Bay Paul Center Publication Co-authorship Network

Top 25 Journals

Proc Natl Acad Sci U S A (56), PLoS One (30), ISME J (30), Appl Environ Microbiol (29), Mol Biol Evol (24), Environ Microbiol (21), Nucleic Acids Res (18), J Bacteriol (18), Science (17), Front Microbiol (17), Biol Bull (17), J Biol Chem (16), Microbiome (13), J Mol Biol (13), European Journal of Protistology (12), J Eukaryot Microbiol (11), Nature (10), Hydrobiologia (10), Genetics (10), BMC Genomics (10), mSystems (8), Gene (8), PLoS Biol (7), Mol Microbiol (7), MBio (7)


2018 (24) | 2017 (34) | 2016 (49) | 2015 (58) | 2014 (66) | 2013 (40) | 2012 (43) | 2011 (39) | 2010 (32) | 2009 (42) | 2008 (36) | 2007 (42) | 2006 (35) | 2005 (42) | 2004 (26) | 2003 (43) | 2002 (43) | 2001 (37) | 2000 (39) | 1999 (28) | 1998 (30) | 1997 (22) | 1996 (22)



Abrams, J.M., Arkhipova, I.R., Belfort, M., Boeke, J.D., Curcio, M.J., Faulkner, G.J., Goodier, J.L., Lehmann, R., and Levin, H.L. (2018). “Meeting report: mobile genetic elements and genome plasticity 2018.MOBILE DNA, 9(ARTN 21).

Arkhipova, I.R. (2018). “Neutral Theory, Transposable Elements, and Eukaryotic Genome Evolution.Mol Biol Evol, 35(6), 1332-1337.

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., and Woyke, T. (2018). “Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (vol 35, pg 725, 2017).NATURE BIOTECHNOLOGY, 36(2), 196-196.

Burnett, K., Edsinger, E., and Albrecht, D.R. (2018). “Rapid and gentle hydrogel encapsulation of living organisms enables long-term microscopy over multiple hours.Communications Biology, 1(1).

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

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., and 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.

Delmont, T.O., and Eren, A.M. (2018). “Linking pangenomes and metagenomes: the Prochlorococcus metapangenome.PEERJ, 6(ARTN e4320).

Delmont, T.O., Quince, C., Shaiber, A., Esen, O.C., Lee, S.T.M., Rappe, M.S., MacLellan, S.L., Lucker, S., and Eren, A.M. (2018). “Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.NATURE MICROBIOLOGY, 3(7), 804-+.

Frère, L., Maignien, L., Chalopin, M., Huvet, A., Rinnert, E., Morrison, H., Kerninon, S., Cassone, A.L., Lambert, C., Reveillaud, J., and 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.

Gilbert, J.A. (2018). “Early-Career Systems Microbiology Scientists.mSystems, 3(2).

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., and Hogan, D.A. (2018). “Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA.mSphere, 3(4).

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., and Karagas, M.R. (2018). “Sex-specific associations of infants’ gut microbiome with arsenic exposure in a US population.Scientific Reports, 8(1), 12627.

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., and Nusslein, K. (2018). “New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes.FRONTIERS IN MICROBIOLOGY, 9(ARTN 1635).

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

Lundgren, S.N., Madan, J.C., Emond, J.A., Morrison, H.G., Christensen, B.C., Karagas, M.R., and Hoen, A.G. (2018). “Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner.MICROBIOME, 6(ARTN 109).

McIntosh, C.M., Chen, L., Shaiber, A., Eren, A.M., and Alegre, M.L. (2018). “Gut microbes contribute to variation in solid organ transplant outcomes in mice.MICROBIOME, 6(ARTN 96).

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., Vu, D., 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., and Jabri, B. (2018). “Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host.NATURE, 557(7706), 580-+.

Peñalver Bernabé, B., Cralle, L., and Gilbert, J.A. (2018). “Systems biology of the human microbiome.Curr Opin Biotechnol, 51 146-153.

Quigley, C.T.C., Morrison, H.G., Mendonca, I.R., and Brawley, S.H. (2018). “A common garden experiment with Porphyra umbilicalis (Rhodophyta) evaluates methods to study spatial differences in the macroalgal microbiome.J Phycol., , ,.

Rodriguez, F., and Arkhipova, I.R. (2018). “Transposable elements and polyploid evolution in animals.CURRENT OPINION IN GENETICS & DEVELOPMENT, 49 115-123.

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

Sheik, C.S., Reese, B.K., Twing, K.I., Sylvan, J.B., Grim, S.L., Schrenk, M.O., Sogin, M.L., and Colwell, F.S. (2018). “Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.FRONTIERS IN MICROBIOLOGY, 9(ARTN 840).

Yushenova, I.A., and Arkhipova, I.R. (2018). “Biochemical properties of bacterial reverse transcriptase-related (rvt) gene products: multimerization, protein priming, and nucleotide preference.Curr Genet., , , .

Zhang, X., Xia, K., Lin, L., Zhang, F., Yu, Y., St Ange, K., Han, X., Edsinger, E., Sohn, J., and Linhardt, R.J. (2018). “Structural and Functional Components of the Skate Sensory Organ Ampullae of Lorenzini.ACS CHEMICAL BIOLOGY, 13(6), 1677-1685.



Amaral-Zettler, L.A., Dragone, N.B., Schell, J., Slikas, B., Murphy, L.G., Morrall, C.E., and 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.

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

Arkhipova, I.R., Yushenova, I.A., and Rodriguez, F. (2017). “Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres.Mol Biol Evol, 34(9), 2245-2257.

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., and 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.

Bowman, J.S., Amaral-Zettler, L.A., J, J.R., C, M.L., and 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.

Courtine, D., Alain, K., Georges, M., Bienvenu, N., Morrison, H.G., Eren, A.M., and 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).

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

Delmont, T.O., and 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.

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

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., and Crump, B.C. (2017). “Bacterial Biogeography across the Amazon River-Ocean Continuum.Front Microbiol, 8 882.

Fan, K.K., Cardona, C., Li, Y.T., Shi, Y., Xiang, X.J., Shen, C.C., Wang, H.F., Gilbert, J.A., and 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.

Franco-Obregon, A., and Gilbert, J.A. (2017). “The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals.mSystems, 2(3).

Gibbons, S.M., Lekberg, Y., Mummey, D.L., Sangwan, N., Ramsey, P.W., and Gilbert, J.A. (2017). “Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem.mSystems, 2(2).

Gilbert, J.A. (2017). “How do we make indoor environments and healthcare settings healthier?Microb Biotechnol, 10(1), 11-13.

Gribble, K.E., and Mark Welch, D.B. (2017). “Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system.BMC Genomics, 18(1), 217.

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

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., and 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.

Knight, R., Callewaert, C., Marotz, C., Hyde, E.R., Debelius, J.W., McDonald, D., and Sogin, M.L. (2017). “The Microbiome and Human Biology.Annu Rev Genomics Hum Genet, 18 65-86.

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., and Lal, R. (2017). “Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium.mSystems, 2(3).

Kuntz, T.M., and Gilbert, J.A. (2017). “Introducing the Microbiome into Precision Medicine.Trends Pharmacol Sci, 38(1), 81-91.

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., and Eren, A.M. (2017). “Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics.Microbiome, 5(1), 50.

Ma, B., Dai, Z., Wang, H., Dsouza, M., Liu, X., He, Y., Wu, J., Rodrigues, J.L., Gilbert, J.A., Brookes, P.C., and 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).

Mackey, K.R.M., Hunter-Cevera, K., Britten, G.L., Murphy, L.G., Sogin, M.L., and 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.

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

Mark Welch, J.L., Hasegawa, Y., McNulty, N.P., Gordon, J.I., and 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.

Perez, T., Rodriguez, F., Fernandez, M., Albornoz, J., and Dominguez, A. (2017). “Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus.Gene, 628(Supplement C), 63-71.

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

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

Schmidt, V., Gomez-Chiarri, M., Roy, C., Smith, K., and Amaral-Zettler, L.A. (2017). “Subtle Microbiome Manipulation Using Probiotics Reduces Antibiotic-Associated Mortality in Fish.Msystems, 2(6).

Smith, M.W., Herfort, L., Fortunato, C.S., Crump, B.C., and 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).

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

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

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

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



Arkhipova, I.R., and Rice, P.A. (2016). “Mobile genetic elements: in silico, in vitro, in vivo.Mol Ecol, 25(5), 1027-1031.

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., and 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.

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., and 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.

Chernikova, D.A., Koestler, D.C., Hoen, A.G., Housman, M.L., Hibberd, P.L., Moore, J.H., Morrison, H.G., Sogin, M.L., Zain-Ul-Abideen, M., and Madan, J.C. (2016). “Fetal exposures and perinatal influences on the stool microbiota of premature infants.J Matern Fetal Neonatal Med, 29(1), 99-105.

Davies, N., Field, D., Gavaghan, D., Holbrook, S.J., Planes, S., Troyer, M., Bonsall, M., Claudet, J., Roderick, G., Schmitt, R.J., Amaral-Zettler, L.A., Berteaux, V., Bossin, H.C., Cabasse, C., Collin, A., Deck, J., Dell, T., Dunne, J., Gates, R., Harfoot, M., Hench, J.L., Hopuare, M., Kirch, P., Kotoulas, G., Kosenkov, A., Kusenko, A., Leichter, J.J., Lenihan, H., Magoulas, A., Martinez, N., Meyer, C., Stoll, B., Swalla, B., Tartakovsky, D.M., Murphy, H.T., Turyshev, S., Valdvinos, F., Williams, R., Wood, S., and Consortium, I. (2016). “Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium.Gigascience, 5(1), 14.

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

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

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., and 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.

Dugas, L.R., Fuller, M., Gilbert, J., and Layden, B.T. (2016). “The obese gut microbiome across the epidemiologic transition.Emerg Themes Epidemiol, 13 2.

Eren, A.M., Sogin, M.L., and Maignien, L. (2016). “Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation.Frontiers in Microbiology, 7 1318.

Fernandez-Gonzalez, N., Huber, J.A., and Vallino, J.J. (2016). “Microbial Communities Are Well Adapted to Disturbances in Energy Input.mSystems, 1(5).

Fortunato, C.S., and Huber, J.A. (2016). “Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent.ISME J, 10(8), 1925-1938.

Gibbons, S.M., Scholz, M., Hutchison, A.L., Dinner, A.R., Gilbert, J.A., and Coleman, M.L. (2016). “Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System.MBIO, 7(6).

Gilbert, J.A. (2016). “mSystems: Learning To Love Systems.mSystems, 1(1).

Gilbert, J.A., and Alverdy, J. (2016). “Stool consistency as a major confounding factor affecting microbiota composition: an ignored variable?Gut, 65(1), 1-2.

Gilbert, J.A., Klyczek, K.K., and Elliott, S.L. (2016). “Introducing the JMBE Themed Issue on Scientific Citizenship.J Microbiol Biol Educ, 17(1), 1-2.

Hogan, D.A., Willger, S.D., Dolben, E.L., Hampton, T.H., Stanton, B.A., Morrison, H.G., Sogin, M.L., Czum, J., and 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.

Kaneko, G., Yoshinaga, T., Gribble, K.E., Mark Welch, D.B., and Ushio, H. (2016). “Measurement of Survival Time in Brachionus Rotifers: Synchronization of Maternal Conditions.J Vis Exp,(113), e54126.

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

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., and 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.

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

Liebeskind, B.J., Hillis, D.M., Zakon, H.H., and Hofmann, H.A. (2016). “Complex Homology and the Evolution of Nervous Systems.Trends Ecol Evol, 31(2), 127-135.

Luria, C.M., Amaral-Zettler, L.A., Ducklow, H.W., and 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.

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., and 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.

Mark Welch, J.L., Rossetti, B.J., Rieken, C.W., Dewhirst, F.E., and 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.

Metcalf, J.L., Xu, Z.Z., Weiss, S., Lax, S., Van Treuren, W., Hyde, E.R., Song, S.J., Amir, A., Larsen, P., Sangwan, N., Haarmann, D., Humphrey, G.C., Ackermann, G., Thompson, L.R., Lauber, C., Bibat, A., Nicholas, C., Gebert, M.J., Petrosino, J.F., Reed, S.C., Gilbert, J.A., Lynne, A.M., Bucheli, S.R., Carter, D.O., and Knight, R. (2016). “Microbial community assembly and metabolic function during mammalian corpse decomposition.Science, 351(6269), 158-162.

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., and 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.

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., and Walsh, E.J. (2016). “Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy.Hydrobiologia, 796(1), 39-58.

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

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

Reveillaud, J., Reddington, E., McDermott, J., Algar, C., Meyer, J.L., Sylva, S., Seewald, J., German, C.R., and 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.

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

Rodriguez, F., and 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.

Sangwan, N., Xia, F., and Gilbert, J.A. (2016). “Recovering complete and draft population genomes from metagenome datasets.Microbiome, 4(1), 8.

Schmidt, V., Amaral-Zettler, L. A., Davidson, J., Summerfelt, S., and 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.

Sharma, A., Gilbert, J.A., and Lal, R. (2016). “(Meta) genomic insights into the pathogenome of Cellulosimicrobium cellulans.Scientific Reports, 6 25527.

Sielaff, M., Schmidt, H., Struck, T.H., Rosenkranz, D., Mark Welch, D.B., Hankeln, T., and 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.

Sun, R., Dsouza, M., Gilbert, J.A., Guo, X., Wang, D., Guo, Z., Ni, Y., and Chu, H. (2016). “Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter.ENVIRONMENTAL MICROBIOLOGY, 18(12), 5137-5150.

Topcuoglu, B.D., Stewart, L.C., Morrison, H.G., Butterfield, D.A., Huber, J.A., and 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).

Utter, D.R., Welch, J.L.M., and Borisy, G.G. (2016). “Individuality, Stability, and Variability of the Plaque Microbiome.FRONTIERS IN MICROBIOLOGY, 7(ARTN 564).

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., and Sogin, M.L. (2016). “Patient-Specific Bacteroides Genome Variants in Pouchitis.MBio, 7(6), e01713-01716.

Walsh, E.A., Kirkpatrick, J.B., Pockalny, R., Sauvage, J., Spivack, A.J., Murray, R.W., Sogin, M.L., and 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.

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

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., and 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).

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., and 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.

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

Yang, T., Weisenhorn, P., Gilbert, J.A., Ni, Y., Sun, R., Shi, Y., and Chu, H. (2016). “Carbon constrains fungal endophyte assemblages along the timberline.Environ Microbiol, 18(8), 2455-2469.

Zheng, Y., Huang, Y., Andersen, R.A., and 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.

Zozaya, M., Ferris, M.J., Siren, J.D., Lillis, R., Myers, L., Nsuami, M.J., Eren, A.M., Brown, J., Taylor, C.M., and 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.



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., and Taha, S.A. (2015). “A unified initiative to harness Earth’s microbiomes.Science, 350.

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

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

Anderson, R.E., Sogin, M.L., and 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.

Angermeyer, A., Crosby, S.C., and 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.

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., and 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.

Bowen, J.L., Weisman, D., Yasuda, M., Jayakumar, A., Morrison, H.G., and 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.

Browne, M.A., Chapman, M.G., Thompson, R.C., Amaral-Zettler, L.A., Jambeck, J., and 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.

Burgsdorf, I., Slaby, B.M., Handley, K.M., Haber, M., Blom, J., Marshall, C.W., Gilbert, J.A., Hentschel, U., and Steindler, L. (2015). “Lifestyle evolution in cyanobacterial symbionts of sponges.MBio, 6(3), e00391-00315.

Chafee, M., Maignien, L., and Simmons, S.L. (2015). “The effects of variable sample biomass on comparative metagenomics.Environ Microbiol, 17(7), 2239-2253.

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

Delmont, T.O., Eren, A.M., Vineis, J.H., and 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.

Ducklow, H.W., Wilson, S.E., Post, A.F., Stammerjohn, S.E., Erickson, M., Lee, S., Lowry, K.E., Sherrell, R.M., and 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.

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

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

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

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., and 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., and 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.

Fortunato, C.S., and Crump, B.C. (2015). “Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient.PLoS One, 10(11), e0140578.

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., and 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.

Gibbons, S.M., and Gilbert, J.A. (2015). “Microbial diversity-exploration of natural ecosystems and microbiomes.Curr Opin Genet Dev, 35 66-72.

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

Gilbert, J.A., and Henry, C. (2015). “Predicting ecosystem emergent properties at multiple scales.Environ Microbiol Rep, 7(1), 20-22.

Gordon, J., Gandhi, P., Shekhawat, G., Frazier, A., Hampton-Marcell, J., and Gilbert, J.A. (2015). “A simple novel device for air sampling by electrokinetic capture.Microbiome, 3(1), 79.

Green, H.C., Fisher, J.C., McLellan, S.L., Sogin, M.L., and Shanks, O.C. (2015). “Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves, Mammalia, and Actinopterygii.Appl Environ Microbiol, 82(5), 1496-1503.

Hoen, A.G., Li, J., Moulton, L.A., O’Toole, G.A., Housman, M.L., Koestler, D.C., Guill, M.F., Moore, J.H., Hibberd, P.L., Morrison, H.G., Sogin, M.L., Karagas, M.R., and Madan, J.C. (2015). “Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis.J Pediatr, 167(1), 138-147 e131-133.

Huang, E.Y., Inoue, T., Leone, V.A., Dalal, S., Touw, K., Wang, Y., Musch, M.W., Theriault, B., Higuchi, K., Donovan, S., Gilbert, J.A., and Chang, E.B. (2015). “Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases.Inflamm Bowel Dis, 21(5), 963-972.

Huber, J.A. (2015). “MICROBIAL ECOLOGY. Making methane down deep.Science, 349(6246), 376-377.

Hunter-Cevera, K.R., Post, A.F., Peacock, E.E., and Sosik, H.M. (2015). “Diversity of Synechococcus at the Martha’s Vineyard Coastal Observatory: Insights from Culture Isolations, Clone Libraries, and Flow Cytometry.Microb Ecol, 71(2), 276-289.

Huo, Y.Y., Cheng, H., Post, A.F., Wang, C.S., Jiang, X.W., Pan, J., Wu, M., and Xu, X.W. (2015). “Ecological functions of uncultured microorganisms in the cobalt-rich ferromanganese crust of a seamount in the central Pacific are elucidated by fosmid sequencing.Acta Oceanologica Sinica, 34(4), 92-113.

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.M., and Joye, S.B. (2015). “Chemical dispersants can suppress the activity of natural oil-degrading microorganisms.Proc Natl Acad Sci U S A, 112(48), 14900-14905.

Kopf, A., Bicak, M., Kottmann, R., Schnetzer, J., Kostadinov, I., Lehmann, K., Fernandez-Guerra, A., Jeanthon, C., Rahav, E., Ullrich, M., Wichels, A., Gerdts, G., Polymenakou, P., Kotoulas, G., Siam, R., Abdallah, R.Z., Sonnenschein, E.C., Cariou, T., O’Gara, F., Jackson, S., Orlic, S., Steinke, M., Busch, J., Duarte, B., Cacador, I., Canning-Clode, J., Bobrova, O., Marteinsson, V., Reynisson, E., Loureiro, C.M., Luna, G.M., Quero, G.M., Loscher, C.R., Kremp, A., DeLorenzo, M.E., Ovreas, L., Tolman, J., LaRoche, J., Penna, A., Frischer, M., Davis, T., Katherine, B., Meyer, C.P., Ramos, S., Magalhaes, C., Jude-Lemeilleur, F., Aguirre-Macedo, M.L., Wang, S., Poulton, N., Jones, S., Collin, R., Fuhrman, J.A., Conan, P., Alonso, C., Stambler, N., Goodwin, K., Yakimov, M.M., Baltar, F., Bodrossy, L., Van De Kamp, J., Frampton, D.M., Ostrowski, M., Van Ruth, P., Malthouse, P., Claus, S., Deneudt, K., Mortelmans, J., Pitois, S., Wallom, D., Salter, I., Costa, R., Schroeder, D.C., Kandil, M.M., Amaral, V., Biancalana, F., Santana, R., Pedrotti, M.L., Yoshida, T., Ogata, H., Ingleton, T., Munnik, K., Rodriguez-Ezpeleta, N., Berteaux-Lecellier, V., Wecker, P., Cancio, I., Vaulot, D., Bienhold, C., Ghazal, H., Chaouni, B., Essayeh, S., Ettamimi, S., Zaid el, H., Boukhatem, N., Bouali, A., Chahboune, R., Barrijal, S., Timinouni, M., El Otmani, F., Bennani, M., Mea, M., Todorova, N., Karamfilov, V., Ten Hoopen, P., Cochrane, G., L’Haridon, S., Bizsel, K.C., Vezzi, A., Lauro, F.M., Martin, P., Jensen, R.M., Hinks, J., Gebbels, S., Rosselli, R., De Pascale, F., Schiavon, R., Dos Santos, A., Villar, E., Pesant, S., Cataletto, B., Malfatti, F., Edirisinghe, R., Silveira, J.A., Barbier, M., Turk, V., Tinta, T., Fuller, W.J., Salihoglu, I., Serakinci, N., Ergoren, M.C., Bresnan, E., Iriberri, J., Nyhus, P.A., Bente, E., Karlsen, H.E., Golyshin, P.N., Gasol, J.M., Moncheva, S., Dzhembekova, N., Johnson, Z., Sinigalliano, C.D., Gidley, M.L., Zingone, A., Danovaro, R., Tsiamis, G., Clark, M.S., Costa, A.C., El Bour, M., Martins, A.M., Collins, R.E., Ducluzeau, A.L., Martinez, J., Costello, M.J., Amaral-Zettler, L.A., Gilbert, J.A., Davies, N., Field, D., and Glockner, F.O. (2015). “The ocean sampling day consortium.Gigascience, 4 27.

Larsen, P.E., Scott, N., Post, A.F., Field, D., Knight, R., Hamada, Y., and Gilbert, J.A. (2015). “Satellite remote sensing data can be used to model marine microbial metabolite turnover.ISME J, 9(1), 166-179.

Lax, S., and Gilbert, J.A. (2015). “Hospital-associated microbiota and implications for nosocomial infections.Trends Mol Med, 21(7), 427-432.

Lax, S., Hampton-Marcell, J.T., Gibbons, S.M., Colares, G.B., Smith, D., Eisen, J.A., and Gilbert, J.A. (2015). “Forensic analysis of the microbiome of phones and shoes.Microbiome, 3 21.

Lax, S., Nagler, C.R., and Gilbert, J.A. (2015). “Our interface with the built environment: immunity and the indoor microbiota.Trends Immunol, 36(3), 121-123.

Liebeskind, B.J., Hillis, D.M., and Zakon, H.H. (2015). “Convergence of ion channel genome content in early animal evolution.Proc Natl Acad Sci U S A, 112(8), E846-851.

Lin, X., Handley, K.M., Gilbert, J.A., and Kostka, J.E. (2015). “Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat.ISME J, 9(12), 2740-2744.

Lüchmann, K.H., Clark, M.S., Bainy, A.C., Gilbert, J.A., Craft, J.A., Chipman, J.K., Thorne, M.A., Mattos, J.J., Siebert, M.N., and Schroeder, D.C. (2015). “Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana.Aquat Toxicol, 166 10-20.

Mackey, K.R.M., Chien, C.T., Post, A.F., Saito, M.A., and Paytan, A. (2015). “Rapid and gradual modes of aerosol trace metal dissolution in seawater.Front Microbiol, 5 794.

Mackey, K.R.M., Post, A.F., McIlvin, M.R., Cutter, G.A., John, S.G., and Saito, M.A. (2015). “Divergent responses of Atlantic coastal and oceanic Synechococcus to iron limitation.Proc Natl Acad Sci U S A, 112(32), 9944-9949.

Moran, Y., Barzilai, M.G., Liebeskind, B.J., and Zakon, H.H. (2015). “Evolution of voltage-gated ion channels at the emergence of Metazoa.J Exp Biol, 218(Pt 4), 515-525.

Newton, R.J., McLellan, S.L., Dila, D.K., Vineis, J.H., Morrison, H.G., Eren, A.M., and Sogin, M.L. (2015). “Sewage reflects the microbiomes of human populations.MBio, 6(2), e02574.

Ochiana, S.O., Bland, N.D., Settimo, L., Campbell, R.K., and Pollastri, M.P. (2015). “Repurposing human PDE4 inhibitors for neglected tropical diseases. Evaluation of analogs of the human PDE4 inhibitor GSK-256066 as inhibitors of PDEB1 of Trypanosoma brucei.Chem Biol Drug Des, 85(5), 549-564.

Quince, C., Ijaz, U.Z., Loman, N., Eren, A.M., Saulnier, D., Russell, J., Haig, S.J., Calus, S.T., Quick, J., Barclay, A., Bertz, M., Blaut, M., Hansen, R., McGrogan, P., Russell, R.K., Edwards, C.A., and Gerasimidis, K. (2015). “Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition.Am J Gastroenterol, 110(12), 1718-1729.

Saito, M.A., Dorsk, A., Post, A.F., McIlvin, M.R., Rappe, M.S., DiTullio, G.R., and Moran, D.M. (2015). “Needles in the blue sea: sub-species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome.Proteomics, 15(20), 3521-3531.

Satinsky, B.M., Fortunato, C.S., Doherty, M., Smith, C.B., Sharma, S., Ward, N.D., Krusche, A.V., Yager, P.L., Richey, J.E., Moran, M.A., and Crump, B.C. (2015). “Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011.Microbiome, 3(1), 39.

Schmidt, V.T., Smith, K.F., Melvin, D.W., and Amaral-Zettler, L.A. (2015). “Community assembly of a euryhaline fish microbiome during salinity acclimation.Mol Ecol, 24(10), 2537-2550.

Shade, A., and Gilbert, J.A. (2015). “Temporal patterns of rarity provide a more complete view of microbial diversity.Trends Microbiol, 23(6), 335-340.

Sielaff, M., Schmidt, H., Struck, T.H., Rosenkranz, D., Mark Welch, D.B., Hankeln, T., and Herlyn, H. (2015). “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.

Signorovitch, A., Hur, J., Gladyshev, E., and Meselson, M. (2015). “Allele Sharing and Evidence for Sexuality in a Mitochondrial Clade of Bdelloid Rotifers.Genetics, 200(2), 581-590.

Snell, T.W., Johnston, R.K., Gribble, K.E., and Mark Welch, D.B. (2015). “Rotifers as experimental tools for investigating aging.Invertebr Reprod Dev, 59(1), 5-10.

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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, 5(9), 1540-1548.

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 Med 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.

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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.Appl Environ Microbiol, 77(21), 7647-7655.

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.J Water Health, 9(1), 37-52.

Gladyshev, E.A., and Arkhipova, I.R. (2011). “A widespread class of reverse transcriptase-related cellular genes.Proc Natl Acad Sci U S A, 108(51), 20311-20316.

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Kamennaya, N.A., and Post, A.F. (2011). “Characterization of cyanate metabolism in marine Synechococcus and Prochlorococcus spp.Appl Environ Microbiol, 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.

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.ISME J, 5(8), 1374-1387.

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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.A., and Guillou, L. (2011). “Eukaryotic richness in the abyss: insights from pyrotag sequencing.PLoS One, 6(4), e18169.

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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.Appl Environ Microbiol, 77(9), 2992-3001.

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.

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Hasegawa, Y., Welch, J.L.M., Valm, A.M., Rieken, C., Sogin, M.L., and Borisy, G.G. (2010). “Imaging Marine Bacteria with Unique 16S rRNA V6 Sequences by Fluorescence in situ Hybridization and Spectral Analysis.Geomicrobiology Journal, 27(3), 251-260.

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McLellan, S.L., Huse, S.M., Mueller-Spitz, S.R., Andreishcheva, E.N., and Sogin, M.L. (2010). “Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent.Environ Microbiol, 12(2), 378-392.

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Smith, H.A., Mark Welch, D.B., and Snell, T.W. (2010). “Molecular evolution of the membrane associated progesterone receptor in the Brachionus plicatilis (Rotifera, Monogononta) species complex.Hydrobiologia, 662(1), 99-106.

Smith, J.L., Barrett, J.E., Tusnady, G., Rejto, L., and Cary, S.C. (2010). “Resolving environmental drivers of microbial community structure in Antarctic soils.Antarctic Science, 22(6), 673-680.

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Mahnke Braam, L.A., Goryshin, I.Y., and Reznikoff, W.S. (1999). “A mechanism for Tn5 inhibition. carboxyl-terminal dimerization.J Biol Chem, 274(1), 86-92.

Meselson, M. (1999). “The challenge of biological and chemical weapons.Bull World Health Organ, 77(2), 102-103.

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Simpson, A.G.B., and Patterson, D.J. (1999). “The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the “Excavate hypothesis”.European Journal of Protistology, 35(4), 353-370.

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