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 2009 Publications

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 a single population of archaea in a hydrothermal vent biofilm.” Environ Microbiol(in press).

Claessens, M., Wickham, S. A., Post, A. F., and Reuter, M. (2009). “A paradox of the ciliates? High cilate diversity in a resource-poor environment.” Mar. Biol., in press.

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.

Gillor, O., Hadas, O., Post, A. F., and Belkin, S. (2009). “Phosphorus and nitrogen in a monomictic fresh water lake: a new insight into nutrient bioavailability.” Freshwater Biol., in press.

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.

Wankel, S. D., Chen, Y., Kendall, C., Post, A. F., and Paytan, A. (2009). “Sources of aerosol nitrate to the Gulf of Aqaba: evidence from δ15N and δ18O of nitrate and trace metal chemistry.” Marine Chem., in press.

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.