2013 Publications

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Akerman, N. H., Butterfield, D. A., and Huber, J. A. (2013). “Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids.” Front Microbiol, 4, 185.

Alliegro, M. C., and Alliegro, M. A. (2013). “Localization of rRNA transcribed spacer domains in the nucleolinus and maternal procentrosomes of surf clam (Spisula) oocytes.” RNA Biol, 10(3), 391-6.

Amaral-Zettler, L. A. (2013). “Eukaryotic diversity at pH extremes.” Frontiers in Microbiology, 3, 441.

Amend, A. S., Oliver, T. A., Amaral-Zettler, L. A., Boetius, A., Fuhrman, J. A., Horner-Devine, M. C., Huse, S. M., Mark Welch, D. B., Martiny, A. C., Ramette, A., Zinger, L., Sogin, M. L., and Martiny, J. B. H. (2013). “Macroecological patterns of marine bacteria on a global scale.” Journal of Biogeography, 40(4), 800-11.

Arkhipova, I. R., Yushenova, I. A., and Rodriguez, F. (2013). “Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families.” Mobile DNA, 4(1), 19.

Arkhipova, I. R., and Rodriguez, F. (2013). “Genetic and epigenetic changes involving (retro)transposons in animal hybrids and polyploids.” Cytogenet Genome Res, 140(2-4), 295-311.

Bennett, S. A., Coleman, M., Huber, J. A., Reddington, E., Kinsey, J. C., McIntyre, C., Seewald, J. S., and German, C. R. (2013). “Trophic regions of a hydrothermal plume dispersing away from an ultramafic-hosted vent-system: Von Damm vent-site, Mid-Cayman Rise.” Geochemistry Geophysics Geosystems, 14(2), 317-327.

Duffy, J. E., Amaral-Zettler, L. A., Fautin, D. G., Paulay, G., Rynearson, T. A., Sosik, H. M., and Stachowicz, J. J. (2013). “Envisioning a Marine Biodiversity Observation Network.” Bioscience, 63(5), 350-361.

Eren, A. M., Maignien, L., Sul, W. J., Murphy, L. G., Grim, S. L., Morrison, H. G., and Sogin, M. L. (2013). “Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.” Methods Ecol Evol, 4(12).

Eren, A. M., Morrison, H. G., Huse, S. M., and Sogin, M. L. (2013). “DRISEE overestimates errors in metagenomic sequencing data.” ” Brief Bioinform.

Eren, A. M., Vineis, J. H., Morrison, H. G., and Sogin, M. L. (2013). “A filtering method to generate high quality short reads using illumina paired-end technology.” PLoS One, 8(6), e66643.

Feehery, G. R., Yigit, E., Oyola, S. O., Langhorst, B. W., Schmidt, V. T., Stewart, F. J., Dimalanta, E. T., Amaral-Zettler, L. A., Davis, T., Quail, M. A., and Pradhan, S. (2013). “A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.” PLoS One, 8(10), e76096.

Fischer, A. H., Tulin, S., Fredman, D., and Smith, J. (2013). “Employing BAC-reporter constructs in the sea anemone Nematostella vectensis.” Integr Comp Biol, 53(5), 832-46.

Flot, J. F., Hespeels, B., Li, X., Noel, B., Arkhipova, I., Danchin, E. G., Hejnol, A., Henrissat, B., Koszul, R., Aury, J. M., Barbe, V., Barthelemy, R. M., Bast, J., Bazykin, G. A., Chabrol, O., Couloux, A., Da Rocha, M., Da Silva, C., Gladyshev, E., Gouret, P., Hallatschek, O., Hecox-Lea, B., Labadie, K., Lejeune, B., Piskurek, O., Poulain, J., Rodriguez, F., Ryan, J. F., Vakhrusheva, O. A., Wajnberg, E., Wirth, B., Yushenova, I., Kellis, M., Kondrashov, A. S., Mark Welch, D. B., Pontarotti, P., Weissenbach, J., Wincker, P., Jaillon, O., and Van Doninck, K. (2013). “Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.” Nature, 500(7463), 453-7.

Fortunato, C. S., Eiler, A., Herfort, L., Needoba, J. A., Peterson, T. D., and Crump, B. C. (2013). “Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin.” ISME J, 7(10), 1899-911.

Gifford, A. H., Alexandru, D. M., Li, Z., Dorman, D. B., Moulton, L. A., Price, K. E., Hampton, T. H., Sogin, M. L., Zuckerman, J. B., Parker, H. W., Stanton, B. A., and O’Toole, G. A. (2013). “Iron supplementation does not worsen respiratory health or alter the sputum microbiome in cystic fibrosis.” J Cyst Fibros, 13(3), 311-8

Gribble, K. E., and Mark Welch, D. B. (2013). “Life-span extension by caloric restriction is determined by type and level of food reduction and by reproductive mode in Brachionus manjavacas (Rotifera).” J Gerontol A Biol Sci Med Sci, 68(4), 349-58.

Gupta, R. W., Tran, L., Norori, J., Ferris, M. J., Eren, A. M., Taylor, C. M., Dowd, S. E., and Penn, D. (2013). “Histamine-2 receptor blockers alter the fecal microbiota in premature infants.” J Pediatr Gastroenterol Nutr, 56(4), 397-400.

Hanson, S. J., Schurko, A. M., Hecox-Lea, B., Welch, D. B., Stelzer, C. P., and Logsdon, J. M., Jr. (2013). “Inventory and phylogenetic analysis of meiotic genes in monogonont rotifers.” J Here’d, 104(3), 357-70..

Hanson, S. J., Stelzer, C. P., Mark Welch, D. B., and Logsdon, J. M., Jr. (2013). “Comparative transcriptome analysis of obligately asexual and cyclically sexual rotifers reveals genes with putative functions in sexual reproduction, dormancy, and asexual egg production.” BMC Genomics, 14, 412.

Helm, R. R., Siebert, S., Tulin, S., Smith, J., and Dunn, C. W. (2013). “Characterization of differential transcript abundance through time during Nematostella vectensis development.” BMC Genomics, 14, 266.

Huse, S. M., Mark Welch, D. B., and Sogin, M. L. (2013). “Sequencing errors, diversity estimates and the rare biosphere”, The Science and Applications of Microbial Genomics: Workshop Summary. Institute of Medicine. Washington, DC: The National Academies Press, pp. 188-207.

Kamennaya, N. A., and Post, A. F. (2013). “Distribution and expression of the cyanate acquisition potential among cyanobacterial populations in oligotrophic marine waters.” Limnology and Oceanography, 58(6), 1959-1971.

Maignien, L., Parkes, R. J., Cragg, B., Niemann, H., Knittel, K., Coulon, S., Akhmetzhanov, A., and Boon, N. (2013). “Anaerobic oxidation of methane in hypersaline cold seep sediments.” FEMS Microbiol Ecol, 83(1), 214-31.

Marteinsson, V. T., 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.” ISME J, 7(2), 427-37.

Materna, S. C., Swartz, S. Z., and Smith, J. (2013). “Notch and Nodal control forkhead factor expression in the specification of multipotent progenitors in sea urchin.” Development, 140(8), 1796-806.

McLellan, S. L., Newton, R. J., Vandewalle, J. L., Shanks, O. C., Huse, S. M., Eren, A. M., and Sogin, M. L. (2013). “Sewage reflects the distribution of human faecal Lachnospiraceae.” Environ Microbiol, 15(8), 2213-27.

Merkel, A. Y., Huber, J. A., Chernyh, N. A., Bonch-Osmolovskaya, E. A., and Lebedinsky, A. V. (2013). “Detection of putatively thermophilic anaerobic methanotrophs in diffuse hydrothermal vent fluids.” Appl Environ Microbiol, 79(3), 915-23.

Meyer, J. L., Akerman, N. H., Proskurowski, G., and Huber, J. A. (2013). “Microbiological characterization of post-eruption “snowblower” vents at Axial Seamount, Juan de Fuca Ridge.” Front Microbiol, 4, 153.

Newton, R. J., Bootsma, M. J., Morrison, H. G., Sogin, M. L., and McLellan, S. L. (2013). “A microbial signature approach to identify fecal pollution in the waters off an urbanized coast of Lake Michigan.” Microb Ecol, 65(4), 1011-23.

Newton, R. J., Huse, S. M., Morrison, H. G., Peake, C. S., Sogin, M. L., and McLellan, S. L. (2013). “Shifts in the microbial community composition of Gulf Coast beaches following beach oiling.” PLoS One, 8(9), e74265.

Price, K. E., Hampton, T. H., Gifford, A. H., Dolben, E. L., Hogan, D. A., Morrison, H. G., Sogin, M. L., and O’Toole, G. A. (2013). “Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation.” Microbiome, 1(1), 27.

Rozhkov, N. V., Schostak, N. G., Zelentsova, E. S., Yushenova, I. A., Zatsepina, O. G., and Evgen’ev, M. B. (2013). “Evolution and dynamics of small RNA response to a retroelement invasion in Drosophila.” Mol Biol Evol, 30(2), 397-408.

Shanks, O. C., Newton, R. J., Kelty, C. A., Huse, S. M., Sogin, M. L., and McLellan, S. L. (2013). “Comparison of the microbial community structures of untreated wastewaters from different geographic locales.” Appl Environ Microbiol, 79(9), 2906-13.

Sul, W. J., Oliver, T. A., Ducklow, H. W., Amaral-Zettler, L. A., and Sogin, M. L. (2013). “Marine bacteria exhibit a bipolar distribution.” Proc Natl Acad Sci U S A, 110(6), 2342-7.

Taylor, R. C., Webb Robertson, B. J., Markillie, L. M., Serres, M. H., Linggi, B. E., Aldrich, J. T., Hill, E. A., Romine, M. F., Lipton, M. S., and Wiley, H. S. (2013). “Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria.” Integr Biol (Camb), 5(11), 1393-406.

Theroux, S., Toney, J., Amaral-Zettler, L., and Huang, Y. S. (2013). “Production and temperature sensitivity of long chain alkenones in the cultured haptophyte Pseudoisochrysis paradoxa.” Organic Geochemistry, 62, 68-73.

Tulin, S., Aguiar, D., Istrail, S., and Smith, J. (2013). “A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems.” Evodevo, 4(1), 16.

Ver Eecke, H. C., Akerman, N. H., Huber, J. A., Butterfield, D. A., and Holden, J. F. (2013). “Growth kinetics and energetics of a deep-sea hyperthermophilic methanogen under varying environmental conditions.” Environ Microbiol Rep, 5(5), 665-71.

Vital, M., Penton, C. R., Wang, Q., Young, V. B., Antonopoulos, D. A., Sogin, M. L., Morrison, H. G., Raffals, L., Chang, E. B., Huffnagle, G. B., Schmidt, T. M., Cole, J. R., and Tiedje, J. M. (2013). “A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community.” Microbiome, 1(1), 8.

Woodring, J. L., Bland, N. D., Ochiana, S. O., Campbell, R. K., and Pollastri, M. P. (2013). “Synthesis and assessment of catechol diether compounds as inhibitors of trypanosomal phosphodiesterase B1 (TbrPDEB1).” Bioorg Med Chem Lett, 23(21), 5971-4

Young, V. B., Raffals, L. H., Huse, S. M., Vital, M., Dai, D., Schloss, P. D., Brulc, J. M., Antonopoulos, D. A., Arrieta, R. L., Kwon, J. H., Reddy, K. G., Hubert, N. A., Grim, S. L., Vineis, J. H., Dalal, S., Morrison, H. G., Eren, A. M., Meyer, F., Schmidt, T. M., Tiedje, J. M., Chang, E. B., and Sogin, M. L. (2013). “Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis.” Microbiome, 1(1), 9.

Zettler, E. R., Mincer, T. J., and Amaral-Zettler, L. A. (2013). “Life in the “plastisphere”: microbial communities on plastic marine debris.” Environ Sci Technol, 47(13), 7137-46.

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