2012 Publications

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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.

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