018-0176-.

Dever, K., Carr, J., Girard, J., Calzarette, D., Remsen, D., Gage, G., Chugunov, I., Weissbourd, B., Cordeiro, M., Miao, J., Marvel-Zuccola, J., Newstein, P., Peramba, K., & Edsinger, E. (2018). “Octocams: A simple scalable system for short-term to lifecycle monitoring of behavior in aquaria.” Paper presented at the Annual Meeting of the Society for Integrative and Comparative Biology, San Francisco, CA.

Edsinger, E., & Dolen, G. (2018). “A Conserved Role for Serotonergic Neurotransmission in Mediating Social Behavior in Octopus.” Curr Biol, 28(19), 3136-3142 e3134. doi:10.1016/j.cub.2018.07.06.

Frere, L., Maignien, L., Chalopin, M., Huvet, A., Rinnert, E., Morrison, H., Kerninon, S., Cassone, A. L., Lambert, C., Reveillaud, J., & Paul-Pont, I. (2018). “Microplastic bacterial communities in the Bay of Brest: Influence of polymer type and size.” Environ Pollut, 242(Pt A), 614-625. doi:10.1016/j.envpol.2018.07.02.

Gilbert, J. A. (2018). “Early-Career Systems Microbiology Scientists.” mSystems, 3(2). doi:10.1128/mSystems.00002-1.

Grahl, N., Dolben, E. L., Filkins, L. M., Crocker, A. W., Willger, S. D., Morrison, H. G., Sogin, M. L., Ashare, A., Gifford, A. H., Jacobs, N. J., Schwartzman, J. D., & Hogan, D. A. (2018). “Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA.” mSphere, 3(4). doi:10.1128/mSphere.00292-1.

Gribble, K. E., Moran, B. M., Jones, S., Corey, E. L., & Mark Welch, D. B. (2018). “Congeneric variability in lifespan extension and onset of senescence suggest active regulation of aging in response to low temperature.” Exp Gerontol, 114, 99-106. doi:10.1016/j.exger.2018.10.02.

Hecox-Lea, B. J., & Mark Welch, D. B. (2018). “Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers.” BMC Evol Biol, 18(1), 177. doi:10.1186/s12862-018-1288-.

Hoen, A. G., Madan, J. C., Li, Z., Coker, M., Lundgren, S. N., Morrison, H. G., Palys, T., Jackson, B. P., Sogin, M. L., Cottingham, K. L., & Karagas, M. R. (2018). “Sex-specific associations of infants’ gut microbiome with arsenic exposure in a US population.” Sci Rep, 8(1), 12627. doi:10.1038/s41598-018-30581-.

Hubbard, C. J., Brock, M. T., van Diepen, L. T., Maignien, L., Ewers, B. E., & Weinig, C. (2018). “The plant circadian clock influences rhizosphere community structure and function.” ISME J, 12, 400-410.

Kroeger, M. E., Delmont, T. O., Eren, A. M., Meyer, K. M., Guo, J., Khan, K., Rodrigues, J. L. M., Bohannan, B. J. M., Tringe, S. G., Borges, C. D., Tiedje, J. M., Tsai, S. M., & Nusslein, K. (2018). “New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes.” Front Microbiol, 9(ARTN 1635), 1635. doi:10.3389/fmicb.2018.0163.

Lang, J. M., Coil, D. A., Neches, R. Y., Brown, W. E., Cavalier, D., Severance, M., Hampton-Marcell, J. T., Gilbert, J. A., & Eisen, J. A. (2018). “Correction: A microbial survey of the International Space Station (ISS).” PeerJ, 5. doi:10.7717/peerj.4029/correction-.

Lundgren, S. N., Madan, J. C., Emond, J. A., Morrison, H. G., Christensen, B. C., Karagas, M. R., & Hoen, A. G. (2018). “Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner.” Microbiome, 6(1), 109. doi:10.1186/s40168-018-0490-.

McIntosh, C. M., Chen, L., Shaiber, A., Eren, A. M., & Alegre, M. L. (2018). “Gut microbes contribute to variation in solid organ transplant outcomes in mice.” Microbiome, 6(1), 96. doi:10.1186/s40168-018-0474-.

Meisel, M., Hinterleitner, R., Pacis, A., Chen, L., Earley, Z. M., Mayassi, T., Pierre, J. F., Ernest, J. D., Galipeau, H. J., Thuille, N., Bouziat, R., Buscarlet, M., Ringus, D. L., Wang, Y., Li, Y., Dinh, V., Kim, S. M., McDonald, B. D., Zurenski, M. A., Musch, M. W., Furtado, G. C., Lira, S. A., Baier, G., Chang, E. B., Eren, A. M., Weber, C. R., Busque, L., Godley, L. A., Verdu, E. F., Barreiro, L. B., & Jabri, B. (2018). “Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host.” Nature, 557(7706), 580-584. doi:10.1038/s41586-018-0125-.

Peñalver Bernabé, B., Cralle, L., & Gilbert, J. A. (2018). “Systems biology of the human microbiome.” Curr Opin Biotechnol, 51, 146-153. doi:10.1016/j.copbio.2018.01.01.

Quigley, C. T. C., Morrison, H. G., Mendonca, I. R., & Brawley, S. H. (2018). “A common garden experiment with Porphyra umbilicalis (Rhodophyta) evaluates methods to study spatial differences in the macroalgal microbiome.” J Phycol, 54(5), 653-664. doi:10.1111/jpy.1276.

Rodriguez, F., & Arkhipova, I. R. (2018). “Transposable elements and polyploid evolution in animals.” Curr Opin Genet Dev, 49, 115-123. doi:10.1016/j.gde.2018.04.00.

Seyler, L. M., McGuinness, L. R., Gilbert, J. A., Biddle, J. F., Gong, D., & Kerkhof, L. J. (2018). “Discerning autotrophy, mixotrophy and heterotrophy in marine TACK archaea from the North Atlantic.” FEMS Microbiol Ecol, 94(3). doi:10.1093/femsec/fiy01.

Sheik, C. S., Reese, B. K., Twing, K. I., Sylvan, J. B., Grim, S. L., Schrenk, M. O., Sogin, M. L., & Colwell, F. S. (2018). “Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.” Front Microbiol, 9(ARTN 840), 840. doi:10.3389/fmicb.2018.0084.

Vakhrusheva, O. A., Mnatsakanova, E. A., Galimov, Y. R., Neretina, T. V., Gerasimov, E. S., Ozerova, S. G., Zalevsky, A. O., Yushenova, I. A., Arkhipova, I. R., Penin, A. A., Logacheva, M. D., Bazykin, G. A., & Kondrashov, A. S. (2018). “Recombination in a natural population of the bdelloid rotifer Adineta vaga.” bioRxiv, 489393. doi:10.1101/48939.

Yushenova, I. A., & Arkhipova, I. R. (2018). “Biochemical properties of bacterial reverse transcriptase-related (rvt) gene products: multimerization, protein priming, and nucleotide preference.” Curr Genet, 64(6), 1287-1301. doi:10.1007/s00294-018-0844-.

Zhang, X., Xia, K., Lin, L., Zhang, F., Yu, Y., St Ange, K., Han, X., Edsinger, E., Sohn, J., & Linhardt, R. J. (2018). “Structural and Functional Components of the Skate Sensory Organ Ampullae of Lorenzini.” ACS Chem Biol, 13(6), 1677-1685. doi:10.1021/acschembio.8b0033.

2017

Amaral-Zettler, L. A., Dragone, N. B., Schell, J., Slikas, B., Murphy, L. G., Morrall, C. E., & Zettler, E. R. (2017). “Comparative mitochondrial and chloroplast genomics of a genetically distinct form of Sargassum contributing to recent “Golden Tides” in the Western Atlantic.” Ecol Evol, 7(2), 516-525. doi:10.1002/ece3.263.

Anderson, R. E., Reveillaud, J., Reddington, E., Delmont, T. O., Eren, A. M., McDermott, J. M., Seewald, J. S., & Huber, J. A. (2017). “Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents.” Nat Commun, 8(1), 1114. doi:10.1038/s41467-017-01228-.

Arkhipova, I. R., Yushenova, I. A., & Rodriguez, F. (2017). “Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres.” Mol Biol Evol, 34(9), 2245-2257. doi:10.1093/molbev/msx15.

Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., Eloe-Fadrosh, E. A., Tringe, S. G., Ivanova, N. N., Copeland, A., Clum, A., Becraft, E. D., Malmstrom, R. R., Birren, B., Podar, M., Bork, P., Weinstock, G. M., Garrity, G. M., Dodsworth, J. A., Yooseph, S., Sutton, G., Glockner, F. O., Gilbert, J. A., Nelson, W. C., Hallam, S. J., Jungbluth, S. P., Ettema, T. J. G., Tighe, S., Konstantinidis, K. T., Liu, W. T., Baker, B. J., Rattei, T., Eisen, J. A., Hedlund, B., McMahon, K. D., Fierer, N., Knight, R., Finn, R., Cochrane, G., Karsch-Mizrachi, I., Tyson, G. W., Rinke, C., Lapidus, A., Meyer, F., Yilmaz, P., Parks, D. H., Eren, A. M., Schriml, L., Banfield, J. F., Hugenholtz, P., Woyke, T., & Consortium, G. S. (2017). “Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.” Nature Biotechnology, 35(8), 725-731. doi:10.1038/nbt.389.

Bowman, J. S., Amaral-Zettler, L. A., J, J. R., C, M. L., & Ducklow, H. W. (2017). “Bacterial community segmentation facilitates the prediction of ecosystem function along the coast of the western Antarctic Peninsula.” ISME J, 11(6), 1460-1471. doi:10.1038/ismej.2016.20.

Courtine, D., Alain, K., Georges, M., Bienvenu, N., Morrison, H. G., Eren, A. M., & Maignien, L. (2017). “Complete Genome Sequence of Hyperthermophilic Archaeon Thermococcus sp.” EXT12c, Isolated from the East Pacific Rise 9 degrees N. Genome Announc, 5(50). doi:10.1128/genomeA.01385-1.

De Tender, C., Schlundt, C., Devriese, L. I., Mincer, T. J., Zettler, E. R., & Amaral-Zettler, L. A. (2017). “A review of microscopy and comparative molecular-based methods to characterize “Plastisphere” communities.” Analytical Methods, 9(14), 2132-2143. doi:10.1039/c7ay00260.

Delmont, T. O., & Eren, A. M. (2017). “Simulations predict microbial responses in the environment? This environment disagrees retrospectively.” Proc Natl Acad Sci U S A, 114(43), E8947-E8949. doi:10.1073/pnas.171218611.

Devetter, M., Fontaneto, D., Jersabek, C. D., Mark Welch, D. B., May, L., & Walsh, E. J. (2017). “Preface: evolving rotifers, evolving science Proceedings of the XIV International Rotifer Symposium.” Hydrobiologia, 796(1), 1-6. doi:10.1007/s10750-017-3241-.

Doherty, M., Yager, P. L., Moran, M. A., Coles, V. J., Fortunato, C. S., Krusche, A. V., Medeiros, P. M., Payet, J. P., Richey, J. E., Satinsky, B. M., Sawakuchi, H. O., Ward, N. D., & Crump, B. C. (2017). “Bacterial Biogeography across the Amazon River-Ocean Continuum.” Front Microbiol, 8, 882. doi:10.3389/fmicb.2017.0088.

Fan, K. K., Cardona, C., Li, Y. T., Shi, Y., Xiang, X. J., Shen, C. C., Wang, H. F., Gilbert, J. A., & Chu, H. Y. (2017). “Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields.” Soil Biology & Biochemistry, 113(Supplement C), 275-284. doi:10.1016/j.soilbio.2017.06.02.

Franco-Obregon, A., & Gilbert, J. A. (2017). “The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals.” mSystems, 2(3). doi:10.1128/mSystems.00018-1.

Gibbons, S. M., Lekberg, Y., Mummey, D. L., Sangwan, N., Ramsey, P. W., & Gilbert, J. A. (2017). “Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem.” mSystems, 2(2). doi:10.1128/mSystems.00178-1.

Gilbert, J. A. (2017). “How do we make indoor environments and healthcare settings healthier?” Microb Biotechnol, 10(1), 11-13. doi:10.1111/1751-7915.1243.

Gribble, K. E., & Mark Welch, D. B. (2017). “Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system.” BMC Genomics, 18(1), 217. doi:10.1186/s12864-017-3540-.

Hasegawa, Y., Mark Welch, J. L., Rossetti, B. J., & Borisy, G. G. (2017). “Preservation of three-dimensional spatial structure in the gut microbiome.” PLoS One, 12(11), e0188257. doi:10.1371/journal.pone.018825.

Herfort, L., Crump, B. C., Fortunato, C. S., McCue, L. A., Campbell, V., Simon, H. M., Baptista, A. M., & Zuber, P. (2017). “Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima.” Microbiologyopen, 6(6), e00522-n/a. doi:10.1002/mbo3.52.

Huang, Y., Dalal, S., Antonopoulos, D., Hubert, N., Raffals, L. H., Dolan, K., Weber, C., Messer, J. S., Jabri, B., Bendelac, A., Eren, A. M., Rubin, D. T., Sogin, M., & Chang, E. B. (2017). “Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis.” Inflamm Bowel Dis, 23(3), 366-378. doi:10.1097/MIB.000000000000102.

Knight, R., Callewaert, C., Marotz, C., Hyde, E. R., Debelius, J. W., McDonald, D., & Sogin, M. L. (2017). “The Microbiome and Human Biology.” Annu Rev Genomics Hum Genet, 18, 65-86. doi:10.1146/annurev-genom-083115-02243.

Kumar, R., Verma, H., Haider, S., Bajaj, A., Sood, U., Ponnusamy, K., Nagar, S., Shakarad, M. N., Negi, R. K., Singh, Y., Khurana, J. P., Gilbert, J. A., & Lal, R. (2017). “Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium.” mSystems, 2(3). doi:10.1128/mSystems.00020-1.

Kuntz, T. M., & Gilbert, J. A. (2017). “Introducing the Microbiome into Precision Medicine.” Trends Pharmacol Sci, 38(1), 81-91. doi:10.1016/j.tips.2016.10.00.

Lee, S. T. M., Kahn, S. A., Delmont, T. O., Shaiber, A., Esen, O. C., Hubert, N. A., Morrison, H. G., Antonopoulos, D. A., Rubin, D. T., & Eren, A. M. (2017). “Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics.” Microbiome, 5(1), 50. doi:10.1186/s40168-017-0270-.

Luria, C. M., Amaral-Zettler, L. A., Ducklow, H. W., Repeta, D. J., Rhyne, A., & Rich, J. J. (2017). “Seasonal shifts in bacterial community responses to phytoplankton-derived dissolved organic matter in the Western Antarctic Peninsula.” Frontiers in Microbiology-Aquatic Microbiology, 8, 2117.

Ma, B., Dai, Z., Wang, H., Dsouza, M., Liu, X., He, Y., Wu, J., Rodrigues, J. L., Gilbert, J. A., Brookes, P. C., & Xu, J. (2017). “Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China.” mSystems, 2(1). doi:10.1128/mSystems.00174-1.

Mackey, K. R. M., Hunter-Cevera, K., Britten, G. L., Murphy, L. G., Sogin, M. L., & Huber, J. A. (2017). “Seasonal Succession and Spatial Patterns of Synechococcus Microdiversity in a Salt Marsh Estuary Revealed through 16S rRNA Gene Oligotyping.” Front Microbiol, 8, 1496. doi:10.3389/fmicb.2017.0149.

Mark Welch, D. B., Jauch, A., Langowski, J., Olins, A. L., & Olins, D. E. (2017). “Transcriptomes reflect the phenotypes of undifferentiated, granulocyte and macrophage forms of HL-60/S4 cells.” Nucleus, 8(2), 222-237. doi:10.1080/19491034.2017.128598.

Mark Welch, J. L., Hasegawa, Y., McNulty, N. P., Gordon, J. I., & Borisy, G. G. (2017). “Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice.” Proc Natl Acad Sci U S A, 114(43), E9105-E9114. doi:10.1073/pnas.171159611.

Perez, T., Rodriguez, F., Fernandez, M., Albornoz, J., & Dominguez, A. (2017). “Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus.” Gene, 628(Supplement C), 63-71. doi:10.1016/j.gene.2017.07.03.

Quince, C., Delmont, T. O., Raguideau, S., Alneberg, J., Darling, A. E., Collins, G., & Eren, A. M. (2017). “DESMAN: a new tool for de novo extraction of strains from metagenomes.” Genome Biol, 18(1), 181. doi:10.1186/s13059-017-1309-.

Rodriguez, F., Kenefick, A. W., & Arkhipova, I. R. (2017). “LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types.” Viruses, 9(4). doi:10.3390/v904007.

Schmidt, V., Gomez-Chiarri, M., Roy, C., Smith, K., & Amaral-Zettler, L. A. (2017). “Subtle Microbiome Manipulation Using Probiotics Reduces Antibiotic-Associated Mortality in Fish.” Msystems, 2(6). doi:UNSP e00133-17 10.1128/mSystems.00133-1.

Smith, M. W., Herfort, L., Fortunato, C. S., Crump, B. C., & Simon, H. M. (2017). “Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary.” Microbiologyopen, 6(4). doi:10.1002/mbo3.46.

Stellato, G., Utter, D. R., Voorhis, A., De Angelis, M., Eren, A. M., & Ercolini, D. (2017). “A Few Pseudomonas Oligotypes Dominate in the Meat and Dairy Processing Environment.” Front Microbiol, 8, 264. doi:10.3389/fmicb.2017.0026.

Sylvan, J. B., Wankel, S. D., LaRowe, D. E., Charoenpong, C. N., Huber, J. A., Moyer, C. L., & Edwards, K. J. (2017). “Evidence for microbial mediation of subseafloor nitrogen redox processes at Loihi Seamount, Hawaii.” Geochimica Et Cosmochimica Acta, 198, 131-150. doi:10.1016/j.gca.2016.10.02.

Teif, V. B., Mallm, J. P., Sharma, T., Mark Welch, D. B., Rippe, K., Eils, R., Langowski, J., Olins, A. L., & Olins, D. E. (2017). “Nucleosome repositioning during differentiation of a human myeloid leukemia cell line.” Nucleus, 8(2), 188-204. doi:10.1080/19491034.2017.129520.

Wilbert, S. A., Mark Welch, J. L., Dewhirst, F. E., & Borisy, G. G. (2017). “Spatial organization of the human tongue dorsum microbiome at the micron scale.” Paper presented at the ASCB/EMBO Meeting, Philadelphia, PA.

Zettler, E. R., Takada, H., Monteleone, B., Mallos, N., Eriksen, M., & Amaral-Zettler, L. A. (2017). “Incorporating citizen science to study plastics in the environment.” Analytical Methods, 9(9), 1392-1403. doi:10.1039/c6ay02716.

2016

Arkhipova, I. R., & Rice, P. A. (2016). “Mobile genetic elements: in silico, in vitro, in vivo.” Mol Ecol, 25(5), 1027-1031. doi:10.1111/mec.1354.

Balint, M., Bahram, M., Eren, A. M., Faust, K., Fuhrman, J. A., Lindahl, B., O’Hara, R. B., Opik, M., Sogin, M. L., Unterseher, M., & Tedersoo, L. (2016). “Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.” FEMS Microbiol Rev, 40(5), 686-700. doi:10.1093/femsre/fuw01.

Britstein, M., Devescovi, G., Handley, K. M., Malik, A., Haber, M., Saurav, K., Teta, R., Costantino, V., Burgsdorf, I., Gilbert, J. A., Sher, N., Venturi, V., & Steindler, L. (2016). “A New N-Acyl Homoserine Lactone Synthase in an Uncultured Symbiont of the Red Sea Sponge Theonella swinhoei.” Appl Environ Microbiol, 82(4), 1274-1285. doi:10.1128/aem.03111-1.

Chernikova, D. A., Koestler, D. C., Hoen, A. G., Housman, M. L., Hibberd, P. L., Moore, J. H., Morrison, H. G., Sogin, M. L., Zain-Ul-Abideen, M., & Madan, J. C. (2016). “Fetal exposures and perinatal influences on the stool microbiota of premature infants.” J Matern Fetal Neonatal Med, 29(1), 99-105. doi:10.3109/14767058.2014.98774.

Davies, N., Field, D., Gavaghan, D., Holbrook, S. J., Planes, S., Troyer, M., Bonsall, M., Claudet, J., Roderick, G., Schmitt, R. J., Amaral-Zettler, L. A., Berteaux, V., Bossin, H. C., Cabasse, C., Collin, A., Deck, J., Dell, T., Dunne, J., Gates, R., Harfoot, M., Hench, J. L., Hopuare, M., Kirch, P., Kotoulas, G., Kosenkov, A., Kusenko, A., Leichter, J. J., Lenihan, H., Magoulas, A., Martinez, N., Meyer, C., Stoll, B., Swalla, B., Tartakovsky, D. M., Murphy, H. T., Turyshev, S., Valdvinos, F., Williams, R., Wood, S., & Consortium, I. (2016). “Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium.” Gigascience, 5(1), 14. doi:10.1186/s13742-016-0118-.

De Filippis, F., Genovese, A., Ferranti, P., Gilbert, J. A., & Ercolini, D. (2016). “Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate.” Sci Rep, 6, 21871. doi:10.1038/srep2187.

Delmont, T. O., & Eren, A. M. (2016). “Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies.” PeerJ, 4, e1839. doi:10.7717/peerj.183.

Denner, D. R., Sangwan, N., Becker, J. B., Hogarth, D. K., Oldham, J., Castillo, J., Sperling, A. I., Solway, J., Naureckas, E. T., Gilbert, J. A., & White, S. R. (2016). “Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways.” J Allergy Clin Immunol, 137(5), 1398-1405 e1393. doi:10.1016/j.jaci.2015.10.01.

Dugas, L. R., Fuller, M., Gilbert, J., & Layden, B. T. (2016). “The obese gut microbiome across the epidemiologic transition.” Emerg Themes Epidemiol, 13, 2. doi:10.1186/s12982-015-0044-.

Eren, A. M., Sogin, M. L., & Maignien, L. (2016). “Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation.” Frontiers in Microbiology, 7, 1318. doi:ARTN 131810.3389/fmicb.2016.0131.

Fernandez-Gonzalez, N., Huber, J. A., & Vallino, J. J. (2016). “Microbial Communities Are Well Adapted to Disturbances in Energy Input.” mSystems, 1(5). doi:10.1128/mSystems.00117-1.

Fortunato, C. S., & Huber, J. A. (2016). “Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent.” ISME J, 10(8), 1925-1938. doi:10.1038/ismej.2015.25.

Gibbons, S. M., Scholz, M., Hutchison, A. L., Dinner, A. R., Gilbert, J. A., & Coleman, M. L. (2016). “Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System.” MBIO, 7(6). doi:10.1128/mBio.01372-1.

Gilbert, J. A. (2016). “mSystems: Learning To Love Systems.” mSystems, 1(1). doi:10.1128/mSystems.00015-1.

Gilbert, J. A., & Alverdy, J. (2016). “Stool consistency as a major confounding factor affecting microbiota composition: an ignored variable?” Gut, 65(1), 1-2. doi:10.1136/gutjnl-2015-31004.

Gilbert, J. A., Klyczek, K. K., & Elliott, S. L. (2016). “Introducing the JMBE Themed Issue on Scientific Citizenship.” J Microbiol Biol Educ, 17(1), 1-2. doi:10.1128/jmbe.v17i1.111.

Hogan, D. A., Willger, S. D., Dolben, E. L., Hampton, T. H., Stanton, B. A., Morrison, H. G., Sogin, M. L., Czum, J., & Ashare, A. (2016). “Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease.” PLoS One, 11(3), e0149998. doi:10.1371/journal.pone.014999.

Kaneko, G., Yoshinaga, T., Gribble, K. E., Mark Welch, D. B., & Ushio, H. (2016). “Measurement of Survival Time in Brachionus Rotifers: Synchronization of Maternal Conditions.” J Vis Exp(113), e54126. doi:10.3791/5412.

Kleindienst, S., Grim, S., Sogin, M., Bracco, A., Crespo-Medina, M., & Joye, S. B. (2016). “Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume.” ISME J, 10(2), 400-415. doi:10.1038/ismej.2015.12.

Kleindienst, S., Seidel, M., Ziervogel, K., Grim, S., Loftis, K., Harrison, S., Malkin, S. Y., Perkins, M. J., Field, J., Sogin, M. L., Dittmar, T., Passow, U., Medeiros, P., & Joye, S. B. (2016). “Reply to Prince et al.: Ability of chemical dispersants to reduce oil spill impacts remains unclear.” Proc Natl Acad Sci U S A, 113(11), E1422-1423. doi:10.1073/pnas.160049811.

Li, H., Yang, X., Weng, B., Su, J., Nie, S., Gilbert, J. A., & Zhu, Y. G. (2016). “The phenological stage of rice growth determines anaerobic ammonium oxidation activity in rhizosphere soil.” SOIL BIOLOGY & BIOCHEMISTRY, 100, 59-65. doi:10.1016/j.soilbio.2016.05.01.

Liebeskind, B. J., Hillis, D. M., Zakon, H. H., & Hofmann, H. A. (2016). “Complex Homology and the Evolution of Nervous Systems.” Trends Ecol Evol, 31(2), 127-135. doi:10.1016/j.tree.2015.12.00.

Luria, C. M., Amaral-Zettler, L. A., Ducklow, H. W., & Rich, J. J. (2016). “Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula.” Front Microbiol, 7(ARTN 1731), 1731. doi:10.3389/fmicb.2016.0173.

Madan, J. C., Hoen, A. G., Lundgren, S. N., Farzan, S. F., Cottingham, K. L., Morrison, H. G., Sogin, M. L., Li, H., Moore, J. H., & Karagas, M. R. (2016). “Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants.” JAMA PEDIATRICS, 170(3), 212-219. doi:10.1001/jamapediatrics.2015.373.

Mark Welch, J. L., Rossetti, B. J., Rieken, C. W., Dewhirst, F. E., & Borisy, G. G. (2016). “Biogeography of a human oral microbiome at the micron scale.” Proc Natl Acad Sci U S A, 113(6), E791-800. doi:10.1073/pnas.152214911.

Metcalf, J. L., Xu, Z. Z., Weiss, S., Lax, S., Van Treuren, W., Hyde, E. R., Song, S. J., Amir, A., Larsen, P., Sangwan, N., Haarmann, D., Humphrey, G. C., Ackermann, G., Thompson, L. R., Lauber, C., Bibat, A., Nicholas, C., Gebert, M. J., Petrosino, J. F., Reed, S. C., Gilbert, J. A., Lynne, A. M., Bucheli, S. R., Carter, D. O., & Knight, R. (2016). “Microbial community assembly and metabolic function during mammalian corpse decomposition.” Science, 351(6269), 158-162. doi:10.1126/science.aad264.

Meyer, J. L., Jaekel, U., Tully, B. J., Glazer, B. T., Wheat, C. G., Lin, H. T., Hsieh, C. C., Cowen, J. P., Hulme, S. M., Girguis, P. R., & Huber, J. A. (2016). “A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge.” Sci Rep, 6, 22541. doi:10.1038/srep2254.

Mills, S., Alcántara-Rodríguez, J. A., Ciros-Pérez, J., Gómez, A., Hagiwara, A., Galindo, K. H., Jersabek, C. D., Malekzadeh-Viayeh, R., Leasi, F., Lee, J.-S., Mark Welch, D. B., Papakostas, S., Riss, S., Segers, H., Serra, M., Shiel, R., Smolak, R., Snell, T. W., Stelzer, C.-P., Tang, C. Q., Wallace, R. L., Fontaneto, D., & Walsh, E. J. (2016). “Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy.” Hydrobiologia, 796(1), 39-58. doi:10.1007/s10750-016-2725-.

O’Brien, S. L., Gibbons, S. M., Owens, S. M., Hampton-Marcell, J., Johnston, E. R., Jastrow, J. D., Gilbert, J. A., Meyer, F., & Antonopoulos, D. A. (2016). “Spatial scale drives patterns in soil bacterial diversity.” Environ Microbiol, 18(6), 2039-2051. doi:10.1111/1462-2920.1323.

Perisin, M., Vetter, M., Gilbert, J. A., & Bergelson, J. (2016). “16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies.” ISME J, 10(4), 1020-1024. doi:10.1038/ismej.2015.16.

Reveillaud, J., Reddington, E., McDermott, J., Algar, C., Meyer, J. L., Sylva, S., Seewald, J., German, C. R., & Huber, J. A. (2016). “Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise.” Environ Microbiol, 18(6), 1970-1987. doi:10.1111/1462-2920.1317.

Rochman, C. M., Browne, M. A., Underwood, A. J., van Franeker, J. A., Hompson, R. C. T., & Amaral-Zettler, L. A. (2016). “The ecological impacts of marine debris: unraveling the demonstrated evidence from what is perceived.” Ecology, 97(2), 302-312. doi:10.1890/14-2070..

Rodriguez, F., & Arkhipova, I. R. (2016). “Multitasking of the piRNA Silencing Machinery: Targeting Transposable Elements and Foreign Genes in the Bdelloid Rotifer Adineta vaga.” Genetics, 203(1), 255-268. doi:10.1534/genetics.116.18673.

Sangwan, N., Xia, F., & Gilbert, J. A. (2016). “Recovering complete and draft population genomes from metagenome datasets.” Microbiome, 4(1), 8. doi:10.1186/s40168-016-0154-.

Schmidt, V., Amaral-Zettler, L. A., Davidson, J., Summerfelt, S., & Good, C. (2016). “The influence of fishmeal-free diets on microbial communities in Atlantic salmon Salmo salar recirculation aquaculture systems.” Appl Environ Microbiol, 82(15), 4470-4481. doi:10.1128/AEM.00902-1.

Sharma, A., Gilbert, J. A., & Lal, R. (2016). “(Meta) genomic insights into the pathogenome of Cellulosimicrobium cellulans.” Scientific Reports, 6, 25527. doi:ARTN 25527 10.1038/srep2552.

Sielaff, M., Schmidt, H., Struck, T. H., Rosenkranz, D., Mark Welch, D. B., Hankeln, T., & Herlyn, H. (2016). “Phylogeny of Syndermata (syn.” Rotifera): Mitochondrial gene order verifies epizoic Seisonidea as sister to endoparasitic Acanthocephala within monophyletic Hemirotifera. Mol Phylogenet Evol, 96, 79-92. doi:10.1016/j.ympev.2015.11.01.

Sun, R., Dsouza, M., Gilbert, J. A., Guo, X., Wang, D., Guo, Z., Ni, Y., & Chu, H. (2016). “Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter.” Environ Microbiol, 18(12), 5137-5150. doi:10.1111/1462-2920.1351.

Topcuoglu, B. D., Stewart, L. C., Morrison, H. G., Butterfield, D. A., Huber, J. A., & Holden, J. F. (2016). “Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents.” Frontiers in Microbiology, 7(ARTN 1240). doi:10.3389/fmicb.2016.0124.

Utter, D. R., Welch, J. L. M., & Borisy, G. G. (2016). “Individuality, Stability, and Variability of the Plaque Microbiome.” FRONTIERS IN MICROBIOLOGY, 7(ARTN 564). doi:10.3389/fmicb.2016.0056.

Vineis, J. H., Ringus, D. L., Morrison, H. G., Delmont, T. O., Dalal, S., Raffals, L. H., Antonopoulos, D. A., Rubin, D. T., Eren, A. M., Chang, E. B., & Sogin, M. L. (2016). “Patient-Specific Bacteroides Genome Variants in Pouchitis.” MBio, 7(6), e01713-01716. doi:10.1128/mBio.01713-1.

Walsh, E. A., Kirkpatrick, J. B., Pockalny, R., Sauvage, J., Spivack, A. J., Murray, R. W., Sogin, M. L., & D’Hondt, S. (2016). “Relationship of Bacterial Richness to Organic Degradation Rate and Sediment Age in Subseafloor Sediment.” Appl Environ Microbiol, 82(16), 4994-4999. doi:10.1128/AEM.00809-1.

Walsh, E. A., Kirkpatrick, J. B., Rutherford, S. D., Smith, D. C., Sogin, M., & D’Hondt, S. (2016). “Bacterial diversity and community composition from seasurface to subseafloor.” ISME J, 10(4), 979-989. doi:10.1038/ismej.2015.17.

Walters, W., Hyde, E. R., Berg-Lyons, D., Ackermann, G., Humphrey, G., Parada, A., Gilbert, J. A., Jansson, J. K., Caporaso, J. G., Fuhrman, J. A., Apprill, A., & Knight, R. (2016). “Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys.” mSystems, 1(1). doi:10.1128/mSystems.00009-1.

Ward, M. A., Pierre, J. F., Leal, R. F., Huang, Y., Shogan, B., Dalal, S. R., Weber, C. R., Leone, V. A., Musch, M. W., An, G. C., Rao, M. C., Rubin, D. T., Raffals, L. E., Antonopoulos, D. A., Sogin, M. L., Hyman, N. H., Alverdy, J. C., & Chang, E. B. (2016). “Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility.” Am J Physiol Gastrointest Liver Physiol, 310(11), G973-988. doi:10.1152/ajpgi.00017.201.

Wardrip, N. C., Dsouza, M., Urgun-Demirtas, M., Snyder, S. W., Gilbert, J. A., & Arnusch, C. J. (2016). “Printing-Assisted Surface Modifications of Patterned Ultrafiltration Membranes.” ACS APPLIED MATERIALS & INTERFACES, 8(44), 30271-30280. doi:10.1021/acsami.6b1133.

Yang, T., Weisenhorn, P., Gilbert, J. A., Ni, Y., Sun, R., Shi, Y., & Chu, H. (2016). “Carbon constrains fungal endophyte assemblages along the timberline.” Environ Microbiol, 18(8), 2455-2469. doi:10.1111/1462-2920.1315.

Zheng, Y., Huang, Y., Andersen, R. A., & Amaral-Zettler, L. A. (2016). “Excluding the di-unsaturated alkenone in the UK37 index strengthens temperature correlation for the common lacustrine and brackish-water haptophytes.” Geochimica et Cosmochimica Acta, 175, 36-46. doi:10.1016/j.gca.2015.11.02.

Zozaya, M., Ferris, M. J., Siren, J. D., Lillis, R., Myers, L., Nsuami, M. J., Eren, A. M., Brown, J., Taylor, C. M., & Martin, D. H. (2016). “Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis.” Microbiome, 4(1), 16. doi:10.1186/s40168-016-0161-.

2015

Alivisatos, A. P., Blaser, M. J., Brodie, E. L., Chun, M., Dangl, J. L., Donohue, T. J., Dorrestein, P. C., Gilbert, J. A., Green, J. L., Jansson, J. K., Knight, R., Maxon, M. E., McFall-Ngai, M. J., Miller, J. F., Pollard, K. S., Ruby, E. G., & Taha, S. A. (2015). “A unified initiative to harness Earth’s microbiomes.” Science, 350. doi:10.1126/science.aac848.

Amaral-Zettler, L. A., Zettler, E. R., Slikas, B., Boyd, G. D., Melvin, D. W., Morrall, C. E., Proskurowski, G., & Mincer, T. J. (2015). “The biogeography of the Plastisphere: implications for policy.” Frontiers in Ecology and the Environment, 13(10), 541-546. doi:10.1890/15001.

Amata, E., Bland, N. D., Campbell, R. K., & Pollastri, M. P. (2015). “Evaluation of pyrrolidine and pyrazolone derivatives as inhibitors of trypanosomal phosphodiesterase B1 (TbrPDEB1).” Tetrahedron Lett, 56(21), 2832-2835. doi:10.1016/j.tetlet.2015.04.06.

Anderson, R. E., Sogin, M. L., & Baross, J. A. (2015). “Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.” FEMS Microbiol Ecol, 91(1), 1-11. doi:10.1093/femsec/fiu01.

Angermeyer, A., Crosby, S. C., & Huber, J. A. (2015). “Decoupled distance-decay patterns between dsrA and 16S rRNA genes among salt marsh sulfate-reducing bacteria.” Environ Microbiol, 18(1), 75-86. doi:10.1111/1462-2920.1282.

Bertrand, E. M., McCrow, J. P., Moustafa, A., Zheng, H., McQuaid, J. B., Delmont, T. O., Post, A. F., Sipler, R. E., Spackeen, J. L., Xu, K., Bronk, D. A., Hutchins, D. A., & Allen, A. E. (2015). “Phytoplankton-bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge.” Proc Natl Acad Sci U S A, 112(32), 9938-9943. doi:10.1073/pnas.150161511.

Bowen, J. L., Weisman, D., Yasuda, M., Jayakumar, A., Morrison, H. G., & Ward, B. B. (2015). “Marine Oxygen-Deficient Zones Harbor Depauperate Denitrifying Communities Compared to Novel Genetic Diversity in Coastal Sediments.” Microb Ecol, 70(2), 311-321. doi:10.1007/s00248-015-0582-.

Browne, M. A., Chapman, M. G., Thompson, R. C., Amaral-Zettler, L. A., Jambeck, J., & Mallos, N. J. (2015). “Spatial and temporal patterns of stranded intertidal marine debris: is there a picture of global change?” Environ Sci Technol, 49(12), 7082-7094. doi:10.1021/es506057.

Burgsdorf, I., Slaby, B. M., Handley, K. M., Haber, M., Blom, J., Marshall, C. W., Gilbert, J. A., Hentschel, U., & Steindler, L. (2015). “Lifestyle evolution in cyanobacterial symbionts of sponges.” MBio, 6(3), e00391-00315. doi:10.1128/mBio.00391-1.

Chafee, M., Maignien, L., & Simmons, S. L. (2015). “The effects of variable sample biomass on comparative metagenomics.” Environ Microbiol, 17(7), 2239-2253. doi:10.1111/1462-2920.1266.

Delmont, T. O., Eren, A. M., Maccario, L., Prestat, E., Esen, O. C., Pelletier, E., Le Paslier, D., Simonet, P., & Vogel, T. M. (2015). “Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics.” Front Microbiol, 6, 358. doi:10.3389/fmicb.2015.0035.

Delmont, T. O., Eren, A. M., Vineis, J. H., & Post, A. F. (2015). “Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica.” Front Microbiol, 6, 1090. doi:10.3389/fmicb.2015.0109.

Ducklow, H. W., Wilson, S. E., Post, A. F., Stammerjohn, S. E., Erickson, M., Lee, S., Lowry, K. E., Sherrell, R. M., & Yager, P. L. (2015). “Particle flux on the continental shelf in the Amundsen Sea Polynya and Western Antarctic Peninsula.” Elementa: Science of the Anthropocene, 3(46), 000046. doi:10.12952/journal.elementa.00004.

Eren, A. M., Esen, O. C., Quince, C., Vineis, J. H., Morrison, H. G., Sogin, M. L., & Delmont, T. O. (2015). “Anvi’o: an advanced analysis and visualization platform for ‘omics data.” PeerJ, 3, e1319. doi:10.7717/peerj.131.

Eren, A. M., Morrison, H. G., Lescault, P. J., Reveillaud, J., Vineis, J. H., & Sogin, M. L. (2015). “Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences.” ISME J, 9(4), 968-979. doi:10.1038/ismej.2014.19.

Eren, A. M., Sogin, M. L., Morrison, H. G., Vineis, J. H., Fisher, J. C., Newton, R. J., & McLellan, S. L. (2015). “A single genus in the gut microbiome reflects host preference and specificity.” ISME J, 9(1), 90-100. doi:10.1038/ismej.2014.9.

Filkins, L. M., Dolben, E. L., Willger, S. D., Gifford, A. H., Sogin, M. L., Morrison, H. G., Grim, S. L., Ashare, A., Schwartzman, J. D., & Hogan, D. (2015). “Bacfun: An Rna-Based Diagnostic for Cystic Fibrosis Respiratory Samples.” Pediatric Pulmonology, 50, 321-321.

Fisher, J. C., Eren, A. M., Green, H. C., Shanks, O. C., Morrison, H. G., Vineis, J. H., Sogin, M. L., & McLellan, S. L. (2015). “Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups.” Appl Environ Microbiol, 81(20), 7023-7033. doi:10.1128/AEM.01524-1.

Fortunato, C. S., & Crump, B. C. (2015). “Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient.” PLoS One, 10(11), e0140578. doi:10.1371/journal.pone.014057.

Fuller, M., Priyadarshini, M., Gibbons, S. M., Angueira, A. R., Brodsky, M., Hayes, M. G., Kovatcheva-Datchary, P., Backhed, F., Gilbert, J. A., Lowe, W. L. Jr., & Layden, B. T. (2015). “The short-chain fatty acid receptor, FFA2, contributes to gestational glucose homeostasis.” Am J Physiol Endocrinol Metab, 309(10), E840-851. doi:10.1152/ajpendo.00171.201.

Gibbons, S. M., & Gilbert, J. A. (2015). “Microbial diversity-exploration of natural ecosystems and microbiomes.” Curr Opin Genet Dev, 35, 66-72. doi:10.1016/j.gde.2015.10.00.

Gibbons, S. M., Schwartz, T., Fouquier, J., Mitchell, M., Sangwan, N., Gilbert, J. A., & Kelley, S. T. (2015). “Ecological succession and viability of human-associated microbiota on restroom surfaces.” Appl Environ Microbiol, 81(2), 765-773. doi:10.1128/AEM.03117-1.

Gilbert, J. A., & Henry, C. (2015). “Predicting ecosystem emergent properties at multiple scales.” Environ Microbiol Rep, 7(1), 20-22. doi:10.1111/1758-2229.1225.

Gordon, J., Gandhi, P., Shekhawat, G., Frazier, A., Hampton-Marcell, J., & Gilbert, J. A. (2015). “A simple novel device for air sampling by electrokinetic capture.” Microbiome, 3(1), 79. doi:10.1186/s40168-015-0141-.

Green, H. C., Fisher, J. C., McLellan, S. L., Sogin, M. L., & Shanks, O. C. (2015). “Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves, Mammalia, and Actinopterygii.” Appl Environ Microbiol, 82(5), 1496-1503. doi:10.1128/AEM.02456-1.

Hoen, A. G., Li, J., Moulton, L. A., O’Toole, G. A., Housman, M. L., Koestler, D. C., Guill, M. F., Moore, J. H., Hibberd, P. L., Morrison, H. G., Sogin, M. L., Karagas, M. R., & Madan, J. C. (2015). “Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis.” J Pediatr, 167(1), 138-147 e131-133. doi:10.1016/j.jpeds.2015.02.04.

Huang, E. Y., Inoue, T., Leone, V. A., Dalal, S., Touw, K., Wang, Y., Musch, M. W., Theriault, B., Higuchi, K., Donovan, S., Gilbert, J. A., & Chang, E. B. (2015). “Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases.” Inflamm Bowel Dis, 21(5), 963-972. doi:10.1097/MIB.000000000000033.

Huber, J. A. (2015). “MICROBIAL ECOLOGY.” Making methane down deep. Science, 349(6246), 376-377. doi:10.1126/science.aac667.

Hunter-Cevera, K. R., Post, A. F., Peacock, E. E., & Sosik, H. M. (2015). “Diversity of Synechococcus at the Martha’s Vineyard Coastal Observatory: Insights from Culture Isolations, Clone Libraries, and Flow Cytometry.” Microb Ecol, 71(2), 276-289. doi:10.1007/s00248-015-0644-.

Huo, Y. Y., Cheng, H., Post, A. F., Wang, C. S., Jiang, X. W., Pan, J., Wu, M., & Xu, X. W. (2015). “Ecological functions of uncultured microorganisms in the cobalt-rich ferromanganese crust of a seamount in the central Pacific are elucidated by fosmid sequencing.” Acta Oceanologica Sinica, 34(4), 92-113. doi:10.1007/s13131-015-0650-.

Kleindienst, S., Seidel, M., Ziervogel, K., Grim, S., Loftis, K., Harrison, S., Malkin, S. Y., Perkins, M. J., Field, J., Sogin, M. L., Dittmar, T., Passow, U., Medeiros, P. M., & Joye, S. B. (2015). “Chemical dispersants can suppress the activity of natural oil-degrading microorganisms.” Proc Natl Acad Sci U S A, 112(48), 14900-14905. doi:10.1073/pnas.150738011.

Kopf, A., Bicak, M., Kottmann, R., Schnetzer, J., Kostadinov, I., Lehmann, K., Fernandez-Guerra, A., Jeanthon, C., Rahav, E., Ullrich, M., Wichels, A., Gerdts, G., Polymenakou, P., Kotoulas, G., Siam, R., Abdallah, R. Z., Sonnenschein, E. C., Cariou, T., O’Gara, F., Jackson, S., Orlic, S., Steinke, M., Busch, J., Duarte, B., Cacador, I., Canning-Clode, J., Bobrova, O., Marteinsson, V., Reynisson, E., Loureiro, C. M., Luna, G. M., Quero, G. M., Loscher, C. R., Kremp, A., DeLorenzo, M. E., Ovreas, L., Tolman, J., LaRoche, J., Penna, A., Frischer, M., Davis, T., Katherine, B., Meyer, C. P., Ramos, S., Magalhaes, C., Jude-Lemeilleur, F., Aguirre-Macedo, M. L., Wang, S., Poulton, N., Jones, S., Collin, R., Fuhrman, J. A., Conan, P., Alonso, C., Stambler, N., Goodwin, K., Yakimov, M. M., Baltar, F., Bodrossy, L., Van De Kamp, J., Frampton, D. M., Ostrowski, M., Van Ruth, P., Malthouse, P., Claus, S., Deneudt, K., Mortelmans, J., Pitois, S., Wallom, D., Salter, I., Costa, R., Schroeder, D. C., Kandil, M. M., Amaral, V., Biancalana, F., Santana, R., Pedrotti, M. L., Yoshida, T., Ogata, H., Ingleton, T., Munnik, K., Rodriguez-Ezpeleta, N., Berteaux-Lecellier, V., Wecker, P., Cancio, I., Vaulot, D., Bienhold, C., Ghazal, H., Chaouni, B., Essayeh, S., Ettamimi, S., Zaid el, H., Boukhatem, N., Bouali, A., Chahboune, R., Barrijal, S., Timinouni, M., El Otmani, F., Bennani, M., Mea, M., Todorova, N., Karamfilov, V., Ten Hoopen, P., Cochrane, G., L’Haridon, S., Bizsel, K. C., Vezzi, A., Lauro, F. M., Martin, P., Jensen, R. M., Hinks, J., Gebbels, S., Rosselli, R., De Pascale, F., Schiavon, R., Dos Santos, A., Villar, E., Pesant, S., Cataletto, B., Malfatti, F., Edirisinghe, R., Silveira, J. A., Barbier, M., Turk, V., Tinta, T., Fuller, W. J., Salihoglu, I., Serakinci, N., Ergoren, M. C., Bresnan, E., Iriberri, J., Nyhus, P. A., Bente, E., Karlsen, H. E., Golyshin, P. N., Gasol, J. M., Moncheva, S., Dzhembekova, N., Johnson, Z., Sinigalliano, C. D., Gidley, M. L., Zingone, A., Danovaro, R., Tsiamis, G., Clark, M. S., Costa, A. C., El Bour, M., Martins, A. M., Collins, R. E., Ducluzeau, A. L., Martinez, J., Costello, M. J., Amaral-Zettler, L. A., Gilbert, J. A., Davies, N., Field, D., & Glockner, F. O. (2015). “The ocean sampling day consortium.” Gigascience, 4, 27. doi:10.1186/s13742-015-0066-.

Larsen, P. E., Scott, N., Post, A. F., Field, D., Knight, R., Hamada, Y., & Gilbert, J. A. (2015). “Satellite remote sensing data can be used to model marine microbial metabolite turnover.” ISME J, 9(1), 166-179. doi:10.1038/ismej.2014.10.

Lax, S., & Gilbert, J. A. (2015). “Hospital-associated microbiota and implications for nosocomial infections.” Trends Mol Med, 21(7), 427-432. doi:10.1016/j.molmed.2015.03.00.

Lax, S., Hampton-Marcell, J. T., Gibbons, S. M., Colares, G. B., Smith, D., Eisen, J. A., & Gilbert, J. A. (2015). “Forensic analysis of the microbiome of phones and shoes.” Microbiome, 3, 21. doi:10.1186/s40168-015-0082-.

Lax, S., Nagler, C. R., & Gilbert, J. A. (2015). “Our interface with the built environment: immunity and the indoor microbiota.” Trends Immunol, 36(3), 121-123. doi:10.1016/j.it.2015.01.00.

Liebeskind, B. J., Hillis, D. M., & Zakon, H. H. (2015). “Convergence of ion channel genome content in early animal evolution.” Proc Natl Acad Sci U S A, 112(8), E846-851. doi:10.1073/pnas.150119511.

Lin, X., Handley, K. M., Gilbert, J. A., & Kostka, J. E. (2015). “Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat.” ISME J, 9(12), 2740-2744. doi:10.1038/ismej.2015.7.

Lüchmann, K. H., Clark, M. S., Bainy, A. C., Gilbert, J. A., Craft, J. A., Chipman, J. K., Thorne, M. A., Mattos, J. J., Siebert, M. N., & Schroeder, D. C. (2015). “Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana.” Aquat Toxicol, 166, 10-20. doi:10.1016/j.aquatox.2015.06.01.

Mackey, K. R. M., Chien, C. T., Post, A. F., Saito, M. A., & Paytan, A. (2015). “Rapid and gradual modes of aerosol trace metal dissolution in seawater.” Front Microbiol, 5, 794. doi:10.3389/fmicb.2014.0079.

Mackey, K. R. M., Post, A. F., McIlvin, M. R., Cutter, G. A., John, S. G., & Saito, M. A. (2015). “Divergent responses of Atlantic coastal and oceanic Synechococcus to iron limitation.” Proc Natl Acad Sci U S A, 112(32), 9944-9949. doi:10.1073/pnas.150944811.

Moran, Y., Barzilai, M. G., Liebeskind, B. J., & Zakon, H. H. (2015). “Evolution of voltage-gated ion channels at the emergence of Metazoa.” J Exp Biol, 218(Pt 4), 515-525. doi:10.1242/jeb.11027.

Newton, R. J., McLellan, S. L., Dila, D. K., Vineis, J. H., Morrison, H. G., Eren, A. M., & Sogin, M. L. (2015). “Sewage reflects the microbiomes of human populations.” MBio, 6(2), e02574. doi:10.1128/mBio.02574-1.

Ochiana, S. O., Bland, N. D., Settimo, L., Campbell, R. K., & Pollastri, M. P. (2015). “Repurposing human PDE4 inhibitors for neglected tropical diseases.” Evaluation of analogs of the human PDE4 inhibitor GSK-256066 as inhibitors of PDEB1 of Trypanosoma brucei. Chem Biol Drug Des, 85(5), 549-564. doi:10.1111/cbdd.1244.

Quince, C., Ijaz, U. Z., Loman, N., Eren, A. M., Saulnier, D., Russell, J., Haig, S. J., Calus, S. T., Quick, J., Barclay, A., Bertz, M., Blaut, M., Hansen, R., McGrogan, P., Russell, R. K., Edwards, C. A., & Gerasimidis, K. (2015). “Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition.” Am J Gastroenterol, 110(12), 1718-1729. doi:10.1038/ajg.2015.35.

Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M. R., Rappe, M. S., DiTullio, G. R., & Moran, D. M. (2015). “Needles in the blue sea: sub-species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome.” Proteomics, 15(20), 3521-3531. doi:10.1002/pmic.20140063.

Satinsky, B. M., Fortunato, C. S., Doherty, M., Smith, C. B., Sharma, S., Ward, N. D., Krusche, A. V., Yager, P. L., Richey, J. E., Moran, M. A., & Crump, B. C. (2015). “Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011.” Microbiome, 3(1), 39. doi:10.1186/s40168-015-0099-.

Schmidt, V. T., Smith, K. F., Melvin, D. W., & Amaral-Zettler, L. A. (2015). “Community assembly of a euryhaline fish microbiome during salinity acclimation.” Mol Ecol, 24(10), 2537-2550. doi:10.1111/mec.1317.

Shade, A., & Gilbert, J. A. (2015). “Temporal patterns of rarity provide a more complete view of microbial diversity.” Trends Microbiol, 23(6), 335-340. doi:10.1016/j.tim.2015.01.00.

Sielaff, M., Schmidt, H., Struck, T. H., Rosenkranz, D., Mark Welch, D. B., Hankeln, T., & Herlyn, H. (2015). “Phylogeny of Syndermata (syn.” Rotifera): Mitochondrial gene order verifies epizoic Seisonidea as sister to endoparasitic Acanthocephala within monophyletic Hemirotifera. Mol Phylogenet Evol, 96, 79-92. doi:10.1016/j.ympev.2015.11.01.

Signorovitch, A., Hur, J., Gladyshev, E., & Meselson, M. (2015). “Allele Sharing and Evidence for Sexuality in a Mitochondrial Clade of Bdelloid Rotifers.” Genetics, 200(2), 581-590. doi:10.1534/genetics.115.17671.

Snell, T. W., Johnston, R. K., Gribble, K. E., & Mark Welch, D. B. (2015). “Rotifers as experimental tools for investigating aging.” Invertebr Reprod Dev, 59(1), 5-10. doi:10.1080/07924259.2014.92551.

Traeger, L. L., Volkening, J. D., Moffett, H., Gallant, J. R., Chen, P. H., Novina, C. D., Phillips, G. N. Jr., Anand, R., Wells, G. B., Pinch, M., Guth, R., Unguez, G. A., Albert, J. S., Zakon, H., Sussman, M. R., & Samanta, M. P. (2015). “Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus).” BMC Genomics, 16, 243. doi:10.1186/s12864-015-1288-.

Van Bonn, W., LaPointe, A., Gibbons, S. M., Frazier, A., Hampton-Marcell, J., & Gilbert, J. A. (2015). “Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management.” Zoo Biol, 34(4), 360-367. doi:10.1002/zoo.2122.

Walsh, E. A., Smith, D. C., Sogin, M. L., & D’Hondt, S. (2015). “Bacterial and archaeal biogeography of the deep chlorophyll maximum in the South Pacific Gyre.” Aquatic Microbial Ecology, 75(1), 1-13. doi:10.3354/ame0174.

Wood, M., Gibbons, S. M., Lax, S., Eshoo-Anton, T. W., Owens, S. M., Kennedy, S., Gilbert, J. A., & Hampton-Marcell, J. T. (2015). “Athletic equipment microbiota are shaped by interactions with human skin.” Microbiome, 3, 25. doi:10.1186/s40168-015-0088-.

Ying, S., Zeng, D. N., Chi, L., Tan, Y., Galzote, C., Cardona, C., Lax, S., Gilbert, J., & Quan, Z. X. (2015). “The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations.” PLoS One, 10(10), e0141842. doi:10.1371/journal.pone.014184.

Zarraonaindia, I., Owens, S. M., Weisenhorn, P., West, K., Hampton-Marcell, J., Lax, S., Bokulich, N. A., Mills, D. A., Martin, G., Taghavi, S., van der Lelie, D., & Gilbert, J. A. (2015). “The soil microbiome influences grapevine-associated microbiota.” MBio, 6(2). doi:10.1128/mBio.02527-1.

2014

Amata, E., Bland, N. D., Hoyt, C. T., Settimo, L., Campbell, R. K., & Pollastri, M. P. (2014). “Repurposing human PDE4 inhibitors for neglected tropical diseases: design, synthesis and evaluation of cilomilast analogues as Trypanosoma brucei PDEB1 inhibitors.” Bioorg Med Chem Lett, 24(17), 4084-4089. doi:10.1016/j.bmcl.2014.07.06.

Anderson, R. E., Sogin, M. L., & Baross, J. A. (2014). “Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics.” PLoS One, 9(10), e109696. doi:10.1371/journal.pone.010969.

Apprill, A., Robbins, J., Eren, A. M., Pack, A. A., Reveillaud, J., Mattila, D., Moore, M., Niemeyer, M., Moore, K. M., & Mincer, T. J. (2014). “Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?” PLoS One, 9(3), e90785. doi:10.1371/journal.pone.009078.

Beliaev, A. S., Romine, M. F., Serres, M. H., Bernstein, H. C., Linggi, B. E., Markillie, L. M., Isern, N. G., Chrisler, W. B., Kucek, L. A., Hill, E. A., Pinchuk, G. E., Bryant, D. A., Wiley, H. S., Fredrickson, J. K., & Konopka, A. (2014). “Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing.” ISME J, 8(11), 2243-2255. doi:10.1038/ismej.2014.6.

Bullerjahn, G. S., & Post, A. F. (2014). “Physiology and molecular biology of aquatic cyanobacteria.” Front Microbiol, 5, 359. doi:10.3389/fmicb.2014.0035.

Celaj, S., Gleeson, M. W., Deng, J., O’Toole, G. A., Hampton, T. H., Toft, M. F., Morrison, H. G., Sogin, M. L., Putra, J., Suriawinata, A. A., & Gorham, J. D. (2014). “The microbiota regulates susceptibility to Fas-mediated acute hepatic injury.” Lab Invest, 94(9), 938-949. doi:10.1038/labinvest.2014.9.

Cusack, D. F., Axsen, J., Shwom, R., Hartzell-Nichols, L., White, S., & Mackey, K. R. M. (2014). “An interdisciplinary assessment of climate engineering strategies.” Frontiers in Ecology and the Environment, 12(5), 280-287. doi:10.1890/13003.

Davies, N., Field, D., Amaral-Zettler, L. A., Bicak, M., Bourlat, S., Coddington, J., Deck, J., Drummond, A., Gilbert, J. A., Glöckner, F. O., Kottmann, R., Meyer, C., Morrison, N., Obst, M., Robbins, R., Schriml, L., Sterk, P., & Stones-Havas, S. (2014). “Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012.” Standards in Genomic Sciences; Vol 9, No 3 (2014): Standards in Genomic Sciences.

Davies, N., Field, D., Amaral-Zettler, L. A., Clark, M. S., Deck, J., Drummond, A., Faith, D. P., Geller, J., Gilbert, J., Glockner, F. O., Hirsch, P. R., Leong, J. A., Meyer, C., Obst, M., Planes, S., Scholin, C., Vogler, A. P., Gates, R. D., Toonen, R., Berteaux-Lecellier, V., Barbier, M., Barker, K., Bertilsson, S., Bicak, M., Bietz, M. J., Bobe, J., Bodrossy, L., Borja, A., Coddington, J., Fuhrman, J., Gerdts, G., Gillespie, R., Goodwin, K., Hanson, P. C., Hero, J. M., Hoekman, D., Jansson, J., Jeanthon, C., Kao, R., Klindworth, A., Knight, R., Kottmann, R., Koo, M. S., Kotoulas, G., Lowe, A. J., Marteinsson, V. T., Meyer, F., Morrison, N., Myrold, D. D., Pafilis, E., Parker, S., Parnell, J. J., Polymenakou, P. N., Ratnasingham, S., Roderick, G. K., Rodriguez-Ezpeleta, N., Schonrogge, K., Simon, N., Valette-Silver, N. J., Springer, Y. P., Stone, G. N., Stones-Havas, S., Sansone, S. A., Thibault, K. M., Wecker, P., Wichels, A., Wooley, J. C., Yahara, T., Zingone, A., & COS, G. O. (2014). “The founding charter of the Genomic Observatories Network.” Gigascience, 3(1), 2. doi:10.1186/2047-217X-3-.

Dejea, C. M., Wick, E. C., Hechenbleikner, E. M., White, J. R., Mark Welch, J. L., Rossetti, B. J., Peterson, S. N., Snesrud, E. C., Borisy, G. G., Lazarev, M., Stein, E., Vadivelu, J., Roslani, A. C., Malik, A. A., Wanyiri, J. W., Goh, K. L., Thevambiga, I., Fu, K., Wan, F., Llosa, N., Housseau, F., Romans, K., Wu, X., McAllister, F. M., Wu, S., Vogelstein, B., Kinzler, K. W., Pardoll, D. M., & Sears, C. L. (2014). “Microbiota organization is a distinct feature of proximal colorectal cancers.” Proc Natl Acad Sci U S A, 111(51), 18321-18326. doi:10.1073/pnas.140619911.

Delmont, T. O., Francioli, D., Jacquesson, S., Laoudi, S., Mathieu, A., Nesme, J., Ceccherini, M. T., Nannipieri, P., Simonet, P., & Vogel, T. M. (2014). “Microbial community development and unseen diversity recovery in inoculated sterile soil.” Biology and Fertility of Soils, 50(7), 1069-1076. doi:10.1007/s00374-014-0925-.

Delmont, T. O., Hammar, K. M., Ducklow, H. W., Yager, P. L., & Post, A. F. (2014). “Phaeocystis antarctica blooms strongly influence bacterial community structures in the Amundsen Sea polynya.” Front Microbiol, 5, 646. doi:10.3389/fmicb.2014.0064.

Durham, B. P., Grote, J., Whittaker, K. A., Bender, S. J., Luo, H., Grim, S. L., Brown, J. M., Casey, J. R., Dron, A., Florez-Leiva, L., Krupke, A., Luria, C. M., Mine, A. H., Nigro, O. D., Pather, S., Talarmin, A., Wear, E. K., Weber, T. S., Wilson, J. M., Church, M. J., DeLong, E. F., Karl, D. M., Steward, G. F., Eppley, J. M., Kyrpides, N. C., Schuster, S., & Rappe, M. S. (2014). “Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome.” Stand Genomic Sci, 9(3), 632-645. doi:10.4056/sigs.499898.

Eren, A. M., Borisy, G. G., Huse, S. M., & Mark Welch, J. L. (2014). “Oligotyping analysis of the human oral microbiome.” Proc Natl Acad Sci U S A, 111(28), E2875-2884. doi:10.1073/pnas.140964411.

Eren, A. M., Morrison, H. G., Huse, S. M., & Sogin, M. L. (2014). “DRISEE overestimates errors in metagenomic sequencing data.” Brief Bioinform, 15(5), 783-787. doi:10.1093/bib/bbt01.

Ferreira, A. J., Siam, R., Setubal, J. C., Moustafa, A., Sayed, A., Chambergo, F. S., Dawe, A. S., Ghazy, M. A., Sharaf, H., Ouf, A., Alam, I., Abdel-Haleem, A. M., Lehvaslaiho, H., Ramadan, E., Antunes, A., Stingl, U., Archer, J. A., Jankovic, B. R., Sogin, M. L., Bajic, V. B., & El-Dorry, H. (2014). “Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.” PLoS One, 9(6), e97338. doi:10.1371/journal.pone.009733.

Field, D., Sterk, P., Kottmann, R., De Smet, J. W., Amaral-Zettler, L. A., Cochrane, G., Cole, J. R., Davies, N., Dawyndt, P., Garrity, G. M., Gilbert, J. A., Glockner, F. O., Hirschman, L., Klenk, H. P., Knight, R., Kyrpides, N., Meyer, F., Karsch-Mizrachi, I., Morrison, N., Robbins, R., San Gil, I., Sansone, S., Schriml, L., Tatusova, T., Ussery, D., Yilmaz, P., White, O., Wooley, J., & Caporaso, G. (2014). “Genomic standards consortium projects.” Stand Genomic Sci, 9(3), 599-601. doi:10.4056/sigs.555968.

Fischer, A. H., Mozzherin, D., Eren, A. M., Lans, K. D., Wilson, N., Cosentino, C., & Smith, J. (2014). “SeaBase: a multispecies transcriptomic resource and platform for gene network inference.” Integr Comp Biol, 54(2), 250-263. doi:10.1093/icb/icu06.

Gallant, J. R., Traeger, L. L., Volkening, J. D., Moffett, H., Chen, P. H., Novina, C. D., Phillips, G. N. Jr., Anand, R., Wells, G. B., Pinch, M., Guth, R., Unguez, G. A., Albert, J. S., Zakon, H. H., Samanta, M. P., & Sussman, M. R. (2014). “Nonhuman genetics.” Genomic basis for the convergent evolution of electric organs. Science, 344(6191), 1522-1525. doi:10.1126/science.125443.

Ghezzi, A., Liebeskind, B. J., Thompson, A., Atkinson, N. S., & Zakon, H. H. (2014). “Ancient association between cation leak channels and Mid1 proteins is conserved in fungi and animals.” Front Mol Neurosci, 7, 15. doi:10.3389/fnmol.2014.0001.

Gifford, A. H., Alexandru, D. M., Li, Z., Dorman, D. B., Moulton, L. A., Price, K. E., Hampton, T. H., Sogin, M. L., Zuckerman, J. B., Parker, H. W., Stanton, B. A., & O’Toole, G. A. (2014). “Iron supplementation does not worsen respiratory health or alter the sputum microbiome in cystic fibrosis.” J Cyst Fibros, 13(3), 311-318. doi:10.1016/j.jcf.2013.11.00.

Gilbert, J. A., Dick, G. J., Jenkins, B., Heidelberg, J., Allen, E., Mackey, K. R., & DeLong, E. F. (2014). “Meeting report: Ocean ‘omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013).” Stand Genomic Sci, 9(3), 1252-1258. doi:10.4056/sigs.574994.

Gilbert, J. A., Jansson, J. K., & Knight, R. (2014). “The Earth Microbiome project: successes and aspirations.” BMC Biol, 12. doi:10.1186/s12915-014-0069-.

Gilbert, J. A., & Neufeld, J. D. (2014). “Life in a World without Microbes.” PLoS Biol, 12(12), e1002020. doi:10.1371/journal.pbio.100202.

Glass, E. M., Dribinsky, Y., Yilmaz, P., Levin, H., Van Pelt, R., Wendel, D., Wilke, A., Eisen, J. A., Huse, S. M., Shipanova, A., Sogin, M. L., Stajich, J., Knight, R., Meyer, F., & Schriml, L. M. (2014). “MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.” ISME J, 8(1), 1-3. doi:10.1038/ismej.2013.17.

Gribble, K. E., Jarvis, G., Bock, M., & Mark Welch, D. B. (2014). “Maternal caloric restriction partially rescues the deleterious effects of advanced maternal age on offspring.” Aging Cell, 13(4), 623-630. doi:10.1111/acel.1221.

Gribble, K. E., Kaido, O., Jarvis, G., & Mark Welch, D. B. (2014). “Patterns of intraspecific variability in the response to caloric restriction.” Exp Gerontol, 51, 28-37. doi:10.1016/j.exger.2013.12.00.

Halliday, E., McLellan, S. L., Amaral-Zettler, L. A., Sogin, M. L., & Gast, R. J. (2014). “Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations.” PLoS One, 9(3), e90815. doi:10.1371/journal.pone.009081.

Hampton, T. H., Green, D. M., Cutting, G. R., Morrison, H. G., Sogin, M. L., Gifford, A. H., Stanton, B. A., & O’Toole, G. A. (2014). “The microbiome in pediatric cystic fibrosis patients: the role of shared environment suggests a window of intervention.” Microbiome, 2, 14. doi:10.1186/2049-2618-2-1.

Huo, Y. Y., Li, Z. Y., You, H., Wang, C. S., Post, A. F., Oren, A., & Xu, X. W. (2014). “Oceanicola antarcticus sp.” nov. and Oceanicola flagellatus sp. nov., moderately halophilic bacteria isolated from seawater. Int J Syst Evol Microbiol, 64(Pt 9), 2975-2979. doi:10.1099/ijs.0.062588-.

Huse, S. M., Mark Welch, D. B., Voorhis, A., Shipunova, A., Morrison, H. G., Eren, A. M., & Sogin, M. L. (2014). “VAMPS: a website for visualization and analysis of microbial population structures.” BMC Bioinformatics, 15(1), 41. doi:10.1186/1471-2105-15-4.

Huse, S. M., Young, V. B., Morrison, H. G., Antonopoulos, D. A., Kwon, J., Dalal, S., Arrieta, R., Hubert, N. A., Shen, L., Vineis, J. H., Koval, J. C., Sogin, M. L., Chang, E. B., & Raffals, L. E. (2014). “Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects.” Microbiome, 2(1), 5. doi:10.1186/2049-2618-2-.

Keeling, P. J., Burki, F., Wilcox, H. M., Allam, B., Allen, E. E., Amaral-Zettler, L. A., Armbrust, E. V., Archibald, J. M., Bharti, A. K., Bell, C. J., Beszteri, B., Bidle, K. D., Cameron, C. T., Campbell, L., Caron, D. A., Cattolico, R. A., Collier, J. L., Coyne, K., Davy, S. K., Deschamps, P., Dyhrman, S. T., Edvardsen, B., Gates, R. D., Gobler, C. J., Greenwood, S. J., Guida, S. M., Jacobi, J. L., Jakobsen, K. S., James, E. R., Jenkins, B., John, U., Johnson, M. D., Juhl, A. R., Kamp, A., Katz, L. A., Kiene, R., Kudryavtsev, A., Leander, B. S., Lin, S., Lovejoy, C., Lynn, D., Marchetti, A., McManus, G., Nedelcu, A. M., Menden-Deuer, S., Miceli, C., Mock, T., Montresor, M., Moran, M. A., Murray, S., Nadathur, G., Nagai, S., Ngam, P. B., Palenik, B., Pawlowski, J., Petroni, G., Piganeau, G., Posewitz, M. C., Rengefors, K., Romano, G., Rumpho, M. E., Rynearson, T., Schilling, K. B., Schroeder, D. C., Simpson, A. G., Slamovits, C. H., Smith, D. R., Smith, G. J., Smith, S. R., Sosik, H. M., Stief, P., Theriot, E., Twary, S. N., Umale, P. E., Vaulot, D., Wawrik, B., Wheeler, G. L., Wilson, W. H., Xu, Y., Zingone, A., & Worden, A. Z. (2014). “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.” PLoS Biol, 12(6), e1001889. doi:10.1371/journal.pbio.100188.

Koskey, A. M., Fisher, J. C., Eren, A. M., Ponce-Terashima, R., Reis, M. G., Blanton, R. E., & McLellan, S. L. (2014). “Blautia and Prevotella sequences distinguish human and animal fecal pollution in Brazil surface waters.” Environ Microbiol Rep, 6(6), 696-704. doi:10.1111/1758-2229.1218.

Kyrpides, N. C., Hugenholtz, P., Eisen, J. A., Woyke, T., Goker, M., Parker, C. T., Amann, R., Beck, B. J., Chain, P. S., Chun, J., Colwell, R. R., Danchin, A., Dawyndt, P., Dedeurwaerdere, T., DeLong, E. F., Detter, J. C., De Vos, P., Donohue, T. J., Dong, X. Z., Ehrlich, D. S., Fraser, C., Gibbs, R., Gilbert, J. A., Gilna, P., Glockner, F. O., Jansson, J. K., Keasling, J. D., Knight, R., Labeda, D., Lapidus, A., Lee, J. S., Li, W. J., Ma, J., Markowitz, V., Moore, E. R., Morrison, M., Meyer, F., Nelson, K. E., Ohkuma, M., Ouzounis, C. A., Pace, N., Parkhill, J., Qin, N., Rossello-Mora, R., Sikorski, J., Smith, D., Sogin, M. L., Stevens, R., Stingl, U., Suzuki, K., Taylor, D., Tiedje, J. M., Tindall, B., Wagner, M., Weinstock, G., Weissenbach, J., White, O., Wang, J., Zhang, L., Zhou, Y. G., Field, D., Whitman, W. B., Garrity, G. M., & Klenk, H. P. (2014). “Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.” PLoS Biol, 12(8), e1001920. doi:10.1371/journal.pbio.100192.

LaBelle, E. V., Marshall, C. W., Gilbert, J. A., & May, H. D. (2014). “Influence of acidic pH on hydrogen and acetate production by an electrosynthetic microbiome.” PLoS One, 9(10), e109935. doi:10.1371/journal.pone.010993.

Lau, M. C., Cameron, C., Magnabosco, C., Brown, C. T., Schilkey, F., Grim, S., Hendrickson, S., Pullin, M., Sherwood Lollar, B., van Heerden, E., Kieft, T. L., & Onstott, T. C. (2014). “Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships.” Front Microbiol, 5, 531. doi:10.3389/fmicb.2014.0053.

Lie, A. A., Liu, Z., Hu, S. K., Jones, A. C., Kim, D. Y., Countway, P. D., Amaral-Zettler, L. A., Cary, S. C., Sherr, E. B., Sherr, B. F., Gast, R. J., & Caron, D. A. (2014). “Investigating microbial eukaryotic diversity from a global census: insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes.” Appl Environ Microbiol, 80(14), 4363-4373. doi:10.1128/AEM.00057-1.

Luria, C. M., Ducklow, H. W., & Amaral-Zettler, L. A. (2014). “Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the western Antarctic Peninsula.” Aquatic Microbial Ecology, 73(2), 107-121. doi:10.3354/ame0170.

Maignien, L., DeForce, E. A., Chafee, M. E., Eren, A. M., & Simmons, S. L. (2014). “Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities.” MBio, 5(1), e00682-00613. doi:10.1128/mBio.00682-1.

Maltz, M. A., Bomar, L., Lapierre, P., Morrison, H. G., McClure, E. A., Sogin, M. L., & Graf, J. (2014). “Metagenomic analysis of the medicinal leech gut microbiota.” Front Microbiol, 5, 151. doi:10.3389/fmicb.2014.0015.

Mark Welch, J. L., Utter, D. R., Rossetti, B. J., Mark Welch, D. B., Eren, A. M., & Borisy, G. G. (2014). “Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping.” Front Microbiol, 5, 568. doi:10.3389/fmicb.2014.0056.

Markham, M. R., & Zakon, H. H. (2014). “Ionic mechanisms of microsecond-scale spike timing in single cells.” J Neurosci, 34(19), 6668-6678. doi:10.1523/JNEUROSCI.0615-14.201.

McLellan, S. L., & Eren, A. M. (2014). “Discovering new indicators of fecal pollution.” Trends Microbiol, 22(12), 697-706. doi:10.1016/j.tim.2014.08.00.

Meyer, J. L., & Huber, J. A. (2014). “Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano.” ISME J, 8(4), 867-880. doi:10.1038/ismej.2013.20.

Moran, Y., & Zakon, H. H. (2014). “The evolution of the four subunits of voltage-gated calcium channels: ancient roots, increasing complexity, and multiple losses.” Genome Biol Evol, 6(9), 2210-2217. doi:10.1093/gbe/evu17.

Nelson, M. C., Morrison, H. G., Benjamino, J., Grim, S. L., & Graf, J. (2014). “Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys.” PLoS One, 9(4), e94249. doi:10.1371/journal.pone.009424.

Ong, W. K., Vu, T. T., Lovendahl, K. N., Llull, J. M., Serres, M. H., Romine, M. F., & Reed, J. L. (2014). “Comparisons of Shewanella strains based on genome annotations, modeling, and experiments.” BMC Syst Biol, 8(1), 31. doi:10.1186/1752-0509-8-3.

Orcutt, B. N., LaRowe, D. E., Lloyd, K. G., Mills, H., Orsi, W., Reese, B. K., Sauvage, J., Huber, J. A., & Amend, J. (2014). “IODP Deep Biosphere Research Workshop report – a synthesis of recent investigations, and discussion of new research questions and drilling targets.” Scientific Drilling, 17, 61-66. doi:10.5194/sd-17-61-201.

Reed, D. C., Algar, C. K., Huber, J. A., & Dick, G. J. (2014). “Gene-centric approach to integrating environmental genomics and biogeochemical models.” Proc Natl Acad Sci U S A, 111(5), 1879-1884. doi:10.1073/pnas.131371311.

Reveillaud, J., Maignien, L., Murat Eren, A., Huber, J. A., Apprill, A., Sogin, M. L., & Vanreusel, A. (2014). “Host-specificity among abundant and rare taxa in the sponge microbiome.” ISME J, 8(6), 1198-1209. doi:10.1038/ismej.2013.22.

Reznikoff, W. S. (2014). “Viewing Francois Jacob (and Jacques Monod) through AGC & T.” Res Microbiol, 165(5), 357-358. doi:10.1016/j.resmic.2014.05.02.

Sadler, N. C., Melnicki, M. R., Serres, M. H., Merkley, E. D., Chrisler, W. B., Hill, E. A., Romine, M. F., Kim, S., Zink, E. M., Datta, S., Smith, R. D., Beliaev, A. S., Konopka, A., & Wright, A. T. (2014). “Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium.” ACS Chem Biol, 9(1), 291-300. doi:10.1021/cb400769.

Saito, M. A., McIlvin, M. R., Moran, D. M., Goepfert, T. J., DiTullio, G. R., Post, A. F., & Lamborg, C. H. (2014). “Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers.” Science, 345(6201), 1173-1177. doi:10.1126/science.125645.

Schmidt, V. T., Reveillaud, J., Zettler, E., Mincer, T. J., Murphy, L., & Amaral-Zettler, L. A. (2014). “Oligotyping reveals community level habitat selection within the genus Vibrio.” Front Microbiol, 5, 563. doi:10.3389/fmicb.2014.0056.

Scientists, G. C. o., Bracken-Grissom, H., Collins, A. G., Collins, T., Crandall, K., Distel, D., Dunn, C., Giribet, G., Haddock, S., Knowlton, N., Martindale, M., Medina, M., Messing, C., O’Brien, S. J., Paulay, G., Putnam, N., Ravasi, T., Rouse, G. W., Ryan, J. F., Schulze, A., Worheide, G., Adamska, M., Bailly, X., Breinholt, J., Browne, W. E., Diaz, M. C., Evans, N., Flot, J. F., Fogarty, N., Johnston, M., Kamel, B., Kawahara, A. Y., Laberge, T., Lavrov, D., Michonneau, F., Moroz, L. L., Oakley, T., Osborne, K., Pomponi, S. A., Rhodes, A., Santos, S. R., Satoh, N., Thacker, R. W., Van de Peer, Y., Voolstra, C. R., Mark Welch, D. B., Winston, J., & Zhou, X. (2014). “The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.” J Hered, 105(1), 1-18. doi:10.1093/jhered/est08.

Shafquat, A., Joice, R., Simmons, S. L., & Huttenhower, C. (2014). “Functional and phylogenetic assembly of microbial communities in the human microbiome.” Trends Microbiol, 22(5), 261-266. doi:10.1016/j.tim.2014.01.01.

Shilova, I. N., Robidart, J. C., James Tripp, H., Turk-Kubo, K., Wawrik, B., Post, A. F., Thompson, A. W., Ward, B., Hollibaugh, J. T., Millard, A., Ostrowski, M., Scanlan, D. J., Paerl, R. W., Stuart, R., & Zehr, J. P. (2014). “A microarray for assessing transcription from pelagic marine microbial taxa.” ISME J, 8(7), 1476-1491. doi:10.1038/ismej.2014..

Smith, J., & Cosentino, C. (2014). “Reliability and Modularity in the Sea Urchin Gene Regulatory Network for Endomesoderm Specification.” Paper presented at the Integrative and Comparative Biology, Austin, TX.

Swan, B. K., Chaffin, M. D., Martinez-Garcia, M., Morrison, H. G., Field, E. K., Poulton, N. J., Masland, E. D., Harris, C. C., Sczyrba, A., Chain, P. S., Koren, S., Woyke, T., & Stepanauskas, R. (2014). “Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres.” PLoS One, 9(4), e95380. doi:10.1371/journal.pone.009538.

Thompson, A., Vo, D., Comfort, C., & Zakon, H. H. (2014). “Expression evolution facilitated the convergent neofunctionalization of a sodium channel gene.” Mol Biol Evol, 31(8), 1941-1955. doi:10.1093/molbev/msu14.

Vallino, J., Algar, C., González, N., & Huber, J. (2014). “Use of Receding Horizon Optimal Control to Solve MaxEP-Based Biogeochemistry Problems.” In R. C. Dewar, C. H. Lineweaver, R. K. Niven, & K. Regenauer-Lieb (Ed.), Beyond the Second Law (pp. 337-359): Springer Berlin Heidelberg.

Vick-Majors, T. J., Priscu, J. C., & Amaral-Zettler, L. A. (2014). “Modular community structure suggests metabolic plasticity during the transition to polar night in ice-covered Antarctic lakes.” ISME J, 8(4), 778-789. doi:10.1038/ismej.2013.19.

Wey-Fabrizius, A. R., Herlyn, H., Rieger, B., Rosenkranz, D., Witek, A., Mark Welch, D. B., Ebersberger, I., & Hankeln, T. (2014). “Transcriptome data reveal Syndermatan relationships and suggest the evolution of endoparasitism in Acanthocephala via an epizoic stage.” PLoS One, 9(2), e88618. doi:10.1371/journal.pone.008861.

Wickham, S. A., Claessens, M., & Post, A. F. (2014). “Ciliates, microbes and nutrients: interactions in the seasonally mixed Gulf of Aqaba.” Journal of Plankton Research, 37(1), 258-271. doi:10.1093/plankt/fbu10.

Willger, S. D., Grim, S. L., Dolben, E. L., Shipunova, A., Hampton, T. H., Morrison, H. G., Filkins, L. M., O’Toole, G. A., Moulton, L. A., Ashare, A., Sogin, M. L., & Hogan, D. A. (2014). “Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis.” Microbiome, 2, 40. doi:10.1186/2049-2618-2-4.

Xu, Y., Vick-Majors, T. J., Morgan-Kiss, R., Priscu, J. C., & Amaral-Zettler, L. A. (2014). “Ciliate diversity, community structure, and novel taxa in lakes of the McMurdo Dry Valleys, Antarctica.” Biol Bull, 227(2), 175-190.

Zakon, H. (2014). “Hibernating mammals pass the acid test: multiple independent evolutions of enhanced proton block of sodium channels in acid-sensing pain receptors.” Brain Behav Evol, 83(4), 245-246. doi:10.1159/00036103.

2013

Akerman, N. H., Butterfield, D. A., & Huber, J. A. (2013). “Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids.” Front Microbiol, 4, 185. doi:10.3389/fmicb.2013.0018.

Alliegro, M. C., & Alliegro, M. A. (2013). “Localization of rRNA transcribed spacer domains in the nucleolinus and maternal procentrosomes of surf clam (Spisula) oocytes.” RNA Biol, 10(3), 391-396. doi:10.4161/rna.2354.

Amend, A. S., Oliver, T. A., Amaral-Zettler, L. A., Boetius, A., Fuhrman, J. A., Horner-Devine, M. C., Huse, S. M., Welch, D. B. M., Martiny, A. C., Ramette, A., Zinger, L., Sogin, M. L., & Martiny, J. B. H. (2013). “Macroecological patterns of marine bacteria on a global scale.” Journal of Biogeography, 40(4), 800-811. doi:10.1111/jbi.1203.

Arkhipova, I. R., & Rodriguez, F. (2013). “Genetic and epigenetic changes involving (retro)transposons in animal hybrids and polyploids.” Cytogenet Genome Res, 140(2-4), 295-311. doi:10.1159/00035206.

Arkhipova, I. R., Yushenova, I. A., & Rodriguez, F. (2013). “Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families.” Mob DNA, 4(1), 19. doi:10.1186/1759-8753-4-1.

Bennett, S. A., Coleman, M., Huber, J. A., Reddington, E., Kinsey, J. C., McIntyre, C., Seewald, J. S., & German, C. R. (2013). “Trophic regions of a hydrothermal plume dispersing away from an ultramafic-hosted vent-system: Von Damm vent-site, Mid-Cayman Rise.” Geochemistry Geophysics Geosystems, 14(2), 317-327. doi:DOI 10.1002/ggge.2006.

Duffy, J. E., Amaral-Zettler, L. A., Fautin, D. G., Paulay, G., Rynearson, T. A., Sosik, H. M., & Stachowicz, J. J. (2013). “Envisioning a Marine Biodiversity Observation Network.” Bioscience, 63(5), 350-361. doi:DOI 10.1525/bio.2013.63.5..

Eren, A. M., Maignien, L., Sul, W. J., Murphy, L. G., Grim, S. L., Morrison, H. G., & Sogin, M. L. (2013). “Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.” Methods Ecol Evol, 4(12). doi:10.1111/2041-210X.1211.

Eren, A. M., Vineis, J. H., Morrison, H. G., & Sogin, M. L. (2013). “A filtering method to generate high quality short reads using illumina paired-end technology.” PLoS One, 8(6), e66643. doi:10.1371/journal.pone.006664.

Feehery, G. R., Yigit, E., Oyola, S. O., Langhorst, B. W., Schmidt, V. T., Stewart, F. J., Dimalanta, E. T., Amaral-Zettler, L. A., Davis, T., Quail, M. A., & Pradhan, S. (2013). “A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.” PLoS One, 8(10), e76096. doi:10.1371/journal.pone.007609.

Fischer, A. H., Tulin, S., Fredman, D., & Smith, J. (2013). “Employing BAC-reporter constructs in the sea anemone Nematostella vectensis.” Integr Comp Biol, 53(5), 832-846. doi:10.1093/icb/ict09.

Flot, J. F., Hespeels, B., Li, X., Noel, B., Arkhipova, I. R., Danchin, E. G., Hejnol, A., Henrissat, B., Koszul, R., Aury, J. M., Barbe, V., Barthelemy, R. M., Bast, J., Bazykin, G. A., Chabrol, O., Couloux, A., Da Rocha, M., Da Silva, C., Gladyshev, E., Gouret, P., Hallatschek, O., Hecox-Lea, B., Labadie, K., Lejeune, B., Piskurek, O., Poulain, J., Rodriguez, F., Ryan, J. F., Vakhrusheva, O. A., Wajnberg, E., Wirth, B., Yushenova, I. A., Kellis, M., Kondrashov, A. S., Mark Welch, D. B., Pontarotti, P., Weissenbach, J., Wincker, P., Jaillon, O., & Van Doninck, K. (2013). “Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.” Nature, 500(7463), 453-457. doi:10.1038/nature1232.

Fortunato, C. S., Eiler, A., Herfort, L., Needoba, J. A., Peterson, T. D., & Crump, B. C. (2013). “Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin.” ISME J, 7(10), 1899-1911. doi:10.1038/ismej.2013.7.

Gribble, K. E., & Mark Welch, D. B. (2013). “Life-span extension by caloric restriction is determined by type and level of food reduction and by reproductive mode in Brachionus manjavacas (Rotifera).” J Gerontol A Biol Sci Med Sci, 68(4), 349-358. doi:10.1093/gerona/gls17.

Gupta, R. W., Tran, L., Norori, J., Ferris, M. J., Eren, A. M., Taylor, C. M., Dowd, S. E., & Penn, D. (2013). “Histamine-2 receptor blockers alter the fecal microbiota in premature infants.” J Pediatr Gastroenterol Nutr, 56(4), 397-400. doi:10.1097/MPG.0b013e318282a8c.

Hanson, S. J., Schurko, A. M., Hecox-Lea, B., Mark Welch, D. B., Stelzer, C. P., & Logsdon, J. M. Jr. (2013). “Inventory and phylogenetic analysis of meiotic genes in monogonont rotifers.” J Hered, 104(3), 357-370. doi:10.1093/jhered/est01.

Hanson, S. J., Stelzer, C. P., Mark Welch, D. B., & Logsdon, J. M. Jr. (2013). “Comparative transcriptome analysis of obligately asexual and cyclically sexual rotifers reveals genes with putative functions in sexual reproduction, dormancy, and asexual egg production.” BMC Genomics, 14, 412. doi:10.1186/1471-2164-14-41.

Helm, R. R., Siebert, S., Tulin, S., Smith, J., & Dunn, C. W. (2013). “Characterization of differential transcript abundance through time during Nematostella vectensis development.” BMC Genomics, 14, 266. doi:10.1186/1471-2164-14-26.

Huse, S. M., Mark Welch, D. B., & Sogin, M. L. (2013). “Sequencing errors, diversity estimates and the rare biosphere The Science and Applications of Microbial Genomics: Workshop Summary (pp.” 188-207). Institute of Medicine. Washington, DC: The National Academies Press.

Kamennaya, N. A., & Post, A. F. (2013). “Distribution and expression of the cyanate acquisition potential among cyanobacterial populations in oligotrophic marine waters.” Limnology and Oceanography, 58(6), 1959-1971. doi:DOI 10.4319/lo.2013.58.6.195.

Light, J. E., Hafner, J. C., Upham, N. S., & Reddington, E. (2013). “Conservation Genetics of Kangaroo Mice, Genus Microdipodops.” Journal of Mammalian Evolution, 20(2), 129-146. doi:10.1007/s10914-012-9193-2.

Liu, C. M., Hungate, B. A., Toblan, A. A. R., Serwadda, D., Ravel, J., Lester, R., Kigozi, G., Aziz, M., Galiwango, R. M., Nalugoda, F., Contente-Cuomo, T. L., Wawer, M. J., Kelm, P., Gray, R. H., & Price, L. B. (2013). “Male circumcision significantly reduces prevalence and load of genital anaerobic bacteria.” MBio, 4. doi:10.1128/mBio.00076-1.

Maignien, L., Parkes, R. J., Cragg, B., Niemann, H., Knittel, K., Coulon, S., Akhmetzhanov, A., & Boon, N. (2013). “Anaerobic oxidation of methane in hypersaline cold seep sediments.” FEMS Microbiol Ecol, 83(1), 214-231. doi:10.1111/j.1574-6941.2012.01466..

Marteinsson, V. T., Runarsson, A., Stefansson, A., Thorsteinsson, T., Johannesson, T., Magnusson, S. H., Reynisson, E., Einarsson, B., Wade, N., Morrison, H. G., & Gaidos, E. (2013). “Microbial communities in the subglacial waters of the Vatnajokull ice cap, Iceland.” ISME J, 7(2), 427-437. doi:10.1038/ismej.2012.9.

Materna, S. C., Swartz, S. Z., & Smith, J. (2013). “Notch and Nodal control forkhead factor expression in the specification of multipotent progenitors in sea urchin.” Development, 140(8), 1796-1806. doi:10.1242/dev.09115.

McLellan, S. L., Newton, R. J., Vandewalle, J. L., Shanks, O. C., Huse, S. M., Eren, A. M., & Sogin, M. L. (2013). “Sewage reflects the distribution of human faecal Lachnospiraceae.” Environ Microbiol, 15(8), 2213-2227. doi:10.1111/1462-2920.1209.

Merkel, A. Y., Huber, J. A., Chernyh, N. A., Bonch-Osmolovskaya, E. A., & Lebedinsky, A. V. (2013). “Detection of putatively thermophilic anaerobic methanotrophs in diffuse hydrothermal vent fluids.” Appl Environ Microbiol, 79(3), 915-923. doi:10.1128/AEM.03034-1.

Meyer, J. L., Akerman, N. H., Proskurowski, G., & Huber, J. A. (2013). “Microbiological characterization of post-eruption “snowblower” vents at Axial Seamount, Juan de Fuca Ridge.” Front Microbiol, 4, 153. doi:10.3389/fmicb.2013.0015.

Newton, R. J., Bootsma, M. J., Morrison, H. G., Sogin, M. L., & McLellan, S. L. (2013). “A microbial signature approach to identify fecal pollution in the waters off an urbanized coast of Lake Michigan.” Microb Ecol, 65(4), 1011-1023. doi:10.1007/s00248-013-0200-.

Newton, R. J., Huse, S. M., Morrison, H. G., Peake, C. S., Sogin, M. L., & McLellan, S. L. (2013). “Shifts in the microbial community composition of Gulf Coast beaches following beach oiling.” PLoS One, 8(9), e74265. doi:10.1371/journal.pone.007426.

Price, K. E., Hampton, T. H., Gifford, A. H., Dolben, E. L., Hogan, D. A., Morrison, H. G., Sogin, M. L., & O’Toole, G. A. (2013). “Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation.” Microbiome, 1(1), 27. doi:10.1186/2049-2618-1-2.

Rozhkov, N. V., Schostak, N. G., Zelentsova, E. S., Yushenova, I. A., Zatsepina, O. G., & Evgen’ev, M. B. (2013). “Evolution and dynamics of small RNA response to a retroelement invasion in Drosophila.” Mol Biol Evol, 30(2), 397-408. doi:10.1093/molbev/mss24.

Shanks, O. C., Newton, R. J., Kelty, C. A., Huse, S. M., Sogin, M. L., & McLellan, S. L. (2013). “Comparison of the microbial community structures of untreated wastewaters from different geographic locales.” Appl Environ Microbiol, 79(9), 2906-2913. doi:10.1128/AEM.03448-1.

Sul, W. J., Oliver, T. A., Ducklow, H. W., Amaral-Zettler, L. A., & Sogin, M. L. (2013). “Marine bacteria exhibit a bipolar distribution.” Proc Natl Acad Sci U S A, 110(6), 2342-2347. doi:10.1073/pnas.121242411.

Taylor, R. C., Webb Robertson, B. J., Markillie, L. M., Serres, M. H., Linggi, B. E., Aldrich, J. T., Hill, E. A., Romine, M. F., Lipton, M. S., & Wiley, H. S. (2013). “Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria.” Integr Biol (Camb), 5(11), 1393-1406. doi:10.1039/c3ib40120.

Theroux, S., Toney, J., Amaral-Zettler, L. A., & Huang, Y. S. (2013). “Production and temperature sensitivity of long chain alkenones in the cultured haptophyte Pseudoisochrysis paradoxa.” Organic Geochemistry, 62, 68-73. doi:DOI 10.1016/j.orggeochem.2013.07.00.

Tulin, S., Aguiar, D., Istrail, S., & Smith, J. (2013). “A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems.” Evodevo, 4(1), 16. doi:10.1186/2041-9139-4-1.

Ver Eecke, H. C., Akerman, N. H., Huber, J. A., Butterfield, D. A., & Holden, J. F. (2013). “Growth kinetics and energetics of a deep-sea hyperthermophilic methanogen under varying environmental conditions.” Environ Microbiol Rep, 5(5), 665-671. doi:10.1111/1758-2229.1206.

Vital, M., Penton, C. R., Wang, Q., Young, V. B., Antonopoulos, D. A., Sogin, M. L., Morrison, H. G., Raffals, L., Chang, E. B., Huffnagle, G. B., Schmidt, T. M., Cole, J. R., & Tiedje, J. M. (2013). “A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community.” Microbiome, 1(1), 8. doi:10.1186/2049-2618-1-.

Woodring, J. L., Bland, N. D., Ochiana, S. O., Campbell, R. K., & Pollastri, M. P. (2013). “Synthesis and assessment of catechol diether compounds as inhibitors of trypanosomal phosphodiesterase B1 (TbrPDEB1).” Bioorg Med Chem Lett, 23(21), 5971-5974. doi:10.1016/j.bmcl.2013.08.05.

Young, V. B., Raffals, L. H., Huse, S. M., Vital, M., Dai, D., Schloss, P. D., Brulc, J. M., Antonopoulos, D. A., Arrieta, R. L., Kwon, J. H., Reddy, K. G., Hubert, N. A., Grim, S. L., Vineis, J. H., Dalal, S., Morrison, H. G., Eren, A. M., Meyer, F., Schmidt, T. M., Tiedje, J. M., Chang, E. B., & Sogin, M. L. (2013). “Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis.” Microbiome, 1(1), 9. doi:10.1186/2049-2618-1-.

Zettler, E. R., Mincer, T. J., & Amaral-Zettler, L. A. (2013). “Life in the “plastisphere”: microbial communities on plastic marine debris.” Environ Sci Technol, 47(13), 7137-7146. doi:10.1021/es401288.

2012

Alliegro, M. C., Hartson, S., & Alliegro, M. A. (2012). “Composition and dynamics of the nucleolinus, a link between the nucleolus and cell division apparatus in surf clam (Spisula) oocytes.” J Biol Chem, 287(9), 6702-6713. doi:10.1074/jbc.M111.28850.

Amaral-Zettler, L. A. (2012). “Eukaryotic diversity at pH extremes.” Front Microbiol, 3, 441. doi:10.3389/fmicb.2012.0044.

Arkhipova, I. R. (2012). “Telomerase, retrotransposons, and evolution.” In N. F. Lue & C. Autexier (Ed.), Telomerases: Chemistry, Biology and Clinical Applications (pp. 265-299). Hoboken, NJ: Wiley and Sons, Inc. .

Arkhipova, I. R., Batzer, M. A., Brosius, J., Feschotte, C., Moran, J. V., Schmitz, J., & Jurka, J. (2012). “Genomic impact of eukaryotic transposable elements.” Mob DNA, 3(1), 19. doi:10.1186/1759-8753-3-1.

Atamna-Ismaeel, N., Finkel, O. M., Glaser, F., Sharon, I., Schneider, R., Post, A. F., Spudich, J. L., von Mering, C., Vorholt, J. A., Iluz, D., Beja, O., & Belkin, S. (2012). “Microbial rhodopsins on leaf surfaces of terrestrial plants.” Environ Microbiol, 14(1), 140-146. doi:10.1111/j.1462-2920.2011.02554..

Beg, Q. K., Zampieri, M., Klitgord, N., Collins, S. B., Altafini, C., Serres, M. H., & Segre, D. (2012). “Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis.” Nucleic Acids Res, 40(15), 7132-7149. doi:10.1093/nar/gks46.

Bowen, J. L., Morrison, H. G., Hobbie, J. E., & Sogin, M. L. (2012). “Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates.” ISME J, 6(11), 2014-2023. doi:10.1038/ismej.2012.4.

Brandt, B. W., Bonder, M. J., Huse, S. M., & Zaura, E. (2012). “TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage.” Nucleic Acids Res, 40(Web Server issue), W82-87. doi:10.1093/nar/gks41.

Breier, J. A., Gomez-Ibanez, D., Reddington, E., Huber, J. A., & Emerson, D. (2012). “A precision multi-sampler for deep-sea hydrothermal microbial mat studies.” Deep-Sea Research Part I-Oceanographic Research Papers, 70(0), 83-90. doi:DOI 10.1016/j.dsr.2012.10.00.

Chandsawangbhuwana, C., Shi, L. Z., Zhu, Q., Alliegro, M. C., & Berns, M. W. (2012). “High-throughput optofluidic system for the laser microsurgery of oocytes.” J Biomed Opt, 17(1), 015001. doi:10.1117/1.JBO.17.1.01500.

Chapman, M., & Alliegro, M. C. (2012). “The karyomastigont as an evolutionary seme.” Q Rev Biol, 87(4), 315-324.

Crump, B. C., Amaral-Zettler, L. A., & Kling, G. W. (2012). “Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils.” ISME J, 6(9), 1629-1639. doi:10.1038/ismej.2012..

Davies, N., Meyer, C., Gilbert, J. A., Amaral-Zettler, L. A., Deck, J., Bicak, M., Rocca-Serra, P., Assunta-Sansone, S., Willis, K., & Field, D. (2012). “A call for an international network of genomic observatories (GOs).” Gigascience, 1(1), 5. doi:10.1186/2047-217X-1-.

Filkins, L. M., Hampton, T. H., Gifford, A. H., Gross, M. J., Hogan, D. A., Sogin, M. L., Morrison, H. G., Paster, B. J., & O’Toole, G. A. (2012). “Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability.” J Bacteriol, 194(17), 4709-4717. doi:10.1128/JB.00566-1.

Finkel, O. M., Burch, A. Y., Elad, T., Huse, S. M., Lindow, S. E., Post, A. F., & Belkin, S. (2012). “Distance-decay relationships partially determine diversity patterns of phyllosphere bacteria on Tamarix trees across the Sonoran Desert [corrected].” Appl Environ Microbiol, 78(17), 6187-6193. doi:10.1128/AEM.00888-1.

Fischer, A. H. L., & Smith, J. (2012). “Evo-devo in the era of gene regulatory networks.” Integr Comp Biol, 52(6), 842-849. doi:10.1093/icb/ics11.

Freitas, S., Hatosy, S., Fuhrman, J. A., Huse, S. M., Mark Welch, D. B., Sogin, M. L., & Martiny, A. C. (2012). “Global distribution and diversity of marine Verrucomicrobia.” ISME J, 6(8), 1499-1505. doi:10.1038/ismej.2012..

Gilbert, J. A., Steele, J. A., Caporaso, J. G., Steinbruck, L., Reeder, J., Temperton, B., Huse, S. M., McHardy, A. C., Knight, R., Joint, I., Somerfield, P., Fuhrman, J. A., & Field, D. (2012). “Defining seasonal marine microbial community dynamics.” ISME J, 6(2), 298-308. doi:10.1038/ismej.2011.10.

Gobet, A., Boer, S. I., Huse, S. M., van Beusekom, J. E., Quince, C., Sogin, M. L., Boetius, A., & Ramette, A. (2012). “Diversity and dynamics of rare and of resident bacterial populations in coastal sands.” ISME J, 6(3), 542-553. doi:10.1038/ismej.2011.13.

Gribble, K. E., & Mark Welch, D. B. (2012). “The mate recognition protein gene mediates reproductive isolation and speciation in the Brachionus plicatilis cryptic species complex.” BMC Evol Biol, 12(1), 134. doi:10.1186/1471-2148-12-13.

Huse, S. M., Ye, Y., Zhou, Y., & Fodor, A. A. (2012). “A core human microbiome as viewed through 16S rRNA sequence clusters.” PLoS One, 7(6), e34242. doi:10.1371/journal.pone.003424.

Kozul-Horvath, C. D., Zandbergen, F., Jackson, B. P., Enelow, R. I., & Hamilton, J. W. (2012). “Effects of low-dose drinking water arsenic on mouse fetal and postnatal growth and development.” PLoS One, 7(5), e38249. doi:10.1371/journal.pone.003824.

Lasek-Nesselquist, E. (2012). “A mitogenomic re-evaluation of the bdelloid phylogeny and relationships among the Syndermata.” PLoS One, 7(8), e43554. doi:10.1371/journal.pone.004355.

Looft, T., Johnson, T. A., Allen, H. K., Bayles, D. O., Alt, D. P., Stedtfeld, R. D., Sul, W. J., Stedtfeld, T. M., Chai, B., Cole, J. R., Hashsham, S. A., Tiedje, J. M., & Stanton, T. B. (2012). “In-feed antibiotic effects on the swine intestinal microbiome.” Proc Natl Acad Sci U S A, 109(5), 1691-1696. doi:10.1073/pnas.112023810.

Mackey, K. R. M., Roberts, K., Lomas, M. W., Saito, M. A., Post, A. F., & Paytan, A. (2012). “Enhanced solubility and ecological impact of atmospheric phosphorus deposition upon extended seawater exposure.” Environ Sci Technol, 46(19), 10438-10446. doi:10.1021/es300799.

Madan, J. C., Koestler, D. C., Stanton, B. A., Davidson, L., Moulton, L. A., Housman, M. L., Moore, J. H., Guill, M. F., Morrison, H. G., Sogin, M. L., Hampton, T. H., Karagas, M. R., Palumbo, P. E., Foster, J. A., Hibberd, P. L., & O’Toole, G. A. (2012). “Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures.” MBio, 3(4). doi:10.1128/mBio.00251-1.

Madan, J. C., Salari, R. C., Saxena, D., Davidson, L., O’Toole, G. A., Moore, J. H., Sogin, M. L., Foster, J. A., Edwards, W. H., Palumbo, P., & Hibberd, P. L. (2012). “Gut microbial colonisation in premature neonates predicts neonatal sepsis.” Arch Dis Child Fetal Neonatal Ed, 97(6), F456-462. doi:10.1136/fetalneonatal-2011-30137.

McCliment, E. A., Nelson, C. E., Carlson, C. A., Alldredge, A. L., Witting, J., & Amaral-Zettler, L. A. (2012). “An all-taxon microbial inventory of the Moorea coral reef ecosystem.” ISME J, 6(2), 309-319. doi:10.1038/ismej.2011.10.

Meeder, E., Mackey, K. R. M., Paytan, A., Shaked, Y., Iluz, D., Stambler, N., Rivlin, T., Post, A. F., & Lazar, B. (2012). “Nitrite dynamics in the open ocean—clues from seasonal and diurnal variations.” Marine Ecology Progress Series, 453, 11-26. doi:10.3354/meps0952.

Ochiana, S. O., Gustafson, A., Bland, N. D., Wang, C., Russo, M. J., Campbell, R. K., & Pollastri, M. P. (2012). “Synthesis and evaluation of human phosphodiesterases (PDE) 5 inhibitor analogs as trypanosomal PDE inhibitors.” Part 2. Tadalafil analogs. Bioorg Med Chem Lett, 22(7), 2582-2584. doi:10.1016/j.bmcl.2012.01.11.

Ozok, A. R., Persoon, I. F., Huse, S. M., Keijser, B. J., Wesselink, P. R., Crielaard, W., & Zaura, E. (2012). “Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments.” Int Endod J, 45(6), 530-541. doi:10.1111/j.1365-2591.2011.02006..

Sansone, S. A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral-Zettler, L. A., Begley, K., Booth, T., Bougueleret, L., Burns, G., Chapman, B., Clark, T., Coleman, L. A., Copeland, J., Das, S., de Daruvar, A., de Matos, P., Dix, I., Edmunds, S., Evelo, C. T., Forster, M. J., Gaudet, P., Gilbert, J., Goble, C., Griffin, J. L., Jacob, D., Kleinjans, J., Harland, L., Haug, K., Hermjakob, H., Ho Sui, S. J., Laederach, A., Liang, S., Marshall, S., McGrath, A., Merrill, E., Reilly, D., Roux, M., Shamu, C. E., Shang, C. A., Steinbeck, C., Trefethen, A., Williams-Jones, B., Wolstencroft, K., Xenarios, I., & Hide, W. (2012). “Toward interoperable bioscience data.” Nat Genet, 44(2), 121-126. doi:10.1038/ng.105.

Siam, R., Mustafa, G. A., Sharaf, H., Moustafa, A., Ramadan, A. R., Antunes, A., Bajic, V. B., Stingl, U., Marsis, N. G., Coolen, M. J., Sogin, M. L., Ferreira, A. J., & Dorry, H. E. (2012). “Unique prokaryotic consortia in geochemically distinct sediments from Red Sea Atlantis II and discovery deep brine pools.” PLoS One, 7(8), e42872. doi:10.1371/journal.pone.004287.

Smith, K. F., Schmidt, V. T., Rosen, G. E., & Amaral-Zettler, L. A. (2012). “Microbial diversity and potential pathogens in ornamental fish aquarium water.” PLoS One, 7(9), e39971. doi:10.1371/journal.pone.003997.

Sogin, M. L. (2012). “Trying to Make Sense of the Microbial Census.” In S. Maloy & R. Kolter (Ed.), Microbes and Evolution: The World That Darwin Never Saw (pp. 31-37). Washington, DC: ASM Press.

Sukenik, A., Kaplan-Levy, R. N., Mark Welch, J. L., & Post, A. F. (2012). “Massive multiplication of genome and ribosomes in dormant cells (akinetes) of Aphanizomenon ovalisporum (Cyanobacteria).” ISME J, 6(3), 670-679. doi:10.1038/ismej.2011.12.

Sun, Y., Cai, Y., Huse, S. M., Knight, R., Farmerie, W. G., Wang, X., & Mai, V. (2012). “A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis.” Brief Bioinform, 13(1), 107-121. doi:10.1093/bib/bbr00.

Takumi, K., Swart, A., Mank, T., Lasek-Nesselquist, E., Lebbad, M., Caccio, S. M., & Sprong, H. (2012). “Population-based analyses of Giardia duodenalis is consistent with the clonal assemblage structure.” Parasit Vectors, 5, 168. doi:10.1186/1756-3305-5-16.

Theroux, S., Huang, Y., & Amaral-Zettler, L. (2012). “Comparative Molecular Microbial Ecology of the Spring Haptophyte Bloom in a Greenland Arctic Oligosaline Lake.” Frontiers in Microbiology, 3, 415.

Toney, J. L., Theroux, S., Andersen, R. A., Coleman, A., Amaral-Zettler, L. A., & Huang, Y. S. (2012). “Culturing of the first 37:4 predominant lacustrine haptophyte: Geochemical, biochemical, and genetic implications.” Geochimica Et Cosmochimica Acta, 78, 51-64. doi:DOI 10.1016/j.gca.2011.11.02.

Valm, A. M., Mark Welch, J. L., & Borisy, G. G. (2012). “CLASI-FISH: principles of combinatorial labeling and spectral imaging.” Syst Appl Microbiol, 35(8), 496-502. doi:10.1016/j.syapm.2012.03.00.

Vandewalle, J. L., Goetz, G. W., Huse, S. M., Morrison, H. G., Sogin, M. L., Hoffmann, R. G., Yan, K., & McLellan, S. L. (2012). “Acinetobacter, Aeromonas and Trichococcus populations dominate the microbial community within urban sewer infrastructure.” Environ Microbiol, 14(9), 2538-2552. doi:10.1111/j.1462-2920.2012.02757..

Ver Eecke, H. C., Butterfield, D. A., Huber, J. A., Lilley, M. D., Olson, E. J., Roe, K. K., Evans, L. J., Merkel, A. Y., Cantin, H. V., & Holden, J. F. (2012). “Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents.” Proc Natl Acad Sci U S A, 109(34), 13674-13679. doi:10.1073/pnas.120663210.

Wang, C., Ashton, T. D., Gustafson, A., Bland, N. D., Ochiana, S. O., Campbell, R. K., & Pollastri, M. P. (2012). “Synthesis and evaluation of human phosphodiesterases (PDE) 5 inhibitor analogs as trypanosomal PDE inhibitors.” Part 1. Sildenafil analogs. Bioorg Med Chem Lett, 22(7), 2579-2581. doi:10.1016/j.bmcl.2012.01.11.

Wolf, B., Schwarzer, A., Cote, A. L., Hampton, T. H., Schwaab, T., Huarte, E., Tomlinson, C. R., Gui, J., Fisher, J. L., Fadul, C. E., Hamilton, J. W., & Ernstoff, M. S. (2012). “Gene expression profile of peripheral blood lymphocytes from renal cell carcinoma patients treated with IL-2, interferon-alpha and dendritic cell vaccine.” PLoS One, 7(12), e50221. doi:10.1371/journal.pone.005022.

Yager, P. L., Sherrell, R. M., Stammerjohn, S. E., Alderkamp, A. C., Schofield, O., Abrahamsen, E. P., Arrigo, K. R., Bertilsson, S., Garay, D. L., Guerrero, R., Lowry, K. E., Moksnes, P. O., Ndungu, K., Post, A. F., Randall-Goodwin, E., Riemann, L., Severmann, S., Thatje, S., van Dijken, G. L., & Wilson, S. (2012). “ASPIRE The Amundsen Sea Polynya International Research Expedition.” Oceanography, 25(3), 40-53. doi:http://dx.doi.org/10.5670/oceanog.2012.73.

2011

Agogue, H., Lamy, D., Neal, P. R., Sogin, M. L., & Herndl, G. J. (2011). “Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing.” Mol Ecol, 20(2), 258-274. doi:10.1111/j.1365-294X.2010.04932..

Akerman, N. H., Price, R. E., Pichler, T., & Amend, J. P. (2011). “Energy sources for chemolithotrophs in an arsenic- and iron-rich shallow-sea hydrothermal system.” Geobiology, 9(5), 436-445. doi:10.1111/j.1472-4669.2011.00291..

Alliegro, M. C. (2011). “The Nucleolinus: A disappearing, forgotten and (maybe) misnamed organelle.” Commun Integr Biol, 4(2), 147-149. doi:10.4161/cib.4.2.1454.

Alliegro, M. C. (2011). “The centrosome and spindle as a ribonucleoprotein complex.” Chromosome Res, 19(3), 367-376. doi:10.1007/s10577-011-9186-.

Amaral-Zettler, L. A., Zettler, E. R., Theroux, S. M., Palacios, C., Aguilera, A., & Amils, R. (2011). “Microbial community structure across the tree of life in the extreme Rio Tinto.” ISME J, 5(1), 42-50. doi:10.1038/ismej.2010.10.

Bland, N. D., Wang, C., Tallman, C., Gustafson, A. E., Wang, Z., Ashton, T. D., Ochiana, S. O., McAllister, G., Cotter, K., Fang, A. P., Gechijian, L., Garceau, N., Gangurde, R., Ortenberg, R., Ondrechen, M. J., Campbell, R. K., & Pollastri, M. P. (2011). “Pharmacological validation of Trypanosoma brucei phosphodiesterases B1 and B2 as druggable targets for African sleeping sickness.” J Med Chem, 54(23), 8188-8194. doi:10.1021/jm201148.

Bogaert, D., Keijser, B., Huse, S. M., Rossen, J., Veenhoven, R., van Gils, E., Bruin, J., Montijn, R., Bonten, M., & Sanders, E. (2011). “Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis.” PLoS One, 6(2), e17035. doi:10.1371/journal.pone.001703.

Bowen, J. L., Ward, B. B., Morrison, H. G., Hobbie, J. E., Valiela, I., Deegan, L. A., & Sogin, M. L. (2011). “Microbial community composition in sediments resists perturbation by nutrient enrichment.” ISME J, 5(9), 1540-1548. doi:10.1038/ismej.2011.2.

Crielaard, W., Zaura, E., Schuller, A. A., Huse, S. M., Montijn, R. C., & Keijser, B. J. (2011). “Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health.” BMC Med Genomics, 4, 22. doi:10.1186/1755-8794-4-2.

Eren, A. M., Zozaya, M., Taylor, C. M., Dowd, S. E., Martin, D. H., & Ferris, M. J. (2011). “Exploring the diversity of Gardnerella vaginalis in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation.” PLoS One, 6(10), e26732. doi:10.1371/journal.pone.002673.

Field, D., Amaral-Zettler, L. A., Cochrane, G., Cole, J. R., Dawyndt, P., Garrity, G. M., Gilbert, J., Glockner, F. O., Hirschman, L., Karsch-Mizrachi, I., Klenk, H. P., Knight, R., Kottmann, R., Kyrpides, N., Meyer, F., San Gil, I., Sansone, S. A., Schriml, L. M., Sterk, P., Tatusova, T., Ussery, D. W., White, O., & Wooley, J. (2011). “The Genomic Standards Consortium.” PLoS Biol, 9(6), e1001088. doi:10.1371/journal.pbio.100108.

Finkel, O. M., Burch, A. Y., Lindow, S. E., Post, A. F., & Belkin, S. (2011). “Geographical location determines the population structure in phyllosphere microbial communities of a salt-excreting desert tree.” Appl Environ Microbiol, 77(21), 7647-7655. doi:10.1128/AEM.05565-1.

Garbuz, D. G., Astakhova, L. N., Zatsepina, O. G., Arkhipova, I. R., Nudler, E., & Evgen’ev, M. B. (2011). “Functional organization of hsp70 cluster in camel (Camelus dromedarius) and other mammals.” PLoS One, 6(11), e27205. doi:10.1371/journal.pone.002720.

Garbuz, D. G., Yushenova, I. A., Zatsepina, O. G., Przhiboro, A. A., Bettencourt, B. R., & Evgen’ev, M. B. (2011). “Organization and evolution of hsp70 clusters strikingly differ in two species of Stratiomyidae (Diptera) inhabiting thermally contrasting environments.” BMC Evol Biol, 11, 74. doi:10.1186/1471-2148-11-7.

Gast, R. J., Moran, D. M., Dennett, M. R., Wurtsbaugh, W. A., & Amaral-Zettler, L. A. (2011). “Amoebae and Legionella pneumophila in saline environments.” J Water Health, 9(1), 37-52. doi:10.2166/wh.2010.10.

Gladyshev, E. A., & Arkhipova, I. R. (2011). “A widespread class of reverse transcriptase-related cellular genes.” Proc Natl Acad Sci U S A, 108(51), 20311-20316. doi:10.1073/pnas.110026610.

Gribble, K. E., Snell, T. W., & Mark Welch, D. B. (2011). “Gene and protein structure of the mate recognition protein gene family in Brachionus manjavacas (Rotifera).” Hydrobiologia, 662(1), 35-42. doi:DOI 10.1007/s10750-010-0482-.

Huse, S. M., & Mark Welch, D. (2011). “Accuracy and quality of massively parallel DNA pyrosequencing In F.” J. de Bruijn (Ed.), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches (pp. 149-156): Wiley and Sons.

Kamennaya, N. A., & Post, A. F. (2011). “Characterization of cyanate metabolism in marine Synechococcus and Prochlorococcus spp.” Appl Environ Microbiol, 77(1), 291-301. doi:10.1128/AEM.01272-1.

Mackey, K. R. M., Bristow, L., Parks, D. R., Altabet, M. A., Post, A. F., & Paytan, A. (2011). “The influence of light on nitrogen cycling and the primary nitrite maximum in a seasonally stratified sea.” Progress in Oceanography, 91(4), 545-560. doi:DOI 10.1016/j.pocean.2011.09.00.

Mark Welch, D. B., & Huse, S. H. (2011). “Microbial diversity in the deep sea and the underexplored “rare biosphere.” In F. J. de Bruijn (Ed.), Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats (pp. 245-252): Wiley and Sons.

Nelson, C. E., Alldredge, A. L., McCliment, E. A., Amaral-Zettler, L. A., & Carlson, C. A. (2011). “Depleted dissolved organic carbon and distinct bacterial communities in the water column of a rapid-flushing coral reef ecosystem.” ISME J, 5(8), 1374-1387. doi:10.1038/ismej.2011.1.

Nuzzio, D. B., Zettler, E. R., Aguilera, A., & Amaral-Zettler, L. A. (2011). “A direct in situ fingerprinting method for acid rock drainage using voltammetric techniques with a single renewable gold microelectrode.” Sci Total Environ, 409(10), 1984-1989. doi:10.1016/j.scitotenv.2011.01.00.

Oleksiak, M. F., Karchner, S. I., Jenny, M. J., Franks, D. G., Mark Welch, D. B., & Hahn, M. E. (2011). “Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site.” BMC Genomics, 12(1), 263. doi:10.1186/1471-2164-12-26.

Pawlowski, J., Christen, R., Lecroq, B., Bachar, D., Shahbazkia, H. R., Amaral-Zettler, L. A., & Guillou, L. (2011). “Eukaryotic richness in the abyss: insights from pyrotag sequencing.” PLoS One, 6(4), e18169. doi:10.1371/journal.pone.001816.

Perry, D. A., Morrison, H. G., & Adam, R. D. (2011). “Optical map of the genotype A1 WB C6 Giardia lamblia genome isolate.” Mol Biochem Parasitol, 180(2), 112-114. doi:10.1016/j.molbiopara.2011.07.00.

Pollastri, M. P., & Campbell, R. K. (2011). “Target repurposing for neglected diseases.” Future Med Chem, 3(10), 1307-1315. doi:10.4155/fmc.11.9.

Post, A. F., Penno, S., Zandbank, K., Paytan, A., Huse, S. M., & Welch, D. M. (2011). “Long term seasonal dynamics of synechococcus population structure in the gulf of aqaba, northern red sea.” Front Microbiol, 2, 131. doi:10.3389/fmicb.2011.0013.

Resing, J. A., Rubin, K. H., Embley, R. W., Lupton, J. E., Baker, E. T., Dziak, R. P., Baumberger, T., Lilley, M. D., Huber, J. A., Shank, T. M., Butterfield, D. A., Clague, D. A., Keller, N. S., Merle, S. G., Buck, N. J., Michael, P. J., Soule, A., Caress, D. W., Walker, S. L., Davis, R., Cowen, J. P., Reysenbach, A. L., & Thomas, H. (2011). “Active submarine eruption of boninite in the northeastern Lau Basin.” Nature Geoscience, 4(11), 799-806. doi:Doi 10.1038/Ngeo127.

Rodrigues, J. L., Serres, M. H., & Tiedje, J. M. (2011). “Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of shewanella species and identify metabolic pathways conserved at the genus level.” Appl Environ Microbiol, 77(15), 5352-5360. doi:10.1128/AEM.00097-1.

Shanks, O. C., Kelty, C. A., Archibeque, S., Jenkins, M., Newton, R. J., McLellan, S. L., Huse, S. M., & Sogin, M. L. (2011). “Community structures of fecal bacteria in cattle from different animal feeding operations.” Appl Environ Microbiol, 77(9), 2992-3001. doi:10.1128/AEM.02988-1.

Shanks, O. C., McLellan, S. L., Huse, S. M., & Sogin, M. L. (2011). “Characterization of Microbial Community Structures in Recreational Waters and Primary Sources of Faecal Pollution with a Next-generation Sequencing Approach.” . In K. Sen & N. J. Ashbolt (Ed.), In Environmental Microbiology: Current Technology and Water Applications. Norfolk, UK: Caister Academic Press.

Smith, H. A., Mark Welch, D. B., & Snell, T. W. (2011). “Molecular evolution of the membrane associated progesterone receptor in the Brachionus plicatilis (Rotifera, Monogononta) species complex.” Hydrobiologia, 662(1), 99-106. doi:10.1007/s10750-010-0484-.

Smith, J., Morgan, J. R., Zottoli, S. J., Smith, P. J., Buxbaum, J. D., & Bloom, O. E. (2011). “Regeneration in the era of functional genomics and gene network analysis.” Biol Bull, 221(1), 18-34.

Sul, W. J., Cole, J. R., Jesus Eda, C., Wang, Q., Farris, R. J., Fish, J. A., & Tiedje, J. M. (2011). “Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering.” Proc Natl Acad Sci U S A, 108(35), 14637-14642. doi:10.1073/pnas.111143510.

Valm, A. M., Mark Welch, J. L., Rieken, C. W., Hasegawa, Y., Sogin, M. L., Oldenbourg, R., Dewhirst, F. E., & Borisy, G. G. (2011). “Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging.” Proc Natl Acad Sci U S A, 108(10), 4152-4157. doi:10.1073/pnas.110113410.

White, J., Gilbert, J. A., Hill, G., Hill, E., Huse, S. M., Weightman, A. J., & Mahenthiralingam, E. (2011). “Culture-independent analysis of bacterial fuel contamination provides insight into the level of concordance with the standard industry practice of aerobic cultivation.” Appl Environ Microbiol, 77(13), 4527-4538. doi:10.1128/AEM.02317-1.

Xia, L. C., Steele, J. A., Cram, J. A., Cardon, Z. G., Simmons, S. L., Vallino, J. J., Fuhrman, J. A., & Sun, F. (2011). “Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates.” BMC Syst Biol, 5 Suppl 2, S15. doi:10.1186/1752-0509-5-S2-S1.

Yelton, A. P., Thomas, B. C., Simmons, S. L., Wilmes, P., Zemla, A., Thelen, M. P., Justice, N., & Banfield, J. F. (2011). “A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes.” PLoS Comput Biol, 7(10), e1002230. doi:10.1371/journal.pcbi.100223.

Yilmaz, P., Gilbert, J. A., Knight, R., Amaral-Zettler, L. A., Karsch-Mizrachi, I., Cochrane, G., Nakamura, Y., Sansone, S. A., Glockner, F. O., & Field, D. (2011). “The genomic standards consortium: bringing standards to life for microbial ecology.” ISME J, 5(10), 1565-1567. doi:10.1038/ismej.2011.3.

Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J. R., Amaral-Zettler, L. A., Gilbert, J. A., Karsch-Mizrachi, I., Johnston, A., Cochrane, G., Vaughan, R., Hunter, C., Park, J., Morrison, N., Rocca-Serra, P., Sterk, P., Arumugam, M., Bailey, M., Baumgartner, L., Birren, B. W., Blaser, M. J., Bonazzi, V., Booth, T., Bork, P., Bushman, F. D., Buttigieg, P. L., Chain, P. S., Charlson, E., Costello, E. K., Huot-Creasy, H., Dawyndt, P., DeSantis, T., Fierer, N., Fuhrman, J. A., Gallery, R. E., Gevers, D., Gibbs, R. A., San Gil, I., Gonzalez, A., Gordon, J. I., Guralnick, R., Hankeln, W., Highlander, S., Hugenholtz, P., Jansson, J., Kau, A. L., Kelley, S. T., Kennedy, J., Knights, D., Koren, O., Kuczynski, J., Kyrpides, N., Larsen, R., Lauber, C. L., Legg, T., Ley, R. E., Lozupone, C. A., Ludwig, W., Lyons, D., Maguire, E., Methe, B. A., Meyer, F., Muegge, B., Nakielny, S., Nelson, K. E., Nemergut, D., Neufeld, J. D., Newbold, L. K., Oliver, A. E., Pace, N. R., Palanisamy, G., Peplies, J., Petrosino, J., Proctor, L., Pruesse, E., Quast, C., Raes, J., Ratnasingham, S., Ravel, J., Relman, D. A., Assunta-Sansone, S., Schloss, P. D., Schriml, L., Sinha, R., Smith, M. I., Sodergren, E., Spo, A., Stombaugh, J., Tiedje, J. M., Ward, D. V., Weinstock, G. M., Wendel, D., White, O., Whiteley, A., Wilke, A., Wortman, J. R., Yatsunenko, T., & Glockner, F. O. (2011). “Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.” Nat Biotechnol, 29(5), 415-420. doi:10.1038/nbt.182.

Zinger, L., Amaral-Zettler, L. A., Fuhrman, J. A., Horner-Devine, M. C., Huse, S. M., Mark Welch, D. B., Martiny, J. B., Sogin, M. L., Boetius, A., & Ramette, A. (2011). “Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems.” PLoS One, 6(9), e24570. doi:10.1371/journal.pone.002457.

2010

Adam, R. D., Nigam, A., Seshadri, V., Martens, C. A., Farneth, G. A., Morrison, H. G., Nash, T. E., Porcella, S. F., & Patel, R. (2010). “The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution.” BMC Genomics, 11(1), 424. doi:10.1186/1471-2164-11-42.

Adey, A., Morrison, H. G., Asan, Xun, X., Kitzman, J. O., Turner, E. H., Stackhouse, B., MacKenzie, A. P., Caruccio, N. C., Zhang, X., & Shendure, J. (2010). “Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.” Genome Biol, 11(12), R119. doi:10.1186/gb-2010-11-12-r11.

Alliegro, M. A., Henry, J. J., & Alliegro, M. C. (2010). “Rediscovery of the nucleolinus, a dynamic RNA-rich organelle associated with the nucleolus, spindle, and centrosomes.” Proc Natl Acad Sci U S A, 107(31), 13718-13723. doi:10.1073/pnas.100846910.

Amaral-Zettler, L. A., Artigas, L. F., Baross, J., Bharathi, L., Boetius, A., Chandramohan, D., Herndl, G., Kogure, K., Neal, P., Pedros-Alio, C., Ramette, A., Schouten, S., Stal, L., Thessen, A., de Leeuw, J., & Sogin, M. L. (2010). “A global census of marine microbes Life in the World’s Oceans: Diversity, Distribution and Abundance (Vol.” 1, pp. 223-245). Oxford: Blackwell Publishing Ltd.

Bodaker, I., Sharon, I., Suzuki, M. T., Feingersch, R., Shmoish, M., Andreishcheva, E., Sogin, M. L., Rosenberg, M., Maguire, M. E., Belkin, S., Oren, A., & Beja, O. (2010). “Comparative community genomics in the Dead Sea: an increasingly extreme environment.” ISME J, 4(3), 399-407. doi:10.1038/ismej.2009.14.

Bordenstein, S. R., Brothers, C., Wolfe, G., Bahr, M., Minckley, R. L., Clark, M. E., Wernegreen, J. J., Bordenstein, S. R., Reznikoff, W. S., & Werren, J. H. (2010). “Using the Wolbachia Bacterial Symbiont to Teach Inquiry-Based Science: A High School Laboratory Series.” American Biology Teacher, 72(8), 478-483. doi:DOI 10.1525/abt.2010.72.8..

Brazelton, W. J., Ludwig, K. A., Sogin, M. L., Andreishcheva, E. N., Kelley, D. S., Shen, C. C., Edwards, R. L., & Baross, J. A. (2010). “Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys.” Proc Natl Acad Sci U S A, 107(4), 1612-1617. doi:10.1073/pnas.090536910.

Chafee, M. E., Funk, D. J., Harrison, R. G., & Bordenstein, S. R. (2010). “Lateral phage transfer in obligate intracellular bacteria (wolbachia): verification from natural populations.” Mol Biol Evol, 27(3), 501-505. doi:10.1093/molbev/msp27.

Fei, D. L., Li, H., Kozul, C. D., Black, K. E., Singh, S., Gosse, J. A., DiRenzo, J., Martin, K. A., Wang, B., Hamilton, J. W., Karagas, M. R., & Robbins, D. J. (2010). “Activation of Hedgehog signaling by the environmental toxicant arsenic may contribute to the etiology of arsenic-induced tumors.” Cancer Res, 70(5), 1981-1988. doi:10.1158/0008-5472.CAN-09-289.

German, C. R., Bowen, A., Coleman, M. L., Honig, D. L., Huber, J. A., Jakuba, M. V., Kinsey, J. C., Kurz, M. D., Leroy, S., McDermott, J. M., de Lepinay, B. M., Nakamura, K., Seewald, J. S., Smith, J. L., Sylva, S. P., Van Dover, C. L., Whitcomb, L. L., & Yoerger, D. R. (2010). “Diverse styles of submarine venting on the ultraslow spreading Mid-Cayman Rise.” Proc Natl Acad Sci U S A, 107(32), 14020-14025. doi:10.1073/pnas.100920510.

Gilg, I. C., Amaral-Zettler, L. A., Countway, P. D., Moorthi, S., Schnetzer, A., & Caron, D. A. (2010). “Phylogenetic affiliations of mesopelagic acantharia and acantharian-like environmental 18S rRNA genes off the southern California coast.” Protist, 161(2), 197-211. doi:10.1016/j.protis.2009.09.00.

Gillor, O., Hadas, O. R. A., Post, A. F., & Belkin, S. (2010). “Phosphorus and nitrogen in a monomictic freshwater lake: employing cyanobacterial bioreporters to gain new insights into nutrient bioavailability.” Freshwater Biology, 55(6), 1182-1190. doi:DOI 10.1111/j.1365-2427.2009.02342..

Gladyshev, E. A., & Arkhipova, I. R. (2010). “Bdelloid rotifers McGraw Hill 2010 Yearbook of Science and Technology (pp.” 37-39). New York, NY: McGraw Hill Inc. .

Gladyshev, E. A., & Arkhipova, I. R. (2010). “A subtelomeric non-LTR retrotransposon Hebe in the bdelloid rotifer Adineta vaga is subject to inactivation by deletions but not 5′ truncations.” Mob DNA, 1(1), 12. doi:10.1186/1759-8753-1-1.

Gladyshev, E. A., & Arkhipova, I. R. (2010). “Genome structure of bdelloid rotifers: shaped by asexuality or desiccation?” J Hered, 101 Suppl 1, S85-93. doi:10.1093/jhered/esq00.

Hasegawa, Y., Welch, J. L. M., Valm, A. M., Rieken, C., Sogin, M. L., & Borisy, G. G. (2010). “Imaging Marine Bacteria with Unique 16S rRNA V6 Sequences by Fluorescence in situ Hybridization and Spectral Analysis.” Geomicrobiology Journal, 27(3), 251-260. doi:Pii 922060090 10.1080/0149045090345680.

Huber, J. A., Cantin, H. V., Huse, S. M., Mark Welch, D. B., Sogin, M. L., & Butterfield, D. A. (2010). “Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts.” FEMS Microbiol Ecol, 73(3), 538-549. doi:10.1111/j.1574-6941.2010.00910..

Huse, S. M., Welch, D. M., Morrison, H. G., & Sogin, M. L. (2010). “Ironing out the wrinkles in the rare biosphere through improved OTU clustering.” Environ Microbiol, 12(7), 1889-1898. doi:10.1111/j.1462-2920.2010.02193..

Karpinets, T. V., Obraztsova, A. Y., Wang, Y., Schmoyer, D. D., Kora, G. H., Park, B. H., Serres, M. H., Romine, M. F., Land, M. L., Kothe, T. B., Fredrickson, J. K., Nealson, K. H., & Uberbacher, E. C. (2010). “Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes.” Funct Integr Genomics, 10(1), 97-110. doi:10.1007/s10142-009-0142-.

Karpinets, T. V., Romine, M. F., Schmoyer, D. D., Kora, G. H., Syed, M. H., Leuze, M. R., Serres, M. H., Park, B. H., Samatova, N. F., & Uberbacher, E. C. (2010). “Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions.” Database (Oxford), 2010, baq012. doi:10.1093/database/baq01.

Keeling, P. J., Corradi, N., Morrison, H. G., Haag, K. L., Ebert, D., Weiss, L. M., Akiyoshi, D. E., & Tzipori, S. (2010). “The reduced genome of the parasitic microsporidian Enterocytozoon bieneusi lacks genes for core carbon metabolism.” Genome Biol Evol, 2, 304-309. doi:10.1093/gbe/evq02.

Lasek-Nesselquist, E., Welch, D. M., & Sogin, M. L. (2010). “The identification of a new Giardia duodenalis assemblage in marine vertebrates and a preliminary analysis of G.” duodenalis population biology in marine systems. Int J Parasitol, 40(9), 1063-1074. doi:10.1016/j.ijpara.2010.02.01.

Lee, H. S., Komarova, Y. A., Nadezhdina, E. S., Anjum, R., Peloquin, J. G., Schober, J. M., Danciu, O., van Haren, J., Galjart, N., Gygi, S. P., Akhmanova, A., & Borisy, G. G. (2010). “Phosphorylation controls autoinhibition of cytoplasmic linker protein-170.” Mol Biol Cell, 21(15), 2661-2673. doi:10.1091/mbc.E09-12-103.

Mark Welch, D. B. (2010). “Monogononta McGraw-Hill Encyclopedia of Science and Technology, 11th Edition (11th Edition ed., Vol.” 1, pp. 1-1): McGraw-Hill.

McLellan, S. L., Huse, S. M., Mueller-Spitz, S. R., Andreishcheva, E. N., & Sogin, M. L. (2010). “Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent.” Environ Microbiol, 12(2), 378-392. doi:10.1111/j.1462-2920.2009.02075..

Morf, L., Spycher, C., Rehrauer, H., Fournier, C. A., Morrison, H. G., & Hehl, A. B. (2010). “The transcriptional response to encystation stimuli in Giardia lamblia is restricted to a small set of genes.” Eukaryot Cell, 9(10), 1566-1576. doi:10.1128/EC.00100-1.

Olins, A. L., Rhodes, G., Mark Welch, D. B., Zwerger, M., & Olins, D. E. (2010). “Lamin B receptor Multi-tasking at the nuclear envelope.” Nucleus-Austin, 1, 53-70. doi:DOI 10.4161/nucl.1.1.1051.

Parfrey, L. W., Grant, J., Tekle, Y. I., Lasek-Nesselquist, E., Morrison, H. G., Sogin, M. L., Patterson, D. J., & Katz, L. A. (2010). “Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life.” Syst Biol, 59(5), 518-533. doi:10.1093/sysbio/syq03.

Schrenk, M. O., Huber, J. A., & Edwards, K. J. (2010). “Microbial provinces in the subseafloor.” Ann Rev Mar Sci, 2(1), 279-304. doi:10.1146/annurev-marine-120308-08100.

Smith, J. L., Barrett, J. E., Tusnady, G., Rejto, L., & Cary, S. C. (2010). “Resolving environmental drivers of microbial community structure in Antarctic soils.” Antarctic Science, 22(6), 673-680. doi:Doi 10.1017/S095410201000076.

Theroux, S. M., D’Andrea, W. D., Toney, J., Amaral-Zettler, L. A., & Huang, Y. (2010). “Phylogenetic diversity and evolutionary relatedness of alkenone-producing haptophyte algae in lakes: Implications for continental paleotemperature reconstructions.” Earth and Planetary Science Letters, 300(3-4), 311-320. doi:DOI 10.1016/j.epsl.2010.10.00.

Wankel, S. D., Chen, Y., Kendall, C., Post, A. F., & Paytan, A. (2010). “Sources of aerosol nitrate to the Gulf of Aqaba: Evidence from δ15N and δ18O of nitrate and trace metal chemistry.” Marine Chemistry, 120 (1-4), 90-99. doi:10.1016/j.marchem.2009.01.01.

Wernegreen, J. J., Kauppinen, S. N., & Degnan, P. H. (2010). “Slip into something more functional: selection maintains ancient frameshifts in homopolymeric sequences.” Mol Biol Evol, 27(4), 833-839. doi:10.1093/molbev/msp29.

2009

Aberle, N., Hansen, T., Boettger-Schnack, R., Burmeister, A., Post, A. F., & Sommer, U. (2009). “Differential routing of ‘new’ nitrogen toward higher trophic levels within the marine food web of the Gulf of Aqaba, Northern Red Sea.” Marine Biology, 157(1), 157-169. doi:10.1007/s00227-009-1306-.

Akiyoshi, D. E., Morrison, H. G., Lei, S., Feng, X., Zhang, Q., Corradi, N., Mayanja, H., Tumwine, J. K., Keeling, P. J., Weiss, L. M., & Tzipori, S. (2009). “Genomic survey of the non-cultivatable opportunistic human pathogen, Enterocytozoon bieneusi.” PLoS Pathog, 5(1), e1000261. doi:10.1371/journal.ppat.100026.

Alliegro, M. C., & Satir, P. (2009). “Origin of the cilium: novel approaches to examine a centriolar evolution hypothesis.” Methods Cell Biol, 94, 53-64. doi:10.1016/S0091-679X(08)94002-.

Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W., & Huse, S. M. (2009). “A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes.” PLoS One, 4(7), e6372. doi:10.1371/journal.pone.000637.

Antonopoulos, D. A., Huse, S. M., Morrison, H. G., Schmidt, T. M., Sogin, M. L., & Young, V. B. (2009). “Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation.” Infect Immun, 77(6), 2367-2375. doi:10.1128/IAI.01520-0.

Aurrecoechea, C., Brestelli, J., Brunk, B. P., Carlton, J. M., Dommer, J., Fischer, S., Gajria, B., Gao, X., Gingle, A., Grant, G., Harb, O. S., Heiges, M., Innamorato, F., Iodice, J., Kissinger, J. C., Kraemer, E., Li, W., Miller, J. A., Morrison, H. G., Nayak, V., Pennington, C., Pinney, D. F., Roos, D. S., Ross, C., Stoeckert, C. J. Jr., Sullivan, S., Treatman, C., & Wang, H. (2009). “GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.” Nucleic Acids Res, 37(Database issue), D526-530. doi:10.1093/nar/gkn63.

Barr, F. D., Krohmer, L. J., Hamilton, J. W., & Sheldon, L. A. (2009). “Disruption of histone modification and CARM1 recruitment by arsenic represses transcription at glucocorticoid receptor-regulated promoters.” PLoS One, 4(8), e6766. doi:10.1371/journal.pone.000676.

Brazelton, W. J., Sogin, M. L., & Baross, J. A. (2009). “Multiple scales of diversification within natural populations of archaea in hydrothermal chimney biofilms.” Environmental Microbiology Reports, 2(2), 236-242.

Claessens, M., Wickham, S. A., Post, A. F., & Reuter, M. (2009). “A paradox of the ciliates?” High ciliate diversity in a resource-poor environment. Marine Biology, 157(3), 483-494. doi:10.1007/s00227-009-1334-.

Dick, G. J., Andersson, A. F., Baker, B. J., Simmons, S. L., Thomas, B. C., Yelton, A. P., & Banfield, J. F. (2009). “Community-wide analysis of microbial genome sequence signatures.” Genome Biol, 10(8), R85. doi:10.1186/gb-2009-10-8-r8.

Gilbert, J. A., Field, D., Swift, P., Newbold, L., Oliver, A., Smyth, T., Somerfield, P. J., Huse, S. M., & Joint, I. (2009). “The seasonal structure of microbial communities in the Western English Channel.” Environ Microbiol, 11(12), 3132-3139. doi:10.1111/j.1462-2920.2009.02017..

Gladyshev, E. A., & Arkhipova, I. R. (2009). “A single-copy IS5-like transposon in the genome of a bdelloid rotifer.” Mol Biol Evol, 26(8), 1921-1929. doi:10.1093/molbev/msp10.

Gladyshev, E. A., & Arkhipova, I. R. (2009). “Rotifer rDNA-specific R9 retrotransposable elements generate an exceptionally long target site duplication upon insertion.” Gene, 448(2), 145-150. doi:10.1016/j.gene.2009.08.01.

Gribble, K. E., Anderson, D. M., & Coats, D. W. (2009). “Sexual and asexual processes in Protoperidinium steidingerae Balech (Dinophyceae), with observations on life-history stages of Protoperidinium depressum (Bailey) Balech (Dinophyceae).” J Eukaryot Microbiol, 56(1), 88-103. doi:10.1111/j.1550-7408.2008.00378..

Hamilton, J. (2009). “The use of microarrays to understand the biology and toxicology of low dose arsenic.” In C. Tomlinson (Ed.), Microarrays: Their design and use, The Biomedical & Life Sciences Collection. Henry Stewart Talks Ltd, London (online at http://hstalks.com/bio).

Huber, J. A., Morrison, H. G., Huse, S. M., Neal, P. R., Sogin, M. L., & Mark Welch, D. B. (2009). “Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure.” Environ Microbiol, 11(5), 1292-1302. doi:10.1111/j.1462-2920.2008.01857..

Hur, J. H., Van Doninck, K., Mandigo, M. L., & Meselson, M. (2009). “Degenerate tetraploidy was established before bdelloid rotifer families diverged.” Mol Biol Evol, 26(2), 375-383. doi:10.1093/molbev/msn26.

Ionescu, D., Penno, S., Hazanov, L., Chernihovsky, M., Rihtman, B., Post, A. F., & Oren, A. (2009). “Distribution of Archaea among the prokaryoplankton in the Gulf of Aqaba.” FEMS Microbiol. Ecol., 69, 425-438.

Kenney, D. E., & Borisy, G. G. (2009). “Thomas Hunt Morgan at the marine biological laboratory: naturalist and experimentalist.” Genetics, 181(3), 841-846. doi:10.1534/genetics.109.10165.

Komarova, Y., De Groot, C. O., Grigoriev, I., Gouveia, S. M., Munteanu, E. L., Schober, J. M., Honnappa, S., Buey, R. M., Hoogenraad, C. C., Dogterom, M., Borisy, G. G., Steinmetz, M. O., & Akhmanova, A. (2009). “Mammalian end binding proteins control persistent microtubule growth.” J Cell Biol, 184(5), 691-706. doi:10.1083/jcb.20080717.

Konstantinidis, K. T., Serres, M. H., Romine, M. F., Rodrigues, J. L., Auchtung, J., McCue, L. A., Lipton, M. S., Obraztsova, A., Giometti, C. S., Nealson, K. H., Fredrickson, J. K., & Tiedje, J. M. (2009). “Comparative systems biology across an evolutionary gradient within the Shewanella genus.” Proc Natl Acad Sci U S A, 106(37), 15909-15914. doi:10.1073/pnas.090200010.

Kozul, C. D., Ely, K. H., Enelow, R. I., & Hamilton, J. W. (2009). “Low-dose arsenic compromises the immune response to influenza A infection in vivo.” Environ Health Perspect, 117(9), 1441-1447. doi:10.1289/ehp.090091.

Kozul, C. D., Hampton, T. H., Davey, J. C., Gosse, J. A., Nomikos, A. P., Eisenhauer, P. L., Weiss, D. J., Thorpe, J. E., Ihnat, M. A., & Hamilton, J. W. (2009). “Chronic exposure to arsenic in the drinking water alters the expression of immune response genes in mouse lung.” Environ Health Perspect, 117(7), 1108-1115. doi:10.1289/ehp.080019.

Lasek-Nesselquist, E., Mark Welch, D. B., Thompson, R. C., Steuart, R. F., & Sogin, M. L. (2009). “Genetic exchange within and between assemblages of Giardia duodenalis.” J Eukaryot Microbiol, 56(6), 504-518. doi:10.1111/j.1550-7408.2009.00443..

Lazarevic, V., Whiteson, K., Huse, S. M., Hernandez, D., Farinelli, L., Osteras, M., Schrenzel, J., & Francois, P. (2009). “Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.” J Microbiol Methods, 79(3), 266-271. doi:10.1016/j.mimet.2009.09.01.

Mackey, K. R. M., Paytan, A., Rivlin, T., & Post, A. F. (2009). “Phytoplankton responses to natural and simulated transitions in nutrient and light regimes in the oligotrophic Red Sea.” Mar. Biol., 156, 1531-1546.

Mark Welch, D. B., Ricci, C., & Meselson, M. (2009). “Bdelloid rotifers: progress in understanding the success of an evolutionary scandal.” In K. Martens, I. Shoen, & P. van Dijk (Ed.), Lost Sex: The Evolutionary Biology of Parthenogenesis (pp. 259-279). Heidelberg: Springer-Verlag.

Nahum, L. A., Goswami, S., & Serres, M. H. (2009). “Protein families reflect the metabolic diversity of organisms and provide support for functional prediction.” Physiol Genomics, 38(3), 250-260. doi:10.1152/physiolgenomics.90244.200.

Paytan, A., Mackey, K. R. M., Chen, Y., Lima, I. D., S.C., D., Mahowald, N., Labiosa, R., & Post, A. F. (2009). “Toxicity of atmospheric aerosols on marine phytoplankton.” Proc Natl Acad Sci U S A, 106(12), 4601-4605. doi:10.1073/pnas.081148610.

Post, A. F., Golan, D., Zandbank, K., & Penno, S. (2009). “Phytoplankton communities of the Gulf of Aqaba, Northern Red Sea.” In F. D. Por (Ed.), A Pocket-Sized Ocean, the Gulf of Aqaba (Eilat), Environment and Biodiversity (pp. 119-134). Jerusalem: Magna Press.

Scanlan, D. J., Ostrowski, M., Mazard, S., Dufresne, A., Garczarek, L., Hess, W. R., Post, A. F., Hagemann, M., Paulsen, I., & Partensky, F. (2009). “Ecological genomics of marine picocyanobacteria.” Microbiol Mol Biol Rev, 73(2), 249-299. doi:10.1128/MMBR.00035-0.

Schober, J. M., Cain, J. M., Komarova, Y. A., & Borisy, G. G. (2009). “Migration and actin protrusion in melanoma cells are regulated by EB1 protein.” Cancer Lett, 284(1), 30-36. doi:10.1016/j.canlet.2009.04.00.

Serres, M. H., Kerr, A. R., McCormack, T. J., & Riley, M. (2009). “Evolution by leaps: gene duplication in bacteria.” Biol Direct, 4, 46. doi:10.1186/1745-6150-4-4.

Smith, J., & Davidson, E. H. (2009). “Regulative recovery in the sea urchin embryo and the stabilizing role of fail-safe gene network wiring.” Proc Natl Acad Sci U S A, 106(43), 18291-18296. doi:10.1073/pnas.091000710.

Snell, T. W., Shearer, T. L., Smith, H. A., Kubanek, J., Gribble, K. E., & Mark Welch, D. B. (2009). “Genetic determinants of mate recognition in Brachionus manjavacas (Rotifera).” BMC Biol, 7, 60. doi:10.1186/1741-7007-7-6.

Sogin, M. L. (2009). “Characterizing Microbial Population Structures through Massively Parallel Sequencing.” In S. S. Epstein (Ed.), Uncultivated Microorganisms (Vol. 10, pp. 278-292): Springe.

Stoeck, T., Behnke, A., Christen, R., Amaral-Zettler, L. A., Rodriguez-Mora, M. J., Chistoserdov, A., Orsi, W., & Edgcomb, V. P. (2009). “Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities.” BMC Biol, 7, 72. doi:10.1186/1741-7007-7-7.

Turanov, A. A., Lobanov, A. V., Fomenko, D. E., Morrison, H. G., Sogin, M. L., Klobutcher, L. A., Hatfield, D. L., & Gladyshev, V. N. (2009). “Genetic code supports targeted insertion of two amino acids by one codon.” Science, 323(5911), 259-261. doi:10.1126/science.116474.

Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., Egholm, M., Henrissat, B., Heath, A. C., Knight, R., & Gordon, J. I. (2009). “A core gut microbiome in obese and lean twins.” Nature, 457(7228), 480-484. doi:10.1038/nature0754.

Van Doninck, K., Mandigo, M. L., Hur, J. H., Wang, P., Guglielmini, J., Milinkovitch, M. C., Lane, W. S., & Meselson, M. (2009). “Phylogenomics of unusual histone H2A Variants in Bdelloid rotifers.” PLoS Genet, 5(3), e1000401. doi:10.1371/journal.pgen.100040.

Wernegreen, J. J., Kauppinen, S. N., Brady, S. G., & Ward, P. S. (2009). “One nutritional symbiosis begat another: phylogenetic evidence that the ant tribe Camponotini acquired Blochmannia by tending sap-feeding insects.” BMC Evol Biol, 9(1), 292. doi:10.1186/1471-2148-9-29.

Wernegreen, J. J., & Wheeler, D. E. (2009). “Remaining flexible in old alliances: functional plasticity in constrained mutualisms.” DNA Cell Biol, 28(8), 371-382. doi:10.1089/dna.2009.087.

Whitman, C. T., Wirth, T. E., Meselson, M., Nissen, S. E., Juma, C., & Daley, G. (2009). “Your inbox, Mr President.” Nature, 457(7227), 258-261. doi:10.1038/457258.

Wilmes, P., Simmons, S. L., Denef, V. J., & Banfield, J. F. (2009). “The dynamic genetic repertoire of microbial communities.” FEMS Microbiol Rev, 33(1), 109-132. doi:10.1111/j.1574-6976.2008.00144..

Witek, A., Herlyn, H., Ebersberger, I., Mark Welch, D. B., & Hankeln, T. (2009). “Support for the monophyletic origin of Gnathifera from phylogenomics.” Mol Phylogenet Evol, 53(3), 1037-1041. doi:10.1016/j.ympev.2009.07.03.

Zaura, E., Keijser, B. J., Huse, S. M., & Crielaard, W. (2009). “Defining the healthy “core microbiome” of oral microbial communities.” BMC Microbiol, 9, 259. doi:10.1186/1471-2180-9-25.

2008

Aguero, F., Al-Lazikani, B., Aslett, M., Berriman, M., Buckner, F. S., Campbell, R. K., Carmona, S., Carruthers, I. M., Chan, A. W., Chen, F., Crowther, G. J., Doyle, M. A., Hertz-Fowler, C., Hopkins, A. L., McAllister, G., Nwaka, S., Overington, J. P., Pain, A., Paolini, G. V., Pieper, U., Ralph, S. A., Riechers, A., Roos, D. S., Sali, A., Shanmugam, D., Suzuki, T., Van Voorhis, W. C., & Verlinde, C. L. (2008). “Genomic-scale prioritization of drug targets: the TDR Targets database.” Nat Rev Drug Discov, 7(11), 900-907. doi:10.1038/nrd268.

Alliegro, M. C. (2008). “The implications of centrosomal RNA.” RNA Biol, 5(4), 198-200. doi:6972 [pii.

Alliegro, M. C., & Alliegro, M. A. (2008). “Centrosomal RNA correlates with intron-poor nuclear genes in Spisula oocytes.” Proc Natl Acad Sci U S A, 105(19), 6993-6997. doi:10.1073/pnas.080229310.

Amaral-Zettler, L. A., Peplies, J., Ramette, A., Fuchs, B., Ludwig, W., & Glockner, F. O. (2008). “Proceedings of the international workshop on Ribosomal RNA technology, April 7-9, 2008, Bremen, Germany.” Syst Appl Microbiol, 31(4), 258-268. doi:10.1016/j.syapm.2008.08.00.

Amaral-Zettler, L. A., Rocca, J. D., Lamontagne, M. G., Dennett, M. R., & Gast, R. J. (2008). “Changes in microbial community structure in the wake of Hurricanes Katrina and Rita.” Environ Sci Technol, 42(24), 9072-9078. doi:doi:10.1021/es801904.

Biddle, J. F., Huse, S. M., Sogin, M. L., & Teske, A. (2008). “Archaeal and bacterial diversity of deep marine subsurface sediments analysed by V6-tag sequencing.” Paper presented at the Poster and Abstract at ICOMM Workshop “Assessing marine microbial diversity: problems and solutions”, Amsterdam, The Netherlands.

Claessens, M., Wickham, S. A., Post, A. F., & Reuter, M. (2008). “Ciliate community in the oligotrophic Gulf of Aqaba, Red Sea.” Aquatic Microbial Ecology, 53(2), 181-190. doi:DOI 10.3354/ame0124.

Davey, J. C., Nomikos, A. P., Wungjiranirun, M., Sherman, J. R., Ingram, L., Batki, C., Lariviere, J. P., & Hamilton, J. W. (2008). “Arsenic as an endocrine disruptor: arsenic disrupts retinoic acid receptor-and thyroid hormone receptor-mediated gene regulation and thyroid hormone-mediated amphibian tail metamorphosis.” Environ Health Perspect, 116(2), 165-172. doi:10.1289/ehp.1013.

Dethlefsen, L., Huse, S. M., Sogin, M. L., & Relman, D. A. (2008). “The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing.” PLoS Biol, 6(11), e280. doi:10.1371/journal.pbio.006028.

Dufresne, A., Ostrowski, M., Scanlan, D. J., Garczarek, L., Mazard, S., Palenik, B. P., Paulsen, I. T., de Marsac, N. T., Wincker, P., Dossat, C., Ferriera, S., Johnson, J., Post, A. F., Hess, W. R., & Partensky, F. (2008). “Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.” Genome Biol, 9(5), R90. doi:10.1186/gb-2008-9-5-r9.

Fredrickson, J. K., Romine, M. F., Beliaev, A. S., Auchtung, J. M., Driscoll, M. E., Gardner, T. S., Nealson, K. H., Osterman, A. L., Pinchuk, G., Reed, J. L., Rodionov, D. A., Rodrigues, J. L., Saffarini, D. A., Serres, M. H., Spormann, A. M., Zhulin, I. B., & Tiedje, J. M. (2008). “Towards environmental systems biology of Shewanella.” Nat Rev Microbiol, 6(8), 592-603. doi:10.1038/nrmicro194.

Gil, I. S., Sheldon, W., Schmidt, T., Servilla, M., Aguilar, R., Gries, C., Gray, T., Field, D., Cole, J., Pan, J. Y., Palanisamy, G., Henshaw, D., O’Brien, M., Kinkel, L., McMahon, K., Kottmann, R., Amaral-Zettler, L. A., Hobbie, J., Goldstein, P., Guralnick, R. P., Brunt, J., & Michener, W. K. (2008). “Defining linkages between the GSC and NSF’s LTER program: how the Ecological Metadata Language (EML) relates to GCDML and other outcomes.” OMICS, 12(2), 151-156. doi:10.1089/omi.2008.001.

Gladyshev, E. A., Meselson, M., & Arkhipova, I. R. (2008). “Massive horizontal gene transfer in bdelloid rotifers.” Science, 320(5880), 1210-1213. doi:10.1126/science.115640.

Gradman, R. J., Ptacin, J. L., Bhasin, A., Reznikoff, W. S., & Goryshin, I. Y. (2008). “A bifunctional DNA binding region in Tn5 transposase.” Mol Microbiol, 67(3), 528-540. doi:10.1111/j.1365-2958.2007.06056..

Gradman, R. J., & Reznikoff, W. S. (2008). “Tn5 synaptic complex formation: role of transposase residue W450.” J Bacteriol, 190(4), 1484-1487. doi:10.1128/JB.01488-0.

Hays, A. M., Lantz, R. C., Rodgers, L. S., Sollome, J. J., Vaillancourt, R. R., Andrew, A. S., Hamilton, J. W., & Camenisch, T. (2008). “Arsenic down-regulates vascular matrix.” Toxicol Pathol 36, 805-817.

Huber, J. A., & Holden, J. F. (2008). “Modeling the impact of diffuse vent microorganisms along mid-ocean ridges and flanks.” In R. P. Lowell, J. S. Seewald, A. Metaxas, & M. R. Perfit (Ed.), Magma to Microbe: Modeling Hydrothermal Processes at Oceanic Spreading Ridges (pp. 215-231). Washington, DC: American Geophysical Union Press.

Huse, S. M., Dethlefsen, L., Huber, J. A., Mark Welch, D. B., Relman, D. A., & Sogin, M. L. (2008). “Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.” PLoS Genet, 4(11), e1000255. doi:10.1371/journal.pgen.100025.

Jost, M. C., Hillis, D. M., Lu, Y., Kyle, J. W., Fozzard, H. A., & Zakon, H. H. (2008). “Toxin-resistant sodium channels: parallel adaptive evolution across a complete gene family.” Mol Biol Evol, 25(6), 1016-1024. doi:10.1093/molbev/msn02.

Kamennaya, N. A., Chernihovsky, M., & Post, A. F. (2008). “The cyanate utilization capacity of marine unicellular Cyanobacteria.” Limnology and Oceanography, 53(6), 2485-2494. doi:DOI 10.4319/lo.2008.53.6.248.

Keijser, B. J., Zaura, E., Huse, S. M., van der Vossen, J. M., Schuren, F. H., Montijn, R. C., ten Cate, J. M., & Crielaard, W. (2008). “Pyrosequencing analysis of the oral microflora of healthy adults.” J Dent Res, 87(11), 1016-1020. doi:87/11/1016 [pii.

Kozul, C. D., Nomikos, A. P., Hampton, T. H., Warnke, L. A., Gosse, J. A., Davey, J. C., Thorpe, J. E., Jackson, B. P., Ihnat, M. A., & Hamilton, J. W. (2008). “Laboratory diet profoundly alters gene expression and confounds genomic analysis in mouse liver and lung.” Chem Biol Interact, 173(2), 129-140. doi:10.1016/j.cbi.2008.02.00.

Lasek-Nesselquist, E., Bogomolni, A. L., Gast, R. J., Mark Welch, D. B., Ellis, J. C., Sogin, M. L., & Moore, M. J. (2008). “Molecular characterization of Giardia intestinalis haplotypes in marine animals: variation and zoonotic potential.” Dis Aquat Organ, 81(1), 39-51. doi:10.3354/dao0193.

Mark Welch, D. B., Mark Welch, J. L., & Meselson, M. (2008). “Evidence for degenerate tetraploidy in bdelloid rotifers.” Proc Natl Acad Sci U S A, 105(13), 5145-5149. doi:10.1073/pnas.080097210.

Nahum, L. A., & Pereira, S. L. (2008). “Phylogenomics, Protein Family Evolution, and the Tree of Life: An Integrated Approach between Molecular Evolution and Computational Intelligence.” In T. Smolinski, M. Milanova, & A.-E. Hassanien (Ed.), Studies in Computational Intelligence (SCI) (Vol. 122, pp. 259-279). Berlin Heidelberg: Springer-Verlag.

Palacios, C., Zettler, E., Amils, R., & Amaral-Zettler, L. (2008). “Contrasting microbial community assembly hypotheses: a reconciling tale from the Rio Tinto.” PLoS One, 3(12), e3853. doi:10.1371/journal.pone.000385.

Riley, M., Staley, J. T., Danchin, A., Wang, T. Z., Brettin, T. S., Hauser, L. J., Land, M. L., & Thompson, L. S. (2008). “Genomics of an extreme psychrophile, Psychromonas ingrahamii.” BMC Genomics, 9(1), 210. doi:10.1186/1471-2164-9-21.

Rull, K., Hallast, P., Uuskula, L., Jackson, J., Punab, M., Salumets, A., Campbell, R. K., & Laan, M. (2008). “Fine-scale quantification of HCG beta gene transcription in human trophoblastic and non-malignant non-trophoblastic tissues.” Mol Hum Reprod, 14(1), 23-31. doi:10.1093/molehr/gam08.

San Gil, I., Sheldon, W., Schmidt, T., Servilla, M., Aguilar, R., Gries, C., Gray, T., Field, D., Cole, J., Yun Pan, J., Palanisamy, G., Henshaw, D., O’Brien, M., Kinkel, L., McMahon, K., Kottmann, R., Amaral-Zettler, L. A., Hobbie, J., Goldstein, P., Guralnick, R. P., Brunt, J., & K., M. W. (2008). “Defining linkages between the GSC and NSF’s LTER program: How the Ecological Metadata Language (EML) relates to GCDML and other outcomes.” OMICS A Journal of Integrative Biology, 12(2), 151-156.

Santelli, C. M., Orcutt, B. N., Banning, E., Bach, W., Moyer, C. L., Sogin, M. L., Staudigel, H., & Edwards, K. J. (2008). “Abundance and diversity of microbial life in ocean crust.” Nature, 453(7195), 653-656. doi:10.1038/nature0689.

Scanlan, D. J., & Post, A. F. (2008). “Chapter 24 – Aspects of Marine Cyanobacterial Nitrogen Physiology and Connection to the Nitrogen Cycle.” In D. G. Capone, D. A. Bronk, M. R. Mulholland, & E. J. Carpenter (Ed.), Nitrogen in the Marine Environment (2nd Edition) (pp. 1073-1095). San Diego: Academic Press.

Schostak, N., Pyatkov, K. I., Zelentsova, E., Arkhipova, I. R., Shagin, D., Shagina, I., Mudrik, E., Blintsov, A., Clark, I., Finnegan, D. J., & Evgen’ev, M. B. (2008). “Molecular dissection of Penelope transposable element regulatory machinery.” Nucleic Acids Res, 36(8), 2522-2529. doi:10.1093/nar/gkm116.

Simmons, S. L., Dibartolo, G., Denef, V. J., Goltsman, D. S., Thelen, M. P., & Banfield, J. F. (2008). “Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation.” PLoS Biol, 6(7), e177. doi:10.1371/journal.pbio.006017.

Smith, J. (2008). “A protocol describing the principles of cis-regulatory analysis in the sea urchin.” Nat Protoc, 3(4), 710-718. doi:10.1038/nprot.2008.3.

Smith, J., & Davidson, E. H. (2008). “Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo.” Proc Natl Acad Sci U S A, 105(51), 20089-20094. doi:10.1073/pnas.080644210.

Smith, J., & Davidson, E. H. (2008). “A new method, using cis-regulatory control, for blocking embryonic gene expression.” Dev Biol, 318(2), 360-365. doi:10.1016/j.ydbio.2008.02.05.

Smith, J., Kraemer, E., Liu, H., Theodoris, C., & Davidson, E. (2008). “A spatially dynamic cohort of regulatory genes in the endomesodermal gene network of the sea urchin embryo.” Dev Biol, 313(2), 863-875. doi:10.1016/j.ydbio.2007.10.04.

Stewart, J. R., Gast, R. J., Fujioka, R. S., Solo-Gabriele, H. M., Meschke, J. S., Amaral-Zettler, L. A., Del Castillo, E., Polz, M. F., Collier, T. K., Strom, M. S., Sinigalliano, C. D., Moeller, P. D., & Holland, A. F. (2008). “The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs.” Environ Health, 7 Suppl 2, S3. doi:10.1186/1476-069X-7-S2-S.

Suga, K., Mark Welch, D. B., Tanaka, Y., Sakakura, Y., & Hagiwara, A. (2008). “Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis.” Molecular Biology and Evolution, 25(6), 1129-1137. doi:DOI 10.1093/molbev/msn05.

Tamas, I., Wernegreen, J. J., Nystedt, B., Kauppinen, S. N., Darby, A. C., Gomez-Valero, L., Lundin, D., Poole, A. M., & Andersson, S. G. (2008). “Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts.” Proc Natl Acad Sci U S A, 105(39), 14934-14939. doi:10.1073/pnas.080655410.

Ye, S., MacEachran, D. P., Hamilton, J. W., O’Toole, G. A., & Stanton, B. A. (2008). “Chemotoxicity of doxorubicin and surface expression of P-glycoprotein (MDR1) is regulated by the Pseudomonas aeruginosa toxin Cif.” Am J Physiol Cell Physiol, 295(3), C807-818. doi:10.1152/ajpcell.00234.200.

2007

Adams, C. D., Schnurr, B., Marko, J. F., & Reznikoff, W. S. (2007). “Pulling apart catalytically active Tn5 synaptic complexes using magnetic tweezers.” J Mol Biol, 367(2), 319-327. doi:10.1016/j.jmb.2006.12.06.

Aguilera, A., Amaral-Zettler, L. A., Souza-Egipsy, V., Zettler, E., & Amils, R. (2007). “Eukaryotic Community Structure from Río Tinto (SW, Spain), a Highly Acidic River.” In J. Seckbach (Ed.), Algae and Cyanobacteria in Extreme Environments (Vol. 11, pp. 465-485): Springer Netherlands.

Aguilera, A., Zettler, E., Gomez, F., Amaral-Zettler, L. A., Rodriguez, N., & Amils, R. (2007). “Distribution and seasonal variability in the benthic eukaryotic community of Rio Tinto (SW, Spain), an acidic, high metal extreme environment.” Syst Appl Microbiol, 30(7), 531-546. doi:10.1016/j.syapm.2007.05.00.

Alliegro, M. C., & Alliegro, M. A. (2007). “Echinonectin is a Del-1-like molecule with regulated expression in sea urchin embryos.” Gene Expr Patterns, 7(6), 651-656. doi:10.1016/j.modgep.2007.03.00.

Baross, J. A., Schrenk, M. O., & Huber, J. A. (2007). “Limits of carbon life on Earth and elsewhere.” In W. T. I. Sullivan & J. A. Baross (Ed.), Planets and Life: The Emerging Science of Astrobiology (pp. 275-291). Cambridge, UK: Cambridge University Press.

Bordenstein, S. R. (2007). “Evolutionary genomics: transdomain gene transfers.” Curr Biol, 17(21), R935-936. doi:10.1016/j.cub.2007.09.02.

Bordenstein, S. R. (2007). “Discover the microbes within: The Wolbachia Project.” Focus on Microbiology Education 14(1), 4-5.

Bordenstein, S. R., & Werren, J. H. (2007). “Bidirectional incompatibility among divergent Wolbachia and incompatibility level differences among closely related Wolbachia in Nasonia.” Heredity (Edinb), 99(3), 278-287. doi:10.1038/sj.hdy.680099.

Chapman, M., & Alliegro, M. C. (2007). “A symbiogenetic origin for the centrosome?” Symbiosis, 44, 23-31.

Chen, Y., Street, J., Golan, D., Post, A. F., & Paytan, A. (2007). “Estimate of atmospheric dry deposition fluxes and associate input of nutrients in the Gulf of Aqaba.” Journal of Geophysical Research, 112, D04309.

Corradi, N., Akiyoshi, D. E., Morrison, H. G., Feng, X., Weiss, L. M., Tzipori, S., & Keeling, P. J. (2007). “Patterns of genome evolution among the microsporidian parasites Encephalitozoon cuniculi, Antonospora locustae and Enterocytozoon bieneusi.” PLoS One, 2(12), e1277. doi:10.1371/journal.pone.000127.

Curcio, M. J., & Belfort, M. (2007). “The beginning of the end: links between ancient retroelements and modern telomerases.” Proc Natl Acad Sci U S A, 104(22), 9107-9108. doi:10.1073/pnas.070322410.

Czyz, A., Stillmock, K. A., Hazuda, D. J., & Reznikoff, W. S. (2007). “Dissecting Tn5 transposition using HIV-1 integrase diketoacid inhibitors.” Biochemistry, 46(38), 10776-10789. doi:10.1021/bi700654.

D’Hondt, S., Inagaki, F., Ferdelman, T., Barker Jørgensen, B., Kato, K., Kemp, P., Sobecky, P., Sogin, M., & Takai, K. (2007). “Exploring Subseafloor Life with the Integrated Ocean Drilling Program.” Sci. Dril., 5, 26-37. doi:10.2204/iodp.sd.5.03.200.

Driscoll, M. E., Romine, M. F., Juhn, F. S., Serres, M. H., McCue, L. A., Beliaev, A. S., Fredrickson, J. K., & Gardner, T. S. (2007). “Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling.” Genome Inform, 18, 287-298. doi:9781860949920_0028 [pii.

Edgcomb, V. P., Molyneaux, S. J., Boer, S., Wirsen, C. O., Saito, M., Atkins, M. S., Lloyd, K., & Teske, A. (2007). “Survival and growth of two heterotrophic hydrothermal vent archaea, Pyrococcus strain GB-D and Thermococcus fumicolans, under low pH and high sulfide concentrations in combination with high temperature and pressure regimes.” Extremophiles, 11(2), 329-342. doi:10.1007/s00792-006-0043-.

Ekanayake, D. K., Mark Welch, D. B., Kieft, R., Hajduk, S., & Dittus, W. P. J. (2007). “Transmission dynamics of Cryptosporidium infection in a natural population of non-human primates at Polonnaruwa, Sri Lanka.” Am J Trop Med Hyg, 77(5), 818-822.

Garczarek, L., Dufresne, A., Rousvoal, S., West, N., Mazard, S., Marie, D., Claustre, H., Raimbault, P., Post, A. F., Scanlan, D., & Partensky, F. (2007). “High vertical and low horizontal microdiversity of Prochlorococcus genotypes in the Mediterranean Sea in summer.” FEMS Microbiology Ecology, 60, 189-206.

Gladyshev, E. A., & Arkhipova, I. R. (2007). “Telomere-associated endonuclease-deficient Penelope-like retroelements in diverse eukaryotes.” Proc Natl Acad Sci U S A, 104(22), 9352-9357. doi:10.1073/pnas.070274110.

Gladyshev, E. A., Meselson, M., & Arkhipova, I. R. (2007). “A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers.” Gene, 390(1-2), 136-145. doi:10.1016/j.gene.2006.09.02.

Gribble, K. E., Nolan, G., & Anderson, D. M. (2007). “Biodiversity, biogeography and potential trophic impact of Protoperidinium spp.” (Dinophyceae) off the southwestern coast of Ireland. Journal of Plankton Research, 29(11), 931-947. doi:DOI 10.1093/plankt/fbm07.

Hegreness, M., & Meselson, M. (2007). “What did Sutton see? Thirty years of confusion over the chromosomal basis of Mendelism.” Genetics, 176(4), 1939-1944. doi:10.1534/genetics.104.7972.

Huber, J. A., Mark Welch, D. B., Morrison, H. G., Huse, S. M., Neal, P. R., Butterfield, D. A., & Sogin, M. L. (2007). “Microbial population structures in the deep marine biosphere.” Science, 318(5847), 97-100. doi:10.1126/science.114668.

Huse, S. M., Huber, J. A., Morrison, H. G., Sogin, M. L., & Mark Welch, D. B. (2007). “Accuracy and quality of massively parallel DNA pyrosequencing.” Genome Biol, 8(7), R143. doi:10.1186/gb-2007-8-7-r14.

Ioannidis, P., Dunning Hotopp, J. C., Sapountzis, P., Siozios, S., Tsiamis, G., Bordenstein, S. R., Baldo, L., Werren, J. H., & Bourtzis, K. (2007). “New criteria for selecting the origin of DNA replication in Wolbachia and closely related bacteria.” BMC Genomics, 8, 182. doi:10.1186/1471-2164-8-18.

Kieft, R., Brand, V., Ekanayake, D. K., Sweeney, K., DiPaolo, C., Reznikoff, W. S., & Sabatini, R. (2007). “JBP2, a SWI2/SNF2-like protein, regulates de novo telomeric DNA glycosylation in bloodstream form Trypanosoma brucei.” Mol Biochem Parasitol, 156(1), 24-31. doi:10.1016/j.molbiopara.2007.06.01.

Leary, P. R., Remsen, D. P., Norton, C. N., Patterson, D. J., & Sarkar, I. N. (2007). “uBioRSS: tracking taxonomic literature using RSS Bioinformatics (Vol.” 23, pp. 1434-1436).

Lo, N., Paraskevopoulos, C., Bourtzis, K., O’Neill, S. L., Werren, J. H., Bordenstein, S. R., & Bandi, C. (2007). “Taxonomic status of the intracellular bacterium Wolbachia pipientis.” Int J Syst Evol Microbiol, 57(Pt 3), 654-657. doi:10.1099/ijs.0.64515-.

Mackey, K. R. M., Calhoun, M., Labiosa, R. G., Street, J. H., Post, A. F., & Paytan, A. (2007). “Phosphorus availability controls phytoplankton community dynamics and taxon specific nutrient status in the Gulf of Aqaba, Red Sea.” Limnology and Oceanography, 52(2), 873-885.

Mark Welch, D. B. (2007). “Bdelloidea McGraw-Hill Encyclopedia of Science and Technology (10th Edition ed., Vol.” 1, pp. 1-1): McGraw-Hill.

Meselson, M., & Mark Welch, D. B. (2007). “Evolution.” Stable heterozygosity? Science, 318(5848), 202-203. doi:10.1126/science.115019.

Morrison, H. G., McArthur, A. G., Gillin, F. D., Aley, S. B., Adam, R. D., Olsen, G. J., Best, A. A., Cande, W. Z., Chen, F., Cipriano, M. J., Davids, B. J., Dawson, S. C., Elmendorf, H. G., Hehl, A. B., Holder, M. E., Huse, S. M., Kim, U. U., Lasek-Nesselquist, E., Manning, G., Nigam, A., Nixon, J. E., Palm, D., Passamaneck, N. E., Prabhu, A., Reich, C. I., Reiner, D. S., Samuelson, J., Svard, S. G., & Sogin, M. L. (2007). “Genomic minimalism in the early diverging intestinal parasite Giardia lamblia.” Science, 317(5846), 1921-1926. doi:10.1126/science.114383.

Morrison, H. G., McArthur, A. G., Gillin, F. D., Aley, S. B., Adam, R. D., Olsen, G. J., Best, A. A., Cande, W. Z., Chen, F., Cipriano, M. J., Davids, B. J., Dawson, S. C., Elmendorf, H. G., Hehl, A. B., Holder, M. E., Huse, S. M., Kim, U. U., Lasek-Nesselquist, E., Manning, G., Nigam, A., Nixon, J. E. J., Palm, D., Passamaneck, N. E., Prabhu, A., Reich, C. I., Reiner, D. S., Samuelson, J., Svard, S. G., & Sogin, M. L. (2007). “Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia.” Science, 317(5846), 1921.

Panagiotis, I., Hotopp, J. C. D., Sapounizis, P., Siozios, S., Tsiamis, G., Bordenstein, S. R., Baldo, L., Werren, J. H., & Bourtzis, K. (2007). “On the origin of DNA replication of Wolbachia and closely related bacteria.” BMC Genomics, 8, 182.

Patterson, D. J., Bhattacharya, D., Cole, J., Dunthorn, M., Logsdon, J., Katz, L., & Wegener-Parfrey, L. (2007). “Classifying protists.” Microbiology today(Feb 07), 44-45.

Patterson, D. J., & Sogin, M. L. (2007). “The micro*scope web tool.” In S. W. T. & J. A. Baross (Ed.), Planets and Life: The emerging Science of Astrobiology (pp. 579-584). Cambridge: Cambridge University Press.

Prabhu, A., Morrison, H. G., Martinez, C. R., 3rd, & Adam, R. D. (2007). “Characterisation of the subtelomeric regions of Giardia lamblia genome isolate WBC6.” Int J Parasitol, 37(5), 503-513. doi:10.1016/j.ijpara.2006.12.01.

Robbins, J. B., Stapleton, M., Stanger, M. J., Smith, D., Dansereau, J. T., Derbyshire, V., & Belfort, M. (2007). “Homing endonuclease I-TevIII: dimerization as a means to a double-strand break.” Nucleic Acids Res, 35(5), 1589-1600. doi:10.1093/nar/gkl117.

Sanogo, Y. O., Dobson, S. L., Bordenstein, S. R., & Novak, R. J. (2007). “Disruption of the Wolbachia surface protein gene wspB by a transposable element in mosquitoes of the Culex pipiens complex (Diptera, Culicidae).” Insect Mol Biol, 16(2), 143-154. doi:10.1111/j.1365-2583.2006.00707..

Simmons, S. L., Bazylinski, D. A., & Edwards, K. J. (2007). “Population dynamics of marine magnetotactic bacteria in a meromictic salt pond described with qPCR.” Environ Microbiol, 9(9), 2162-2174. doi:10.1111/j.1462-2920.2007.01330..

Simmons, S. L., & Edwards, K. J. (2007). “Unexpected diversity in populations of the many-celled magnetotactic prokaryote.” Environ Microbiol, 9(1), 206-215. doi:10.1111/j.1462-2920.2006.01129..

Simmons, S. L., & Edwards, K. J. (2007). “Geobiology of magnetotactic bacteria.” In D. Schüler (Ed.), Magnetoreception and Magnetosomes in Bacteria (pp. 77-102). Berlin: Springer-Verlag.

Sinigalliano, C. D., Gidley, M. L., Shibata, T., Whitman, D., Dixon, T. H., Laws, E., Hou, A., Bachoon, D., Brand, L., Amaral-Zettler, L. A., Gast, R. J., Steward, G. F., Nigro, O. D., Fujioka, R., Betancourt, W. Q., Vithanage, G., Mathews, J., Fleming, L. E., & Solo-Gabriele, H. M. (2007). “Impacts of Hurricanes Katrina and Rita on the microbial landscape of the New Orleans area.” Proc Natl Acad Sci U S A, 104(21), 9029-9034. doi:10.1073/pnas.061055210.

Slagter-Jager, J. G., Puzis, L., Gutgsell, N. S., Belfort, M., & Jain, C. (2007). “Functional defects in transfer RNAs lead to the accumulation of ribosomal RNA precursors.” RNA, 13(4), 597-605. doi:10.1261/rna.31940.

Smith, J., Theodoris, C., & Davidson, E. H. (2007). “A gene regulatory network subcircuit drives a dynamic pattern of gene expression.” Science, 318(5851), 794-797. doi:10.1126/science.114652.

Sogin, M. L., Patterson, D. J., & McArthur, A. (2007). “The origin and diversification of eukaryotes.” In S. W. T. & J. A. Baross (Ed.), Planets and Life: The emerging Science of Astrobiology (pp. 265-274). Cambridge: Cambridge University Press.

Suga, K., Mark Welch, D. B., Tanaka, Y., Sakakura, Y., & Hagiwara, A. (2007). “Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis.” PLoS One, 2(7), e671. doi:10.1371/journal.pone.000067.

Vaezeslami, S., Sterling, R., & Reznikoff, W. S. (2007). “Site-directed mutagenesis studies of tn5 transposase residues involved in synaptic complex formation.” J Bacteriol, 189(20), 7436-7441. doi:10.1128/JB.00524-0.

Van Roey, P., Pereira, B., Li, Z., Hiraga, K., Belfort, M., & Derbyshire, V. (2007). “Crystallographic and mutational studies of Mycobacterium tuberculosis recA mini-inteins suggest a pivotal role for a highly conserved aspartate residue.” J Mol Biol, 367(1), 162-173. doi:10.1016/j.jmb.2006.12.05.

Wells, L. E., Armstrong, J. C., & Huber, J. A. (2007). “Disciplinary aspirations and educational opportunities.” In W. T. I. Sullivan & J. A. Baross (Ed.), Planets and Life: The Emerging Science of Astrobiology (pp. 547-557). Cambridge: Cambridge University Press.

Wernegreen, J. J. (2007). “Genomic signatures of intracellularity: Evolutionary patterns and paces in bacterial mutalists and parasites.” In M. J. Pallen, K. E. Nelson, & G. M. Preston (Ed.), Bacterial Pathogenomics (pp. 196-212). Washington, DC: ASM Press.

Winterberg, K. M., & Reznikoff, W. S. (2007). “Screening transposon mutant libraries using full-genome oligonucleotide microarrays.” Methods Enzymol, 421, 110-125. doi:10.1016/S0076-6879(06)21011-.

Winterberg, K. M., & Reznikoff, W. S. (2007). “Transposon-based strategies for the identification of essential bacterial genes.” In A. Osterman & S. Gerdes (Ed.), Gene Essentiality at Genome Scale: Protocols and Bioinformatics. Totowa, NJ: Humana Press.

2006

Adams, C. D., Schnurr, B., Skoko, D., Marko, J. F., & Reznikoff, W. S. (2006). “Tn5 transposase loops DNA in the absence of Tn5 transposon end sequences.” Mol Microbiol, 62(6), 1558-1568. doi:10.1111/j.1365-2958.2006.05471..

Alliegro, M. C., Alliegro, M. A., & Palazzo, R. E. (2006). “Centrosome-associated RNA in surf clam oocytes.” Proc Natl Acad Sci U S A, 103(24), 9034-9038. doi:10.1073/pnas.060285910.

Amaral-Zettler, L. A., Cole, J., Laatsch, A. D., Nerad, T. A., Anderson, O. R., & Reysenbach, A. L. (2006). “Vannella epipetala n.” sp. isolated from the leaf surface of Spondias mombin (Anacardiaceae) growing in the dry forest of Costa Rica. J Eukaryot Microbiol, 53(6), 522-530. doi:10.1111/j.1550-7408.2006.00143..

Arkhipova, I. R. (2006). “Distribution and phylogeny of Penelope-like elements in eukaryotes.” Syst Biol, 55(6), 875-885.

Bach, W., Edwards, K. J., Hayes, J. M., Huber, J. A., Sievert, S. M., & Sogin, M. L. (2006). “Energy in the dark: Fuel for life in the deep ocean and beyond.” Eos Transactions, American Geophysical Union, 87(7), 73-78.

Baldo, L., Bordenstein, S., Wernegreen, J. J., & Werren, J. H. (2006). “Widespread recombination throughout Wolbachia genomes.” Mol Biol Evol, 23(2), 437-449. doi:10.1093/molbev/msj04.

Baldo, L., Dunning Hotopp, J. C., Jolley, K. A., Bordenstein, S. R., Biber, S. A., Choudhury, R. R., Hayashi, C., Maiden, M. C., Tettelin, H., & Werren, J. H. (2006). “Multilocus sequence typing system for the endosymbiont Wolbachia pipientis.” Appl Environ Microbiol, 72(11), 7098-7110. doi:10.1128/AEM.00731-0.

Beauregard, A., Chalamcharla, V. R., Piazza, C. L., Belfort, M., & Coros, C. J. (2006). “Bipolar localization of the group II intron Ll.LtrB is maintained in Escherichia coli deficient in nucleoid condensation, chromosome partitioning and DNA replication.” Mol Microbiol, 62(3), 709-722. doi:10.1111/j.1365-2958.2006.05419..

Biddle, J. F., Lipp, J. S., Lever, M. A., Lloyd, K. G., Sorensen, K. B., Anderson, R., Fredricks, H. F., Elvert, M., Kelly, T. J., Schrag, D. P., Sogin, M. L., Brenchley, J. E., Teske, A., House, C. H., & Hinrichs, K. U. (2006). “Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru.” Proc Natl Acad Sci U S A, 103(10), 3846-3851. doi:10.1073/pnas.060003510.

Bordenstein, S. R., Marshall, M. L., Fry, A. J., Kim, U., & Wernegreen, J. J. (2006). “The tripartite associations between bacteriophage, Wolbachia, and arthropods.” PLoS Pathog, 2(5), e43. doi:10.1371/journal.ppat.002004.

Cantarel, B. L., Morrison, H. G., & Pearson, W. (2006). “Exploring the relationship between sequence similarity and accurate phylogenetic trees.” Mol Biol Evol, 23(11), 2090-2100. doi:10.1093/molbev/msl08.

Consortium, S. U. G. S. (2006). “The genome of the sea urchin Strongylocentrotus purpuratus.” Science, 314, 941-952.

D’Andrea, W. J., Lage, M., Martiny, J. B. H., Laatsch, A. D., Amaral-Zettler, L. A., Sogin, M. L., & Huang, Y. S. (2006). “Alkenone producers inferred from well-preserved 18S rDNA in Greenland lake sediments.” Journal of Geophysical Research-Biogeosciences, 111(G3). doi:Artn G0301310.1029/2005jg00012.

Huber, J. A., Butterfield, D. A., & Baross, J. A. (2006). “Diversity and distribution of subseafloor Thermococcales populations in diffuse hydrothermal vents at an active deep-sea volcano in the northeast Pacific Ocean.” Journal of Geophysical Research-Biogeosciences, 111(G4). doi:ARTN G04016 10.1029/2005jg00009.

Huber, J. A., Johnson, H. P., Butterfield, D. A., & Baross, J. A. (2006). “Microbial life in ridge flank crustal fluids.” Environ Microbiol, 8(1), 88-99. doi:10.1111/j.1462-2920.2005.00872..

Hutchinson, L., Mustard, J., Gendrin, A., Fernandez Remolar, D., Amils, R., & Amaral-Zettler, L. A. (2006). “Finding Mineralogically Interesting Targets for Exploration from Spatially Coarse Visible and Near IR Spectra.” Earth and Planetary Science Letters, 252, 201-214.

Ley, R. E., Harris, J. K., Wilcox, J., Spear, J. R., Miller, S. R., Bebout, B. M., Maresca, J. A., Bryant, D. A., Sogin, M. L., & Pace, N. R. (2006). “Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat.” Appl Environ Microbiol, 72(5), 3685-3695. doi:10.1128/AEM.72.5.3685-3695.200.

Liu, Q., Derbyshire, V., Belfort, M., & Edgell, D. R. (2006). “Distance determination by GIY-YIG intron endonucleases: discrimination between repression and cleavage functions.” Nucleic Acids Res, 34(6), 1755-1764. doi:10.1093/nar/gkl07.

Mühling, M., Fuller, N. J., Somerfield, P. J., Post, A. F., Wilson, W. H., Scanlan, D. J., Joint, I., & Mann, N. H. (2006). “High resolution genetic diversity studies of marine Synechococcus using rpoC1-based Restriction Fragment Length Polymorphism.” Aquatic Microbial Ecology, 45, 263-275.

Murray, S., Hoppenrath, M., Preisfeld, A., Larsen, J., Yoshimatsu, S., Toriumi, S., & Patterson, D. J. (2006). “Phylogenetics of Rhinodinium broomeense gen.” et sp nov., a peridinioid, sand-dwelling dinoflagellate (Dinophyceae). Journal of Phycology, 42(4), 934-942. doi:DOI 10.1111/j.1529-8817.2006.00241..

Paraskevopoulos, C., Bordenstein, S. R., Wernegreen, J. J., Werren, J. H., & Bourtzis, K. (2006). “Toward a Wolbachia multilocus sequence typing system: discrimination of Wolbachia strains present in Drosophila species.” Curr Microbiol, 53(5), 388-395. doi:10.1007/s00284-006-0054-.

Patterson, D. J., Remsen, D., Marino, W. A., & Norton, C. (2006). “Taxonomic indexing–extending the role of taxonomy.” Syst Biol, 55(3), 367-373. doi:10.1080/1063515050054168.

Penno, S., Lindell, D., & Post, A. F. (2006). “Diversity of Synechococcus and Prochlorococcus populations determined from DNA sequences of the N-regulatory gene ntcA.” Environ Microbiol, 8(7), 1200-1211. doi:10.1111/j.1462-2920.2006.01010..

Post, A. F. (2006). “The Genus Prochlorococcus.” In M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, & E. Stackebrandt (Ed.), The Prokaryotes (pp. 1099-1110): Springer US.

Remsen, D. P., Norton, C., & Patterson, D. J. (2006). “Taxonomic informatics tools for the electronic Nomenclator Zoologicus.” Biol Bull, 210(1), 18-24. doi:210/1/18 [pii.

Reznikoff, W. S. (2006). “Tn5 transposition: a molecular tool for studying protein structure-function.” Biochem Soc Trans, 34(Pt 2), 320-323. doi:10.1042/BST2006032.

Riley, M., Abe, T., Arnaud, M. B., Berlyn, M. K., Blattner, F. R., Chaudhuri, R. R., Glasner, J. D., Horiuchi, T., Keseler, I. M., Kosuge, T., Mori, H., Perna, N. T., Plunkett, G., 3rd, Rudd, K. E., Serres, M. H., Thomas, G. H., Thomson, N. R., Wishart, D., & Wanner, B. L. (2006). “Escherichia coli K-12: a cooperatively developed annotation snapshot–2005.” Nucleic Acids Res, 34(1), 1-9. doi:10.1093/nar/gkj40.

Schon, I., & Arkhipova, I. R. (2006). “Two families of non-LTR retrotransposons, Syrinx and Daphne, from the Darwinulid ostracod, Darwinula stevensoni.” Gene, 371(2), 296-307. doi:10.1016/j.gene.2005.12.00.

Serres, M. H., & Riley, M. (2006). “Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions versus experiments.” J Bacteriol, 188(13), 4601-4609. doi:10.1128/JB.01787-0.

Silva, G. H., Belfort, M., Wende, W., & Pingoud, A. (2006). “From monomeric to homodimeric endonucleases and back: engineering novel specificity of LAGLIDADG enzymes.” J Mol Biol, 361(4), 744-754. doi:10.1016/j.jmb.2006.06.06.

Simmons, S. L., Bazylinski, D. A., & Edwards, K. J. (2006). “South-seeking magnetotactic bacteria in the Northern Hemisphere.” Science, 311(5759), 371-374. doi:10.1126/science.112284.

Slagter-Jager, J. G., Allen, G. S., Smith, D., Hahn, I. A., Frank, J., & Belfort, M. (2006). “Visualization of a group II intron in the 23S rRNA of a stable ribosome.” Proc Natl Acad Sci U S A, 103(26), 9838-9843. doi:10.1073/pnas.060395610.

Sogin, M. L., Morrison, H. G., Huber, J. A., Mark Welch, D. B., Huse, S. M., Neal, P. R., Arrieta, J. M., & Herndl, G. J. (2006). “Microbial diversity in the deep sea and the underexplored “rare biosphere”.” Proc Natl Acad Sci U S A, 103(32), 12115-12120. doi:10.1073/pnas.060512710.

Steiniger, M., Adams, C. D., Marko, J. F., & Reznikoff, W. S. (2006). “Defining characteristics of Tn5 Transposase non-specific DNA binding.” Nucleic Acids Res, 34(9), 2820-2832. doi:10.1093/nar/gkl17.

Steiniger, M., Metzler, J., & Reznikoff, W. S. (2006). “Mutation of Tn5 transposase beta-loop residues affects all steps of Tn5 transposition: the role of conformational changes in Tn5 transposition.” Biochemistry, 45(51), 15552-15562. doi:10.1021/bi061227.

Wegener-Parfrey, L., Barbero, E., Lasser, B., Dunthorn, M., Bhattacharya, D., Patterson, D. J., & Katz, L. (2006). “Evaluating support for the current classification of eukaryotic diversity.” PLOS Genetics, 2, 2062-2073.

2005

Alliegro, M. C., & Alliegro, M. A. (2005). “Differential expression of tyrosinated tubulin in Spisula solidissima polar bodies.” Dev Dyn, 232(1), 216-220. doi:10.1002/dvdy.2020.

Amaral-Zettler, L. A., Laatsch, A. D., Zettler, E., Nerad, T. A., Cole, J., Diaz, F. C., Diaz, J., Janzen, D. H., Sittenfeld, A., Mason, O., & Reysenbach, A. L. (2005). “A microbial observatory of caterpillars: isolation and molecular characterization of protists associated with the saturniid moth caterpillar Rothschildia lebeau.” J Eukaryot Microbiol, 52(2), 107-115. doi:10.1111/j.1550-7408.2005.05202008..

Amils, R., González-Toril, E., Gómez, F., Fernández-Remolar, D., Rodríguez, N., Malki, M., Zuluaga, J., Aguilera, A., & Amaral-Zettler, L. A. (2005). “Importance of Chemolithotrophy for Early Life on Earth: The Tinto River (Iberian Pyritic Belt) Case.” In J. Seckbach (Ed.), Origins (Vol. 6, pp. 463-480): Springer Netherlands.

Arkhipova, I. R. (2005). “Mobile genetic elements and sexual reproduction.” Cytogenet Genome Res, 110(1-4), 372-382. doi:10.1159/00008496.

Arkhipova, I. R., & Meselson, M. (2005). “Diverse DNA transposons in rotifers of the class Bdelloidea.” Proc Natl Acad Sci U S A, 102(33), 11781-11786. doi:10.1073/pnas.050533310.

Arkhipova, I. R., & Meselson, M. (2005). “Deleterious transposable elements and the extinction of asexuals.” Bioessays, 27(1), 76-85. doi:10.1002/bies.2015.

Ason, B., Knauss, D. J., Balke, A. M., Merkel, G., Skalka, A. M., & Reznikoff, W. S. (2005). “Targeting Tn5 transposase identifies human immunodeficiency virus type 1 inhibitors.” Antimicrob Agents Chemother, 49(5), 2035-2043. doi:10.1128/AAC.49.5.2035-2043.200.

Bahr, M., Crump, B. C., Klepac-Ceraj, V., Teske, A., Sogin, M. L., & Hobbie, J. E. (2005). “Molecular characterization of sulfate-reducing bacteria in a New England salt marsh.” Environ Microbiol, 7(8), 1175-1185. doi:10.1111/j.1462-2920.2005.00796..

Belfort, M. (2005). “Back to Basics: Structure, Function, Evolution and Application of Homing Endonucleases and Inteins.” In M. Belfort, D. Wood, B. Stoddard, & V. Derbyshire (Ed.), Homing Endonucleases and Inteins (pp. 1-10): Springer Berlin Heidelberg.

Blocker, F. J., Mohr, G., Conlan, L. H., Qi, L., Belfort, M., & Lambowitz, A. M. (2005). “Domain structure and three-dimensional model of a group II intron-encoded reverse transcriptase.” RNA, 11(1), 14-28. doi:10.1261/rna.718110.

Bordenstein, S., & Rosengaus, R. B. (2005). “Discovery of a novel Wolbachia super group in Isoptera.” Curr Microbiol, 51(6), 393-398. doi:10.1007/s00284-005-0084-.

Bordenstein, S. R., & Reznikoff, W. S. (2005). “Mobile DNA in obligate intracellular bacteria.” Nat Rev Microbiol, 3(9), 688-699. doi:10.1038/nrmicro123.

Casiraghi, M., Bordenstein, S. R., Baldo, L., Lo, N., Beninati, T., Wernegreen, J. J., Werren, J. H., & Bandi, C. (2005). “Phylogeny of Wolbachia pipientis based on gltA, groEL and ftsZ gene sequences: clustering of arthropod and nematode symbionts in the F supergroup, and evidence for further diversity in the Wolbachia tree.” Microbiology, 151(Pt 12), 4015-4022. doi:10.1099/mic.0.28313-.

Conlan, L. H., Stanger, M. J., Ichiyanagi, K., & Belfort, M. (2005). “Localization, mobility and fidelity of retrotransposed Group II introns in rRNA genes.” Nucleic Acids Res, 33(16), 5262-5270. doi:10.1093/nar/gki81.

Coros, C. J., Landthaler, M., Piazza, C. L., Beauregard, A., Esposito, D., Perutka, J., Lambowitz, A. M., & Belfort, M. (2005). “Retrotransposition strategies of the Lactococcus lactis Ll.LtrB group II intron are dictated by host identity and cellular environment.” Mol Microbiol, 56(2), 509-524. doi:10.1111/j.1365-2958.2005.04554..

Degnan, P. H., Lazarus, A. B., & Wernegreen, J. J. (2005). “Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects.” Genome Res, 15(8), 1023-1033. doi:10.1101/gr.377130.

Dhillon, A., Goswami, S., Riley, M., Teske, A., & Sogin, M. L. (2005). “Domain evolution and functional diversification of sulfite reductases.” Astrobiology, 5(1), 18-29. doi:10.1089/ast.2005.5.1.

Dhillon, A., Lever, M., Lloyd, K. G., Albert, D. B., Sogin, M. L., & Teske, A. (2005). “Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin.” Appl Environ Microbiol, 71(8), 4592-4601. doi:10.1128/AEM.71.8.4592-4601.200.

Evgen’ev, M. B., & Arkhipova, I. R. (2005). “Penelope-like elements–a new class of retroelements: distribution, function and possible evolutionary significance.” Cytogenet Genome Res, 110(1-4), 510-521. doi:10.1159/00008498.

Fry, A. J., & Wernegreen, J. J. (2005). “The roles of positive and negative selection in the molecular evolution of insect endosymbionts.” Gene, 355, 1-10. doi:10.1016/j.gene.2005.05.02.

Fuller, N. J., Marie, D., Yallop, M., Rivlin, T., West, N. J., Post, A. F., & Scanlan, D. J. (2005). “Dynamics of community structure and P status of picocyanobacterial populations in the Gulf of Aqaba, Red Sea during 1999-2000.” Limnology and Oceanography, 50(1), 363-375.

Gould, R. M., Morrison, H. G., Gilland, E., & Campbell, R. K. (2005). “Myelin tetraspan family proteins but no non-tetraspan family proteins are present in the ascidian (Ciona intestinalis) genome.” Biol Bull, 209(1), 49-66.

Herbeck, J. T., Degnan, P. H., & Wernegreen, J. J. (2005). “Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria).” Mol Biol Evol, 22(3), 520-532. doi:10.1093/molbev/msi03.

Hiraga, K., Derbyshire, V., Dansereau, J. T., Van Roey, P., & Belfort, M. (2005). “Minimization and stabilization of the Mycobacterium tuberculosis recA intein.” J Mol Biol, 354(4), 916-926. doi:10.1016/j.jmb.2005.09.08.

Kolker, E., Picone, A. F., Galperin, M. Y., Romine, M. F., Higdon, R., Makarova, K. S., Kolker, N., Anderson, G. A., Qiu, X., Auberry, K. J., Babnigg, G., Beliaev, A. S., Edlefsen, P., Elias, D. A., Gorby, Y. A., Holzman, T., Klappenbach, J. A., Konstantinidis, K. T., Land, M. L., Lipton, M. S., McCue, L. A., Monroe, M., Pasa-Tolic, L., Pinchuk, G., Purvine, S., Serres, M. H., Tsapin, S., Zakrajsek, B. A., Zhu, W., Zhou, J., Larimer, F. W., Lawrence, C. E., Riley, M., Collart, F. R., Yates, J. R., 3rd, Smith, R. D., Giometti, C. S., Nealson, K. H., Fredrickson, J. K., & Tiedje, J. M. (2005). “Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.” Proc Natl Acad Sci U S A, 102(6), 2099-2104. doi:10.1073/pnas.040911110.

Kysela, D. T., Palacios, C., & Sogin, M. L. (2005). “Serial analysis of V6 ribosomal sequence tags (SARST-V6): a method for efficient, high-throughput analysis of microbial community composition.” Environ Microbiol, 7(3), 356-364. doi:10.1111/j.1462-2920.2004.00712..

Lee, W. J., Simpson, A. G. B., & Patterson, D. J. (2005). “Free-living heterotrophic flagellates from freshwater sites in Tasmania (Australia), a field survey.” Acta Protozoologica, 44(4), 321-350.

Lindell, D., Penno, S., Al-Qutob, M., David, E., Korpal, T., Lazar, B., & Post, A. F. (2005). “Expression of the N-stress response gene ntcA reveals N-sufficient Synechococcus populations in the oligotrophic northern Red Sea.” Limnology and Oceanography, 50, 1932-1944.

Mark Welch, D. B. (2005). “Bayesian and Maximum Likelihood Analyses of Rotifer–Acanthocephalan Relationships.” Hydrobiologia, 546(1), 47-54. doi:10.1007/s10750-005-4100-.

Mark Welch, D. B., & Mark Welch, J. L. (2005). “The potential of genomic approaches to rotifer ecology.” In A. Herzig, R. Gulati, C. Jersabek, & L. May (Ed.), Rotifera X (Vol. 181, pp. 101-108): Springer Netherlands.

Mehta, M. P., Huber, J. A., & Baross, J. A. (2005). “Incidence of novel and potentially archaeal nitrogenase genes in the deep Northeast Pacific Ocean.” Environ Microbiol, 7(10), 1525-1534. doi:10.1111/j.1462-2920.2005.00836..

Messerli, M. A., Amaral-Zettler, L. A., Zettler, E., Jung, S. K., Smith, P. J., & Sogin, M. L. (2005). “Life at acidic pH imposes an increased energetic cost for a eukaryotic acidophile.” J Exp Biol, 208(Pt 13), 2569-2579. doi:10.1242/jeb.0166.

Miao, J., Wu, W., Spielmann, T., Belfort, M., Derbyshire, V., & Belfort, G. (2005). “Single-step affinity purification of toxic and non-toxic proteins on a fluidics platform.” Lab Chip, 5(3), 248-253. doi:10.1039/b413292.

Mühling, M., Fuller, N. J., Millard, A., Scanlan, D. J., Post, A. F., Wilson, W. H., & Mann, N. H. (2005). “Genetic diversity of marine picoplankton (Synechococcus) blooms and covariance of the associated virioplankton population.” Environ Microbiol, 7(4), 499-508.

Murray, S., Flo Jorgensen, M., Ho, S. Y., Patterson, D. J., & Jermiin, L. S. (2005). “Improving the analysis of dinoflagellate phylogeny based on rDNA.” Protist, 156(3), 269-286. doi:10.1016/j.protis.2005.05.00.

Noel, C., Dufernez, F., Gerbod, D., Edgcomb, V. P., Delgado-Viscogliosi, P., Ho, L. C., Singh, M., Wintjens, R., Sogin, M. L., Capron, M., Pierce, R., Zenner, L., & Viscogliosi, E. (2005). “Molecular phylogenies of Blastocystis isolates from different hosts: implications for genetic diversity, identification of species, and zoonosis.” J Clin Microbiol, 43(1), 348-355. doi:10.1128/JCM.43.1.348-355.200.

Post, A. F. (2005). “Nutrient Limitation of Marine Cyanobacteria.” In J. Huisman, H. P. Matthijs, & P. Visser (Ed.), Harmful Cyanobacteria (Vol. 3, pp. 87-107): Springer Netherlands.

Roland, S., Bahr, M., Olendzenski, L., & Patterson, D. J. (2005). “Switch on micro*scope.” The Science Teacher(February ), 47-49.

Schaber, J., Rispe, C., Wernegreen, J. J., Buness, A., Delmotte, F., Silva, F. J., & Moya, A. (2005). “Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria.” Gene, 352, 109-117. doi:10.1016/j.gene.2005.04.00.

Serres, M. H., & Riley, M. (2005). “Gene fusions and gene duplications: relevance to genomic annotation and functional analysis.” BMC Genomics, 6, 33. doi:10.1186/1471-2164-6-3.

Sheehan, K. B., Patterson, D. J., Dicks, B. L., & Henson, J. M. (2005). “Seen and unseen: discovering the microbes of Yellowstone.” A Falcon Guide, Montana State University, Helena. Montana, 128.

Smith, D., Zhong, J., Matsuura, M., Lambowitz, A. M., & Belfort, M. (2005). “Recruitment of host functions suggests a repair pathway for late steps in group II intron retrohoming.” Genes Dev, 19(20), 2477-2487. doi:10.1101/gad.134510.

Sogin, M. L., Patterson, D. J., & McArthur, A. G. (2005). “Molecular and traditional approaches in the study of diversity and diversification of eukaryotes.” In J. Barros & W. Sullivan (Ed.), Planets & Life: The Emerging Science of Astrobiology: Cambridge University Press.

Van Roey, P., Belfort, M., & Derbyshire, V. (2005). “Homing endonuclease I-TevI: an atypical zinc finger with a novel function.” In S. Iuchi (Ed.), Zinc finger proteins: from atomic contact to cellular function (Vol. 1, pp. 35-38): Georgetown: Landes Bioscience, New York: Kluwer Academic/Plenum Publishers.

Wagner, R. Jr., & Meselson, M. (2005). “Repair tracts in mismatched DNA heteroduplexes.” 1976. DNA Repair (Amst), 4(1), 126-130; discussion 103-124, 131.

Weiland, M. E., McArthur, A. G., Morrison, H. G., Sogin, M. L., & Svard, S. G. (2005). “Annexin-like alpha giardins: a new cytoskeletal gene family in Giardia lamblia.” Int J Parasitol, 35(6), 617-626. doi:10.1016/j.ijpara.2004.12.00.

Wernegreen, J. J. (2005). “For better or worse: genomic consequences of intracellular mutualism and parasitism.” Curr Opin Genet Dev, 15(6), 572-583. doi:10.1016/j.gde.2005.09.01.

Winterberg, K. M., Luecke, J., Bruegl, A. S., & Reznikoff, W. S. (2005). “Phenotypic screening of Escherichia coli K-12 Tn5 insertion libraries, using whole-genome oligonucleotide microarrays.” Appl Environ Microbiol, 71(1), 451-459. doi:10.1128/AEM.71.1.451-459.200.

2004

Ason, B., & Reznikoff, W. S. (2004). “A high-throughput assay for Tn5 Tnp-induced DNA cleavage.” Nucleic Acids Res, 32(10), e83. doi:10.1093/nar/gnh08.

Ason, B., & Reznikoff, W. S. (2004). “DNA sequence bias during Tn5 transposition.” J Mol Biol, 335(5), 1213-1225. doi:S0022283603014499 [pii.

Best, A. A., Morrison, H. G., McArthur, A. G., Sogin, M. L., & Olsen, G. J. (2004). “Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia.” Genome Res, 14(8), 1537-1547. doi:10.1101/gr.225660.

Bordenstein, S. R., & Wernegreen, J. J. (2004). “Bacteriophage flux in endosymbionts (Wolbachia): infection frequency, lateral transfer, and recombination rates.” Mol Biol Evol, 21(10), 1981-1991. doi:10.1093/molbev/msh21.

Butterfield, D. A., Lilley, M. D., Huber, J. A., Roe, K. K., Embley, R. W., Baross, J. A., & Massoth, G. J. (2004). “Mixing, reaction, and microbial activity in the sub-seafloor revealed by temporal and spatial variation in diffuse flow vents at Axial Volcano.” In W. S. D. Wilcock, E. F. DeLong, D. S. Kelley, J. A. Baross, & S. C. Cary (Ed.), The subseafloor biosphere at mid-ocean ridges (Vol. Geophysical Monograph 144, pp. 269-289). Washington, D.C.: American Geophysical Union.

Crump, B. C., Hopkinson, C. S., Sogin, M. L., & Hobbie, J. E. (2004). “Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time.” Appl Environ Microbiol, 70(3), 1494-1505.

Degnan, P. H., Lazarus, A. B., Brock, C. D., & Wernegreen, J. J. (2004). “Host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of camponotus species and their endosymbionts, candidatus blochmannia.” Syst Biol, 53(1), 95-110. doi:JPADCD2N0F198Q0X [pii.

Edgell, D. R., Derbyshire, V., Van Roey, P., LaBonne, S., Stanger, M. J., Li, Z., Boyd, T. M., Shub, D. A., & Belfort, M. (2004). “Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor.” Nat Struct Mol Biol, 11(10), 936-944. doi:10.1038/nsmb82.

Edgell, D. R., Stanger, M. J., & Belfort, M. (2004). “Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host thymidylate synthase gene.” J Mol Biol, 343(5), 1231-1241. doi:10.1016/j.jmb.2004.09.00.

Lease, R. A., Smith, D., McDonough, K., & Belfort, M. (2004). “The small noncoding DsrA RNA is an acid resistance regulator in Escherichia coli.” J Bacteriol, 186(18), 6179-6185. doi:10.1128/JB.186.18.6179-6185.200.

Mark Welch, D. B., Cummings, M. P., Hillis, D. M., & Meselson, M. (2004). “Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families.” Proc Natl Acad Sci U S A, 101(6), 1622-1625. doi:10.1073/pnas.213668610.

Mark Welch, J. L., Mark Welch, D. B., & Meselson, M. (2004). “Cytogenetic evidence for asexual evolution of bdelloid rotifers.” Proc Natl Acad Sci U S A, 101(6), 1618-1621. doi:10.1073/pnas.030767710.

Meselson, M. (2004). “Explorations in the land of DNA and beyond.” Nat Med, 10(10), 1034-1037. doi:10.1038/nm1004-103.

Murray, S., & Patterson, D. J. (2004). “Cabra matta, gen.” nov., sp nov., a new benthic, heterotrophic dinoflagellate. European Journal of Phycology, 39(2), 229-234. doi:Doi 10.1080/096702604200020215.

Powell, W. H., Morrison, H. G., Weil, E. J., Karchner, S. I., Sogin, M. L., Stegeman, J. J., & Hahn, M. E. (2004). “Cloning and analysis of the CYP1A promoter from the atlantic killifish (Fundulus heteroclitus).” Mar Environ Res, 58(2-5), 119-124. doi:10.1016/j.marenvres.2004.03.00.

Pyatkov, K. I., Arkhipova, I. R., Malkova, N. V., Finnegan, D. J., & Evgen’ev, M. B. (2004). “Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements.” Proc Natl Acad Sci U S A, 101(41), 14719-14724. doi:10.1073/pnas.040628110.

Pyatkov, K. I., Arkhipova, I. R., Malkova, N. V., Finnegan, D. J., & Evgen’ev, M. B. (2004). “Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements.” Proc Natl Acad Sci U S A, 101(41), 14719-14724. doi:10.1073/pnas.040628110.

Reznikoff, W. S., Bordenstein, S. R., & Apodaca, J. (2004). “Comparative sequence analysis of IS50/Tn5 transposase.” J Bacteriol, 186(24), 8240-8247. doi:10.1128/JB.186.24.8240-8247.200.

Reznikoff, W. S., Goryshin, I. Y., & Jendrisak, J. J. (2004). “Tn5 as a molecular genetics tool: In vitro transposition and the coupling of in vitro technologies with in vivo transposition.” Methods Mol Biol, 260, 83-96. doi:10.1385/1-59259-755-6:08.

Serres, M. H., Goswami, S., & Riley, M. (2004). “GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins.” Nucleic Acids Res, 32(Database issue), D300-302. doi:10.1093/nar/gkh08.

Serres, M. H., & Riley, M. (2004). “Structural domains, protein modules, and sequence similarities enrich our understanding of the Shewanella oneidensis MR-1 proteome.” OMICS, 8(4), 306-321. doi:10.1089/omi.2004.8.30.

Silva, G. H., & Belfort, M. (2004). “Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI.” Nucleic Acids Res, 32(10), 3156-3168. doi:10.1093/nar/gkh61.

Silva-Pinhati, A. C., Bacci, M. Jr., Hinkle, G., Sogin, M. L., Pagnocca, F. C., Martins, V. G., Bueno, O. C., & Hebling, M. J. (2004). “Low variation in ribosomal DNA and internal transcribed spacers of the symbiotic fungi of leaf-cutting ants (Attini: Formicidae).” Braz J Med Biol Res, 37(10), 1463-1472. doi:/S0100-879X200400100000.

Simmons, S. L., Sievert, S. M., Frankel, R. B., Bazylinski, D. A., & Edwards, K. J. (2004). “Spatiotemporal distribution of marine magnetotactic bacteria in a seasonally stratified coastal salt pond.” Appl Environ Microbiol, 70(10), 6230-6239. doi:10.1128/AEM.70.10.6230-6239.200.

Steiniger-White, M., Rayment, I., & Reznikoff, W. S. (2004). “Structure/function insights into Tn5 transposition.” Curr Opin Struct Biol, 14(1), 50-57. doi:10.1016/j.sbi.2004.01.00.

Wernegreen, J. J. (2004). “Endosymbiosis: lessons in conflict resolution.” PLoS Biol, 2(3), E68. doi:10.1371/journal.pbio.002006.

Wernegreen, J. J., & Funk, D. J. (2004). “Mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome.” J Mol Evol, 59(6), 849-858. doi:10.1007/s00239-003-0192-.

2003

Alappat, S. R., Zhang, M., Zhao, X., Alliegro, M. A., Alliegro, M. C., & Burdsal, C. A. (2003). “Mouse pigpen encodes a nuclear protein whose expression is developmentally regulated during craniofacial morphogenesis.” Dev Dyn, 228(1), 59-71. doi:10.1002/dvdy.1035.

Amaral-Zettler, L. A., Messerli, M. A., Laatsch, A. D., Smith, P. J., & Sogin, M. L. (2003). “From genes to genomes: beyond biodiversity in Spain’s Rio Tinto.” Biol Bull, 204(2), 205-209.

Arkhipova, I. R., Pyatkov, K. I., Meselson, M., & Evgen’ev, M. B. (2003). “Retroelements containing introns in diverse invertebrate taxa.” Nat Genet, 33(2), 123-124. doi:10.1038/ng107.

Belfort, M. (2003). “Two for the price of one: a bifunctional intron-encoded DNA endonuclease-RNA maturase.” Genes Dev, 17(23), 2860-2863. doi:10.1101/gad.116250.

Bordenstein, S. R. (2003). “Symbiosis and the origin of species.” In K. Bourtzis & T. Miller (Ed.), Insect Symbiosis (Vol. 1, pp. 283-304). New York: CRC Press.

Bordenstein, S. R., Fitch, D. H., & Werren, J. H. (2003). “Absence of wolbachia in nonfilariid nematodes.” J Nematol, 35(3), 266-270.

Bordenstein, S. R., Uy, J. J., & Werren, J. H. (2003). “Host genotype determines cytoplasmic incompatibility type in the haplodiploid genus Nasonia.” Genetics, 164(1), 223-233.

Busse, I., Patterson, D. J., & Preisfeld, A. (2003). “Phylogeny of phagotrophic euglenids (Euglenozoa): A molecular approach based on culture material and environmental samples.” Journal of Phycology, 39(4), 828-836. doi:DOI 10.1046/j.1529-8817.2003.02178..

Dhillon, A., Teske, A., Dillon, J., Stahl, D. A., & Sogin, M. L. (2003). “Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin.” Appl Environ Microbiol, 69(5), 2765-2772.

Edgell, D. R., Stanger, M. J., & Belfort, M. (2003). “Importance of a single base pair for discrimination between intron-containing and intronless alleles by endonuclease I-BmoI.” Curr Biol, 13(11), 973-978. doi:S0960982203003403 [pii.

Fuller, N. J., Marie, D., Partensky, F., Vaulot, D., Post, A. F., & Scanlan, D. J. (2003). “Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea.” Appl Environ Microbiol, 69(5), 2430-2443.

Gillor, O., Harush, A., Hadas, O., Post, A. F., & Belkin, S. (2003). “A Synechococcus PglnA::luxAB fusion for estimation of nitrogen bioavailability to freshwater cyanobacteria.” Appl Environ Microbiol, 69(3), 1465-1474.

Goryshin, I. Y., Naumann, T. A., Apodaca, J., & Reznikoff, W. S. (2003). “Chromosomal deletion formation system based on Tn5 double transposition: use for making minimal genomes and essential gene analysis.” Genome Res, 13(4), 644-653. doi:10.1101/gr.61140.

Herbeck, J. T., Funk, D. J., Degnan, P. H., & Wernegreen, J. J. (2003). “A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: slightly deleterious mutations in the chaperonin groEL.” Genetics, 165(4), 1651-1660.

Herbeck, J. T., Wall, D. P., & Wernegreen, J. J. (2003). “Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia.” Microbiology, 149(Pt 9), 2585-2596.

Huber, J. A., Butterfield, D. A., & Baross, J. A. (2003). “Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption.” FEMS Microbiol Ecol, 43(3), 393-409. doi:10.1111/j.1574-6941.2003.tb01080..

Ichiyanagi, K., Beauregard, A., & Belfort, M. (2003). “A bacterial group II intron favors retrotransposition into plasmid targets.” Proc Natl Acad Sci U S A, 100(26), 15742-15747. doi:10.1073/pnas.253665910.

Johnson, H. P., & Party, L. S. (2003). “Probing for life in the ocean crust with the LEXEN program.” Eos, Trans. AGU., 84, 109-112.

Lee, W. J., Brandt, S. M., Vors, N., & Patterson, D. J. (2003). “Darwin’s heterotrophic flagellates.” Ophelia, 57(2), 63-98.

Linz-McGillem, L. A., & Alliegro, M. C. (2003). “Myosin II in retinal pigmented epithelial cells: evidence for an association with membranous vesicles.” Exp Eye Res, 76(5), 543-552. doi:S0014483503000319 [pii.

Liu, Q., Belle, A., Shub, D. A., Belfort, M., & Edgell, D. R. (2003). “SegG endonuclease promotes marker exclusion and mediates co-conversion from a distant cleavage site.” J Mol Biol, 334(1), 13-23. doi:S0022283603011628 [pii.

Man, D., Wang, W., Sabehi, G., Aravind, L., Post, A. F., Massana, R., Spudich, E. N., Spudich, J. L., & Beja, O. (2003). “Diversification and spectral tuning in marine proteorhodopsins.” EMBO J, 22(8), 1725-1731. doi:10.1093/emboj/cdg18.

Mark Welch, D. B., & Meselson, M. (2003). “Oocyte nuclear DNA content and GC proportion in rotifers of the anciently asexual Class Bdelloidea.” Biological Journal of the Linnean Society, 79(1), 85-91. doi:10.1046/j.1095-8312.2003.00180..

Medina, M., Collins, A. G., Taylor, J. W., Valentine, J. W., Lipps, J. H., Amaral-Zettler, L. A., & Sogin, M. L. (2003). “Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa.” International Journal of Astrobiology, 2, 203-211.

Meselson, M. (2003). “Interview with Matthew Meselson.” Bioessays, 25(12), 1236-1246. doi:10.1002/bies.1037.

Nixon, J. E., Field, J., McArthur, A. G., Sogin, M. L., Yarlett, N., Loftus, B. J., & Samuelson, J. (2003). “Iron-dependent hydrogenases of Entamoeba histolytica and Giardia lamblia: activity of the recombinant entamoebic enzyme and evidence for lateral gene transfer.” Biol Bull, 204(1), 1-9.

Noble, M., Smith, J., Power, J., & Mayer-Proschel, M. (2003). “Redox state as a central modulator of precursor cell function.” Parkinson’s Disease: The Life Cycle of the Dopamine Neuron, 991, 251-271.

Noel, C., Peyronnet, C., Gerbod, D., Edgcomb, V. P., Delgado-Viscogliosi, P., Sogin, M. L., Capron, M., Viscogliosi, E., & Zenner, L. (2003). “Phylogenetic analysis of Blastocystis isolates from different hosts based on the comparison of small-subunit rRNA gene sequences.” Mol Biochem Parasitol, 126(1), 119-123. doi:S0166685102002463 [pii.

O’Kelly, C. J., Silberman, J. D., Amaral-Zettler, L. A., Nerad, T. A., & Sogin, M. L. (2003). “Monopylocystis visvesvarai n.” gen., n. sp. and Sawyeria marylandensis n. gen., n. sp.: two new amitochondrial heterolobosean amoebae from anoxic environments. Protist, 154(2), 281-290. doi:10.1078/14344610332216656.

Patterson, D. J. (2003). “Progressing towards a biological names register.” Nature, 422(6933), 661. doi:10.1038/422661.

Patterson, D. J., Remsen, D., & Norton, C. (2003). “Comment on Zoological record and registration of new names in zoology.” Bulletin of Zoological Nomenclature, 60, 297-299.

Peglar, M. T., Amaral-Zettler, L. A., Anderson, O. R., Nerad, T. A., Gillevet, P. M., Mullen, T. E., Frasca, S. Jr., Silberman, J. D., O’Kelly, C. J., & Sogin, M. L. (2003). “Two new small-subunit ribosomal RNA gene lineages within the subclass gymnamoebia.” J Eukaryot Microbiol, 50(3), 224-232.

Peterson, G., & Reznikoff, W. (2003). “Tn5 transposase active site mutations suggest position of donor backbone DNA in synaptic complex.” J Biol Chem, 278(3), 1904-1909. doi:10.1074/jbc.M20896820.

Reiner, D. S., Hetsko, M. L., Meszaros, J. G., Sun, C. H., Morrison, H. G., Brunton, L. L., & Gillin, F. D. (2003). “Calcium signaling in excystation of the early diverging eukaryote, Giardia lamblia.” J Biol Chem, 278(4), 2533-2540. doi:10.1074/jbc.M20803320.

Reznikoff, W. S. (2003). “Tn5 as a model for understanding DNA transposition.” Mol Microbiol, 47(5), 1199-1206. doi:3382 [pii.

Rocap, G., Larimer, F. W., Lamerdin, J., Malfatti, S., Chain, P., Ahlgren, N. A., Arellano, A., Coleman, M., Hauser, L., Hess, W. R., Johnson, Z. I., Land, M., Lindell, D., Post, A. F., Regala, W., Shah, M., Shaw, S. L., Steglich, C., Sullivan, M. B., Ting, C. S., Tolonen, A., Webb, E. A., Zinser, E. R., & Chisholm, S. W. (2003). “Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation.” Nature, 424(6952), 1042-1047. doi:10.1038/nature0194.

Schroeckh, S., Lee, W. J., & Patterson, D. J. (2003). “Free-living heterotrophic euglenids from freshwater sites in mainland Australia.” Hydrobiologia, 493(1-3), 131-166. doi:Doi 10.1023/A:102545780142.

Seshadri, V., McArthur, A. G., Sogin, M. L., & Adam, R. D. (2003). “Giardia lamblia RNA polymerase II: amanitin-resistant transcription.” J Biol Chem, 278(30), 27804-27810. doi:10.1074/jbc.M30331620.

Sogin, M. L., & Jennings, D. E. (2003). “Introduction.” Biol Bull, 204(2), 159. doi:10.1086/BBLv204n2p15.

Steglich, C., Post, A. F., & Hess, W. R. (2003). “Analysis of natural populations of Prochlorococcus spp.” in the northern Red Sea using phycoerythrin gene sequences. Environ Microbiol, 5(8), 681-690. doi:DOI 10.1046/j.1462-2920.2003.00456..

Teske, A., Dhillon, A., & Sogin, M. L. (2003). “Genomic markers of ancient anaerobic microbial pathways: sulfate reduction, methanogenesis, and methane oxidation.” Biol Bull, 204(2), 186-191.

Walker, G., Silberman, J. D., Karpov, S. A., Preisfeld, A., Foster, P., Ol Frolov, A., Novozhilov, Y., & Sogin, M. L. (2003). “An ultrastructural and molecular study of Hyperamoeba dachnyaya,n.” sp., and its relationship to the mycetozoan slime moulds. European Journal of Protistology, 39, 319-336.

Wernegreen, J. J., Degnan, P. H., Lazarus, A. B., Palacios, C., & Bordenstein, S. R. (2003). “Genome evolution in an insect cell: distinct features of an ant-bacterial partnership.” Biol Bull, 204(2), 221-231.

Zeidner, G., Preston, C. M., Delong, E. F., Massana, R., Post, A. F., Scanlan, D. J., & Beja, O. (2003). “Molecular diversity among marine picophytoplankton as revealed by psbA analyses.” Environ Microbiol, 5(3), 212-216. doi:DOI 10.1046/j.1462-2920.2003.00403..

2002

Al Qassab, S., Lee, W. J., Murray, S., & Patterson, D. J. (2002). “Flagellates from stromatolites and surrounding sediments in Shark Bay, Western Australia.” Acta. Protozoologica, 41, 91-144.

Alliegro, M. C. (2002). “Coiled body heterogeneity induced by G(1) arrest with amiloride + bumetanide.” Exp Cell Res, 279(1), 111-117. doi:S0014482702955989 [pii.

Alliegro, M. C., & Alliegro, M. A. (2002). “Nuclear injection of anti-pigpen antibodies inhibits endothelial cell division.” J Biol Chem, 277(21), 19037-19041. doi:10.1074/jbc.M20073720.

Amaral-Zettler, L. A., Gomez, F., Zettler, E., Keenan, B. G., Amils, R., & Sogin, M. L. (2002). “Microbiology: eukaryotic diversity in Spain’s River of Fire.” Nature, 417(6885), 137. doi:10.1038/417137.

Ason, B., & Reznikoff, W. S. (2002). “Mutational analysis of the base flipping event found in Tn5 transposition.” J Biol Chem, 277(13), 11284-11291. doi:10.1074/jbc.M11111920.

Belfort, M., Derbyshire, V., Cousineau, B., & Lambowitz, A. M. (2002). “Mobile introns: pathway and proteins.” In R. Craig, M. Craigie, Gellert, & A. M. Lambowitz (Ed.), Mobile DNA II (pp. 761-783). Washington, DC: ASM Press.

Boelen, P., Post, A. F., Veldhuis, M. J., & Buma, A. G. (2002). “Diel patterns of UVBR-induced DNA damage in picoplankton size fractions from the Gulf of Aqaba, Red Sea.” Microb Ecol, 44(2), 164-174. doi:10.1007/s00248-002-1002-.

Dean, A. B., Stanger, M. J., Dansereau, J. T., Van Roey, P., Derbyshire, V., & Belfort, M. (2002). “Zinc finger as distance determinant in the flexible linker of intron endonuclease I-TevI.” Proc Natl Acad Sci U S A, 99(13), 8554-8561. doi:10.1073/pnas.08225369.

Delvinquier, B. L. J., & Patterson, D. J. (2002). “Order Slopalinida.” In J. J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (pp. 754-759). Lawrence, Kansas: Society of Protozoologists.

Dyer, K. D., Linz-Mcgillem, L. A., Alliegro, M. A., & Alliegro, M. C. (2002). “Receptor-bound uPA is reversibly protected from inhibition by low molecular weight inhibitors.” Cell Biol Int, 26(4), 327-335. doi:10.1006/cbir.2001.085.

Edgcomb, V. P., Kysela, D. T., Teske, A., de Vera Gomez, A., & Sogin, M. L. (2002). “Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment.” Proc Natl Acad Sci U S A, 99(11), 7658-7662. doi:10.1073/pnas.06218639.

Edgcomb, V. P., Simpson, A. G., Zettler, L. A., Nerad, T. A., Patterson, D. J., Holder, M. E., & Sogin, M. L. (2002). “Pelobionts are degenerate protists: insights from molecules and morphology.” Mol Biol Evol, 19(6), 978-982.

Gerbod, D., Noel, C., Dolan, M. F., Edgcomb, V. P., Kitade, O., Noda, S., Dufernez, F., Ohkuma, M., Kudo, T., Capron, M., Sogin, M. L., & Viscogliosi, E. (2002). “Molecular phylogeny of parabasalids inferred from small subunit rRNA sequences, with emphasis on the Devescovinidae and Calonymphidae (Trichomonadea).” Mol Phylogenet Evol, 25(3), 545-556. doi:S1055790302003007 [pii.

Gillor, O., Hadas, O., Post, A. F., & Belkin, S. (2002). “Phosphorus bioavailability monitoring by a bioluminescent cyanobacterial sensor strain.” Journal of Phycology, 38, 107-105.

Holtzendorff, J., Marie, D., Post, A. F., Partensky, F., Rivlin, A., & Hess, W. R. (2002). “Synchronized expression of ftsZ in natural Prochlorococcus populations of the Red Sea.” Environ Microbiol, 4(11), 644-653.

Huber, J. A., Butterfield, D. A., & Baross, J. A. (2002). “Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat.” Appl Environ Microbiol, 68(4), 1585-1594.

Ichiyanagi, K., Beauregard, A., Lawrence, S., Smith, D., Cousineau, B., & Belfort, M. (2002). “Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets.” Mol Microbiol, 46(5), 1259-1272.

Katoh, M., & Kuma, M. (2002). “Mafft: a novel method for rapid multiple sequence alignment based on fast Fourier transform.” Nucleic Acids Res, 30. doi:10.1093/nar/gkf43.

Langford, T. D., Silberman, J. D., Weiland, M. E., Svard, S. G., McCaffery, J. M., Sogin, M. L., & Gillin, F. D. (2002). “Giardia lamblia: identification and characterization of Rab and GDI proteins in a genome survey of the ER to Golgi endomembrane system.” Exp Parasitol, 101(1), 13-24. doi.

Lee, W. J., & Patterson, D. J. (2002). “Optimising the extraction of bacteria, heterotrophic protists and diatoms, and estimating their abundance and biomass from intertidal sandy sediments.” Journal of the Korean Society of Oceanography, 37, 58-65.

Lee, W. J., & Patterson, D. J. (2002). “Abundance and biomass of heterotrophic flagellates, and factors controlling their abundance and distribution in sediments of Botany Bay.” Microb Ecol, 43(4), 467-481. doi:10.1007/s00248-002-2000-.

Lindell, D., Erdner, D., Marie, D., Claustre, H., Prasil, O., Le Gall, F., Rippka, R., Partensky, F., Scanlan, D. J., & Post, A. F. (2002). “Contrasting expression of ntcA and amt in Prochlorococcus sp.” strain PCC 9511. Journal of Phycology, 38(6), 1113-1124.

Lovell, S., Goryshin, I. Y., Reznikoff, W. R., & Rayment, I. (2002). “Two-metal active site binding of a Tn5 transposase synaptic complex.” Nat Struct Biol, 9(4), 278-281. doi:10.1038/nsb77.

Mark Welch, D. B. (2002). “Rotifera McGraw-Hill Yearbook of Science & Technology (Vol.” 1, pp. 304-306). New York: McGraw Hill.

Mikrjukov, K. A., Patterson, D. J., & Siemensma, F. J. (2002). “Phylum Heliozoa In J.” J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa (2nd ed., pp. 860-871). Lawrence, Kansas: Society of Protozoologists.

Moore, L. R., Post, A. F., Rocap, G., & Chisholm, S. W. (2002). “Differential nitrogen utilization of the marine cyanobacteria Prochlorococcus and Synechococcus.” Limnology and Oceanography, 47(4), 989-996.

Morrison, H. G., Zamora, G., Campbell, R. K., & Sogin, M. L. (2002). “Inferring protein function from genomic sequence: Giardia lamblia expresses a phosphatidylinositol kinase-related kinase similar to yeast and mammalian TOR.” Comp Biochem Physiol B Biochem Mol Biol, 133(4), 477-491.

Murray, S., & Patterson, D. J. (2002). “The benthic dinoflagellate genus Amphidinium in south-eastern Australian waters, including three new species.” European Journal of Phycology, 37(2), 279-298. doi:Doi 10.1017/S096702620200359.

Murray, S., & Patterson, D. J. (2002). “Amphidiniopsis korewalensis sp.” nov., a new heterotrophic benthic dinoflagellates. Phycologica, 41, 382-388.

Naumann, T. A., Goryshin, I. Y., & Reznikoff, W. S. (2002). “Production of combinatorial libraries of fused genes by sequential transposition reactions.” Nucleic Acids Res, 30(21), e119.

Naumann, T. A., & Reznikoff, W. S. (2002). “Tn5 transposase active site mutants.” J Biol Chem, 277(20), 17623-17629. doi:10.1074/jbc.M20074220.

Naumann, T. A., & Reznikoff, W. S. (2002). “Tn5 transposase with an altered specificity for transposon ends.” J Bacteriol, 184(1), 233-240.

Nixon, J. E., Wang, A., Field, J., Morrison, H. G., McArthur, A. G., Sogin, M. L., Loftus, B. J., & Samuelson, J. (2002). “Evidence for lateral transfer of genes encoding ferredoxins, nitroreductases, NADH oxidase, and alcohol dehydrogenase 3 from anaerobic prokaryotes to Giardia lamblia and Entamoeba histolytica.” Eukaryot Cell, 1(2), 181-190.

Nixon, J. E., Wang, A., Morrison, H. G., McArthur, A. G., Sogin, M. L., Loftus, B. J., & Samuelson, J. (2002). “A spliceosomal intron in Giardia lamblia.” Proc Natl Acad Sci U S A, 99(6), 3701-3705. doi:10.1073/pnas.04270029.

Pahl, N., Homsi, S., Morrison, H. G., & Gould, R. M. (2002). “mRNAs located in Squalus acanthias (spiny dogfish) oligodendrocyte processes.” Biol Bull, 203(2), 217-218.

Palacios, C., & Wernegreen, J. J. (2002). “A strong effect of AT mutational bias on amino acid usage in Buchnera is mitigated at high-expression genes.” Mol Biol Evol, 19(9), 1575-1584.

Patterson, D. J. (2002). “Changing views of protistan systematics: the taxonomy of protozoa – an overview.” In J. J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (pp. 2-9). Lawrence, Kansas: Society of Protozoologists.

Patterson, D. J. (2002). “Residual heterotrophic stramenopiles.” In J. J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (pp. 751-754). Lawrence, Kansas: Society of Protozoologists.

Patterson, D. J., Rogerson, A., & Vors, N. (2002). “Class Heterolobosea.” In J. J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (pp. 1104-1111). Lawrence, Kansas: Society of Protozoologists.

Patterson, D. J., Simpson, A. G. B., & Rogerson, A. (2002). “Amoebae of uncertain affinities In J.” J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (pp. 804-827). Lawrence, Kansas: Society of Protozoologists.

Patterson, D. J., Vors, N., Simpson, A. G. B., & O’Kelly, C. J. (2002). “Residual free-living and predatory heterotrophic flagellates.” In J. J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (2nd edition ed., pp. 1302-1328). Lawrence, Kansas: Society of Protozoologists.

Podar, M., Mullineaux, L., Huang, H. R., Perlman, P. S., & Sogin, M. L. (2002). “Bacterial group II introns in a deep-sea hydrothermal vent environment.” Appl Environ Microbiol, 68(12), 6392-6398.

Post, A. F., Dedej, Z., Gottlieb, R., Li, H., Thomas, D., El-Absawy, M., El-Naggar, A., El-Gharabawi, M., & Sommer, U. (2002). “Spatial and temporal distribution of Trichodesmium spp.” in the stratified waters of the Gulf of Aqaba (northern Red Sea). Marine Ecology Progress Series, 239, 241-250.

Reznikoff, W. S. (2002). “Molecular basis of Tn5 transposition Molecular Genetics Biophysics and Medicine Today, Bresler Memorial Lectures (pp.” 292-297): Russian Academy of Sciences, St. Petersburg Scientific Center RAS, Konstantinov Petersburg Nuclear Physics Institute RAS.

Reznikoff, W. S. (2002). “Tn5 transposition.” In N. Craig, R. Craigie, M. Gellert, & A. Lambowitz (Ed.), Mobile DNA II (pp. 403-421). Washington, DC: ASM Press.

Rogerson, A., & Patterson, D. J. (2002). “The naked ramicristate amoebae (Gymnamoebae) In J.” J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (pp. 1023-1053). Lawrence, Kansas: Society of Protozoologists.

Simpson, A. G., Roger, A. J., Silberman, J. D., Leipe, D. D., Edgcomb, V. P., Jermiin, L. S., Patterson, D. J., & Sogin, M. L. (2002). “Evolutionary history of “early-diverging” eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia.” Mol Biol Evol, 19(10), 1782-1791.

Simpson, A. G. B., & Patterson, D. J. (2002). “Family Colpodellidae Simpson & Patterson, 19965.” In J. J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition. Lawrence, Kansas: Society of Protozoologists.

Sommer, U., Berninger, U.-G., Boettger-Schnack, R., Hansen, T., Stibor, H., Schnack-Schiel, S. B., Cornils, A., Hagen, W., Wickham, S., Al-Najjar, T., & Post, A. F. (2002). “Grazing during the spring bloom in the Gulf of Aqaba and the Northern Red Sea.” Marine Ecology Progress Series, 239, 251-261.

Steiniger-White, M., Bhasin, A., Lovell, S., Rayment, I., & Reznikoff, W. S. (2002). “Evidence for “unseen” transposase–DNA contacts.” J Mol Biol, 322(5), 971-982. doi:S002228360200877X [pii.

Tamas, I., Klasson, L., Canback, B., Naslund, A. K., Eriksson, A. S., Wernegreen, J. J., Sandstrom, J. P., Moran, N. A., & Andersson, S. G. (2002). “50 million years of genomic stasis in endosymbiotic bacteria.” Science, 296(5577), 2376-2379. doi:10.1126/science.107127.

Teske, A., Hinrichs, K. U., Edgcomb, V., de Vera Gomez, A., Kysela, D., Sylva, S. P., Sogin, M. L., & Jannasch, H. W. (2002). “Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities.” Appl Environ Microbiol, 68(4), 1994-2007.

Van Roey, P., Meehan, L., Kowalski, J. C., Belfort, M., & Derbyshire, V. (2002). “Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI.” Nat Struct Biol, 9(11), 806-811. doi:10.1038/nsb85.

Wernegreen, J. J. (2002). “Genome evolution in bacterial endosymbionts of insects.” Nat Rev Genet, 3(11), 850-861. doi:10.1038/nrg93.

Wernegreen, J. J., Lazarus, A. B., & Degnan, P. H. (2002). “Small genome of Candidatus Blochmannia, the bacterial endosymbiont of Camponotus, implies irreversible specialization to an intracellular lifestyle.” Microbiology, 148(Pt 8), 2551-2556.

Wu, W., Wood, D. W., Belfort, G., Derbyshire, V., & Belfort, M. (2002). “Intein-mediated purification of cytotoxic endonuclease I-TevI by insertional inactivation and pH-controllable splicing.” Nucleic Acids Res, 30(22), 4864-4871.

2001

Alliegro, M. C. (2001). “Pigpen and endothelial cell differentiation.” Cell Biol Int, 25(7), 577-584. doi:10.1006/cbir.2000.073.

Amaral-Zettler, L. A., Nerad, T. A., O’Kelly, C. J., & Sogin, M. L. (2001). “The nucleariid amoebae: more protists at the animal-fungal boundary.” J Eukaryot Microbiol, 48(3), 293-297.

Arkhipova, I. R. (2001). “[Transposable elements in the Animal Kingdom].” Mol Biol (Mosk), 35(2), 196-207.

Arkhipova, I. R. (2001). “Retrotransposons.” In E. C. R. Reeve (Ed.), Encyclopedia of Genetics. London: Fitzroy Dearborn Publishers.

Arkhipova, I. R., & Morrison, H. G. (2001). “Three retrotransposon families in the genome of Giardia lamblia: two telomeric, one dead.” Proc Natl Acad Sci U S A, 98(25), 14497-14502. doi:10.1073/pnas.23149479.

Barbieri, E., Paster, B. J., Hughes, D., Zurek, L., Moser, D. P., Teske, A., & Sogin, M. L. (2001). “Phylogenetic characterization of epibiotic bacteria in the accessory nidamental gland and egg capsules of the squid Loligo pealei (Cephalopoda:Loliginidae).” Environ Microbiol, 3(3), 151-167.

Bordenstein, S. R., & Drapeau, M. D. (2001). “Genotype-by-environment interaction and the Dobzhansky-Muller model of postzygotic isolation.” Journal of Evolutionary Biology, 14(3), 490-501. doi:Doi 10.1046/J.1420-9101.2001.00289..

Bordenstein, S. R., O’Hara, F. P., & Werren, J. H. (2001). “Wolbachia-induced incompatibility precedes other hybrid incompatibilities in Nasonia.” Nature, 409(6821), 707-710. doi:10.1038/3505554.

Brugerolle, G., & Patterson, D. J. (2001). “Ultrastructure of Joenina pulchella Grassi, 1917 (Protista, Parabasalia), a reassessment of evolutionary trends in the parabasalids, and a new order Cristamonadida for devescovinid, calonymphid and lophomonad flagellates.” Organisms Diversity & Evolution, 1(2), 147-160. doi:Doi 10.1078/1439-6092-0001.

Corduneanu, A., & Bishop, C. M. (2001). “Variational Bayesian model selection for mixture distributions.” In T. Jaakkola & T. Richardson (Ed.), Artificial intelligence and statistics 2001. United States: Morgan Kaufmann.

Edgcomb, V. P., Roger, A. J., Simpson, A. G., Kysela, D. T., & Sogin, M. L. (2001). “Evolutionary relationships among “jakobid” flagellates as indicated by alpha- and beta-tubulin phylogenies.” Mol Biol Evol, 18(4), 514-522.

Funk, D. J., Wernegreen, J. J., & Moran, N. A. (2001). “Intraspecific variation in symbiont genomes: bottlenecks and the aphid-buchnera association.” Genetics, 157(2), 477-489.

Gerbod, D., Edgcomb, V. P., Noel, C., Vanacova, S., Wintjens, R., Tachezy, J., Sogin, M. L., & Viscogliosi, E. (2001). “Phylogenetic relationships of class II fumarase genes from trichomonad species.” Mol Biol Evol, 18(8), 1574-1584.

Gerbod, D., Edgcomb, V. P., Noel, C., Zenner, L., Wintjens, R., Delgado-Viscogliosi, P., Holder, M. E., Sogin, M. L., & Viscogliosi, E. (2001). “Phylogenetic position of the trichomonad parasite of turkeys, Histomonas meleagridis (Smith) Tyzzer, inferred from small subunit rRNA sequence.” J Eukaryot Microbiol, 48(4), 498-504.

Karpov, S. A., Sogin, M. L., & Silberman, J. D. (2001). “Rootlet homology, taxonomy, and phylogeny of bicosoecids based on 18S rRNA gene sequences.” Protistology, 21, 34-47.

Lee, D. D., & Seung, H. S. (2001). “Algorithms for non-negative matrix factorization.” Adv Neural Inf Process Syst, 13.

Lindell, D., & Post, A. F. (2001). “Ecological aspects of ntcA gene expression and its use as an indicator of the nitrogen status of marine Synechococcus spp.” Appl Environ Microbiol, 67(8), 3340-3349. doi:10.1128/AEM.67.8.3340-3349.200.

Mark Welch, D. B. (2001). “Early contributions of molecular phylogenetics to understanding the evolution of Rotifera.” Hydrobiologia, 446-447(1), 315-322. doi:10.1023/A:101750292328.

Mark Welch, D. B., & Meselson, M. (2001). “A survey of introns in three genes of rotifers.” In L. Sanoamuang, H. Segers, R. J. Shiel, & R. D. Gulati (Ed.), Rotifera IX (Vol. 153, pp. 333-336): Springer Netherlands.

Mark Welch, D. B., & Meselson, M. S. (2001). “Rates of nucleotide substitution in sexual and anciently asexual rotifers.” Proc Natl Acad Sci U S A, 98(12), 6720-6724. doi:10.1073/pnas.11114459.

McArthur, A. G., Knodler, L. A., Silberman, J. D., Davids, B. J., Gillin, F. D., & Sogin, M. L. (2001). “The evolutionary origins of eukaryotic protein disulfide isomerase domains: new evidence from the Amitochondriate protist Giardia lamblia.” Mol Biol Evol, 18(8), 1455-1463.

Medina, M., Collins, A. G., Silberman, J. D., & Sogin, M. L. (2001). “Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA.” Proc Natl Acad Sci U S A, 98(17), 9707-9712. doi:10.1073/pnas.17131699.

Mikrjukov, K. A., & Patterson, D. J. (2001). “Taxonomy and phylogeny of heliozoa.” III. Actinophryids. Acta Protozoologica, 40(1), 3-25.

Morrison, H. G., Roger, A. J., Nystul, T. G., Gillin, F. D., & Sogin, M. L. (2001). “Giardia lamblia expresses a proteobacterial-like DnaK homolog.” Mol Biol Evol, 18(4), 530-541.

Patterson, D. J., & Burford, M. A. (2001). “A guide to the protozoa of marine aquaculture ponds.” Collingwood, Australia: CSIRO Publishing.

Pevzner, P., Tang, H., & Waterman, M. (2001). “An Eulerian path approach to DNA fragment assembly.” Proc Natl Acad Sci USA, 98. doi:10.1073/pnas.17128509.

Podar, M., Haddock, S. H., Sogin, M. L., & Harbison, G. R. (2001). “A molecular phylogenetic framework for the phylum Ctenophora using 18S rRNA genes.” Mol Phylogenet Evol, 21(2), 218-230. doi:10.1006/mpev.2001.103.

Schreiter, P., Gillor, O., Post, A. F., Belkin, S., Schmid, R. D., & Bachmann, T. T. (2001). “Monitoring of phosphorus availability in water by an immobilized lumniscent cyanobacterial reporter strain.” Biosensors and Bioelectronics, 16, 811-818.

Serres, M. H., Gopal, S., Nahum, L. A., Liang, P., Gaasterland, T., & Riley, M. (2001). “A functional update of the Escherichia coli K-12 genome.” Genome Biol, 2(9), RESEARCH0035.

Simpson, A. G., & Patterson, D. J. (2001). “On core jakobids and excavate taxa: the ultrastructure of Jakoba incarcerata.” J Eukaryot Microbiol, 48(4), 480-492.

Smith, R., Kavanagh, E., Morrison, H. G., & Gould, R. M. (2001). “Messenger RNAs located in spiny dogfish oligodendrocyte processes.” Biol Bull, 201(2), 255-256.

Stihl, A., Sommer, U., & Post, A. F. (2001). “Alkaline phosphatase activities among populations of the colony-forming diazotrophic cyanobacterium Trichodesmium spp.” (cyanobacteria) in the Red Sea. Journal of Phycology, 37(2), 310-317. doi:Doi 10.1046/J.1529-8817.2001.037002310..

Torino, J. L., Burger, M. S., Reznikoff, C. A., & Swaminathan, S. (2001). “Role of TP53 in repair of N-(deoxyguanosin-8-yl)-4-aminobiphenyl adducts in human transitional cell carcinoma of the urinary bladder.” Carcinogenesis, 22(1), 147-154.

Twining, S. S., Goryshin, I. Y., Bhasin, A., & Reznikoff, W. S. (2001). “Functional characterization of arginine 30, lysine 40, and arginine 62 in Tn5 transposase.” J Biol Chem, 276(25), 23135-23143. doi:10.1074/jbc.M01074820.

Van Roey, P., Waddling, C. A., Fox, K. M., Belfort, M., & Derbyshire, V. (2001). “Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.” EMBO J, 20(14), 3631-3637. doi:10.1093/emboj/20.14.363.

Walker, G., Simpson, A. G. B., Edgcomb, V. P., Sogin, M. L., & Patterson, D. J. (2001). “Ultrastructural identities of Mastigamoeba Protozoologica punctachora, Mastigamoeba simplex and Mastigella commutans and assessment of hypotheses of relatedness of the pelobionts (Protista).” Europ. J. Protistol, 37, 25-49.

Welling, M., & Weber, M. (2001). “Positive tensor factorization.” Pattern Recognit Lett, 22. doi:10.1016/S0167-8655(01)00070-.

Wernegreen, J. J., & Moran, N. A. (2001). “Vertical transmission of biosynthetic plasmids in aphid endosymbionts (Buchnera).” J Bacteriol, 183(2), 785-790. doi:10.1128/JB.183.2.785-790.200.

Wernegreen, J. J., Richardson, A. O., & Moran, N. A. (2001). “Parallel acceleration of evolutionary rates in symbiont genes underlying host nutrition.” Mol Phylogenet Evol, 19(3), 479-485. doi:10.1006/mpev.2001.092.

West, N. J., Schoenhuber, W. A., Fuller, N. J., Walsby, A. E., Amann, R. I., Rippka, R., Post, A. F., & Scanlan, D. J. (2001). “Identification and enumeration of Prochlorococcus sp.” in natural communities by in situ hybridization using 16S rRNA-targeted oligonucleotides and tyramide signal amplification. Microbiology, 147, 1731-1744.

Wu, C. H., Madabusi, L., Nishioka, H., Emanuel, P., Sypes, M., Arkhipova, I. R., & Gilmour, D. S. (2001). “Analysis of core promoter sequences located downstream from the TATA element in the hsp70 promoter from Drosophila melanogaster.” Mol Cell Biol, 21(5), 1593-1602. doi:10.1128/MCB.21.5.1593-1602.200.

2000

Alliegro, M. C. (2000). “A C-terminal carbohydrate-binding domain in the endothelial cell regulatory protein, pigpen: new function for an EWS family member.” Exp Cell Res, 255(2), 270-277. doi:10.1006/excr.1999.477.

Alliegro, M. C. (2000). “Effects of dithiothreitol on protein activity unrelated to thiol-disulfide exchange: for consideration in the analysis of protein function with Cleland’s reagent.” Anal Biochem, 282(1), 102-106. doi:10.1006/abio.2000.455.

Amaral-Zettler, L. A., Anderson, O. R., Nerad, T. A., & Sogin, M. L. (2000). “The phylogenetic position of Comandonia operculata and its implications for the taxonomy of the genus Acanthamoeba.” In S. Billot-Bonef, P. A. Cabanes, F. Marciano-Cabral, P. Pernin, & E. Pringuez (Ed.), IXth International Meeting on the Biology and Pathogenicity of Free-Living Amoebae Proceedings (pp. 235-242). Paris, France: John Libbey Eurotext.

Amaral-Zettler, L. A., & Caron, D. A. (2000). “New insights into the phylogeny of the Acantharea based on SSU rRNA gene sequencing.” European Journal of Protistology, 36, 34-39.

Amaral-Zettler, L. A., Nerad, T. A., O’Kelly, C. J., Peglar, M. T., Gillevet, P. M., Silberman, J. D., & Sogin, M. L. (2000). “A molecular reassessment of the Leptomyxid amoebae.” Protist, 151(3), 275-282. doi:10.1078/1434-4610-0002.

Arkhipova, I. R., & Meselson, M. (2000). “Transposable elements in sexual and ancient asexual taxa.” Proc Natl Acad Sci U S A, 97(26), 14473-14477. doi:10.1073/pnas.97.26.1447.

Bernard, C., Simpson, A. G. B., & Patterson, D. J. (2000). “Some free-living flagellates (protista) from anoxic habitats.” Ophelia, 52(2), 113-142.

Bhasin, A., Goryshin, I. Y., Steiniger-White, M., York, D., & Reznikoff, W. S. (2000). “Characterization of a Tn5 pre-cleavage synaptic complex.” J Mol Biol, 302(1), 49-63. doi:10.1006/jmbi.2000.404.

Bordenstein, S. R., Drapeau, M. D., & Werren, J. H. (2000). “Intraspecific variation in sexual isolation in the jewel wasp Nasonia.” Evolution, 54(2), 567-573.

Bouzat, J. L., McNeil, L. K., Robertson, H. M., Solter, L. F., Nixon, J. E., Beever, J. E., Gaskins, H. R., Olsen, G., Subramaniam, S., Sogin, M. L., & Lewin, H. A. (2000). “Phylogenomic analysis of the alpha proteasome gene family from early-diverging eukaryotes.” J Mol Evol, 51(6), 532-543. doi:10.1007/s002390010117 [pii.

Clark, M. A., Moran, N. A., Baumann, P., & Wernegreen, J. J. (2000). “Cospeciation between bacterial endosymbionts (Buchnera) and a recent radiation of aphids (Uroleucon) and pitfalls of testing for phylogenetic congruence.” Evolution, 54(2), 517-525.

Cousineau, B., Lawrence, S., Smith, D., & Belfort, M. (2000). “Retrotransposition of a bacterial group II intron.” Nature, 404(6781), 1018-1021. doi:10.1038/3501002.

Davies, D. R., Goryshin, I. Y., Reznikoff, W. S., & Rayment, I. (2000). “Three-dimensional structure of the Tn5 synaptic complex transposition intermediate.” Science, 289(5476), 77-85. doi:8656 [pii.

Delgado-Viscogliosi, P., Viscogliosi, E., Gerbod, D., Kulda, J., Sogin, M. L., & Edgcomb, V. P. (2000). “Molecular phylogeny of parabasalids based on small subunit rRNA sequences, with emphasis on the Trichomonadinae subfamily.” J Eukaryot Microbiol, 47(1), 70-75.

Edgell, D. R., Belfort, M., & Shub, D. A. (2000). “Barriers to intron promiscuity in bacteria.” J Bacteriol, 182(19), 5281-5289.

Funk, D. J., Helbling, L., Wernegreen, J. J., & Moran, N. A. (2000). “Intraspecific phylogenetic congruence among multiple symbiont genomes.” Proc Biol Sci, 267(1461), 2517-2521. doi:10.1098/rspb.2000.131.

Goryshin, I. Y., Jendrisak, J., Hoffman, L. M., Meis, R., & Reznikoff, W. S. (2000). “Insertional transposon mutagenesis by electroporation of released Tn5 transposition complexes.” Nat Biotechnol, 18(1), 97-100. doi:10.1038/7201.

Gould, R. M., Freund, C. M., Engler, J., & Morrison, H. G. (2000). “Optimization of homogenization conditions used to isolate mRNAs in processes of myelinating oligodendrocytes.” Biol Bull, 199(2), 215-217.

Hoffman, L. M., Jendrisak, J. J., Meis, R. J., Goryshin, I. Y., & Reznikoff, W. S. (2000). “Transposome insertional mutagenesis and direct sequencing of microbial genomics.” Genetica, 108, 19-24.

Lease, R. A., & Belfort, M. (2000). “A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures.” Proc Natl Acad Sci U S A, 97(18), 9919-9924. doi:10.1073/pnas.17028149.

Lease, R. A., & Belfort, M. (2000). “Riboregulation by DsrA RNA: trans-actions for global economy.” Mol Microbiol, 38(4), 667-672.

Lee, W. J., & Patterson, D. J. (2000). “Heterotrophic flagellates (Protista) from marine sediments of Botany Bay, Australia.” Journal of Natural History, 34(4), 483-562. doi:Doi 10.1080/00222930029943.

Liang, P., Serres, M. H., & Riley, M. (2000). “Genes and Proteins of Escherichia coli K-12 (GenProtEC).” Nucleic Acids Research, 26(1), 54.

Mark Welch, D. B. (2000). “Evidence from a protein-coding gene that acanthocephalans are rotifers.” Invertebrate Biology, 119(1), 17-26. doi:10.1111/j.1744-7410.2000.tb00170..

Mark Welch, D. B., & Meselson, M. (2000). “Evidence for the Evolution of Bdelloid Rotifers Without Sexual Reproduction or Genetic Exchange.” Science, 288(5469), 1211-1215. doi:10.1126/science.288.5469.121.

McArthur, A. G., Morrison, H. G., Nixon, J. E., Passamaneck, N. Q., Kim, U., Hinkle, G., Crocker, M. K., Holder, M. E., Farr, R., Reich, C. I., Olsen, G. E., Aley, S. B., Adam, R. D., Gillin, F. D., & Sogin, M. L. (2000). “The Giardia genome project database.” FEMS Microbiol Lett, 189(2), 271-273.

Mohr, G., Smith, D., Belfort, M., & Lambowitz, A. M. (2000). “Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences.” Genes Dev, 14(5), 559-573.

Moran, N. A., & Wernegreen, J. J. (2000). “Lifestyle evolution in symbiotic bacteria: insights from genomics.” Trends Ecol Evol, 15(8), 321-326. doi:S0169534700019029 [pii.

Naumann, T. A., & Reznikoff, W. S. (2000). “Trans catalysis in Tn5 transposition.” Proc Natl Acad Sci U S A, 97(16), 8944-8949. doi:10.1073/pnas.16010799.

Neal, R. M. (2000). “Markov chain sampling methods for Dirichlet process mixture models.” J Comp Graph, 9.

Noel, R. J. Jr., & Reznikoff, W. S. (2000). “Structural studies of lacUV5-RNA polymerase interactions in vitro.” Ethylation interference and missing nucleoside analysis. J Biol Chem, 275(11), 7708-7712.

Patterson, D. J., & Lee, W. J. (2000). “Geographic distribution and diversity of free-living heterotrophic flagellates.” In J. Green & B. S. C. Leadbeater (Ed.), The Flagellates (pp. 269-287): Taylor and Francis.

Riley, M., & Serres, M. H. (2000). “Interim report on genomics of Escherichia coli.” Annu Rev Microbiol, 54, 341-411. doi:10.1146/annurev.micro.54.1.34.

Serres, M. H., Fladmark, K. E., & Doskeland, S. O. (2000). “An ultrasensitive competitive binding assay for the detection of toxins affecting protein phosphatases.” Toxicon, 38(3), 347-360. doi:DOI: 10.1016/S0041-0101(99)00163-.

Serres, M. H., & Riley, M. (2000). “MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products.” Microb Comp Genomics, 5(4), 205-222.

Serres, M. H., Riley, M., M.Dworkin, & et al. (2000). “Genomics and metabolism in Escherichia coli The Prokaryotes: An Evolving Electronic Database for the Microbiological Community (Vol.” 3rd edition (release 3.2), pp. www.prokaryotes.com). New York: Springer-Verlag.

Simpson, A. G. B., Bernard, C., & Patterson, D. J. (2000). “The ultrastructure of Trimastix marina Kent, 1880 (eukaryota), an excavate flagellate.” European Journal of Protistology, 36(3), 229-251.

Sogin, M. L. (2000). “Evolution of Eukaryotic Ribosomal RNA Genes.” In S. Parker (Ed.), McGraw-Hill Yearbook of Science and Technology. New York, NY: McGraw-Hill.

Steiniger-White, M., & Reznikoff, W. S. (2000). “The C-terminal alpha helix of Tn5 transposase is required for synaptic complex formation.” J Biol Chem, 275(30), 23127-23133. doi:10.1074/jbc.M00341120.

Wang, Q., Li, H., & Post, A. F. (2000). “Nitrate assimilation genes of the marine diazotrophic, filamentous cyanobacterium Trichodesmium sp.” strain WH9601. J Bacteriol, 182(6), 1764-1767.

Wernegreen, J. J., & Moran, N. A. (2000). “Decay of mutualistic potential in aphid endosymbionts through silencing of biosynthetic loci: Buchnera of Diuraphis.” Proc Biol Sci, 267(1451), 1423-1431. doi:10.1098/rspb.2000.115.

Wernegreen, J. J., Ochman, H., Jones, I. B., & Moran, N. A. (2000). “Decoupling of genome size and sequence divergence in a symbiotic bacterium.” J Bacteriol, 182(13), 3867-3869.

Wood, D. W., Derbyshire, V., Wu, W., Chartrain, M., Belfort, M., & Belfort, G. (2000). “Optimized single-step affinity purification with a self-cleaving intein applied to human acidic fibroblast growth factor.” Biotechnol Prog, 16(6), 1055-1063. doi:10.1021/bp000085.

Wu, G., McArthur, A. G., Fiser, A., Sali, A., Sogin, M. L., & Mllerm, M. (2000). “Core histones of the amitochondriate protist, Giardia lamblia.” Mol Biol Evol, 17(8), 1156-1163.

1999

Amaral-Zettler, L. A., Anderson, O. R., & Caron, D. A. (1999). “Towards a molecular phylogeny of colonial spumellarian radiolaria.” Marine Micropaleontology, 36, 67-79.

Anderson, O. R., Gastrich, M. D., & Amaral-Zettler, L. A. (1999). “Fine structure of the colonial radiolarian Collozoum serpentinum (Polycystinea: Spumellarida) with consideration of its taxonomic status and the recommendation for the reestablishment of the genus Collophidium (Haeckel).” Marine Micropaleontology, 36(81-9).

Bhasin, A., Goryshin, I. Y., & Reznikoff, W. S. (1999). “Hairpin formation in Tn5 transposition.” J Biol Chem, 274(52), 37021-37029.

Davies, D. R., Mahnke Braam, L., Reznikoff, W. S., & Rayment, I. (1999). “The three-dimensional structure of a Tn5 transposase-related protein determined to 2.9-A resolution.” J Biol Chem, 274(17), 11904-11913.

Dixon, T. C., Meselson, M., Guillemin, J., & Hanna, P. C. (1999). “Anthrax.” N Engl J Med, 341(11), 815-826. doi:10.1056/NEJM19990909341110.

Doehmer, J., Buters, J. T., Luch, A., Soballa, V., Baird, W. M., Morisson, H. G., Stegeman, J. J., Townsend, A. J., Greenlee, W. F., Glatt, H. R., Seidel, A., Jacob, J., & Greim, H. (1999). “Molecular studies on the toxifying effects by genetically engineered cytochromes P450.” Drug Metab Rev, 31(2), 423-435. doi:10.1081/DMR-10010192.

Gould, R., Freund, C., Palmer, F., Knapp, P. E., Huang, J., Morrison, H., & Feinstein, D. L. (1999). “Messenger RNAs for Kinesins and Dynein are Located in Neural Processes.” The Biological Bulletin, 197(2), 259-260. doi:10.2307/154263.

Gould, R., Freund, C., Palmer, F., Knapp, P. E., Huang, J., Morrison, H. G., & Feinstein, D. L. (1999). “Messenger RNAs for kinesins and dynein are located in neural processes.” Biol Bull, 197(2), 259-260.

Kohler, A., Jostarndt-Fogen, K., Rottner, K., Alliegro, M. C., & Draeger, A. (1999). “Intima-like smooth muscle cells: developmental link between endothelium and media?” Anat Embryol (Berl), 200(3), 313-323.

Lee, W. J., Blackmore, R., & Patterson, D. J. (1999). “Australian records of two lesser known genera of heterotrophic euglenids – Chasmostoma Massart 1920 and Jenningsia Schaeffer 1918.” Protistology, 1, 10-16.

Lee, W. J., & Patterson, D. J. (1999). “Are communities of heterotrophic flagellates determined by their geography?” In W. Ponder & D. Lunney (Ed.), The other 99%. The conservation and biodiversity of Invertebrates (pp. 232-235). Mosman, Sydney: Trans. R. Soc. New South Wales.

Lindell, D., Padan, E., & Post, A. F. (1999). “The effect of ammonium on NtcA expression, nitrate and nitrite uptake in marine Synechococcus sp.” strain WH 7803. In L. Charpy & A. W. D. Larkum (Ed.), Marine Cyanoabacteria (pp. 273-278). Monaco: Bulletin de l’Institut Oceanographique, special issue N° 19.

Mahnke Braam, L. A., Goryshin, I. Y., & Reznikoff, W. S. (1999). “A mechanism for Tn5 inhibition.” carboxyl-terminal dimerization. J Biol Chem, 274(1), 86-92.

Meselson, M. (1999). “The challenge of biological and chemical weapons.” Bull World Health Organ, 77(2), 102-103.

Orgel, L., Hearn, M. A., Bada, J., Barros, J., Chapman, C., Drake, M., Kerridge, J., Race, M., Sogin, M. L., & Squyres, S. (1999). “Sample return from small solar system bodies.” Adv. Space Res., 25, 239-248.

Patterson, D. J. (1999). “The Diversity of Eukaryotes.” Am Nat, 154(S4), S96-S124. doi:10.1086/30328.

Patterson, D. J., Simpson, A. G., & Weerakoon, N. (1999). “Free-living flagellates from anoxic habitats and the assembly of the eukaryotic cell.” Biol Bull, 196(3), 381-383; discussion 383-384.

Post, A. F. (1999). “The Prochlorophytes – An Algal Enigma.” Biology of chlorophyll a/b containing photosynthetic prokaryotes. In J. Seckbach (Ed.), Enigmatic microorganisms and life in extreme environments (pp. 115-125). Dordrecht: Kluwer Academic Publishers.

Reznikoff, W. S., Bhasin, A., Davies, D. R., Goryshin, I. Y., Mahnke, L. A., Naumann, T., Rayment, I., Steiniger-White, M., & Twining, S. S. (1999). “Tn5: A molecular window on transposition.” Biochem Biophys Res Commun, 266(3), 729-734. doi:10.1006/bbrc.1999.189.

Roger, A. J., Morrison, H. G., & Sogin, M. L. (1999). “Primary structure and phylogenetic relationships of a malate dehydrogenase gene from Giardia lamblia.” J Mol Evol, 48(6), 750-755.

Sanchez, L. B., Morrison, H. G., Sogin, M. L., & Muller, M. (1999). “Cloning and sequencing of an acetyl-CoA synthetase (ADP-forming) gene from the amitochondriate protist, Giardia lamblia.” Gene, 233(1-2), 225-231.

Silberman, J. D., Clark, C. G., Diamond, L. S., & Sogin, M. L. (1999). “Phylogeny of the genera Entamoeba and Endolimax as deduced from small-subunit ribosomal RNA sequences.” Mol Biol Evol, 16(12), 1740-1751.

Simpson, A. G. B., & Patterson, D. J. (1999). “The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the “Excavate hypothesis”.” European Journal of Protistology, 35(4), 353-370.

Sogin, M. L. (1999). “Concluding Remarks.” Biol Bull, 196(3), 415-416. doi:10.1086/BBLv196n3p41.

Sogin, M. L. (1999). “Introductory remarks.” BIOLOGICAL BULLETIN, 196(3), 307-307.

Teske, A., Sogin, M. L., Nielsen, L. P., & Jannasch, H. W. (1999). “Phylogenetic relationships of a large marine Beggiatoa.” Syst Appl Microbiol, 22(1), 39-44. doi:10.1016/S0723-2020(99)80026-.

Weerakoon, N. D., Harper, J. D. I., Simpson, A. G. B., & Patterson, D. J. (1999). “Centrin in the groove: immunolocalisation of centrin and microtubules in the putatively primitive protist Chilomastix cuspidata (Retortamonadida).” Protoplasma, 210(1-2), 75-84. doi:Doi 10.1007/Bf0131495.

Wernegreen, J. J., & Moran, N. A. (1999). “Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes.” Mol Biol Evol, 16(1), 83-97.

Wernegreen, J. J., & Riley, M. A. (1999). “Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages.” Mol Biol Evol, 16(1), 98-113.

Yigit, H., & Reznikoff, W. S. (1999). “Escherichia coli DNA topoisomerase I copurifies with Tn5 transposase, and Tn5 transposase inhibits topoisomerase I.” J Bacteriol, 181(10), 3185-3192.

Zaman, V., Zaki, M., Howe, J., Ng, M., Leipe, D. D., Sogin, M. L., & Silberman, J. D. (1999). “Hyperamoeba isolated from human feces: Description and phylogenetic affinity.” European Journal of Protistology, 35(2), 197-207.

1998

Alliegro, M. C. (1998). “Myosin-carbohydrate interactions.” Cell Motil Cytoskeleton, 39(3), 191-194. doi:10.1002/(SICI)1097-0169(1998)39:33.0.CO;2-.

Alliegro, M. C., & Alliegro, M. A. (1998). “Protein heterogeneity in the coiled body compartment.” Exp Cell Res, 239(1), 60-68. doi:10.1006/excr.1997.386.

Amaral-Zettler, L. A., Anderson, O. R., & Caron, D. A. (1998). “Insights on the diversity within a “species” of Thalassicolla (Spumellarida) based on 16S-like ribosomal RNA gene sequencing.” J Eukaryot Microbiol, 45(5), 488-496.

Bordenstein, S. R., & Werren, J. H. (1998). “Effects of A and B Wolbachia and host genotype on interspecies cytoplasmic incompatibility in Nasonia.” Genetics, 148(4), 1833-1844.

Clark, C. G., Silberman, J. D., Diamond, L. S., & Sogin, M. L. (1998). “Molecular systematics of the intestinal amoebae.” In G. H. Coombs, K. Vickerman, M. A. Sleigh, & A. Warren (Ed.), Evolutionary Relationships Among Protozoa (pp. 169-180): Chapman & Hall.

Cousineau, B., Smith, D., Lawrence-Cavanagh, S., Mueller, J. E., Yang, J., Mills, D., Manias, D., Dunny, G., Lambowitz, A. M., & Belfort, M. (1998). “Retrohoming of a bacterial group II intron: mobility via complete reverse splicing, independent of homologous DNA recombination.” Cell, 94(4), 451-462. doi:DOI: 10.1016/S0092-8674(00)81586-.

Derbyshire, V., & Belfort, M. (1998). “Lightning strikes twice: intron-intein coincidence.” Proc Natl Acad Sci U S A, 95(4), 1356-1357.

Edgcomb, V., Viscogliosi, E., Simpson, A. G. B., Delgado-Viscogliosi, P., Roger, A. J., & Sogin, M. L. (1998). “New insights into the phylogeny of trichomonads inferred from small subunit rRNA sequences.” Protist, 149(4), 359-366.

Fladmark, K. E., Serres, M. H., Larsen, N. L., Yasumoto, T., Aune, T., & Doskeland, S. O. (1998). “Sensitive detection of apoptogenic toxins in suspension cultures of rat and salmon hepatocytes.” Toxicon, 36(8), 1101-1114. doi:DOI: 10.1016/S0041-0101(98)00083-.

Goryshin, I. Y., Miller, J. A., Kil, Y. V., Lanzov, V. A., & Reznikoff, W. S. (1998). “Tn5/IS50 target recognition.” Proc Natl Acad Sci U S A, 95(18), 10716-10721.

Goryshin, I. Y., & Reznikoff, W. S. (1998). “Tn5 in vitro transposition.” J Biol Chem, 273(13), 7367-7374.

Heep, T., Rohozinski, J., Simpson, A. G. B., & Patterson, D. J. (1998). “Stentor amethystinus (Ciliophora, Heterotrichida), a common member of fresh-water plankton in Australia.” Records of the Australian Museum, 50, 211-216.

Henze, K., Morrison, H. G., Sogin, M. L., & MullerM. (1998). “Sequence and phylogenetic position of a class II aldolase gene in the amitochondriate protist, Giardia lamblia.” Gene, 222(2), 163-168.

Lee, W. J., & Patterson, D. J. (1998). “Diversity and geographic distribution of free-living heterotrophic flagellates – Analysis by PRIMER.” Protist, 149(3), 229-244.

Li, H., Veldhuis, M. J. W., & Post, A. F. (1998). “Alkaline phosphatase activities among planktonic communities in the northern Red Sea.” Marine Ecology Progress Series, 173, 107-115.

Lindell, D., Padan, E., & Post, A. F. (1998). “Regulation of ntcA expression and nitrite uptake in the marine Synechococcus sp.” strain WH 7803. J Bacteriol, 180(7), 1878-1886.

Mahnke Braam, L. A., & Reznikoff, W. S. (1998). “Functional characterization of the Tn5 transposase by limited proteolysis.” J Biol Chem, 273(18), 10908-10913.

Mark Welch, D. B., & Meselson, M. (1998). “Measurements of the genome size of the monogonont rotifer Brachionus plicatilis and of the bdelloid rotifers Philodina roseola and Habrotrocha constricta.” Hydrobiologia, 387/388, 395-402.

Mark Welch, D. B., & Meselson, M. (1998). “Karyotypes of bdelloid rotifers from three families.” Hydrobiologia, 387/388, 403-407.

Meselson, M. S., & Stahl, F. W. (1998). “Young Jan.” Genetics, 148(4), 1413-1414.

Morrison, H. G., Weil, E. J., Karchner, S. I., Sogin, M. L., & Stegeman, J. J. (1998). “Molecular cloning of CYP1A from the estuarine fish Fundulus heteroclitus and phylogenetic analysis of CYP1 genes: update with new sequences.” Comp Biochem Physiol C Pharmacol Toxicol Endocrinol, 121(1-3), 231-240.

Noel, R. J. Jr., & Reznikoff, W. S. (1998). “CAP, the -45 region, and RNA polymerase: three partners in transcription initiation at lacP1 in Escherichia coli.” J Mol Biol, 282(3), 495-504. doi:10.1006/jmbi.1998.204.

Roger, A. J., Svard, S. G., Tovar, J., Clark, C. G., Smith, M. W., Gillin, F. D., & Sogin, M. L. (1998). “A mitochondrial-like chaperonin 60 gene in Giardia lamblia: evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria.” Proc Natl Acad Sci U S A, 95(1), 229-234.

Smith, M. W., Aley, S. B., Sogin, M. L., Gillin, F. D., & Evans, G. A. (1998). “Sequence survey of the Giardia lamblia genome.” Mol Biochem Parasitol, 95(2), 267-280.

Sogin, M. L., & Silberman, J. D. (1998). “Evolution of the protists and protistan parasites from the perspective of molecular systematics.” Int J Parasitol, 28(1), 11-20. doi:DOI: 10.1016/S0020-7519(97)00181-.

Stegeman, J. J., Soballa, V., Morrison, H. G., Jacob, J., & Doehmer, J. (1998). “Catalytic Properties of Scup Cytochrome P4501A Expressed in Chinese Hamster V79 Cells.” Marine Environmental Research, 46, 395-395.

Tong, S. M., Nygaard, K., Bernard, C., Vors, N., & Patterson, D. J. (1998). “Heterotrophic flagellates from the water column in Port Jackson, Sydney, Australia.” European Journal of Protistology, 34(2), 162-194.

Yahel, G., Post, A. F., Fabricius, K., Marie, D., Vaulot, D., & Genin, A. (1998). “Phytoplankton distribution and grazing near coral reefs.” Limnology and Oceanography, 43(4), 551-563.

Yigit, H., & Reznikoff, W. S. (1998). “Escherichia coli DNA topoisomerase I and suppression of killing by Tn5 transposase overproduction: topoisomerase I modulates Tn5 transposition.” J Bacteriol, 180(22), 5866-5874.

York, D., Welch, K., Goryshin, I. Y., & Reznikoff, W. S. (1998). “Simple and efficient generation in vitro of nested deletions and inversions: Tn5 intramolecular transposition.” Nucleic Acids Res, 26(8), 1927-1933. doi:doi: 10.1093/nar/26.8.192.

Zhou, M., Bhasin, A., & Reznikoff, W. S. (1998). “Molecular genetic analysis of transposase-end DNA sequence recognition: cooperativity of three adjacent base-pairs in specific interaction with a mutant Tn5 transposase.” J Mol Biol, 276(5), 913-925. doi:10.1006/jmbi.1997.157.

1997

Alliegro, M. C., & Alliegro, M. A. (1997). “Identification of a new coiled body component.” Exp Cell Res, 231(2), 386-390.

Alliegro, M. C., & Linz, L. A. (1997). “Novel characteristics of a myosin isolated from mammalian retinal pigment epithelial and endothelial cells.” J Biol Chem, 272(13), 8759-8763.

Amaral-Zettler, L. A., Sogin, M. L., & Caron, D. A. (1997). “Phylogenetic relationships between the Acantharea and the Polycystinea: a molecular perspective on Haeckel’s Radiolaria.” Proc Natl Acad Sci U S A, 94(21), 11411-11416.

Arkhipova, I. R., Li, J., & Meselson, M. (1997). “On the mode of gene-dosage compensation in Drosophila.” Genetics, 145(3), 729-736.

Bernard, C., Simpson, A. G., & Patterson, D. J. (1997). “An ultrastructural study of a free-living retortamonad, Chilomastix cuspidata (Larsen & Patterson 1990) n.” comb. (Retortamonadida, Protista). European Journal of Protistology, 33, 254-265.

Brugerolle, G., & Patterson, D. J. (1997). “Ultrastructure of Trimastix convexa Hollande, an amitochondriate anaerobic flagellate with a previously undescribed organization.” European Journal of Protistology, 33(2), 121-130.

Czarniecki, D., Noel, R. J. Jr., & Reznikoff, W. S. (1997). “The -45 region of the Escherichia coli lac promoter: CAP-dependent and CAP-independent transcription.” J Bacteriol, 179(2), 423-429.

Danilevskaya, O. N., Arkhipova, I. R., Traverse, K. L., & Pardue, M. L. (1997). “Promoting in tandem: the promoter for telomere transposon HeT-A and implications for the evolution of retroviral LTRs.” Cell, 88(5), 647-655. doi:DOI: 10.1016/S0092-8674(00)81907-.

Ekelund, F., & Patterson, D. J. (1997). “Some heterotrophic flagellates from a cultivated garden soil in Australia.” Archiv Fur Protistenkunde, 148(4), 461-478.

Hinkle, G., Morrison, H. G., & Sogin, M. L. (1997). “Genes coding for reverse transcriptase, DNA-directed RNA polymerase, and chitin synthase from the microsporidian Spraguea lophii.” Biol Bull, 193(2), 250-251.

Post, A. F., & Arieli, B. (1997). “Photosynthesis of Prochlorothrix hollandica under Sulfide-Rich Anoxic Conditions.” Appl Environ Microbiol, 63(9), 3507-3511.

Simpson, A. G., Bernard, C., Fenchel, T., & Patterson, D. J. (1997). “The organisation of Mastigamoeba schizophrenia n.” sp.: More evidence of ultrastructural idiosyncrasy and simplicity in pelobiont protests. European Journal of Protistology, 33, 87-98.

Simpson, A. G., van den Hoff, J., Bernard, C., Burton, H., & Patterson, D. J. (1997). “The ultrastructure and systematic position of the euglenozoan Postgaardi mariagerensis, Fenchel et al.” Arch. Protistenk, 147, 213-225.

Sogin, M. L. (1997). “History assignment: when was the mitochondrion founded?” Current Opinions in Genetics & Development, 7, 792-799.

Sogin, M. L. (1997). “Organelle origins: energy-producing symbionts in early eukaryotes?” Curr Biol, 7(5), R315-317.

Tong, S., Vors, N., & Patterson, D. J. (1997). “Heterotrophic flagellates, centrohelid heliozoa and filose amoebae from marine and freshwater sites in the Antarctic.” Polar Biology, 18(2), 91-106. doi:Doi 10.1007/S00300005016.

Wernegreen, J. J., Harding, E. E., & Riley, M. A. (1997). “Rhizobium gone native: unexpected plasmid stability of indigenous Rhizobium leguminosarum.” Proc Natl Acad Sci U S A, 94(10), 5483-5488.

Yigit, H., & Reznikoff, W. S. (1997). “Examination of the Tn5 transposase overproduction phenotype in Escherichia coli and localization of a suppressor of transposase overproduction killing that is an allele of rpoH.” J Bacteriol, 179(5), 1704-1713.

York, D., & Reznikoff, W. S. (1997). “DNA binding and phasing analyses of Tn5 transposase and a monomeric variant.” Nucleic Acids Res, 25(11), 2153-2160.

Zettler, L. A., Sogin, M. L., & Caron, D. A. (1997). “Phylogenetic relationships between the Acantharea and the Polycystinea: a molecular perspective on Haeckel’s Radiolaria.” Proc Natl Acad Sci U S A, 94(21), 11411-11416.

Zhou, M., & Reznikoff, W. S. (1997). “Tn5 transposase mutants that alter DNA binding specificity.” J Mol Biol, 271(3), 362-373. doi:10.1006/jmbi.1997.118.

Zhou, Q., Hinkle, G., Sogin, M. L., & Dionne, V. E. (1997). “Phylogenetic analysis of olfactory receptor genes from mudpuppy (Necturus maculosus).” Biol Bull, 193(2), 248-250.

1996

Agamalian, N. S., Arkhipova, I. R., Surkov, S. A., & Il’in Iu, V. (1996). “[Regulating polyadenylation of jockey mobile genetic element transcripts belonging to the LINE class, in Drosophila cell culture].” Mol Biol (Mosk), 30(4), 818-828.

Alliegro, M. C., & Alliegro, M. A. (1996). “A nuclear protein regulated during the transition from active to quiescent phenotype in cultured endothelial cells.” Dev Biol, 174(2), 288-297. doi:10.1006/dbio.1996.007.

Bahr, M., Hobbie, J. E., & Sogin, M. L. (1996). “Bacterial diversity in an arctic lake: A freshwater SAR11 cluster.” Aquatic Microbial Ecology, 11(3), 271-277. doi:DOI 10.3354/ame01127.

Dwivedi, K., Post, A. F., & Bullerjahn, G. S. (1996). “Cloning and functional analysis of the pmmA gene encoding phosphomannomutase from the photosynthetic prokaryote Prochlorothrix hollandica.” Biochim Biophys Acta, 1290(3), 210-214.

Ekebom, J., Patterson, D. J., & Vors, N. (1996). “Heterotrophic flagellates from coral reef sediments (Great Barrier Reef, Australia).” Archiv Fur Protistenkunde, 146(3-4), 251-272.

Hammerschmidt, B., Schlegel, M., Lynn, D. H., Leipe, D. D., Sogin, M. L., & Raikov, I. B. (1996). “Insights into the evolution of nuclear dualism in the ciliates revealed by phylogenetic analysis of rRNA sequences.” J Eukaryot Microbiol, 43(3), 225-230.

Jilk, R. A., York, D., & Reznikoff, W. S. (1996). “The organization of the outside end of transposon Tn5.” J Bacteriol, 178(6), 1671-1679.

Leipe, D. D., Tong, S. M., Goggin, C. L., Slemenda, S. B., Pieniazek, N. J., & Sogin, M. L. (1996). “16S-like rDNA sequences from Developayella elegans, Labyrinthuloides haliotidis, and Proteromonas lacertae confirm that the stramenopiles are a primarily heterotrophic group.” European Journal of Protistology, 32(4), 449-458.

O’Kelly, C. J., & Patterson, D. J. (1996). “The flagellar apparatus of Cafeteria roenbergensis Fenchel & Patterson 1988 (Bicosoecales = Bicosoecida).” European Journal of Protistology, 32, 216-226.

Patterson, D. J. (1996). “Free-living Freshwater Protozoa.” New South Wales, Australia: Manson Wiley and University of New South Wales Presses.

Patterson, D. J. (1996). “Morphology and natural habitats.” In O. R. Anderson & M. Druger (Ed.), Explore the World Using Protozoa (pp. 28-34). Virginia: National Science Teachers Association.

Patterson, D. J., & Simpson, A. G. B. (1996). “Heterotrophic flagellates from coastal marine and hypersaline sediments in Western Australia.” European Journal of Protistology, 32(4), 423-448.

Record, J., M. T., Reznikoff, W. S., & Schlax, P. J. (1996). “Escherichia coli RNA polymerase (E_70), promoters, and the kinetics of the steps of transcription initiation.” In Neidhardt, Curtiss, Ingraham, Lin, Low, Magasanik, Reznikoff, Riley, Schaechter, & Umbarger (Ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd edition (pp. 792-820): American Society of Microbiology.

Relman, D. A., Schmidt, T. M., Gajadhar, A., Sogin, M. L., Cross, J., Yoder, K., Sethabutr, O., & Echeverria, P. (1996). “Molecular phylogenetic analysis of Cyclospora, the human intestinal pathogen, suggests that it is closely related to Eimeria species.” Journal of Infectious Diseases, 173(2), 440-445.

Santamaria-Fries, M., Fajardo, L. F., Sogin, M. L., Olson, P. D., & Relman, D. A. (1996). “Lethal infection by a previously unrecognised metazoan parasite.” Lancet, 347(9018), 1797-1801.

Schaechter, M., Curtiss III, R., Ingraham, J. L., Lin, E. C. C., Low, K. B., Magasanik, B., Neidhardt, F. C., Reznikoff, W. S., Riley, M., & Umbarger, H. E. (1996). “The view from here.” In Neidhardt, Curtiss, Ingraham, Lin, Low, Magasanik, Reznikoff, Riley, Schaechter, & Umbarger (Ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd edition (pp. 2817-2822): American Society of Microbiology.

Schlegel, M., Lom, J., Stechmann, A., Bernhard, D., Leipe, D., Dykova, I., & Sogin, M. L. (1996). “Phylogenetic analysis of complete small subunit ribosomal RNA coding region of Myxidium lieberkuehni: Evidence that Myxozoa are Metazoa and related to the Bilateria.” Archiv Fur Protistenkunde, 147(1), 1-9.

Serres, M. H., & Ensign, J. C. (1996). “Endogenous ADP-ribosylation of proteins in Mycobacterium smegmatis.” J Bacteriol, 178(20), 6074-6077.

Silberman, J. D., Clark, C. G., & Sogin, M. L. (1996). “Dientamoeba fragilis shares a recent common evolutionary history with the trichomonads.” Mol Biochem Parasitol, 76(1-2), 311-314.

Silberman, J. D., Sogin, M. L., Leipe, D. D., & Clark, C. G. (1996). “Human parasite finds taxonomic home.” Nature, 380(6573), 398. doi:10.1038/380398a.

Simpson, A. G. B., & Patterson, D. J. (1996). “Ultrastructure and identification of the predatory flagellate Colpodella pugnax Cienkowski (Apicomplexa) with a description of Colpodella turpis n sp and a review of the genus.” Systematic Parasitology, 33(3), 187-198. doi:Doi 10.1007/Bf0153120.

Sogin, M. L., & Hinkle, G. (1996). “Common Measures for Studies of Biodiversity: Molecular phylogeny in the eukaryotic microbial world.” In M. L. Reaka-Kudla, D. E. Wilson, & E. O. Wilson (Ed.), Biodiversity II: Understanding and Protecting Our Biological Resources (pp. 109-122). Washington, DC: Joseph Henry Press.

Sogin, M. L., Morrison, H. G., Hinkle, G., & Silberman, J. D. (1996). “Ancestral relationships of the major eukaryotic lineages.” Microbiologia, 12(1), 17-28.

Sogin, M. L., Silberman, J. D., Hinkle, G., & Morrison, H. G. (1996). “Problems with Molecular Diversity in the Eukarya.” In D. M. Roberts, P. Sharp, G. Alderson, & M. A. Collins (Ed.), Society for General Microbiology Symposium 54: Evolution of Microbial Life (pp. 167-184). Cambridge, MA: Cambridge University Press.

Tavormina, P. L., Reznikoff, W. S., & Gross, C. A. (1996). “Identifying interacting regions in the beta subunit of Escherichia coli RNA polymerase.” J Mol Biol, 258(2), 213-223. doi:10.1006/jmbi.1996.024.

Udomkit, A., Forbes, S., McClean, C., Arkhipova, I. R., & Finnegan, D. J. (1996). “Control of expression of the I factor, a LINE-like transposable element in Drosophila melanogaster.” EMBO J, 15(12), 3174-3181.

York, D., & Reznikoff, W. S. (1996). “Purification and biochemical analyses of a monomeric form of Tn5 transposase.” Nucleic Acids Res, 24(19), 3790-3796. doi:6t0287 [pii.