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Group: iSEEM - with tag ploscb08 [73 articles]

Neue Artikel von Mitliedern der Gruppe iSEEM Gruppe with tag ploscb08
  • notes The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.
    PLoS ONE, Vol. 3, No. 1. (2008)
    by SJ Williamson, DB Rusch, S Yooseph, AL Halpern, KB Heidelberg, JI Glass, C Andrews-Pfannkoch, D Fadrosh, CS Miller, G Sutton, M Frazier, JC Venter
    posted to empirical metagenomics ploscb08 virus by jlgreen to the group iSEEM on 2008-08-18 19:04:16 as ** along with 2 people and 2 groups jdelcampo mjetten Microbial-Ecology microbiology_nijmegen
  • 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
    posted to binning metagenomic ploscb08 by jlgreen to the group iSEEM on 2008-08-15 04:37:39 as ** along with 4 people and 1 group alexl mjetten werwiesel djkt microbiology_nijmegen
  • Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
    Genome Research
    by Shannon
    posted to diversity networks ploscb08 by jlgreen to the group iSEEM on 2008-08-12 20:19:42 as **
  • Toward a census of bacteria in soil.
    PLoS Comput Biol, Vol. 2, No. 7. (21 July 2006)
    by PD Schloss, J Handelsman
    posted to 16s diversity estimator ploscb08 by jlgreen to the group iSEEM on 2008-08-08 23:52:21 as ** along with 3 people and 2 groups azazello fornstar mjetten anammox microbiology_nijmegen
  • 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
    posted to diversity method ploscb08 rarefaction review by jlgreen to the group iSEEM on 2008-08-08 23:51:10 as ** along with 2 people mcox Olaf_Ilzins
  • MEGAN analysis of metagenomic data
    Genome Res.
    by Huson
    posted to metagenomic ploscb08 by jlgreen to the group iSEEM on 2008-08-08 07:37:12 as **
  • 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
  • Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment
    PNAS
    by Biddle
    posted to empirical metagenomic ploscb08 pyrosequening whole-genome-amplification by jlgreen to the group iSEEM on 2008-08-07 17:14:09 as read along with 1 person and 1 group djkt Green Lab
  • The rational exploration of microbial diversity
    ISME (2008)
    by Christopher Quince, Thomas P Curtis, William T Sloan
    posted to 16s diversity estimator metagenomic parametric ploscb08 by jlgreen to the group iSEEM on 2008-08-04 20:30:02 as read along with 1 person and 1 group djkt Green Lab
  • AN INCIDENCE-BASED RICHNESS ESTIMATOR FOR QUADRATS SAMPLED WITHOUT REPLACEMENT
    Ecology (2008)
    by Tsung-Jen Shen, Fangliang He
    posted to diversity estimator ploscb08 by jlgreen to the group iSEEM on 2008-08-04 19:38:58 as read along with 1 group Green Lab
  • 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 to the group iSEEM on 2008-08-04 17:18:34 as read along with 1 group Green Lab
  • 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
    posted to phylogenetics alignment ploscb08 sequence by jlgreen to the group iSEEM on 2008-07-27 23:19:57 as read along with 22 people and 2 groups marti bpcusack chad_davis hpaces dinnes gjuggler djkt ArtemPankin phoenixzxl jago marck imtechnology aprasad zwang bmaust bpb michaelbarton Schmidtc AbnerCYH gulsacan emptyhb nuin Khavkin's lab Green Lab
  • 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
    posted to clone diversity fingerprinting pcr ploscb08 review by jlgreen to the group iSEEM on 2008-07-26 00:50:56 as read along with 4 people and 3 groups vaulot jdelcampo djkt skembel Papers recommended by the Roscoff Plankton Group Microbial-Ecology Green Lab
  • Microbiology in the post-genomic era
    Nature Reviews Microbiology, Vol. 6, No. 6. (13 May 2008), pp. 419-430.
    by Duccio Medini, Davide Serruto, Julian Parkhill, David A Relman, Claudio Donati, Richard Moxon, Stanley Falkow, Rino Rappuoli
    posted to metagenomic pangenome ploscb08 review by jlgreen to the group iSEEM on 2008-07-26 00:43:25 as read along with 2 people and 1 group jyuh Huub_odc Green Lab
  • 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
    posted to metagenomic metatranscriptomics ocean ploscb08 by jlgreen to the group iSEEM on 2008-07-25 23:53:06 as read along with 4 people and 2 groups mcox tmmurali vaulot mjetten microbiology_nijmegen Green Lab
  • Metagenomics: DNA sequencing of environmental samples
    Nature Reviews Genetics, Vol. 6, No. 11. (01 November 2005), pp. 805-814.
    by Susannah G Tringe, Edward M Rubin
    posted to metagenomic ploscb08 review by jlgreen to the group iSEEM on 2008-07-25 23:40:45 as read along with 2 people and 1 group carpi mcox Green Lab
  • 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.
    by Jiao, Nianzhi, Zhang, Yao, Zeng, Yonghui, Hong, Ning, Liu, Rulong, Chen, Feng, Wang, Pinxian
    posted to ocean ploscb08 by jlgreen to the group iSEEM on 2008-07-25 23:38:10 as ** along with 1 group Green Lab
  • 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.
    by Yutin, Natalya, Suzuki, T Marcelino, Teeling, Hanno, Weber, Marc, Venter, J Craig, Rusch, B Douglas, Beja, Oded
    posted to biogeography gos metagenomic ploscb08 by jlgreen to the group iSEEM on 2008-07-25 23:36:32 as ** along with 2 people and 1 group jmeppley vrich Green Lab
  • Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments
    Environmental Microbiology, Vol. 10, No. 4. (April 2008), pp. 1039-1056.
    by Sharma, K Adrian, Zhaxybayeva, Olga, Papke, R Thane, Doolittle, W Ford
    posted to diversity gos ocean phylogenetics ploscb08 rhodopsin by jlgreen to the group iSEEM on 2008-07-25 23:34:52 as read along with 1 group Green Lab
  • 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
    posted to metagenomic ocean ploscb08 virus by jlgreen to the group iSEEM on 2008-07-25 23:32:18 as ** along with 3 people and 3 groups dayjm dchughes wxg119 G4ID Genetics-of-Gambling Green Lab
  • 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
    posted to phylogenetics ploscb08 by jlgreen to the group iSEEM on 2008-07-25 23:31:12 as ** along with 12 people and 6 groups ana nickluscombe michC bluto agg19954 TaqSys azazello Thaverkamp larsjuhljensen rvgomes mjetten djkt structural_bioinformatics Bioinformatics EBI-regulation Microbial-Ecology microbiology_nijmegen Green Lab
  • 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
    posted to methods ploscb08 phylogenetics by jlgreen to the group iSEEM on 2008-07-25 23:29:06 as ** along with 4 people and 2 groups bluto azazello wenhan djkt MBLAB Green Lab
  • 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
    posted to assembly binning metagenomic methods ploscb08 simulation by jlgreen to the group iSEEM on 2008-07-25 23:27:12 as ** along with 10 people and 4 groups Yanno oamg jmeppley bluto azazello GustavoLacerda carlk alexl mjetten djkt Glimcher_Lab Bioinformatics microbiology_nijmegen Green Lab
  • Genomic patterns of recombination, clonal divergence and environment in marine microbial populations
    by Konstantinos T Konstantinidis, Edward F Delong
    posted to ocean ploscb08 popgen by jlgreen to the group iSEEM on 2008-07-25 23:14:11 as ** along with 1 person and 1 group djkt Green Lab
  • 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
    posted to metagenomic ocean ploscb08 by jlgreen to the group iSEEM on 2008-07-25 23:06:56 as ** along with 1 person and 1 group jmeppley Green Lab
  • 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
    posted to diversity egts metagenomic ploscb08 by jlgreen to the group iSEEM on 2008-07-25 22:59:38 as ** along with 11 people and 3 groups jmeppley AaronDarling azazello wenhan sgoetz bluto vrich sanchezbuelna mcox mjetten djkt anammox microbiology_nijmegen Green Lab
  • 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
    posted to diversity empirical metagenomic ocean ploscb08 traits by jlgreen to the group iSEEM on 2008-07-25 22:57:43 as ** along with 11 people and 3 groups eoghanharr dayjm jmeppley michC bluto jdelcampo beatrizfernandez mjetten mcox vrich djkt Microbial-Ecology microbiology_nijmegen Green Lab
  • Spatial scaling of microbial biodiversity
    Trends in Ecology & Evolution, Vol. 21, No. 9. (September 2006), pp. 501-507.
    by Jessica Green, Brendan J Bohannan
    posted to biogeography diversity ploscb08 review by jlgreen to the group iSEEM on 2008-07-25 22:45:27 as ** along with 5 people and 2 groups jmeppley cmm mcox vrich djkt FAB-lab Green Lab
  • 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
    posted to arisa biogeography diversity ocean ploscb08 by jlgreen to the group iSEEM on 2008-07-25 22:42:18 as ** along with 3 people and 3 groups skato_toyaku vaulot djkt Green Lab Microbial-Ecology Papers recommended by the Roscoff Plankton Group
  • 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
    posted to biogeography diversity metagenomic ploscb08 by jlgreen to the group iSEEM on 2008-07-25 22:40:27 as ** along with 2 people and 1 group dayjm djkt Green Lab
  • The power of species sorting: Local factors drive bacterial community composition over a wide range of spatial scales
    Proceedings of the National Academy of Sciences
    by Katleen, Karl Cottenie‡, Koenraad Muylaert§, Nele Vloemans*, Erik Jeppesen‖, Jose-Maria Conde-Porcuna**, Klaus Schwenk††, Gabriel Zwart‡‡, 11, 12, 13
    posted to biogeography diversity ploscb08 by jlgreen to the group iSEEM on 2008-07-25 22:35:01 as ** along with 1 group Green Lab
  • 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
    posted to biogeography diversity microarray ploscb08 by jlgreen to the group iSEEM on 2008-07-25 22:15:23 as ** along with 1 person and 1 group skato_toyaku Green Lab
  • The Human Microbiome Project
    Nature, Vol. 449, pp. 804-810.
    by Peter J Turnbaugh, Ruth E Ley, Micah Hamady, Claire M Fraser-Liggett, Rob Knight, Jeffrey I Gordon
    posted to assembly biogeography diversity microbiome ploscb08 review by jlgreen to the group iSEEM on 2008-07-25 21:05:09 as read along with 1 person and 1 group djkt Green Lab
  • Multivariate analyses in microbial ecology
    Vol. 62 (2007), pp. 142-160.
    by Alban Ramette
    posted to ploscb08 statistics by jlgreen to the group iSEEM on 2008-07-25 18:51:52 as ** along with 1 person and 1 group djkt Green Lab
  • Inference of population genetic parameters in metagenomics: A clean look at messy data
    Genome Res., Vol. 16, No. 10. (1 October 2006), pp. 1320-1327.
    by Philip L Johnson, Montgomery Slatkin
    posted to metagenomic ploscb08 popgen by djkt to the group iSEEM on 2008-07-24 23:14:44 as read along with 2 people jmeppley bluto
  • 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
  • Spatial scaling of microbial eukaryote diversity
    Nature, Vol. 432, No. 7018. (09 December 2004), pp. 747-750.
    by Jessica L Green, Andrew J Holmes, Mark Westoby, Ian Oliver, David Briscoe, Mark Dangerfield, Michael Gillings, Andrew J Beattie
    posted to biogeography empirical method ploscb08 by djkt to the group iSEEM on 2008-07-24 19:04:48 as read
  • The diversity and biogeography of soil bacterial communities.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 3. (17 January 2006), pp. 626-631.
    by N Fierer, RB Jackson
    posted to biogeography empirical method ploscb08 by djkt to the group iSEEM on 2008-07-24 19:03:48 as read
  • Larger Islands House More Bacterial Taxa
    Science, Vol. 308, No. 5730. (24 June 2005), 1884.
    by Thomas Bell, Duane Ager, Ji-Inn Song, Jonathan A Newman, Ian P Thompson, Andrew K Lilley, Christopher J van der Gast
    posted to biogeography empirical method ploscb08 by djkt to the group iSEEM on 2008-07-24 19:02:53 as read
  • 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
  • The application of rarefaction techniques to molecular inventories of microbial diversity.
    Methods Enzymol, Vol. 397 (2005), pp. 292-308.
    by JB Hughes, JJ Hellmann
    posted to diversity method ploscb08 by djkt to the group iSEEM on 2008-07-24 19:00:05 as read along with 1 person rabu
  • Quantitative and Qualitative beta Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities
    Appl. Environ. Microbiol., Vol. 73, No. 5. (1 March 2007), pp. 1576-1585.
    by Catherine A Lozupone, Micah Hamady, Scott T Kelley, Rob Knight
    posted to diversity method ploscb08 by djkt to the group iSEEM on 2008-07-24 18:59:15 as read along with 1 person Olaf_Ilzins
  • Global patterns in bacterial diversity
    by Catherine A Lozupone, Rob Knight
    posted to diversity ploscb08 review by djkt to the group iSEEM on 2008-07-24 18:58:06 as read
  • 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
    posted to diversity ploscb08 review by djkt to the group iSEEM on 2008-07-24 18:56:17 as read along with 1 person and 1 group kinestetika microbiology_nijmegen
  • Bioinformatics for whole-genome shotgun sequencing of microbial communities.
    PLoS Comput Biol, Vol. 1, No. 2. (July 2005)
    by K Chen, L Pachter
    posted to metagenomic ploscb08 review by djkt to the group iSEEM on 2008-07-24 18:53:51 as *** along with 7 people and 2 groups knaseanka ana jmeppley dullhunk bluto wenhan druvus structural_bioinformatics Bioinformatics
  • 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 1 person sconlan
  • An application of statistics to comparative metagenomics.
    BMC Bioinformatics, Vol. 7, No. 1. (20 March 2006)
    by Beltran Rodriguez-Brito, Forest Rohwer, Robert Edwards
    posted to distance diversity metabolic metagenomic method ploscb08 by djkt to the group iSEEM on 2008-07-24 18:48:40 as *** along with 4 people knaseanka bluto jmeppley carpi
  • 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
  • UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context
    BMC Bioinformatics, Vol. 7 (07 August 2006), 371.
    by Catherine Lozupone, Micah Hamady, Rob Knight
    posted to diversity method phylogenetics ploscb08 by djkt to the group iSEEM on 2008-07-24 18:45:57 as read along with 1 person mcox
  • 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
    posted to diversity method phylogenetics ploscb08 by djkt to the group iSEEM on 2008-07-24 18:45:14 as read along with 4 people and 1 group jmeppley Thaverkamp mcox Olaf_Ilzins Microbial-Ecology
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