Bay Paul Center Publications

Alliegro, MC; Hartson, S; Alliegro, MA. 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.

Amend, AS; Oliver, TA; Amaral-Zettler, LA; Boetius, A; Fuhrman, JA; Horner-Devine, MC; Huse, SM; Mark Welch, DB; Martiny, AC; Ramette, A; Zinger, L; Sogin, ML; Martiny, JBH. 2012. Macroecological Patterns of Marine Bacteria on a Global Scale. Journal of Biogeography 40(4): 800-11.

Arkhipova, IR. 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, IR; Batzer, MA; Brosius, J; Feschotte, C; Moran, JV; Schmitz, J; Jurka, J. 2012. Genomic Impact of Eukaryotic Transposable Elements. Mobile DNA 3(1): 19.

Atamna-Ismaeel, N; Finkel, OM; Glaser, F; Sharon, I; Schneider, R; Post, AF; Spudich, JL; von Mering, C; Vorholt, JA; Iluz, D; Beja, O; Belkin, S. 2012. Microbial Rhodopsins on Leaf Surfaces of Terrestrial Plants. Environmental Microbiology 14(1): 140-46.

Beg, QK; Zampieri, M; Klitgord, N; Collins, SB; Altafini, C; Serres, MH; 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, JL; Morrison, HG; Hobbie, JE; Sogin, ML. 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, BW; Bonder, MJ; Huse, SM; 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, JA; Gomez-Ibanez, D; Reddington, E; Huber, JA; 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, LZ; Zhu, Q; Alliegro, MC; Berns, MW. 2012. High-throughput Automated Optofluidic System for the Laser Microsurgery of Non-adherent Oocytes. J Biomed Optics (17): 015001

Chapman, M; Alliegro, MC. 2012. The Karyomastigont as an Evolutionary Seme. Quart Rev Biol 87(4): 315-24.

Crump, BC; Amaral-Zettler, LA; Kling, GW. 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, JA; Amaral-Zettler, LA; Deck, J; Bicak, M; Rocca-Serra, P; Assunta-Sansone, S; Willis, K; Field, D. 2012. A Call for an International Network of Genomic Observatories (GOs). Giga Science (1): 5.

Filkins, LM; Hampton, TH; Gifford, AH; Gross, MJ; Hogan, DA; Sogin, ML; Morrison, HG; Paster, BJ; O’Toole, GA. 2012. Prevalence of Streptococci and Increased Polymicrobial Diversity Associated With Cystic Fibrosis Patient Stability. Journal of Bacteriology 194(17): 4709-17.

Finkel, OM; Burch, AY; Elad, T; Huse, SM; Lindow, SE; Post, AF; 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.

Freitas, S; Hatosy, S; Fuhrman, JA; Huse, SM; Mark Welch, DB; Sogin, ML; Martiny, AC. 2012. Global Distribution and Diversity of Marine Verrucomicrobia. The ISME Journal 6(8): 1499-505.

Gobet, A; Boer, SI; Huse, SM; van Beusekom, JE; Quince, C; Sogin, ML; Boetius, A; Ramette, A. 2012. Diversity and Dynamics of Rare and of Resident Bacterial Populations in Coastal Sands. The ISME Journal 6, 542–53; doi: 10.1038/ismej.2011.132; published online 6 October 2011.

Gribble, KE; Mark Welch, DB. 2012. Lifespan Extension by Caloric Restriction is Determined by Type and Level of Food Reduction and by Reproductive Mode in Brachionus manjavacas (Rotifera). The Journals of Gerontology Series A: Biological Sciences and Medical Sciences doi: 10.1093/gerona/gls170.

Gribble, KE; Mark Welch, DB. 2012. The Mate Recognition Protein Gene Mediates Reproductive Isolation and Speciation in the Brachionus plicatilis Cryptic Species Complex. BMC Evolutionary Biology 12(1): 134.

Gupta, RW; Tran, L; Norori, J; Ferris, MJ; Eren, AM; Taylor, CM; Dowd, SE; Penn, D. 2012. Histamine-2 Receptor Blockers Alter the Fecal Microbiota in Premature Infants. Journal of pediatric gastroenterology and nutrition.

Huse, SM; Ye, Y; Zhou, Y; Fodor, AA. 2012. A Core Human Microbiome as Viewed Through 16S rRNA Sequence Clusters. PLoS ONE 7(6): e34242.

Kozul-Horvath, CD; Zandbergen, F; Jackson, BP; Enelow, RI; Hamilton, JW. 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, JE; Hafner, JC; Upham, NS; Reddington, E. 2012. Conservation Genetics of Kangaroo Mice, Genus Microdipodops. Journal of Mammalian Evolution

Looft, T; Johnson, TA; Allen, HK; Bayles, DO; Alt, DP; Stedtfeld, RD; Sul, WJ; Stedtfeld, TM; Chai, B; Cole, JR; Hashsham, SA; Tiedje, JM; Stanton, TB. 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, KRM; Roberts, K; Lomas, MW; Saito, MA; Post, AF; Paytan, A. 2012. Enhanced Solubility and Ecological Impact of Atmospheric Phosphorus Deposition Upon Extended Seawater Exposure. Environmental Science & Technology 46(19): 10438-46.

Madan, JC; Koestler, DC; Stanton, BA; Davidson, L; Moulton, LA; Housman, ML; Moore, JH; Guill, MF; Morrison, HG; Sogin, ML; Hampton, TH; Karagas, MR; Palumbo, PE; Foster, JA; Hibberd, PL; O’Toole, GA. 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, JC; Salari, RC; Saxena, D; Davidson, L; O’Toole, GA; Moore, JH; Sogin, ML; Foster, JA; Edwards, WH; Palumbo, P; Hibberd, PL. 2012. Gut Microbial Colonisation in Premature Neonates Predicts Neonatal Sepsis. Archives of disease in childhood. Fetal and neonatal edition 97(6): F456-62.

McCliment, EA; Nelson, CE; Carlson, CA; Alldredge, AL; Witting, J; Amaral-Zettler, LA. 2012. An All-taxon Microbial Inventory of the Moorea Coral Reef Ecosystem. The ISME Journal 6(2): 309-19.

Meeder, E; Mackey, KRM; Paytan, A; Shaked, Y; Iluz, D; Stambler, N; Rivlin, T; Post, AF; Lazar, B. 2012. Nitrite Dynamics in the Open Oceanóclues from Seasonal and Diurnal Variations. Marine Ecology Progress Series (453): 11-26.

Ochiana, SO; Gustafson, A; Bland, ND; Wang, C; Russo, MJ; Campbell, RK; Pollastri, MP. 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, AR; Persoon, IF; Huse, SM; Keijser, BJ; Wesselink, PR; Crielaard, W; 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, AF; Rihtman, B; 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, SA; 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, LA; Copeland, J; Das, S; de Daruvar, A; de Matos, P; Dix, I; Edmunds, S; Evelo, CT; Forster, MJ; Gaudet, P; Gilbert, J; Goble, C; Griffin, JL; Jacob, D; Kleinjans, J; Harland, L; Haug, K; Hermjakob, H; Ho Sui, SJ; Laederach, A; Liang, S; Marshall, S; McGrath, A; Merrill, E; Reilly, D; Roux, M; Shamu, CE; Shang, CA; Steinbeck, C; Trefethen, A; Williams-Jones, B; Wolstencroft, K; Xenarios, I; Hide, W. 2012. Toward Interoperable Bioscience Data. Nature Genetics 44(2): 121-6.

Siam, R; Mustafa, GA; Sharaf, H; Moustafa, A; Ramadan, AR; Antunes, A; Bajic, VB; Stingl, U; Marsis, NGR; Coolen, MJL; Sogin, M; Ferreira, AJS; Dorry, HE. 2012. Unique Prokaryotic Consortia in Geochemically Distinct Sediments from Red Sea Atlantis II and Discovery Deep Brine Pools. PLoS ONE 7(8): e42872.

Smith, KF; Schmidt, V; Rosen, GE; Amaral-Zettler, L. 2012. Microbial Diversity and Potential Pathogens in Ornamental Fish Aquarium Water. PLoS ONE 7(9): e39971.

Sukenik, A; Kaplan-Levy, RN; Mark Welch, JL; Post, AF. 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, SM; Knight, R; Farmerie, WG; Wang, X; 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, El; Lebbad, M; Caccio, SM; 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, SH; Reynisson, E; Einarsson, B; Wade, N; Morrison, HG; Gaidos, E. 2013. Microbial Communities in the Subglacial Waters of the Vatnajokull Ice Cap, Iceland. The ISME Journal 7(2): 427-37.

Toney, JL; Theroux, S; Andersen, RA; Coleman, A; Amaral-Zettler, L; 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, AM; Mark Welch, JL; Borisy, GG. 2012. CLASI-FISH: Principles of Combinatorial Labeling and Spectral Imaging. Systematic and Applied Microbiology, 35(8): 496-502.

Vandewalle, JL; Goetz, GW; Huse, SM; Morrison, HG; Sogin, ML; Hoffmann, RG; Yan, K; McLellan, SL. 2012. Acinetobacter, Aeromonas and Trichococcus Populations Dominate the Microbial Community Within Urban Sewer Infrastructure. Environmental Microbiology 14(9): 2538-52.

Ver Eecke, HC; Butterfield, DA; Huber, JA; Lilley, MD; Olson, EJ; Roe, KK; Evans, LJ; Merkel, AY; Cantin, HV; Holden, JF. 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, TD; Gustafson, A; Bland, ND; Ochiana, SO; Campbell, RK; Pollastri, MP. 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, AL; Hampton, TH; Schwaab, T; Huarte, E; Tomlinson, CR; Gui, J; Fisher, JL; Fadul, CE; Hamilton, JW; Ernstoff, MS. 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, PL; Sherrell, RM; Stammerjohn, SE; Alderkamp, AC; Schofield, O; Abrahamsen, EP; Arrigo, KR; Bertilsson, S; Garay, DL; Guerrero, R; Lowry, KE; Moksnes, PO; Ndungu, K; Post, AF; Randall-Goodwin, E; Riemann, L; Severmann, S; Thatje, S; van Dijken, GL; Wilson, S. 2012. ASPIRE: The Amundsen Sea Polynya International Research Expedition. Oceanography 25(3): 40-53.