JBPC Publications: 2011 - 2020

Years

2020 (27) | 2019 (46) | 2018 (32) | 2017 (37) | 2016 (49) | 2015 (58) | 2014 (68) | 2013 (42) | 2012 (47) | 2011 (42) | 2000-2010 | 1996-1999

2020

Utter DR, Borisy GG, Eren AM, Cavanaugh CM, Mark Welch JL. Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity. Genome Biol. 2020 Dec 16;21(1):293. doi: 10.1186/s13059-020-02200-2. PMID: 33323129; PMCID: PMC7739467.

Shaiber A, Willis AD, Delmont TO, Roux S, Chen LX, Schmid AC, Yousef M, Watson AR, Lolans K, Esen ÖC, Lee STM, Downey N, Morrison HG, Dewhirst FE, Mark Welch JL, Eren AM. Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. Genome Biol. 2020 Dec 16;21(1):292. doi: 10.1186/s13059-020-02195-w. PMID: 33323122; PMCID: PMC7739484.

Vakhrusheva OA, Mnatsakanova EA, Galimov YR, Neretina TV, Gerasimov ES, Naumenko SA, Ozerova SG, Zalevsky AO, Yushenova IA, Rodriguez F, Arkhipova IR, Penin AA, Logacheva MD, Bazykin GA, Kondrashov AS. Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga. Nat Commun. 2020 Dec 18;11(1):6421. doi: 10.1038/s41467-020-19614-y. PMID: 33339818; PMCID: PMC7749112.

Arkhipova IR. Metagenome Proteins and Database Contamination. mSphere. 2020 Nov 4;5(6):e00854-20. doi: 10.1128/mSphere.00854-20. PMID: 33148820; PMCID: PMC7643828.

Sieber CMK, Paul BG, Castelle CJ, Hu P, Tringe SG, Valentine DL, Andersen GL, Banfield JF. Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community. mBio. 2019 Nov 12;10(6):e02128-19. doi: 10.1128/mBio.02128-19. PMID: 31719174; PMCID: PMC6851277.

Vallota-Eastman A, Arrington EC, Meeken S, Roux S, Dasari K, Rosen S, Miller JF, Valentine DL, Paul BG. Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria. BMC Genomics. 2020 Sep 25;21(1):664. doi: 10.1186/s12864-020-07052-5. PMID: 32977771; PMCID: PMC7517822.

Mark Welch JL, Ramírez-Puebla ST, Borisy GG. Oral Microbiome Geography: Micron-Scale Habitat and Niche. Cell Host Microbe. 2020 Aug 12;28(2):160-168. doi: 10.1016/j.chom.2020.07.009. PMID: 32791109; PMCID: PMC7604680.

Quigley CTC, Capistrant-Fossa KA, Morrison HG, Johnson LE, Morozov A, Hertzberg VS, Brawley SH. Bacterial Communities Show Algal Host (Fucus spp.)/Zone Differentiation Across the Stress Gradient of the Intertidal Zone. Front Microbiol. 2020 Sep 24;11:563118. doi: 10.3389/fmicb.2020.563118. PMID: 33072025; PMCID: PMC7541829.

Funikov SY, Rezvykh AP, Kulikova DA, Zelentsova ES, Protsenko LA, Chuvakova LN, Tyukmaeva VI, Arkhipova IR, Evgen’ev MB. Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins. Sci Rep. 2020 Jul 17;10(1):11893. doi: 10.1038/s41598-020-68879-2. PMID: 32681087; PMCID: PMC7368049.

Fowler BL, Neubert MG, Hunter-Cevera KR, Olson RJ, Shalapyonok A, Solow AR, Sosik HM. Dynamics and functional diversity of the smallest phytoplankton on the Northeast US Shelf. Proc Natl Acad Sci U S A. 2020 Jun 2;117(22):12215-12221. doi: 10.1073/pnas.1918439117. Epub 2020 May 15. PMID: 32414929; PMCID: PMC7275697.

Hernández CM, van Daalen SF, Caswell H, Neubert MG, Gribble KE. A demographic and evolutionary analysis of maternal effect senescence. Proc Natl Acad Sci U S A. 2020 Jul 14;117(28):16431-16437. doi: 10.1073/pnas.1919988117. PMID: 32601237; PMCID: PMC7368264.

Lemonnier, C., Perennou, M., Eveillard, D., Fernandez-Guerra, A., Leynaert, A., Marie, L., Morrison H. G., Memery L., Paillard C.,  Maignien, L. Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area. FRONTIERS IN MARINE SCIENCE. 2020 Jun 09; 7, 13 pages. doi:10.3389/fmars.2020.00376

Schlundt C, Mark Welch JL, Knochel AM, Zettler ER, Amaral-Zettler LA. Spatial structure in the “Plastisphere”: Molecular resources for imaging microscopic communities on plastic marine debris. Mol Ecol Resour. 2020 May;20(3):620-634. doi: 10.1111/1755-0998.13119. PMID: 31782619; PMCID: PMC7318237.

Hunter-Cevera KR, Neubert MG, Olson RJ, Shalapyonok A, Solow AR, Sosik HM. Seasons of Syn. Limnol Oceanogr. 2020 May;65(5):1085-1102. doi: 10.1002/lno.11374. Epub 2019 Nov 19. PMID: 32612307; PMCID: PMC7319482.

Antosca K, Hoen AG, Palys T, Hilliard M, Morrison HG, Coker M, Madan J, Karagas MR. Reliability of stool microbiome methods for DNA yields and sequencing among infants and young children. Microbiologyopen. 2020 May;9(5):e1018. doi: 10.1002/mbo3.1018. Epub 2020 Mar 12. PMID: 32166902; PMCID: PMC7221451.

Chakraborty, A, Ruff, SE, Dong, X, Ellefson, ED, Li, C, Brooks, JM, McBee, J, Bernard, BB, & Hubert, CRJ. Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres. Proc Natl Acad Sci U S A.  2020 May; 117(20), 11029-11037. doi: 10.1073/pnas.2002289117 PMID: 32354993; PMCID: PMC7245137

Grettenberger, CL, McCauley Rench, RL, Gruen, DS, Mills, DB, Carney, C, Brainard, J, Hamasaki, H, Ramirez, R, Watanabe, Y, Amaral-Zettler, LA, Ohmoto, H, & Macalady, JL. Microbial population structure in a stratified, acidic pit lake in the Iberian Pyrite Belt. GEOMICROBIOLOGY JOURNAL. 2020 Apr11; 37(7), 623-634. doi: 10.1080/01490451.2020.1751748.

Chen, LX, Anantharaman, K, Shaiber, A, Eren, AM, & Banfield, JF. Accurate and complete genomes from metagenomes. Genome Research. 2020 March 30(3), 315-333. doi: 10.1101/gr.258640.119  PMID: 32188701; PMCID: PMC7111523

Dai, Z, Sevillano-Rivera, MC, Calus, ST, Bautista-de Los Santos, QM, Eren, AM, van der Wielen, P, Ijaz, UZ, & Pinto, AJ. Disinfection exhibits systematic impacts on the drinking water microbiome. Microbiome. 2020 March20; 8(1), 42. doi: 10.1186/s40168-020-00813-0. PMID: 32197656; PMCID: PMC7085177

Wilbert SA, Mark Welch JL, Borisy GG. Spatial Ecology of the Human Tongue Dorsum Microbiome. Cell Rep. 2020 Mar 24;30(12):4003-4015.e3. doi: 10.1016/j.celrep.2020.02.097. PMID: 32209464; PMCID: PMC7179516.

Amaral-Zettler LA, Zettler ER, Mincer TJ. Ecology of the plastisphere. Nat Rev Microbiol. 2020 Mar;18(3):139-151. doi: 10.1038/s41579-019-0308-0. PMID: 31937947.

Rossetti BJ, Wilbert SA, Mark Welch JL, Borisy GG, Nagy JG. Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs. Bioinformatics. 2020 Feb 1;36(3):910-917. doi: 10.1093/bioinformatics/btz674. PMID: 31504202; PMCID: PMC7523684.

Kuloyo, O, Ruff, SE, Cahill, A, Connors, L, Zorz, JK, Hrabe de Angelis, I, Nightingale, M, Mayer, B, & Strous, M. Methane oxidation and methylotroph population dynamics in groundwater mesocosms. Environ Microbiology. 2020 Feb03; 22(4), 1222-1237. doi: 10.1111/1462-2920.14929 PMID: 32017377; PMCID: PMC7187433

Bhatnagar, S, Cowley, ES, Kopf, SH, Castro, SP, Kearney, S, Dawson, SC, Hanselmann, K, & Ruff, SE. Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom. Environmental Microbiome. 2020 Jan; 15(1). doi: 10.1186/s40793-019-0348-0 

Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR, Madan JC. Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study. BJOG. 2020 Jan;127(2):217-227. doi: 10.1111/1471-0528.15799. PMID: 31006170; PMCID: PMC6803026.

Gurdebeke PR,  Mertens KN, Pospelova V, Matsuoka K, Li Z, Gribble KE, Gu H, Bogus K, Vrielinck H & Louwye S. Taxonomic revision, phylogeny, and cyst wall composition of the dinoflagellate cyst genus Votadinium Reid (Dinophyceae, Peridiniales, Protoperidiniaceae), Palynology. 2020; 44:2,310-335, doi: 10.1080/01916122.2019.1580627

Martiny JBH, Whiteson KL, Bohannan BJM, David LA, Hynson NA, McFall-Ngai M, Rawls JF, Schmidt TM, Abdo Z, Blaser MJ, Bordenstein S, Bréchot C, Bull CT, Dorrestein P, Eisen JA, Garcia-Pichel F, Gilbert J, Hofmockel KS, Holtz ML, Knight R, Mark Welch DB, McDonald D, Methé B, Mouncey NJ, Mueller NT, Pfister CA, Proctor L, Sachs JL. The emergence of microbiome centres. Nat Microbiol. 2020 Jan;5(1):2-3. doi: 10.1038/s41564-019-0644-x. PMID: 31857734.

2019

Lundgren SN, Madan JC, Karagas MR, Morrison HG, Hoen AG, Christensen BC. Microbial Communities in Human Milk Relate to Measures of Maternal Weight. Front Microbiol. 2019 Dec 20;10:2886. doi: 10.3389/fmicb.2019.02886. PMID: 31921063; PMCID: PMC6933483.

Sharko FS, Nedoluzhko AV, Lê BM, Tsygankova SV, Boulygina ES, Rastorguev SM, Sokolov AS, Rodriguez F, Mazur AM, Polilov AA, Benton R, Evgen’ev MB, Arkhipova IR, Prokhortchouk EB, Skryabin KG. A partial genome assembly of the miniature parasitoid wasp, Megaphragma amalphitanum. PLoS One. 2019 Dec 23;14(12):e0226485. doi: 10.1371/journal.pone.0226485. PMID: 31869362; PMCID: PMC6927652.

Antosca KM, Chernikova DA, Price CE, Ruoff KL, Li K, Guill MF, Sontag NR, Morrison HG, Hao S, Drumm ML, MacKenzie TA, Dorman DB, Feenan LM, Williams MA, Dessaint J, Yuan IH, Aldrich BJ, Moulton LA, Ting L, Martinez-Del Campo A, Stewart EJ, Karagas MR, O’Toole GA, Madan JC. Altered Stool Microbiota of Infants with Cystic Fibrosis Shows a Reduction in Genera Associated with Immune Programming from Birth. J Bacteriol. 2019 Jul 24;201(16):e00274-19. doi: 10.1128/JB.00274-19. PMID: 31209076; PMCID: PMC6657602.

Ivashkin E, Melnikova V, Kurtova A, Brun NR, Obukhova A, Khabarova MY, Yakusheff A, Adameyko I, Gribble KE, Voronezhskaya EE. Transglutaminase Activity Determines Nuclear Localization of Serotonin Immunoreactivity in the Early Embryos of Invertebrates and Vertebrates. ACS Chem Neurosci. 2019 Aug 21;10(8):3888-3899. doi: 10.1021/acschemneuro.9b00346. Epub 2019 Jul 23. PMID: 31291540.

Mark Welch JL, Dewhirst FE, Borisy GG. Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis. Annu Rev Microbiol. 2019 Sep 8;73:335-358. doi: 10.1146/annurev-micro-090817-062503. Epub 2019 Jun 10. PMID: 31180804; PMCID: PMC7153577.

Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ, Boetius A, Boyd PW, Classen AT, Crowther TW, Danovaro R, Foreman CM, Huisman J, Hutchins DA, Jansson JK, Karl DM, Koskella B, Mark Welch DB, Martiny JBH, Moran MA, Orphan VJ, Reay DS, Remais JV, Rich VI, Singh BK, Stein LY, Stewart FJ, Sullivan MB, van Oppen MJH, Weaver SC, Webb EA, Webster NS. Scientists’ warning to humanity: microorganisms and climate change. Nat Rev Microbiol. 2019 Sep;17(9):569-586. doi: 10.1038/s41579-019-0222-5. Epub 2019 Jun 18. PMID: 31213707; PMCID: PMC7136171.

Blommaert J, Riss S, Hecox-Lea B, Mark Welch DB, Stelzer CP. Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex. BMC Genomics. 2019 Jun 7;20(1):466. doi: 10.1186/s12864-019-5859-y. PMID: 31174483; PMCID: PMC6555955.

Gurdebeke, P. R., Mertens, K. N., Pospelova, V., Matsuoka, K., Li, Z., Gribble, K. E., Gu, H., Bogus, K., Vrielinck, H., & Louwye, S. (2019). “Taxonomic revision, phylogeny, and cyst wall composition of the dinoflagellate cyst genus Votadinium Reid (Dinophyceae, Peridiniales, Protoperidiniaceae).” Palynology, 1-26. doi:10.1080/01916122.2019.158062.

Kivenson V, Lemkau KL, Pizarro O, Yoerger DR, Kaiser C, Nelson RK, Carmichael C, Paul BG, Reddy CM, Valentine DL. Ocean Dumping of Containerized DDT Waste Was a Sloppy Process. Environ Sci Technol. 2019 Mar 19;53(6):2971-2980. doi: 10.1021/acs.est.8b05859. Epub 2019 Mar 4. PMID: 30829032.

Dobay A, Haas C, Fucile G, Downey N, Morrison HG, Kratzer A, Arora N. Microbiome-based body fluid identification of samples exposed to indoor conditions. Forensic Sci Int Genet. 2019 May;40:105-113. doi: 10.1016/j.fsigen.2019.02.010. Epub 2019 Feb 11. PMID: 30785061.

Lutz HL, Ramírez-Puebla ST, Abbo L, Durand A, Schlundt C, Gottel NR, Sjaarda AK, Hanlon RT, Gilbert JA, Mark Welch JL. A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis. mSystems. 2019 May 14;4(4):e00177-19. doi: 10.1128/mSystems.00177-19. PMID: 31098396; PMCID:
PMC6517690.

Arkhipova IR, Yushenova IA. Giant Transposons in Eukaryotes: Is Bigger Better? Genome Biol Evol. 2019 Mar 1;11(3):906-918. doi: 10.1093/gbe/evz041. PMID: 30796812; PMCID: PMC6431247.

Hubbard CJ, Li B, McMinn R, Brock MT, Maignien L, Ewers BE, Kliebenstein D, Weinig C. The effect of rhizosphere microbes outweighs host plant genetics in reducing insect herbivory. Mol Ecol. 2019 Apr;28(7):1801-1811. doi: 10.1111/mec.14989. Epub 2019 Feb 6. PMID: 30582660.

Bock MJ, Jarvis GC, Corey EL, Stone EE, Gribble KE. Maternal age alters offspring lifespan, fitness, and lifespan extension under caloric restriction. Sci Rep. 2019 Feb 28;9(1):3138. doi: 10.1038/s41598-019-40011-z. PMID: 30816287; PMCID: PMC6395700.

Trigodet F, Larché N, Morrison HG, Jebbar M, Thierry D, Maignien L. Electroactive Bacteria Associated With Stainless Steel Ennoblement in Seawater. Front Microbiol. 2019 Feb 7;10:170. doi: 10.3389/fmicb.2019.00170. PMID: 30792705; PMCID: PMC6374330.

Ecklu-Mensah, G., Sackey, S. T., Morrison, H. G., Sogin, M. L., Murphy, L. G., & Reznikoff, W. S. (2019). Assessment of bacterial diversity in western Accra, Ghana, drinking water samples. JOURNAL OF WATER SANITATION AND HYGIENE FOR DEVELOPMENT, 9(4), 644-661. doi:10.2166/washdev.2019.123

Bhatnagar, S., Cowley, E. S., Kopf, S. H., Castro, S. P., Kearney, S., Dawson, S. C., Hanselmann, K., & Ruff, S. E. (2019). “Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom.” bioRxiv, 604504. doi:10.1101/60450.

Bono, L. M., Orton, R. J., Peredo, E. L., Morrison, H. G., Sistrom, M., Simmons, S., & Turner, P. E. (2019). “Spatiotemporal dynamics of RNA virus diversity in a phyllosphere microbial community.” bioRxiv, 772475. doi:10.1101/77247.

Coker, M. O., Hoen, A. G., Dade, E., Lundgren, S., Li, Z., Wong, A. D., Zens, M. S., Palys, T. J., Morrison, H. G., Sogin, M. L., Baker, E. R., Karagas, M. R., & Madan, J. C. (2019). “Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study.” BJOG, 0(0), 0. doi:10.1111/1471-0528.1579.

Cramm, M. A., Chakraborty, A., Li, C., Ruff, S. E., Jorgensen, B. B., & Hubert, C. R. J. (2019). “Freezing Tolerance of Thermophilic Bacterial Endospores in Marine Sediments.” Front Microbiol, 10, 945. doi:10.3389/fmicb.2019.0094.

Delmont, T. O., Kiefl, E., Kilinc, O., Esen, O. C., Uysal, I., Rappe, M. S., Giovannoni, S., & Eren, A. M. (2019). “Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade.” Elife, 8(ARTN e46497). doi:10.7554/eLife.4649.

Edsinger, E., Pnini, R., Ono, N., Yanagisawa, R., Dever, K., & Miller, J. (2019). “Social tolerance in Octopus laqueus – a maximal entropy model.” bioRxiv, 526905. doi:10.1101/52690.

Fiore-Donno, A. M., Richter-Heitmann, T., Degrune, F., Dumack, K., Regan, K., Mahran, S., Boeddinghaus, R., Rillig, M., Friedrich, M. W., Kandeler, E., & Bonkowski, M. (2019). “Environmental selection and spatiotemporal structure of a major group of soil protists (Rhizaria: Cercozoa) in a temperate grassland.” bioRxiv, 531970. doi:10.1101/53197.

Funikov, S. Y., Rezvykh, A. P., Kulikova, D. A., Zelentsova, E. S., Chuvakova, L. N., Tyukmaeva, V. I., Arkhipova, I. R., & Evgen’ev, M. B. (2019). “Insulator proteins contribute to expression of gene loci repositioned into heterochromatin in the course of Drosophila evolution.” bioRxiv, 802371. doi:10.1101/80237.

Goldmann, K., Boeddinghaus, R. S., Klemmer, S., Regan, K. M., Heintz-Buschart, A., Fischer, M., Prati, D., Piepho, H. P., Berner, D., Marhan, S., Kandeler, E., Buscot, F., & Wubet, T. (2019). “Unraveling spatiotemporal variability of arbuscular mycorrhizal fungi in a temperate grassland plot.” Environ Microbiol, 0(0). doi:10.1111/1462-2920.1465.

Han, M., Dsouza, M., Zhou, C., Li, H., Zhang, J., Chen, C., Yao, Q., Zhong, C., Zhou, H., Gilbert, J. A., Wang, Z., & Ning, K. (2019). “Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake.” Genomics Proteomics Bioinformatics, 17(1), 76-90. doi:10.1016/j.gpb.2018.04.00.

McKay, L. J., Dlakic, M., Fields, M. W., Delmont, T. O., Eren, A. M., Jay, Z. J., Klingelsmith, K. B., Rusch, D. B., & Inskeep, W. P. (2019). “Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota.” Nat Microbiol, 4(4), 614-622. doi:10.1038/s41564-019-0362-.

Mincer, T. J., Zettler, E. R., & Amaral-Zettler, L. A. (2019). “Biofilms on Plastic Debris and Their Influence on Marine Nutrient Cycling, Productivity, and Hazardous Chemical Mobility.” In H. Takada & H. K. Karapanagioti (Ed.), Hazardous Chemicals Associated with Plastics in the Marine Environment (pp. 221-233): Cham: Springer International Publishing.

Nedoluzhko, A. V., Sharko, F. S., Lê, B. M., Tsygankova, S. V., Boulygina, E. S., Rastorguev, S. M., Sokolov, A. S., Rodriguez, F., Mazur, A. M., Polilov, A. A., Benton, R., Evgen’ev, M. B., Arkhipova, I. R., Prokhortchouk, E. B., & Skryabin, K. G. (2019). “A draft genome sequence of the miniature parasitoid wasp, Megaphragma amalphitanum.” bioRxiv, 579052. doi:10.1101/57905.

Nissimov, J. I., Talmy, D., Haramaty, L., Fredricks, H. F., Zelzion, E., Knowles, B., Eren, A. M., Vandzura, R., Laber, C. P., Schieler, B. M., Johns, C. T., More, K. D., Coolen, M. J. L., Follows, M. J., Bhattacharya, D., Van Mooy, B. A. S., & Bidle, K. D. (2019). “Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology.” Environ Microbiol, 21(6), 2182-2197. doi:10.1111/1462-2920.1463.

Peramba, K. B., & Edsinger, E. (2019). “Imaging the neuromuscular systems of cephalopod arms and suckers.” Paper presented at the Annual Meeting of the Society for Integrative and Comparative Biology, Tampa, FL.

Peramba, K. B., Nash, C., Walters, D., Hackworth, L., Schumm, M., Pineda, O., & Edsinger, E. (2019). “Squid Monday: Characterizing population structure in Doryteuthis pealeii.” Paper presented at the Annual Meeting of the Society for Integrative and Comparative Biology, Tampa, FL.

Perez Castro, S., Cleland, E. E., Wagner, R., Sawad, R. A., & Lipson, D. A. (2019). “Soil microbial responses to drought and exotic plants shift carbon metabolism.” ISME J, 13(7), 1776-1787. doi:10.1038/s41396-019-0389-.

Puritty, C. E., Esch, E. H., Castro, S. P., Ryan, E. M., Lipson, D. A., & Cleland, E. E. (2019). “Drought in Southern California coastal sage scrub reduces herbaceous biomass of exotic species more than native species, but exotic growth recovers quickly when drought ends.” Plant Ecology, 220(2), 151-169. doi:10.1007/s11258-019-00912-.

Reveillaud, J., Bordenstein, S. R., Cruaud, C., Shaiber, A., Esen, O. C., Weill, M., Makoundou, P., Lolans, K., Watson, A. R., Rakotoarivony, I., Bordenstein, S. R., & Eren, A. M. (2019). “The Wolbachia mobilome in Culex pipiens includes a putative plasmid.” Nat Commun, 10(1), 1051. doi:10.1038/s41467-019-08973-.

Richter, N., Longo, W. M., George, S., Shipunova, A., Huang, Y., & Amaral-Zettler, L. (2019). “Phylogenetic diversity in freshwater-dwelling Isochrysidales haptophytes with implications for alkenone production.” Geobiology, 17(3), 272-280. doi:10.1111/gbi.1233.

Rossetti, B. J., Wilbert, S. A., Mark Welch, J. L., Borisy, G. G., & Nagy, J. G. (2019). “Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs.” bioRxiv, 674. doi:10.1093/bioinformatics/btz67.

Ruff, S. E. (2019). “Microbial communities and metabolisms at hydrocarbon seeps.” In A. Teske & V. Carvalho (Ed.), Marine Hydrocarbon Seeps – Microbiology and Biogeochemistry of a Global Marine Habitat (pp. 280): Springer.

Ruff, S. E., Felden, J., Gruber-Vodicka, H. R., Marcon, Y., Knittel, K., Ramette, A., & Boetius, A. (2019). “In situ development of a methanotrophic microbiome in deep-sea sediments.” ISME J, 13(1), 197-213. doi:10.1038/s41396-018-0263-.

Sevillano, M., Dai, Z., Calus, S., Bautista-de los Santos, Q. M., Eren, A. M., van der Wielen, P. W. J. J., Ijaz, U. Z., & Pinto, A. J. (2019). “Disinfectant residuals in drinking water systems select for mycobacterial populations with intrinsic antimicrobial resistance.” bioRxiv, 675561. doi:10.1101/67556.

Shaiber, A., & Eren, A. M. (2019). “Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories.” MBio, 10(3), e00725-00719. doi:10.1128/mBio.00725-1.

Theroux, S., Huang, Y. S., Toney, J. L., Andersen, R., Nyren, P., Bohn, R., Salacup, J., Murphy, L., & Amaral-Zettler, L. (2019). “Successional blooms of alkenone-producing haptophytes in Lake George, North Dakota: Implications for continental paleoclimate reconstructions.” Limnology and Oceanography, 0(0), 11311. doi:10.1002/lno.1131.

Trigodet, F., Larché, N., Morrison, H. G., Maignien, L., & Thierry, D. (2019). “Influence of dissolved oxygen content on the bacteria‐induced ennoblement of stainless steels in seawater and its consequence on the localized corrosion risk.” Materials and Corrosion, 0(0). doi:10.1002/maco.20191122.

Watterson, W. J., Tanyeri, M., Watson, A. R., Cham, C. M., Shan, Y., Chang, E. B., Eren, A. M., & Tay, S. (2019). “High-throughput isolation and sorting of gut microbes reduce biases of traditional cultivation strategies.” bioRxiv, 759969. doi:10.1101/75996.

Yeoman, C. J., Brutscher, L. M., Esen, O. C., Ibaoglu, F., Fowler, C., Eren, A. M., Wanner, K., & Weaver, D. K. (2019). “Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus).” PeerJ, 7, e7548. doi:10.7717/peerj.754.

2018

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.

2017

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/j.tips.2016.10.00.

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.

2016

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.

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., & 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. doi:10.3109/14767058.2014.98774.

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., & Consortium, I. (2016). “Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium.” Gigascience, 5(1), 14. doi:10.1186/s13742-016-0118-.

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.

Dugas, L. R., Fuller, M., Gilbert, J., & Layden, B. T. (2016). “The obese gut microbiome across the epidemiologic transition.” Emerg Themes Epidemiol, 13, 2. doi:10.1186/s12982-015-0044-.

Eren, A. M., Sogin, M. L., & Maignien, L. (2016). “Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation.” Frontiers in Microbiology, 7, 1318. doi:ARTN 131810.3389/fmicb.2016.0131.

Fernandez-Gonzalez, N., Huber, J. A., & Vallino, J. J. (2016). “Microbial Communities Are Well Adapted to Disturbances in Energy Input.” mSystems, 1(5). doi:10.1128/mSystems.00117-1.

Fortunato, C. S., & 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. doi:10.1038/ismej.2015.25.

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.

Gilbert, J. A. (2016). “mSystems: Learning To Love Systems.” mSystems, 1(1). doi:10.1128/mSystems.00015-1.

Gilbert, J. A., & Alverdy, J. (2016). “Stool consistency as a major confounding factor affecting microbiota composition: an ignored variable?” Gut, 65(1), 1-2. doi:10.1136/gutjnl-2015-31004.

Gilbert, J. A., Klyczek, K. K., & Elliott, S. L. (2016). “Introducing the JMBE Themed Issue on Scientific Citizenship.” J Microbiol Biol Educ, 17(1), 1-2. doi:10.1128/jmbe.v17i1.111.

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.

Kaneko, G., Yoshinaga, T., Gribble, K. E., Mark Welch, D. B., & Ushio, H. (2016). “Measurement of Survival Time in Brachionus Rotifers: Synchronization of Maternal Conditions.” J Vis Exp(113), e54126. doi:10.3791/5412.

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.

Liebeskind, B. J., Hillis, D. M., Zakon, H. H., & Hofmann, H. A. (2016). “Complex Homology and the Evolution of Nervous Systems.” Trends Ecol Evol, 31(2), 127-135. doi:10.1016/j.tree.2015.12.00.

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.

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., & Knight, R. (2016). “Microbial community assembly and metabolic function during mammalian corpse decomposition.” Science, 351(6269), 158-162. doi:10.1126/science.aad264.

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-.

2015

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-.

Green, H. C., Fisher, J. C., McLellan, S. L., Sogin, M. L., & 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. doi:10.1128/AEM.02456-1.

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., & 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. doi:10.1016/j.jpeds.2015.02.04.

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., & Chang, E. B. (2015). “Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases.” Inflamm Bowel Dis, 21(5), 963-972. doi:10.1097/MIB.000000000000033.

Huber, J. A. (2015). “MICROBIAL ECOLOGY.” Making methane down deep. Science, 349(6246), 376-377. doi:10.1126/science.aac667.

Hunter-Cevera, K. R., Post, A. F., Peacock, E. E., & 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. doi:10.1007/s00248-015-0644-.

Huo, Y. Y., Cheng, H., Post, A. F., Wang, C. S., Jiang, X. W., Pan, J., Wu, M., & 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. doi:10.1007/s13131-015-0650-.

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., & 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. doi:10.1073/pnas.150738011.

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., & Glockner, F. O. (2015). “The ocean sampling day consortium.” Gigascience, 4, 27. doi:10.1186/s13742-015-0066-.

Larsen, P. E., Scott, N., Post, A. F., Field, D., Knight, R., Hamada, Y., & Gilbert, J. A. (2015). “Satellite remote sensing data can be used to model marine microbial metabolite turnover.” ISME J, 9(1), 166-179. doi:10.1038/ismej.2014.10.

Lax, S., & Gilbert, J. A. (2015). “Hospital-associated microbiota and implications for nosocomial infections.” Trends Mol Med, 21(7), 427-432. doi:10.1016/j.molmed.2015.03.00.

Lax, S., Hampton-Marcell, J. T., Gibbons, S. M., Colares, G. B., Smith, D., Eisen, J. A., & Gilbert, J. A. (2015). “Forensic analysis of the microbiome of phones and shoes.” Microbiome, 3, 21. doi:10.1186/s40168-015-0082-.

Lax, S., Nagler, C. R., & Gilbert, J. A. (2015). “Our interface with the built environment: immunity and the indoor microbiota.” Trends Immunol, 36(3), 121-123. doi:10.1016/j.it.2015.01.00.

Liebeskind, B. J., Hillis, D. M., & 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. doi:10.1073/pnas.150119511.

Lin, X., Handley, K. M., Gilbert, J. A., & 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. doi:10.1038/ismej.2015.7.

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., & 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. doi:10.1016/j.aquatox.2015.06.01.

Mackey, K. R. M., Chien, C. T., Post, A. F., Saito, M. A., & Paytan, A. (2015). “Rapid and gradual modes of aerosol trace metal dissolution in seawater.” Front Microbiol, 5, 794. doi:10.3389/fmicb.2014.0079.

Mackey, K. R. M., Post, A. F., McIlvin, M. R., Cutter, G. A., John, S. G., & 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. doi:10.1073/pnas.150944811.

Moran, Y., Barzilai, M. G., Liebeskind, B. J., & Zakon, H. H. (2015). “Evolution of voltage-gated ion channels at the emergence of Metazoa.” J Exp Biol, 218(Pt 4), 515-525. doi:10.1242/jeb.11027.

Newton, R. J., McLellan, S. L., Dila, D. K., Vineis, J. H., Morrison, H. G., Eren, A. M., & Sogin, M. L. (2015). “Sewage reflects the microbiomes of human populations.” MBio, 6(2), e02574. doi:10.1128/mBio.02574-1.

Ochiana, S. O., Bland, N. D., Settimo, L., Campbell, R. K., & 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. doi:10.1111/cbdd.1244.

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., & 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. doi:10.1038/ajg.2015.35.

Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M. R., Rappe, M. S., DiTullio, G. R., & 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. doi:10.1002/pmic.20140063.

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., & Crump, B. C. (2015). “Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011.” Microbiome, 3(1), 39. doi:10.1186/s40168-015-0099-.

Schmidt, V. T., Smith, K. F., Melvin, D. W., & Amaral-Zettler, L. A. (2015). “Community assembly of a euryhaline fish microbiome during salinity acclimation.” Mol Ecol, 24(10), 2537-2550. doi:10.1111/mec.1317.

Shade, A., & Gilbert, J. A. (2015). “Temporal patterns of rarity provide a more complete view of microbial diversity.” Trends Microbiol, 23(6), 335-340. doi:10.1016/j.tim.2015.01.00.

Sielaff, M., Schmidt, H., Struck, T. H., Rosenkranz, D., Mark Welch, D. B., Hankeln, T., & 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. doi:10.1016/j.ympev.2015.11.01.

Signorovitch, A., Hur, J., Gladyshev, E., & Meselson, M. (2015). “Allele Sharing and Evidence for Sexuality in a Mitochondrial Clade of Bdelloid Rotifers.” Genetics, 200(2), 581-590. doi:10.1534/genetics.115.17671.

Snell, T. W., Johnston, R. K., Gribble, K. E., & Mark Welch, D. B. (2015). “Rotifers as experimental tools for investigating aging.” Invertebr Reprod Dev, 59(1), 5-10. doi:10.1080/07924259.2014.92551.

Traeger, L. L., Volkening, J. D., Moffett, H., Gallant, J. R., Chen, P. H., Novina, C. D., Phillips, G. N. Jr., Anand, R., Wells, G. B., Pinch, M., Guth, R., Unguez, G. A., Albert, J. S., Zakon, H., Sussman, M. R., & Samanta, M. P. (2015). “Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus).” BMC Genomics, 16, 243. doi:10.1186/s12864-015-1288-.

Van Bonn, W., LaPointe, A., Gibbons, S. M., Frazier, A., Hampton-Marcell, J., & Gilbert, J. A. (2015). “Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management.” Zoo Biol, 34(4), 360-367. doi:10.1002/zoo.2122.

Walsh, E. A., Smith, D. C., Sogin, M. L., & D’Hondt, S. (2015). “Bacterial and archaeal biogeography of the deep chlorophyll maximum in the South Pacific Gyre.” Aquatic Microbial Ecology, 75(1), 1-13. doi:10.3354/ame0174.

Wood, M., Gibbons, S. M., Lax, S., Eshoo-Anton, T. W., Owens, S. M., Kennedy, S., Gilbert, J. A., & Hampton-Marcell, J. T. (2015). “Athletic equipment microbiota are shaped by interactions with human skin.” Microbiome, 3, 25. doi:10.1186/s40168-015-0088-.

Ying, S., Zeng, D. N., Chi, L., Tan, Y., Galzote, C., Cardona, C., Lax, S., Gilbert, J., & Quan, Z. X. (2015). “The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations.” PLoS One, 10(10), e0141842. doi:10.1371/journal.pone.014184.

Zarraonaindia, I., Owens, S. M., Weisenhorn, P., West, K., Hampton-Marcell, J., Lax, S., Bokulich, N. A., Mills, D. A., Martin, G., Taghavi, S., van der Lelie, D., & Gilbert, J. A. (2015). “The soil microbiome influences grapevine-associated microbiota.” MBio, 6(2). doi:10.1128/mBio.02527-1.

2014

Amata, E., Bland, N. D., Hoyt, C. T., Settimo, L., Campbell, R. K., & Pollastri, M. P. (2014). “Repurposing human PDE4 inhibitors for neglected tropical diseases: design, synthesis and evaluation of cilomilast analogues as Trypanosoma brucei PDEB1 inhibitors.” Bioorg Med Chem Lett, 24(17), 4084-4089. doi:10.1016/j.bmcl.2014.07.06.

Anderson, R. E., Sogin, M. L., & Baross, J. A. (2014). “Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics.” PLoS One, 9(10), e109696. doi:10.1371/journal.pone.010969.

Apprill, A., Robbins, J., Eren, A. M., Pack, A. A., Reveillaud, J., Mattila, D., Moore, M., Niemeyer, M., Moore, K. M., & Mincer, T. J. (2014). “Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?” PLoS One, 9(3), e90785. doi:10.1371/journal.pone.009078.

Beliaev, A. S., Romine, M. F., Serres, M. H., Bernstein, H. C., Linggi, B. E., Markillie, L. M., Isern, N. G., Chrisler, W. B., Kucek, L. A., Hill, E. A., Pinchuk, G. E., Bryant, D. A., Wiley, H. S., Fredrickson, J. K., & Konopka, A. (2014). “Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing.” ISME J, 8(11), 2243-2255. doi:10.1038/ismej.2014.6.

Bullerjahn, G. S., & Post, A. F. (2014). “Physiology and molecular biology of aquatic cyanobacteria.” Front Microbiol, 5, 359. doi:10.3389/fmicb.2014.0035.

Celaj, S., Gleeson, M. W., Deng, J., O’Toole, G. A., Hampton, T. H., Toft, M. F., Morrison, H. G., Sogin, M. L., Putra, J., Suriawinata, A. A., & Gorham, J. D. (2014). “The microbiota regulates susceptibility to Fas-mediated acute hepatic injury.” Lab Invest, 94(9), 938-949. doi:10.1038/labinvest.2014.9.

Cusack, D. F., Axsen, J., Shwom, R., Hartzell-Nichols, L., White, S., & Mackey, K. R. M. (2014). “An interdisciplinary assessment of climate engineering strategies.” Frontiers in Ecology and the Environment, 12(5), 280-287. doi:10.1890/13003.

Davies, N., Field, D., Amaral-Zettler, L. A., Bicak, M., Bourlat, S., Coddington, J., Deck, J., Drummond, A., Gilbert, J. A., Glöckner, F. O., Kottmann, R., Meyer, C., Morrison, N., Obst, M., Robbins, R., Schriml, L., Sterk, P., & Stones-Havas, S. (2014). “Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012.” Standards in Genomic Sciences; Vol 9, No 3 (2014): Standards in Genomic Sciences.

Davies, N., Field, D., Amaral-Zettler, L. A., Clark, M. S., Deck, J., Drummond, A., Faith, D. P., Geller, J., Gilbert, J., Glockner, F. O., Hirsch, P. R., Leong, J. A., Meyer, C., Obst, M., Planes, S., Scholin, C., Vogler, A. P., Gates, R. D., Toonen, R., Berteaux-Lecellier, V., Barbier, M., Barker, K., Bertilsson, S., Bicak, M., Bietz, M. J., Bobe, J., Bodrossy, L., Borja, A., Coddington, J., Fuhrman, J., Gerdts, G., Gillespie, R., Goodwin, K., Hanson, P. C., Hero, J. M., Hoekman, D., Jansson, J., Jeanthon, C., Kao, R., Klindworth, A., Knight, R., Kottmann, R., Koo, M. S., Kotoulas, G., Lowe, A. J., Marteinsson, V. T., Meyer, F., Morrison, N., Myrold, D. D., Pafilis, E., Parker, S., Parnell, J. J., Polymenakou, P. N., Ratnasingham, S., Roderick, G. K., Rodriguez-Ezpeleta, N., Schonrogge, K., Simon, N., Valette-Silver, N. J., Springer, Y. P., Stone, G. N., Stones-Havas, S., Sansone, S. A., Thibault, K. M., Wecker, P., Wichels, A., Wooley, J. C., Yahara, T., Zingone, A., & COS, G. O. (2014). “The founding charter of the Genomic Observatories Network.” Gigascience, 3(1), 2. doi:10.1186/2047-217X-3-.

Dejea, C. M., Wick, E. C., Hechenbleikner, E. M., White, J. R., Mark Welch, J. L., Rossetti, B. J., Peterson, S. N., Snesrud, E. C., Borisy, G. G., Lazarev, M., Stein, E., Vadivelu, J., Roslani, A. C., Malik, A. A., Wanyiri, J. W., Goh, K. L., Thevambiga, I., Fu, K., Wan, F., Llosa, N., Housseau, F., Romans, K., Wu, X., McAllister, F. M., Wu, S., Vogelstein, B., Kinzler, K. W., Pardoll, D. M., & Sears, C. L. (2014). “Microbiota organization is a distinct feature of proximal colorectal cancers.” Proc Natl Acad Sci U S A, 111(51), 18321-18326. doi:10.1073/pnas.140619911.

Delmont, T. O., Francioli, D., Jacquesson, S., Laoudi, S., Mathieu, A., Nesme, J., Ceccherini, M. T., Nannipieri, P., Simonet, P., & Vogel, T. M. (2014). “Microbial community development and unseen diversity recovery in inoculated sterile soil.” Biology and Fertility of Soils, 50(7), 1069-1076. doi:10.1007/s00374-014-0925-.

Delmont, T. O., Hammar, K. M., Ducklow, H. W., Yager, P. L., & Post, A. F. (2014). “Phaeocystis antarctica blooms strongly influence bacterial community structures in the Amundsen Sea polynya.” Front Microbiol, 5, 646. doi:10.3389/fmicb.2014.0064.

Durham, B. P., Grote, J., Whittaker, K. A., Bender, S. J., Luo, H., Grim, S. L., Brown, J. M., Casey, J. R., Dron, A., Florez-Leiva, L., Krupke, A., Luria, C. M., Mine, A. H., Nigro, O. D., Pather, S., Talarmin, A., Wear, E. K., Weber, T. S., Wilson, J. M., Church, M. J., DeLong, E. F., Karl, D. M., Steward, G. F., Eppley, J. M., Kyrpides, N. C., Schuster, S., & Rappe, M. S. (2014). “Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome.” Stand Genomic Sci, 9(3), 632-645. doi:10.4056/sigs.499898.

Eren, A. M., Borisy, G. G., Huse, S. M., & Mark Welch, J. L. (2014). “Oligotyping analysis of the human oral microbiome.” Proc Natl Acad Sci U S A, 111(28), E2875-2884. doi:10.1073/pnas.140964411.

Eren, A. M., Morrison, H. G., Huse, S. M., & Sogin, M. L. (2014). “DRISEE overestimates errors in metagenomic sequencing data.” Brief Bioinform, 15(5), 783-787. doi:10.1093/bib/bbt01.

Ferreira, A. J., Siam, R., Setubal, J. C., Moustafa, A., Sayed, A., Chambergo, F. S., Dawe, A. S., Ghazy, M. A., Sharaf, H., Ouf, A., Alam, I., Abdel-Haleem, A. M., Lehvaslaiho, H., Ramadan, E., Antunes, A., Stingl, U., Archer, J. A., Jankovic, B. R., Sogin, M. L., Bajic, V. B., & El-Dorry, H. (2014). “Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.” PLoS One, 9(6), e97338. doi:10.1371/journal.pone.009733.

Field, D., Sterk, P., Kottmann, R., De Smet, J. W., Amaral-Zettler, L. A., Cochrane, G., Cole, J. R., Davies, N., Dawyndt, P., Garrity, G. M., Gilbert, J. A., Glockner, F. O., Hirschman, L., Klenk, H. P., Knight, R., Kyrpides, N., Meyer, F., Karsch-Mizrachi, I., Morrison, N., Robbins, R., San Gil, I., Sansone, S., Schriml, L., Tatusova, T., Ussery, D., Yilmaz, P., White, O., Wooley, J., & Caporaso, G. (2014). “Genomic standards consortium projects.” Stand Genomic Sci, 9(3), 599-601. doi:10.4056/sigs.555968.

Fischer, A. H., Mozzherin, D., Eren, A. M., Lans, K. D., Wilson, N., Cosentino, C., & Smith, J. (2014). “SeaBase: a multispecies transcriptomic resource and platform for gene network inference.” Integr Comp Biol, 54(2), 250-263. doi:10.1093/icb/icu06.

Gallant, J. R., Traeger, L. L., Volkening, J. D., Moffett, H., Chen, P. H., Novina, C. D., Phillips, G. N. Jr., Anand, R., Wells, G. B., Pinch, M., Guth, R., Unguez, G. A., Albert, J. S., Zakon, H. H., Samanta, M. P., & Sussman, M. R. (2014). “Nonhuman genetics.” Genomic basis for the convergent evolution of electric organs. Science, 344(6191), 1522-1525. doi:10.1126/science.125443.

Ghezzi, A., Liebeskind, B. J., Thompson, A., Atkinson, N. S., & Zakon, H. H. (2014). “Ancient association between cation leak channels and Mid1 proteins is conserved in fungi and animals.” Front Mol Neurosci, 7, 15. doi:10.3389/fnmol.2014.0001.

Gifford, A. H., Alexandru, D. M., Li, Z., Dorman, D. B., Moulton, L. A., Price, K. E., Hampton, T. H., Sogin, M. L., Zuckerman, J. B., Parker, H. W., Stanton, B. A., & O’Toole, G. A. (2014). “Iron supplementation does not worsen respiratory health or alter the sputum microbiome in cystic fibrosis.” J Cyst Fibros, 13(3), 311-318. doi:10.1016/j.jcf.2013.11.00.

Gilbert, J. A., Dick, G. J., Jenkins, B., Heidelberg, J., Allen, E., Mackey, K. R., & DeLong, E. F. (2014). “Meeting report: Ocean ‘omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013).” Stand Genomic Sci, 9(3), 1252-1258. doi:10.4056/sigs.574994.

Gilbert, J. A., Jansson, J. K., & Knight, R. (2014). “The Earth Microbiome project: successes and aspirations.” BMC Biol, 12. doi:10.1186/s12915-014-0069-.

Gilbert, J. A., & Neufeld, J. D. (2014). “Life in a World without Microbes.” PLoS Biol, 12(12), e1002020. doi:10.1371/journal.pbio.100202.

Glass, E. M., Dribinsky, Y., Yilmaz, P., Levin, H., Van Pelt, R., Wendel, D., Wilke, A., Eisen, J. A., Huse, S. M., Shipanova, A., Sogin, M. L., Stajich, J., Knight, R., Meyer, F., & Schriml, L. M. (2014). “MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.” ISME J, 8(1), 1-3. doi:10.1038/ismej.2013.17.

Gribble, K. E., Jarvis, G., Bock, M., & Mark Welch, D. B. (2014). “Maternal caloric restriction partially rescues the deleterious effects of advanced maternal age on offspring.” Aging Cell, 13(4), 623-630. doi:10.1111/acel.1221.

Gribble, K. E., Kaido, O., Jarvis, G., & Mark Welch, D. B. (2014). “Patterns of intraspecific variability in the response to caloric restriction.” Exp Gerontol, 51, 28-37. doi:10.1016/j.exger.2013.12.00.

Halliday, E., McLellan, S. L., Amaral-Zettler, L. A., Sogin, M. L., & Gast, R. J. (2014). “Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations.” PLoS One, 9(3), e90815. doi:10.1371/journal.pone.009081.

Hampton, T. H., Green, D. M., Cutting, G. R., Morrison, H. G., Sogin, M. L., Gifford, A. H., Stanton, B. A., & O’Toole, G. A. (2014). “The microbiome in pediatric cystic fibrosis patients: the role of shared environment suggests a window of intervention.” Microbiome, 2, 14. doi:10.1186/2049-2618-2-1.

Huo, Y. Y., Li, Z. Y., You, H., Wang, C. S., Post, A. F., Oren, A., & Xu, X. W. (2014). “Oceanicola antarcticus sp.” nov. and Oceanicola flagellatus sp. nov., moderately halophilic bacteria isolated from seawater. Int J Syst Evol Microbiol, 64(Pt 9), 2975-2979. doi:10.1099/ijs.0.062588-.

Huse, S. M., Mark Welch, D. B., Voorhis, A., Shipunova, A., Morrison, H. G., Eren, A. M., & Sogin, M. L. (2014). “VAMPS: a website for visualization and analysis of microbial population structures.” BMC Bioinformatics, 15(1), 41. doi:10.1186/1471-2105-15-4.

Huse, S. M., Young, V. B., Morrison, H. G., Antonopoulos, D. A., Kwon, J., Dalal, S., Arrieta, R., Hubert, N. A., Shen, L., Vineis, J. H., Koval, J. C., Sogin, M. L., Chang, E. B., & Raffals, L. E. (2014). “Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects.” Microbiome, 2(1), 5. doi:10.1186/2049-2618-2-.

Keeling, P. J., Burki, F., Wilcox, H. M., Allam, B., Allen, E. E., Amaral-Zettler, L. A., Armbrust, E. V., Archibald, J. M., Bharti, A. K., Bell, C. J., Beszteri, B., Bidle, K. D., Cameron, C. T., Campbell, L., Caron, D. A., Cattolico, R. A., Collier, J. L., Coyne, K., Davy, S. K., Deschamps, P., Dyhrman, S. T., Edvardsen, B., Gates, R. D., Gobler, C. J., Greenwood, S. J., Guida, S. M., Jacobi, J. L., Jakobsen, K. S., James, E. R., Jenkins, B., John, U., Johnson, M. D., Juhl, A. R., Kamp, A., Katz, L. A., Kiene, R., Kudryavtsev, A., Leander, B. S., Lin, S., Lovejoy, C., Lynn, D., Marchetti, A., McManus, G., Nedelcu, A. M., Menden-Deuer, S., Miceli, C., Mock, T., Montresor, M., Moran, M. A., Murray, S., Nadathur, G., Nagai, S., Ngam, P. B., Palenik, B., Pawlowski, J., Petroni, G., Piganeau, G., Posewitz, M. C., Rengefors, K., Romano, G., Rumpho, M. E., Rynearson, T., Schilling, K. B., Schroeder, D. C., Simpson, A. G., Slamovits, C. H., Smith, D. R., Smith, G. J., Smith, S. R., Sosik, H. M., Stief, P., Theriot, E., Twary, S. N., Umale, P. E., Vaulot, D., Wawrik, B., Wheeler, G. L., Wilson, W. H., Xu, Y., Zingone, A., & Worden, A. Z. (2014). “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.” PLoS Biol, 12(6), e1001889. doi:10.1371/journal.pbio.100188.

Koskey, A. M., Fisher, J. C., Eren, A. M., Ponce-Terashima, R., Reis, M. G., Blanton, R. E., & McLellan, S. L. (2014). “Blautia and Prevotella sequences distinguish human and animal fecal pollution in Brazil surface waters.” Environ Microbiol Rep, 6(6), 696-704. doi:10.1111/1758-2229.1218.

Kyrpides, N. C., Hugenholtz, P., Eisen, J. A., Woyke, T., Goker, M., Parker, C. T., Amann, R., Beck, B. J., Chain, P. S., Chun, J., Colwell, R. R., Danchin, A., Dawyndt, P., Dedeurwaerdere, T., DeLong, E. F., Detter, J. C., De Vos, P., Donohue, T. J., Dong, X. Z., Ehrlich, D. S., Fraser, C., Gibbs, R., Gilbert, J. A., Gilna, P., Glockner, F. O., Jansson, J. K., Keasling, J. D., Knight, R., Labeda, D., Lapidus, A., Lee, J. S., Li, W. J., Ma, J., Markowitz, V., Moore, E. R., Morrison, M., Meyer, F., Nelson, K. E., Ohkuma, M., Ouzounis, C. A., Pace, N., Parkhill, J., Qin, N., Rossello-Mora, R., Sikorski, J., Smith, D., Sogin, M. L., Stevens, R., Stingl, U., Suzuki, K., Taylor, D., Tiedje, J. M., Tindall, B., Wagner, M., Weinstock, G., Weissenbach, J., White, O., Wang, J., Zhang, L., Zhou, Y. G., Field, D., Whitman, W. B., Garrity, G. M., & Klenk, H. P. (2014). “Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.” PLoS Biol, 12(8), e1001920. doi:10.1371/journal.pbio.100192.

LaBelle, E. V., Marshall, C. W., Gilbert, J. A., & May, H. D. (2014). “Influence of acidic pH on hydrogen and acetate production by an electrosynthetic microbiome.” PLoS One, 9(10), e109935. doi:10.1371/journal.pone.010993.

Lau, M. C., Cameron, C., Magnabosco, C., Brown, C. T., Schilkey, F., Grim, S., Hendrickson, S., Pullin, M., Sherwood Lollar, B., van Heerden, E., Kieft, T. L., & Onstott, T. C. (2014). “Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships.” Front Microbiol, 5, 531. doi:10.3389/fmicb.2014.0053.

Lie, A. A., Liu, Z., Hu, S. K., Jones, A. C., Kim, D. Y., Countway, P. D., Amaral-Zettler, L. A., Cary, S. C., Sherr, E. B., Sherr, B. F., Gast, R. J., & Caron, D. A. (2014). “Investigating microbial eukaryotic diversity from a global census: insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes.” Appl Environ Microbiol, 80(14), 4363-4373. doi:10.1128/AEM.00057-1.

Luria, C. M., Ducklow, H. W., & Amaral-Zettler, L. A. (2014). “Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the western Antarctic Peninsula.” Aquatic Microbial Ecology, 73(2), 107-121. doi:10.3354/ame0170.

Maignien, L., DeForce, E. A., Chafee, M. E., Eren, A. M., & Simmons, S. L. (2014). “Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities.” MBio, 5(1), e00682-00613. doi:10.1128/mBio.00682-1.

Maltz, M. A., Bomar, L., Lapierre, P., Morrison, H. G., McClure, E. A., Sogin, M. L., & Graf, J. (2014). “Metagenomic analysis of the medicinal leech gut microbiota.” Front Microbiol, 5, 151. doi:10.3389/fmicb.2014.0015.

Mark Welch, J. L., Utter, D. R., Rossetti, B. J., Mark Welch, D. B., Eren, A. M., & Borisy, G. G. (2014). “Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping.” Front Microbiol, 5, 568. doi:10.3389/fmicb.2014.0056.

Markham, M. R., & Zakon, H. H. (2014). “Ionic mechanisms of microsecond-scale spike timing in single cells.” J Neurosci, 34(19), 6668-6678. doi:10.1523/JNEUROSCI.0615-14.201.

McLellan, S. L., & Eren, A. M. (2014). “Discovering new indicators of fecal pollution.” Trends Microbiol, 22(12), 697-706. doi:10.1016/j.tim.2014.08.00.

Meyer, J. L., & Huber, J. A. (2014). “Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano.” ISME J, 8(4), 867-880. doi:10.1038/ismej.2013.20.

Moran, Y., & Zakon, H. H. (2014). “The evolution of the four subunits of voltage-gated calcium channels: ancient roots, increasing complexity, and multiple losses.” Genome Biol Evol, 6(9), 2210-2217. doi:10.1093/gbe/evu17.

Nelson, M. C., Morrison, H. G., Benjamino, J., Grim, S. L., & Graf, J. (2014). “Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys.” PLoS One, 9(4), e94249. doi:10.1371/journal.pone.009424.

Ong, W. K., Vu, T. T., Lovendahl, K. N., Llull, J. M., Serres, M. H., Romine, M. F., & Reed, J. L. (2014). “Comparisons of Shewanella strains based on genome annotations, modeling, and experiments.” BMC Syst Biol, 8(1), 31. doi:10.1186/1752-0509-8-3.

Orcutt, B. N., LaRowe, D. E., Lloyd, K. G., Mills, H., Orsi, W., Reese, B. K., Sauvage, J., Huber, J. A., & Amend, J. (2014). “IODP Deep Biosphere Research Workshop report – a synthesis of recent investigations, and discussion of new research questions and drilling targets.” Scientific Drilling, 17, 61-66. doi:10.5194/sd-17-61-201.

Reed, D. C., Algar, C. K., Huber, J. A., & Dick, G. J. (2014). “Gene-centric approach to integrating environmental genomics and biogeochemical models.” Proc Natl Acad Sci U S A, 111(5), 1879-1884. doi:10.1073/pnas.131371311.

Reveillaud, J., Maignien, L., Murat Eren, A., Huber, J. A., Apprill, A., Sogin, M. L., & Vanreusel, A. (2014). “Host-specificity among abundant and rare taxa in the sponge microbiome.” ISME J, 8(6), 1198-1209. doi:10.1038/ismej.2013.22.

Reznikoff, W. S. (2014). “Viewing Francois Jacob (and Jacques Monod) through AGC & T.” Res Microbiol, 165(5), 357-358. doi:10.1016/j.resmic.2014.05.02.

Sadler, N. C., Melnicki, M. R., Serres, M. H., Merkley, E. D., Chrisler, W. B., Hill, E. A., Romine, M. F., Kim, S., Zink, E. M., Datta, S., Smith, R. D., Beliaev, A. S., Konopka, A., & Wright, A. T. (2014). “Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium.” ACS Chem Biol, 9(1), 291-300. doi:10.1021/cb400769.

Saito, M. A., McIlvin, M. R., Moran, D. M., Goepfert, T. J., DiTullio, G. R., Post, A. F., & Lamborg, C. H. (2014). “Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers.” Science, 345(6201), 1173-1177. doi:10.1126/science.125645.

Schmidt, V. T., Reveillaud, J., Zettler, E., Mincer, T. J., Murphy, L., & Amaral-Zettler, L. A. (2014). “Oligotyping reveals community level habitat selection within the genus Vibrio.” Front Microbiol, 5, 563. doi:10.3389/fmicb.2014.0056.

Scientists, G. C. o., Bracken-Grissom, H., Collins, A. G., Collins, T., Crandall, K., Distel, D., Dunn, C., Giribet, G., Haddock, S., Knowlton, N., Martindale, M., Medina, M., Messing, C., O’Brien, S. J., Paulay, G., Putnam, N., Ravasi, T., Rouse, G. W., Ryan, J. F., Schulze, A., Worheide, G., Adamska, M., Bailly, X., Breinholt, J., Browne, W. E., Diaz, M. C., Evans, N., Flot, J. F., Fogarty, N., Johnston, M., Kamel, B., Kawahara, A. Y., Laberge, T., Lavrov, D., Michonneau, F., Moroz, L. L., Oakley, T., Osborne, K., Pomponi, S. A., Rhodes, A., Santos, S. R., Satoh, N., Thacker, R. W., Van de Peer, Y., Voolstra, C. R., Mark Welch, D. B., Winston, J., & Zhou, X. (2014). “The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.” J Hered, 105(1), 1-18. doi:10.1093/jhered/est08.

Shafquat, A., Joice, R., Simmons, S. L., & Huttenhower, C. (2014). “Functional and phylogenetic assembly of microbial communities in the human microbiome.” Trends Microbiol, 22(5), 261-266. doi:10.1016/j.tim.2014.01.01.

Shilova, I. N., Robidart, J. C., James Tripp, H., Turk-Kubo, K., Wawrik, B., Post, A. F., Thompson, A. W., Ward, B., Hollibaugh, J. T., Millard, A., Ostrowski, M., Scanlan, D. J., Paerl, R. W., Stuart, R., & Zehr, J. P. (2014). “A microarray for assessing transcription from pelagic marine microbial taxa.” ISME J, 8(7), 1476-1491. doi:10.1038/ismej.2014..

Smith, J., & Cosentino, C. (2014). “Reliability and Modularity in the Sea Urchin Gene Regulatory Network for Endomesoderm Specification.” Paper presented at the Integrative and Comparative Biology, Austin, TX.

Swan, B. K., Chaffin, M. D., Martinez-Garcia, M., Morrison, H. G., Field, E. K., Poulton, N. J., Masland, E. D., Harris, C. C., Sczyrba, A., Chain, P. S., Koren, S., Woyke, T., & Stepanauskas, R. (2014). “Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres.” PLoS One, 9(4), e95380. doi:10.1371/journal.pone.009538.

Thompson, A., Vo, D., Comfort, C., & Zakon, H. H. (2014). “Expression evolution facilitated the convergent neofunctionalization of a sodium channel gene.” Mol Biol Evol, 31(8), 1941-1955. doi:10.1093/molbev/msu14.

Vallino, J., Algar, C., González, N., & Huber, J. (2014). “Use of Receding Horizon Optimal Control to Solve MaxEP-Based Biogeochemistry Problems.” In R. C. Dewar, C. H. Lineweaver, R. K. Niven, & K. Regenauer-Lieb (Ed.), Beyond the Second Law (pp. 337-359): Springer Berlin Heidelberg.

Vick-Majors, T. J., Priscu, J. C., & Amaral-Zettler, L. A. (2014). “Modular community structure suggests metabolic plasticity during the transition to polar night in ice-covered Antarctic lakes.” ISME J, 8(4), 778-789. doi:10.1038/ismej.2013.19.

Wey-Fabrizius, A. R., Herlyn, H., Rieger, B., Rosenkranz, D., Witek, A., Mark Welch, D. B., Ebersberger, I., & Hankeln, T. (2014). “Transcriptome data reveal Syndermatan relationships and suggest the evolution of endoparasitism in Acanthocephala via an epizoic stage.” PLoS One, 9(2), e88618. doi:10.1371/journal.pone.008861.

Wickham, S. A., Claessens, M., & Post, A. F. (2014). “Ciliates, microbes and nutrients: interactions in the seasonally mixed Gulf of Aqaba.” Journal of Plankton Research, 37(1), 258-271. doi:10.1093/plankt/fbu10.

Willger, S. D., Grim, S. L., Dolben, E. L., Shipunova, A., Hampton, T. H., Morrison, H. G., Filkins, L. M., O’Toole, G. A., Moulton, L. A., Ashare, A., Sogin, M. L., & Hogan, D. A. (2014). “Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis.” Microbiome, 2, 40. doi:10.1186/2049-2618-2-4.

Xu, Y., Vick-Majors, T. J., Morgan-Kiss, R., Priscu, J. C., & Amaral-Zettler, L. A. (2014). “Ciliate diversity, community structure, and novel taxa in lakes of the McMurdo Dry Valleys, Antarctica.” Biol Bull, 227(2), 175-190.

Zakon, H. (2014). “Hibernating mammals pass the acid test: multiple independent evolutions of enhanced proton block of sodium channels in acid-sensing pain receptors.” Brain Behav Evol, 83(4), 245-246. doi:10.1159/00036103.

2013

Akerman, N. H., Butterfield, D. A., & Huber, J. A. (2013). “Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids.” Front Microbiol, 4, 185. doi:10.3389/fmicb.2013.0018.

Alliegro, M. C., & Alliegro, M. A. (2013). “Localization of rRNA transcribed spacer domains in the nucleolinus and maternal procentrosomes of surf clam (Spisula) oocytes.” RNA Biol, 10(3), 391-396. doi:10.4161/rna.2354.

Amend, A. S., Oliver, T. A., Amaral-Zettler, L. A., Boetius, A., Fuhrman, J. A., Horner-Devine, M. C., Huse, S. M., Welch, D. B. M., Martiny, A. C., Ramette, A., Zinger, L., Sogin, M. L., & Martiny, J. B. H. (2013). “Macroecological patterns of marine bacteria on a global scale.” Journal of Biogeography, 40(4), 800-811. doi:10.1111/jbi.1203.

Arkhipova, I. R., & Rodriguez, F. (2013). “Genetic and epigenetic changes involving (retro)transposons in animal hybrids and polyploids.” Cytogenet Genome Res, 140(2-4), 295-311. doi:10.1159/00035206.

Arkhipova, I. R., Yushenova, I. A., & Rodriguez, F. (2013). “Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families.” Mob DNA, 4(1), 19. doi:10.1186/1759-8753-4-1.

Bennett, S. A., Coleman, M., Huber, J. A., Reddington, E., Kinsey, J. C., McIntyre, C., Seewald, J. S., & German, C. R. (2013). “Trophic regions of a hydrothermal plume dispersing away from an ultramafic-hosted vent-system: Von Damm vent-site, Mid-Cayman Rise.” Geochemistry Geophysics Geosystems, 14(2), 317-327. doi:DOI 10.1002/ggge.2006.

Duffy, J. E., Amaral-Zettler, L. A., Fautin, D. G., Paulay, G., Rynearson, T. A., Sosik, H. M., & Stachowicz, J. J. (2013). “Envisioning a Marine Biodiversity Observation Network.” Bioscience, 63(5), 350-361. doi:DOI 10.1525/bio.2013.63.5..

Eren, A. M., Maignien, L., Sul, W. J., Murphy, L. G., Grim, S. L., Morrison, H. G., & Sogin, M. L. (2013). “Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.” Methods Ecol Evol, 4(12). doi:10.1111/2041-210X.1211.

Eren, A. M., Vineis, J. H., Morrison, H. G., & Sogin, M. L. (2013). “A filtering method to generate high quality short reads using illumina paired-end technology.” PLoS One, 8(6), e66643. doi:10.1371/journal.pone.006664.

Feehery, G. R., Yigit, E., Oyola, S. O., Langhorst, B. W., Schmidt, V. T., Stewart, F. J., Dimalanta, E. T., Amaral-Zettler, L. A., Davis, T., Quail, M. A., & Pradhan, S. (2013). “A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.” PLoS One, 8(10), e76096. doi:10.1371/journal.pone.007609.

Fischer, A. H., Tulin, S., Fredman, D., & Smith, J. (2013). “Employing BAC-reporter constructs in the sea anemone Nematostella vectensis.” Integr Comp Biol, 53(5), 832-846. doi:10.1093/icb/ict09.

Flot, J. F., Hespeels, B., Li, X., Noel, B., Arkhipova, I. R., Danchin, E. G., Hejnol, A., Henrissat, B., Koszul, R., Aury, J. M., Barbe, V., Barthelemy, R. M., Bast, J., Bazykin, G. A., Chabrol, O., Couloux, A., Da Rocha, M., Da Silva, C., Gladyshev, E., Gouret, P., Hallatschek, O., Hecox-Lea, B., Labadie, K., Lejeune, B., Piskurek, O., Poulain, J., Rodriguez, F., Ryan, J. F., Vakhrusheva, O. A., Wajnberg, E., Wirth, B., Yushenova, I. A., Kellis, M., Kondrashov, A. S., Mark Welch, D. B., Pontarotti, P., Weissenbach, J., Wincker, P., Jaillon, O., & Van Doninck, K. (2013). “Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.” Nature, 500(7463), 453-457. doi:10.1038/nature1232.

Fortunato, C. S., Eiler, A., Herfort, L., Needoba, J. A., Peterson, T. D., & Crump, B. C. (2013). “Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin.” ISME J, 7(10), 1899-1911. doi:10.1038/ismej.2013.7.

Gribble, K. E., & Mark Welch, D. B. (2013). “Life-span extension by caloric restriction is determined by type and level of food reduction and by reproductive mode in Brachionus manjavacas (Rotifera).” J Gerontol A Biol Sci Med Sci, 68(4), 349-358. doi:10.1093/gerona/gls17.

Gupta, R. W., Tran, L., Norori, J., Ferris, M. J., Eren, A. M., Taylor, C. M., Dowd, S. E., & Penn, D. (2013). “Histamine-2 receptor blockers alter the fecal microbiota in premature infants.” J Pediatr Gastroenterol Nutr, 56(4), 397-400. doi:10.1097/MPG.0b013e318282a8c.

Hanson, S. J., Schurko, A. M., Hecox-Lea, B., Mark Welch, D. B., Stelzer, C. P., & Logsdon, J. M. Jr. (2013). “Inventory and phylogenetic analysis of meiotic genes in monogonont rotifers.” J Hered, 104(3), 357-370. doi:10.1093/jhered/est01.

Hanson, S. J., Stelzer, C. P., Mark Welch, D. B., & Logsdon, J. M. Jr. (2013). “Comparative transcriptome analysis of obligately asexual and cyclically sexual rotifers reveals genes with putative functions in sexual reproduction, dormancy, and asexual egg production.” BMC Genomics, 14, 412. doi:10.1186/1471-2164-14-41.

Helm, R. R., Siebert, S., Tulin, S., Smith, J., & Dunn, C. W. (2013). “Characterization of differential transcript abundance through time during Nematostella vectensis development.” BMC Genomics, 14, 266. doi:10.1186/1471-2164-14-26.

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

Kamennaya, N. A., & Post, A. F. (2013). “Distribution and expression of the cyanate acquisition potential among cyanobacterial populations in oligotrophic marine waters.” Limnology and Oceanography, 58(6), 1959-1971. doi:DOI 10.4319/lo.2013.58.6.195.

Light, J. E., Hafner, J. C., Upham, N. S., & Reddington, E. (2013). “Conservation Genetics of Kangaroo Mice, Genus Microdipodops.” Journal of Mammalian Evolution, 20(2), 129-146. doi:10.1007/s10914-012-9193-2.

Liu, C. M., Hungate, B. A., Toblan, A. A. R., Serwadda, D., Ravel, J., Lester, R., Kigozi, G., Aziz, M., Galiwango, R. M., Nalugoda, F., Contente-Cuomo, T. L., Wawer, M. J., Kelm, P., Gray, R. H., & Price, L. B. (2013). “Male circumcision significantly reduces prevalence and load of genital anaerobic bacteria.” MBio, 4. doi:10.1128/mBio.00076-1.

Maignien, L., Parkes, R. J., Cragg, B., Niemann, H., Knittel, K., Coulon, S., Akhmetzhanov, A., & Boon, N. (2013). “Anaerobic oxidation of methane in hypersaline cold seep sediments.” FEMS Microbiol Ecol, 83(1), 214-231. doi:10.1111/j.1574-6941.2012.01466..

Marteinsson, V. T., Runarsson, A., Stefansson, A., Thorsteinsson, T., Johannesson, T., Magnusson, S. H., Reynisson, E., Einarsson, B., Wade, N., Morrison, H. G., & Gaidos, E. (2013). “Microbial communities in the subglacial waters of the Vatnajokull ice cap, Iceland.” ISME J, 7(2), 427-437. doi:10.1038/ismej.2012.9.

Materna, S. C., Swartz, S. Z., & Smith, J. (2013). “Notch and Nodal control forkhead factor expression in the specification of multipotent progenitors in sea urchin.” Development, 140(8), 1796-1806. doi:10.1242/dev.09115.

McLellan, S. L., Newton, R. J., Vandewalle, J. L., Shanks, O. C., Huse, S. M., Eren, A. M., & Sogin, M. L. (2013). “Sewage reflects the distribution of human faecal Lachnospiraceae.” Environ Microbiol, 15(8), 2213-2227. doi:10.1111/1462-2920.1209.

Merkel, A. Y., Huber, J. A., Chernyh, N. A., Bonch-Osmolovskaya, E. A., & Lebedinsky, A. V. (2013). “Detection of putatively thermophilic anaerobic methanotrophs in diffuse hydrothermal vent fluids.” Appl Environ Microbiol, 79(3), 915-923. doi:10.1128/AEM.03034-1.

Meyer, J. L., Akerman, N. H., Proskurowski, G., & Huber, J. A. (2013). “Microbiological characterization of post-eruption “snowblower” vents at Axial Seamount, Juan de Fuca Ridge.” Front Microbiol, 4, 153. doi:10.3389/fmicb.2013.0015.

Newton, R. J., Bootsma, M. J., Morrison, H. G., Sogin, M. L., & McLellan, S. L. (2013). “A microbial signature approach to identify fecal pollution in the waters off an urbanized coast of Lake Michigan.” Microb Ecol, 65(4), 1011-1023. doi:10.1007/s00248-013-0200-.

Newton, R. J., Huse, S. M., Morrison, H. G., Peake, C. S., Sogin, M. L., & McLellan, S. L. (2013). “Shifts in the microbial community composition of Gulf Coast beaches following beach oiling.” PLoS One, 8(9), e74265. doi:10.1371/journal.pone.007426.

Price, K. E., Hampton, T. H., Gifford, A. H., Dolben, E. L., Hogan, D. A., Morrison, H. G., Sogin, M. L., & O’Toole, G. A. (2013). “Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation.” Microbiome, 1(1), 27. doi:10.1186/2049-2618-1-2.

Rozhkov, N. V., Schostak, N. G., Zelentsova, E. S., Yushenova, I. A., Zatsepina, O. G., & Evgen’ev, M. B. (2013). “Evolution and dynamics of small RNA response to a retroelement invasion in Drosophila.” Mol Biol Evol, 30(2), 397-408. doi:10.1093/molbev/mss24.

Shanks, O. C., Newton, R. J., Kelty, C. A., Huse, S. M., Sogin, M. L., & McLellan, S. L. (2013). “Comparison of the microbial community structures of untreated wastewaters from different geographic locales.” Appl Environ Microbiol, 79(9), 2906-2913. doi:10.1128/AEM.03448-1.

Sul, W. J., Oliver, T. A., Ducklow, H. W., Amaral-Zettler, L. A., & Sogin, M. L. (2013). “Marine bacteria exhibit a bipolar distribution.” Proc Natl Acad Sci U S A, 110(6), 2342-2347. doi:10.1073/pnas.121242411.

Taylor, R. C., Webb Robertson, B. J., Markillie, L. M., Serres, M. H., Linggi, B. E., Aldrich, J. T., Hill, E. A., Romine, M. F., Lipton, M. S., & Wiley, H. S. (2013). “Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria.” Integr Biol (Camb), 5(11), 1393-1406. doi:10.1039/c3ib40120.

Theroux, S., Toney, J., Amaral-Zettler, L. A., & Huang, Y. S. (2013). “Production and temperature sensitivity of long chain alkenones in the cultured haptophyte Pseudoisochrysis paradoxa.” Organic Geochemistry, 62, 68-73. doi:DOI 10.1016/j.orggeochem.2013.07.00.

Tulin, S., Aguiar, D., Istrail, S., & Smith, J. (2013). “A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems.” Evodevo, 4(1), 16. doi:10.1186/2041-9139-4-1.

Ver Eecke, H. C., Akerman, N. H., Huber, J. A., Butterfield, D. A., & Holden, J. F. (2013). “Growth kinetics and energetics of a deep-sea hyperthermophilic methanogen under varying environmental conditions.” Environ Microbiol Rep, 5(5), 665-671. doi:10.1111/1758-2229.1206.

Vital, M., Penton, C. R., Wang, Q., Young, V. B., Antonopoulos, D. A., Sogin, M. L., Morrison, H. G., Raffals, L., Chang, E. B., Huffnagle, G. B., Schmidt, T. M., Cole, J. R., & Tiedje, J. M. (2013). “A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community.” Microbiome, 1(1), 8. doi:10.1186/2049-2618-1-.

Woodring, J. L., Bland, N. D., Ochiana, S. O., Campbell, R. K., & Pollastri, M. P. (2013). “Synthesis and assessment of catechol diether compounds as inhibitors of trypanosomal phosphodiesterase B1 (TbrPDEB1).” Bioorg Med Chem Lett, 23(21), 5971-5974. doi:10.1016/j.bmcl.2013.08.05.

Young, V. B., Raffals, L. H., Huse, S. M., Vital, M., Dai, D., Schloss, P. D., Brulc, J. M., Antonopoulos, D. A., Arrieta, R. L., Kwon, J. H., Reddy, K. G., Hubert, N. A., Grim, S. L., Vineis, J. H., Dalal, S., Morrison, H. G., Eren, A. M., Meyer, F., Schmidt, T. M., Tiedje, J. M., Chang, E. B., & Sogin, M. L. (2013). “Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis.” Microbiome, 1(1), 9. doi:10.1186/2049-2618-1-.

Zettler, E. R., Mincer, T. J., & Amaral-Zettler, L. A. (2013). “Life in the “plastisphere”: microbial communities on plastic marine debris.” Environ Sci Technol, 47(13), 7137-7146. doi:10.1021/es401288.

2012

Alliegro, M. C., Hartson, S., & Alliegro, M. A. (2012). “Composition and dynamics of the nucleolinus, a link between the nucleolus and cell division apparatus in surf clam (Spisula) oocytes.” J Biol Chem, 287(9), 6702-6713. doi:10.1074/jbc.M111.28850.

Amaral-Zettler, L. A. (2012). “Eukaryotic diversity at pH extremes.” Front Microbiol, 3, 441. doi:10.3389/fmicb.2012.0044.

Arkhipova, I. R. (2012). “Telomerase, retrotransposons, and evolution.” In N. F. Lue & C. Autexier (Ed.), Telomerases: Chemistry, Biology and Clinical Applications (pp. 265-299). Hoboken, NJ: Wiley and Sons, Inc. .

Arkhipova, I. R., Batzer, M. A., Brosius, J., Feschotte, C., Moran, J. V., Schmitz, J., & Jurka, J. (2012). “Genomic impact of eukaryotic transposable elements.” Mob DNA, 3(1), 19. doi:10.1186/1759-8753-3-1.

Atamna-Ismaeel, N., Finkel, O. M., Glaser, F., Sharon, I., Schneider, R., Post, A. F., Spudich, J. L., von Mering, C., Vorholt, J. A., Iluz, D., Beja, O., & Belkin, S. (2012). “Microbial rhodopsins on leaf surfaces of terrestrial plants.” Environ Microbiol, 14(1), 140-146. doi:10.1111/j.1462-2920.2011.02554..

Beg, Q. K., Zampieri, M., Klitgord, N., Collins, S. B., Altafini, C., Serres, M. H., & Segre, D. (2012). “Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis.” Nucleic Acids Res, 40(15), 7132-7149. doi:10.1093/nar/gks46.

Bowen, J. L., Morrison, H. G., Hobbie, J. E., & Sogin, M. L. (2012). “Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates.” ISME J, 6(11), 2014-2023. doi:10.1038/ismej.2012.4.

Brandt, B. W., Bonder, M. J., Huse, S. M., & Zaura, E. (2012). “TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage.” Nucleic Acids Res, 40(Web Server issue), W82-87. doi:10.1093/nar/gks41.

Breier, J. A., Gomez-Ibanez, D., Reddington, E., Huber, J. A., & Emerson, D. (2012). “A precision multi-sampler for deep-sea hydrothermal microbial mat studies.” Deep-Sea Research Part I-Oceanographic Research Papers, 70(0), 83-90. doi:DOI 10.1016/j.dsr.2012.10.00.

Chandsawangbhuwana, C., Shi, L. Z., Zhu, Q., Alliegro, M. C., & Berns, M. W. (2012). “High-throughput optofluidic system for the laser microsurgery of oocytes.” J Biomed Opt, 17(1), 015001. doi:10.1117/1.JBO.17.1.01500.

Chapman, M., & Alliegro, M. C. (2012). “The karyomastigont as an evolutionary seme.” Q Rev Biol, 87(4), 315-324.

Crump, B. C., Amaral-Zettler, L. A., & Kling, G. W. (2012). “Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils.” ISME J, 6(9), 1629-1639. doi:10.1038/ismej.2012..

Davies, N., Meyer, C., Gilbert, J. A., Amaral-Zettler, L. A., Deck, J., Bicak, M., Rocca-Serra, P., Assunta-Sansone, S., Willis, K., & Field, D. (2012). “A call for an international network of genomic observatories (GOs).” Gigascience, 1(1), 5. doi:10.1186/2047-217X-1-.

Filkins, L. M., Hampton, T. H., Gifford, A. H., Gross, M. J., Hogan, D. A., Sogin, M. L., Morrison, H. G., Paster, B. J., & O’Toole, G. A. (2012). “Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability.” J Bacteriol, 194(17), 4709-4717. doi:10.1128/JB.00566-1.

Finkel, O. M., Burch, A. Y., Elad, T., Huse, S. M., Lindow, S. E., Post, A. F., & Belkin, S. (2012). “Distance-decay relationships partially determine diversity patterns of phyllosphere bacteria on Tamarix trees across the Sonoran Desert [corrected].” Appl Environ Microbiol, 78(17), 6187-6193. doi:10.1128/AEM.00888-1.

Fischer, A. H. L., & Smith, J. (2012). “Evo-devo in the era of gene regulatory networks.” Integr Comp Biol, 52(6), 842-849. doi:10.1093/icb/ics11.

Freitas, S., Hatosy, S., Fuhrman, J. A., Huse, S. M., Mark Welch, D. B., Sogin, M. L., & Martiny, A. C. (2012). “Global distribution and diversity of marine Verrucomicrobia.” ISME J, 6(8), 1499-1505. doi:10.1038/ismej.2012..

Gilbert, J. A., Steele, J. A., Caporaso, J. G., Steinbruck, L., Reeder, J., Temperton, B., Huse, S. M., McHardy, A. C., Knight, R., Joint, I., Somerfield, P., Fuhrman, J. A., & Field, D. (2012). “Defining seasonal marine microbial community dynamics.” ISME J, 6(2), 298-308. doi:10.1038/ismej.2011.10.

Gobet, A., Boer, S. I., Huse, S. M., van Beusekom, J. E., Quince, C., Sogin, M. L., Boetius, A., & Ramette, A. (2012). “Diversity and dynamics of rare and of resident bacterial populations in coastal sands.” ISME J, 6(3), 542-553. doi:10.1038/ismej.2011.13.

Gribble, K. E., & Mark Welch, D. B. (2012). “The mate recognition protein gene mediates reproductive isolation and speciation in the Brachionus plicatilis cryptic species complex.” BMC Evol Biol, 12(1), 134. doi:10.1186/1471-2148-12-13.

Huse, S. M., Ye, Y., Zhou, Y., & Fodor, A. A. (2012). “A core human microbiome as viewed through 16S rRNA sequence clusters.” PLoS One, 7(6), e34242. doi:10.1371/journal.pone.003424.

Kozul-Horvath, C. D., Zandbergen, F., Jackson, B. P., Enelow, R. I., & Hamilton, J. W. (2012). “Effects of low-dose drinking water arsenic on mouse fetal and postnatal growth and development.” PLoS One, 7(5), e38249. doi:10.1371/journal.pone.003824.

Lasek-Nesselquist, E. (2012). “A mitogenomic re-evaluation of the bdelloid phylogeny and relationships among the Syndermata.” PLoS One, 7(8), e43554. doi:10.1371/journal.pone.004355.

Looft, T., Johnson, T. A., Allen, H. K., Bayles, D. O., Alt, D. P., Stedtfeld, R. D., Sul, W. J., Stedtfeld, T. M., Chai, B., Cole, J. R., Hashsham, S. A., Tiedje, J. M., & Stanton, T. B. (2012). “In-feed antibiotic effects on the swine intestinal microbiome.” Proc Natl Acad Sci U S A, 109(5), 1691-1696. doi:10.1073/pnas.112023810.

Mackey, K. R. M., Roberts, K., Lomas, M. W., Saito, M. A., Post, A. F., & Paytan, A. (2012). “Enhanced solubility and ecological impact of atmospheric phosphorus deposition upon extended seawater exposure.” Environ Sci Technol, 46(19), 10438-10446. doi:10.1021/es300799.

Madan, J. C., Koestler, D. C., Stanton, B. A., Davidson, L., Moulton, L. A., Housman, M. L., Moore, J. H., Guill, M. F., Morrison, H. G., Sogin, M. L., Hampton, T. H., Karagas, M. R., Palumbo, P. E., Foster, J. A., Hibberd, P. L., & O’Toole, G. A. (2012). “Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures.” MBio, 3(4). doi:10.1128/mBio.00251-1.

Madan, J. C., Salari, R. C., Saxena, D., Davidson, L., O’Toole, G. A., Moore, J. H., Sogin, M. L., Foster, J. A., Edwards, W. H., Palumbo, P., & Hibberd, P. L. (2012). “Gut microbial colonisation in premature neonates predicts neonatal sepsis.” Arch Dis Child Fetal Neonatal Ed, 97(6), F456-462. doi:10.1136/fetalneonatal-2011-30137.

McCliment, E. A., Nelson, C. E., Carlson, C. A., Alldredge, A. L., Witting, J., & Amaral-Zettler, L. A. (2012). “An all-taxon microbial inventory of the Moorea coral reef ecosystem.” ISME J, 6(2), 309-319. doi:10.1038/ismej.2011.10.

Meeder, E., Mackey, K. R. M., Paytan, A., Shaked, Y., Iluz, D., Stambler, N., Rivlin, T., Post, A. F., & Lazar, B. (2012). “Nitrite dynamics in the open ocean—clues from seasonal and diurnal variations.” Marine Ecology Progress Series, 453, 11-26. doi:10.3354/meps0952.

Ochiana, S. O., Gustafson, A., Bland, N. D., Wang, C., Russo, M. J., Campbell, R. K., & Pollastri, M. P. (2012). “Synthesis and evaluation of human phosphodiesterases (PDE) 5 inhibitor analogs as trypanosomal PDE inhibitors.” Part 2. Tadalafil analogs. Bioorg Med Chem Lett, 22(7), 2582-2584. doi:10.1016/j.bmcl.2012.01.11.

Ozok, A. R., Persoon, I. F., Huse, S. M., Keijser, B. J., Wesselink, P. R., Crielaard, W., & Zaura, E. (2012). “Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments.” Int Endod J, 45(6), 530-541. doi:10.1111/j.1365-2591.2011.02006..

Sansone, S. A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral-Zettler, L. A., Begley, K., Booth, T., Bougueleret, L., Burns, G., Chapman, B., Clark, T., Coleman, L. A., Copeland, J., Das, S., de Daruvar, A., de Matos, P., Dix, I., Edmunds, S., Evelo, C. T., Forster, M. J., Gaudet, P., Gilbert, J., Goble, C., Griffin, J. L., Jacob, D., Kleinjans, J., Harland, L., Haug, K., Hermjakob, H., Ho Sui, S. J., Laederach, A., Liang, S., Marshall, S., McGrath, A., Merrill, E., Reilly, D., Roux, M., Shamu, C. E., Shang, C. A., Steinbeck, C., Trefethen, A., Williams-Jones, B., Wolstencroft, K., Xenarios, I., & Hide, W. (2012). “Toward interoperable bioscience data.” Nat Genet, 44(2), 121-126. doi:10.1038/ng.105.

Siam, R., Mustafa, G. A., Sharaf, H., Moustafa, A., Ramadan, A. R., Antunes, A., Bajic, V. B., Stingl, U., Marsis, N. G., Coolen, M. J., Sogin, M. L., Ferreira, A. J., & Dorry, H. E. (2012). “Unique prokaryotic consortia in geochemically distinct sediments from Red Sea Atlantis II and discovery deep brine pools.” PLoS One, 7(8), e42872. doi:10.1371/journal.pone.004287.

Smith, K. F., Schmidt, V. T., Rosen, G. E., & Amaral-Zettler, L. A. (2012). “Microbial diversity and potential pathogens in ornamental fish aquarium water.” PLoS One, 7(9), e39971. doi:10.1371/journal.pone.003997.

Sogin, M. L. (2012). “Trying to Make Sense of the Microbial Census.” In S. Maloy & R. Kolter (Ed.), Microbes and Evolution: The World That Darwin Never Saw (pp. 31-37). Washington, DC: ASM Press.

Sukenik, A., Kaplan-Levy, R. N., Mark Welch, J. L., & Post, A. F. (2012). “Massive multiplication of genome and ribosomes in dormant cells (akinetes) of Aphanizomenon ovalisporum (Cyanobacteria).” ISME J, 6(3), 670-679. doi:10.1038/ismej.2011.12.

Sun, Y., Cai, Y., Huse, S. M., Knight, R., Farmerie, W. G., Wang, X., & Mai, V. (2012). “A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis.” Brief Bioinform, 13(1), 107-121. doi:10.1093/bib/bbr00.

Takumi, K., Swart, A., Mank, T., Lasek-Nesselquist, E., Lebbad, M., Caccio, S. M., & Sprong, H. (2012). “Population-based analyses of Giardia duodenalis is consistent with the clonal assemblage structure.” Parasit Vectors, 5, 168. doi:10.1186/1756-3305-5-16.

Theroux, S., Huang, Y., & Amaral-Zettler, L. (2012). “Comparative Molecular Microbial Ecology of the Spring Haptophyte Bloom in a Greenland Arctic Oligosaline Lake.” Frontiers in Microbiology, 3, 415.

Toney, J. L., Theroux, S., Andersen, R. A., Coleman, A., Amaral-Zettler, L. A., & Huang, Y. S. (2012). “Culturing of the first 37:4 predominant lacustrine haptophyte: Geochemical, biochemical, and genetic implications.” Geochimica Et Cosmochimica Acta, 78, 51-64. doi:DOI 10.1016/j.gca.2011.11.02.

Valm, A. M., Mark Welch, J. L., & Borisy, G. G. (2012). “CLASI-FISH: principles of combinatorial labeling and spectral imaging.” Syst Appl Microbiol, 35(8), 496-502. doi:10.1016/j.syapm.2012.03.00.

Vandewalle, J. L., Goetz, G. W., Huse, S. M., Morrison, H. G., Sogin, M. L., Hoffmann, R. G., Yan, K., & McLellan, S. L. (2012). “Acinetobacter, Aeromonas and Trichococcus populations dominate the microbial community within urban sewer infrastructure.” Environ Microbiol, 14(9), 2538-2552. doi:10.1111/j.1462-2920.2012.02757..

Ver Eecke, H. C., Butterfield, D. A., Huber, J. A., Lilley, M. D., Olson, E. J., Roe, K. K., Evans, L. J., Merkel, A. Y., Cantin, H. V., & Holden, J. F. (2012). “Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents.” Proc Natl Acad Sci U S A, 109(34), 13674-13679. doi:10.1073/pnas.120663210.

Wang, C., Ashton, T. D., Gustafson, A., Bland, N. D., Ochiana, S. O., Campbell, R. K., & Pollastri, M. P. (2012). “Synthesis and evaluation of human phosphodiesterases (PDE) 5 inhibitor analogs as trypanosomal PDE inhibitors.” Part 1. Sildenafil analogs. Bioorg Med Chem Lett, 22(7), 2579-2581. doi:10.1016/j.bmcl.2012.01.11.

Wolf, B., Schwarzer, A., Cote, A. L., Hampton, T. H., Schwaab, T., Huarte, E., Tomlinson, C. R., Gui, J., Fisher, J. L., Fadul, C. E., Hamilton, J. W., & Ernstoff, M. S. (2012). “Gene expression profile of peripheral blood lymphocytes from renal cell carcinoma patients treated with IL-2, interferon-alpha and dendritic cell vaccine.” PLoS One, 7(12), e50221. doi:10.1371/journal.pone.005022.

Yager, P. L., Sherrell, R. M., Stammerjohn, S. E., Alderkamp, A. C., Schofield, O., Abrahamsen, E. P., Arrigo, K. R., Bertilsson, S., Garay, D. L., Guerrero, R., Lowry, K. E., Moksnes, P. O., Ndungu, K., Post, A. F., Randall-Goodwin, E., Riemann, L., Severmann, S., Thatje, S., van Dijken, G. L., & Wilson, S. (2012). “ASPIRE The Amundsen Sea Polynya International Research Expedition.” Oceanography, 25(3), 40-53. doi:http://dx.doi.org/10.5670/oceanog.2012.73.

2011

Agogue, H., Lamy, D., Neal, P. R., Sogin, M. L., & Herndl, G. J. (2011). “Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing.” Mol Ecol, 20(2), 258-274. doi:10.1111/j.1365-294X.2010.04932..

Akerman, N. H., Price, R. E., Pichler, T., & Amend, J. P. (2011). “Energy sources for chemolithotrophs in an arsenic- and iron-rich shallow-sea hydrothermal system.” Geobiology, 9(5), 436-445. doi:10.1111/j.1472-4669.2011.00291..

Alliegro, M. C. (2011). “The Nucleolinus: A disappearing, forgotten and (maybe) misnamed organelle.” Commun Integr Biol, 4(2), 147-149. doi:10.4161/cib.4.2.1454.

Alliegro, M. C. (2011). “The centrosome and spindle as a ribonucleoprotein complex.” Chromosome Res, 19(3), 367-376. doi:10.1007/s10577-011-9186-.

Amaral-Zettler, L. A., Zettler, E. R., Theroux, S. M., Palacios, C., Aguilera, A., & Amils, R. (2011). “Microbial community structure across the tree of life in the extreme Rio Tinto.” ISME J, 5(1), 42-50. doi:10.1038/ismej.2010.10.

Bland, N. D., Wang, C., Tallman, C., Gustafson, A. E., Wang, Z., Ashton, T. D., Ochiana, S. O., McAllister, G., Cotter, K., Fang, A. P., Gechijian, L., Garceau, N., Gangurde, R., Ortenberg, R., Ondrechen, M. J., Campbell, R. K., & Pollastri, M. P. (2011). “Pharmacological validation of Trypanosoma brucei phosphodiesterases B1 and B2 as druggable targets for African sleeping sickness.” J Med Chem, 54(23), 8188-8194. doi:10.1021/jm201148.

Bogaert, D., Keijser, B., Huse, S. M., Rossen, J., Veenhoven, R., van Gils, E., Bruin, J., Montijn, R., Bonten, M., & Sanders, E. (2011). “Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis.” PLoS One, 6(2), e17035. doi:10.1371/journal.pone.001703.

Bowen, J. L., Ward, B. B., Morrison, H. G., Hobbie, J. E., Valiela, I., Deegan, L. A., & Sogin, M. L. (2011). “Microbial community composition in sediments resists perturbation by nutrient enrichment.” ISME J, 5(9), 1540-1548. doi:10.1038/ismej.2011.2.

Crielaard, W., Zaura, E., Schuller, A. A., Huse, S. M., Montijn, R. C., & 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. doi:10.1186/1755-8794-4-2.

Eren, A. M., Zozaya, M., Taylor, C. M., Dowd, S. E., Martin, D. H., & 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. doi:10.1371/journal.pone.002673.

Field, D., Amaral-Zettler, L. A., Cochrane, G., Cole, J. R., Dawyndt, P., Garrity, G. M., Gilbert, J., Glockner, F. O., Hirschman, L., Karsch-Mizrachi, I., Klenk, H. P., Knight, R., Kottmann, R., Kyrpides, N., Meyer, F., San Gil, I., Sansone, S. A., Schriml, L. M., Sterk, P., Tatusova, T., Ussery, D. W., White, O., & Wooley, J. (2011). “The Genomic Standards Consortium.” PLoS Biol, 9(6), e1001088. doi:10.1371/journal.pbio.100108.

Finkel, O. M., Burch, A. Y., Lindow, S. E., Post, A. F., & 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. doi:10.1128/AEM.05565-1.

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.

Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J. R., Amaral-Zettler, L. A., Gilbert, J. A., Karsch-Mizrachi, I., Johnston, A., Cochrane, G., Vaughan, R., Hunter, C., Park, J., Morrison, N., Rocca-Serra, P., Sterk, P., Arumugam, M., Bailey, M., Baumgartner, L., Birren, B. W., Blaser, M. J., Bonazzi, V., Booth, T., Bork, P., Bushman, F. D., Buttigieg, P. L., Chain, P. S., Charlson, E., Costello, E. K., Huot-Creasy, H., Dawyndt, P., DeSantis, T., Fierer, N., Fuhrman, J. A., Gallery, R. E., Gevers, D., Gibbs, R. A., San Gil, I., Gonzalez, A., Gordon, J. I., Guralnick, R., Hankeln, W., Highlander, S., Hugenholtz, P., Jansson, J., Kau, A. L., Kelley, S. T., Kennedy, J., Knights, D., Koren, O., Kuczynski, J., Kyrpides, N., Larsen, R., Lauber, C. L., Legg, T., Ley, R. E., Lozupone, C. A., Ludwig, W., Lyons, D., Maguire, E., Methe, B. A., Meyer, F., Muegge, B., Nakielny, S., Nelson, K. E., Nemergut, D., Neufeld, J. D., Newbold, L. K., Oliver, A. E., Pace, N. R., Palanisamy, G., Peplies, J., Petrosino, J., Proctor, L., Pruesse, E., Quast, C., Raes, J., Ratnasingham, S., Ravel, J., Relman, D. A., Assunta-Sansone, S., Schloss, P. D., Schriml, L., Sinha, R., Smith, M. I., Sodergren, E., Spo, A., Stombaugh, J., Tiedje, J. M., Ward, D. V., Weinstock, G. M., Wendel, D., White, O., Whiteley, A., Wilke, A., Wortman, J. R., Yatsunenko, T., & Glockner, F. O. (2011). “Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.” Nat Biotechnol, 29(5), 415-420. doi:10.1038/nbt.182.

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.