Publications

Bay Paul Center Publication Co-authorship Network

Top 25 Journals

Proc Natl Acad Sci U S A (67), PLoS One (51), ISME J (38), Appl Environ Microbiol (35), Nature (28), Science (24), Nucleic Acids Res (24), Environ Microbiol (23), Mol Biol Evol (21), J Bacteriol (18), J Biol Chem (16), Microbiome (15), Biol Bull (15), J Mol Biol (14), Front Microbiol (13), European Journal of Protistology (12), BMC Genomics (12), Genome Biol (11), J Eukaryot Microbiol (10), Genome Res (10), Genetics (10), Nat Biotechnol (9), MBio (9), Hydrobiologia (9), PLoS Biol (7)

Years

2016 (40) | 2015 (85) | 2014 (106) | 2013 (72) | 2012 (80) | 2011 (59) | 2010 (44) | 2009 (49) | 2008 (43) | 2007 (51) | 2006 (40) | 2005 (54) | 2004 (33) | 2003 (44) | 2002 (47) | 2001 (38) | 2000 (42) | 1999 (27) | 1998 (32) | 1997 (23) | 1996 (22)

 

2016

Zozaya, M., Ferris, M. J., Siren, J. D., Lillis, R., Myers, L., Nsuami, M. J., Eren, A. M., Brown, J., Taylor, C. M., and Martin, D. H. (2016). “Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis.Microbiome, 4(1), 1-10.

Zheng, Y., Huang, Y., Andersen, R. A., and 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.

Yang, T., Weisenhorn, P., Gilbert, J. A., Ni, Y., Sun, R., Shi, Y., and Chu, H. (2016). “Carbon constrains fungal endophyte assemblages along the timberline.Environmental Microbiology, 18(8), 2455-2469.

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., and Chang, E. B. (2016). “Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility.American Journal of Physiology-Gastrointestinal and Liver Physiology, 310(11), G973-G988.

Walsh, E. A., Kirkpatrick, J. B., Pockalny, R., Sauvage, J., Spivack, A. J., Murray, R. W., Sogin, M. L., and D’Hondt, S. (2016). “Relationship of Bacterial Richness to Organic Degradation Rate and Sediment Age in Subseafloor Sediment.Applied and Environmental Microbiology, 82(16), 4994-4999.

Utter, D. R., Mark Welch, J. L., and Borisy, G. G. (2016). “Individuality, Stability, and Variability of the Plaque Microbiome.Frontiers in Microbiology, 7, 564.

Topçuoğlu, B. D., Stewart, L. C., Morrison, H. G., Butterfield, D. A., Huber, J. A., and Holden, J. F. (2016). “Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents.Frontiers in Microbiology, 7, 1240.

Sielaff, M., Schmidt, H., Struck, T. H., Rosenkranz, D., Mark Welch, D. B., Hankeln, T., and Herlyn, H. (2016). “Phylogeny of Syndermata (syn. Rotifera): Mitochondrial gene order verifies epizoic Seisonidea as sister to endoparasitic Acanthocephala within monophyletic Hemirotifera.Molecular Phylogenetics and Evolution, 96, 79-92.

Sharma, A., Gilbert, J. A., and Lal, R. (2016). “(Meta)genomic insights into the pathogenome of Cellulosimicrobium cellulans.Scientific Reports, 6, 25527.

Schmidt, V., Amaral-Zettler, L. A., Davidson, J., Summerfelt, S., and 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), 4470-81.

Sangwan, N., Xia, F., and Gilbert, J. A. (2016). “Recovering complete and draft population genomes from metagenome datasets.Microbiome, 4(1), 8.

Rodriguez, F., and 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.

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

Reveillaud, J., Reddington, E., McDermott, J., Algar, C., Meyer, J. L., Sylva, S., Seewald, J., German, C. R., and Huber, J. A. (2016). “Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise.Environ Microbiol, 18(6), 1970-87.

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

O’Brien, S. L., Gibbons, S. M., Owens, S. M., Hampton-Marcell, J., Johnston, E. R., Jastrow, J. D., Gilbert, J. A., Meyer, F., and Antonopoulos, D. A. (2016). “Spatial scale drives patterns in soil bacterial diversity.Environ Microbiol, 18(6), 2039-51.

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., and Walsh, E. J. (2016). “Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy.Hydrobiologia, 10.1007/s10750-016-2725-7, 1-20.

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., and 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.

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., and Knight, R. (2016). “Microbial community assembly and metabolic function during mammalian corpse decomposition.Science, 351(6269), 158-62.

Mark Welch, J. L., Rossetti, B. J., Rieken, C. W., Dewhirst, F. E., and 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.

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., and Karagas, M. R. (2016). “Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants.JAMA Pediatr, 170(3), 212-9.

Liebeskind, B. J., Hillis, D. M., Zakon, H. H., and Hofmann, H. A. (2016). “Complex Homology and the Evolution of Nervous Systems.Trends Ecol Evol, 31(2), 127-35.

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., and 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), E1422-3.

Kaneko, G., Yoshinaga, T., Gribble, K. E., Welch, D. M., and Ushio, H. (2016). “Measurement of Survival Time in Brachionus Rotifers: Synchronization of Maternal Conditions.doi:10.3791/54126(113), e54126.

Hogan, D. A., Willger, S. D., Dolben, E. L., Hampton, T. H., Stanton, B. A., Morrison, H. G., Sogin, M. L., Czum, J., and 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.

Green, H. C., Fisher, J. C., McLellan, S. L., Sogin, M. L., and Shanks, O. C. (2016). “Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves, Mammalia, and Actinopterygii.Applied and Environmental Microbiology, 82(5), 1496-1503.

Gilbert, J. A., Klyczek, K. K., and Elliott, S. L. (2016). “Introducing the JMBE Themed Issue on Scientific Citizenship.Journal of Microbiology & Biology Education, 17(1), 1-2.

Gilbert, J. A., and Alverdy, J. (2016). “Stool consistency as a major confounding factor affecting microbiota composition: an ignored variable?Gut, 65(1), 1-2.

Fortunato, C. S., and Huber, J. A. (2016). “Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent.ISME J, 10(8), 1925-38.

Eren, A. M., Sogin, M. L., and Maignien, L. (2016). “Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation.Frontiers in Microbiology, 7, 1318.

Dugas, L. R., Fuller, M., Gilbert, J., and Layden, B. T. (2016). “The obese gut microbiome across the epidemiologic transition.Emerg Themes Epidemiol, 13(1), 2.

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., and White, S. R. (2016). “Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways.Journal of Allergy and Clinical Immunology, 137(5), 1398-1405.e3.

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

De Filippis, F., Genovese, A., Ferranti, P., Gilbert, J. A., and Ercolini, D. (2016). “Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate.Scientific Reports, 6, 21871.

Davies, N., Field, D., Gavaghan, D., Holbrook, S. J., Planes, S., Troyer, M., Bonsall, M., Claudet, J., Roderick, G., Schmitt, R. J., 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., and Wood, S. (2016). “Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium.GigaScience, 5(1), 1-4.

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., and 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.

Canani, R. B., Sangwan, N., Stefka, A. T., Nocerino, R., Paparo, L., Aitoro, R., Calignano, A., Khan, A. A., Gilbert, J. A., and Nagler, C. R. (2016). “Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants.ISME J, 10(3), 742-750.

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., and Steindler, L. (2016). “A New N-Acyl Homoserine Lactone Synthase in an Uncultured Symbiont of the Red Sea Sponge Theonella swinhoei.Applied and Environmental Microbiology, 82(4), 1274-1285.

Bálint, M., Bahram, M., Eren, A. M., Faust, K., Fuhrman, J. A., Lindahl, B., Hara, R. B., Öpik, M., Sogin, M. L., Unterseher, M., and Tedersoo, L. (2016). “Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.FEMS Microbiology Reviews, 40(5), 686.

Arkhipova, I. R., and Rice, P. A. (2016). “Mobile genetic elements: in silico, in vitro, in vivo.Mol Ecol, 25(5), 1027-31.

 

2015

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., and Gilbert, J. A. (2015). “The soil microbiome influences grapevine-associated microbiota.MBio, 6(2).

Ying, S., Zeng, D. N., Chi, L., Tan, Y., Galzote, C., Cardona, C., Lax, S., Gilbert, J., and 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.

Yang, T., Weisenhorn, P., Gilbert, J. A., Ni, Y., Sun, R., Shi, Y., and Chu, H. (2015). “Carbon constrains fungal endophyte assemblages along the timberline.Environ Microbiol, 10.1111/1462-2920.13153.

Wood, M., Gibbons, S. M., Lax, S., Eshoo-Anton, T. W., Owens, S. M., Kennedy, S., Gilbert, J. A., and Hampton-Marcell, J. T. (2015). “Athletic equipment microbiota are shaped by interactions with human skin.Microbiome, 3, 25.

Walsh, E. A., Smith, D. C., Sogin, M. L., and 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.

Van Bonn, W., LaPointe, A., Gibbons, S. M., Frazier, A., Hampton-Marcell, J., and Gilbert, J. (2015). “Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management.Zoo Biol, 34(4), 360-7.

Traxler, M. F., and Kolter, R. (2015). “Natural products in soil microbe interactions and evolution.Nat Prod Rep, 32.

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., and 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.

Soranno, P. A., Bissell, E. G., Cheruvelil, K. S., Christel, S. T., Collins, S. M., and Fergus, C. E. (2015). “Building a multi-scaled geospatial temporal ecology database from disparate data sources: fostering open science and data reuse.Gigascience, 4.

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

Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., and Zdobnov, E. M. (2015). “BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.Bioinformatics, 31.

Signorovitch, A., Hur, J., Gladyshev, E., and Meselson, M. (2015). “Allele Sharing and Evidence for Sexuality in a Mitochondrial Clade of Bdelloid Rotifers.Genetics, 200(2), 581-90.

Sielaff, M., Schmidt, H., Struck, T. H., Rosenkranz, D., Mark Welch, D. B., Hankeln, T., and 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.

Shade, A., and Gilbert, J. A. (2015). “Temporal patterns of rarity provide a more complete view of microbial diversity.Trends Microbiol, 23(6), 335-40.

Schmidt, V. T., Smith, K. F., Melvin, D. W., and Amaral-Zettler, L. A. (2015). “Community assembly of a euryhaline fish microbiome during salinity acclimation.Mol Ecol, 24(10), 2537-50.

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., and Crump, B. C. (2015). “Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011.Microbiome, 3(1), 1-8.

Sangwan, N., Lambert, C., Sharma, A., Gupta, V., Khurana, P., and Khurana, J. P. (2015). “Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes.Environ Microbiol Rep, 7.

Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M. R., Rappe, M. S., DiTullio, G. R., and 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), 3521-31.

Reese, A. T., Savage, A., Youngsteadt, E., McGuire, K. L., Koling, A., Watkins, O., Frank, S. D., and Dunn, R. R. (2015). “Urban stress is associated with variation in microbial species composition-but not richness-in Manhattan.ISME J, 10.

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., and Gerasimidis, K. (2015). “Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition.Am J Gastroenterol, 110(12), 1718-29.

Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., and Tyson, G. W. (2015). “CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.Genome Res, 25.

Ochiana, S. O., Bland, N. D., Settimo, L., Campbell, R. K., and 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), 549-64.

Newton, R. J., McLellan, S. L., Dila, D. K., Vineis, J. H., Morrison, H. G., Eren, A. M., and Sogin, M. L. (2015). “Sewage reflects the microbiomes of human populations.MBio, 6(2), e02574.

Moran, Y., Barzilai, M. G., Liebeskind, B. J., and Zakon, H. H. (2015). “Evolution of voltage-gated ion channels at the emergence of Metazoa.J Exp Biol, 218(Pt 4), 515-25.

Moczek, A. P., Sears, K. E., Stollewerk, A., Wittkopp, P. J., Diggle, P., Dworkin, I., Ledon-Rettig, C., Matus, D. Q., Roth, S., Abouheif, E., Brown, F. D., Chiu, C. H., Cohen, C. S., Tomaso, A. W., Gilbert, S. F., Hall, B., Love, A. C., Lyons, D. C., Sanger, T. J., Smith, J., Specht, C., Vallejo-Marin, M., and Extavour, C. G. (2015). “The significance and scope of evolutionary developmental biology: a vision for the 21st century.Evol Dev, 17(3), 198-219.

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., and Karagas, M. R. (2015). “Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants.JAMA Pediatr, 10.1001/jamapediatrics.2015.3732, 1-8.

Mackey, K. R. M., Post, A. F., McIlvin, M. R., Cutter, G. A., John, S. G., and Saito, M. A. (2015). “Divergent responses of Atlantic coastal and oceanic Synechococcus to iron limitation.Proc Natl Acad Sci U S A, 112(32), 9944-9.

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

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., and 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.

Liu, C. M., Hungate, B. A., Toblan, A. A. R., Ravel, J., Prodger, J. L., Serwadda, D., Kigozi, G., Galiwango, R. M., Nalugoda, F., Kelm, P., Wawer, M. J., Price, L. B., and Gray, R. H. (2015). “Penile microbiota and female partner bacterial vaginosis in Rakai, Uganda.MBio, 6.

Lin, X., Handley, K. M., Gilbert, J. A., and 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), 2740-4.

Liebeskind, B. J., Hillis, D. M., and Zakon, H. H. (2015). “Convergence of ion channel genome content in early animal evolution.Proc Natl Acad Sci U S A, 112(8), E846-51.

Lax, S., Nagler, C. R., and Gilbert, J. A. (2015). “Our interface with the built environment: immunity and the indoor microbiota.Trends Immunol, 36(3), 121-3.

Lax, S., Hampton-Marcell, J. T., Gibbons, S. M., Colares, G. B., Smith, D., Eisen, J. A., and Gilbert, J. A. (2015). “Forensic analysis of the microbiome of phones and shoes.Microbiome, 3, 21.

Lax, S., and Gilbert, J. A. (2015). “Hospital-associated microbiota and implications for nosocomial infections.Trends Mol Med, 21(7), 427-32.

Larsen, P. E., Scott, N., Post, A. F., Field, D., Knight, R., Hamada, Y., and Gilbert, J. A. (2015). “Satellite remote sensing data can be used to model marine microbial metabolite turnover.ISME J, 9(1), 166-79.

Larigauderie, A. (2015). “The Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES): a call to action.GAIA Ecol Perspect Sci Soc, 24.

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., et al. (2015). “The ocean sampling day consortium.Gigascience, 4, 27.

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., and Joye, S. B. (2015). “Chemical dispersants can suppress the activity of natural oil-degrading microorganisms.Proc Natl Acad Sci U S A, 112(48), 14900-5.

Kleindienst, S., Grim, S., Sogin, M., Bracco, A., Crespo-Medina, M., and Joye, S. B. (2015). “Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume.ISME J, 10(2), 400-15.

Kang, D. D., Froula, J., Egan, R., and Wang, Z. (2015). “MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.PeerJ, 3.

Ji, P., Parks, J., Edwards, M. A., and Pruden, A. (2015). “Impact of water chemistry, pipe material and stagnation on the building plumbing microbiome.PLoS One, 10.

Huo, Y. Y., Cheng, H., Post, A. F., Wang, C. S., Jiang, X. W., Pan, J., Wu, M., and 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.

Hunter-Cevera, K. R., Post, A. F., Peacock, E. E., and 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), 276-89.

Huber, J. A. (2015). “MICROBIAL ECOLOGY. Making methane down deep.Science, 349(6246), 376-7.

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., and Chang, E. B. (2015). “Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases.Inflamm Bowel Dis, 21(5), 963-72.

Hua, Z.-S., Han, Y.-J., Chen, L.-X., Liu, J., Hu, M., and Li, S.-J. (2015). “Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics.ISME J, 9.

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., and Madan, J. C. (2015). “Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis.J Pediatr, 167(1), 138-47 e1-3.

Hilton, J. A., Satinsky, B. M., Doherty, M., Zielinski, B., and Zehr, J. P. (2015). “Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume.ISME J, 9.

Gordon, J., Gandhi, P., Shekhawat, G., Frazier, A., Hampton-Marcell, J., and Gilbert, J. A. (2015). “A simple novel device for air sampling by electrokinetic capture.Microbiome, 3(1), 79.

Gilbert, J. A., and Henry, C. (2015). “Predicting ecosystem emergent properties at multiple scales.Environ Microbiol Rep, 7(1), 20-2.

Gibbons, S. M., Schwartz, T., Fouquier, J., Mitchell, M., Sangwan, N., Gilbert, J. A., and Kelley, S. T. (2015). “Ecological succession and viability of human-associated microbiota on restroom surfaces.Appl Environ Microbiol, 81(2), 765-73.

Gibbons, S. M., Schwartz, T., Fouquier, J., Mitchell, M., Sangwan, N., and Gilbert, J. A. (2015). “Ecological succession and viability of human-associated microbiota on restroom surfaces.Appl Environ Microbiol, 81.

Gibbons, S. M., and Gilbert, J. A. (2015). “Microbial diversity-exploration of natural ecosystems and microbiomes.Curr Opin Genet Dev, 35, 66-72.

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., and Layden, B. T. (2015). “The short-chain fatty acid receptor, FFA2, contributes to gestational glucose homeostasis.Am J Physiol Endocrinol Metab, 309(10), E840-51.

Fortunato, C. S., and Crump, B. C. (2015). “Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient.PLoS One, 10(11), e0140578.

Fisher, J. C., Eren, A. M., Green, H. C., Shanks, O. C., Morrison, H. G., Vineis, J. H., Sogin, M. L., and 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), 7023-33.

Fisch, K. M., Meißner, T., Gioia, L., Ducom, J. C., Carland, T. M., Loguercio, S., and Su, A. I. (2015). “Omics Pipe: a community-based framework for reproducible multi-omics data analysis.Bioinformatics, 31.

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., and Hogan, D. (2015). “Bacfun: An Rna-Based Diagnostic for Cystic Fibrosis Respiratory Samples.Pediatric Pulmonology, 50, 321-321.

Filippidou, S., Junier, T., Wunderlin, T., Lo, C. C., Li, P. E., Chain, P. S., and Junier, P. (2015). “Under-detection of endospore-forming firmicutes in metagenomic data.Comput Struct Biotechnol J, 13.

Felczykowska, A., Krajewska, A., Zielińska, S., and Los, J. M. (2015). “Sampling, metadata and DNA extraction—important steps in metagenomic studies.Acta Biochim Pol, 62.

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

Eren, A. M., Morrison, H. G., Lescault, P. J., Reveillaud, J., Vineis, J. H., and Sogin, M. L. (2015). “Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences.ISME J, 9(4), 968-79.

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

Ehrenberg, R. (2015). “Urban microbe come out of the shadows.Nature, 522.

Ducklow, H. W., Wilson, S. E., Post, A. F., Stammerjohn, S. E., Erickson, M., Lee, S., Lowry, K. E., Sherrell, R. M., and 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.

Dubilier, N., McFall-Ngai, M., and Zhao, L. (2015). “Microbiology: create a global microbiome effort.Nature, 526.

Deng, X., Naccache, S. N., Ng, T., Federman, S., Li, L., and Chiu, C. Y. (2015). “An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data.Nucleic Acids Res, 43.

Delmont, T. O., Eren, A. M., Vineis, J. H., and 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.

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

Cressey, D. (2015). “Tropical paradise inspires virtual ecology lab.Nature, 517.

Chafee, M., Maignien, L., and Simmons, S. L. (2015). “The effects of variable sample biomass on comparative metagenomics.Environ Microbiol, 17(7), 2239-53.

Burgsdorf, I., Slaby, B. M., Handley, K. M., Haber, M., Blom, J., Marshall, C. W., Gilbert, J. A., Hentschel, U., and Steindler, L. (2015). “Lifestyle evolution in cyanobacterial symbionts of sponges.MBio, 6(3), e00391-15.

Browne, M. A., Chapman, M. G., Thompson, R. C., Amaral-Zettler, L. A., Jambeck, J., and 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), 7082-94.

Brown, C. T., Hug, L. A., Thomas, B. C., Sharon, I., Castelle, C. J., and Singh, A. (2015). “Unusual biology across a group comprising more than 15 % of domain Bacteria.Nature, 523.

Brown, C. T. (2015). “Strain recovery from metagenomes.Nat Biotechnol, 33.

Bowen, J. L., Weisman, D., Yasuda, M., Jayakumar, A., Morrison, H. G., and Ward, B. B. (2015). “Marine Oxygen-Deficient Zones Harbor Depauperate Denitrifying Communities Compared to Novel Genetic Diversity in Coastal Sediments.Microb Ecol, 70(2), 311-21.

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., and 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), 9938-43.

Baker, B. J., Lazar, C. S., Teske, A. P., and Dick, G. J. (2015). “Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria.Microbiome, 3.

Angermeyer, A., Crosby, S. C., and 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.

Anderson, R. E., Sogin, M. L., and 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.

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

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

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., and Taha, S. A. (2015). “A unified initiative to harness Earth’s microbiomes.Science, 350.

Afshinnekoo, E., Meydan, C., Chowdhury, S., Jaroudi, D., Boyer, C., Bernstein, N., Maritz, J. M., Reeves, D., Gandara, J., Chhangawala, S., Ahsanuddin, S., Simmons, A., Nessel, T., Sundaresh, B., Pereira, E., Jorgensen, E., Kolokotronis, S., Kirchberger, N., Garcia, I., Gandara, D., Dhanraj, S., Nawrin, T., Saletore, Y., Alexander, N., Vijay, P., Hénaff, E. M., Zumbo, P., Walsh, M., O’Mullan, G. D., Tighe, S., Dudley, J. T., Dunaif, A., Ennis, S., O’Halloran, E., Magalhaes, T. R., Boone, B., Jones, A. L., Muth, T. R., Paolantonio, K. S., Alter, E., Schadt, E. E., Garbarino, J., Prill, R. J., Carlton, J. M., Levy, S., and Mason, C. E. (2015). “Modern methods for delineating metagenomic complexity.Cell Sys, 1.

 

2014

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), 245-6.

Xu, Y., Vick-Majors, T. J., Morgan-Kiss, R., Priscu, J. C., and Amaral-Zettler, L. A. (2014). “Ciliate diversity, community structure, and novel taxa in lakes of the McMurdo Dry Valleys, Antarctica.Biol Bull, 227(2), 175-90.

Wu, Y.-W., Tang, Y.-H., Tringe, S. G., Simmons, B. A., and Singer, S. W. (2014). “MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm.Microbiome, 2.

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., and Hogan, D. A. (2014). “Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis.Microbiome, 2, 40.

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

Wey-Fabrizius, A. R., Herlyn, H., Rieger, B., Rosenkranz, D., Witek, A., Mark Welch, D. B., Ebersberger, I., and 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.

Weng, S. L., Chiu, C. M., Lin, F. M., Huang, W. C., Liang, C., Yang, T., Yang, T. L., Liu, C. Y., Wu, W. Y., Chang, Y. A., Chang, T. H., and Huang, H. D. (2014). “Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality.PLoS One, 9.

Vick-Majors, T. J., Priscu, J. C., and 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), 778-89.

Vázquez-Castellanos, J. F., García-López, R., Pérez-Brocal, V., Pignatelli, M., and Moya, A. (2014). “Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut.BMC Genomics, 15.

Thompson, A., Vo, D., Comfort, C., and Zakon, H. H. (2014). “Expression evolution facilitated the convergent neofunctionalization of a sodium channel gene.Mol Biol Evol, 31(8), 1941-55.

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., and Stepanauskas, R. (2014). “Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres.PLoS One, 9(4), e95380.

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., and Zehr, J. P. (2014). “A microarray for assessing transcription from pelagic marine microbial taxa.ISME J, 8(7), 1476-91.

Shafquat, A., Joice, R., Simmons, S. L., and Huttenhower, C. (2014). “Functional and phylogenetic assembly of microbial communities in the human microbiome.Trends Microbiol, 22(5), 261-6.

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., and Zhou, X. (2014). “The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.J Hered, 105(1), 1-18.

Scholz, M., Lo, C.-C., and Chain, P. S. G. (2014). “Improved assemblies using a source-agnostic pipeline for metagenomic assembly by merging (MeGAMerge) of contigs.Sci Rep, 4.

Schmidt, V. T., Reveillaud, J., Zettler, E., Mincer, T. J., Murphy, L., and Amaral-Zettler, L. A. (2014). “Oligotyping reveals community level habitat selection within the genus Vibrio.Front Microbiol, 5, 563.

Sawakuchi, H. O., Bastviken, D., Sawakuchi, A. O., Krusche, A. V., Ballester, M. V. R., and Richey, J. E. (2014). “Methane emissions from Amazonian Rivers and their contribution to the global methane budget.Global Change Biol, 20.

Satinsky, B. M., Zielinski, B. L., Doherty, M., Smith, C. B., Sharma, S., and Paul, J. H. (2014). “The Amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the Amazon River plume, June 2010.Microbiome, 2.

Satinsky, B. M., Crump, B. C., Smith, C. B., Sharma, S., Zielinski, B. L., and Doherty, M. (2014). “Microspatial gene expression patterns in the Amazon River Plume.Proc Natl Acad Sci U S A, 111.

Salikhov, K., Sacomoto, G., and Kucherov, G. (2014). “Using cascading Bloom filters to improve the memory usage for de Brujin graphs.Algorithms Mol Biol AMB, 9.

Saito, M. A., McIlvin, M. R., Moran, D. M., Goepfert, T. J., DiTullio, G. R., Post, A. F., and Lamborg, C. H. (2014). “Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers.Science, 345(6201), 1173-7.

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., and Wright, A. T. (2014). “Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium.ACS Chem Biol, 9(1), 291-300.

Rodriguez-R, L. M., and Konstantinidis, K. T. (2014). “Estimating coverage in metagenomic data sets and why it matters.ISME J, 8.

Rodriguez-R, L. M., and Konstantinidis, K. T. (2014). “Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets.Bioinforma Oxf Engl, 30.

Reznikoff, W. S. (2014). “Viewing Francois Jacob (and Jacques Monod) through AGC & T.Res Microbiol, 165(5), 357-8.

Reveillaud, J., Maignien, L., Murat Eren, A., Huber, J. A., Apprill, A., Sogin, M. L., and Vanreusel, A. (2014). “Host-specificity among abundant and rare taxa in the sponge microbiome.ISME J, 8(6), 1198-209.

Reed, D. C., Algar, C. K., Huber, J. A., and 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.

Reed, D. C., Algar, C. K., Huber, J. A., and Dick, G. J. (2014). “Gene-centric approach to integrating environmental genomics and biogeochemical models.Proc Natl Acad Sci U S A, 111(5), 1879-84.

Orcutt, B. N., LaRowe, D. E., Lloyd, K. G., Mills, H., Orsi, W., Reese, B. K., Sauvage, J., Huber, J. A., and 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.

Ong, W. K., Vu, T. T., Lovendahl, K. N., Llull, J. M., Serres, M. H., Romine, M. F., and Reed, J. L. (2014). “Comparisons of Shewanella strains based on genome annotations, modeling, and experiments.BMC Syst Biol, 8(1), 31.

Ofek-Lalzar, M., Sela, N., Goldman-Voronov, M., Green, S. J., Hadar, Y., and Minz, D. (2014). “Niche and host-associated functional signatures of the root surface microbiome.Nat Commun, 5.

Nielsen, H. B., Almeida, M., Juncker, A. S., Rasmussen, S., Li, J., and Sunagawa, S. (2014). “Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.Nat Biotechnol, 32.

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

Muzny, C. A., and Schwebke, J. R. (2014). “Suspected heterosexual transmission of bacterial vaginosis without seminal fluid exposure.Sex Transm Dis, 41.

Moran, Y., and 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), 2210-7.

Meyer, J. L., and Huber, J. A. (2014). “Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano.ISME J, 8(4), 867-80.

McLellan, S. L., and Eren, A. M. (2014). “Discovering new indicators of fecal pollution.Trends Microbiol, 22(12), 697-706.

McInerny, G. J., Chen, M., Freeman, R., Gavaghan, D., Meyer, M., and Rowland, F. (2014). “Information visualisation for science and policy: engaging users and avoiding bias.Trends Ecol Evol, 29.

McInerny, G. J., Chen, M., Freeman, R., Gavaghan, D., Meyer, M., and Rowland, F. (2014). “Information visualisation for science and policy: engaging users and avoiding bias.Trends Ecol Evol, 29.

Mason, C. E., and Shi, L. (2014). “A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium.Nature Biotech, 32.

Mason, C. E., and Shi, L. (2014). “A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium.Nature Biotech, 32.

Mason, C. E., Porter, S., and Smith, T. (2014). “Characterizing Multi-omic data in systems biology.Adv Exp Med Biol, 799.

Mason, C. E., Porter, S., and Smith, T. (2014). “Characterizing Multi-omic data in systems biology.Adv Exp Med Biol, 799.

Markham, M. R., and Zakon, H. H. (2014). “Ionic mechanisms of microsecond-scale spike timing in single cells.J Neurosci, 34(19), 6668-78.

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

Maltz, M. A., Bomar, L., Lapierre, P., Morrison, H. G., McClure, E. A., Sogin, M. L., and Graf, J. (2014). “Metagenomic analysis of the medicinal leech gut microbiota.Front Microbiol, 5, 151.

Maignien, L., DeForce, E. A., Chafee, M. E., Eren, A. M., and Simmons, S. L. (2014). “Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities.MBio, 5(1), e00682-13.

Luria, C. M., Ducklow, H. W., and 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.

Luo, H., and Moran, M. A. (2014). “Evolutionary ecology of the marine roseobacter clade.Microbiol Mol Biol Rev, 78.

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., and 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), 4363-73.

Li, S., and Mason, C. E. (2014). “The pivotal regulatory landscape of RNA modifications.Annu Rev Genomics Hum Genet, 15.

Li, S., and Mason, C. E. (2014). “The pivotal regulatory landscape of RNA modifications.Annu Rev Genomics Hum Genet, 15.

Li, S., Labaj, P., Zumbo, R., Shi, W., Phan, J., Wu, L., Wang, M., Thierry-Mieg, J., Thierry-Mieg, D., Shi, L., Kreil, D., and Mason, C. E. (2014). “Detecting and correcting systematic variation from large-scale RNA sequencing.Nat Biotechnol, 32.

Li, S., Labaj, P., Zumbo, R., Shi, W., Phan, J., Wu, L., Wang, M., Thierry-Mieg, J., Thierry-Mieg, D., Shi, L., Kreil, D., and Mason, C. E. (2014). “Detecting and correcting systematic variation from large-scale RNA sequencing.Nat Biotechnol, 32.

Leung, M. H., Wilkins, D., Li, E. K., Kong, F. K., and Lee, P. K. (2014). “Indoor-air microbiome in an urban subway network: diversity and dynamics.Appl Environ Microbiol, 80.

Leung, M. H., Wilkins, D., Li, E. K., Kong, F. K., and Lee, P. K. (2014). “Indoor-air microbiome in an urban subway network: diversity and dynamics.Appl Environ Microbiol, 80.

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., and 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.

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

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., 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., 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., and Klenk, H. P. (2014). “Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.PLoS Biol, 12(8), e1001920.

Koskey, A. M., Fisher, J. C., Eren, A. M., Ponce-Terashima, R., Reis, M. G., Blanton, R. E., and 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.

Koren, S., Treangen, T. J., Hill, C. M., Pop, M., and Phillippy, A. M. (2014). “Automated ensemble assembly and validation of microbial genomes.BMC Bioinformatics, 15.

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., and 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.

Imelfort, M., Parks, D., Woodcroft, B. J., Dennis, P., Hugenholtz, P., and Tyson, G. W. (2014). “GroopM: an automated tool for the recovery of population genomes from related metagenomes.PeerJ, 2.

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., and 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.

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

Huo, Y. Y., Li, Z. Y., You, H., Wang, C. S., Post, A. F., Oren, A., and 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), 2975-9.

Handley, K. M., Bartels, D., O’Loughlin, E. J., Williams, K. H., Trimble, W. L., and Skinner, K. (2014). “The complete genome sequence for putative H2- and S-oxidizer candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome.Environ Microbiol, 16.

Hampton, T. H., Green, D. M., Cutting, G. R., Morrison, H. G., Sogin, M. L., Gifford, A. H., Stanton, B. A., and 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.

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

Gribble, K. E., Kaido, O., Jarvis, G., and Mark Welch, D. B. (2014). “Patterns of intraspecific variability in the response to caloric restriction.Exp Gerontol, 51, 28-37.

Gribble, K. E., Jarvis, G., Bock, M., and Mark Welch, D. B. (2014). “Maternal caloric restriction partially rescues the deleterious effects of advanced maternal age on offspring.Aging Cell, 13(4), 623-30.

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., Stajich, J., Knight, R., Meyer, F., and 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.

Gilbert, J. A., and Neufeld, J. D. (2014). “Life in a World without Microbes.PLoS Biol, 12(12), e1002020.

Gilbert, J. A., Jansson, J. K., and Knight, R. (2014). “The Earth Microbiome project: successes and aspirations.BMC Biol, 12.

Gilbert, J. A., Jansson, J. K., and Knight, R. (2014). “The Earth Microbiome project: successes and aspirations.BMC Biol, 12.

Gilbert, J. A., Dick, G. J., Jenkins, B., Heidelberg, J., Allen, E., Mackey, K. R., and 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), 1252-8.

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., and 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), 311-8.

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

Ghai, R., Mizuno, C. M., Picazo, A., Camacho, A., and Rodriguez-Valera, F. (2014). “Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing.Mol Ecol, 23.

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., and Sussman, M. R. (2014). “Nonhuman genetics. Genomic basis for the convergent evolution of electric organs.Science, 344(6191), 1522-5.

Fischer, A. H., Mozzherin, D., Eren, A. M., Lans, K. D., Wilson, N., Cosentino, C., and Smith, J. (2014). “SeaBase: a multispecies transcriptomic resource and platform for gene network inference.Integr Comp Biol, 54(2), 250-63.

Firth, C., Bhat, M., Firth, M. A., Williams, S. H., Frye, M. J., Simmonds, P., Conte, J. M., Ng, J., Garcia, J., Bhuva, N. P., Lee, B., Che, X., Quan, P. L., and Lipkin, W. I. (2014). “Detection of zoonotic pathogens and characterization of novel viruses carried by commensal Rattus norvegicus in New York City.MBio, 5.

Firth, C., Bhat, M., Firth, M. A., Williams, S. H., Frye, M. J., Simmonds, P., Conte, J. M., Ng, J., Garcia, J., Bhuva, N. P., Lee, B., Che, X., Quan, P. L., and Lipkin, W. I. (2014). “Detection of zoonotic pathogens and characterization of novel viruses carried by commensal Rattus norvegicus in New York City.MBio, 5.

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., and Caporaso, G. (2014). “Genomic standards consortium projects.Stand Genomic Sci, 9(3), 599-601.

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., Bajic, V. B., and El-Dorry, H. (2014). “Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.PLoS One, 9(6), e97338.

Eren, A. M., Morrison, H. G., Huse, S. M., and Sogin, M. L. (2014). “DRISEE overestimates errors in metagenomic sequencing data.Brief Bioinform, 15(5), 783-7.

Eren, A. M., Borisy, G. G., Huse, S. M., and Mark Welch, J. L. (2014). “Oligotyping analysis of the human oral microbiome.Proc Natl Acad Sci U S A, 111(28), E2875-84.

Earl, D., Nguyen, N., Hickey, G., Harris, R. S., Fitzgerald, S., and Beal, K. (2014). “Alignathon: a competitive assessment of whole-genome alignment methods.Genome Res, 24.

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., and 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), 632-45.

Donia, M. S., Cimermancic, P., Schulze, C. J., Wieland Brown, L. C., Martin, J., Mitreva, M., Clardy, J., Linington, R. G., and Fischbach, M. A. (2014). “A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics.Cell, 158.

Donia, M. S., Cimermancic, P., Schulze, C. J., Wieland Brown, L. C., Martin, J., Mitreva, M., Clardy, J., Linington, R. G., and Fischbach, M. A. (2014). “A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics.Cell, 158.

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

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

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., and Sears, C. L. (2014). “Microbiota organization is a distinct feature of proximal colorectal cancers.Proc Natl Acad Sci U S A, 111(51), 18321-6.

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., and COS, G. O. (2014). “The founding charter of the Genomic Observatories Network.Gigascience, 3(1), 2.

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., and 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.

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

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., and Gorham, J. D. (2014). “The microbiota regulates susceptibility to Fas-mediated acute hepatic injury.Lab Invest, 94(9), 938-49.

Cao, C., Jiang, W., Wang, B., Fang, J., Lang, J., Tian, G., Jiang, J., and Zhu, T. F. (2014). “Inhalable microorganisms in Beijing’s PM2.5 and PM10 pollutants during a severe smog event.Environ Sci Technol, 48.

Cao, C., Jiang, W., Wang, B., Fang, J., Lang, J., Tian, G., Jiang, J., and Zhu, T. F. (2014). “Inhalable microorganisms in Beijing’s PM2.5 and PM10 pollutants during a severe smog event.Environ Sci Technol, 48.

Bullerjahn, G. S., and Post, A. F. (2014). “Physiology and molecular biology of aquatic cyanobacteria.Front Microbiol, 5, 359.

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., and Konopka, A. (2014). “Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing.ISME J, 8(11), 2243-55.

Apprill, A., Robbins, J., Eren, A. M., Pack, A. A., Reveillaud, J., Mattila, D., Moore, M., Niemeyer, M., Moore, K. M., and 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.

Anderson, R. E., Sogin, M. L., and Baross, J. A. (2014). “Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics.PLoS One, 9(10), e109696.

Amata, E., Bland, N. D., Hoyt, C. T., Settimo, L., Campbell, R. K., and 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), 4084-9.

Alneberg, J., Bjarnason, B. S., Bruijn, I., Schirmer, M., Quick, J., and Ijaz, U. Z. (2014). “Binning metagenomic contigs by coverage and composition.Nat Methods, 11.

 

2013

Zettler, E. R., Mincer, T. J., and Amaral-Zettler, L. A. (2013). “Life in the “plastisphere”: microbial communities on plastic marine debris.Environ Sci Technol, 47(13), 7137-46.

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., and 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.

Yooseph, S., Andrews-Pfannkoch, C., Tenney, A., McQuaid, J., Williamson, S., Thiagarajan, M., Brami, D., Zeigler-Allen, L., Hoffman, J., Goll, J. B., Fadrosh, D., Glass, J., Adams, M. D., Friedman, R., and Venter, J. C. (2013). “A metagenomic framework for the study of airborne microbial communities.PLoS One, 8.

Yooseph, S., Andrews-Pfannkoch, C., Tenney, A., McQuaid, J., Williamson, S., Thiagarajan, M., Brami, D., Zeigler-Allen, L., Hoffman, J., Goll, J. B., Fadrosh, D., Glass, J., Adams, M. D., Friedman, R., and Venter, J. C. (2013). “A metagenomic framework for the study of airborne microbial communities.PLoS One, 8.

Woodring, J. L., Bland, N. D., Ochiana, S. O., Campbell, R. K., and Pollastri, M. P. (2013). “Synthesis and assessment of catechol diether compounds as inhibitors of trypanosomal phosphodiesterase B1 (TbrPDEB1).Bioorg Med Chem Lett, 23(21), 5971-4.

Ward, N. D., Keil, R. G., Medeiros, P. M., Brito, D. C., Cunha, A. C., and Dittmar, T. (2013). “Degradation of terrestrially derived macromolecules in the Amazon River.Nat Geosci, 6.

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., and Tiedje, J. M. (2013). “A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community.Microbiome, 1(1), 8.

Vicedomini, R., Vezzi, F., Scalabrin, S., Arvestad, L., and Policriti, A. (2013). “GAM-NGS: genomic assemblies merger for next generation sequencing.BMC Bioinformatics, 14.

Ver Eecke, H. C., Akerman, N. H., Huber, J. A., Butterfield, D. A., and Holden, J. F. (2013). “Growth kinetics and energetics of a deep-sea hyperthermophilic methanogen under varying environmental conditions.Environ Microbiol Rep, 5(5), 665-71.

Tulin, S., Aguiar, D., Istrail, S., and 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.

Theroux, S., Toney, J., Amaral-Zettler, L. A., and Huang, Y. S. (2013). “Production and temperature sensitivity of long chain alkenones in the cultured haptophyte Pseudoisochrysis paradoxa.Organic Geochemistry, 62, 68-73.

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., and Wiley, H. S. (2013). “Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria.Integr Biol (Camb), 5(11), 1393-406.

Sul, W. J., Oliver, T. A., Ducklow, H. W., Amaral-Zettler, L. A., and Sogin, M. L. (2013). “Marine bacteria exhibit a bipolar distribution.Proc Natl Acad Sci U S A, 110(6), 2342-7.

Sharon, I., Morowitz, M. J., Thomas, B. C., Costello, E. K., Relman, D. A., and Banfield, J. F. (2013). “Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization.Genome Res, 23.

Shanks, O. C., Newton, R. J., Kelty, C. A., Huse, S. M., Sogin, M. L., and McLellan, S. L. (2013). “Comparison of the microbial community structures of untreated wastewaters from different geographic locales.Appl Environ Microbiol, 79(9), 2906-13.

Satinsky, B. M., Gifford, S. M., Crump, B. C., and Moran, M. A. (2013). “Use of internal standards for quantitative metatranscriptome and metagenome analysis.Method Enzymol, 531.

Rung, J., and Brazma, A. (2013). “Reuse of public genome-wide gene expression data.Nat Rev Genet, 14.

Rung, J., and Brazma, A. (2013). “Reuse of public genome-wide gene expression data.Nat Rev Genet, 14.

Rozhkov, N. V., Schostak, N. G., Zelentsova, E. S., Yushenova, I. A., Zatsepina, O. G., and 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.

Rosenfeld, J., and Mason, C. E. (2013). “Pervasive sequence patents cover the entire human genome.Genome Med, 5.

Rosenfeld, J., and Mason, C. E. (2013). “Pervasive sequence patents cover the entire human genome.Genome Med, 5.

Roller, M., Lucić, V., Nagy, I., Perica, T., and Vlahovicek, K. (2013). “Environmental shaping of codon usage and functional adaptation across microbial communities.Nucleic Acids Res, 41.

Robertson, C. E., Baumgartner, L. K., Harris, J. K., Peterson, K. L., Stevens, M. J., Frank, D. N., and Pace, N. R. (2013). “Culture-independent analysis of aerosol microbiology in a metropolitan subway system.Appl Environ Microbiol, 79.

Robertson, C. E., Baumgartner, L. K., Harris, J. K., Peterson, K. L., Stevens, M. J., Frank, D. N., and Pace, N. R. (2013). “Culture-independent analysis of aerosol microbiology in a metropolitan subway system.Appl Environ Microbiol, 79.

Rienzi, S. C., Sharon, I., Wrighton, K. C., Koren, O., Hug, L. A., and Thomas, B. C. (2013). “The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria.eLife, 2.

Purves, D., Scharlemann, J., Harfoot, M., Newbold, T., Tittensor, D. P., and Hutton, J. (2013). “Ecosystems: time to model all life on Earth.Nature, 493.

Purves, D., Scharlemann, J., Harfoot, M., Newbold, T., Tittensor, D. P., and Hutton, J. (2013). “Ecosystems: time to model all life on Earth.Nature, 493.

Price, K. E., Hampton, T. H., Gifford, A. H., Dolben, E. L., Hogan, D. A., Morrison, H. G., Sogin, M. L., and O’Toole, G. A. (2013). “Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation.Microbiome, 1(1), 27.

Newton, R. J., Huse, S. M., Morrison, H. G., Peake, C. S., Sogin, M. L., and McLellan, S. L. (2013). “Shifts in the microbial community composition of Gulf Coast beaches following beach oiling.PLoS One, 8(9), e74265.

Newton, R. J., Bootsma, M. J., Morrison, H. G., Sogin, M. L., and 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), 1011-23.

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

Merkel, A. Y., Huber, J. A., Chernyh, N. A., Bonch-Osmolovskaya, E. A., and Lebedinsky, A. V. (2013). “Detection of putatively thermophilic anaerobic methanotrophs in diffuse hydrothermal vent fluids.Appl Environ Microbiol, 79(3), 915-23.

McLellan, S. L., Newton, R. J., Vandewalle, J. L., Shanks, O. C., Huse, S. M., Eren, A. M., and Sogin, M. L. (2013). “Sewage reflects the distribution of human faecal Lachnospiraceae.Environ Microbiol, 15(8), 2213-27.

Materna, S. C., Swartz, S. Z., and Smith, J. (2013). “Notch and Nodal control forkhead factor expression in the specification of multipotent progenitors in sea urchin.Development, 140(8), 1796-806.

Marteinsson, V. T., Runarsson, A., Stefansson, A., Thorsteinsson, T., Johannesson, T., Magnusson, S. H., Reynisson, E., Einarsson, B., Wade, N., Morrison, H. G., and Gaidos, E. (2013). “Microbial communities in the subglacial waters of the Vatnajokull ice cap, Iceland.ISME J, 7(2), 427-37.

Maignien, L., Parkes, R. J., Cragg, B., Niemann, H., Knittel, K., Coulon, S., Akhmetzhanov, A., and Boon, N. (2013). “Anaerobic oxidation of methane in hypersaline cold seep sediments.FEMS Microbiol Ecol, 83(1), 214-31.

Mace, G. (2013). “Ecology must evolve.Nature, 503.

Mace, G. (2013). “Ecology must evolve.Nature, 503.

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., and Price, L. B. (2013). “Male circumcision significantly reduces prevalence and load of genital anaerobic bacteria.MBio, 4.

Kantor, R. S., Wrighton, K. C., Handley, K. M., Sharon, I., Hug, L. A., and Castelle, C. J. (2013). “Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla.mBio, 4.

Kamennaya, N. A., and 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.

Hunt, M., Kikuchi, T., Sanders, M., Newbold, C., Berriman, M., and Otto, T. D. (2013). “REAPR: a universal tool for genome assembly evaluation.Genome Biol, 14.

Helm, R. R., Siebert, S., Tulin, S., Smith, J., and Dunn, C. W. (2013). “Characterization of differential transcript abundance through time during Nematostella vectensis development.BMC Genomics, 14, 266.

Hanson, S. J., Stelzer, C. P., Mark Welch, D. B., and 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.

Hanson, S. J., Schurko, A. M., Hecox-Lea, B., Mark Welch, D. B., Stelzer, C. P., and Logsdon, J. M. Jr. (2013). “Inventory and phylogenetic analysis of meiotic genes in monogonont rotifers.J Hered, 104(3), 357-70.

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

Gribble, K. E., and 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), 349-58.

Garcia, S. L., McMahon, K. D., Martinez-Garcia, M., Srivastava, A., Sczyrba, A., and Stepanauskas, R. (2013). “Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton.ISME J, 7.

Fortunato, C. S., Eiler, A., Herfort, L., Needoba, J. A., Peterson, T. D., and Crump, B. C. (2013). “Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin.ISME J, 7(10), 1899-911.

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., and Van Doninck, K. (2013). “Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.Nature, 500(7463), 453-7.

Fischer, A. H., Tulin, S., Fredman, D., and Smith, J. (2013). “Employing BAC-reporter constructs in the sea anemone Nematostella vectensis.Integr Comp Biol, 53(5), 832-46.

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., and Pradhan, S. (2013). “A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.PLoS One, 8(10), e76096.

Eren, A. M., Vineis, J. H., Morrison, H. G., and Sogin, M. L. (2013). “A filtering method to generate high quality short reads using illumina paired-end technology.PLoS One, 8(6), e66643.

Eren, A. M., Maignien, L., Sul, W. J., Murphy, L. G., Grim, S. L., Morrison, H. G., and Sogin, M. L. (2013). “Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.Methods Ecol Evol, 4(12).

Eppinger, M., Daugherty, S., Agrawal, S., Galens, K., Sengamalay, N., and Sadzewicz, L. (2013). “Whole-genome draft sequences of 26 enterohemorrhagic Escherichia coli O157:H7 strains.Genome Announc, 1.

Edwards, D. J., and Holt, K. E. (2013). “Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data.Microb Inform Exp, 3.

Duffy, J. E., Amaral-Zettler, L. A., Fautin, D. G., Paulay, G., Rynearson, T. A., Sosik, H. M., and Stachowicz, J. J. (2013). “Envisioning a Marine Biodiversity Observation Network.Bioscience, 63(5), 350-361.

Conceição, T., Diamantino, F., Coelho, C., Lencastre, H., and Aires-de-Sousa, M. (2013). “Contamination of public buses with MRSA in Lisbon, Portugal: a possible transmission route of major MRSA clones within the community.PLoS One, 8.

Conceição, T., Diamantino, F., Coelho, C., Lencastre, H., and Aires-de-Sousa, M. (2013). “Contamination of public buses with MRSA in Lisbon, Portugal: a possible transmission route of major MRSA clones within the community.PLoS One, 8.

Clark, S. C., Egan, R., Frazier, P. I., and Wang, Z. (2013). “ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.Bioinforma Oxf Engl, 29.

Castelle, C. J., Hug, L. A., Wrighton, K. C., Thomas, B. C., Williams, K. H., and Wu, D. (2013). “Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment.Nat Commun, 4.

Cameron, P., Corne, D. W., Mason, C. E., and Rosenfeld, J. (2013). “Crowdfunding genomics and bioinformatics.Genome Biol, 14.

Cameron, P., Corne, D. W., Mason, C. E., and Rosenfeld, J. (2013). “Crowdfunding genomics and bioinformatics.Genome Biol, 14.

Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., and Birol, I. (2013). “Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.GigaScience, 2.

Bennett, S. A., Coleman, M., Huber, J. A., Reddington, E., Kinsey, J. C., McIntyre, C., Seewald, J. S., and 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.

Arkhipova, I. R., Yushenova, I. A., and 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.

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

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

Alliegro, M. C., and 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), 391-6.

Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K. L., Tyson, G. W., and Nielsen, P. H. (2013). “Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.Nat Biotechnol, 31.

Akhter, S., Bailey, B. A., Salamon, P., Aziz, R. K., and Edwards, R. A. (2013). “Applying Shannon’s information theory to bacterial and phage genomes and metagenomes.Sci Rep, 3.

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

 

2012

Zhao, Y., Tang, H., and Ye, Y. (2012). “RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data.Bioinformatics, 28.

Zhang, Z., Li, J., Cui, P., Ding, F., Li, A., and Townsend, J. P. (2012). “Codon deviation coefficient: a novel measure for estimating codon usage bias and its statistical significance.BMC Bioinformatics, 13.

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., and Wilson, S. (2012). “ASPIRE The Amundsen Sea Polynya International Research Expedition.Oceanography, 25(3), 40-53.

Wu, M., and Scott, A. J. (2012). “Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.Bioinformatics, 28.

Wrighton, K. C., Thomas, B. C., Sharon, I., Miller, C. S., Castelle, C. J., and VerBerkmoes, N. C. (2012). “Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla.Science, 337.

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., and 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.

Wang, C., Ashton, T. D., Gustafson, A., Bland, N. D., Ochiana, S. O., Campbell, R. K., and 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), 2579-81.

Vezzi, F., Narzisi, G., and Mishra, B. (2012). “Reevaluating assembly evaluations with feature response curves: GAGE and Assemblathons.PLoS One, 7.

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., and Holden, J. F. (2012). “Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents.Proc Natl Acad Sci U S A, 109(34), 13674-9.

Vandewalle, J. L., Goetz, G. W., Huse, S. M., Morrison, H. G., Sogin, M. L., Hoffmann, R. G., Yan, K., and McLellan, S. L. (2012). “Acinetobacter, Aeromonas and Trichococcus populations dominate the microbial community within urban sewer infrastructure.Environ Microbiol, 14(9), 2538-52.

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

Treangen, T. J., and Salzberg, S. L. (2012). “Repetitive DNA and next-generation sequencing: computational challenges and solutions.Nat Rev Genet, 13.

Toney, J. L., Theroux, S., Andersen, R. A., Coleman, A., Amaral-Zettler, L. A., and 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.

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

Takumi, K., Swart, A., Mank, T., Lasek-Nesselquist, E., Lebbad, M., Caccio, S. M., and Sprong, H. (2012). “Population-based analyses of Giardia duodenalis is consistent with the clonal assemblage structure.Parasit Vectors, 5, 168.

Sun, Y., Cai, Y., Huse, S. M., Knight, R., Farmerie, W. G., Wang, X., and Mai, V. (2012). “A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis.Brief Bioinform, 13(1), 107-21.

Sukenik, A., Kaplan-Levy, R. N., Mark Welch, J. L., and Post, A. F. (2012). “Massive multiplication of genome and ribosomes in dormant cells (akinetes) of Aphanizomenon ovalisporum (Cyanobacteria).ISME J, 6(3), 670-9.

Srinivasan, S., Hoffman, N. G., Morgan, M. T., Matsen, F. A., Fiedler, T. L., Hall, R. W., Ross, F. J., McCoy, C. O., Bumgarner, R., Marrazzo, J. M., and Fredricks, D. N. (2012). “Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria.PLoS One, 7.

Spencer, R. G. M., Hernes, P. J., Aufdenkampe, A. K., Baker, A., Gulliver, P., and Stubbins, A. (2012). “An initial investigation into the organic matter biogeochemistry of the Congo River.Geochim Cosmochim Ac, 84.

Smith, K. F., Schmidt, V. T., Rosen, G. E., and Amaral-Zettler, L. A. (2012). “Microbial diversity and potential pathogens in ornamental fish aquarium water.PLoS One, 7(9), e39971.

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., Ferreira, A. J., and 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.

Schatz, M. C., and Phillippy, A. M. (2012). “The rise of a digital immune system.Giga Sci, 1.

Schatz, M. C., and Phillippy, A. M. (2012). “The rise of a digital immune system.Giga Sci, 1.

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., and Hide, W. (2012). “Toward interoperable bioscience data.Nat Genet, 44(2), 121-6.

Salzberg, S. L., Phillippy, A. M., Zimin, A., Puiu, D., Magoc, T., and Koren, S. (2012). “GAGE: a critical evaluation of genome assemblies and assembly algorithms.Genome Res, 22.

Rosa, P. S., Brooks, J. P., Deych, E., Boone, E. L., Edwards, D. J., Wang, Q., Sodergren, E., Weinstock, G., and Shannon, W. D. (2012). “Hypothesis testing and power calculations for taxonomic-based human microbiome data.PLoS One, 7.

Rosa, P. S., Brooks, J. P., Deych, E., Boone, E. L., Edwards, D. J., Wang, Q., Sodergren, E., Weinstock, G., and Shannon, W. D. (2012). “Hypothesis testing and power calculations for taxonomic-based human microbiome data.PLoS One, 7.

Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., and Zhang, F. (2012). “A metagenome-wide association study of gut microbiota in type 2 diabetes.Nature, 490.

Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., and Boursnell, C. (2012). “The Pfam protein families database.Nucleic Acids Res, 40.

Peng, Y., Leung, H. C. M., Yiu, S. M., and Chin, F. Y. L. (2012). “IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.Bioinforma Oxf Engl, 28.

Pell, J., Hintze, A., Canino-Koning, R., Howe, A., Tiedje, J. M., and Brown, C. T. (2012). “Scaling metagenome sequence assembly with probabilistic de Bruijn graphs.Proc Natl Acad Sci U S A, 109.

Ozok, A. R., Persoon, I. F., Huse, S. M., Keijser, B. J., Wesselink, P. R., Crielaard, W., and 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), 530-41.

Ochiana, S. O., Gustafson, A., Bland, N. D., Wang, C., Russo, M. J., Campbell, R. K., and 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), 2582-4.

Nelson, D. E., Dong, Q., Pol, B. V. D., Toh, E., Fan, B., Katz, B. P., Mi, D., Rong, R., Weinstock, G. M., Sodergren, E., and Fortenberry, J. D. (2012). “Bacterial communities of the Coronal Sulcus and Distal Urethra of adolescent males.PLoS One, 7.

Namiki, T., Hachiya, T., Tanaka, H., and Sakakibara, Y. (2012). “MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.Nucleic Acids Res, 40.

Mende, D. R., Waller, A. S., Sunagawa, S., Järvelin, A. I., Chan, M. M., and Arumugam, M. (2012). “Assessment of metagenomic assembly using simulated next generation sequencing data.PLoS One, 7.

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

McCliment, E. A., Nelson, C. E., Carlson, C. A., Alldredge, A. L., Witting, J., and Amaral-Zettler, L. A. (2012). “An all-taxon microbial inventory of the Moorea coral reef ecosystem.ISME J, 6.

McCliment, E. A., Nelson, C. E., Carlson, C. A., Alldredge, A. L., Witting, J., and Amaral-Zettler, L. A. (2012). “An all-taxon microbial inventory of the Moorea coral reef ecosystem.ISME J, 6(2), 309-19.

Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G., and Neufeld, J. D. (2012). “PANDAseq: paired-end assembler for illumina sequences.BMC Bioinformatics, 13.

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., and Hibberd, P. L. (2012). “Gut microbial colonisation in premature neonates predicts neonatal sepsis.Arch Dis Child Fetal Neonatal Ed, 97(6), F456-62.

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., and 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).

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

Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., and Yuan, J. (2012). “SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.GigaSci, 1.

Luo, C., Tsementzi, D., Kyrpides, N. C., and Konstantinidis, K. T. (2012). “Individual genome assembly from complex community short-read metagenomic datasets.ISME J, 6.

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., and Stanton, T. B. (2012). “In-feed antibiotic effects on the swine intestinal microbiome.Proc Natl Acad Sci U S A, 109(5), 1691-6.

Light, J. E., Hafner, J. C., Upham, N. S., and Reddington, E. (2012). “Conservation Genetics of Kangaroo Mice, Genus Microdipodops.Journal of Mammalian Evolution, 10.1007/s10914-012-9193-2.

Lasek-Nesselquist, E. (2012). “A mitogenomic re-evaluation of the bdelloid phylogeny and relationships among the Syndermata.PLoS One, 7(8), e43554.

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

Karr, J. R., Sanghvi, J. C., Macklin, D. N., Gutschow, M. V., Jacobs, J. M., and Bolival, B. (2012). “A whole-cell computational model predicts phenotype from genotype.Cell, 150.

Karr, J. R., Sanghvi, J. C., Macklin, D. N., Gutschow, M. V., Jacobs, J. M., and Bolival, B. (2012). “A whole-cell computational model predicts phenotype from genotype.Cell, 150.

Iverson, V., Morris, R. M., Frazar, C. D., Berthiaume, C. T., Morales, R. L., and Armbrust, E. V. (2012). “Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota.Science, 335.

Huse, S. M., Ye, Y., Zhou, Y., and Fodor, A. A. (2012). “A core human microbiome as viewed through 16S rRNA sequence clusters.PLoS One, 7(6), e34242.

Gribble, K. E., and 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.

Gobet, A., Boer, S. I., Huse, S. M., van Beusekom, J. E., Quince, C., Sogin, M. L., Boetius, A., and Ramette, A. (2012). “Diversity and dynamics of rare and of resident bacterial populations in coastal sands.ISME J, 6(3), 542-53.

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., and Field, D. (2012). “Defining seasonal marine microbial community dynamics.ISME J, 6(2), 298-308.

Fuchsman, C. A., Staley, J. T., Oakley, B. B., Kirkpatrick, J. B., and Murray, J. W. (2012). “Free-living and aggregate-associated Planctomycetes in the Black Sea.Fems Microbiol Ecol, 80.

Freitas, S., Hatosy, S., Fuhrman, J. A., Huse, S. M., Mark Welch, D. B., Sogin, M. L., and Martiny, A. C. (2012). “Global distribution and diversity of marine Verrucomicrobia.ISME J, 6(8), 1499-505.

Fischer, A. H. L., and Smith, J. (2012). “Evo-devo in the era of gene regulatory networks.Integr Comp Biol, 52(6), 842-9.

Finkel, O. M., Burch, A. Y., Elad, T., Huse, S. M., Lindow, S. E., Post, A. F., and 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), 6187-93.

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

Fethers, K., Twin, J., Fairley, C. K., Fowkes, F. J. I., Garland, S. M., Fehler, G., Morton, A. M., Hocking, J. S., Tabrizi, S. N., and Bradshaw, C. S. (2012). “Bacterial vaginosis (BV) candidate bacteria: Associations with BV and behavioural practices in sexually-experienced and inexperienced women.PLoS One, 7.

Duyzend, M. H., Clark, C. T., Simmons, S. L., Johnson, W. B., Larson, A. M., Leconte, A. M., Wills, A. W., Ginder-Vogel, M., Wilhelm, A. K., Czechowicz, J. A., and Alberg, D. G. (2012). “Synthesis and evaluation of substrate analogue inhibitors of trypanothione reductase.J Enzyme Inhib Med Chem, 27(6), 784-94.

Dupont, C. L., Rusch, D. B., Yooseph, S., Lombardo, M.-J., Alexander Richter, R., and Valas, R. (2012). “Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.ISME J, 6.

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

Crump, B. C., Amaral-Zettler, L. A., and Kling, G. W. (2012). “Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils.ISME J, 6(9), 1629-39.

Cohen, C. R., Lingappa, J. R., Baeten, J. M., Ngayo, M. O., Spiegel, C. A., Hong, T., Donnell, D., Celum, C., Kapiga, S., Delany, S., and Bukusi, E. A. (2012). “Bacterial vaginosis associated with increased risk of female-to-male HIV-1 transmission: a prospective cohort analysis among African couples.PLoS Med, 9.

Chapman, M., and Alliegro, M. C. (2012). “The karyomastigont as an evolutionary seme.Q Rev Biol, 87(4), 315-24.

Chandsawangbhuwana, C., Shi, L. Z., Zhu, Q., Alliegro, M. C., and Berns, M. W. (2012). “High-throughput optofluidic system for the laser microsurgery of oocytes.J Biomed Opt, 17(1), 015001.

Breier, J. A., Gomez-Ibanez, D., Reddington, E., Huber, J. A., and 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.

Brandt, B. W., Bonder, M. J., Huse, S. M., and Zaura, E. (2012). “TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage.Nucleic Acids Res, 40(Web Server issue), W82-7.

Bowen, J. L., Morrison, H. G., Hobbie, J. E., and Sogin, M. L. (2012). “Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates.ISME J, 6(11), 2014-23.

Boisvert, S., Raymond, F., Godzaridis, E., Laviolette, F., and Corbeil, J. (2012). “Ray Meta: scalable de novo metagenome assembly and profiling.Genome Biol, 13.

Beg, Q. K., Zampieri, M., Klitgord, N., Collins, S. B., Altafini, C., Serres, M. H., and 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), 7132-49.

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., and Kulikov, A. S. (2012). “SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.J Comput Biol J Comput Mol Cell Biol, 19.

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., and Belkin, S. (2012). “Microbial rhodopsins on leaf surfaces of terrestrial plants.Environ Microbiol, 14(1), 140-6.

Arkhipova, I. R., Batzer, M. A., Brosius, J., Feschotte, C., Moran, J. V., Schmitz, J., and Jurka, J. (2012). “Genomic impact of eukaryotic transposable elements.Mob DNA, 3(1), 19.

Amend, A. S., Oliver, T. A., Amaral-Zettler, L. A., Boetius, A., Fuhrman, J. A., Horner-Devine, M. C., Huse, S. M., Mark Welch, D. B., Martiny, A. C., Ramette, A., Zinger, L., Sogin, M. L., and Martiny, J. B. H. (2012). “Macroecological patterns of marine bacteria on a global scale.Journal of Biogeography, 40(4), 800-811.

Amaral-Zettler, L. A. (2012). “Eukaryotic diversity at pH extremes.Front Microbiol, 3, 441.

Alliegro, M. C., Hartson, S., and 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), 6702-13.

 

2011

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

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., and 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), 415-20.

Yilmaz, P., Gilbert, J. A., Knight, R., Amaral-Zettler, L. A., Karsch-Mizrachi, I., Cochrane, G., Nakamura, Y., Sansone, S. A., Glockner, F. O., and Field, D. (2011). “The genomic standards consortium: bringing standards to life for microbial ecology.ISME J, 5(10), 1565-7.

Yelton, A. P., Thomas, B. C., Simmons, S. L., Wilmes, P., Zemla, A., Thelen, M. P., Justice, N., and 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.

Xia, L. C., Steele, J. A., Cram, J. A., Cardon, Z. G., Simmons, S. L., Vallino, J. J., Fuhrman, J. A., and 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.

White, J., Gilbert, J., Hill, G., Hill, E., Huse, S. M., Weightman, A. J., and 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), 4527-38.

Valm, A. M., Mark Welch, J. L., Rieken, C. W., Hasegawa, Y., Sogin, M. L., Oldenbourg, R., Dewhirst, F. E., and 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), 4152-7.

Sul, W. J., Cole, J. R., Jesus Eda, C., Wang, Q., Farris, R. J., Fish, J. A., and 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), 14637-42.

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

Smith, H. A., Snell, T. W., Serra, M., Hecox-Lea, B., and Mark Welch, D. (2011). “Molecular evolution of the membrane associated progesterone receptor within the Brachionus plicatilis (Rotifera) cryptic species complex.Hydrobiolgia (662), 99-106.

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

Rodrigues, J. L., Serres, M. H., and 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), 5352-60.

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., and Thomas, H. (2011). “Active submarine eruption of boninite in the northeastern Lau Basin.Nature Geoscience, 4(11), 799-806.

Ravel, J., Gajer, P., Abdo, Z., Schneider, G. M., Koenig, S. S., McCulle, S. L., Karlebach, S., Gorle, R., Russell, J., Tacket, C. O., Brotman, R. M., Davis, C. C., Ault, K., Peralta, L., and Forney, L. J. (2011). “Vaginal microbiome of reproductive-age women.Proc Natl Acad Sci U S A, 108.

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

Pollastri, M. P., and Campbell, R. K. (2011). “Target repurposing for neglected diseases.Future Med Chem, 3(10), 1307-15.

Piwowar, H. A., Vision, T. J., and Whitlock, M. C. (2011). “Data archiving is a good investment.Nature, 473.

Piwowar, H. A., Vision, T. J., and Whitlock, M. C. (2011). “Data archiving is a good investment.Nature, 473.

Pignatelli, M., and Moya, A. (2011). “Evaluating the fidelity of de novo short read metagenomic assembly using simulated data.PLoS One, 6.

Perry, D. A., Morrison, H. G., and Adam, R. D. (2011). “Optical map of the genotype A1 WB C6 Giardia lamblia genome isolate.Mol Biochem Parasitol, 180(2), 112-4.

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

Oleksiak, M. F., Karchner, S. I., Jenny, M. J., Franks, D. G., Mark Welch, D. B., and 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.

Nuzzio, D. B., Zettler, E. R., Aguilera, A., and 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), 1984-9.

Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D., and Bertilsson, S. (2011). “A guide to the natural history of freshwater lake bacteria.Microbiol Mol Biol Rev, 75.

Nelson, C. E., Alldredge, A. L., McCliment, E. A., Amaral-Zettler, L. A., and 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), 1374-87.

Nalbantoglu, O. U., Way, S. F., Hinrichs, S. H., and Sayood, K. (2011). “RAIphy: phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles.BMC Bioinformatics, 12.

Morowitz, M. J., Denef, V. J., Costello, E. K., Thomas, B. C., Poroyko, V., and Relman, D. A. (2011). “Strain-resolved community genomic analysis of gut microbial colonization in a premature infant.Proc Natl Acad Sci U S A, 108.

Mackey, K. R. M., Bristow, L., Parks, D. R., Altabet, M. A., Post, A. F., and 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.

Mackelprang, R., Waldrop, M. P., DeAngelis, K. M., David, M. M., Chavarria, K. L., and Blazewicz, S. J. (2011). “Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.Nature, 480.

Kamennaya, N. A., and Post, A. F. (2011). “Characterization of cyanate metabolism in marine Synechococcus and Prochlorococcus spp.Appl Environ Microbiol, 77(1), 291-301.

Hess, M., Sczyrba, A., Egan, R., Kim, T.-W., Chokhawala, H., and Schroth, G. (2011). “Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.Science, 331.

Heilbronner, S., Holden, M. T. G., Tonder, A., Geoghegan, J. A., Foster, T. J., and Parkhill, J. (2011). “Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors.FEMS Microbiol Lett, 322.

Gribble, K. E., Snell, T. W., and 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.

Gladyshev, E. A., and Arkhipova, I. R. (2011). “A widespread class of reverse transcriptase-related cellular genes.Proc Natl Acad Sci U S A, 108(51), 20311-6.

Gilbert, J. A., and Dupont, C. L. (2011). “Microbial metagenomics: beyond the genome.Ann Rev Mar Sci, 3.

Ghai, R., Rodriguez-Valera, F., McMahon, K. D., Toyama, D., Rinke, R., and Cristina Souza De Oliveira, T. (2011). “Metagenomics of the water column in the pristine upper course of the Amazon river.PLoS One, 6.

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

Garbuz, D. G., Yushenova, I. A., Zatsepina, O. G., Przhiboro, A. A., Bettencourt, B. R., and 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.

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

Finkel, O. M., Burch, A. Y., Lindow, S. E., Post, A. F., and Belkin, S. (2011). “Geographical location determines the population structure in phyllosphere microbial communities of a salt-excreting desert tree.Appl Environ Microbiol, 77(21), 7647-55.

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., and Wooley, J. (2011). “The Genomic Standards Consortium.PLoS Biol, 9(6), e1001088.

Fethers, K. A., Fairley, C. K., Morton, A., Hocking, J. S., Fehler, G., Kennedy, L. J., and Bradshaw, C. S. (2011). “Low incidence of bacterial vaginosis in cohort of young Australian women.Sex Transm Dis, 38.

Eren, A. M., Zozaya, M., Taylor, C. M., Dowd, S. E., Martin, D. H., and 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.

Eren, A. M., Zozaya, M., Taylor, C. M., Dowd, S. E., Martin, D. H., and 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.

Dong, Q., Nelson, D. E., Toh, E., Diao, L., Gao, X., Fortenberry, J. D., and Pol, B. (2011). “The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens.PLoS One, 6.

Crielaard, W., Zaura, E., Schuller, A. A., Huse, S. M., Montijn, R. C., and 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.

Chou, S. H., Feske, S. K., Simmons, S. L., Konigsberg, R. G., Orzell, S. C., Marckmann, A., Bourget, G., Bauer, D. J., De Jager, P. L., Du, R., Arai, K., Lo, E. H., and Ning, M. M. (2011). “Elevated peripheral neutrophils and matrix metalloproteinase 9 as biomarkers of functional outcome following subarachnoid hemorrhage.Transl Stroke Res, 2(4), 600-7.

Charuvaka, A., and Rangwala, H. (2011). “Evaluation of short read metagenomic assembly.BMC Genomics, 12.

Bowen, J. L., Ward, B. B., Morrison, H. G., Hobbie, J. E., Valiela, I., Deegan, L. A., and Sogin, M. L. (2011). “Microbial community composition in sediments resists perturbation by nutrient enrichment.ISME J, 5(9), 1540-8.

Botzman, M., and Margalit, H. (2011). “Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles.Genome Biol, 12.

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

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., and 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), 8188-94.

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

Alliegro, M. C. (2011). “The centrosome and spindle as a ribonucleoprotein complex.Chromosome Res, 19(3), 367-76.

Alliegro, M. C. (2011). “The Nucleolinus: A disappearing, forgotten and (maybe) misnamed organelle.Commun Integr Biol, 4(2), 147-9.

Akerman, N. H., Price, R. E., Pichler, T., and Amend, J. P. (2011). “Energy sources for chemolithotrophs in an arsenic- and iron-rich shallow-sea hydrothermal system.Geobiology, 9(5), 436-45.

Agogue, H., Lamy, D., Neal, P. R., Sogin, M. L., and Herndl, G. J. (2011). “Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing.Mol Ecol, 20(2), 258-74.

Adam, T. C., Schmitt, R. J., Holbrook, S. J., Brooks, A. J., Edmunds, P. J., and Carpenter, R. C. (2011). “Herbivory, connectivity, and ecosystem resilience: response of a coral reef to a large-scale perturbation.PLoS One, 6.

Adam, T. C., Schmitt, R. J., Holbrook, S. J., Brooks, A. J., Edmunds, P. J., and Carpenter, R. C. (2011). “Herbivory, connectivity, and ecosystem resilience: response of a coral reef to a large-scale perturbation.PLoS One, 6.

 

2010

Zozaya-Hinchliffe, M., Lillis, R., Martin, D. H., and Ferris, M. J. (2010). “Quantitative PCR assessments of bacterial species in women with and without bacterial vaginosis.J Clin Microbiol, 48.

Wernegreen, J. J., Kauppinen, S. N., and Degnan, P. H. (2010). “Slip into something more functional: selection maintains ancient frameshifts in homopolymeric sequences.Mol Biol Evol, 27(4), 833-9.

Wankel, S. D., Chen, Y., Kendall, C., Post, A. F., and 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.

Vieira-Silva, S., and Rocha, E. P. (2010). “The systemic imprint of growth and its uses in ecological (meta)genomics.PLoS Genet, 6.

Vieira-Silva, S., and Rocha, E. P. (2010). “The systemic imprint of growth and its uses in ecological (meta)genomics.PLoS Genet, 6.

Theroux, S. M., D’Andrea, W. D., Toney, J., Amaral-Zettler, L. A., and 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.

Smith, J. L., Barrett, J. E., Tusnady, G., Rejto, L., and Cary, S. C. (2010). “Resolving environmental drivers of microbial community structure in Antarctic soils.Antarctic Science, 22(6), 673-680.

Smith, H. A., Mark Welch, D. B., and Snell, T. W. (2010). “Molecular evolution of the membrane associated progesterone receptor in the Brachionus plicatilis (Rotifera, Monogononta) species complex.Hydrobiologia, 662(1), 99-106.

Schrenk, M. O., Huber, J. A., and Edwards, K. J. (2010). “Microbial provinces in the subseafloor.Ann Rev Mar Sci, 2(1), 279-304.

Price, L. B., Liu, C. M., Johnson, K. E., Aziz, M., Lau, M. K., Bowers, J., Ravel, J., Keim, P. S., Serwadda, D., Wawer, M. J., and Gray, R. H. (2010). “The effects of circumcision on the penis microbiome.PLoS One, 5.

Parfrey, L. W., Grant, J., Tekle, Y. I., Lasek-Nesselquist, E., Morrison, H. G., Sogin, M. L., Patterson, D. J., and Katz, L. A. (2010). “Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life.Syst Biol, 59(5), 518-33.

Olins, A. L., Rhodes, G., Mark Welch, D. B., Zwerger, M., and Olins, D. E. (2010). “Lamin B receptor Multi-tasking at the nuclear envelope.Nucleus-Austin, 1, 53-70.

Nelson, D. E., Pol, B., Dong, Q., Revanna, K. V., Fan, B., Easwaran, S., Sodergren, E., Weinstock, G. M., Diao, L., and Fortenberry, J. D. (2010). “Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection.PLoS One, 5.

Morf, L., Spycher, C., Rehrauer, H., Fournier, C. A., Morrison, H. G., and 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), 1566-76.

McLellan, S. L., Huse, S. M., Mueller-Spitz, S. R., Andreishcheva, E. N., and Sogin, M. L. (2010). “Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent.Environ Microbiol, 12(2), 378-92.

Ling, Z., Kong, J., Liu, F., Zhu, H., Chen, X., Wang, Y., Li, L., Nelson, K. E., Xia, Y., and Xiang, C. (2010). “Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis.BMC Genomics, 11.

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., and Borisy, G. G. (2010). “Phosphorylation controls autoinhibition of cytoplasmic linker protein-170.Mol Biol Cell, 21(15), 2661-73.

Lasek-Nesselquist, E., Welch, D. M., and 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), 1063-74.

Keeling, P. J., Corradi, N., Morrison, H. G., Haag, K. L., Ebert, D., Weiss, L. M., Akiyoshi, D. E., and Tzipori, S. (2010). “The reduced genome of the parasitic microsporidian Enterocytozoon bieneusi lacks genes for core carbon metabolism.Genome Biol Evol, 2, 304-9.

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., and 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.

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., and 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.

Huse, S. M., Welch, D. M., Morrison, H. G., and Sogin, M. L. (2010). “Ironing out the wrinkles in the rare biosphere through improved OTU clustering.Environ Microbiol, 12(7), 1889-98.

Huber, J. A., Cantin, H. V., Huse, S. M., Mark Welch, D. B., Sogin, M. L., and Butterfield, D. A. (2010). “Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts.FEMS Microbiol Ecol, 73(3), 538-49.

Hasegawa, Y., Welch, J. L. M., Valm, A. M., Rieken, C., Sogin, M. L., and 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.

Gribble, K. E., Snell, T. W., and Mark Welch, D. B. (2010). “Gene and protein structure of the mate recognition protein gene family in Brachionus manjavacas (Rotifera).Hydrobiologia, 662(1), 35-42.

Gladyshev, E. A., and 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.

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

Gillor, O., Hadas, O. R. A., Post, A. F., and 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.

Gilg, I. C., Amaral-Zettler, L. A., Countway, P. D., Moorthi, S., Schnetzer, A., and 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.

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., and 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), 14020-5.

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., and 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), 1981-8.

Dudley, J. T., and Butte, A. J. (2010). “In silico research in the era of cloud computing.Nat Biotechnol, 28.

Dudley, J. T., and Butte, A. J. (2010). “In silico research in the era of cloud computing.Nat Biotechnol, 28.

Davidsen, T., Beck, E., Ganapathy, A., Montgomery, R., Zafar, N., and Yang, Q. (2010). “The comprehensive microbial resource.Nucleic Acids Res, 38.

Chafee, M. E., Funk, D. J., Harrison, R. G., and Bordenstein, S. R. (2010). “Lateral phage transfer in obligate intracellular bacteria (wolbachia): verification from natural populations.Mol Biol Evol, 27(3), 501-5.

Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., and Gordon, J. I. (2010). “QIIME allows analysis of high-throughput community sequencing data.Nat Methods, 7.

Brotman, R. M., Klebanoff, M. A., Nansel, T. R., Yu, K. F., Andrews, W. W., Zhang, J., and Schwebke, J. R. (2010). “Bacterial vaginosis assessed by gram stain and diminished colonization resistance to incident gonococcal, chlamydial, and trichomonal genital infection.J Infect Dis, 202.

Brazelton, W. J., Ludwig, K. A., Sogin, M. L., Andreishcheva, E. N., Kelley, D. S., Shen, C. C., Edwards, R. L., and 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), 1612-7.

Bordenstein, S. R., Brothers, C., Wolfe, G., Bahr, M., Minckley, R. L., Clark, M. E., Wernegreen, J. J., Bordenstein, S. R., Reznikoff, W. S., and 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.

Boisvert, S., Laviolette, F., and Corbeil, J. (2010). “Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.J Comput Biol, 17.

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., and Beja, O. (2010). “Comparative community genomics in the Dead Sea: an increasingly extreme environment.ISME J, 4(3), 399-407.

Alliegro, M. A., Henry, J. J., and 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), 13718-23.

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

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

 

2009

Zaura, E., Keijser, B. J., Huse, S. M., and Crielaard, W. (2009). “Defining the healthy “core microbiome” of oral microbial communities.BMC Microbiol, 9, 259.

Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., and Ivanova, N. N. (2009). “A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.Nature, 462.

Witek, A., Herlyn, H., Ebersberger, I., Mark Welch, D. B., and Hankeln, T. (2009). “Support for the monophyletic origin of Gnathifera from phylogenomics.Mol Phylogenet Evol, 53(3), 1037-41.

Wilmes, P., Simmons, S. L., Denef, V. J., and Banfield, J. F. (2009). “The dynamic genetic repertoire of microbial communities.FEMS Microbiol Rev, 33(1), 109-32.

Whitman, C. T., Wirth, T. E., Meselson, M., Nissen, S. E., Juma, C., and Daley, G. (2009). “Your inbox, Mr President.Nature, 457(7227), 258-61.

Wernegreen, J. J., and Wheeler, D. E. (2009). “Remaining flexible in old alliances: functional plasticity in constrained mutualisms.DNA Cell Biol, 28(8), 371-82.

Wernegreen, J. J., Kauppinen, S. N., Brady, S. G., and 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.

Van Doninck, K., Mandigo, M. L., Hur, J. H., Wang, P., Guglielmini, J., Milinkovitch, M. C., Lane, W. S., and Meselson, M. (2009). “Phylogenomics of unusual histone H2A Variants in Bdelloid rotifers.PLoS Genet, 5(3), e1000401.

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., and Gordon, J. I. (2009). “A core gut microbiome in obese and lean twins.Nature, 457(7228), 480-4.

Turanov, A. A., Lobanov, A. V., Fomenko, D. E., Morrison, H. G., Sogin, M. L., Klobutcher, L. A., Hatfield, D. L., and Gladyshev, V. N. (2009). “Genetic code supports targeted insertion of two amino acids by one codon.Science, 323(5911), 259-61.

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

Snell, T. W., Shearer, T. L., Smith, H. A., Kubanek, J., Gribble, K. E., and Mark Welch, D. B. (2009). “Genetic determinants of mate recognition in Brachionus manjavacas (Rotifera).BMC Biol, 7, 60.

Smith, J., and 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), 18291-6.

Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J. M., and Birol, İ. (2009). “ABySS: a parallel assembler for short read sequence data.Genome Res, 19.

Serres, M. H., Kerr, A. R., McCormack, T. J., and Riley, M. (2009). “Evolution by leaps: gene duplication in bacteria.Biol Direct, 4, 46.

Schober, J. M., Cain, J. M., Komarova, Y. A., and Borisy, G. G. (2009). “Migration and actin protrusion in melanoma cells are regulated by EB1 protein.Cancer Lett, 284(1), 30-6.

Scanlan, D. J., Ostrowski, M., Mazard, S., Dufresne, A., Garczarek, L., Hess, W. R., Post, A. F., Hagemann, M., Paulsen, I., and Partensky, F. (2009). “Ecological genomics of marine picocyanobacteria.Microbiol Mol Biol Rev, 73(2), 249-99.

Paytan, A., Mackey, K. R. M., Chen, Y., Lima, I. D., S.C., D., Mahowald, N., Labiosa, R., and Post, A. F. (2009). “Toxicity of atmospheric aerosols on marine phytoplankton.Proc Natl Acad Sci U S A, 106(12), 4601-5.

Nahum, L. A., Goswami, S., and Serres, M. H. (2009). “Protein families reflect the metabolic diversity of organisms and provide support for functional prediction.Physiol Genomics, 38(3), 250-60.

Mackey, K. R. M., Paytan, A., Rivlin, T., and 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.

Lazarevic, V., Whiteson, K., Huse, S. M., Hernandez, D., Farinelli, L., Osteras, M., Schrenzel, J., and Francois, P. (2009). “Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.J Microbiol Methods, 79(3), 266-71.

Lasek-Nesselquist, E., Mark Welch, D. B., Thompson, R. C., Steuart, R. F., and Sogin, M. L. (2009). “Genetic exchange within and between assemblages of Giardia duodenalis.J Eukaryot Microbiol, 56(6), 504-18.

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., and 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), 1108-15.

Kozul, C. D., Ely, K. H., Enelow, R. I., and Hamilton, J. W. (2009). “Low-dose arsenic compromises the immune response to influenza A infection in vivo.Environ Health Perspect, 117(9), 1441-7.

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., and Tiedje, J. M. (2009). “Comparative systems biology across an evolutionary gradient within the Shewanella genus.Proc Natl Acad Sci U S A, 106(37), 15909-14.

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., and Akhmanova, A. (2009). “Mammalian end binding proteins control persistent microtubule growth.J Cell Biol, 184(5), 691-706.

Kim, T. K., Thomas, S. M., Ho, M., Sharma, S., Reich, C. I., Frank, J. A., Yeater, K. M., Biggs, D. R., Nakamura, N., Stumpf, R., Leigh, S. R., Tapping, R. I., Blanke, S. R., Slauch, J. M., Gaskins, H. R., Weisbaum, J. S., Olsen, G. J., Hoyer, L. L., and Wilson, B. A. (2009). “Heterogeneity of vaginal microbial communities within individuals.J Clin Microbiol, 47.

Kenney, D. E., and Borisy, G. G. (2009). “Thomas Hunt Morgan at the marine biological laboratory: naturalist and experimentalist.Genetics, 181(3), 841-6.

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

Hur, J. H., Van Doninck, K., Mandigo, M. L., and Meselson, M. (2009). “Degenerate tetraploidy was established before bdelloid rotifer families diverged.Mol Biol Evol, 26(2), 375-83.

Huber, J. A., Morrison, H. G., Huse, S. M., Neal, P. R., Sogin, M. L., and Mark Welch, D. B. (2009). “Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure.Environ Microbiol, 11(5), 1292-302.

Gribble, K. E., Anderson, D. M., and 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.

Gray, R. H., Kigozi, G., Serwadda, D., Makumbi, F., Nalugoda, F., Watya, S., Moulton, L., Chen, M. Z., Sewankambo, N. K., Kiwanuka, N., Sempijja, V., Lutalo, T., Kagayii, J., Wabwire-Mangen, F., Ridzon, R., Bacon, M., and Wawer, M. J. (2009). “The effects of male circumcision on female partners’ genital tract symptoms and vaginal infections in a randomized trial in Rakai, Uganda.Am J Obstet Gynecol, 200.

Gladyshev, E. A., and Arkhipova, I. R. (2009). “Rotifer rDNA-specific R9 retrotransposable elements generate an exceptionally long target site duplication upon insertion.Gene, 448(2), 145-50.

Gladyshev, E. A., and Arkhipova, I. R. (2009). “A single-copy IS5-like transposon in the genome of a bdelloid rotifer.Mol Biol Evol, 26(8), 1921-9.

Gilbert, J. A., Field, D., Swift, P., Newbold, L., Oliver, A., Smyth, T., Somerfield, P. J., Huse, S. M., and Joint, I. (2009). “The seasonal structure of microbial communities in the Western English Channel.Environ Microbiol, 11(12), 3132-9.

Fethers, K. A., Fairley, C. K., Morton, A., Hocking, J. S., Hopkins, C., Kennedy, L. J., Fehler, G., and Bradshaw, C. S. (2009). “Early sexual experiences and risk factors for bacterial vaginosis.J Infect Dis, 200.

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

Dick, G. J., Andersson, A. F., Baker, B. J., Simmons, S. L., Thomas, B. C., and Yelton, A. P. (2009). “Community-wide analysis of microbial genome sequence signatures.Genome Biol, 10.

Claessens, M., Wickham, S. A., Post, A. F., and Reuter, M. (2009). “A paradox of the ciliates? High ciliate diversity in a resource-poor environment.Marine Biology, 157(3), 483-494.

Chain, P. S. G., Grafham, D. V., Fulton, R. S., Fitzgerald, M. G., Hostetler, J., and Muzny, D. (2009). “Genomics. Genome project standards in a new era of sequencing.Science, 326.

Brazelton, W. J., Sogin, M. L., and Baross, J. A. (2009). “Multiple scales of diversification within natural populations of archaea in hydrothermal chimney biofilms.Environmental Microbiology Reports, 2(2), 236-42.

Barr, F. D., Krohmer, L. J., Hamilton, J. W., and 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.

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., and 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), D526-30.

Antonopoulos, D. A., Huse, S. M., Morrison, H. G., Schmidt, T. M., Sogin, M. L., and Young, V. B. (2009). “Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation.Infect Immun, 77(6), 2367-75.

Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W., and 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.

Alliegro, M. C., and Satir, P. (2009). “Origin of the cilium: novel approaches to examine a centriolar evolution hypothesis.Methods Cell Biol, 94, 53-64.

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., and Tzipori, S. (2009). “Genomic survey of the non-cultivatable opportunistic human pathogen, Enterocytozoon bieneusi.PLoS Pathog, 5(1), e1000261.

Aberle, N., Hansen, T., Boettger-Schnack, R., Burmeister, A., Post, A. F., and 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.

 

2008

Zozaya-Hinchliffe, M., Martin, D. H., and Ferris, M. J. (2008). “Prevalence and abundance of uncultivated Megasphaera-like bacteria in the human vaginal environment.Appl Environ Microbiol, 74.

Zerbino, D. R., and Birney, E. (2008). “Velvet: algorithms for de novo short read assembly using de Bruijn graphs.Genome Res, 18.

Ye, S., MacEachran, D. P., Hamilton, J. W., O’Toole, G. A., and 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), C807-18.

Wu, M., and Eisen, J. A. (2008). “A simple, fast, and accurate method of phylogenomic inference.Genome Biol, 9.

Tamas, I., Wernegreen, J. J., Nystedt, B., Kauppinen, S. N., Darby, A. C., Gomez-Valero, L., Lundin, D., Poole, A. M., and 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), 14934-9.

Suga, K., Mark Welch, D. B., Tanaka, Y., Sakakura, Y., and 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.

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., and Holland, A. F. (2008). “The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs.Environ Health, 7 Suppl 2, S3.

Smith, J., Kraemer, E., Liu, H., Theodoris, C., and Davidson, E. (2008). “A spatially dynamic cohort of regulatory genes in the endomesodermal gene network of the sea urchin embryo.Dev Biol, 313(2), 863-75.

Smith, J., and Davidson, E. H. (2008). “A new method, using cis-regulatory control, for blocking embryonic gene expression.Dev Biol, 318(2), 360-5.

Smith, J., and 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), 20089-94.

Smith, J. (2008). “A protocol describing the principles of cis-regulatory analysis in the sea urchin.Nat Protoc, 3(4), 710-8.

Simmons, S. L., Dibartolo, G., Denef, V. J., Goltsman, D. S., Thelen, M. P., and 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.

Schostak, N., Pyatkov, K. I., Zelentsova, E., Arkhipova, I. R., Shagin, D., Shagina, I., Mudrik, E., Blintsov, A., Clark, I., Finnegan, D. J., and Evgen’ev, M. B. (2008). “Molecular dissection of Penelope transposable element regulatory machinery.Nucleic Acids Res, 36(8), 2522-9.

Santelli, C. M., Orcutt, B. N., Banning, E., Bach, W., Moyer, C. L., Sogin, M. L., Staudigel, H., and Edwards, K. J. (2008). “Abundance and diversity of microbial life in ocean crust.Nature, 453(7195), 653-6.

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., and 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 A Journal of Integrative Biology, 12(2), 151-156.

Rull, K., Hallast, P., Uuskula, L., Jackson, J., Punab, M., Salumets, A., Campbell, R. K., and 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.

Riley, M., Staley, J. T., Danchin, A., Wang, T. Z., Brettin, T. S., Hauser, L. J., Land, M. L., and Thompson, L. S. (2008). “Genomics of an extreme psychrophile, Psychromonas ingrahamii.BMC Genomics, 9(1), 210.

Palacios, C., Zettler, E., Amils, R., and Amaral-Zettler, L. (2008). “Contrasting microbial community assembly hypotheses: a reconciling tale from the Rio Tinto.PLoS One, 3(12), e3853.

Oakley, B. B., Fiedler, T. L., Marrazzo, J. M., and Fredricks, D. N. (2008). “Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis.Appl Environ Microbiol, 74.

Mark Welch, D. B., Mark Welch, J. L., and Meselson, M. (2008). “Evidence for degenerate tetraploidy in bdelloid rotifers.Proc Natl Acad Sci U S A, 105(13), 5145-9.

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

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., and Hamilton, J. W. (2008). “Laboratory diet profoundly alters gene expression and confounds genomic analysis in mouse liver and lung.Chem Biol Interact, 173(2), 129-40.

Keijser, B. J., Zaura, E., Huse, S. M., van der Vossen, J. M., Schuren, F. H., Montijn, R. C., ten Cate, J. M., and Crielaard, W. (2008). “Pyrosequencing analysis of the oral microflora of healthy adults.J Dent Res, 87(11), 1016-20.

Kamennaya, N. A., Chernihovsky, M., and Post, A. F. (2008). “The cyanate utilization capacity of marine unicellular Cyanobacteria.Limnology and Oceanography, 53(6), 2485-2494.

Jost, M. C., Hillis, D. M., Lu, Y., Kyle, J. W., Fozzard, H. A., and Zakon, H. H. (2008). “Toxin-resistant sodium channels: parallel adaptive evolution across a complete gene family.Mol Biol Evol, 25(6), 1016-24.

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

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

Gradman, R. J., and Reznikoff, W. S. (2008). “Tn5 synaptic complex formation: role of transposase residue W450.J Bacteriol, 190(4), 1484-7.

Gradman, R. J., Ptacin, J. L., Bhasin, A., Reznikoff, W. S., and Goryshin, I. Y. (2008). “A bifunctional DNA binding region in Tn5 transposase.Mol Microbiol, 67(3), 528-40.

Gladyshev, E. A., Meselson, M., and Arkhipova, I. R. (2008). “Massive horizontal gene transfer in bdelloid rotifers.Science, 320(5880), 1210-3.

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., and 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), 151-6.

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., and Tiedje, J. M. (2008). “Towards environmental systems biology of Shewanella.Nat Rev Microbiol, 6(8), 592-603.

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., and Partensky, F. (2008). “Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.Genome Biol, 9(5), R90.

Dimise, E. J., Widboom, P. F., and Bruner, S. D. (2008). “Structure elucidation and biosynthesis of fuscachelins, peptide siderophores from the moderate thermophile Thermobifida fusca.Proc Natl Acad Sci U S A, 105.

Dimise, E. J., Widboom, P. F., and Bruner, S. D. (2008). “Structure elucidation and biosynthesis of fuscachelins, peptide siderophores from the moderate thermophile Thermobifida fusca.Proc Natl Acad Sci U S A, 105.

Dethlefsen, L., Huse, S. M., Sogin, M. L., and 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.

Davey, J. C., Nomikos, A. P., Wungjiranirun, M., Sherman, J. R., Ingram, L., Batki, C., Lariviere, J. P., and 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), 165-72.

Claessens, M., Wickham, S. A., Post, A. F., and Reuter, M. (2008). “Ciliate community in the oligotrophic Gulf of Aqaba, Red Sea.Aquatic Microbial Ecology, 53(2), 181-190.

Amaral-Zettler, L. A., Rocca, J. D., Lamontagne, M. G., Dennett, M. R., and Gast, R. J. (2008). “Changes in microbial community structure in the wake of Hurricanes Katrina and Rita.Environ Sci Technol, 42(24), 9072-8.

Amaral-Zettler, L. A., Peplies, J., Ramette, A., Fuchs, B., Ludwig, W., and Glockner, F. O. (2008). “Proceedings of the international workshop on Ribosomal RNA technology, April 7-9, 2008, Bremen, Germany.Syst Appl Microbiol, 31(4), 258-68.

Alliegro, M. C., and Alliegro, M. A. (2008). “Centrosomal RNA correlates with intron-poor nuclear genes in Spisula oocytes.Proc Natl Acad Sci U S A, 105(19), 6993-7.

Alliegro, M. C. (2008). “The implications of centrosomal RNA.RNA Biol, 5(4), 198-200.

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., and Verlinde, C. L. (2008). “Genomic-scale prioritization of drug targets: the TDR Targets database.Nat Rev Drug Discov, 7(11), 900-7.

 

2007

Zhou, X., Brown, C. J., Abdo, Z., Davis, C. C., Hansmann, M. A., Joyce, P., Foster, J. A., and Forney, L. J. (2007). “Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women.ISME J, 1.

Winterberg, K. M., and Reznikoff, W. S. (2007). “Screening transposon mutant libraries using full-genome oligonucleotide microarrays.Methods Enzymol, 421, 110-25.

Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R. (2007). “Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.Appl Environ Microbiol, 73.

Van Roey, P., Pereira, B., Li, Z., Hiraga, K., Belfort, M., and Derbyshire, V. (2007). “A Pivotal, highly conserved aspartate in the Mtu recA intein is proximal to and functional at both termini.J Mol Biol, 367, 162-73.

Van Roey, P., Pereira, B., Li, Z., Hiraga, K., Belfort, M., and 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), 162-73.

Vaezeslami, S., Sterling, R., and Reznikoff, W. S. (2007). “Site-directed mutagenesis studies of tn5 transposase residues involved in synaptic complex formation.J Bacteriol, 189(20), 7436-41.

Suga, K., Mark Welch, D. B., Tanaka, Y., Sakakura, Y., and Hagiwara, A. (2007). “Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis.PLoS One, 2(7), e671.

Sommer, D. D., Delcher, A. L., Salzberg, S. L., and Pop, M. (2007). “Minimus: a fast, lightweight genome assembler.BMC Bioinformatics, 8.

Smith, J., Theodoris, C., and Davidson, E. H. (2007). “A gene regulatory network subcircuit drives a dynamic pattern of gene expression.Science, 318(5851), 794-7.

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

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., and 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), 9029-34.

Simmons, S. L., and Edwards, K. J. (2007). “Unexpected diversity in populations of the many-celled magnetotactic prokaryote.Environ Microbiol, 9(1), 206-15.

Simmons, S. L., Bazylinski, D. A., and Edwards, K. J. (2007). “Population dynamics of marine magnetotactic bacteria in a meromictic salt pond described with qPCR.Environ Microbiol, 9(9), 2162-74.

Sanogo, Y. O., Dobson, S. L., Bordenstein, S. R., and 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), 143-54.

Robbins, J. B., Stapleton, M., Stanger, M. J., Smith, D., Dansereau, J. T., Derbyshire, V., and Belfort, M. (2007). “Homing endonuclease I-TevIII: dimerization as a means to a double-strand break.Nucleic Acids Res, 35(5), 1589-600.

Ramette, A., and Tiedje, J. M. (2007). “Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution.Microb Ecol, 53.

Prabhu, A., Morrison, H. G., Martinez, C. R., 3rd, and Adam, R. D. (2007). “Characterisation of the subtelomeric regions of Giardia lamblia genome isolate WBC6.Int J Parasitol, 37(5), 503-13.

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

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

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., and Sogin, M. L. (2007). “Genomic minimalism in the early diverging intestinal parasite Giardia lamblia.Science, 317(5846), 1921-6.

Meselson, M., and Mark Welch, D. B. (2007). “Evolution. Stable heterozygosity?Science, 318(5848), 202-3.

Mavromatis, K., Ivanova, N., Barry, K., Shapiro, H., Goltsman, E., and McHardy, A. C. (2007). “Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.Nat Methods, 4.

Lo, N., Paraskevopoulos, C., Bourtzis, K., O’Neill, S. L., Werren, J. H., Bordenstein, S. R., and Bandi, C. (2007). “Taxonomic status of the intracellular bacterium Wolbachia pipientis.Int J Syst Evol Microbiol, 57(Pt 3), 654-7.

Kieft, R., Brand, V., Ekanayake, D. K., Sweeney, K., DiPaolo, C., Reznikoff, W. S., and 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.

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

Huse, S. M., Huber, J. A., Morrison, H. G., Sogin, M. L., and Mark Welch, D. B. (2007). “Accuracy and quality of massively-parrallel DNA pyrosequencing.Genome Biology, 8, R143.

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

Hu, Y., Phelan, V., Ntai, I., Farnet, C. M., Zazopoulos, E., and Bachmann, B. O. (2007). “Benzodiazepine biosynthesis in Streptomyces refuineus.Chem Biol, 14.

Hu, Y., Phelan, V., Ntai, I., Farnet, C. M., Zazopoulos, E., and Bachmann, B. O. (2007). “Benzodiazepine biosynthesis in Streptomyces refuineus.Chem Biol, 14.

Hegreness, M., and Meselson, M. (2007). “What did Sutton see? Thirty years of confusion over the chromosomal basis of Mendelism.Genetics, 176(4), 1939-44.

Gribble, K. E., Nolan, G., and 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.

Gladyshev, E. A., Meselson, M., and Arkhipova, I. R. (2007). “A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers.Gene, 390(1-2), 136-45.

Gladyshev, E. A., and Arkhipova, I. R. (2007). “Telomere-associated endonuclease-deficient Penelope-like retroelements in diverse eukaryotes.Proc Natl Acad Sci U S A, 104(22), 9352-7.

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

Fredricks, D. N., Fiedler, T. L., Thomas, K. K., Oakley, B. B., and Marrazzo, J. M. (2007). “Targeted PCR for detection of vaginal bacteria associated with bacterial vaginosis.J Clin Microbiol, 45.

Ekanayake, D. K., Mark Welch, D. B., Kieft, R., Hajduk, S., and 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), 818-22.

Edgcomb, V. P., Molyneaux, S. J., Boer, S., Wirsen, C. O., Saito, M., Atkins, M. S., Lloyd, K., and 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), 329-42.

Driscoll, M. E., Romine, M. F., Juhn, F. S., Serres, M. H., McCue, L. A., Beliaev, A. S., Fredrickson, J. K., and Gardner, T. S. (2007). “Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling.Genome Inform, 18, 287-98.

Czyz, A., Stillmock, K. A., Hazuda, D. J., and Reznikoff, W. S. (2007). “Dissecting Tn5 transposition using HIV-1 integrase diketoacid inhibitors.Biochemistry, 46(38), 10776-89.

Curcio, M. J., and Belfort, M. (2007). “The beginning of the end: links between ancient retroelements and modern telomerases.Proc Natl Acad Sci U S A, 104(22), 9107-8.

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

Clark, W. C. (2007). “Sustainability science: a room of its own.Proc Natl Acad Sci U S A, 104.

Clark, W. C. (2007). “Sustainability science: a room of its own.Proc Natl Acad Sci U S A, 104.

Chen, Y., Street, J., Golan, D., Post, A. F., and 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.

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

Bordenstein, S. R., and Werren, J. H. (2007). “Bidirectional incompatibility among divergent Wolbachia and incompatibility level differences among closely related Wolbachia in Nasonia.Heredity (Edinb), 99(3), 278-87.

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

Bordenstein, S. R. (2007). “Evolutionary genomics: transdomain gene transfers.Curr Biol, 17(21), R935-6.

Alliegro, M. C., and Alliegro, M. A. (2007). “Echinonectin is a Del-1-like molecule with regulated expression in sea urchin embryos.Gene Expr Patterns, 7(6), 651-6.

Aguilera, A., Zettler, E., Gomez, F., Amaral-Zettler, L. A., Rodriguez, N., and 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), 531-46.

Adams, C. D., Schnurr, B., Marko, J. F., and Reznikoff, W. S. (2007). “Pulling apart catalytically active Tn5 synaptic complexes using magnetic tweezers.J Mol Biol, 367(2), 319-27.

 

2006

Wendl, M. C. (2006). “A general coverage theory for shotgun DNA sequencing.J Comput Biol J Comput Mol Cell Biol, 13.

Wegener-Parfrey, L., Barbero, E., Lasser, B., Dunthorn, M., Bhattacharya, D., Patterson, D. J., and Katz, L. (2006). “Evaluating support for the current classification of eukaryotic diversity.PLOS Genetics, 2, 2062-73.

Suzuki, R., and Shimodaira, H. (2006). “Pvclust: an R package for assessing the uncertainty in hierarchical clustering.Bioinformatics, 22.

Steiniger, M., Metzler, J., and 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), 15552-62.

Steiniger, M., Adams, C. D., Marko, J. F., and Reznikoff, W. S. (2006). “Defining characteristics of Tn5 Transposase non-specific DNA binding.Nucleic Acids Res, 34(9), 2820-32.

Spieck, E., Hartwig, C., McCormack, I., Maixner, F., Wagner, M., and Lipski, A. (2006). “Selective enrichment and molecular characterization of a previously uncultured Nitrospira-like bacterium from activated sludge.Environ Microbiol, 8.

Sogin, M. L., Morrison, H. G., Huber, J. A., Mark Welch, D. B., Huse, S. M., Neal, P. R., Arrieta, J. M., and Herndl, G. J. (2006). “Microbial diversity in the deep sea and the underexplored “rare biosphere”.Proc Natl Acad Sci U S A, 103(32), 12115-20.

Slagter-Jager, J. G., Allen, G. S., Smith, D., Hahn, I. A., Frank, J., and 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), 9838-43.

Simmons, S. L., Bazylinski, D. A., and Edwards, K. J. (2006). “South-seeking magnetotactic bacteria in the Northern Hemisphere.Science, 311(5759), 371-4.

Silva, G. H., Belfort, M., Wende, W., and Pingoud, A. (2006). “From monomeric to homodimeric endonucleases and back: engineering novel specificity of LAGLIDADG enzymes.J Mol Biol, 361(4), 744-54.

Serres, M. H., and Riley, M. (2006). “Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions versus experiments.J Bacteriol, 188(13), 4601-9.

Schon, I., and Arkhipova, I. R. (2006). “Two families of non-LTR retrotransposons, Syrinx and Daphne, from the Darwinulid ostracod, Darwinula stevensoni.Gene, 371(2), 296-307.

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., and Wanner, B. L. (2006). “Escherichia coli K-12: a cooperatively developed annotation snapshot–2005.Nucleic Acids Res, 34(1), 1-9.

Reznikoff, W. S. (2006). “Tn5 transposition: a molecular tool for studying protein structure-function.Biochem Soc Trans, 34(Pt 2), 320-3.

Remsen, D. P., Norton, C., and Patterson, D. J. (2006). “Taxonomic informatics tools for the electronic Nomenclator Zoologicus.Biol Bull, 210(1), 18-24.

Penno, S., Lindell, D., and Post, A. F. (2006). “Diversity of Synechococcus and Prochlorococcus populations determined from DNA sequences of the N-regulatory gene ntcA.Environ Microbiol, 8(7), 1200-11.

Patterson, D. J., Remsen, D., Marino, W. A., and Norton, C. (2006). “Taxonomic indexing–extending the role of taxonomy.Syst Biol, 55(3), 367-73.

Paraskevopoulos, C., Bordenstein, S. R., Wernegreen, J. J., Werren, J. H., and Bourtzis, K. (2006). “Toward a Wolbachia multilocus sequence typing system: discrimination of Wolbachia strains present in Drosophila species.Curr Microbiol, 53(5), 388-95.

Murray, S., Hoppenrath, M., Preisfeld, A., Larsen, J., Yoshimatsu, S., Toriumi, S., and 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.

Mühling, M., Fuller, N. J., Somerfield, P. J., Post, A. F., Wilson, W. H., Scanlan, D. J., Joint, I., and 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.

Liu, Q., Derbyshire, V., Belfort, M., and Edgell, D. R. (2006). “Distance determination by GIY-YIG intron endonucleases: discrimination between repression and cleavage functions.Nucleic Acids Res, 34(6), 1755-64.

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., and Pace, N. R. (2006). “Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat.Appl Environ Microbiol, 72(5), 3685-95.

Hutchinson, L., Mustard, J., Gendrin, A., Fernandez Remolar, D., Amils, R., and Amaral-Zettler, L. (2006). “Finding Mineralogically Interesting Targets for Exploration from Spatially Coarse Visible and Near IR Spectra.Earth and Planetary Science Letters, 252, 201-14.

Huber, J. A., Johnson, H. P., Butterfield, D. A., and Baross, J. A. (2006). “Microbial life in ridge flank crustal fluids.Environ Microbiol, 8(1), 88-99.

Huber, J. A., Butterfield, D. A., and 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).

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

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

Check, E. (2006). “Treasure island: pinning down a model ecosystem.Nature, 439.

Check, E. (2006). “Treasure island: pinning down a model ecosystem.Nature, 439.

Cantarel, B. L., Morrison, H. G., and Pearson, W. (2006). “Exploring the relationship between sequence similarity and accurate phylogenetic trees.Mol Biol Evol, 23(11), 2090-100.

Bordenstein, S. R., Marshall, M. L., Fry, A. J., Kim, U., and Wernegreen, J. J. (2006). “The tripartite associations between bacteriophage, Wolbachia, and arthropods.PLoS Pathog, 2(5), e43.

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., and Hinrichs, K. U. (2006). “Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru.Proc Natl Acad Sci U S A, 103(10), 3846-51.

Beauregard, A., Chalamcharla, V. R., Piazza, C. L., Belfort, M., and 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), 709-22.

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., and Werren, J. H. (2006). “Multilocus sequence typing system for the endosymbiont Wolbachia pipientis.Appl Environ Microbiol, 72(11), 7098-110.

Baldo, L., Bordenstein, S., Wernegreen, J. J., and Werren, J. H. (2006). “Widespread recombination throughout Wolbachia genomes.Mol Biol Evol, 23(2), 437-49.

Bach, W., Edwards, K. J., Hayes, J. M., Huber, J. A., Sievert, S. M., and 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.

Arkhipova, I. R. (2006). “Distribution and phylogeny of Penelope-like elements in eukaryotes.Syst Biol, 55(6), 875-85.

Amaral-Zettler, L. A., Cole, J., Laatsch, A. D., Nerad, T. A., Anderson, O. R., and 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), 522-30.

Alliegro, M. C., Alliegro, M. A., and Palazzo, R. E. (2006). “Centrosome-associated RNA in surf clam oocytes.Proc Natl Acad Sci U S A, 103(24), 9034-8.

Adams, C. D., Schnurr, B., Skoko, D., Marko, J. F., and Reznikoff, W. S. (2006). “Tn5 transposase loops DNA in the absence of Tn5 transposon end sequences.Mol Microbiol, 62(6), 1558-68.

 

2005

Winterberg, K. M., Luecke, J., Bruegl, A. S., and Reznikoff, W. S. (2005). “Phenotypic screening of Escherichia coli K-12 Tn5 insertion libraries, using whole-genome oligonucleotide microarrays.Appl Environ Microbiol, 71(1), 451-9.

Wernegreen, J. J. (2005). “For better or worse: genomic consequences of intracellular mutualism and parasitism.Curr Opin Genet Dev, 15(6), 572-83.

Weiland, M. E., McArthur, A. G., Morrison, H. G., Sogin, M. L., and Svard, S. G. (2005). “Annexin-like alpha giardins: a new cytoskeletal gene family in Giardia lamblia.Int J Parasitol, 35(6), 617-26.

Wagner, R. Jr., and Meselson, M. (2005). “Repair tracts in mismatched DNA heteroduplexes. 1976.DNA Repair (Amst), 4(1), 126-30; discussion 103-4, 131.

Smith, D., Zhong, J., Matsuura, M., Lambowitz, A. M., and Belfort, M. (2005). “Recruitment of host functions suggests a repair pathway for late steps in group II intron retrohoming.Genes Dev, 19(20), 2477-87.

Simmons, S. L., Cummings, J. A., Clemens, L. G., and Nunez, A. A. (2005). “Exposure to PCB 77 affects the maternal behavior of rats.Physiol Behav, 84(1), 81-6.

Simmons, S. L. (2005). “Extinguishing the flames of manager burnout with CPR.Neonatal Netw, 24(4), 59-60.

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

Sha, B. E., Zariffard, M. R., Wang, Q. J., Chen, H. Y., Bremer, J., Cohen, M. H., and Spear, G. T. (2005). “Female genital-tract HIV load correlates inversely with Lactobacillus species but positively with bacterial vaginosis and Mycoplasma hominis.J Infect Dis, 191.

Serres, M. H., and Riley, M. (2005). “Gene fusions and gene duplications: relevance to genomic annotation and functional analysis.BMC Genomics, 6, 33.

Schaber, J., Rispe, C., Wernegreen, J. J., Buness, A., Delmotte, F., Silva, F. J., and Moya, A. (2005). “Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria.Gene, 352, 109-17.

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

Polaszek, A. (2005). “A universal register for animal names.Nature, 437(7058), 477.

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., and 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), 348-55.

Murray, S., Flo Jorgensen, M., Ho, S. Y., Patterson, D. J., and Jermiin, L. S. (2005). “Improving the analysis of dinoflagellate phylogeny based on rDNA.Protist, 156(3), 269-86.

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

Miao, J., Wu, W., Spielmann, T., Belfort, M., Derbyshire, V., and Belfort, G. (2005). “Single-step affinity purification of toxic and non-toxic proteins on a fluidics platform.Lab Chip, 5(3), 248-53.

Messerli, M. A., Amaral-Zettler, L. A., Zettler, E., Jung, S. K., Smith, P. J., and Sogin, M. L. (2005). “Life at acidic pH imposes an increased energetic cost for a eukaryotic acidophile.J Exp Biol, 208(Pt 13), 2569-79.

Mehta, M. P., Huber, J. A., and Baross, J. A. (2005). “Incidence of novel and potentially archaeal nitrogenase genes in the deep Northeast Pacific Ocean.Environ Microbiol, 7(10), 1525-34.

Mark Welch, D. B. (2005). “Bayesian and Maximum Likelihood Analyses of Rotifer–Acanthocephalan Relationships.Hydrobiologia, 546(1), 47-54.

Lozupone, C., and Knight, R. (2005). “UniFrac: a new phylogenetic method for comparing microbial communities.Appl Environ Microbiol, 71.

Lindell, D., Penno, S., Al-Qutob, M., David, E., Korpal, T., Lazar, B., and 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.

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

Larsson, P. G., and Forsum, U. (2005). “Bacterial vaginosis—a disturbed bacterial flora and treatment enigma.APMIS, 113.

Larsson, P. G., Bergstrom, M., Forsum, U., Jacobsson, B., Strand, A., and Wolner-Hanssen, P. (2005). “Bacterial vaginosis. Transmission, role in genital tract infection and pregnancy outcome: an enigma.APMIS, 113.

Kysela, D. T., Palacios, C., and 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), 356-64.

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., and 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), 2099-104.

Hyman, R. W., Fukushima, M., Diamond, L., Kumm, J., Giudice, L. C., and Davis, R. W. (2005). “Microbes on the human vaginal epithelium.Proc Natl Acad Sci U S A, 102.

Hiraga, K., Derbyshire, V., Dansereau, J. T., Van Roey, P., and Belfort, M. (2005). “Minimization and stabilization of the Mycobacterium tuberculosis recA intein.J Mol Biol, 354(4), 916-26.

Herbeck, J. T., Degnan, P. H., and 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), 520-32.

Gould, R. M., Morrison, H. G., Gilland, E., and 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.

Giovannoni, S. J., Tripp, H. J., Givan, S., Podar, M., Vergin, K. L., and Baptista, D. (2005). “Genome streamlining in a cosmopolitan oceanic bacterium.Science, 309.

Fuller, N. J., Marie, D., Yallop, M., Rivlin, T., West, N. J., Post, A. F., and 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.

Fry, A. J., and Wernegreen, J. J. (2005). “The roles of positive and negative selection in the molecular evolution of insect endosymbionts.Gene, 355, 1-10.

Fredricks, D. N., Fiedler, T. L., and Marrazzo, J. M. (2005). “Molecular identification of bacteria associated with bacterial vaginosis.N Engl J Med, 353.

Forsum, U., Holst, E., Larsson, P. G., Vasquez, A., Jakobsson, T., and Mattsby-Baltzer, I. (2005). “Bacterial vaginosis—a microbiological and immunological enigma.APMIS, 113.

Forsum, U., Hallen, A., and Larsson, P. G. (2005). “Bacterial vaginosis—a laboratory and clinical diagnostics enigma.APMIS, 113.

Evgen’ev, M. B., and Arkhipova, I. R. (2005). “Penelope-like elements–a new class of retroelements: distribution, function and possible evolutionary significance.Cytogenet Genome Res, 110(1-4), 510-21.

Dhillon, A., Lever, M., Lloyd, K. G., Albert, D. B., Sogin, M. L., and 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), 4592-601.

Dhillon, A., Goswami, S., Riley, M., Teske, A., and Sogin, M. L. (2005). “Domain evolution and functional diversification of sulfite reductases.Astrobiology, 5(1), 18-29.

Degnan, P. H., Lazarus, A. B., and Wernegreen, J. J. (2005). “Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects.Genome Res, 15(8), 1023-33.

Coros, C. J., Landthaler, M., Piazza, C. L., Beauregard, A., Esposito, D., Perutka, J., Lambowitz, A. M., and 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), 509-24.

Conlan, L. H., Stanger, M. J., Ichiyanagi, K., and Belfort, M. (2005). “Localization, mobility and fidelity of retrotransposed Group II introns in rRNA genes.Nucleic Acids Res, 33(16), 5262-70.

Casiraghi, M., Bordenstein, S. R., Baldo, L., Lo, N., Beninati, T., Wernegreen, J. J., Werren, J. H., and 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), 4015-22.

Bordenstein, S. R., and Reznikoff, W. S. (2005). “Mobile DNA in obligate intracellular bacteria.Nat Rev Microbiol, 3(9), 688-99.

Bordenstein, S., and Rosengaus, R. B. (2005). “Discovery of a novel Wolbachia super group in Isoptera.Curr Microbiol, 51(6), 393-8.

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

Bahr, M., Crump, B. C., Klepac-Ceraj, V., Teske, A., Sogin, M. L., and Hobbie, J. E. (2005). “Molecular characterization of sulfate-reducing bacteria in a New England salt marsh.Environ Microbiol, 7(8), 1175-85.

Ason, B., Knauss, D. J., Balke, A. M., Merkel, G., Skalka, A. M., and Reznikoff, W. S. (2005). “Targeting Tn5 transposase identifies human immunodeficiency virus type 1 inhibitors.Antimicrob Agents Chemother, 49(5), 2035-43.

Arkhipova, I. R., and Meselson, M. (2005). “Deleterious transposable elements and the extinction of asexuals.Bioessays, 27(1), 76-85.

Arkhipova, I. R., and Meselson, M. (2005). “Diverse DNA transposons in rotifers of the class Bdelloidea.Proc Natl Acad Sci U S A, 102(33), 11781-6.

Arkhipova, I. R. (2005). “Mobile genetic elements and sexual reproduction.Cytogenet Genome Res, 110(1-4), 372-82.

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., and 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), 107-15.

Alliegro, M. C., and Alliegro, M. A. (2005). “Differential expression of tyrosinated tubulin in Spisula solidissima polar bodies.Dev Dyn, 232(1), 216-20.

 

2004

Zhou, X., Bent, S. J., Schneider, M. G., Davis, C. C., Islam, M. R., and Forney, L. J. (2004). “Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods.Microbiology, 150.

Wernegreen, J. J., and Funk, D. J. (2004). “Mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome.J Mol Evol, 59(6), 849-58.

Wernegreen, J. J. (2004). “Endosymbiosis: lessons in conflict resolution.PLoS Biol, 2(3), E68.

Verhelst, R., Verstraelen, H., Claeys, G., Verschraegen, G., Delanghe, J., Simaey, L., Ganck, C., Temmerman, M., and Vaneechoutte, M. (2004). “Cloning of 16S rRNA genes amplified from normal and disturbed vaginal microflora suggests a strong association between Atopobium vaginae, Gardnerella vaginalis and bacterial vaginosis.BMC Microbiol, 4.

Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., and Richardson, P. M. (2004). “Community structure and metabolism through reconstruction of microbial genomes from the environment.Nature, 428.

Steiniger-White, M., Rayment, I., and Reznikoff, W. S. (2004). “Structure/function insights into Tn5 transposition.Curr Opin Struct Biol, 14(1), 50-7.

Simmons, S. L., Sievert, S. M., Frankel, R. B., Bazylinski, D. A., and Edwards, K. J. (2004). “Spatiotemporal distribution of marine magnetotactic bacteria in a seasonally stratified coastal salt pond.Appl Environ Microbiol, 70(10), 6230-9.

Silva-Pinhati, A. C., Bacci, M. Jr., Hinkle, G., Sogin, M. L., Pagnocca, F. C., Martins, V. G., Bueno, O. C., and 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), 1463-72.

Silva, G. H., and Belfort, M. (2004). “Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI.Nucleic Acids Res, 32(10), 3156-68.

Serres, M. H., and Riley, M. (2004). “Structural domains, protein modules, and sequence similarities enrich our understanding of the Shewanella oneidensis MR-1 proteome.OMICS, 8(4), 306-21.

Serres, M. H., Goswami, S., and Riley, M. (2004). “GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins.Nucleic Acids Res, 32(Database issue), D300-2.

Reznikoff, W. S., Goryshin, I. Y., and 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.

Reznikoff, W. S., Bordenstein, S. R., and Apodaca, J. (2004). “Comparative sequence analysis of IS50/Tn5 transposase.J Bacteriol, 186(24), 8240-7.

Pyatkov, K. I., Arkhipova, I. R., Malkova, N. V., Finnegan, D. J., and Evgen’ev, M. B. (2004). “Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements.Proc Natl Acad Sci U S A, 101(41), 14719-24.

Pyatkov, K. I., Arkhipova, I. R., Malkova, N. V., Finnegan, D. J., and Evgen’ev, M. B. (2004). “Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements.Proc Natl Acad Sci U S A, 101(41), 14719-24.

Powell, W. H., Morrison, H. G., Weil, E. J., Karchner, S. I., Sogin, M. L., Stegeman, J. J., and Hahn, M. E. (2004). “Cloning and analysis of the CYP1A promoter from the atlantic killifish (Fundulus heteroclitus).Mar Environ Res, 58(2-5), 119-24.

Murray, S., and Patterson, D. J. (2004). “Cabra matta, gen. nov., sp nov., a new benthic, heterotrophic dinoflagellate.European Journal of Phycology, 39(2), 229-234.

Meselson, M. (2004). “Explorations in the land of DNA and beyond.Nat Med, 10(10), 1034-7.

Mark Welch, J. L., Mark Welch, D. B., and Meselson, M. (2004). “Cytogenetic evidence for asexual evolution of bdelloid rotifers.Proc Natl Acad Sci U S A, 101(6), 1618-21.

Mark Welch, D. B., Cummings, M. P., Hillis, D. M., and 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), 1622-5.

Lease, R. A., Smith, D., McDonough, K., and Belfort, M. (2004). “The small noncoding DsrA RNA is an acid resistance regulator in Escherichia coli.J Bacteriol, 186(18), 6179-85.

Kodama, Y., and Watanabe, K. (2004). “Sulfuricurvum kujiense gen. nov., sp. nov., a facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium isolated from an underground crude-oil storage cavity.Int J Syst Evol Microbiol, 54.

Hood, L., Heath, J. R., Phelps, M. E., and Lin, B. (2004). “Systems biology and new technologies enable predictive and preventative medicine.Science, 306.

Hood, L., Heath, J. R., Phelps, M. E., and Lin, B. (2004). “Systems biology and new technologies enable predictive and preventative medicine.Science, 306.

Ferris, M. J., Masztal, A., Aldridge, K. E., Fortenberry, J. D., Fidel, P. L., and Martin, D. H. (2004). “Association of Atopobium vaginae, a recently described metronidazole resistant anaerobe, with bacterial vaginosis.BMC Infect Dis, 4.

Edgell, D. R., Stanger, M. J., and 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), 1231-41.

Edgell, D. R., Derbyshire, V., Van Roey, P., LaBonne, S., Stanger, M. J., Li, Z., Boyd, T. M., Shub, D. A., and Belfort, M. (2004). “Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor.Nat Struct Mol Biol, 11(10), 936-44.

Degnan, P. H., Lazarus, A. B., Brock, C. D., and 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.

Crump, B. C., Hopkinson, C. S., Sogin, M. L., and Hobbie, J. E. (2004). “Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time.Appl Environ Microbiol, 70(3), 1494-505.

Bordenstein, S. R., and Wernegreen, J. J. (2004). “Bacteriophage flux in endosymbionts (Wolbachia): infection frequency, lateral transfer, and recombination rates.Mol Biol Evol, 21(10), 1981-91.

Best, A. A., Morrison, H. G., McArthur, A. G., Sogin, M. L., and Olsen, G. J. (2004). “Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia.Genome Res, 14(8), 1537-47.

Ason, B., and Reznikoff, W. S. (2004). “DNA sequence bias during Tn5 transposition.J Mol Biol, 335(5), 1213-25.

Ason, B., and Reznikoff, W. S. (2004). “A high-throughput assay for Tn5 Tnp-induced DNA cleavage.Nucleic Acids Res, 32(10), e83.

 

2003

Zeidner, G., Preston, C. M., Delong, E. F., Massana, R., Post, A. F., Scanlan, D. J., and Beja, O. (2003). “Molecular diversity among marine picophytoplankton as revealed by psbA analyses.Environmental Microbiology, 5(3), 212-216.

Wernegreen, J. J., Degnan, P. H., Lazarus, A. B., Palacios, C., and Bordenstein, S. R. (2003). “Genome evolution in an insect cell: distinct features of an ant-bacterial partnership.Biol Bull, 204(2), 221-31.

Walker, G., Silberman, J. D., Karpov, S. A., Preisfeld, A., Foster, P., Ol Frolov, A., Novozhilov, Y., and 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, 319-36.

Teske, A., Dhillon, A., and Sogin, M. L. (2003). “Genomic markers of ancient anaerobic microbial pathways: sulfate reduction, methanogenesis, and methane oxidation.Biol Bull, 204(2), 186-91.

Steglich, C., Post, A. F., and Hess, W. R. (2003). “Analysis of natural populations of Prochlorococcus spp. in the northern Red Sea using phycoerythrin gene sequences.Environmental Microbiology, 5(8), 681-690.

Sogin, M. L., and Jennings, D. E. (2003). “Proceedings of a workshop sponsored by The Center for Advanced Studies in the Space Life Sciences at the MBL – 1 to 3 May 2002 – Introduction.Biological Bulletin, 204(2), 159-159.

Seshadri, V., McArthur, A. G., Sogin, M. L., and Adam, R. D. (2003). “Giardia lamblia RNA polymerase II: amanitin-resistant transcription.J Biol Chem, 278(30), 27804-10.

Schroeckh, S., Lee, W. J., and Patterson, D. J. (2003). “Free-living heterotrophic euglenids from freshwater sites in mainland Australia.Hydrobiologia, 493(1-3), 131-166.

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., and Chisholm, S. W. (2003). “Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation.Nature, 424(6952), 1042-7.

Reznikoff, W. S. (2003). “Tn5 as a model for understanding DNA transposition.Mol Microbiol, 47(5), 1199-206.

Reiner, D. S., Hetsko, M. L., Meszaros, J. G., Sun, C. H., Morrison, H. G., Brunton, L. L., and Gillin, F. D. (2003). “Calcium signaling in excystation of the early diverging eukaryote, Giardia lamblia.J Biol Chem, 278(4), 2533-40.

Peterson, G., and Reznikoff, W. (2003). “Tn5 transposase active site mutations suggest position of donor backbone DNA in synaptic complex.J Biol Chem, 278(3), 1904-9.

Patterson, D. J., Remsen, D., and Norton, C. (2003). “Comment on Zoological record and registration of new names in zoology.Bulletin of Zoological Nomenclature, 60, 297-99.

Patterson, D. J. (2003). “Progressing towards a biological names register.Nature, 422(6933), 661.

Onderdonk, A. B., Lee, M. L., Lieberman, E., Delaney, M. L., and Tuomala, R. E. (2003). “Quantitative microbiologic models for preterm delivery.J Clin Microbiol, 41.

O’Kelly, C. J., Silberman, J. D., Amaral-Zettler, L. A., Nerad, T. A., and 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), 281-90.

Noel, C., Peyronnet, C., Gerbod, D., Edgcomb, V. P., Delgado-Viscogliosi, P., Sogin, M. L., Capron, M., Viscogliosi, E., and 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), 119-23.

Noble, M., Smith, J., Power, J., and 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.

Nixon, J. E., Field, J., McArthur, A. G., Sogin, M. L., Yarlett, N., Loftus, B. J., and 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.

Meselson, M. (2003). “Interview with Matthew Meselson.Bioessays, 25(12), 1236-46.

Medina, M., Collins, A. G., Taylor, J. W., Valentine, J. W., Lipps, J. H., Amaral-Zettler, L. A., and Sogin, M. L. (2003). “Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa.International Journal of Astrobiology, 2, 203-11.

Mark Welch, D. B., and 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.

Man, D., Wang, W., Sabehi, G., Aravind, L., Post, A. F., Massana, R., Spudich, E. N., Spudich, J. L., and Beja, O. (2003). “Diversification and spectral tuning in marine proteorhodopsins.EMBO J, 22(8), 1725-31.

Liu, Q., Belle, A., Shub, D. A., Belfort, M., and 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.

Linz-McGillem, L. A., and Alliegro, M. C. (2003). “Myosin II in retinal pigmented epithelial cells: evidence for an association with membranous vesicles.Exp Eye Res, 76(5), 543-52.

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

Johnson, H. P., and Party, L. S. (2003). “Probing for life in the ocean crust with the LEXEN program.Eos, Trans. AGU., 84, 109-12.

Ichiyanagi, K., Beauregard, A., and Belfort, M. (2003). “A bacterial group II intron favors retrotransposition into plasmid targets.Proc Natl Acad Sci U S A, 100(26), 15742-7.

Huber, J. A., Butterfield, D. A., and Baross, J. A. (2003). “Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption.FEMS Microbiol Ecol, 43(3), 393-409.

Herbeck, J. T., Wall, D. P., and 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), 2585-96.

Herbeck, J. T., Funk, D. J., Degnan, P. H., and 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), 1651-60.

Haft, D. H., Selengut, J. D., and White, O. (2003). “The TIGRFAMs database of protein families.Nucleic Acids Res, 31.

Goryshin, I. Y., Naumann, T. A., Apodaca, J., and 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), 644-53.

Gillor, O., Harush, A., Hadas, O., Post, A. F., and Belkin, S. (2003). “A Synechococcus PglnA::luxAB fusion for estimation of nitrogen bioavailability to freshwater cyanobacteria.Appl Environ Microbiol, 69(3), 1465-74.

Fuller, N. J., Marie, D., Partensky, F., Vaulot, D., Post, A. F., and 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), 2430-43.

Edgell, D. R., Stanger, M. J., and 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), 973-8.

Dhillon, A., Teske, A., Dillon, J., Stahl, D. A., and Sogin, M. L. (2003). “Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin.Appl Environ Microbiol, 69(5), 2765-72.

Busse, I., Patterson, D. J., and 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.

Bordenstein, S. R., Uy, J. J., and Werren, J. H. (2003). “Host genotype determines cytoplasmic incompatibility type in the haplodiploid genus Nasonia.Genetics, 164(1), 223-33.

Bordenstein, S. R., Fitch, D. H., and Werren, J. H. (2003). “Absence of wolbachia in nonfilariid nematodes.J Nematol, 35(3), 266-70.

Belfort, M. (2003). “Two for the price of one: a bifunctional intron-encoded DNA endonuclease-RNA maturase.Genes Dev, 17(23), 2860-3.

Arkhipova, I. R., Pyatkov, K. I., Meselson, M., and Evgen’ev, M. B. (2003). “Retroelements containing introns in diverse invertebrate taxa.Nat Genet, 33(2), 123-4.

Amaral-Zettler, L. A., Messerli, M. A., Laatsch, A. D., Smith, P. J., and Sogin, M. L. (2003). “From genes to genomes: beyond biodiversity in Spain’s Rio Tinto.Biol Bull, 204(2), 205-9.

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

 

2002

Wu, W., Wood, D. W., Belfort, G., Derbyshire, V., and Belfort, M. (2002). “Intein-mediated purification of cytotoxic endonuclease I-TevI by insertional inactivation and pH-controllable splicing.Nucleic Acids Res, 30(22), 4864-71.

Wernegreen, J. J., Lazarus, A. B., and 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), 2551-6.

Wernegreen, J. J. (2002). “Genome evolution in bacterial endosymbionts of insects.Nat Rev Genet, 3(11), 850-61.

Vitousek, P. M. (2002). “Oceanic islands as model systems for ecological studies.J Biogeogr, 29.

Vitousek, P. M. (2002). “Oceanic islands as model systems for ecological studies.J Biogeogr, 29.

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

Teske, A., Hinrichs, K. U., Edgcomb, V., de Vera Gomez, A., Kysela, D., Sylva, S. P., Sogin, M. L., and 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.

Tamas, I., Klasson, L., Canback, B., Naslund, A. K., Eriksson, A. S., Wernegreen, J. J., Sandstrom, J. P., Moran, N. A., and Andersson, S. G. (2002). “50 million years of genomic stasis in endosymbiotic bacteria.Science, 296(5577), 2376-9.

Steiniger-White, M., Bhasin, A., Lovell, S., Rayment, I., and Reznikoff, W. S. (2002). “Evidence for “unseen” transposase–DNA contacts.J Mol Biol, 322(5), 971-82.

Sommer, U., Berninger, U.-G., R., B.-S., Hansen, T., Stibor, H., Schnack-Schiel, S. B., Cornils, A., Hagen, W., Wickham, S., Al-Najjar, T., and 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.

Simpson, A. G., Roger, A. J., Silberman, J. D., Leipe, D. D., Edgcomb, V. P., Jermiin, L. S., Patterson, D. J., and 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), 1782-91.

Richey, J. E., Melack, J. M., Aufdenkampe, A. K., Ballester, V. M., and Hess, L. L. (2002). “Outgassing from Amazonian rivers and wetlands as a large tropical source of atmospheric CO2.Nature, 416.

Power, J., Mayer-Pröschel, M., Smith, J., and Noble, M. (2002). “Oligodendrocyte precursor cells from different brain regions express divergent properties consistent with the differing time courses of myelination in these regions.Developmental Biology, 245(2), 362-375.

Post, A. F., Dedej, Z., Gottlieb, R., Li, H., Thomas, D., El-Absawy, M., El-Naggar, A., El-Gharabawi, M., and 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.

Podar, M., Mullineaux, L., Huang, H. R., Perlman, P. S., and Sogin, M. L. (2002). “Bacterial group II introns in a deep-sea hydrothermal vent environment.Appl Environ Microbiol, 68(12), 6392-8.

Palacios, C., and 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), 1575-84.

Pahl, N., Homsi, S., Morrison, H. G., and Gould, R. M. (2002). “mRNAs located in Squalus acanthias (spiny dogfish) oligodendrocyte processes.Biol Bull, 203(2), 217-8.

Nixon, J. E., Wang, A., Morrison, H. G., McArthur, A. G., Sogin, M. L., Loftus, B. J., and Samuelson, J. (2002). “A spliceosomal intron in Giardia lamblia.Proc Natl Acad Sci U S A, 99(6), 3701-5.

Nixon, J. E., Wang, A., Field, J., Morrison, H. G., McArthur, A. G., Sogin, M. L., Loftus, B. J., and 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), 181-90.

Naumann, T. A., and Reznikoff, W. S. (2002). “Tn5 transposase with an altered specificity for transposon ends.J Bacteriol, 184(1), 233-40.

Naumann, T. A., and Reznikoff, W. S. (2002). “Tn5 transposase active site mutants.J Biol Chem, 277(20), 17623-9.

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

Murray, S., and Patterson, D. J. (2002). “Amphidiniopsis korewalensis sp. nov., a new heterotrophic benthic dinoflagellates.Phycologica, 41, 382-88.

Murray, S., and 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.

Morrison, H. G., Zamora, G., Campbell, R. K., and 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), 477-91.

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

Marrazzo, J. M., Koutsky, L. A., Eschenbach, D. A., Agnew, K., Stine, K., and Hillier, S. L. (2002). “Characterization of vaginal flora and bacterial vaginosis in women who have sex with women.J Infect Dis, 185.

Lovell, S., Goryshin, I. Y., Reznikoff, W. R., and Rayment, I. (2002). “Two-metal active site binding of a Tn5 transposase synaptic complex.Nat Struct Biol, 9(4), 278-81.

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

Lee, W. J., and 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), 467-81.

Lee, W. J., and 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.

Langford, T. D., Silberman, J. D., Weiland, M. E., Svard, S. G., McCaffery, J. M., Sogin, M. L., and 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.

Ichiyanagi, K., Beauregard, A., Lawrence, S., Smith, D., Cousineau, B., and Belfort, M. (2002). “Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets.Mol Microbiol, 46(5), 1259-72.

Huber, J. A., Butterfield, D. A., and Baross, J. A. (2002). “Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat.Appl Environ Microbiol, 68(4), 1585-94.

Holtzendorff, J., Marie, D., Post, A. F., Partensky, F., Rivlin, A., and Hess, W. R. (2002). “Synchronized expression of ftsZ in natural Prochlorococcus populations of the Red Sea.Environ Microbiol, 4(11), 644-53.

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

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., and 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), 545-56.

Edgcomb, V. P., Simpson, A. G., Zettler, L. A., Nerad, T. A., Patterson, D. J., Holder, M. E., and Sogin, M. L. (2002). “Pelobionts are degenerate protists: insights from molecules and morphology.Mol Biol Evol, 19(6), 978-82.

Edgcomb, V. P., Kysela, D. T., Teske, A., de Vera Gomez, A., and Sogin, M. L. (2002). “Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment.Proc Natl Acad Sci U S A, 99(11), 7658-62.

Dyer, K. D., Linz-Mcgillem, L. A., Alliegro, M. A., and Alliegro, M. C. (2002). “Receptor-bound uPA is reversibly protected from inhibition by low molecular weight inhibitors.Cell Biol Int, 26(4), 327-35.

Dean, A. B., Stanger, M. J., Dansereau, J. T., Van Roey, P., Derbyshire, V., and 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), 8554-61.

Boelen, P., Post, A. F., Veldhuis, M. J., and 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), 164-74.

Ason, B., and Reznikoff, W. S. (2002). “Mutational analysis of the base flipping event found in Tn5 transposition.J Biol Chem, 277(13), 11284-91.

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

Alliegro, M. C., and Alliegro, M. A. (2002). “Nuclear injection of anti-pigpen antibodies inhibits endothelial cell division.J Biol Chem, 277(21), 19037-41.

Alliegro, M. C. (2002). “Coiled body heterogeneity induced by G(1) arrest with amiloride + bumetanide.Exp Cell Res, 279(1), 111-7.

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

 

2001

Wu, C. H., Madabusi, L., Nishioka, H., Emanuel, P., Sypes, M., Arkhipova, I. R., and 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), 1593-602.

West, N. J., Schoenhuber, W. A., Fuller, N. J., Walsby, A. E., Amann, R. I., Rippka, R., Post, A. F., and 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.

Wernegreen, J. J., Richardson, A. O., and Moran, N. A. (2001). “Parallel acceleration of evolutionary rates in symbiont genes underlying host nutrition.Mol Phylogenet Evol, 19(3), 479-85.

Wernegreen, J. J., and Moran, N. A. (2001). “Vertical transmission of biosynthetic plasmids in aphid endosymbionts (Buchnera).J Bacteriol, 183(2), 785-90.

Walker, G., Simpson, A. G. B., Edgcomb, V. P., Sogin, M. L., and 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.

Van Roey, P., Waddling, C. A., Fox, K. M., Belfort, M., and Derbyshire, V. (2001). “Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.EMBO J, 20(14), 3631-7.

Twining, S. S., Goryshin, I. Y., Bhasin, A., and Reznikoff, W. S. (2001). “Functional characterization of arginine 30, lysine 40, and arginine 62 in Tn5 transposase.J Biol Chem, 276(25), 23135-43.

Torino, J. L., Burger, M. S., Reznikoff, C. A., and 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), 147-54.

Stihl, A., Sommer, U., and 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.

Smith, R., Kavanagh, E., Morrison, H. G., and Gould, R. M. (2001). “Messenger RNAs located in spiny dogfish oligodendrocyte processes.Biol Bull, 201(2), 255-6.

Simpson, A. G., and Patterson, D. J. (2001). “On core jakobids and excavate taxa: the ultrastructure of Jakoba incarcerata.J Eukaryot Microbiol, 48(4), 480-92.

Serres, M. H., Gopal, S., Nahum, L. A., Liang, P., Gaasterland, T., and Riley, M. (2001). “A functional update of the Escherichia coli K-12 genome.Genome Biol, 2(9), RESEARCH0035.

Schreiter, P., Gillor, O., Post, A. F., Belkin, S., Schmid, R. D., and Bachmann, T. T. (2001). “Monitoring of phosphorus availability in water by an immobilized lumniscent cyanobacterial reporter strain.Biosensors and Bioelectronics, 16, 811-818.

Podar, M., Haddock, S. H., Sogin, M. L., and Harbison, G. R. (2001). “A molecular phylogenetic framework for the phylum Ctenophora using 18S rRNA genes.Mol Phylogenet Evol, 21(2), 218-30.

Nebel, G., Dragsted, J., and Vega, A. S. (2001). “Litter fall, biomass and net primary production in flood plain forests in the Peruvian Amazon.Forest Ecol Manag, 150.

Morrison, H. G., Roger, A. J., Nystul, T. G., Gillin, F. D., and Sogin, M. L. (2001). “Giardia lamblia expresses a proteobacterial-like DnaK homolog.Mol Biol Evol, 18(4), 530-41.

Mikrjukov, K. A., and Patterson, D. J. (2001). “Taxonomy and phylogeny of heliozoa. III. Actinophryids.Acta Protozoologica, 40(1), 3-25.

Medina, M., Collins, A. G., Silberman, J. D., and 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), 9707-12.

McArthur, A. G., Knodler, L. A., Silberman, J. D., Davids, B. J., Gillin, F. D., and 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), 1455-63.

Mark Welch, D. B., and Meselson, M. S. (2001). “Rates of nucleotide substitution in sexual and anciently asexual rotifers.Proc Natl Acad Sci U S A, 98(12), 6720-4.

Mark Welch, D. B. (2001). “Early contributions of molecular phylogenetics to understanding the evolution of Rotifera.Hydrobiologia, 446-447(1), 315-322.

Lindell, D., and 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), 3340-9.

Karpov, S. A., Sogin, M. L., and Silberman, J. D. (2001). “Rootlet homology, taxonomy, and phylogeny of bicosoecids based on 18S rRNA gene sequences.Protistology, 21, 34-47.

Gerbod, D., Edgcomb, V. P., Noel, C., Zenner, L., Wintjens, R., Delgado-Viscogliosi, P., Holder, M. E., Sogin, M. L., and 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.

Funk, D. J., Wernegreen, J. J., and Moran, N. A. (2001). “Intraspecific variation in symbiont genomes: bottlenecks and the aphid-buchnera association.Genetics, 157(2), 477-89.

Edgcomb, V. P., Roger, A. J., Simpson, A. G., Kysela, D. T., and Sogin, M. L. (2001). “Evolutionary relationships among “jakobid” flagellates as indicated by alpha- and beta-tubulin phylogenies.Mol Biol Evol, 18(4), 514-22.

Cu-Uvin, S., Hogan, J. W., Caliendo, A. M., Harwell, J., Mayer, K. H., and Carpenter, C. C. (2001). “Association between bacterial vaginosis and expression of human immunodeficiency virus type 1 RNA in the female genital tract.Clin Infect Dis, 33.

Brugerolle, G., and 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.

Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., Gaasterland, T., Glenisson, P., Holstege, F. C., Kim, I. F., Markowitz, V., Matese, J. C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J., and Vingron, M. (2001). “Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.Nat Genet, 29.

Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., Gaasterland, T., Glenisson, P., Holstege, F. C., Kim, I. F., Markowitz, V., Matese, J. C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J., and Vingron, M. (2001). “Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.Nat Genet, 29.

Bordenstein, S. R., O’Hara, F. P., and Werren, J. H. (2001). “Wolbachia-induced incompatibility precedes other hybrid incompatibilities in Nasonia.Nature, 409(6821), 707-10.

Bordenstein, S. R., and Drapeau, M. D. (2001). “Genotype-by-environment interaction and the Dobzhansky-Muller model of postzygotic isolation.Journal of Evolutionary Biology, 14(3), 490-501.

Barbieri, E., Paster, B. J., Hughes, D., Zurek, L., Moser, D. P., Teske, A., and 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), 151-67.

Balas, C. E., Williams, A. T., Simmons, S. L., and Ergin, A. (2001). “A statistical riverine litter propagation model.Mar Pollut Bull, 42(11), 1169-76.

Arkhipova, I. R., and 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), 14497-502.

Arkhipova, I. R. (2001). “[Transposable elements in the Animal Kingdom].Mol Biol (Mosk), 35(2), 196-207.

Amaral-Zettler, L. A., Nerad, T. A., O’Kelly, C. J., and Sogin, M. L. (2001). “The nucleariid amoebae: more protists at the animal-fungal boundary.J Eukaryot Microbiol, 48(3), 293-7.

Alliegro, M. C. (2001). “Pigpen and endothelial cell differentiation.Cell Biol Int, 25(7), 577-84.

 

2000

Wu, G., McArthur, A. G., Fiser, A., Sali, A., Sogin, M. L., and Mllerm, M. (2000). “Core histones of the amitochondriate protist, Giardia lamblia.Mol Biol Evol, 17(8), 1156-63.

Wood, D. W., Derbyshire, V., Wu, W., Chartrain, M., Belfort, M., and Belfort, G. (2000). “Optimized single-step affinity purification with a self-cleaving intein applied to human acidic fibroblast growth factor.Biotechnol Prog, 16(6), 1055-63.

Wernegreen, J. J., Ochman, H., Jones, I. B., and Moran, N. A. (2000). “Decoupling of genome size and sequence divergence in a symbiotic bacterium.J Bacteriol, 182(13), 3867-9.

Wernegreen, J. J., and Moran, N. A. (2000). “Decay of mutualistic potential in aphid endosymbionts through silencing of biosynthetic loci: Buchnera of Diuraphis.Proc Biol Sci, 267(1451), 1423-31.

Wang, Q., Li, H., and Post, A. F. (2000). “Nitrate assimilation genes of the marine diazotrophic, filamentous cyanobacterium Trichodesmium sp. strain WH9601.J Bacteriol, 182(6), 1764-7.

Steiniger-White, M., and Reznikoff, W. S. (2000). “The C-terminal alpha helix of Tn5 transposase is required for synaptic complex formation.J Biol Chem, 275(30), 23127-33.

Smith, J., Ladi, E., Mayer-Proschel, M., and Noble, M. (2000). “Redox state is a central modulator of the balance between self-renewal and differentiation in a dividing glial precursor cell.Proc Natl Acad Sci U S A, 97(18), 10032-7.

Simpson, A. G. B., Bernard, C., and Patterson, D. J. (2000). “The ultrastructure of Trimastix marina Kent, 1880 (eukaryota), an excavate flagellate.European Journal of Protistology, 36(3), 229-251.

Serres, M. H., and Riley, M. (2000). “MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products.Microb Comp Genomics, 5(4), 205-22.

Serres, M. H., Fladmark, K. E., and Doskeland, S. O. (2000). “An ultrasensitive competitive binding assay for the detection of toxins affecting protein phosphatases.Toxicon, 38(3), 347-60.

Riley, M., and Serres, M. H. (2000). “Interim report on genomics of Escherichia coli.Annu Rev Microbiol, 54, 341-411.

Noel, R. J. Jr., and Reznikoff, W. S. (2000). “Structural studies of lacUV5-RNA polymerase interactions in vitro. Ethylation interference and missing nucleoside analysis.J Biol Chem, 275(11), 7708-12.

Naumann, T. A., and Reznikoff, W. S. (2000). “Trans catalysis in Tn5 transposition.Proc Natl Acad Sci U S A, 97(16), 8944-9.

Moran, N. A., and Wernegreen, J. J. (2000). “Lifestyle evolution in symbiotic bacteria: insights from genomics.Trends Ecol Evol, 15(8), 321-326.

Mohr, G., Smith, D., Belfort, M., and 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), 559-73.

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., and Sogin, M. L. (2000). “The Giardia genome project database.FEMS Microbiol Lett, 189(2), 271-3.

Mark Welch, D. B., and Meselson, M. (2000). “Evidence for the Evolution of Bdelloid Rotifers Without Sexual Reproduction or Genetic Exchange.Science, 288(5469), 1211-1215.

Mark Welch, D. B. (2000). “Evidence from a protein-coding gene that acanthocephalans are rotifers.Invertebrate Biology, 119(1), 17-26.

Lee, W. J., and Patterson, D. J. (2000). “Heterotrophic flagellates (Protista) from marine sediments of Botany Bay, Australia.Journal of Natural History, 34(4), 483-562.

Lease, R. A., and Belfort, M. (2000). “Riboregulation by DsrA RNA: trans-actions for global economy.Mol Microbiol, 38(4), 667-72.

Lease, R. A., and 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), 9919-24.

Hoffman, L. M., Jendrisak, J. J., Meis, R. J., Goryshin, I. Y., and Reznikoff, W. S. (2000). “Transposome insertional mutagenesis and direct sequencing of microbial genomics.Genetica, 108, 19-24.

Hanson, J. M., McGregor, J. A., Hillier, S. L., Eschenbach, D. A., Kreutner, A. K., Galask, R. P., and Martens, M. (2000). “Metronidazole for bacterial vaginosis. A comparison of vaginal gel vs. oral therapy.J Reprod Med, 45.

Gould, R. M., Freund, C. M., Engler, J., and Morrison, H. G. (2000). “Optimization of homogenization conditions used to isolate mRNAs in processes of myelinating oligodendrocytes.Biol Bull, 199(2), 215-7.

Goryshin, I. Y., Jendrisak, J., Hoffman, L. M., Meis, R., and Reznikoff, W. S. (2000). “Insertional transposon mutagenesis by electroporation of released Tn5 transposition complexes.Nat Biotechnol, 18(1), 97-100.

Funk, D. J., Helbling, L., Wernegreen, J. J., and Moran, N. A. (2000). “Intraspecific phylogenetic congruence among multiple symbiont genomes.Proc Biol Sci, 267(1461), 2517-21.

Edgell, D. R., Belfort, M., and Shub, D. A. (2000). “Barriers to intron promiscuity in bacteria.J Bacteriol, 182(19), 5281-9.

Delgado-Viscogliosi, P., Viscogliosi, E., Gerbod, D., Kulda, J., Sogin, M. L., and 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), 70-5.

Davies, D. R., Goryshin, I. Y., Reznikoff, W. S., and Rayment, I. (2000). “Three-dimensional structure of the Tn5 synaptic complex transposition intermediate.Science, 289(5476), 77-85.

Cousineau, B., Lawrence, S., Smith, D., and Belfort, M. (2000). “Retrotransposition of a bacterial group II intron.Nature, 404(6781), 1018-21.

Clark, M. A., Moran, N. A., Baumann, P., and 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), 517-25.

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., and Lewin, H. A. (2000). “Phylogenomic analysis of the alpha proteasome gene family from early-diverging eukaryotes.J Mol Evol, 51(6), 532-43.

Bordenstein, S. R., Drapeau, M. D., and Werren, J. H. (2000). “Intraspecific variation in sexual isolation in the jewel wasp Nasonia.Evolution, 54(2), 567-73.

Bhasin, A., Goryshin, I. Y., Steiniger-White, M., York, D., and Reznikoff, W. S. (2000). “Characterization of a Tn5 pre-cleavage synaptic complex.J Mol Biol, 302(1), 49-63.

Bernard, C., Simpson, A. G. B., and Patterson, D. J. (2000). “Some free-living flagellates (protista) from anoxic habitats.Ophelia, 52(2), 113-142.

Arkhipova, I. R., and Meselson, M. (2000). “Transposable elements in sexual and ancient asexual taxa.Proc Natl Acad Sci U S A, 97(26), 14473-7.

Arkhipova, I. R., and Meselson, M. (2000). “Transposable elements in sexual and ancient asexual taxa.Proc Natl Acad Sci U S A, 97(26), 14473-14477.

Arkhipova, I. R., and Meselson, M. (2000). “Transposable elements in sexual and ancient asexual taxa.Proc Natl Acad Sci U S A, 97(26), 14473-14477.

Amaral-Zettler, L. A., Nerad, T. A., O’Kelly, C. J., Peglar, M. T., Gillevet, P. M., Silberman, J. D., and Sogin, M. L. (2000). “A molecular reassessment of the Leptomyxid amoebae.Protist, 151(3), 275-82.

Amaral-Zettler, L. A., and Caron, D. A. (2000). “New insights into the phylogeny of the Acantharea based on SSU rRNA gene sequencing.European Journal of Protistology, 36, 34-9.

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), 102-6.

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), 270-7.

 

1999

Zaman, V., Zaki, M., Howe, J., Ng, M., Leipe, D. D., Sogin, M. L., and Silberman, J. D. (1999). “Hyperamoeba isolated from human feces: Description and phylogenetic affinity.European Journal of Protistology, 35(2), 197-207.

Yigit, H., and Reznikoff, W. S. (1999). “Escherichia coli DNA topoisomerase I copurifies with Tn5 transposase, and Tn5 transposase inhibits topoisomerase I.J Bacteriol, 181(10), 3185-92.

Wernegreen, J. J., and 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.

Wernegreen, J. J., and Moran, N. A. (1999). “Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes.Mol Biol Evol, 16(1), 83-97.

Weerakoon, N. D., Harper, J. D. I., Simpson, A. G. B., and 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.

Teske, A., Sogin, M. L., Nielsen, L. P., and Jannasch, H. W. (1999). “Phylogenetic relationships of a large marine Beggiatoa.Syst Appl Microbiol, 22(1), 39-44.

Sogin, M. L. (1999). “A molecular point of view (introductory and concluding remarks.Biol. Bull, 196, 415-16.

Simpson, A. G. B., and Patterson, D. J. (1999). “The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the “Excavate hypothesis”.European Journal of Protistology, 35(4), 353-370.

Silberman, J. D., Clark, C. G., Diamond, L. S., and Sogin, M. L. (1999). “Phylogeny of the genera Entamoeba and Endolimax as deduced from small-subunit ribosomal RNA sequences.Mol Biol Evol, 16(12), 1740-51.

Sanchez, L. B., Morrison, H. G., Sogin, M. L., and Muller, M. (1999). “Cloning and sequencing of an acetyl-CoA synthetase (ADP-forming) gene from the amitochondriate protist, Giardia lamblia.Gene, 233(1-2), 225-31.

Roger, A. J., Morrison, H. G., and Sogin, M. L. (1999). “Primary structure and phylogenetic relationships of a malate dehydrogenase gene from Giardia lamblia.J Mol Evol, 48(6), 750-5.

Reznikoff, W. S., Bhasin, A., Davies, D. R., Goryshin, I. Y., Mahnke, L. A., Naumann, T., Rayment, I., Steiniger-White, M., and Twining, S. S. (1999). “Tn5: A molecular window on transposition.Biochem Biophys Res Commun, 266(3), 729-34.

Patterson, D. J., Simpson, A. G., and Weerakoon, N. (1999). “Free-living flagellates from anoxic habitats and the assembly of the eukaryotic cell.Biol Bull, 196(3), 381-3; discussion 383-4.

Patterson, D. J. (1999). “The Diversity of Eukaryotes.Am Nat, 154(S4), S96-S124.

Orgel, L., Hearn, M. A., Bada, J., Barros, J., Chapman, C., Drake, M., Kerridge, J., Race, M., Sogin, M. L., and Squyres, S. (1999). “Sample return from small solar system bodies.Adv. Space Res., 25, 239-48.

Meselson, M. (1999). “The challenge of biological and chemical weapons.Bull World Health Organ, 77(2), 102-3.

Mahnke Braam, L. A., Goryshin, I. Y., and Reznikoff, W. S. (1999). “A mechanism for Tn5 inhibition. carboxyl-terminal dimerization.J Biol Chem, 274(1), 86-92.

Lee, W. J., Blackmore, R., and 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.

Kohler, A., Jostarndt-Fogen, K., Rottner, K., Alliegro, M. C., and Draeger, A. (1999). “Intima-like smooth muscle cells: developmental link between endothelium and media?Anat Embryol (Berl), 200(3), 313-23.

Huang, X., and Madan, A. (1999). “CAP3: a DNA sequence assembly program.Genome Res, 9.

Gould, R., Freund, C., Palmer, F., Knapp, P. E., Huang, J., Morrison, H., and Feinstein, D. L. (1999). “Messenger RNAs for kinesins and dynein are located in neural processes.Biol Bull, 197(2), 259-60.

Doehmer, J., Buters, J. T., Luch, A., Soballa, V., Baird, W. M., Morisson, H., Stegeman, J. J., Townsend, A. J., Greenlee, W. F., Glatt, H. R., Seidel, A., Jacob, J., and Greim, H. (1999). “Molecular studies on the toxifying effects by genetically engineered cytochromes P450.Drug Metab Rev, 31(2), 423-35.

Dixon, T. C., Meselson, M., Guillemin, J., and Hanna, P. C. (1999). “Anthrax.N Engl J Med, 341(11), 815-26.

Davies, D. R., Mahnke Braam, L., Reznikoff, W. S., and Rayment, I. (1999). “The three-dimensional structure of a Tn5 transposase-related protein determined to 2.9-A resolution.J Biol Chem, 274(17), 11904-13.

Bhasin, A., Goryshin, I. Y., and Reznikoff, W. S. (1999). “Hairpin formation in Tn5 transposition.J Biol Chem, 274(52), 37021-9.

Anderson, O. R., Gastrich, M. D., and 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).

Amaral-Zettler, L. A., Anderson, O. R., and Caron, D. A. (1999). “Towards a molecular phylogeny of colonial spumellarian radiolaria.Marine Micropaleontology, 36, 67-79.

 

1998

Zhou, M., Bhasin, A., and 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), 913-25.

York, D., Welch, K., Goryshin, I. Y., and Reznikoff, W. S. (1998). “Simple and efficient generation in vitro of nested deletions and inversions: Tn5 intramolecular transposition.Nucleic Acids Res, 26(8), 1927-33.

Yigit, H., and 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), 5866-74.

Yahel, G., Post, A. F., Fabricius, K., Marie, D., Vaulot, D., and Genin, A. (1998). “Phytoplankton distribution and grazing near coral reefs.Limnology and Oceanography, 43(4), 551-563.

Tong, S. M., Nygaard, K., Bernard, C., Vors, N., and Patterson, D. J. (1998). “Heterotrophic flagellates from the water column in Port Jackson, Sydney, Australia.European Journal of Protistology, 34(2), 162-194.

Stegeman, J. J., Soballa, V., Morrison, H. G., Jacob, J., and Doehmer, J. (1998). “Catalytic Properties of Scup Cytochrome P4501A Expressed in Chinese Hamster V79 Cells.Marine Environmental Research, 46, 395-395.

Sogin, M. L., and Silberman, J. D. (1998). “Evolution of the protists and protistan parasites from the perspective of molecular systematics.Int J Parasitol, 28(1), 11-20.

Smith, M. W., Aley, S. B., Sogin, M. L., Gillin, F. D., and Evans, G. A. (1998). “Sequence survey of the Giardia lamblia genome.Mol Biochem Parasitol, 95(2), 267-80.

Roger, A. J., Svard, S. G., Tovar, J., Clark, C. G., Smith, M. W., Gillin, F. D., and 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), 229-34.

Noel, R. J. Jr., and 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.

Morrison, H. G., Weil, E. J., Karchner, S. I., Sogin, M. L., and 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), 231-40.

Meselson, M. S., and Stahl, F. W. (1998). “Young Jan.Genetics, 148(4), 1413-4.

Mark Welch, D. B., and Meselson, M. (1998). “Karyotypes of bdelloid rotifers from three families.Hydrobiologia, 387/388, 403-07.

Mark Welch, D. B., and 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.

Mahnke Braam, L. A., and Reznikoff, W. S. (1998). “Functional characterization of the Tn5 transposase by limited proteolysis.J Biol Chem, 273(18), 10908-13.

Lindell, D., Padan, E., and Post, A. F. (1998). “Regulation of ntcA expression and nitrite uptake in the marine Synechococcus sp. strain WH 7803.J Bacteriol, 180(7), 1878-86.

Li, H., Veldhuis, M. J. W., and Post, A. F. (1998). “Alkaline phosphatase activities among planktonic communities in the northern Red Sea.Marine Ecology Progress Series, 173, 107-115.

Lee, W. J., and Patterson, D. J. (1998). “Diversity and geographic distribution of free-living heterotrophic flagellates – Analysis by PRIMER.Protist, 149(3), 229-244.

Hill, G. B. (1998). “Preterm birth: associations with genital and possibly oral microflora.Ann Periodontol, 3.

Henze, K., Morrison, H. G., Sogin, M. L., and MullerM. (1998). “Sequence and phylogenetic position of a class II aldolase gene in the amitochondriate protist, Giardia lamblia.Gene, 222(2), 163-8.

Heep, T., Rohozinski, J., Simpson, A. G. B., and Patterson, D. J. (1998). “Stentor amethystinus (Ciliophora, Heterotrichida), a common member of fresh-water plankton in Australia.Records of the Australian Museum, 50, 211-16.

Goryshin, I. Y., and Reznikoff, W. S. (1998). “Tn5 in vitro transposition.J Biol Chem, 273(13), 7367-74.

Goryshin, I. Y., Miller, J. A., Kil, Y. V., Lanzov, V. A., and Reznikoff, W. S. (1998). “Tn5/IS50 target recognition.Proc Natl Acad Sci U S A, 95(18), 10716-21.

Fladmark, K. E., Serres, M. H., Larsen, N. L., Yasumoto, T., Aune, T., and Doskeland, S. O. (1998). “Sensitive detection of apoptogenic toxins in suspension cultures of rat and salmon hepatocytes.Toxicon, 36(8), 1101-14.

Field, C. B., Behrenfeld, M. J., Randerson, J. T., and Falkowski, P. (1998). “Primary production of the biosphere: integrating terrestrial and oceanic components.Science, 281.

Edgcomb, V., Viscogliosi, E., Simpson, A. G. B., Delgado-Viscogliosi, P., Roger, A. J., and Sogin, M. L. (1998). “New insights into the phylogeny of trichomonads inferred from small subunit rRNA sequences.Protist, 149(4), 359-366.

Derbyshire, V., and Belfort, M. (1998). “Lightning strikes twice: intron-intein coincidence.Proc Natl Acad Sci U S A, 95(4), 1356-7.

Cousineau, B., Smith, D., Lawrence-Cavanagh, S., Mueller, J. E., Yang, J., Mills, D., Manias, D., Dunny, G., Lambowitz, A. M., and Belfort, M. (1998). “Retrohoming of a bacterial group II intron: mobility via complete reverse splicing, independent of homologous DNA recombination.Cell, 94(4), 451-62.

Bordenstein, S. R., and Werren, J. H. (1998). “Effects of A and B Wolbachia and host genotype on interspecies cytoplasmic incompatibility in Nasonia.Genetics, 148(4), 1833-44.

Amaral-Zettler, L. A., Anderson, O. R., and 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), 488-96.

Alliegro, M. C., and Alliegro, M. A. (1998). “Protein heterogeneity in the coiled body compartment.Exp Cell Res, 239(1), 60-8.

Alliegro, M. C. (1998). “Myosin-carbohydrate interactions.Cell Motil Cytoskeleton, 39(3), 191-4.

 

1997

Zhou, Q., Hinkle, G., Sogin, M. L., and Dionne, V. E. (1997). “Phylogenetic analysis of olfactory receptor genes from mudpuppy (Necturus maculosus).Biol Bull, 193(2), 248-50.

Zhou, M., and Reznikoff, W. S. (1997). “Tn5 transposase mutants that alter DNA binding specificity.J Mol Biol, 271(3), 362-73.

Zettler, L. A., Sogin, M. L., and 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), 11411-6.

York, D., and Reznikoff, W. S. (1997). “DNA binding and phasing analyses of Tn5 transposase and a monomeric variant.Nucleic Acids Res, 25(11), 2153-60.

Yigit, H., and 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), 1704-13.

Wernegreen, J. J., Harding, E. E., and Riley, M. A. (1997). “Rhizobium gone native: unexpected plasmid stability of indigenous Rhizobium leguminosarum.Proc Natl Acad Sci U S A, 94(10), 5483-8.

Tong, S., Vors, N., and 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.

Sogin, M. L. (1997). “Organelle origins: energy-producing symbionts in early eukaryotes?Curr Biol, 7(5), R315-7.

Sogin, M. L. (1997). “History assignment: when was the mitochondrion founded?Current Opinions in Genetics & Development, 7, 792-99.

Simpson, A. G., van den Hoff, J., Bernard, C., Burton, H., and Patterson, D. J. (1997). “The ultrastructure and systematic position of the euglenozoan Postgaardi mariagerensis, Fenchel et al.Arch. Protistenk, 147, 213-25.

Simpson, A. G., Bernard, C., Fenchel, T., and 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.

Post, A. F., and Arieli, B. (1997). “Photosynthesis of Prochlorothrix hollandica under Sulfide-Rich Anoxic Conditions.Appl Environ Microbiol, 63(9), 3507-11.

Hinkle, G., Morrison, H. G., and 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), 250-1.

Ekelund, F., and Patterson, D. J. (1997). “Some heterotrophic flagellates from a cultivated garden soil in Australia.Archiv Fur Protistenkunde, 148(4), 461-478.

Danilevskaya, O. N., Arkhipova, I. R., Traverse, K. L., and 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), 647-55.

Czarniecki, D., Noel, R. J. Jr., and Reznikoff, W. S. (1997). “The -45 region of the Escherichia coli lac promoter: CAP-dependent and CAP-independent transcription.J Bacteriol, 179(2), 423-9.

Brugerolle, G., and 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.

Bernard, C., Simpson, A. G., and 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, 254-65.

Arkhipova, I. R., Li, J., and Meselson, M. (1997). “On the mode of gene-dosage compensation in Drosophila.Genetics, 145(3), 729-36.

Amaral-Zettler, L. A., Sogin, M. L., and 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), 11411-6.

Altschul, S., Madden, T., Schaeffer, A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. (1997). “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.Nucleic Acids Res, 25.

Alliegro, M. C., and Linz, L. A. (1997). “Novel characteristics of a myosin isolated from mammalian retinal pigment epithelial and endothelial cells.J Biol Chem, 272(13), 8759-63.

Alliegro, M. C., and Alliegro, M. A. (1997). “Identification of a new coiled body component.Exp Cell Res, 231(2), 386-90.

 

1996

York, D., and Reznikoff, W. S. (1996). “Purification and biochemical analyses of a monomeric form of Tn5 transposase.Nucleic Acids Res, 24(19), 3790-6.

Udomkit, A., Forbes, S., McClean, C., Arkhipova, I. R., and Finnegan, D. J. (1996). “Control of expression of the I factor, a LINE-like transposable element in Drosophila melanogaster.EMBO J, 15(12), 3174-81.

Tavormina, P. L., Reznikoff, W. S., and Gross, C. A. (1996). “Identifying interacting regions in the beta subunit of Escherichia coli RNA polymerase.J Mol Biol, 258(2), 213-23.

Sogin, M. L., Morrison, H. G., Hinkle, G., and Silberman, J. D. (1996). “Ancestral relationships of the major eukaryotic lineages.Microbiologia, 12(1), 17-28.

Simpson, A. G. B., and 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.

Silberman, J. D., Sogin, M. L., Leipe, D. D., and Clark, C. G. (1996). “Human parasite finds taxonomic home.Nature, 380(6573), 398.

Silberman, J. D., Clark, C. G., and Sogin, M. L. (1996). “Dientamoeba fragilis shares a recent common evolutionary history with the trichomonads.Mol Biochem Parasitol, 76(1-2), 311-4.

Serres, M. H., and Ensign, J. C. (1996). “Endogenous ADP-ribosylation of proteins in Mycobacterium smegmatis.J Bacteriol, 178(20), 6074-7.

Schlegel, M., Lom, J., Stechmann, A., Bernhard, D., Leipe, D., Dykova, I., and 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.

Santamaria-Fries, M., Fajardo, L. F., Sogin, M. L., Olson, P. D., and Relman, D. A. (1996). “Lethal infection by a previously unrecognised metazoan parasite.Lancet, 347(9018), 1797-801.

Relman, D. A., Schmidt, T. M., Gajadhar, A., Sogin, M. L., Cross, J., Yoder, K., Sethabutr, O., and 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.

Patterson, D. J., and Simpson, A. G. B. (1996). “Heterotrophic flagellates from coastal marine and hypersaline sediments in Western Australia.European Journal of Protistology, 32(4), 423-448.

O’Kelly, C. J., and Patterson, D. J. (1996). “The flagellar apparatus of Cafeteria roenbergensis Fenchel & Patterson 1988 (Bicosoecales = Bicosoecida).European Journal of Protistology, 32, 216-26.

Leipe, D. D., Tong, S. M., Goggin, C. L., Slemenda, S. B., Pieniazek, N. J., and 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.

Jilk, R. A., York, D., and Reznikoff, W. S. (1996). “The organization of the outside end of transposon Tn5.J Bacteriol, 178(6), 1671-9.

Hammerschmidt, B., Schlegel, M., Lynn, D. H., Leipe, D. D., Sogin, M. L., and 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), 225-30.

Ekebom, J., Patterson, D. J., and Vors, N. (1996). “Heterotrophic flagellates from coral reef sediments (Great Barrier Reef, Australia).Archiv Fur Protistenkunde, 146(3-4), 251-272.

Dwivedi, K., Post, A. F., and 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), 210-4.

Bahr, M., Hobbie, J. E., and Sogin, M. L. (1996). “Bacterial diversity in an arctic lake: A freshwater SAR11 cluster.Aquatic Microbial Ecology, 11(3), 271-277.

Alliegro, M. C., and Alliegro, M. A. (1996). “Identification of a new coiled body component.Exp Cell Res, 227(2), 386-90.

Alliegro, M. C., and Alliegro, M. A. (1996). “A nuclear protein regulated during the transition from active to quiescent phenotype in cultured endothelial cells.Dev Biol, 174(2), 288-97.

Agamalian, N. S., Arkhipova, I. R., Surkov, S. A., and 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), 818-28.

Print Friendly