Top 25 Journals

Proc Natl Acad Sci U S A (56), ISME J (33), PLoS One (31), Appl Environ Microbiol (29), Environ Microbiol (26), Mol Biol Evol (24), Front Microbiol (21), Nucleic Acids Res (18), J Bacteriol (17), Biol Bull (17), Microbiome (15), Science (14), J Biol Chem (14), J Mol Biol (13), Nature (11), BMC Genomics (11), bioRxiv (10), J Eukaryot Microbiol (10), Genetics (10), mSystems (9), Hydrobiologia (9), European Journal of Protistology (9), MBio (8), Limnology and Oceanography (8), Gene (8)


2018 (32) | 2017 (37) | 2016 (49) | 2015 (58) | 2014 (68) | 2013 (42) | 2012 (47) | 2011 (42) | 2000-2010 | 1996-1999


Abrams, J. M., Arkhipova, I. R.Belfort, M., Boeke, J. D., Joan Curcio, M., Faulkner, G. J., Goodier, J. L., Lehmann, R., & Levin, H. L. (2018). “Meeting report: mobile genetic elements and genome plasticity 2018.” Mob DNA, 9(ARTN 21), 21. doi:10.1186/s13100-018-0126-.

Amaral-Zettler, L. A., Schmidt, V., & Smith, K. F. (2018). “Microbial Community and Potential Pathogen Shifts Along an Ornamental Fish Supply Chain.” Microorganisms, 6(3). doi:10.3390/microorganisms603009.

Arkhipova, I. R. (2018). “Neutral Theory, Transposable Elements, and Eukaryotic Genome Evolution.” Mol Biol Evol, 35(6), 1332-1337. doi:10.1093/molbev/msy08.

Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., Eloe-Fadrosh, E. A., Tringe, S. G., Ivanova, N. N., Copeland, A., Clum, A., Becraft, E. D., Malmstrom, R. R., Birren, B., Podar, M., Bork, P., Weinstock, G. M., Garrity, G. M., Dodsworth, J. A., Yooseph, S., Sutton, G., Glockner, F. O., Gilbert, J. A., Nelson, W. C., Hallam, S. J., Jungbluth, S. P., Ettema, T. J. G., Tighe, S., Konstantinidis, K. T., Liu, W. T., Baker, B. J., Rattei, T., Eisen, J. A., Hedlund, B., McMahon, K. D., Fierer, N., Knight, R., Finn, R., Cochrane, G., Karsch-Mizrachi, I., Tyson, G. W., Rinke, C., Genome Standards, C., Lapidus, A., Meyer, F., Yilmaz, P., Parks, D. H., Eren, A. M., Schriml, L., Banfield, J. F., Hugenholtz, P., & Woyke, T. (2018). “Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.” Nat Biotechnol, 36(2), 196. doi:10.1038/nbt0218-196.

Burnett, K., Edsinger, E., & Albrecht, D. R. (2018). “Rapid and gentle hydrogel encapsulation of living organisms enables long-term microscopy over multiple hours.” Commun Biol, 1(1), 73. doi:10.1038/s42003-018-0079-.

Chafee, M., Fernandez-Guerra, A., Buttigieg, P. L., Gerdts, G., Eren, A. M., Teeling, H., & Amann, R. I. (2018). “Recurrent patterns of microdiversity in a temperate coastal marine environment.” ISME J, 12(1), 237-252. doi:10.1038/ismej.2017.16.

Chernikova, D. A., Madan, J. C., Housman, M. L., Zain-Ul-Abideen, M., Lundgren, S. N., Morrison, H. G.Sogin, M. L., Williams, S. M., Moore, J. H., Karagas, M. R., & Hoen, A. G. (2018). “The premature infant gut microbiome during the first 6 weeks of life differs based on gestational maturity at birth.” Pediatr Res, 84(1), 71-79. doi:10.1038/s41390-018-0022-.

Crognale, S., Venturi, S., Tassi, F., Rossetti, S., Rashed, H., Cabassi, J., Capecchiacci, F., Nisi, B., Vaselli, O., Morrison, H. G.Sogin, M. L., & Fazi, S. (2018). “Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of the Solfatara Crater (Campi Flegrei, southern Italy).” FEMS Microbiol Ecol, 94(12), fiy190-fiy190. doi:10.1093/femsec/fiy19.

Delmont, T. O., & Eren, A. M. (2018). “Linking pangenomes and metagenomes: the Prochlorococcus metapangenome.” PeerJ, 6(ARTN e4320), e4320. doi:10.7717/peerj.432.

Delmont, T. O., Quince, C., Shaiber, A., Esen, O. C., Lee, S. T., Rappe, M. S., McLellan, S. L., Lucker, S., & Eren, A. M. (2018). “Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.” Nat Microbiol, 3(7), 804-813. doi:10.1038/s41564-018-0176-.

Dever, K., Carr, J., Girard, J., Calzarette, D., Remsen, D., Gage, G., Chugunov, I., Weissbourd, B., Cordeiro, M., Miao, J., Marvel-Zuccola, J., Newstein, P., Peramba, K., & Edsinger, E. (2018). “Octocams: A simple scalable system for short-term to lifecycle monitoring of behavior in aquaria.” Paper presented at the Annual Meeting of the Society for Integrative and Comparative Biology, San Francisco, CA.

Edsinger, E., & Dolen, G. (2018). “A Conserved Role for Serotonergic Neurotransmission in Mediating Social Behavior in Octopus.” Curr Biol, 28(19), 3136-3142 e3134. doi:10.1016/j.cub.2018.07.06.

Frere, L., Maignien, L., Chalopin, M., Huvet, A., Rinnert, E., Morrison, H., Kerninon, S., Cassone, A. L., Lambert, C., Reveillaud, J., & Paul-Pont, I. (2018). “Microplastic bacterial communities in the Bay of Brest: Influence of polymer type and size.” Environ Pollut, 242(Pt A), 614-625. doi:10.1016/j.envpol.2018.07.02.

Gilbert, J. A. (2018). “Early-Career Systems Microbiology Scientists.” mSystems, 3(2). doi:10.1128/mSystems.00002-1.

Grahl, N., Dolben, E. L., Filkins, L. M., Crocker, A. W., Willger, S. D., Morrison, H. G.Sogin, M. L., Ashare, A., Gifford, A. H., Jacobs, N. J., Schwartzman, J. D., & Hogan, D. A. (2018). “Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA.” mSphere, 3(4). doi:10.1128/mSphere.00292-1.

Gribble, K. E., Moran, B. M., Jones, S., Corey, E. L., & Mark Welch, D. B. (2018). “Congeneric variability in lifespan extension and onset of senescence suggest active regulation of aging in response to low temperature.” Exp Gerontol, 114, 99-106. doi:10.1016/j.exger.2018.10.02.

Hecox-Lea, B. J., & Mark Welch, D. B. (2018). “Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers.” BMC Evol Biol, 18(1), 177. doi:10.1186/s12862-018-1288-.

Hoen, A. G., Madan, J. C., Li, Z., Coker, M., Lundgren, S. N., Morrison, H. G., Palys, T., Jackson, B. P., Sogin, M. L., Cottingham, K. L., & Karagas, M. R. (2018). “Sex-specific associations of infants’ gut microbiome with arsenic exposure in a US population.” Sci Rep, 8(1), 12627. doi:10.1038/s41598-018-30581-.

Hubbard, C. J., Brock, M. T., van Diepen, L. T., Maignien, L., Ewers, B. E., & Weinig, C. (2018). “The plant circadian clock influences rhizosphere community structure and function.” ISME J, 12, 400-410.

Kroeger, M. E., Delmont, T. O., Eren, A. M., Meyer, K. M., Guo, J., Khan, K., Rodrigues, J. L. M., Bohannan, B. J. M., Tringe, S. G., Borges, C. D., Tiedje, J. M., Tsai, S. M., & Nusslein, K. (2018). “New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes.” Front Microbiol, 9(ARTN 1635), 1635. doi:10.3389/fmicb.2018.0163.

Lang, J. M., Coil, D. A., Neches, R. Y., Brown, W. E., Cavalier, D., Severance, M., Hampton-Marcell, J. T., Gilbert, J. A., & Eisen, J. A. (2018). “Correction: A microbial survey of the International Space Station (ISS).” PeerJ, 5. doi:10.7717/peerj.4029/correction-.

Lundgren, S. N., Madan, J. C., Emond, J. A., Morrison, H. G., Christensen, B. C., Karagas, M. R., & Hoen, A. G. (2018). “Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner.” Microbiome, 6(1), 109. doi:10.1186/s40168-018-0490-.

McIntosh, C. M., Chen, L., Shaiber, A., Eren, A. M., & Alegre, M. L. (2018). “Gut microbes contribute to variation in solid organ transplant outcomes in mice.” Microbiome, 6(1), 96. doi:10.1186/s40168-018-0474-.

Meisel, M., Hinterleitner, R., Pacis, A., Chen, L., Earley, Z. M., Mayassi, T., Pierre, J. F., Ernest, J. D., Galipeau, H. J., Thuille, N., Bouziat, R., Buscarlet, M., Ringus, D. L., Wang, Y., Li, Y., Dinh, V., Kim, S. M., McDonald, B. D., Zurenski, M. A., Musch, M. W., Furtado, G. C., Lira, S. A., Baier, G., Chang, E. B., Eren, A. M., Weber, C. R., Busque, L., Godley, L. A., Verdu, E. F., Barreiro, L. B., & Jabri, B. (2018). “Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host.” Nature, 557(7706), 580-584. doi:10.1038/s41586-018-0125-.

Peñalver Bernabé, B., Cralle, L., & Gilbert, J. A. (2018). “Systems biology of the human microbiome.” Curr Opin Biotechnol, 51, 146-153. doi:10.1016/j.copbio.2018.01.01.

Quigley, C. T. C., Morrison, H. G., Mendonca, I. R., & Brawley, S. H. (2018). “A common garden experiment with Porphyra umbilicalis (Rhodophyta) evaluates methods to study spatial differences in the macroalgal microbiome.” J Phycol, 54(5), 653-664. doi:10.1111/jpy.1276.

Rodriguez, F., & Arkhipova, I. R. (2018). “Transposable elements and polyploid evolution in animals.” Curr Opin Genet Dev, 49, 115-123. doi:10.1016/j.gde.2018.04.00.

Seyler, L. M., McGuinness, L. R., Gilbert, J. A., Biddle, J. F., Gong, D., & Kerkhof, L. J. (2018). “Discerning autotrophy, mixotrophy and heterotrophy in marine TACK archaea from the North Atlantic.” FEMS Microbiol Ecol, 94(3). doi:10.1093/femsec/fiy01.

Sheik, C. S., Reese, B. K., Twing, K. I., Sylvan, J. B., Grim, S. L., Schrenk, M. O., Sogin, M. L., & Colwell, F. S. (2018). “Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.” Front Microbiol, 9(ARTN 840), 840. doi:10.3389/fmicb.2018.0084.

Vakhrusheva, O. A., Mnatsakanova, E. A., Galimov, Y. R., Neretina, T. V., Gerasimov, E. S., Ozerova, S. G., Zalevsky, A. O., Yushenova, I. A.Arkhipova, I. R., Penin, A. A., Logacheva, M. D., Bazykin, G. A., & Kondrashov, A. S. (2018). “Recombination in a natural population of the bdelloid rotifer Adineta vaga.” bioRxiv, 489393. doi:10.1101/48939.

Yushenova, I. A., & Arkhipova, I. R. (2018). “Biochemical properties of bacterial reverse transcriptase-related (rvt) gene products: multimerization, protein priming, and nucleotide preference.” Curr Genet, 64(6), 1287-1301. doi:10.1007/s00294-018-0844-.

Zhang, X., Xia, K., Lin, L., Zhang, F., Yu, Y., St Ange, K., Han, X., Edsinger, E., Sohn, J., & Linhardt, R. J. (2018). “Structural and Functional Components of the Skate Sensory Organ Ampullae of Lorenzini.” ACS Chem Biol, 13(6), 1677-1685. doi:10.1021/acschembio.8b0033.


Amaral-Zettler, L. A., Dragone, N. B., Schell, J., Slikas, B., Murphy, L. G., Morrall, C. E., & Zettler, E. R. (2017). “Comparative mitochondrial and chloroplast genomics of a genetically distinct form of Sargassum contributing to recent “Golden Tides” in the Western Atlantic.” Ecol Evol, 7(2), 516-525. doi:10.1002/ece3.263.

Anderson, R. E., Reveillaud, J.Reddington, E., Delmont, T. O., Eren, A. M., McDermott, J. M., Seewald, J. S., & Huber, J. A. (2017). “Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents.” Nat Commun, 8(1), 1114. doi:10.1038/s41467-017-01228-.

Arkhipova, I. R.Yushenova, I. A., & Rodriguez, F. (2017). “Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres.” Mol Biol Evol, 34(9), 2245-2257. doi:10.1093/molbev/msx15.

Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., Eloe-Fadrosh, E. A., Tringe, S. G., Ivanova, N. N., Copeland, A., Clum, A., Becraft, E. D., Malmstrom, R. R., Birren, B., Podar, M., Bork, P., Weinstock, G. M., Garrity, G. M., Dodsworth, J. A., Yooseph, S., Sutton, G., Glockner, F. O., Gilbert, J. A., Nelson, W. C., Hallam, S. J., Jungbluth, S. P., Ettema, T. J. G., Tighe, S., Konstantinidis, K. T., Liu, W. T., Baker, B. J., Rattei, T., Eisen, J. A., Hedlund, B., McMahon, K. D., Fierer, N., Knight, R., Finn, R., Cochrane, G., Karsch-Mizrachi, I., Tyson, G. W., Rinke, C., Lapidus, A., Meyer, F., Yilmaz, P., Parks, D. H., Eren, A. M., Schriml, L., Banfield, J. F., Hugenholtz, P., Woyke, T., & Consortium, G. S. (2017). “Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.” Nature Biotechnology, 35(8), 725-731. doi:10.1038/nbt.389.

Bowman, J. S., Amaral-Zettler, L. A., J, J. R., C, M. L., & Ducklow, H. W. (2017). “Bacterial community segmentation facilitates the prediction of ecosystem function along the coast of the western Antarctic Peninsula.” ISME J, 11(6), 1460-1471. doi:10.1038/ismej.2016.20.

Courtine, D., Alain, K., Georges, M., Bienvenu, N., Morrison, H. G.Eren, A. M., & Maignien, L. (2017). “Complete Genome Sequence of Hyperthermophilic Archaeon Thermococcus sp.” EXT12c, Isolated from the East Pacific Rise 9 degrees N. Genome Announc, 5(50). doi:10.1128/genomeA.01385-1.

De Tender, C., Schlundt, C., Devriese, L. I., Mincer, T. J., Zettler, E. R., & Amaral-Zettler, L. A. (2017). “A review of microscopy and comparative molecular-based methods to characterize “Plastisphere” communities.” Analytical Methods, 9(14), 2132-2143. doi:10.1039/c7ay00260.

Delmont, T. O., & Eren, A. M. (2017). “Simulations predict microbial responses in the environment? This environment disagrees retrospectively.” Proc Natl Acad Sci U S A, 114(43), E8947-E8949. doi:10.1073/pnas.171218611.

Devetter, M., Fontaneto, D., Jersabek, C. D., Mark Welch, D. B., May, L., & Walsh, E. J. (2017). “Preface: evolving rotifers, evolving science Proceedings of the XIV International Rotifer Symposium.” Hydrobiologia, 796(1), 1-6. doi:10.1007/s10750-017-3241-.

Doherty, M., Yager, P. L., Moran, M. A., Coles, V. J., Fortunato, C. S., Krusche, A. V., Medeiros, P. M., Payet, J. P., Richey, J. E., Satinsky, B. M., Sawakuchi, H. O., Ward, N. D., & Crump, B. C. (2017). “Bacterial Biogeography across the Amazon River-Ocean Continuum.” Front Microbiol, 8, 882. doi:10.3389/fmicb.2017.0088.

Fan, K. K., Cardona, C., Li, Y. T., Shi, Y., Xiang, X. J., Shen, C. C., Wang, H. F., Gilbert, J. A., & Chu, H. Y. (2017). “Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields.” Soil Biology & Biochemistry, 113(Supplement C), 275-284. doi:10.1016/j.soilbio.2017.06.02.

Franco-Obregon, A., & Gilbert, J. A. (2017). “The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals.” mSystems, 2(3). doi:10.1128/mSystems.00018-1.

Gibbons, S. M., Lekberg, Y., Mummey, D. L., Sangwan, N., Ramsey, P. W., & Gilbert, J. A. (2017). “Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem.” mSystems, 2(2). doi:10.1128/mSystems.00178-1.

Gilbert, J. A. (2017). “How do we make indoor environments and healthcare settings healthier?” Microb Biotechnol, 10(1), 11-13. doi:10.1111/1751-7915.1243.

Gribble, K. E., & Mark Welch, D. B. (2017). “Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system.” BMC Genomics, 18(1), 217. doi:10.1186/s12864-017-3540-.

Hasegawa, Y.Mark Welch, J. L., Rossetti, B. J., & Borisy, G. G. (2017). “Preservation of three-dimensional spatial structure in the gut microbiome.” PLoS One, 12(11), e0188257. doi:10.1371/journal.pone.018825.

Herfort, L., Crump, B. C., Fortunato, C. S., McCue, L. A., Campbell, V., Simon, H. M., Baptista, A. M., & Zuber, P. (2017). “Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima.” Microbiologyopen, 6(6), e00522-n/a. doi:10.1002/mbo3.52.

Huang, Y., Dalal, S., Antonopoulos, D., Hubert, N., Raffals, L. H., Dolan, K., Weber, C., Messer, J. S., Jabri, B., Bendelac, A., Eren, A. M., Rubin, D. T., Sogin, M., & Chang, E. B. (2017). “Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis.” Inflamm Bowel Dis, 23(3), 366-378. doi:10.1097/MIB.000000000000102.

Knight, R., Callewaert, C., Marotz, C., Hyde, E. R., Debelius, J. W., McDonald, D., & Sogin, M. L. (2017). “The Microbiome and Human Biology.” Annu Rev Genomics Hum Genet, 18, 65-86. doi:10.1146/annurev-genom-083115-02243.

Kumar, R., Verma, H., Haider, S., Bajaj, A., Sood, U., Ponnusamy, K., Nagar, S., Shakarad, M. N., Negi, R. K., Singh, Y., Khurana, J. P., Gilbert, J. A., & Lal, R. (2017). “Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium.” mSystems, 2(3). doi:10.1128/mSystems.00020-1.

Kuntz, T. M., & Gilbert, J. A. (2017). “Introducing the Microbiome into Precision Medicine.” Trends Pharmacol Sci, 38(1), 81-91. doi:10.1016/

Lee, S. T. M., Kahn, S. A., Delmont, T. O., Shaiber, A., Esen, O. C., Hubert, N. A., Morrison, H. G., Antonopoulos, D. A., Rubin, D. T., & Eren, A. M. (2017). “Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics.” Microbiome, 5(1), 50. doi:10.1186/s40168-017-0270-.

Luria, C. M., Amaral-Zettler, L. A., Ducklow, H. W., Repeta, D. J., Rhyne, A., & Rich, J. J. (2017). “Seasonal shifts in bacterial community responses to phytoplankton-derived dissolved organic matter in the Western Antarctic Peninsula.” Frontiers in Microbiology-Aquatic Microbiology, 8, 2117.

Ma, B., Dai, Z., Wang, H., Dsouza, M., Liu, X., He, Y., Wu, J., Rodrigues, J. L., Gilbert, J. A., Brookes, P. C., & Xu, J. (2017). “Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China.” mSystems, 2(1). doi:10.1128/mSystems.00174-1.

Mackey, K. R. M., Hunter-Cevera, K., Britten, G. L., Murphy, L. G.Sogin, M. L., & Huber, J. A. (2017). “Seasonal Succession and Spatial Patterns of Synechococcus Microdiversity in a Salt Marsh Estuary Revealed through 16S rRNA Gene Oligotyping.” Front Microbiol, 8, 1496. doi:10.3389/fmicb.2017.0149.

Mark Welch, D. B., Jauch, A., Langowski, J., Olins, A. L., & Olins, D. E. (2017). “Transcriptomes reflect the phenotypes of undifferentiated, granulocyte and macrophage forms of HL-60/S4 cells.” Nucleus, 8(2), 222-237. doi:10.1080/19491034.2017.128598.

Mark Welch, J. L.Hasegawa, Y., McNulty, N. P., Gordon, J. I., & Borisy, G. G. (2017). “Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice.” Proc Natl Acad Sci U S A, 114(43), E9105-E9114. doi:10.1073/pnas.171159611.

Perez, T., Rodriguez, F., Fernandez, M., Albornoz, J., & Dominguez, A. (2017). “Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus.” Gene, 628(Supplement C), 63-71. doi:10.1016/j.gene.2017.07.03.

Quince, C., Delmont, T. O., Raguideau, S., Alneberg, J., Darling, A. E., Collins, G., & Eren, A. M. (2017). “DESMAN: a new tool for de novo extraction of strains from metagenomes.” Genome Biol, 18(1), 181. doi:10.1186/s13059-017-1309-.

Rodriguez, F., Kenefick, A. W., & Arkhipova, I. R. (2017). “LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types.” Viruses, 9(4). doi:10.3390/v904007.

Schmidt, V., Gomez-Chiarri, M., Roy, C., Smith, K., & Amaral-Zettler, L. A. (2017). “Subtle Microbiome Manipulation Using Probiotics Reduces Antibiotic-Associated Mortality in Fish.” Msystems, 2(6). doi:UNSP e00133-17 10.1128/mSystems.00133-1.

Smith, M. W., Herfort, L., Fortunato, C. S., Crump, B. C., & Simon, H. M. (2017). “Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary.” Microbiologyopen, 6(4). doi:10.1002/mbo3.46.

Stellato, G., Utter, D. R., Voorhis, A., De Angelis, M., Eren, A. M., & Ercolini, D. (2017). “A Few Pseudomonas Oligotypes Dominate in the Meat and Dairy Processing Environment.” Front Microbiol, 8, 264. doi:10.3389/fmicb.2017.0026.

Sylvan, J. B., Wankel, S. D., LaRowe, D. E., Charoenpong, C. N., Huber, J. A., Moyer, C. L., & Edwards, K. J. (2017). “Evidence for microbial mediation of subseafloor nitrogen redox processes at Loihi Seamount, Hawaii.” Geochimica Et Cosmochimica Acta, 198, 131-150. doi:10.1016/j.gca.2016.10.02.

Teif, V. B., Mallm, J. P., Sharma, T., Mark Welch, D. B., Rippe, K., Eils, R., Langowski, J., Olins, A. L., & Olins, D. E. (2017). “Nucleosome repositioning during differentiation of a human myeloid leukemia cell line.” Nucleus, 8(2), 188-204. doi:10.1080/19491034.2017.129520.

Wilbert, S. A., Mark Welch, J. L., Dewhirst, F. E., & Borisy, G. G. (2017). “Spatial organization of the human tongue dorsum microbiome at the micron scale.” Paper presented at the ASCB/EMBO Meeting, Philadelphia, PA.

Zettler, E. R., Takada, H., Monteleone, B., Mallos, N., Eriksen, M., & Amaral-Zettler, L. A. (2017). “Incorporating citizen science to study plastics in the environment.” Analytical Methods, 9(9), 1392-1403. doi:10.1039/c6ay02716.


Arkhipova, I. R., & Rice, P. A. (2016). “Mobile genetic elements: in silico, in vitro, in vivo.” Mol Ecol, 25(5), 1027-1031. doi:10.1111/mec.1354.

Balint, M., Bahram, M., Eren, A. M., Faust, K., Fuhrman, J. A., Lindahl, B., O’Hara, R. B., Opik, M., Sogin, M. L., Unterseher, M., & Tedersoo, L. (2016). “Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.” FEMS Microbiol Rev, 40(5), 686-700. doi:10.1093/femsre/fuw01.

Britstein, M., Devescovi, G., Handley, K. M., Malik, A., Haber, M., Saurav, K., Teta, R., Costantino, V., Burgsdorf, I., Gilbert, J. A., Sher, N., Venturi, V., & Steindler, L. (2016). “A New N-Acyl Homoserine Lactone Synthase in an Uncultured Symbiont of the Red Sea Sponge Theonella swinhoei.” Appl Environ Microbiol, 82(4), 1274-1285. doi:10.1128/aem.03111-1.

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De Filippis, F., Genovese, A., Ferranti, P., Gilbert, J. A., & Ercolini, D. (2016). “Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate.” Sci Rep, 6, 21871. doi:10.1038/srep2187.

Delmont, T. O., & Eren, A. M. (2016). “Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies.” PeerJ, 4, e1839. doi:10.7717/peerj.183.

Denner, D. R., Sangwan, N., Becker, J. B., Hogarth, D. K., Oldham, J., Castillo, J., Sperling, A. I., Solway, J., Naureckas, E. T., Gilbert, J. A., & White, S. R. (2016). “Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways.” J Allergy Clin Immunol, 137(5), 1398-1405 e1393. doi:10.1016/j.jaci.2015.10.01.

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Gibbons, S. M., Scholz, M., Hutchison, A. L., Dinner, A. R., Gilbert, J. A., & Coleman, M. L. (2016). “Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System.” MBIO, 7(6). doi:10.1128/mBio.01372-1.

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Hogan, D. A., Willger, S. D., Dolben, E. L., Hampton, T. H., Stanton, B. A., Morrison, H. G.Sogin, M. L., Czum, J., & Ashare, A. (2016). “Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease.” PLoS One, 11(3), e0149998. doi:10.1371/journal.pone.014999.

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Kleindienst, S., Grim, S., Sogin, M., Bracco, A., Crespo-Medina, M., & Joye, S. B. (2016). “Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume.” ISME J, 10(2), 400-415. doi:10.1038/ismej.2015.12.

Kleindienst, S., Seidel, M., Ziervogel, K., Grim, S., Loftis, K., Harrison, S., Malkin, S. Y., Perkins, M. J., Field, J., Sogin, M. L., Dittmar, T., Passow, U., Medeiros, P., & Joye, S. B. (2016). “Reply to Prince et al.: Ability of chemical dispersants to reduce oil spill impacts remains unclear.” Proc Natl Acad Sci U S A, 113(11), E1422-1423. doi:10.1073/pnas.160049811.

Li, H., Yang, X., Weng, B., Su, J., Nie, S., Gilbert, J. A., & Zhu, Y. G. (2016). “The phenological stage of rice growth determines anaerobic ammonium oxidation activity in rhizosphere soil.” SOIL BIOLOGY & BIOCHEMISTRY, 100, 59-65. doi:10.1016/j.soilbio.2016.05.01.

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Luria, C. M., Amaral-Zettler, L. A., Ducklow, H. W., & Rich, J. J. (2016). “Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula.” Front Microbiol, 7(ARTN 1731), 1731. doi:10.3389/fmicb.2016.0173.

Madan, J. C., Hoen, A. G., Lundgren, S. N., Farzan, S. F., Cottingham, K. L., Morrison, H. G.Sogin, M. L., Li, H., Moore, J. H., & Karagas, M. R. (2016). “Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants.” JAMA PEDIATRICS, 170(3), 212-219. doi:10.1001/jamapediatrics.2015.373.

Mark Welch, J. L., Rossetti, B. J., Rieken, C. W., Dewhirst, F. E., & Borisy, G. G. (2016). “Biogeography of a human oral microbiome at the micron scale.” Proc Natl Acad Sci U S A, 113(6), E791-800. doi:10.1073/pnas.152214911.

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Meyer, J. L., Jaekel, U., Tully, B. J., Glazer, B. T., Wheat, C. G., Lin, H. T., Hsieh, C. C., Cowen, J. P., Hulme, S. M., Girguis, P. R., & Huber, J. A. (2016). “A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge.” Sci Rep, 6, 22541. doi:10.1038/srep2254.

Mills, S., Alcántara-Rodríguez, J. A., Ciros-Pérez, J., Gómez, A., Hagiwara, A., Galindo, K. H., Jersabek, C. D., Malekzadeh-Viayeh, R., Leasi, F., Lee, J.-S., Mark Welch, D. B., Papakostas, S., Riss, S., Segers, H., Serra, M., Shiel, R., Smolak, R., Snell, T. W., Stelzer, C.-P., Tang, C. Q., Wallace, R. L., Fontaneto, D., & Walsh, E. J. (2016). “Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy.” Hydrobiologia, 796(1), 39-58. doi:10.1007/s10750-016-2725-.

O’Brien, S. L., Gibbons, S. M., Owens, S. M., Hampton-Marcell, J., Johnston, E. R., Jastrow, J. D., Gilbert, J. A., Meyer, F., & Antonopoulos, D. A. (2016). “Spatial scale drives patterns in soil bacterial diversity.” Environ Microbiol, 18(6), 2039-2051. doi:10.1111/1462-2920.1323.

Perisin, M., Vetter, M., Gilbert, J. A., & Bergelson, J. (2016). “16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies.” ISME J, 10(4), 1020-1024. doi:10.1038/ismej.2015.16.

Reveillaud, J.Reddington, E., McDermott, J., Algar, C., Meyer, J. L., Sylva, S., Seewald, J., German, C. R., & Huber, J. A. (2016). “Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise.” Environ Microbiol, 18(6), 1970-1987. doi:10.1111/1462-2920.1317.

Rochman, C. M., Browne, M. A., Underwood, A. J., van Franeker, J. A., Hompson, R. C. T., & Amaral-Zettler, L. A. (2016). “The ecological impacts of marine debris: unraveling the demonstrated evidence from what is perceived.” Ecology, 97(2), 302-312. doi:10.1890/14-2070..

Rodriguez, F., & Arkhipova, I. R. (2016). “Multitasking of the piRNA Silencing Machinery: Targeting Transposable Elements and Foreign Genes in the Bdelloid Rotifer Adineta vaga.” Genetics, 203(1), 255-268. doi:10.1534/genetics.116.18673.

Sangwan, N., Xia, F., & Gilbert, J. A. (2016). “Recovering complete and draft population genomes from metagenome datasets.” Microbiome, 4(1), 8. doi:10.1186/s40168-016-0154-.

Schmidt, V., Amaral-Zettler, L. A., Davidson, J., Summerfelt, S., & Good, C. (2016). “The influence of fishmeal-free diets on microbial communities in Atlantic salmon Salmo salar recirculation aquaculture systems.” Appl Environ Microbiol, 82(15), 4470-4481. doi:10.1128/AEM.00902-1.

Sharma, A., Gilbert, J. A., & Lal, R. (2016). “(Meta) genomic insights into the pathogenome of Cellulosimicrobium cellulans.” Scientific Reports, 6, 25527. doi:ARTN 25527 10.1038/srep2552.

Sielaff, M., Schmidt, H., Struck, T. H., Rosenkranz, D., Mark Welch, D. B., Hankeln, T., & Herlyn, H. (2016). “Phylogeny of Syndermata (syn.” Rotifera): Mitochondrial gene order verifies epizoic Seisonidea as sister to endoparasitic Acanthocephala within monophyletic Hemirotifera. Mol Phylogenet Evol, 96, 79-92. doi:10.1016/j.ympev.2015.11.01.

Sun, R., Dsouza, M., Gilbert, J. A., Guo, X., Wang, D., Guo, Z., Ni, Y., & Chu, H. (2016). “Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter.” Environ Microbiol, 18(12), 5137-5150. doi:10.1111/1462-2920.1351.

Topcuoglu, B. D., Stewart, L. C., Morrison, H. G., Butterfield, D. A., Huber, J. A., & Holden, J. F. (2016). “Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents.” Frontiers in Microbiology, 7(ARTN 1240). doi:10.3389/fmicb.2016.0124.

Utter, D. R., Welch, J. L. M., & Borisy, G. G. (2016). “Individuality, Stability, and Variability of the Plaque Microbiome.” FRONTIERS IN MICROBIOLOGY, 7(ARTN 564). doi:10.3389/fmicb.2016.0056.

Vineis, J. H., Ringus, D. L., Morrison, H. G., Delmont, T. O., Dalal, S., Raffals, L. H., Antonopoulos, D. A., Rubin, D. T., Eren, A. M., Chang, E. B., & Sogin, M. L. (2016). “Patient-Specific Bacteroides Genome Variants in Pouchitis.” MBio, 7(6), e01713-01716. doi:10.1128/mBio.01713-1.

Walsh, E. A., Kirkpatrick, J. B., Pockalny, R., Sauvage, J., Spivack, A. J., Murray, R. W., Sogin, M. L., & D’Hondt, S. (2016). “Relationship of Bacterial Richness to Organic Degradation Rate and Sediment Age in Subseafloor Sediment.” Appl Environ Microbiol, 82(16), 4994-4999. doi:10.1128/AEM.00809-1.

Walsh, E. A., Kirkpatrick, J. B., Rutherford, S. D., Smith, D. C., Sogin, M., & D’Hondt, S. (2016). “Bacterial diversity and community composition from seasurface to subseafloor.” ISME J, 10(4), 979-989. doi:10.1038/ismej.2015.17.

Walters, W., Hyde, E. R., Berg-Lyons, D., Ackermann, G., Humphrey, G., Parada, A., Gilbert, J. A., Jansson, J. K., Caporaso, J. G., Fuhrman, J. A., Apprill, A., & Knight, R. (2016). “Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys.” mSystems, 1(1). doi:10.1128/mSystems.00009-1.

Ward, M. A., Pierre, J. F., Leal, R. F., Huang, Y., Shogan, B., Dalal, S. R., Weber, C. R., Leone, V. A., Musch, M. W., An, G. C., Rao, M. C., Rubin, D. T., Raffals, L. E., Antonopoulos, D. A., Sogin, M. L., Hyman, N. H., Alverdy, J. C., & Chang, E. B. (2016). “Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility.” Am J Physiol Gastrointest Liver Physiol, 310(11), G973-988. doi:10.1152/ajpgi.00017.201.

Wardrip, N. C., Dsouza, M., Urgun-Demirtas, M., Snyder, S. W., Gilbert, J. A., & Arnusch, C. J. (2016). “Printing-Assisted Surface Modifications of Patterned Ultrafiltration Membranes.” ACS APPLIED MATERIALS & INTERFACES, 8(44), 30271-30280. doi:10.1021/acsami.6b1133.

Yang, T., Weisenhorn, P., Gilbert, J. A., Ni, Y., Sun, R., Shi, Y., & Chu, H. (2016). “Carbon constrains fungal endophyte assemblages along the timberline.” Environ Microbiol, 18(8), 2455-2469. doi:10.1111/1462-2920.1315.

Zheng, Y., Huang, Y., Andersen, R. A., & Amaral-Zettler, L. A. (2016). “Excluding the di-unsaturated alkenone in the UK37 index strengthens temperature correlation for the common lacustrine and brackish-water haptophytes.” Geochimica et Cosmochimica Acta, 175, 36-46. doi:10.1016/j.gca.2015.11.02.

Zozaya, M., Ferris, M. J., Siren, J. D., Lillis, R., Myers, L., Nsuami, M. J., Eren, A. M., Brown, J., Taylor, C. M., & Martin, D. H. (2016). “Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis.” Microbiome, 4(1), 16. doi:10.1186/s40168-016-0161-.


Alivisatos, A. P., Blaser, M. J., Brodie, E. L., Chun, M., Dangl, J. L., Donohue, T. J., Dorrestein, P. C., Gilbert, J. A., Green, J. L., Jansson, J. K., Knight, R., Maxon, M. E., McFall-Ngai, M. J., Miller, J. F., Pollard, K. S., Ruby, E. G., & Taha, S. A. (2015). “A unified initiative to harness Earth’s microbiomes.” Science, 350. doi:10.1126/science.aac848.

Amaral-Zettler, L. A., Zettler, E. R., Slikas, B., Boyd, G. D., Melvin, D. W., Morrall, C. E., Proskurowski, G., & Mincer, T. J. (2015). “The biogeography of the Plastisphere: implications for policy.” Frontiers in Ecology and the Environment, 13(10), 541-546. doi:10.1890/15001.

Amata, E., Bland, N. D., Campbell, R. K., & Pollastri, M. P. (2015). “Evaluation of pyrrolidine and pyrazolone derivatives as inhibitors of trypanosomal phosphodiesterase B1 (TbrPDEB1).” Tetrahedron Lett, 56(21), 2832-2835. doi:10.1016/j.tetlet.2015.04.06.

Anderson, R. E., Sogin, M. L., & Baross, J. A. (2015). “Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.” FEMS Microbiol Ecol, 91(1), 1-11. doi:10.1093/femsec/fiu01.

Angermeyer, A., Crosby, S. C., & Huber, J. A. (2015). “Decoupled distance-decay patterns between dsrA and 16S rRNA genes among salt marsh sulfate-reducing bacteria.” Environ Microbiol, 18(1), 75-86. doi:10.1111/1462-2920.1282.

Bertrand, E. M., McCrow, J. P., Moustafa, A., Zheng, H., McQuaid, J. B., Delmont, T. O., Post, A. F., Sipler, R. E., Spackeen, J. L., Xu, K., Bronk, D. A., Hutchins, D. A., & Allen, A. E. (2015). “Phytoplankton-bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge.” Proc Natl Acad Sci U S A, 112(32), 9938-9943. doi:10.1073/pnas.150161511.

Bowen, J. L., Weisman, D., Yasuda, M., Jayakumar, A., Morrison, H. G., & Ward, B. B. (2015). “Marine Oxygen-Deficient Zones Harbor Depauperate Denitrifying Communities Compared to Novel Genetic Diversity in Coastal Sediments.” Microb Ecol, 70(2), 311-321. doi:10.1007/s00248-015-0582-.

Browne, M. A., Chapman, M. G., Thompson, R. C., Amaral-Zettler, L. A., Jambeck, J., & Mallos, N. J. (2015). “Spatial and temporal patterns of stranded intertidal marine debris: is there a picture of global change?” Environ Sci Technol, 49(12), 7082-7094. doi:10.1021/es506057.

Burgsdorf, I., Slaby, B. M., Handley, K. M., Haber, M., Blom, J., Marshall, C. W., Gilbert, J. A., Hentschel, U., & Steindler, L. (2015). “Lifestyle evolution in cyanobacterial symbionts of sponges.” MBio, 6(3), e00391-00315. doi:10.1128/mBio.00391-1.

Chafee, M., Maignien, L., & Simmons, S. L. (2015). “The effects of variable sample biomass on comparative metagenomics.” Environ Microbiol, 17(7), 2239-2253. doi:10.1111/1462-2920.1266.

Delmont, T. O., Eren, A. M., Maccario, L., Prestat, E., Esen, O. C., Pelletier, E., Le Paslier, D., Simonet, P., & Vogel, T. M. (2015). “Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics.” Front Microbiol, 6, 358. doi:10.3389/fmicb.2015.0035.

Delmont, T. O., Eren, A. M.Vineis, J. H., & Post, A. F. (2015). “Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica.” Front Microbiol, 6, 1090. doi:10.3389/fmicb.2015.0109.

Ducklow, H. W., Wilson, S. E., Post, A. F., Stammerjohn, S. E., Erickson, M., Lee, S., Lowry, K. E., Sherrell, R. M., & Yager, P. L. (2015). “Particle flux on the continental shelf in the Amundsen Sea Polynya and Western Antarctic Peninsula.” Elementa: Science of the Anthropocene, 3(46), 000046. doi:10.12952/journal.elementa.00004.

Eren, A. M., Esen, O. C., Quince, C., Vineis, J. H.Morrison, H. G.Sogin, M. L., & Delmont, T. O. (2015). “Anvi’o: an advanced analysis and visualization platform for ‘omics data.” PeerJ, 3, e1319. doi:10.7717/peerj.131.

Eren, A. M.Morrison, H. G., Lescault, P. J., Reveillaud, J.Vineis, J. H., & Sogin, M. L. (2015). “Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences.” ISME J, 9(4), 968-979. doi:10.1038/ismej.2014.19.

Eren, A. M.Sogin, M. L.Morrison, H. G.Vineis, J. H., Fisher, J. C., Newton, R. J., & McLellan, S. L. (2015). “A single genus in the gut microbiome reflects host preference and specificity.” ISME J, 9(1), 90-100. doi:10.1038/ismej.2014.9.

Filkins, L. M., Dolben, E. L., Willger, S. D., Gifford, A. H., Sogin, M. L.Morrison, H. G.Grim, S. L., Ashare, A., Schwartzman, J. D., & Hogan, D. (2015). “Bacfun: An Rna-Based Diagnostic for Cystic Fibrosis Respiratory Samples.” Pediatric Pulmonology, 50, 321-321.

Fisher, J. C., Eren, A. M., Green, H. C., Shanks, O. C., Morrison, H. G.Vineis, J. H.Sogin, M. L., & McLellan, S. L. (2015). “Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups.” Appl Environ Microbiol, 81(20), 7023-7033. doi:10.1128/AEM.01524-1.

Fortunato, C. S., & Crump, B. C. (2015). “Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient.” PLoS One, 10(11), e0140578. doi:10.1371/journal.pone.014057.

Fuller, M., Priyadarshini, M., Gibbons, S. M., Angueira, A. R., Brodsky, M., Hayes, M. G., Kovatcheva-Datchary, P., Backhed, F., Gilbert, J. A., Lowe, W. L. Jr., & Layden, B. T. (2015). “The short-chain fatty acid receptor, FFA2, contributes to gestational glucose homeostasis.” Am J Physiol Endocrinol Metab, 309(10), E840-851. doi:10.1152/ajpendo.00171.201.

Gibbons, S. M., & Gilbert, J. A. (2015). “Microbial diversity-exploration of natural ecosystems and microbiomes.” Curr Opin Genet Dev, 35, 66-72. doi:10.1016/j.gde.2015.10.00.

Gibbons, S. M., Schwartz, T., Fouquier, J., Mitchell, M., Sangwan, N., Gilbert, J. A., & Kelley, S. T. (2015). “Ecological succession and viability of human-associated microbiota on restroom surfaces.” Appl Environ Microbiol, 81(2), 765-773. doi:10.1128/AEM.03117-1.

Gilbert, J. A., & Henry, C. (2015). “Predicting ecosystem emergent properties at multiple scales.” Environ Microbiol Rep, 7(1), 20-22. doi:10.1111/1758-2229.1225.

Gordon, J., Gandhi, P., Shekhawat, G., Frazier, A., Hampton-Marcell, J., & Gilbert, J. A. (2015). “A simple novel device for air sampling by electrokinetic capture.” Microbiome, 3(1), 79. doi:10.1186/s40168-015-0141-.

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Garbuz, D. G., Astakhova, L. N., Zatsepina, O. G., Arkhipova, I. R., Nudler, E., & Evgen’ev, M. B. (2011). “Functional organization of hsp70 cluster in camel (Camelus dromedarius) and other mammals.” PLoS One, 6(11), e27205. doi:10.1371/journal.pone.002720.

Garbuz, D. G., Yushenova, I. A., Zatsepina, O. G., Przhiboro, A. A., Bettencourt, B. R., & 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. doi:10.1186/1471-2148-11-7.

Gast, R. J., Moran, D. M., Dennett, M. R., Wurtsbaugh, W. A., & Amaral-Zettler, L. A. (2011). “Amoebae and Legionella pneumophila in saline environments.” J Water Health, 9(1), 37-52. doi:10.2166/wh.2010.10.

Gladyshev, E. A., & Arkhipova, I. R. (2011). “A widespread class of reverse transcriptase-related cellular genes.” Proc Natl Acad Sci U S A, 108(51), 20311-20316. doi:10.1073/pnas.110026610.

Gribble, K. E., Snell, T. W., & Mark Welch, D. B. (2011). “Gene and protein structure of the mate recognition protein gene family in Brachionus manjavacas (Rotifera).” Hydrobiologia, 662(1), 35-42. doi:DOI 10.1007/s10750-010-0482-.

Huse, S. M., & 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 (pp. 149-156): Wiley and Sons.

Kamennaya, N. A., & Post, A. F. (2011). “Characterization of cyanate metabolism in marine Synechococcus and Prochlorococcus spp.” Appl Environ Microbiol, 77(1), 291-301. doi:10.1128/AEM.01272-1.

Mackey, K. R. M., Bristow, L., Parks, D. R., Altabet, M. A., Post, A. F., & 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. doi:DOI 10.1016/j.pocean.2011.09.00.

Mark Welch, D. B., & 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 (pp. 245-252): Wiley and Sons.

Nelson, C. E., Alldredge, A. L., McCliment, E. A., Amaral-Zettler, L. A., & Carlson, C. A. (2011). “Depleted dissolved organic carbon and distinct bacterial communities in the water column of a rapid-flushing coral reef ecosystem.” ISME J, 5(8), 1374-1387. doi:10.1038/ismej.2011.1.

Nuzzio, D. B., Zettler, E. R., Aguilera, A., & 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(10), 1984-1989. doi:10.1016/j.scitotenv.2011.01.00.

Oleksiak, M. F., Karchner, S. I., Jenny, M. J., Franks, D. G., Mark Welch, D. B., & 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. doi:10.1186/1471-2164-12-26.

Pawlowski, J., Christen, R., Lecroq, B., Bachar, D., Shahbazkia, H. R., Amaral-Zettler, L. A., & Guillou, L. (2011). “Eukaryotic richness in the abyss: insights from pyrotag sequencing.” PLoS One, 6(4), e18169. doi:10.1371/journal.pone.001816.

Perry, D. A., Morrison, H. G., & Adam, R. D. (2011). “Optical map of the genotype A1 WB C6 Giardia lamblia genome isolate.” Mol Biochem Parasitol, 180(2), 112-114. doi:10.1016/j.molbiopara.2011.07.00.

Pollastri, M. P., & Campbell, R. K. (2011). “Target repurposing for neglected diseases.” Future Med Chem, 3(10), 1307-1315. doi:10.4155/fmc.11.9.

Post, A. F., Penno, S., Zandbank, K., Paytan, A., Huse, S. M., & Welch, D. M. (2011). “Long term seasonal dynamics of synechococcus population structure in the gulf of aqaba, northern red sea.” Front Microbiol, 2, 131. doi:10.3389/fmicb.2011.0013.

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., & Thomas, H. (2011). “Active submarine eruption of boninite in the northeastern Lau Basin.” Nature Geoscience, 4(11), 799-806. doi:Doi 10.1038/Ngeo127.

Rodrigues, J. L., Serres, M. H., & Tiedje, J. M. (2011). “Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of shewanella species and identify metabolic pathways conserved at the genus level.” Appl Environ Microbiol, 77(15), 5352-5360. doi:10.1128/AEM.00097-1.

Shanks, O. C., Kelty, C. A., Archibeque, S., Jenkins, M., Newton, R. J., McLellan, S. L., Huse, S. M., & Sogin, M. L. (2011). “Community structures of fecal bacteria in cattle from different animal feeding operations.” Appl Environ Microbiol, 77(9), 2992-3001. doi:10.1128/AEM.02988-1.

Shanks, O. C., McLellan, S. L., Huse, S. M., & 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 & N. J. Ashbolt (Ed.), In Environmental Microbiology: Current Technology and Water Applications. Norfolk, UK: Caister Academic Press.

Smith, H. A., Mark Welch, D. B., & Snell, T. W. (2011). “Molecular evolution of the membrane associated progesterone receptor in the Brachionus plicatilis (Rotifera, Monogononta) species complex.” Hydrobiologia, 662(1), 99-106. doi:10.1007/s10750-010-0484-.

Smith, J., Morgan, J. R., Zottoli, S. J., Smith, P. J., Buxbaum, J. D., & Bloom, O. E. (2011). “Regeneration in the era of functional genomics and gene network analysis.” Biol Bull, 221(1), 18-34.

Sul, W. J., Cole, J. R., Jesus Eda, C., Wang, Q., Farris, R. J., Fish, J. A., & Tiedje, J. M. (2011). “Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering.” Proc Natl Acad Sci U S A, 108(35), 14637-14642. doi:10.1073/pnas.111143510.

Valm, A. M.Mark Welch, J. L., Rieken, C. W., Hasegawa, Y.Sogin, M. L., Oldenbourg, R., Dewhirst, F. E., & Borisy, G. G. (2011). “Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging.” Proc Natl Acad Sci U S A, 108(10), 4152-4157. doi:10.1073/pnas.110113410.

White, J., Gilbert, J. A., Hill, G., Hill, E., Huse, S. M., Weightman, A. J., & 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.” Appl Environ Microbiol, 77(13), 4527-4538. doi:10.1128/AEM.02317-1.

Xia, L. C., Steele, J. A., Cram, J. A., Cardon, Z. G., Simmons, S. L., Vallino, J. J., Fuhrman, J. A., & Sun, F. (2011). “Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates.” BMC Syst Biol, 5 Suppl 2, S15. doi:10.1186/1752-0509-5-S2-S1.

Yelton, A. P., Thomas, B. C., Simmons, S. L., Wilmes, P., Zemla, A., Thelen, M. P., Justice, N., & Banfield, J. F. (2011). “A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes.” PLoS Comput Biol, 7(10), e1002230. doi:10.1371/journal.pcbi.100223.

Yilmaz, P., Gilbert, J. A., Knight, R., Amaral-Zettler, L. A., Karsch-Mizrachi, I., Cochrane, G., Nakamura, Y., Sansone, S. A., Glockner, F. O., & Field, D. (2011). “The genomic standards consortium: bringing standards to life for microbial ecology.” ISME J, 5(10), 1565-1567. doi:10.1038/ismej.2011.3.

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Zinger, L., Amaral-Zettler, L. A., Fuhrman, J. A., Horner-Devine, M. C., Huse, S. M.Mark Welch, D. B., Martiny, J. B., Sogin, M. L., Boetius, A., & Ramette, A. (2011). “Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems.” PLoS One, 6(9), e24570. doi:10.1371/journal.pone.002457.