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Group: iSEEM - library [167 articles]

Recent papers posted by members of the iSEEM group
  • Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth
    Science, Vol. 322, No. 5899. (10 October 2008), pp. 275-278.
    by Dylan Chivian, Eoin L Brodie, Eric J Alm, David E Culley, Paramvir S Dehal, Todd Z Desantis, Thomas M Gihring, Alla Lapidus, Li-Hung Lin, Stephen R Lowry, Duane P Moser, Paul M Richardson, Gordon Southam, Greg Wanger, Lisa M Pratt, Gary L Andersen, Terry C Hazen, Fred J Brockman, Adam P Arkin, Tullis C Onstott
    posted to microbe metagenomic by djkt to the group iSEEM on 2008-10-10 18:11:34 as ** along with 4 people and 1 group Katje dinnes neils kinestetika microbiology_nijmegen
  • Functional metagenomic profiling of nine biomes
    Nature, Vol. 455, No. 7214. (October 2008), pp. 830-830.
    by Elizabeth A Dinsdale, Robert A Edwards, Dana Hall, Florent Angly, Mya Breitbart, Jennifer M Brulc, Mike Furlan, Christelle Desnues, Matthew Haynes, Linlin Li, Lauren Mcdaniel, Mary A Moran, Karen E Nelson, Christina Nilsson, Robert Olson, John Paul, Beltran R Brito, Yijun Ruan, Brandon K Swan, Rick Stevens, David L Valentine, Rebecca V Thurber, Linda Wegley, Bryan A White, Forest Rohwer
    posted to metagenomic empirical by djkt to the group iSEEM on 2008-10-08 20:45:02 as **
  • Site-Specific Evolutionary Rates in Proteins Are Better Modeled as Non-Independent and Strictly Relative
    Bioinformatics (28 July 2008), btn395.
    by Andrew D Fernandes, William R Atchley
    posted to protein evolution by djkt to the group iSEEM on 2008-09-29 18:04:02 as *** along with 1 person sunhwan
  • Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000186.
    by Steven L Salzberg, Daniel D Sommer, Daniela Puiu, Vincent T Lee
    posted to sequencing microbes by djkt to the group iSEEM on 2008-09-26 18:51:36 as ** along with 5 people and 3 groups druvus vaulot Katje stajich semrich Papers recommended by the Roscoff Plankton Group microbiology_nijmegen Berkeley Mycology
  • Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics
    Environmental Microbiology, Vol. 10, No. 3. (March 2008), pp. 727-737.
    by Robidart, C Julie, Bench, R Shellie, Feldman, A Robert, Novoradovsky, Alexey, Podell, B Sheila, Gaasterland, Terry, Allen, E Eric, Felbeck, Horst
    posted to symbiosis metagenomic by djkt to the group iSEEM on 2008-09-17 19:12:03 as **
  • Microbial ecology of four coral atolls in the Northern Line Islands.
    PLoS ONE, Vol. 3, No. 2. (2008)
    by EA Dinsdale, O Pantos, S Smriga, RA Edwards, F Angly, L Wegley, M Hatay, D Hall, E Brown, M Haynes, L Krause, E Sala, SA Sandin, RV Thurber, BL Willis, F Azam, N Knowlton, F Rohwer
    posted to ocean environmental empirical ecology by djkt to the group iSEEM on 2008-09-17 19:10:36 as ** along with 1 person bluto
  • Bacterial carbon processing by generalist species in the coastal ocean
    Nature (27 January 2008)
    by Xiaozhen Mou, Shulei Sun, Robert A Edwards, Robert E Hodson, Mary A Moran
    posted to ocean environmental empirical ecology by djkt to the group iSEEM on 2008-09-17 19:08:06 as ** along with 3 people and 1 group cmzmasek mjetten vrich microbiology_nijmegen
  • Quantitative assessment of protein function prediction from metagenomics shotgun sequences
    Proceedings of the National Academy of Sciences, Vol. 104, No. 35. (28 August 2007), pp. 13913-13918.
    by ED Harrington, AH Singh, T Doerks, I Letunic, C von Mering, LJ Jensen, J Raes, P Bork
    posted to protein metagenomic functional by djkt to the group iSEEM on 2008-09-17 19:05:23 as ** along with 3 people michC bluto larsjuhljensen
  • MEGAN analysis of metagenomic data
    Genome Research, Vol. 17, No. 3., 377.
    by Huson
    posted to phylogenetics otu diversity by djkt to the group iSEEM on 2008-09-17 19:00:57 as **
  • CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads
    ArXiv e-prints, Vol. 708 (August 2007)
    by S Chatterji, I Yamazaki, Z Bai, J Eisen
    posted to otu by djkt to the group iSEEM on 2008-09-17 18:57:49 as ** along with 1 person azazello
  • Metagenomics: Read length matters
    Appl. Environ. Microbiol. (11 January 2008), AEM.02181-07.
    by Eric K Wommack, Jaysheel Bhavsar, Jacques Ravel
    posted to sequencing by djkt to the group iSEEM on 2008-09-17 18:54:27 as ** along with 10 people and 3 groups vaulot jmeppley azazello kinestetika Thaverkamp skato_toyaku rvgomes alexisfjdufresne alexl bluto Papers recommended by the Roscoff Plankton Group Microbial-Ecology microbiology_nijmegen
  • Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks
    BMC Bioinformatics, Vol. 7 (06 June 2006), 284.
    by June S Oh, Je-Gun Joung, Jeong-Ho Chang, Byoung-Tak Zhang
    posted to phylogenetic metabolic by djkt to the group iSEEM on 2008-09-17 18:52:21 as **
  • Get the most out of your metagenome: computational analysis of environmental sequence data.
    Current opinion in microbiology, Vol. 10, No. 5. (October 2007), pp. 490-498.
    by J Raes, KU Foerstner, P Bork
    posted to minimess metagenomic by djkt to the group iSEEM on 2008-09-17 18:46:49 as **
  • Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis.
    Journal of clinical microbiology, Vol. 45, No. 1. (January 2007), pp. 39-46.
    by D Alland, DW Lacher, MH Hazbón, AS Motiwala, W Qi, RD Fleischmann, TS Whittam
    posted to simulation by djkt to the group iSEEM on 2008-09-10 22:44:46 as **
  • Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis.
    Journal of bacteriology, Vol. 185, No. 11. (June 2003), pp. 3392-3399.
    by D Alland, TS Whittam, MB Murray, MD Cave, MH Hazbon, K Dix, M Kokoris, A Duesterhoeft, JA Eisen, CM Fraser, RD Fleischmann
    posted to simulation by djkt to the group iSEEM on 2008-09-10 22:44:25 as **
  • Modeling genome evolution with a diffusion approximation of a birth-and-death process.
    Bioinformatics, Vol. 21 Suppl 3 (1 November 2005)
    by GP Karev, FS Berezovskaya, EV Koonin
    posted to simulation by djkt to the group iSEEM on 2008-09-10 22:43:22 as ** along with 1 person knaseanka
  • High bacterivory by the smallest phytoplankton in the North Atlantic Ocean
    Nature (10 August 2008)
    by Mikhail V Zubkov, Glen A Tarran
    posted to protistists ecology bacteria by djkt to the group iSEEM on 2008-09-10 19:27:39 as ** along with 2 people and 2 groups hwright vaulot Papers recommended by the Roscoff Plankton Group Microbial-Ecology
  • Metagenomics reveals our incomplete knowledge of global diversity.
    Bioinformatics (Oxford, England) (13 July 2008)
    by Miguel Pignatelli, Gabriel Aparicio, Ignacio Blanquer, Vicente Hernández, Andrés Moya, Javier Tamames
    posted to metagenomic diversity by djkt to the group iSEEM on 2008-09-05 19:09:34 as read along with 4 people and 2 groups vaulot reyez bootsy nuin Papers recommended by the Roscoff Plankton Group Microbial-Ecology
  • Phylocom: software for the analysis of phylogenetic community structure and trait evolution
    Bioinformatics, Vol. 24, No. 18. (15 September 2008), pp. 2098-2100.
    by Campbell O Webb, David D Ackerly, Steven W Kembel
    posted to no-tag by djkt to the group iSEEM on 2008-09-05 19:04:27 as *** along with 1 person and 1 group skembel phylocom
  • The bacterial species definition in the genomic era.
    Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1475. (29 November 2006), pp. 1929-1940.
    by KT Konstantinidis, A Ramette, JM Tiedje
    posted to genomic_similarity by djkt to the group iSEEM on 2008-09-04 00:51:05 as ** along with 3 people and 2 groups jmeppley kinestetika Thaverkamp Microbial-Ecology microbiology_nijmegen
  • Towards a genome-based taxonomy for prokaryotes.
    J Bacteriol, Vol. 187, No. 18. (September 2005), pp. 6258-6264.
    by KT Konstantinidis, JM Tiedje
    posted to genomic_similarity by djkt to the group iSEEM on 2008-09-04 00:50:30 as ** along with 2 people balajis gelack
  • Genomic insights that advance the species definition for prokaryotes.
    Proc Natl Acad Sci U S A, Vol. 102, No. 7. (15 February 2005), pp. 2567-2572.
    by KT Konstantinidis, JM Tiedje
    posted to genomic_similarity by djkt to the group iSEEM on 2008-09-04 00:17:33 as ** along with 3 people and 1 group jmeppley Thaverkamp rvgomes Microbial-Ecology
  • Significant contribution of Archaea to extant biomass in marine subsurface sediments
    Nature (20 July 2008)
    by Julius S Lipp, Yuki Morono, Fumio Inagaki, Kai-Uwe Hinrichs
    posted to archaea ecology empirical metagenomic microbe ocean by djkt to the group iSEEM on 2008-08-20 20:15:03 as *** along with 1 person neils
  • 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
  • The Airborne Metagenome in an Indoor Urban Environment
    PLoS ONE, Vol. 3, No. 4. (2 April 2008), e1862.
    by Susannah G Tringe, Tao Zhang, Xuguo Liu, Yiting Yu, Wah H Lee, Jennifer Yap, Fei Yao, Sim T Suan, Seah K Ing, Matthew Haynes, Forest Rohwer, Chia L Wei, Patrick Tan, James Bristow, Edward M Rubin, Yijun Ruan
    posted to 16s empirical metagenomic by djkt to the group iSEEM on 2008-08-15 17:55:03 as *** along with 1 person semrich
  • 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
  • A HIERARCHICAL MODEL FOR SPATIAL CAPTURE–RECAPTURE DATA
    by J Royle, K Young
    posted to density sampling by jlgreen to the group iSEEM on 2008-08-14 21:09:30 as ** along with 1 group Green Lab
  • Inferring Evolutionary Process from Phylogenetic Tree Shape
    by Mooers
    posted to phylogenetics sampling by jlgreen to the group iSEEM on 2008-08-14 21:02:54 as ** along with 1 group Green Lab
  • 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 **
  • Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil
    Science, Vol. 309, No. 5739. (26 August 2005), pp. 1387-1390.
    by Jason Gans, Murray Wolinsky, John Dunbar
    posted to diversity empirical kinetics by jlgreen to the group iSEEM on 2008-08-12 07:08:08 as ** along with 4 people knaseanka jmeppley paleorthid djkt
  • 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
  • Spatial and Temporal Patterns in the Microbial Diversity of a Meromictic Soda Lake in Washington State
    Appl. Environ. Microbiol., Vol. 74, No. 15. (1 August 2008), pp. 4877-4888.
    by Pedro A Dimitriu, Holly C Pinkart, Brent M Peyton, Melanie R Mormile
    posted to dgge diversity by jlgreen to the group iSEEM on 2008-08-07 22:53:55 as ** along with 1 group 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
  • Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques
    Nature Reviews Microbiology, Vol. 6, No. 5., pp. 339-348.
    by Rudolf Amann, Bernhard M Fuchs
    posted to 16s abundance diversity fish review by jlgreen to the group iSEEM on 2008-08-05 23:33:12 as read along with 4 people and 4 groups Katje vrich vaulot Huub_odc microbiology_nijmegen Microbial-Ecology Papers recommended by the Roscoff Plankton Group 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
  • Beta Diversity in Spatially Implicit Neutral Models: A New Way to Assess Species Migration
    American Naturalist (2008)
    by François Munoz, Pierre Couteron, BR Ramesh1
    posted to beta diversity neutral by jlgreen to the group iSEEM on 2008-08-04 20:20:06 as ** along with 1 group Green Lab
  • Species Synchrony and Its Drivers: Neutral and Nonneutral Community Dynamics in Fluctuating Environments
    American Naturalist (2008)
    by Michel Loreau, Claire de Mazancourt
    posted to assembly community neutral by jlgreen to the group iSEEM on 2008-08-04 20:15:48 as ** along with 1 group Green Lab
  • Disentangling interactions between adaptive divergence and gene flow when ecology drives diversification
    Ecology Letters, Vol. 0, No. 0. (0), pp. ???-???.
    by Katja Rasanen, Andrew P Hendry
    posted to adaptation dispersal divergence evolution by jlgreen to the group iSEEM on 2008-08-04 20:09:12 as ** along with 1 person and 1 group cellison Green Lab
  • Ecological consequences of genetic diversity
    Ecology Letters, Vol. 11, No. 6. (June 2008), pp. 609-623.
    by Hughes, A Randall, Inouye, D Brian, Johnson, TJ Marc, Underwood, Nora, Vellend, Mark
    posted to diversity genetic by jlgreen to the group iSEEM on 2008-08-04 20:06:45 as ** along with 1 group Green Lab
  • Less lineages more trait variation: phylogenetically clustered plant communities are functionally more diverse
    Ecology Letters, Vol. 11, No. 8. (August 2008), pp. 809-819.
    by Prinzing, Andreas, Reiffers, Reineke, Braakhekke, G Wim, Hennekens, M Stephan, Tackenberg, Oliver, Ozinga, A Wim, Schaminee, HJ Joop, Van Groenendael, M Jan
    posted to assembly community diversity functional phylogenetics by jlgreen to the group iSEEM on 2008-08-04 20:03:09 as read along with 1 group Green Lab
  • CONSEQUENCES OF DOMINANCE: A REVIEW OF EVENNESS EFFECTS ON LOCAL AND REGIONAL ECOSYSTEM PROCESSES
    Ecology (2008)
    by Helmut Hillebrand, Danuta M Bennett, Marc W Cadotte
    posted to diversity ecology by jlgreen to the group iSEEM on 2008-08-04 19:59:15 as ** along with 1 group Green Lab
  • The evolutionary ecology of metacommunities.
    Trends in ecology & evolution (Personal edition), Vol. 23, No. 6. (June 2008), pp. 311-317.
    by MC Urban, MA Leibold, P Amarasekare, L De Meester, R Gomulkiewicz, ME Hochberg, CA Klausmeier, N Loeuille, C de Mazancourt, J Norberg, JH Pantel, SY Strauss, M Vellend, MJ Wade
    posted to assembly community metacommunity review by jlgreen to the group iSEEM on 2008-08-04 19:54:56 as read along with 2 people and 1 group skumagai 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
  • COMMUNITY ASSEMBLY IN THE PRESENCE OF DISTURBANCE: A MICROCOSM EXPERIMENT
    Ecology (2008)
    by Shivani N Patel
    posted to assembly community by jlgreen to the group iSEEM on 2008-08-04 19:36:57 as ** along with 1 group Green Lab
  • ON THE RELATIONSHIP BETWEEN REGIONAL AND LOCAL SPECIES RICHNESS: A TEST OF SATURATION THEORY
    Ecology (2008)
    by Brian M Starzomski1, Raenelle L Parker, Diane S Srivastava
    posted to diversity by jlgreen to the group iSEEM on 2008-08-04 19:35:14 as ** 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
  • 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 by jlgreen to the group iSEEM on 2008-08-04 17:17:30 as ** along with 1 group Green Lab
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