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Tag ploscb08 [75 articles]

Recent papers classified by the tag ploscb08.
  • Biogeography: An Emerging Cornerstone for Understanding Prokaryotic Diversity, Ecology, and Evolution
    Microbial Ecology, Vol. 53, No. 2. (February 2007), pp. 197-207.
  • Biogeography and Ecological Setting of Indian Ocean Hydrothermal Vents
    Science, Vol. 294, No. 5543. (26 October 2001), pp. 818-823.
  • Comparative Metagenomics of Microbial Communities
    Science, Vol. 308, No. 5721. (22 April 2005), pp. 554-557.
    by Susannah G Tringe, Christian von Mering, Arthur Kobayashi, Asaf A Salamov, Kevin Chen, Hwai W Chang, Mircea Podar, Jay M Short, Eric J Mathur, John C Detter, Peer Bork, Philip Hugenholtz, Edward M Rubin
  • Metagenomic Analysis of Coastal RNA Virus Communities
    Science, Vol. 312, No. 5781. (23 June 2006), pp. 1795-1798.
    by Alexander I Culley, Andrew S Lang, Curtis A Suttle
  • The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.
    PLoS ONE, Vol. 3, No. 1. (2008)
  • Biodiversity and biogeography of phages in modern stromatolites and thrombolites
    Nature (02 March 2008)
    by Christelle Desnues, Beltran Rodriguez-Brito, Steve Rayhawk, Scott Kelley, Tuong Tran, Matthew Haynes, Hong Liu, Mike Furlan, Linda Wegley, Betty Chau, Yijun Ruan, Dana Hall, Florent E Angly, Robert A Edwards, Linlin Li, Rebecca V Thurber, Pamela R Reid, Janet Siefert, Valeria Souza, David L Valentine, Brandon K Swan, Mya Breitbart, Forest Rohwer
  • Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes
    Environmental Microbiology, Vol. 9, No. 6. (June 2007), pp. 1464-1475.
  • From the Cover: A latitudinal diversity gradient in planktonic marine bacteria
    Proceedings of the National Academy of Sciences, Vol. 105, No. 22. (3 June 2008), pp. 7774-7778.
    by Jed A Fuhrman, Joshua A Steele, Ian Hewson, Michael S Schwalbach, Mark V Brown, Jessica L Green, James H Brown
  • Evolution of Mammals and Their Gut Microbes
    Science, Vol. 320, No. 5883. (20 June 2008), pp. 1647-1651.
    by Ruth E Ley, Micah Hamady, Catherine Lozupone, Peter J Turnbaugh, Rob R Ramey, Stephen J Bircher, Michael L Schlegel, Tammy A Tucker, Mark D Schrenzel, Rob Knight, Jeffrey I Gordon
  • Status of the Microbial Census
    Microbiol. Mol. Biol. Rev., Vol. 68, No. 4. (1 December 2004), pp. 686-691.
    by Patrick D Schloss, Jo Handelsman
  • Molecular diversity and ecology of microbial plankton
    Nature, Vol. 437, No. 7057. (14 September 2005), pp. 343-348.
    by Stephen J Giovannoni, Ulrich Stingl
  • Spatial scaling of microbial biodiversity
    Trends in Ecology & Evolution, Vol. 21, No. 9. (September 2006), pp. 501-507.
    by Jessica Green, Brendan J Bohannan
  • Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior
    Science, Vol. 311, No. 5760. (27 January 2006), pp. 496-503.
    by Edward F Delong, Christina M Preston, Tracy Mincer, Virginia Rich, Steven J Hallam, Niels-Ulrik Frigaard, Asuncion Martinez, Matthew B Sullivan, Robert Edwards, Beltran R Brito, Sallie W Chisholm, David M Karl
  • Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness
    ISME J, Vol. 2, No. 6. (28 February 2008), pp. 642-655.
    by Liyou Wu, Xueduan Liu, Matthew W Fields, Dorothea K Thompson, Christopher E Bagwell, James M Tiedje, Terry C Hazen, Jizhong Zhou
    posted to diversity microarray ploscb08 by jlgreen on 2008-08-04 17:18:34 as ** along with 2 groups iSEEM Green Lab
  • Tracking microbial biodiversity through molecular and genomic ecology.
    Research in microbiology, Vol. 159, No. 1. (b 2008), pp. 67-73.
  • Distinct distribution pattern of abundance and diversity of aerobic anoxygenic phototrophic bacteria in the global ocean
    Environmental Microbiology, Vol. 9, No. 12. (December 2007), pp. 3091-3099.
    posted to ocean ploscb08 by jlgreen on 2008-07-25 23:38:10 as ** along with 2 groups Green Lab iSEEM
  • Species divergence and the measurement of microbial diversity
    FEMS Microbiology Reviews (July 2008), pp. 557-578.
    by Catherine A Lozupone, Rob Knight
  • Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
    Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635.
    by Ari Loytynoja, Nick Goldman
  • The evolutionary ecology of metacommunities.
    Trends in ecology & evolution (Personal edition), Vol. 23, No. 6. (June 2008), pp. 311-317.
  • Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes
    PLoS Biology, Vol. 5, No. 3. (1 March 2007), e82.
    by Jonathan A Eisen
  • Deciphering the evolution and metabolism of an anammox bacterium from a community genome
    Nature, Vol. 440, No. 7085., pp. 790-794.
    by Marc Strous, Eric Pelletier, Sophie Mangenot, Thomas Rattei, Angelika Lehner, Michael W Taylor, Matthias Horn, Holger Daims, Delphine Bartol-Mavel, Patrick Wincker, Valã©rie Barbe, Nuria Fonknechten, David Vallenet, Bã©atrice Segurens, Chantal Schenowitz-Truong, Claudine Mã©digue, Astrid Collingro, Berend Snel, Bas E Dutilh, Huub, Chris van der Drift, Irina Cirpus, Katinka T van de Pas-Schoonen, Harry R Harhangi, Laura van Niftrik, Markus Schmid, Jan Keltjens, Jack van de Vossenberg, Boran Kartal, Harald Meier, Dmitrij Frishman, Martijn A Huynen, Hans-Werner Mewes, Jean Weissenbach, Mike SM Jetten, Michael Wagner, Denis Le Paslier
  • Toward a census of bacteria in soil.
    PLoS Comput Biol, Vol. 2, No. 7. (21 July 2006)
  • Spatial scaling of functional gene diversity across various microbial taxa
    Proceedings of the National Academy of Sciences, Vol. 105, No. 22. (3 June 2008), pp. 7768-7773.
    by Jizhong Zhou, Sanghoon Kang, Christopher W Schadt, Charles T Garten
  • Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
    Nature, Vol. 450, No. 7169., pp. 560-565.
    by Falk Warnecke, Peter Luginbühl, Natalia Ivanova, Majid Ghassemian, Toby H Richardson, Justin T Stege, Michelle Cayouette, Alice C Mchardy, Gordana Djordjevic, Nahla Aboushadi, Rotem Sorek, Susannah G Tringe, Mircea Podar, Hector G Martin, Victor Kunin, Daniel Dalevi, Julita Madejska, Edward Kirton, Darren Platt, Ernest Szeto, Asaf Salamov, Kerrie Barry, Natalia Mikhailova, Nikos C Kyrpides, Eric G Matson, Elizabeth A Ottesen, Xinning Zhang, Myriam Hernández, Catalina Murillo, Luis G Acosta, Isidore Rigoutsos, Giselle Tamayo, Brian D Green, Cathy Chang, Edward M Rubin, Eric J Mathur, Dan E Robertson, Philip Hugenholtz, Jared R Leadbetter
  • Metagenomics: application of genomics to uncultured microorganisms.
    Microbiol Mol Biol Rev, Vol. 68, No. 4. (December 2004), pp. 669-685.
  • The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity.
    The ISME journal (8 May 2008)
    by Stephen J J Bent, Larry J J Forney
  • Genomic Islands and the Ecology and Evolution of Prochlorococcus
    Science, Vol. 311, No. 5768. (24 March 2006), pp. 1768-1770.
    by Maureen L Coleman, Matthew B Sullivan, Adam C Martiny, Claudia Steglich, Kerrie Barry, Edward F Delong, Sallie W Chisholm
  • Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments
    Environmental Microbiology, Vol. 10, No. 4. (April 2008), pp. 1039-1056.
    posted to gos ocean ploscb08 by jlgreen on 2008-07-25 23:34:52 as ** along with 2 groups Green Lab iSEEM
  • Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
    Nat Methods (29 April 2007)
    by Konstantinos Mavromatis, Natalia Ivanova, Kerrie Barry, Harris Shapiro, Eugene Goltsman, Alice C C McHardy, Isidore Rigoutsos, Asaf Salamov, Frank Korzeniewski, Miriam Land, Alla Lapidus, Igor Grigoriev, Paul Richardson, Philip Hugenholtz, Nikos C C Kyrpides
  • Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton
    Science, Vol. 320, No. 5879. (23 May 2008), pp. 1081-1085.
    by Dana E Hunt, Lawrence A David, Dirk Gevers, Sarah P Preheim, Eric J Alm, Martin F Polz
  • Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments
    Science, Vol. 315, No. 5815. (23 February 2007), pp. 1126-1130.
    by C von Mering, P Hugenholtz, J Raes, SG Tringe, T Doerks, LJ Jensen, N Ward, P Bork
  • Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data
    Biology Direct, Vol. 2 (07 November 2007), 27.
    by Larry J Wilhelm, James H Tripp, Scott A Givan, Daniel P Smith, Stephen J Giovannoni
  • Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?
    ISME J, Vol. 2, No. 6. (0000), pp. 579-589.
    by John H Paul
    posted to genomics phage ploscb08 by jlgreen on 2008-08-04 17:17:29 as ** along with 2 groups Green Lab iSEEM
  • Accurate phylogenetic classification of variable-length DNA fragments
    Nature Methods, Vol. 4, No. 1. (10 December 2006), pp. 63-72.
    by Alice C Mchardy, Héctor G Martín, Aristotelis Tsirigos, Philip Hugenholtz, Isidore Rigoutsos
  • Community genomics in microbial ecology and evolution
    Nature Reviews Microbiology, Vol. 3, No. 6. (01 June 2005), pp. 489-498.
    by Eric E Allen, Jillian F Banfield
  • Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness.
    Applied and environmental microbiology, Vol. 71, No. 3. (March 2005), pp. 1501-1506.
    posted to ploscb08 otu method diversity by djkt to the group iSEEM on 2008-07-24 18:21:56 as read along with 3 people melissa_wos mcox sconlan
  • Phylogenetic Approaches for Describing and Comparing the Diversity of Microbial Communities
    Appl. Environ. Microbiol., Vol. 68, No. 8. (1 August 2002), pp. 3673-3682.
    by Andrew P Martin
  • Binning sequences using very sparse labels within a metagenome
    BMC Bioinformatics, Vol. 9 (28 April 2008), 215.
    by Chon-Kit K Chan, Arthur L Hsu, Saman K Halgamuge, Sen-Lin Tang
  • A taxa-area relationship for bacteria
    Nature, Vol. 432, No. 7018. (09 December 2004), pp. 750-753.
    by Claire C Horner-Devine, Melissa Lage, Jennifer B Hughes, Brendan JM Bohannan
    posted to biogeography method ploscb08 by djkt to the group iSEEM on 2008-07-24 19:01:07 as read along with 1 person mcox
  • From the Cover: Microbial community gene expression in ocean surface waters
    Proceedings of the National Academy of Sciences, Vol. 105, No. 10. (11 March 2008), pp. 3805-3810.
    by Jorge Frias-Lopez, Yanmei Shi, Gene W Tyson, Maureen L Coleman, Stephan C Schuster, Sallie W Chisholm, Edward F Delong
  • The marine viromes of four oceanic regions.
    PLoS Biol, Vol. 4, No. 11. (November 2006)
    by FE Angly, B Felts, M Breitbart, P Salamon, RA Edwards, C Carlson, AM Chan, M Haynes, S Kelley, H Liu, JM Mahaffy, JE Mueller, J Nulton, R Olson, R Parsons, S Rayhawk, CA Suttle, F Rohwer
    posted to distance diversity empirical method ploscb08 virus by djkt to the group iSEEM on 2008-07-24 18:47:14 as *** along with 4 people balicea bluto xingxu jlgreen
  • Evaluating different approaches that test whether microbial communities have the same structure.
    The ISME journal, Vol. 2, No. 3. (March 2008), pp. 265-275.
    by PD Schloss
    posted to diversity ploscb08 review by djkt to the group iSEEM on 2008-07-24 18:50:14 as *** along with 2 people skembel sconlan
  • Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation
    PLoS Biology, Vol. 6, No. 7. (1 July 2008), e177.
    by Sheri L Simmons, Genevieve Dibartolo, Vincent J Denef, Daniela S Goltsman, Michael P Thelen, Jillian F Banfield
    posted to empirical metagenomic ploscb08 popgen by djkt to the group iSEEM on 2008-07-24 01:22:37 as ***
  • Taxonomic distribution of large DNA viruses in the sea
    Genome Biology, Vol. 9, No. 7. (2008)
    by Adam Monier, Jean M Claverie, Hiroyuki Ogata
    posted to empirical metagenomic phylogenetics ploscb08 virus by djkt to the group iSEEM on 2008-07-24 01:28:02 as ** along with 1 person neils
  • EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences.
    International journal of systematic and evolutionary microbiology, Vol. 57, No. Pt 10. (October 2007), pp. 2259-2261.
    by J Chun, JH Lee, Y Jung, M Kim, S Kim, BK Kim, YW Lim
    posted to 16s method ploscb08 webtool by djkt to the group iSEEM on 2008-07-24 18:25:58 as read
  • FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries
    BMC Bioinformatics, Vol. 7, No. 1. (2006)
    by Yanan Yu, Mya Breitbart, Pat Mcnairnie, Forest Rohwer
    posted to 16s method ploscb08 webtool by djkt to the group iSEEM on 2008-07-24 23:08:05 as read
  • Trends in Selenium Utilization in Marine Microbial World Revealed through the Analysis of the Global Ocean Sampling (GOS) Project
    PLoS Genet, Vol. 4, No. 6. (13 June 2008), e1000095.
    by Yan Zhang, Vadim N Gladyshev
    posted to biogeography gos metagenomic ploscb08 by djkt to the group iSEEM on 2008-07-24 01:32:28 as read along with 1 person xingxu
  • What is the extent of prokaryotic diversity?
    Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1475. (29 November 2006), pp. 2023-2037.
    by TP Curtis, IM Head, M Lunn, S Woodcock, PD Schloss, WT Sloan
  • Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples.
    Applied and environmental microbiology, Vol. 67, No. 9. (September 2001), pp. 4374-4376.
    by DR Singleton, MA Furlong, SL Rathbun, WB Whitman
    posted to 16s diversity ecology method ploscb08 by djkt to the group iSEEM on 2008-07-24 18:41:42 as read along with 1 person mcox
  • Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions
    ISME J, Vol. 2, No. 8. (May 2008), pp. 865-886.
    by Ana-Belen Martin-Cuadrado, Francisco Rodriguez-Valera, David Moreira, Jose C Alba, Elena Ivars-Martinez, Matthew R Henn, Emmanuel Talla, Purificacion Lopez-Garcia
    posted to diversity metagenomic ploscb08 by jlgreen to the group iSEEM on 2008-08-08 01:16:06 as ** along with 1 person and 1 group djkt Green Lab
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