Publications

2014

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., 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.

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, Article first published online: 24 MAR 2014.

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.

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.

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.

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.

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., Eren, A. M., 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.

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.

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.

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." Frontiers in Microbiology, 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), 800-11.

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." Mobile DNA, 4(1), 19.

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

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.

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., 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., 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., Welch, D. B., Stelzer, C. P., and Logsdon, J. M., Jr. (2013). "Inventory and phylogenetic analysis of meiotic genes in monogonont rotifers." J Here'd, 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.

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

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., 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." The Journal of biological chemistry, 287(9), 6702-13.

Arkhipova, I.R. (2012). Telomerase, retrotransposons, and evolution. In: Telomerases: Chemistry, Biology and Clinical Applications, pp. 265-99. N.F. Lue and C. Autexier, eds. John Wiley and Sons, Inc.: Hoboken, NJ.

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. Mobile 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." Environmental Microbiology, 14(1), 140-46.

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 Research, 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." The ISME journal, 6(11), 2014–23.

Brandt, B.W., Bonder, M.J., Huse, S.M., Zaura, E. (2012). TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W82-7. Epub 2012 May 22.

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 automated optofluidic system for the laser microsurgery of non-adherent oocytes. J. Biomed. Optics. 17:015001

Chapman, M., and Alliegro, M. C. (2012). "The karyomastigont as an evolutionary seme." Quart. 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." The ISME journal, 6(9), 1629-39.

Davies, N., Meyer, C., Gilbert, J. A., Amaral-Zettler, L. A., Deck, J., Bicak, M., Rocca-Serra, P., Assunta-Sansone, S., Willis, K., and Field, D. (2012). "A call for an international network of genomic observatories (GOs)." Giga Science, 1, 5.

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." Journal of Bacteriology, 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." Applied and Environmental Microbiology, 78(17), 6187-93.

Fischer, A. H. L., and Smith, J. (2012). "Evo-devo in the era of gene regulatory networks." Integrative and comparative biology, 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." The ISME journal, 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. The ISME Journal (2012) 6, 542–53; doi:10.1038/ismej.2011.132; published online 6 October 2011.

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 Evolutionary Biology 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.

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." Proceedings of the National Academy of Sciences of the United States of America, 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." Environmental Science & Technology, 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." Archives of disease in childhood. Fetal and neonatal edition, 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." The ISME journal, 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." Bioorganic & medicinal chemistry letters, 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." International endodontic journal, 45(6), 530-41.

Post, A. F., Rihtman, B., and Wang, Q. (2012). "Decoupling of ammonium regulation and ntcA transcription in the diazotrophic marine cyanobacterium Trichodesmium sp. IMS101." The ISME journal(6), 629-37.

Rozhkov NV, Schostak NG, Zelentsova ES, Yushenova IA, Zatsepina OG, Evgen'ev MB. (2012). Evolution and dynamics of small RNA response to a retroelement invasion in Drosophila. Mol Biol Evol. doi: 10.1093/molbev/mss241. Epub Oct 18.

Sansone, S. A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral-Zettler, L., 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." Nature genetics, 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. R., Coolen, M. J. L., Sogin, M., Ferreira, A. J. S., 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., Rosen, G. E., and Amaral-Zettler, L. (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)." The ISME Journal(6), 670-79.

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." Briefings in bioinformatics, 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." Parasites & vectors, 5, 168.

Thor Marteinsson, V., 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." The ISME journal, 7(2), 427-37.

Toney, J. L., Theroux, S., Andersen, R. A., Coleman, A., Amaral-Zettler, L., 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." Systematic and Applied Microbiology, 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." Environmental Microbiology, 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." Proceedings of the National Academy of Sciences of the United States of America, 109, 13674-79.

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." Bioorganic & medicinal chemistry letters, 22(7), 2579-81.

Wolf, B., Schwarzer, A., Côté, 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." Molecular Ecology, 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), 436-445.

Alliegro, M. (2011). "The centrosome and spindle as a ribonucleoprotein complex." Chromosome Research, 19(3), 367-376.

Alliegro, M. C. (2011). "The Nucleolinus: A disappearing, forgotten and (maybe) misnamed organelle." Communicative & integrative biology, 4(2), 147-9.

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." The ISME journal, 5(1), 42-50.

Bland, N. D., Cuihua, W. C., Tallman, C., Gustafson, A. E., Wang, Z., Ashton, T. D., Ochiana, S. O., McAllister, G., Cotter, K., Fang, A. P., Gechijian, L., Garceau, N., Gangurde, R., Ortenberg, R., Ondrechen, M. J., Campbell, R. K., and Pollastri, M. P. (2011). "Pharmacological Validation of Trypanosoma brucei Phosphodiesterases B1 and B2 as Druggable Targets for African Sleeping Sickness." Journal of Medicinal Chemistry, 54(23), 8188-94.

Bogaert, D., Keijser, B., Huse, S., 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.

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 Medical 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., 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." Applied and Environmental Microbiology, 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." Journal of Water and Health, 9(1), 37-52.

Gilbert, J. A., Steele, J. A., Caporaso, J. G., Steinbruck, L., Reeder, J., Temperton, B., Huse, S., McHardy, A. C., Knight, R., Joint, I., Somerfield, P., Fuhrman, J. A., and Field, D. (2011). "Defining seasonal marine microbial community dynamics." The ISME journal.

Gladyshev, E. A., and Arkhipova, I. R. (2011). "A widespread class of reverse transcriptase-related cellular genes." Proc. Natl. Acad. Sci. USA(51), 20311-20316.

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), 35–42.

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

Kamennaya, N. A., and Post, A. F. (2011). "Characterization of cyanate metabolism in marine Synechococcus and Prochlorococcus spp." Applied and Environmental Microbiology, 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.

Mark Welch, D. B., and Huse, S. H. (2011). "Microbial diversity in the deep sea and the underexplored “rare biosphere", in F. J. de Bruijn, (ed.), Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. Wiley and Sons, pp. 245-52.

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." The ISME journal.

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.

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., 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." Molecular and Biochemical Parasitology.

Pollastri, M. P., and Campbell, R. K. (2011). "Target repurposing for neglected diseases." Future medicinal chemistry, 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." Frontiers in Microbiology, 2, 131.

Post, A. F., Rihtman, B., and Wang, Q. (2011). "Decoupling of ammonium regulation and ntcA transcription in the diazotrophic marine cyanobacterium Trichodesmium sp. IMS101." The ISME journal.

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 Geosci, advance online publication.

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 genus level." Applied and Environmental Microbiology, 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." Applied and Environmental Microbiology, 77(9), 2992-3001.

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

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." The Biological bulletin, 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." Proceedings of the National Academy of Sciences of the United States of America, 108(35), 14637-42.

Valm, A. M., 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." Proceedings of the National Academy of Sciences of the United States of America, 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." Applied and Environmental Microbiology, 77(13), 4527-38.

Xia, L., Steele, J., Cram, J., Cardon, Z., Simmons, S., Vallino, J., Fuhrman, J., and Sun, F. (2011). "Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates." BMC Systems Biology, 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 Computational Biology, 7(10), e1002230.

Yilmaz, P., Gilbert, J. A., Knight, R., Amaral-Zettler, L., 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), 1565-1567.

Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J. R., Amaral-Zettler, L., 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." Nature biotechnology, 29(5), 415-420.

Zinger, L., Amaral-Zettler, L. A., Fuhrman, J. A., Horner-Devine, M. C., Huse, S. M., Welch, D. B. M., Martiny, J. B. H., 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

Aberle, N., Hansen, T., Böttger-Schnack, R., Burmeister, A., Post, A. F., and Sommer, U. (2010). "Trophodynamic interactions of zooplankton communities in the northern Gulf of Aqaba." Mar. Biol., 157, 157-69.

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.

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.

Amaral-Zettler, L. A., Zettler, E. R., Theroux, S. M., Palacios, C., Aguilera, A., and Amils, R. (2010). "Microbial community structure across the tree of life in the extreme Rio Tinto." ISME J.

Amaral-Zettler, L., Artigas, L. F., Baross, J., Bharathi, L., Boetius, A., Chandramohan, D., Herndl, G., Kogure, K., Neal, P., Pedros-Alio, C., Ramette, A., Schouten, S., Stal, L., Thessen, A., de Leeuw, J., and Sogin, M. (2010). "A global census of marine microbes", Life in the World's Oceans: Diversity, Distribution and Abundance. Oxford: Blackwell Publishing Ltd., pp. 223-45.

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, 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." The American Biology Teacher, 72, 478-83.

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.

Claessens, M., Wickham, S. A., Post, A. F., and Reuter, M. (2010). "A paradox of the ciliates? High cilate diversity in a resource-poor environment." Mar. Biol., 157, 483-94.

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.

Gast, R. J., Moran, D. M., Dennett, M. R., Wurtsbaugh, W. A., and Amaral-Zettler, L. A. (2010). "Amoebae and pathogenic Legionella pneumophila in saline environments." Journal of Water and Health, doi:10.2166/wh.2010.103.

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, 14020-14025.

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., Post, A. F., and Belkin, S. (2010). "Phosphorus and nitrogen in a monomictic fresh water lake: a new insight into nutrient bioavailability." Freshwater Biol., 55(3), 1182-90.

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

Gladyshev, E. A., and Arkhipova, I. R. (2010). "A subtelomeric non-LTR retrotransposon Hebe in the bdelloid rotifer Adineta vaga is subject to inactivation by deletions but not 5' truncations." Mob DNA, 1(1), 12.

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

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

Hasegawa, Y., Mark Welch, J. L., Valm, A. M., Rieken, C. W., 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), 251-60.

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, 538-49.

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

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

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), Jul6;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, 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 CLIP-170." Mol Biol Cell.

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.

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

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., and Snell, T. (2010). "Molecular evolution of the membrane associated progesterone receptor within the Brachionus plicatilis (Rotifera, Monogononta) species complex." Hydrobiologia, 662:99–106.

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), 673-80.

Stock, S.P., Bordenstein, S.R., Odden, J., Oldenburg, D., Reznikoff, W., Selosse, M.-A., and Werren, J.H. (2010).  Symbiosis instruction: Considerations from the Education Workshop at the 6th ISS Congress.  Symbiosis 51, 67-73.

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, 311-20.
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 Chem., 120 (1-4), 90-99.

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 Chem., 120 (1-4), 90-99.

2009

Aberle, N., Hansen, T., Böttger-Schnack, R., Holzman, R., Post, A. F., and Sommer, U. (2009). "Trophodynamic interactions of zooplankton communities in the northern Gulf of Aqaba." Mar. Biol., in press.

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." Meth. Cell Biol., 94, 51-63.

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.

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. (2009). "Comparative community genomics in the Dead Sea: an increasingly extreme environment." ISME J.

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., and Joint, I. (2009). "The seasonal structure of microbial communities in the Western English Channel." Environ Microbiol.

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

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

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." Mol Biol Evol, 26(2), 375-83.

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.

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. (2009a). "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. (2009b). "Chronic exposure to arsenic in the drinking water alters the expression of immune response genes in mouse lung." Environ Health Perspect, 117(7), 1108-15.

Kozul, C. D., Horvath, R. J., Bomberger, J. M., and Hamilton, J. W. (2009c). "Arsenic decreases chemotaxis of bone marrow derived dendritic cells." in review.

Lasek-Nesselquist, E., Welch, D. M., 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., 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.

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.

McLellan, S. L., Huse, S. M., Mueller-Spitz, S. R., Andreishcheva, E. N., and Sogin, M. L. (2009). "Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent." Environ Microbiol.

Nahum, L. A., Goswami, S., and Serres, M. H. (2009). "Protein Families Reflect Metabolic Diversity of Organisms and Provide Support for Functional Prediction." Physiol Genomics, 38, 250-60.

Paytan, A., Mackey, K. R. M., Chen, Y., Lima, I. D., S.C., D., and Post, A. F. (2009). "Toxicity of atmospheric aerosols on marine phytoplankton." Proc. Natl. Acad. Sci., 106(12), 4601-4605.

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

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), 249-299.

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

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

Sogin, M. L. (2009). Characterizing Microbial Population Structures through Massively Parallel Sequencing: “Uncultivated Microorganisms”: Springer

Stoeck, T., Behnke, A., Christen, R., Amaral-Zettler, L., 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. (2009a). "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. (2009b). "Slip into something more functional: Selection maintains ancient frameshifts in homopolymeric sequences." Mol Biol Evol.

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

Alliegro, M. C. and M. A. Alliegro (2008). "Centrosomal RNA correlates with intron-poor nuclear genes in Spisula oocytes." Proc Natl Acad Sci USA (105): 6993-97.

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

Souza-Egipsy, V., González-Toril E., Zettler, E., Amaral-Zettler, L., Aguilera, A. and Amils, R. 2008. Prokaryotic community structure in algal photosynthetic biofilms from extreme acidic streams in Río Tinto (Huelva, Spain). International Microbiology.doi: 10.2436/20.1501.01.xx.

Amaral-Zettler, L. A., J. D. Rocca, M. G. Lamontagne, M. R. Dennett and R. J. Gast (2008). "Changes in microbial community structure in the wake of Hurricanes Katrina and Rita." Environmental Science & Technology 42(24): 9072-9078

Aurrecoechea, C., J. Brestelli, B. P. Brunk, J. M. Carlton, J. Dommer, S. Fischer, B. Gajria, X. Gao, A. Gingle, G. Grant, O. S. Harb, M. Heiges, F. Innamorato, J. Iodice, J. C. Kissinger, E. Kraemer, W. Li, J. A. Miller, H. G. Morrison, V. Nayak, C. Pennington, D. F. Pinney, D. S. Roos, C. Ross, C. J. Stoeckert, Jr., S. Sullivan, C. Treatman and H. Wang (2008). "GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis." Nucl. Acids Res.: gkn631.

Davey, J. C., A. P. Nomikos, M. Wungjiranirun, J. R. Sherman, L. Ingram, C. Batki, J. P. Lariviere and J. W. Hamilton (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., S. Huse, M. L. Sogin and D. A. Relman (2008). "The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing." PLoS Biology 6(11): e280.

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

Gil, I. S., W. Sheldon, T. Schmidt, M. Servilla, R. Aguilar, C. Gries, T. Gray, D. Field, J. Cole, J. Y. Pan, G. Palanisamy, D. Henshaw, M. O'Brien, L. Kinkel, K. McMahon, R. Kottmann, L. Amaral-Zettler, J. Hobbie, P. Goldstein, R. P. Guralnick, J. Brunt and W. K. Michener (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. and M. Meselson (2008). "Extreme resistance of bdelloid rotifers to ionizing radiation." Proc Natl Acad Sci USA 105(13): 5139-5144.

Gladyshev, E. A., M. Meselson and I. R. Arkhipova (2008). "Massive Horizontal Gene Transfer in Bdelloid Rotifers." Science 320(5880): 1210-1213.

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

Gradman, R. J. and W. S. Reznikoff (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., Camenisch, T.  “Arsenic down-regulates vascular matrix.” Toxicol Pathol 36:805-817, 2008.

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

Huse, S. M., L. Dethlefsen, J. A. Huber, D. M. Welch, D. A. Relman and M. L. Sogin (2008). "Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing." PLoS Genetics 4(11): e1000255.

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

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

Kozul, C. D., A. P. Nomikos, T. H. Hampton, L. A. Warnke, J. A. Gosse, J. C. Davey, J. E. Thorpe, B. P. Jackson, M. A. Ihnat and J. W. Hamilton (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., A. L. Bogomolni, R. J. Gast, D. M. Welch, J. C. Ellis, M. L. Sogin and M. J. Moore (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., J. L. Mark Welch and M. Meselson (2008). "Evidence for degenerate tetraploidy in bdelloid rotifers." Proc Natl Acad Sci U S A.

Nahum, L. A. and S. L. Pereira (2008). Phylogenomics, Protein Family Evolution, and the Tree of Life: An Integrated Approach between Molecular Evolution and Computational Intelligence. Studies in Computational Intelligence (SCI). T. Smolinski, M. Milanova and A.-E. Hassanien. Berlin Heidelberg, Springer-Verlag. 122: 259-79.

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

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

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

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

Schostak, N., K. I. Pyatkov, E. Zelentsova, I. R. Arkhipova, D. Shagin, I. Shagina, E. Mudrik, A. Blintsov, I. Clark, D. J. Finnegan and M. B. Evgen'ev (2008). "Molecular dissection of Penelope transposable element regulatory machinery." Nucleic Acids Res. 36(8): 2522-2529.

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

Souza-Egipsy, V., González-Toril E., Zettler, E., Amaral-Zettler, L., Aguilera, A. and Amils, R. 2008. Prokaryotic community structure in algal photosynthetic biofilms from extreme acidic streams in Río Tinto (Huelva, Spain). International Microbiology.11: 251-260

Suga, K., D. B. Mark Welch, Y. Tanaka, Y. Sakakura and A. Hagiwara (2008). "Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis." Molecular Biology and Evolution 25(4): 1129-37.

Tamas, I., J. J. Wernegreen, B. Nystedt, S. N. Kauppinen, A. C. Darby, L. Gomez-Valero, D. Lundin, A. M. Poole and S. G. Andersson (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.

Turnbaugh, P. J., M. Hamady, T. Yatsunenko, B. L. Cantarel, A. Duncan, R. E. Ley, M. L. Sogin, W. J. Jones, B. A. Roe, J. P. Affourtit, M. Egholm, B. Henrissat, A. C. Heath, R. Knight and J. I. Gordon (2008). "A core gut microbiome in obese and lean twins." Nature.

Ye, S., MacEachran, D.P., Hamilton, J.W., O’Toole, G.A, Stanton, B.A. “Surface expression of P-glycoprotein is regulated by the Pseudomonas aeruginosa toxin Cif.” Am J Physiol: Cell Physiol 295:C807-C818, 2008.

2007

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., J.A. Huber, H.G. Morrison, M.L. Sogin, and D.M. Welch, Accuracy and quality of massively parallel DNA pyrosequencing.  Genome Biol, 2007. 8(7): p. R143.

Morrison, H.G., A.G. McArthur, F.D. Gillin, S.B. Aley, R.D. Adam, G.J. Olsen, A.A. Best, W.Z. Cande, F. Chen, M.J. Cipriano, B.J. Davids, S.C. Dawson, H.G. Elmendorf, A.B. Hehl, M.E. Holder, S.M. Huse, U.U. Kim, E. Lasek-Nesselquist, G. Manning, A. Nigam, J.E.  Nixon, D. Palm, N.E. Passamaneck, A. Prabhu, C.I. Reich, D.S. Reiner, J. Samuelson, S.G. Svard, and M.L. Sogin, Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science, 2007. 317(5846): p. 1921-6.

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

Corradi, N., D.E. Akiyoshi, H.G. Morrison, X. Feng,  L.M. Weiss,  S. Tzipori, and P.J. Keeling, Patterns of Genome Evolution among  the Microsporidian Parasites Encephalitozoon cuniculi, Antonospora locustae, and Enterocytozoon bieneusi.  PloS ONE, 2007. 2(12):e1277. Giardia publication and establishment of giardiadb.org site.

Leary, P. R., Remsen, D.P., Norton, C. N. Patterson,. D. J. and Sarkar, I. N. 2007. Bioinformatics, 23: 1434-1436

Patterson, David J. and Sogin, M. L. 2007.  The micro*scope web tool. pp 579-584 in  Sullivan W. T., Baross, J. A., (eds)  Planets and Life: The emerging Science of Astrobiology.  Cambridge University Press, Cambridge.

Sogin, M. l., Patterson, David J. and McArthur, A. 2007. The origin and diversification of eukaryotes. pp 265-274  in Sullivan W. T., Baross, J. A., (eds)  Planets and Life: The emerging Science of Astrobiology. Cambridge University Press, Cambridge.

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.

Senior Scientist D Patterson established the Bioidiversity Informatics group at the MBL with its flagship role of establishing the informatics environment for the Encyclopedia of Life.  The group attracts further support from the Ellison Medical Foundation to use the informatics infrastructure to develop a macroscope and tools to assist investigations of aging.

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

Alliegro, M.C. and M.A. Alliegro 2007.  Echinonectin is a Del-1—     like molecule with regulated expression in sea urchin embryos. Gene Expr. Patterns 7:651-657.

Alliegro, M.C and M.A. Alliegro 2007. Analysis of centrosome-associated nucleic acids reveals a unique family of genes. Proc Natl Acad Sci USA, in press.

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

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

Baross, J.A., Schrenk, M.O, and J.A. Huber.  2007.  Limits of Carbon Life on Earth and Elsewhere.  In W.T. Sullivan III and J.A Baross (eds.), 275-291.  Planets and Life: The Emerging Science of Astrobiology, Cambridge University Press, Cambridge, UK.

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

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." American Journal of Tropical Medicine and Hygiene, 77(5), 818-22.

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

Meselson, M. and D.B. Mark Welch. 2007. Stable heterozygosity? Science318: 202-203.

Gribble, K.E., G. Nolan, and D.M. Anderson. 2007. Biodiversity, biogeography and potential trophic impact of Protoperidinium spp. (Dinophyceae) of the southwestern coast of Ireland. Journal of Plankton Research 29 (11): 931-947 (2007).

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

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

Gladyshev E.A, Arkhipova I.R. (2007). Telomere-associated endonuclease-deficient Penelope-like retroelements in diverse eukaryotes. Proc Natl Acad Sci USA 104(22):9352-9357. Featured as a cover story in the May 29 PNAS issue, and in the MBL press release 6/13/07.

Gladyshev E.A, Meselson M., Arkhipova I.R. (2007). A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers. Gene 390(1-2):136-145.

The first Northeast Mobile DNA meeting organized by the Mobile Genetic Element Cluster took place on April 13-15, 2007, in Woods Hole, MA. It featured 16 talks and 12 poster presentations, and attracted about 40 participants from 8 states, including PIs, post-doctoral scholars, and graduate students. The opening lecture was presented by Matthew Meselson, the recipient of the 2004 Lasker Award for Special Achievement in Medical Science.

The Cluster also celebrated the Mobile DNA Month in Woods Hole in September 2007 by hosting two seminars presented by leading mobile DNAresearchers:9/21/2007 Marlene Belfort, Ph.D.

NYS Dept. of Health, Wadsworth Center for Medical Sciences Adjunct Scientist, Josephine Bay Paul Center, MBL "Genetic Invaders: Introns as retrotransposons" 9/28/2007 Daniel F. Voytas, Ph.D.Iowa State University Transposable elements and genome organization: the influence of chromatin on retrotransposon target specificity.

Edgcomb, V.E., S J. Molyneaux, S. Boer, C.O. Wirsen, M.S. Atkins, K.G. Lloyd, and A. Teske. 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 11:329-342. DOI 10.1007/s00792-006-0043-0.

Teske, A. 2007. Enigmatic Archaeal and Eukaryotic Life at hydrothermal vents and in marine subsurface sediments. Chapter in: Cellular Origins, Life in Extreme Habitats, and Astrobiology (COLE) (Series Editor, J. Seckbach). Springer.

Hines, M.E. P. T. Visscher, A. P. Teske, and R. Devereux. 2007. Sulfur Cycling. Chapter 42 in: ASM Manual of Environmental Microbiology, 3rd edition. (C.J. Huerst, R.L. Crawford, J.L. Garland, D.A. Lipson, A. L. Mills, and L. Stetzenbach, editors). ASM Press, Washington DC.

Teske, A, H. Cypionka, J.G. Holt, and N.R. Krieg. 2007. Enrichment and Isolation. Chapter 11 in: Methods for General and Molecular Microbiology, 3rd edition. (C.A. Reddy, T.J. Beveridge, J.A. Breznak, G. Marzluf, T.M. Schmidt, L.R. Snyder, Editors). ASM Press, Washington DC.

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

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. J. Geophys. Res. 112, D04309.

Garczarek L., Dufresne A., Rousvoal1 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 Microbiol. Ecol. 60, 189-206.

Wernegreen, J.J.  2007. Genomic signatures of intracellularity: Evolutionary patterns and paces in bacterial mutualists and parasites.  Pp. 196-212 in  Bacterial Pathogenomics, M. J. Pallen, K. E. Nelson, and G. M. Preston, Eds. ASM Press, Washington, DC.

Lo, N., C. Paraskevopoulos, K. Bourtzis, S.L. O'Neill, J.H. Werren, S.R. Bordenstein, and C. Bandi. (2007) Taxonomic status of the intracellular bacterium Wolbachia pipientis. International Journal of Systematics and Evolutionary Microbiology 57: 654-657.

Sanogo, Y.O., S.L. Dobson, S.R. Bordenstein, and R.J. Novak. (2007) Disruption of the Wolbachia surface protein gene wspB by a transposable element in mosquitoes of the Culex pipiens complex (Diptera: Culicidae). Insect Molecular Biology 16(2): 143-154.

Bordenstein, S.R. and J.H. Werren. (2007) Bidirectional incompatibility among divergent Wolbachia and incompatibility level differences among closely related Wolbachia in Nasonia. Heredity 99: 278-287.

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

Bordenstein, S.R. (2007) Discover the microbes within: The Wolbachia project. Focus on Microbiology Education 14:1, Special Issue on K-12 Education.

Bordenstein, S.R. (2007) Evolutionary genomics: Transdomain gene transfers. Current Biology 17:R935-936.

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

Jost MC, Lu, Y, Kyle J, Fozzard H, Hillis DM, Zakon H (2008) "Toxin-resistant sodium channels: Parallel adaptive evolution across a complete gene family". Molecular Biology & Evolution (in press).

Winterberg, K.M. and W.S. Reznikoff. (2007). Screening Transposon Mutant Libraries Using Full-Genome Oligonucleotide Microarrays. In: Advanced Bacterial Genetics: Use of Transposons and Phage for Genomic Engineering, Methods in Enzymology Series, (Kelly T. Hughes and Stanley R. Maloy, Eds.) Elsevier Inc., San Diego, CA. Vol. 421, pp. 110-125.

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

Adams, C.D., B. Schnurr, J.F. Marko, and W.S. Reznikoff (2007).    Pulling apart catalytically active Tn5 synaptic complexes using  magnetic tweezers. J. Mol. Biol. 367, 319-327.

Kieft, R., V. Brand, K. Sweeney, D.K. Ekanayake, C. DiPaolo, W.S. Reznikoff and R. Sabatini (2007).  JBP2, a SWI2/SNF2-like protein, regulates de-novo telomeric DNA glycosylation in bloodstream form Trypanosoma brucei.  Molecular and Biochemical Parasitology.  156, 24-31.

Vaezeslami, S., R. Sterling, and W.S. Reznikoff (2007).  Site-directed mutagenesis studies of Tn5 transposase residues involved in synaptic complex formation.  J. Bacteriol.  189, 7436-7441.

Czyz, A., K. Stillmock, D. Hazuda, and W.S. Reznikoff (2007).  Dissecting Tn5 transposition using HIV-1 integrase diketoacid inhibitors.  Biochemistry. 46, 10776-10789.

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

Morrison, H.G., A.G. McArthur, F.D. Gillin, S.B. Aley, R.D. Adam, G.J. Olsen, A.A. Best, W.Z. Cande, F. Chen, M.J. Cipriano, B.J. Davids, S.C. Dawson, H.G. Elmendorf, A.B. Hehl, M.E. Holder, S.M. Huse, U.U. Kim, E. Lasek-Nesselquist, G. Manning, A. Nigam, J.E.  Nixon, D. Palm, N.E. Passamaneck, A.Prabhu, C.I. Reich, D.S. Reiner, J. Samuelson, S.G. Svard, and M.L. Sogin, Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science, 2007. 317(5846): p. 1921-6.

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

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

2006

Sogin, M.L., Morrison, H.G., Huber, J.A., Mark Welch, D., Huse, S.M., Neal, P.R., Arrieta, J.M., and G.J. Herndl.  2006.  Microbial diversity in the deep sea and the  under-explored “rare biosphere.”  Proc. Natl. Acad. Sci. USA.  103:12115-12120.

Aguilera, A., Amaral Zettler, L. A., Souza-Egipsy, V., Zettler, E., and Amils, R. Eukaryotic community structure from Rio Tinto (SW, Spain), a highly acidic river In. (ed. Seckbach, J.), Extremophilic algae, cyanobacteria and non-photosynthetic protists: From Prokaryotes to Astrobiology. 2006. In press.

Amaral-Zettler, L. A., Cole, J., Laatsch, A. D., Nerad, T. A., Anderson, O. R. & Reysenbach, A-L., 2006. Vannella epipetala n. sp. Isolated from the Leaf Surface of Spondias mombin (Anacardiaceae) Growing in the Dry Forest of Costa Rica. Journal of Eukaryotic Microbiology. 53(6):522-530.

Arkhipova, I.R. (2006) Distribution and Phylogeny of Penelope-like elements in Eukaryotes. Syst. Biol., 55(6): 875-885.

Bach, W., K.J. Edwards, J.M. Hayes, J.A. Huber, S.M. Sievert and M.L. Sogin. Energy in the Dark: Fuel for Life in the Deep Ocean and Beyond. Eos 87(7): 73, 78 (2006).

Baldo, L., S.R. Bordenstein, J.J. Wernegreen and J.H. Werren. (2006) Widespread recombination throughout Wolbachia genomes. Molecular Biology and  Evolution 23: 437-449.

Baldo, L., Dunning-Hotopp, J., Bordenstein, S.R., Biber, S.A., Jollie, K., Tettelin, H., Maiden M., Hayashi, C., and J.H. Werren. (2006) A Multilocus Sequence Typing system for the endosymbiont Wolbachia. Applied and Environmental Microbiology 72(11): 7098-7110.

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

Bordenstein, S.R., M.L. Marshall, A.J. Fry, U. Kim, and J.J Wernegreen. (2006) The tripartite associations of bacteriophage, Wolbachia, and arthropods PLoS Pathogens 2 (5): 384-393.

Clelland, E., Kohli, G., Campbell, R.K., Sharma, S., Shimasaki, S. and Peng, C. Bone morphogenetic protein 15 in the zebrafish ovary: cDNA cloning, genomic organization, tissue distribution and role in oocyte maturation. Endocrinology 147:201-209. (2006)

D’Andrea, W. J., Lage, M., Martiny, J. B. H,. Laatsch, A.D., Amaral-Zettler, L. A., Sogin, M.L., and Y. Huang. 2006. Alkenone producers inferred from well-preserved 18S rDNA in Greenland lake sediments. J. Geophys. Res. 111, G03013, doi:10.1029/2005JG000121.

Davids, B.J., D.S. Reiner, S.R. Birkeland, S.P. Preheim, M.J. Cipriano, A.G. McArthur, & F.D. Gillin. 2006. A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein. PLoS ONE, 1, e44.

Dyhrman, S.T., S.T. Haley, S.R. Birkeland, L.L. Wurch, M.J. Cipriano, & A.G. McArthur. 2006. Long-SAGE (serial analysis of gene expression) for gene discovery and transcriptome profiling in the widespread marine coccolithophore Emiliania huxleyi. Applied and Environmental Microbiology, 72, 252-260.

Faulkner, S.D., M.W. Oli, R. Kieft, L. Cotlin, J. Widener, A. Shiflett, M.J. Cipriano, S.E. Pacocha, S.R. Birkeland, S.L. Hajduk & A.G. McArthur. 2006. In vitro generation of human HDL resistant Trypanosoma brucei brucei. Eukaryotic Cell, 5, 1276-1286.

Golden D.E. and Hajduk, S.L.  (2006) The importance of RNA structure in RNA editing and a potential proofreading mechanism for correct guide RNA:pre-mRNA binary complex formation. J. Molec. Biol. 359, 585-596.

Goldstone, H.M. & J.J. Stegeman. 2006. A revised evolutionary history of the CYP1A subfamily: gene duplication, gene conversion, and positive selection. 2006. Journal of Molecular Evolution, 62, 708-717.

Goldstone, H.M. & J.J. Stegeman. 2006. Molecular mechanisms of 2,3,7,8-tetrachlorodibenzo-p-dioxin cardiovascular embryotoxicity. 2006. Drug Metabolism Reviews, 38, 261-289.

Greenberg, R.M. (2006) Praziquantel: Mechanism of action. In: "Parasitic Flatworms: Molecular Biology, Biochemistry, Immunology and Physiology" (A. Maule, Marks, N.J., eds.)., pp. 269-281, CABI, Oxfordshire, UK.

Hutchison, L. Mustard, J., Gendrin, A., Fernández-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: 201-214.

Jeziorski, M.C. and Greenberg, R.M. (2006) Voltage-gated Ca2+ channel subunits from schistosomes and other platyhelminths: potential role in praziquantel action. (2006) Int. J. Parasitol. 36, 625-632.

Kohn, A.B., Lea, J., Moroz, L.L, and Greenberg, R.M. (2006) Schistosoma mansoni: Use of a fluorescent indicator to detect nitric oxide and related species in living parasites. Experimental Parasitology 113, 130-133.

Ley, R.E., J.K. Harris, J. Wilcox, J.R. Spear, S.R. Miller, B.M. Bebout, J.A. Maresca, D.A. Bryant, M.L. Sogin, and N.R. Pace. Unexpected diversity and complexity from the Guerrero Negro hypersaline microbial mat. Applied and Environmental Microbiology 72: 3685-3695 (2006).

Messerli, S.M., Birkeland, S.R., Bernier, J., Cipriano, M.J., Morgan, W., McArthur, A.G., and Greenberg, R.M. Nitric oxide-dependent changes in Schistosoma mansoni gene expression. Mol. Biochem. Parasitol., in press.

Messerli, S.M., W. Morgan, S.R. Birkeland, J. Bernier, M.J. Cipriano, A.G. McArthur & R.M. Greenberg. 2006. Nitric oxide-dependent changes in Schistosoma mansoni gene expression. Molecular and Biochemical Parasitology, 150, 367-370.

Mukherjee, M., M.T. Brown, A.G. McArthur & P.J. Johnson. 2006. Proteins of the glycine decarboxylase complex in the hydrogenosome of Trichomonas vaginalis. Eukaryotic Cell, 5, 2062-2071.

Murray, S.,  Hoppenrath, M.,  Preisfeld, A., Larsen, J., Yoshimatsu, S., Topriumi, S., and Patterson, D. J. 2006. Phylogenetics of Rhinodinium broomeense gen. et sp. nov., a peridinioid, sand-dwelling dinoflagellate (Dinophyceae). J. Phycol. 42, 934–942

Paraskevopoulos, C., S.R. Bordenstein, J.J. Wernegreen, J.H. Werren, and K. Bourtzis. (2006) Towards a Wolbachia multilocus sequence typing system: Discrimination of Wolbachia strains present in Drosophila species. Current Microbiology 53(5): 388-395.

Patterson. D. J., Remsen, D., Norton, C., Marino, W. 2006. Taxonomic Indexing—extending the role of Taxonomy. Systematic Biology, 55: 367-373.

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

Schoen, I., and Arkhipova, I.R. (2006). Two families of non-LTR retrotransposons, Syrinx and Daphne, from the Darwinulid ostracod, Darwinula stevensoni. Gene, 371(2): 296-30

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

Simpson, A. G. B. and Patterson, D. J. 2006.  Current perspectives on high-level groupings of protists. In Katz, L and Bhattacharya. D., Genomics and Evolution of Microbial Eukaryotes, Oxford University press, pp 7-30.

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

Williams, D.L., A.A. Sayed, D. Ray, & A.G. McArthur. 2006. Schistosoma mansoni albumin, a major defense against oxidative damage, was acquired by lateral gene transfer from a mammalian host. 2006. Molecular and Biochemical Parasitology, 150, 359-363.
Toxicological Sciences, 92, 394-407.

Prabhu A, Morrison HG, Martinez CR 3rd, Adam RD. 2006. "Characterisation of the subtelomeric regions of Giardia lamblia genome isolate WBC6". Int J Parasitol. 37(5):503-13.

Cantarel BL, Morrison HG, Pearson W. 2006. "Exploring the relationship between sequence similarity and accurate phylogenetic trees". Mol Biol Evol. 23(11):2090-100.

Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G 3rd, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL. 2006. "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005". Nucleic Acids Res. 34(1):1-9.

Oli MW, Cotlin LF, Shiflett AM, Hajduk, SL. (2006) Serum resistance-associated protein blocks lysosomal targeting of trypanosome lytic factor in Trypanosoma brucei.  Eukaryot Cell. 5,132-9.

Hajduk, S.L. (2006) Perspective:  Timing sexual development of parasites. Science 313, 626-627.

Ochsenreiter, T. and Hajduk, S.L. (2006) Alternative editing of mRNA generates protein diversity.  EMBO Reports 7, 1128-1133.

Shiflett, A.M. Faulkner, S.D., Cotlin, L.F., Widener, J., Stephens, N., and Hajduk, S.L. (2006) African Trypanosomes: Intracellular Trafficking of Host Defense Molecules. Eukaryot. Microb. 54,18-21.

Ochsenreiter, T. Cipriano, M. and Hajduk, S.L. (2007) KISS: The Kinetoplastid Editing Sequence Search Tool.  RNA 13, 1-4.

Gladyshev, E.G., Meselson, M., Arkhipova, I.R. (2006) A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers. Gene; doi 10.1016 j. gene.2006.09.025

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

Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G 3rd, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL. Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res., 2006 Jan 5;34(1):1-9. Print 2006.

Inagaki, F., T. Nunoura, S. Nakagawa, A. Teske, M. Lever, A. Lauer, M. Suzuki, K. Takai, M. Delwiche, F.S. Colwell, K.H. Nealson, K. Horikoshi, S.L. D'Hondt, and B.B. Jørgensen. 2006. Biogeographical distribution and diversity of microbes in methane-hydrate bearing deep marine sediments on the Pacific Ocean Margin. Proc. Natl. Acad. Sci. USA. 103(8):2815-2820.

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

Kubota A, Iwata H, Goldstone HM, Kim EY, Stegeman JJ, Tanabe S. 2006. "Cytochrome P450 1A4 and 1A5 in common cormorant (Phalacrocorax carbo): evolutionary relationships and functional implications associated with dioxin and related compounds". Toxicol Sci. 92(2):394-408.

Gribble, K.E. and D.M. Anderson.  2006.  Molecular phylogeny of the heterotrophic dinoflagellates, Protoperidinium, Diplopsalis, and Preperidinium (Dinophyceae), inferred from LSU rDNA. Journal of Phycology 42, 1081-1095.

Bach, W., Edward, K.J, Hayes, J.M., Huber, J.A., Sievert, S.M., and M.L. Sogin.  2006. Energy in the dark: Fuel for life in the deep ocean and beyond.  Eos, Trans. AGU.  87:73-  78.

Huber, J.A., Butterfield, D.A., Johnson, H.P., and J.A. Baross.  2006.  Microbial life in ridge flank crustal fluids.  Environmental Microbiology.  88:88-99.

Huber, J.A., Butterfield, D.A, and Baross, J.A.  2006.  Diversity and distribution of   subseafloor Thermococcales populations in diffuse hydrothermal vents at an active deep-sea volcano in the northeast Pacific Ocean.  J. Geophys. Res. 111:G04016,   doi:10.1029/2005JG000097.

Messerli, S. M., Prabhakar, S., Tang, Y., Maymood, U., Giovannini, M., Weissleder, R., Bronson, R., Martuza, R., Rabkin, S., & Breakefield, X. O. (2006).  Treatment of schwannomas  with an oncolytic HSV recombinant virus in murine models of neurofibromatosis type 2. Human Gene Therapy, 17: 1-11.

Messerli, S. M. and Greenberg, R. M. (2006). Cnidarian toxins and voltage-gated ion channels. Marine Drugs, 4:70-81.

Messerli, S. M., Morgan, W, Birkeland, S. R., McArthur, A. G., & Greenberg, R. M. (2006).  NO-dependent changes in Schistosoma mansoni gene expression identified by SAGE. Molecular and Biochemical Parasitology, 150: 367-70.

2005

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

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

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

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

Bordenstein, S. and R. B. Rosengaus (2005). "Discovery of a novel wolbachia supergroup in isoptera." Curr Microbiol 51(6): 393-8.

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

Casiraghi, M., S. R. Bordenstein, L. Baldo, N. Lo, T. Beninati, J. J. Wernegreen, J. H. Werren and C. Bandi (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.

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

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

Dhillon, A., M. Lever, K. G. Lloyd, D. B. Albert, M. L. Sogin and A. Teske (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.

DiPaolo, C., R. Kieft, M. Cross and R. Sabatini (2005). "Regulation of trypanosome DNA glycosylation by a SWI2/SNF2-like protein." Mol Cell 17(3): 441-51.

Evgen'ev, M. B. and I. R. Arkhipova (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 J. J. Wernegreen (2005). "The roles of positive and negative selection in the molecular evolution of insect endosymbionts." Gene 355: 1-10.

Golden, D. E. and S. L. Hajduk (2005). "The 3'-untranslated region of cytochrome oxidase II mRNA functions in RNA editing of African trypanosomes exclusively as a cis guide RNA." Rna 11(1): 29-37.

Gould, R. M., H. G. Morrison, E. Gilland and R. K. Campbell (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.

Greenberg, R. M. (2005). "Are Ca2+ channels targets of praziquantel action?" Int J Parasitol 35(1): 1-9.

Herbeck, J. T., P. H. Degnan and J. J. Wernegreen (2005). "Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria)." Mol Biol Evol 22(3): 520-32.

Kolker, E., A. F. Picone, M. Y. Galperin, M. F. Romine, R. Higdon, K. S. Makarova, N.
Kolker, G. A. Anderson, X. Qiu, K. J. Auberry, G. Babnigg, A. S. Beliaev, P. Edlefsen, D. A. Elias, Y. A. Gorby, T. Holzman, J. A. Klappenbach, K. T. Konstantinidis, M. L. Land, M. S. Lipton, L. A. McCue, M. Monroe, L. Pasa-Tolic, G. Pinchuk, S. Purvine, M. H. Serres, S. Tsapin, B. A. Zakrajsek, W. Zhu, J. Zhou, F. W. Larimer, C. E. Lawrence, M. Riley, F. R. Collart, J. R. Yates, 3rd, R. D. Smith, C. S. Giometti, K. H. Nealson, J. K. Fredrickson and J. M. Tiedje (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., C. Palacios and M. L. Sogin (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., A. G. B. Simpson and D. J. Patterson (2005). "Free-living heterotrophic flagellates from freshwater sites in Tasmania (Australia), a field survey." Acta Protozoologica 44: 321-350.

Mark Welch, D. B. (2005). "Bayesian and maximum likelihood analyses of rotifer-acanthocephalan relationships." Hydrobiologia 546: 47-54.

Mark Welch, D. B. and J. L. Mark Welch (2005). "Genomic approaches to rotifer ecology." Hydrobiologia 546: 101-108.

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

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

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

Noel, C., F. Dufernez, D. Gerbod, V. P. Edgcomb, P. Delgado-Viscogliosi, L. C. Ho, M. Singh, R. Wintjens, M. L. Sogin, M. Capron, R. Pierce, L. Zenner and E. Viscogliosi (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.

Palm, D., M. Weiland, A. G. McArthur, J. Winiecka-Krusnell, M. J. Cipriano, S. R. Birkeland, S. E. Pacocha, B. Davids, F. Gillin, E. Linder and S. Svard (2005). "Developmental changes in the adhesive disk during Giardia differentiation." Mol Biochem Parasitol 141(2): 199-207.

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

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

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

Serres, M. H. and M. Riley (2005). "Gene fusions and gene duplications: relevance to genomic annotation and functional analysis." BMC Genomics 6(1): 33.

Sheehan, K. B., D. J. Patterson, B. L. Dicks and J. B. Henson (2005). Seen and Unseen, discovering the microbes of Yellowstone. Nashville, TN, Falcon Press.

Shiflett, A. M., J. R. Bishop, A. Pahwa and S. L. Hajduk (2005). "Human high density lipoproteins are platforms for the assembly of multi-component innate immune complexes." J Biol Chem 280(38): 32578-85.

Toaldo, C. B., R. Kieft, A. Dirks-Mulder, R. Sabatini, H. G. van Luenen and P. Borst (2005). "A minor fraction of base J in kinetoplastid nuclear DNA is bound by the J-binding protein 1." Mol Biochem Parasitol 143(1): 111-5.

van Luenen, H. G., R. Kieft, R. Mussmann, M. Engstler, B. ter Riet and P. Borst (2005). "Trypanosomes change their transferrin receptor expression to allow effective uptake of host transferrin." Mol Microbiol 58(1): 151-65.

Weiland, M. E., A. G. McArthur, H. G. Morrison, M. L. Sogin and S. G. Svard (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.

Wilson, J. Y., A. G. McArthur and J. J. Stegeman (2005). "Characterization of a cetacean aromatase (CYP19) and the phylogeny and functional conservation of vertebrate aromatase." General and Comparative Endocrinology 140: 74-83.

Zettler, L. A., A. D. Laatsch, E. Zettler, T. A. Nerad, J. Cole, F. C. Diaz, J. Diaz, D. H. Janzen, A. Sittenfeld, O. Mason and A. L. Reysenbach (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.

2004

Amils 2004; Best, Morrison et al. 2004; Bordenstein and Wernegreen 2004; Crump, Hopkinson et al. 2004; Degnan, Lazarus et al. 2004; Herbeck, Degnan et al. 2004; Imrie, Ferguson et al. 2004; Mark Welch, Cummings et al. 2004; Mark Welch, Mark Welch et al. 2004; Milkman 2004; Murray 2004; Powell, Morrison et al. 2004; Pyatkov, Arkhipova et al. 2004; Reznikoff, Bordenstein et al. 2004; Serres M.H 2004; Serres, Goswami et al. 2004; Silva-Pinhati, Bacci et al. 2004; Wernegreen 2004; Wernegreen and Funk 2004; Wood, Sabatini et al. 2004

Amils, R., González-Toril, E., Gómez, F., Fernánadez-Remolar, D., Rodríguez, N., Malki, M., Aguilera, A. & Amaral-Zettler, L.A. (2004). Chemolithotrophy for early life on Earth: the Tinto River (Iberian Pyritic Belt) case. Origins. J. Seckbach. The Netherlands, Kluwer Publishers: 463-480.

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

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

Crump, B. C., C. S. Hopkinson, M. L. Sogin and J. E. Hobbie (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., A. B. Lazarus, C. D. Brock and J. J. Wernegreen (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.

Imrie, H., D. J. Ferguson, M. Carter, J. Drain, A. Schiflett, S. L. Hajduk and K. P. Day (2004). "Light and electron microscopical observations of the effects of high-density lipoprotein on growth of Plasmodium falciparum in vitro." Parasitology 128(Pt 6): 577-84.

Mark Welch, D. B., M. P. Cummings, D. M. Hillis and M. Meselson (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.

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

Milkman, R. (2004). Horizontal Transfer, Genomic Diversity, and Genomic Differentiation. Microbial Evolution: Gene Establishment, Survival, and Exchange. R. V. M. a. M. J. Day. Washington, DC, ASM Press: 297-318.

Murray, S. a. P., D.J. (2004). "Cabra matta gen. nov., sp. Nov., a new heterotrophic benthic dinoflagellate." European Journal of Phycology 39: 229-234.

Powell, W. H., H. G. Morrison, E. J. Weil, S. I. Karchner, M. L. Sogin, J. J. Stegeman and M. E. Hahn (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., I. R. Arkhipova, N. V. Malkova, D. J. Finnegan and M. B. Evgen'ev (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., S. R. Bordenstein and J. Apodaca (2004). "Comparative sequence analysis of IS50/Tn5 transposase." J Bacteriol 186(24): 8240-7.

Serres M.H, R. M. (2004). "Structural domains, protein modules and sequence similarities enrich our understanding of the Shewanella oneidensis MR-1 proteome." OMICS 8(4): 306-321.

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

Silva-Pinhati, A. C., M. Bacci, Jr., G. Hinkle, M. L. Sogin, F. C. Pagnocca, V. G. Martins, O. C. Bueno and M. J. Hebling (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.

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

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

Wood, Z. A., R. S. Sabatini and S. L. Hajduk (2004). "RNA ligase; picking up the pieces." Mol Cell 13(4): 455-6.

2003

Amaral Zettler, L. A., M. A. Messerli, et al. (2003). "From Genes to Genomes: Beyond Biodiversity in Spain's Rio Tinto." Biol Bull 204(2): 205-9.

Bordenstein, S. R. (2003). Symbiosis and the origin of species. Insect Symbiosis. K. Bourtzis and T. Miller. New York, CRC Press: 283-304.

Bordenstein, S. R., D. H. A. Fitch, et al. (2003). "Absence of Wolbachia in nonfilariid nematodes." Journal of Nematology 35(3): 266-270.

Bordenstein, S. R., J. J. Uy, et al. (2003). "Host genotype determines cytoplasmic incompatibility type in the haplodiploid genus nasonia." Genetics 164(1): 223-233.

Busse, I., D. J. Patterson, et al. (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., A. Teske, et al. (2003). "Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin." Appl Environ Microbiol 69(5): 2765-72.

Herbeck, J. T., D. J. Funk, et al. (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., D. P. Wall, et al. (2003). "Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia." Microbiology 149(Pt 9): 2585-96.

Lee, W. J., S. M. Brandt, et al. (2003). "Darwin's heterotrophic flagellates." Ophelia 57: 63-98.

Mark Welch, D. B. and M. Meselson (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.

McArthur, A. G. and M. G. Harasewych (2003). Molecular systematics and the major lineages of the Gastropoda. Molecular systematics and phylogeography of Mollusks. C. Lydeard & D. Lindberg. Washington, DC, Smithsonian Institution Press: 140-160.

McArthur, A. G., T. Hegelund, et al. (2003). "Phylogenetic analysis of the cytochrome P450 3 (CYP3) gene family." J Mol Evol 57(2): 200-11.

Milkman, R., E. Jaeger, et al. (2003). "Molecular evolution of the Escherichia coli chromosome. VI. Two regions of high effective recombination." Genetics 163(2): 475-83.

Nixon, J. E., J. Field, et al. (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.

Noel, C., C. Peyronnet, et al. (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., J. D. Silberman, et al. (2003). "Monopylocystis visvesvarai and Sawyeria marylandensis:  Two New Amitochondrial Heterolobosean Amoebae from Anoxic Environments." Protist 154: 281-290.

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

Patterson, D. J., D. Remsen, et al. (2003). "Comment on Zoological record and registration of new names in zoology." Bulletin of Zoological Nomenclature 60: 297-299.

Peglar, M. T., L. A. Amaral Zettler, et al. (2003). "Two new small-subunit ribosomal RNA gene lineages within the subclass gymnamoebia." J Eukaryot Microbiol 50(3): 224-32.

Priest, J. W. and S. L. Hajduk (2003). "Trypanosoma brucei cytochrome c1 is imported into mitochondria along an unusual pathway." J Biol Chem 278(17): 15084-94.

Reiner, D. S., M. L. Hetsko, et al. (2003). "Calcium signaling in excystation of the early diverging eukaryote, Giardia lamblia." J Biol Chem 278(4): 2533-40.

Schroeckh, S., W. J. Lee, et al. (2003). "Free-living heterotrophic euglenids from freshwater sites in mainland Australia." Hydrobiologia 493(1): 131-166.

Seshadri, V., A. G. McArthur, et al. (2003). "Giardia lamblia RNA polymerase II: amanitin-resistant transcription." J Biol Chem 278(30): 27804-10.

Sherrer, R. L., A. E. Yermovsky-Kammerer, et al. (2003). "A sequence motif within trypanosome precursor tRNAs influences abundance and mitochondrial localization." Mol Cell Biol 23(24): 9061-72.

Sogin, M. and D. E. Jennings (2003). "Introduction." Biol Bull 204(2): 159.

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

Voit, E. O. and M. Riley (2003). "Extending knowledge of Escherichia coli metabolism by modeling and experiment." Genome Biol 4(11): 235.

Wernegreen, J. J., P. H. Degnan, et al. (2003). "Genome evolution in an insect cell: distinct features of an ant-bacterial partnership." Biol Bull 204(2): 221-31.

2002

Arkhipova, I.R. & H.G. Morrison. 2001. Three retrotransposon families in the genome of Giardia lamblia: Two telomeric, one dead. Proc. Natl. Acad. Sci. USA 98:14497-14502.

Arkhipova, I.R., K.I. Pyatkov, M. Meselson, & M.B. Evgenev. 2003. Retroelements containing introns in diverse invertebrate taxa. Nature Genetics 33:123-124.

Cross, M., R. Kieft, Sabatini, R., A. Dirks-Mulder, I. Chaves & P. Borst. 2002. J-binding protein increases the level and retention of the unusual base J in trypanosome DNA.  Mol. Micro. 46:37-47.

Dehal, P., Y. Satou, R.K. Campbell, J. Chapman, B. Degnan, et al.  2002. The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science 298:2157-2167.

Edgcomb, V.P., D.T. Kysela, A. Teske, A. de Vera Gómez & M.L. Sogin. 2002. Benthic eukaryotic diversity in a hydrothermal vent. Proc. Natl. Acad. Sci. 99: 7658-7662.

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

García-Verela, M., M. P. Cummings, G. Pérez-Ponce de León, S. L. Gardner & J. P. Laclette. 2002. Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala). Molecular Phylogenetics and Evolution 23: 288-292.

Laan, M., Richmond, H., He, C., & Campbell, R.K. 2002. Zebrafish as a Model for Vertebrate Reproduction: Characterization of the First Functional Zebrafish (Danio rerio) Gonadotropin Receptor.  Gen. Comp. Endocrinol. 125: 349-364.

Langford, T.D., J.D. Silberman, M.E-L. Weiland, S.G. Svärd, J.M.McCaffery, M.L. Sogin & F.D. Gillin. 2002. Giardia lamblia: Identification and characterization of Rab and GDI proteins in a genome survey of the ER to Golgi endomembrane system. Experimental Parasitology 101: 13-24.

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

Nixon, J.E.J., A. Wang, J. Field, H.G. Morrison, A.G. McArthur, M.L.  Sogin, B.J. Loftus, & J. Samuelson. 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. Eukaryotic Cell 1:181-190.

Nixon, J.E.J., A. Wang, H.G. Morrison, A.G. McArthur, M.L. Sogin, B.  Loftus, & J. Samuelson. 2002. A spliceosomal intron in Giardia intestinalis. Proceedings of the National Academy of Sciences USA 99:3701-3705.

Palacios, C., D.T. Kysela & M.L. Sogin. 2002. Serial Analysis of rRNAs (SARS): A novel molecular strategy for  sampling microbial diversity throughout the universe. Proceedings of the Second European Workshop on Exo/Astrobiology Graz, Austria, 16-19 September 2002 (ESA SP-518, November 2002), p. 481.

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