Publications

Top 25 Journals

Proc Natl Acad Sci U S A (48), PLoS One (25), Appl Environ Microbiol (24), ISME J (21), Mol Biol Evol (19), J Bacteriol (19), Nucleic Acids Res (17), J Biol Chem (16), Environ Microbiol (16), J Mol Biol (14), Biol Bull (14), Science (12), European Journal of Protistology (12), Nature (11), J Eukaryot Microbiol (10), Hydrobiologia (8), Genetics (8), BMC Genomics (8), Mol Microbiol (7), Gene (7), Protist (6), Microbiome (6), Limnology and Oceanography (6), PLoS Biol (5), Mol Biochem Parasitol (5)

Years

2014 (47) | 2013 (42) | 2012 (43) | 2011 (40) | 2010 (28) | 2009 (45) | 2008 (36) | 2007 (42) | 2006 (35) | 2005 (45) | 2004 (25) | 2003 (42) | 2002 (43) | 2001 (34) | 2000 (39) | 1999 (26) | 1998 (30) | 1997 (22) | 1996 (22)

2014

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.

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.

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., Steven Wiley, H., Fredrickson, J. K., and Konopka, A. (2014). “Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing.ISME J, 10.1038/ismej.2014.69.

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.

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.

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.

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, 10.1073/pnas.1406199111.

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-E2884.

Eren, A. M., Morrison, H. G., Lescault, P. J., Reveillaud, J., Vineis, J. H., and Sogin, M. L. (2014). “Minimum Entropy Decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences.ISME Journal, In Press.

Eren, A. M., Sogin, M. L., Morrison, H. G., Vineis, J. H., Fisher, J. C., Newton, R. J., and McLellan, S. L. (2014). “A single genus in the gut microbiome reflects host preference and specificity.ISME J, 10.1038/ismej.2014.97.

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.

Gibbons, S. M., Schwartz, T., Fouquier, J., Mitchell, M., Sangwan, N., Gilbert, J. A., and Kelley, S. T. (2014). “Ecological succession and viability of human-associated microbiota on restroom surfaces.Appl Environ Microbiol, 10.1128/AEM.03117-14.

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.

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.

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.

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.

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.

Huo, Y.-Y., Cheng, H., Post, A. F., Wang, C.-S., Jiang, X.-W., Pan, J., Wu, M., and Xu, X.-W. (2014). “Ecological functions of uncultured microorganisms in the cobalt-rich ferromanganese crust of a seamount in the Central Pacific are elucidated by fosmid Sequencing.Acta Oceanologia Sinica, in press.

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.

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.

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.

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.

Koskey, A. M., Fisher, J. C., Eren, A. M., Terashima, R. P., 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.Environmental Microbiology Reports, 10.1111/1758-2229.12189.

Larsen, P. E., Scott, N., Post, A. F., Field, D., Knight, R., Hamada, Y., and Gilbert, J. A. (2014). “Satellite remote sensing data can be used to model marine microbial metabolite turnover.ISME J, 10.1038/ismej.2014.107.

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.Frontiers in Microbiology, 5.

Lie, A. A. Y., 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.

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.

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.

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.

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.Frontiers in Microbiology, 5.

McLellan, S. L., and Eren, A. M. (2014). “Discovering new indicators of fecal pollution.Trends Microbiol, 10.1016/j.tim.2014.08.002, in press.

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.

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.

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.

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.Sci. Dril., 17, 61-66.

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.

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.

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.

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.

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

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.

Snell, T. W., Johnston, R. K., Gribble, K. E., and Mark Welch, D. B. (2014). “Rotifers as experimental tools for investigating aging.Invertebrate Reproduction & Development, 10.1080/07924259.2014.925516, 1-6.

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.

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.

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.

Willger, S. D., Grim, S. L., Dolben, F., 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, In Press.

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.Biological Bulletin, In Press.

2013

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.

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.

Amaral-Zettler, L. A. (2013). “Eukaryotic diversity at pH extremes.Front Microbiol, 3, 441.

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.

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.

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.

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.

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.

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).

Eren, A. M., Morrison, H. G., Huse, S. M., and Sogin, M. L. (2013). “DRISEE overestimates errors in metagenomic sequencing data.Brief Bioinform, 10.1093/bib/bbt010.

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.

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.

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.

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.

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.

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. (2013). “Iron supplementation does not worsen respiratory health or alter the sputum microbiome in cystic fibrosis.J Cyst Fibros, 13(3), 311-8.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

2012

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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 Tamrix Trees across the Sonoran Desert.Appl Environ Microbiol, 78(17), 6187-93.

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

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.

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.

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.

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.

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.

Lasek-Nesselquist, E. (2012). “A Mitogenomic Re-Evaluation of the Bdelloid Phylogeny and Relationships among the Syndermata.PLoS One, 7(8), e43554.

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.

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.

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.

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).

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.

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.

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 oceanóclues from seasonal and diurnal variations.Marine Ecology Progress Series, 453, 11-26.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

2011

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.

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.

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

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

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.

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.

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.

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.

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.

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.

Field, D., Amaral-Zettler, L. A., Cochrane, G., Cole, J. R., Dawyndt, P., Garrity, G. M., Gilbert, J., Gl√∂ckner, 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.

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.

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.

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.

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.

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. (2011). “Defining seasonal marine microbial community dynamics.ISME J, 6(2), 298-308.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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., Gil, I. S., 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., Spor, 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.

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.

2010

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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, 10.1007/s10750-010-0482-6, 1-8.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Smith, H., Mark Welch, D. B., and Snell, T. (2010). “Molecular evolution of the membrane associated progesterone receptor within the Brachionus plicatilis (Rotifera, Monogononta) species complex.Hydrobiologia, 10.1007/s10750-010-0484-4, 1-8-8.

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.

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.

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.

2009

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.

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.

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.

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.

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.

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.

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.

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.

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), 483-94.

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.

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.

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.

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.

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.

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.

Hur, J. H., Van Doninck, K., Mandigo, M. L., and Meselson, M. (2009). “Degenerate Tetraploidy Was Established Before Bdelloid Rotifer Families Diverged.Molecular Biology and Evolution, 26(2), 375-383.

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.

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. (2009). “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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Schrenk, M. O., Huber, J. A., and Edwards, K. J. (2009). “Microbial Provinces in the Subseafloor.Ann Rev Mar Sci, 2(1), 279-304.

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

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.

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.

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.

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.

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.

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.

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.

Wernegreen, J. J., Kauppinen, S. N., and Degnan, P. H. (2009). “Slip into something more functional: Selection maintains ancient frameshifts in homopolymeric sequences.Mol Biol Evol, 27(4), 833-9.

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.

Whitman, C. T., Wirth, T. E., Meselson, M., Nissen, S. E., Juma, C., and Daley, G. (2009). “Your inbox, Mr President.Nature, 457(7227), 258-261.

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.

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.

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.

2008

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

Gladyshev, E. A., Meselson, M., and Arkhipova, I. R. (2008). “Massive Horizontal Gene Transfer in Bdelloid Rotifers.Science, 320(5880), 1210-3.

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.

Gradman, R. J., and Reznikoff, W. S. (2008). “Tn5 Synaptic Complex Formation: Role of Transposase Residue W450.J Bacteriol, 190(4), 1484-7.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Riley, M., Staley, J. T., Danhin, A., Wang, T., 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.

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.

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.

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.

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.

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.

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

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., and Davidson, E. H. (2008). “A new method, using cis-regulatory control, for blocking embryonic gene expression.Developmental Biology, 318(2), 360-365.

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.

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.

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.

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.

2007

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.

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.

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.

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

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

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Gradman, R. J., and Reznikoff, W. S. (2007). “Tn5 Synaptic Complex Formation: The role of Transposase Residue W450.J Bacteriol, 190(4), 1484-7.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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

2006

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.

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.

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.

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

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.

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

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.

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.

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.

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.

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.

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

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

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

2005

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

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.

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

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

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

Polaszek, A., Agosti, D., Alonso-Zarazaga, M., Beccaloni, G., de Place Bjorn, P., Bouchet, P., Brothers, D. J., Cranbrook, E. o., Evenhuis, N., Godfray, H. C. J., Johnson, N. F., Krell, F. T., Lipscomb, D., Lyal, C. H. C., Mace, G. M., Mawatari, S., Miller, S. E., Minelli, A., Morris, S., Ng, P. K. L., Patterson, D. J., Pyle, R. L., Robinson, N., Rogo, L., Taverne, J., Thompson, F. C., van Tol, J., Wheeler, Q. D., and Wilson, E. O. (2005). “A universal register for animal names.Nature, 437(7058), 477.

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

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

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

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.

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

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.

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.

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.

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.

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

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.

2004

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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

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.

2003

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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

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.

Noble, M., Smith, J., Power, J., and Mayer-Proschel, M. (2003). “Redox state as a central modulator of precursor cell function.Ann N Y Acad Sci. , 991, 251-271.

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.

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.

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

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

2002

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.

Alliegro, M. C. (2002). “Coiled body heterogeneity induced by G(1) arrest with amiloride + bumetanide.Exp Cell Res, 279(1), 111-7.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

2001

Alliegro, M. C. (2001). “Pigpen and endothelial cell differentiation.Cell Biol Int, 25(7), 577-84.

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.

Arkhipova, I. R. (2001). “[Transposable elements in the Animal Kingdom].Mol Biol (Mosk), 35(2), 196-207.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Mark Welch, D. B. (2001). “Early contributions of molecular phylogenetics to understanding the evolution of Rotifera.Hydrobiologia, 446-447(1), 315-322.

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.

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.

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.

Mikrjukov, K. A., and Patterson, D. J. (2001). “Taxonomy and phylogeny of heliozoa. III. Actinophryids.Acta Protozoologica, 40(1), 3-25.

Morrison, H. G., Roger, A. J., Nystul, T. G., Gillin, F. D., and Sogin, M. L. (2001). “Giardia lamblia expresses a proteobacterial-like DnaK homolog.Mol Biol Evol, 18(4), 530-41.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Wernegreen, J. J., and Moran, N. A. (2001). “Vertical transmission of biosynthetic plasmids in aphid endosymbionts (Buchnera).J Bacteriol, 183(2), 785-90.

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.

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.

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.

2000

Alliegro, M. C. (2000). “A C-terminal carbohydrate-binding domain in the endothelial cell regulatory protein, pigpen: new function for an EWS family member.Exp Cell Res, 255(2), 270-7.

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.

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.

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.

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.

Bernard, C., Simpson, A. G. B., and Patterson, D. J. (2000). “Some free-living flagellates (protista) from anoxic habitats.Ophelia, 52(2), 113-142.

Bhasin, A., Goryshin, I. Y., Steiniger-White, M., York, D., and Reznikoff, W. S. (2000). “Characterization of a Tn5 pre-cleavage synaptic complex.J Mol Biol, 302(1), 49-63.

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.

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.

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.

Cousineau, B., Lawrence, S., Smith, D., and Belfort, M. (2000). “Retrotransposition of a bacterial group II intron.Nature, 404(6781), 1018-21.

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.

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.

Edgell, D. R., Belfort, M., and Shub, D. A. (2000). “Barriers to intron promiscuity in bacteria.J Bacteriol, 182(19), 5281-9.

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.

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.

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.

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.

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.

Lease, R. A., and Belfort, M. (2000). “Riboregulation by DsrA RNA: trans-actions for global economy.Mol Microbiol, 38(4), 667-72.

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.

Mark Welch, D. B. (2000). “Evidence from a protein-coding gene that acanthocephalans are rotifers.Invertebrate Biology, 119(1), 17-26.

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.

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.

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.

Moran, N. A., and Wernegreen, J. J. (2000). “Lifestyle evolution in symbiotic bacteria: insights from genomics.Trends Ecol Evol, 15(8), 321-326.

Naumann, T. A., and Reznikoff, W. S. (2000). “Trans catalysis in Tn5 transposition.Proc Natl Acad Sci U S A, 97(16), 8944-9.

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.

Riley, M., and Serres, M. H. (2000). “Interim report on genomics of Escherichia coli.Annu Rev Microbiol, 54, 341-411.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

1999

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.

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).

Bhasin, A., Goryshin, I. Y., and Reznikoff, W. S. (1999). “Hairpin formation in Tn5 transposition.J Biol Chem, 274(52), 37021-9.

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.

Dixon, T. C., Meselson, M., Guillemin, J., and Hanna, P. C. (1999). “Anthrax.N Engl J Med, 341(11), 815-26.

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.

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.

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.

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.

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.

Meselson, M. (1999). “The challenge of biological and chemical weapons.Bull World Health Organ, 77(2), 102-3.

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.

Patterson, D. J. (1999). “The Diversity of Eukaryotes.Am Nat, 154(S4), S96-S124.

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.

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.

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.

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.

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.

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.

Sogin, M. L. (1999). “A molecular point of view (introductory and concluding remarks.Biol. Bull, 196, 415-16.

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.

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.

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.

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.

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.

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.

1998

Alliegro, M. C. (1998). “Myosin-carbohydrate interactions.Cell Motil Cytoskeleton, 39(3), 191-4.

Alliegro, M. C., and Alliegro, M. A. (1998). “Protein heterogeneity in the coiled body compartment.Exp Cell Res, 239(1), 60-8.

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.

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.

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.

Derbyshire, V., and Belfort, M. (1998). “Lightning strikes twice: intron-intein coincidence.Proc Natl Acad Sci U S A, 95(4), 1356-7.

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.

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.

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.

Goryshin, I. Y., and Reznikoff, W. S. (1998). “Tn5 in vitro transposition.J Biol Chem, 273(13), 7367-74.

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.

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.

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.

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.

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.

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.

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.

Mark Welch, D. B., and Meselson, M. (1998). “Karyotypes of bdelloid rotifers from three families.Hydrobiologia, 387/388, 403-07.

Meselson, M. S., and Stahl, F. W. (1998). “Young Jan.Genetics, 148(4), 1413-4.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

1997

Alliegro, M. C., and Alliegro, M. A. (1997). “Identification of a new coiled body component.Exp Cell Res, 231(2), 386-90.

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.

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.

Arkhipova, I. R., Li, J., and Meselson, M. (1997). “On the mode of gene-dosage compensation in Drosophila.Genetics, 145(3), 729-36.

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.

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.

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.

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.

Ekelund, F., and Patterson, D. J. (1997). “Some heterotrophic flagellates from a cultivated garden soil in Australia.Archiv Fur Protistenkunde, 148(4), 461-478.

Hinkle, G., Morrison, H. G., 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.

Post, A. F., and Arieli, B. (1997). “Photosynthesis of Prochlorothrix hollandica under Sulfide-Rich Anoxic Conditions.Appl Environ Microbiol, 63(9), 3507-11.

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.

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.

Sogin, M. L. (1997). “History assignment: when was the mitochondrion founded?Current Opinions in Genetics & Development, 7, 792-99.

Sogin, M. L. (1997). “Organelle origins: energy-producing symbionts in early eukaryotes?Curr Biol, 7(5), R315-7.

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.

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.

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.

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.

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.

Zhou, M., and Reznikoff, W. S. (1997). “Tn5 transposase mutants that alter DNA binding specificity.J Mol Biol, 271(3), 362-73.

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.

1996

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.

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.

Alliegro, M. C., and Alliegro, M. A. (1996). “Identification of a new coiled body component.Exp Cell Res, 227(2), 386-90.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Serres, M. H., and Ensign, J. C. (1996). “Endogenous ADP-ribosylation of proteins in Mycobacterium smegmatis.J Bacteriol, 178(20), 6074-7.

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.

Silberman, J. D., Sogin, M. L., Leipe, D. D., and Clark, C. G. (1996). “Human parasite finds taxonomic home.Nature, 380(6573), 398.

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.

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.

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.

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.

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.

Print Friendly