December 20, 2014

Bay Paul Center Publications

Agogue, H; Lamy, D; Neal, PR; Sogin, ML; Herndl, GJ. 2011. Water Mass-Specificity of Bacterial Communities in the North Atlantic Revealed by Massively Parallel Sequencing. Molecular Ecology 20(2): 258-74.

Akerman, NH; Price, RE; Pichler, T; Amend, JP. 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, MC. 2011. The Nucleolinus: A Disappearing, Forgotten and (maybe) Misnamed Organelle. Communicative & Integrative Biology 4(2): 147-9.

Amaral Zettler, LA; Zettler, ER; Theroux, SM; Palacios, C; Aguilera, A; Amils, R. 2011. Microbial Community Structure Across the Tree of Life in the Extreme Rio Tinto. The ISME Journal 5(1): 42-50.

Bland, ND; Cuihua, WC; Tallman, C; Gustafson, AE; Wang, Z; Ashton, TD; Ochiana, SO; McAllister, G; Cotter, K; Fang, AP; Gechijian, L; Garceau, N; Gangurde, R; Ortenberg, R; Ondrechen, MJ; Campbell, RK; Pollastri, MP. 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; Sanders, E. 2011. Variability and Diversity of Nasopharyngeal microbiota in Children: A Metagenomic Analysis. PLoS ONE 6(2): e17035.

Bowen, JL; Ward, BB; Morrison, HG; Hobbie, JE; Valiela, I; Deegan, LA; Sogin, ML. 2011. Microbial Community Composition in Sediments Resists Perturbation by Nutrient Enrichment. ISME Journal 5(9): 1540-1548.

Crielaard, W; Zaura, E; Schuller, AA; Huse, SM; Montijn, RC; Keijser, BJ. 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, AM; Zozaya, M; Taylor, CM; Dowd, SE; Martin, DH; Ferris, MJ. 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, JR; Dawyndt, P; Garrity, GM; Gilbert, J; Glöckner, FO; Hirschman, L; Karsch-Mizrachi, I; Klenk, HP; Knight, R; Kottmann, R; Kyrpides, N; Meyer, F; San Gil, I; Sansone, SA; Schriml, LM; Sterk, P; Tatusova, T; Ussery, DW; White, O; Wooley, J. 2011. The Genomic Standards Consortium. PLoS Biol 9(6): e1001088.

Finkel, OM; Burch, AY; Lindow, SE; Post, AF; 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, DG; Astakhova, LN; Zatsepina, OG; Arkhipova, IR; Nudler, E; Evgen’ev, MB. 2011. Functional Organization of hsp70 Cluster in Camel (Camelus dromedarius) and Other Mammals. PLoS ONE 6(11): e27205.

Garbuz, DG; Yushenova, IA; Zatsepina, OG; Przhiboro, AA; Bettencourt, BR; Evgen’ev, MB. 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, RJ; Moran, DM; Dennett, MR; Wurtsbaugh, WA; Amaral Zettler, LA. 2011. Amoebae and Legionella pneumophila in Saline Environments. Journal of Water and Health 9(1): 37-52.

Gilbert, JA; Steele, JA; Caporaso, JG; Steinbruck, L; Reeder, J; Temperton, B; Huse, S; McHardy, AC; Knight, R; Joint, I; Somerfield, P; Fuhrman, JA; Field, D. 2011. Defining Seasonal Marine Microbial Community Dynamics. The ISME Journal, doi:10.1038/ismej.2011.107.

Gladyshev, EA; Arkhipova, IR. 2011. A Widespread Class of Reverse Transcriptase-related Cellular Genes. PNAS USA (51): 0311-20316.

Gobet, A; Boer, SI; Huse, SM; van Beusekom, JE; Quince, C; Sogin, ML; Boetius, A; Ramette, A. 2011. Diversity and Dynamics of Rare and of Resident Bacterial Populations in Coastal Sands. The ISME Journal, doi: 10.1038/ismej.2011.132.

Gribble, KE; Snell, TW; Mark Welch, DB. 2011. Gene and Protein Structure of the Mate Recognition Protein Gene Family in Brachionus manjavacas (Rotifera). Hydrobiologi (662): 35–42.

Huse, SM, 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, NA; Post, AF. 2011. Characterization of Cyanate Metabolism in Marine Synechococcus and Prochlorococcus spp. Applied and Environmental Microbiology 77(1): 291-301.

Mark Welch, DB; Huse, SH. 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.

McCliment, EA; Nelson, CE; Carlson, CA; Alldredge, AL; Witting, J; Amaral Zettler, LA. 2011. An All-taxon Microbial Inventory of the Moorea Coral Reef Ecosystem. The ISME Journal, doi: 10.1038/ismej.2011.108.

Nelson, CE; Alldredge, AL; McCliment, EA; Amaral Zettler, LA; Carlson, CA. 2011. Depleted Dissolved Organic Carbon and Distinct Bacterial Communities in the Water Column of a Rapid-Flushing Coral Reef Ecosystem. The ISME Journal 5(8), 1374-1387.

Nuzzio, DB; Zettler, ER; Aguilera, A; Amaral Zettler, LA. 2011. A Direct in situ Fingerprinting Method for Acid Rock Drainage Using Voltammetric Techniques with a Single Renewable Gold Microelectrode. Sci Total Environ 409(10): 1984-9.

Oleksiak, MF; Karchner, SI; Jenny, MJ; Franks, DG; Mark Welch, DB; Hahn, ME. 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, HR; Amaral Zettler, L; Guillou, L. 2011. Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing. PLoS ONE, 6(4): e18169.

Perry, DA; Morrison, HG; Adam, RD. 2011. Optical Map of the Genotype A1 WB C6 Giardia lamblia Genome Isolate. Molecular and Biochemical Parasitology 180(2): 112-4

Pollastri, MP; Campbell, RK 2011. Target Repurposing for Neglected Diseases. Future Medicinal Chemistry 3(10): 1307-15.

Post, AF; Penno, S; Zandbank, K; Paytan, A; Huse, SM; Welch, DM. 2011. Long-term Seasonal Dynamics of Synechococcus Population Structure in the Gulf of Aqaba, Northern Red Sea. Frontiers in Microbiology 2, 131.

Post, AF; Rihtman, B; Wang, Q. 2011. Decoupling of Ammonium Regulation   and ntcA Transcription in the Diazotrophic Marine Cyanobacterium Trichodesmium sp. IMS101. The ISME Journal, doi:10.1038/ismej.2011.121.

Resing, JA; Rubin, KH; Embley, RW; Lupton, JE; Baker, ET; Dziak, RP; Baumberger, T; Lilley, MD; Huber, JA; Shank, TM; Butterfield, DA; Clague, DA; Keller, NS; Merle, SG; Buck, NJ; Michael, PJ; Soule, A; Caress, DW; Walker, SL; Davis, R; Cowen, JP; Reysenbach, AL; Thomas, H. 2011. Active Submarine Eruption of Boninite in the Northeastern Lau Basin. Nature Geosci, 4(11):

799–806.

Rodrigues, JL; Serres, MH; Tiedje, JM. 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, OC; Kelty, CA; Archibeque, S; Jenkins, M; Newton, RJ; McLellan, SL; Huse, SM; Sogin, ML. 2011. Community Structures of Fecal Bacteria in Cattle from Different Animal Feeding Operations. Applied and Environmental Microbiology  77(9): 2992-3001.

Shanks, OC; McLellan, SL; Huse, SM; Sogin, ML. 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.), Environmental Microbiology: Current Technology and Water Applications. Norfolk, UK: Caister Academic Press.

Smith, HA; Snell, TW; Serra, M; Hecox-Lea, B; 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, JR; Zottoli, SJ; Smith, PJ; Buxbaum, JD; Bloom, OE. 2011. Regeneration in the Era of Functional Genomics and Gene Network Analysis. The Biological Bulletin 221(1): 18-34.

Sukenik, A; Kaplan-Levy, RN; Welch, JL; Post, AF. 2011. Massive Multiplication of Genome and Ribosomes in Dormant Cells (akinetes) of Aphanizomenon ovalisporum (Cyanobacteria). The ISME Journal, doi: 10.1038/ismej.2011.128.

Sul, WJ; Cole, JR; Jesus Eda, C; Wang, Q; Farris, RJ; Fish, JA; Tiedje, JM. 2011. Bacterial Community Comparisons by Taxonomy-supervised Analysis Independent of Sequence Alignment and Clustering. Proc Natl Acad Sci U S A 108(35): 14637-42.

Valm, AM; Welch, JL; Rieken, CW; Hasegawa, Y; Sogin, ML; Oldenbourg, R; Dewhirst, FE; Borisy, GG. 2011. Systems-level Analysis of Microbial Community Organization Through Combinatorial Labeling and Spectral Imaging. Proc Natl Acad Sci U S A 108(10): 4152-7.

White, J; Gilbert, J; Hill, G; Hill, E; Huse, SM; Weightman, AJ; 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; 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, AP; Thomas, BC; Simmons, SL; Wilmes, P; Zemla, A; Thelen, MP; Justice, N; Banfield, JF. 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, JA; Knight, R; Amaral Zettler, L; Karsch-Mizrachi, I; Cochrane, G; Nakamura, Y; Sansone, SA; Glockner, FO; Field, D. 2011. The Genomic Standards Consortium: Bringing Standards to Life for Microbial Ecology. ISME Journal 5(10): 1565-1567.

Yilmaz, P; Kottmann, R; Field, D; Knight, R; Cole, JR; Amaral Zettler, L; Gilbert, JA; 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, BW; Blaser, MJ; Bonazzi, V; Booth, T; Bork, P; Bushman, FD; Buttigieg, PL; Chain, PS; Charlson, E; Costello, EK; Huot-Creasy, H; Dawyndt, P; Desantis, T; Fierer, N; Fuhrman, JA; Gallery, RE; Gevers, D; Gibbs, RA; Gil, IS; Gonzalez, A; Gordon, JI; Guralnick, R; Hankeln, W; Highlander, S; Hugenholtz, P; Jansson, J; Kau, AL; Kelley, ST; Kennedy, J; Knights, D; Koren, O; Kuczynski, J; Kyrpides, N; Larsen, R; Lauber, CL; Legg, T; Ley, RE; Lozupone, CA; Ludwig, W; Lyons, D; Maguire, E; Methe, BA; Meyer, F; Muegge, B; Nakielny, S; Nelson, KE; Nemergut, D; Neufeld, JD; Newbold, LK; Oliver, AE; Pace, NR; Palanisamy, G; Peplies, J; Petrosino, J; Proctor, L; Pruesse, E; Quast, C; Raes, J; Ratnasingham, S; Ravel, J; Relman, DA; Assunta-Sansone, S; Schloss, PD; Schriml, L; Sinha, R; Smith, MI; Sodergren, E; Spor, A; Stombaugh, J; Tiedje, JM; Ward, DV; Weinstock, GM; Wendel, D; White, O; Whiteley, A; Wilke, A; Wortman, JR; Yatsunenko, T; Glockner, FO. 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, LA; Fuhrman, JA; Horner-Devine, MC; Huse, SM; Welch, DBM; Martiny, JBH; Sogin, M; Boetius, A; Ramette, A. 2011. Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems. PLoS ONE  6(9): e24570.