2011 Publications

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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.

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