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Group: iSEEM - library [205 articles]

Neue Artikel von Mitliedern der Gruppe iSEEM Gruppe
  • Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities
    Annual Review of Microbiology, Vol. 62, No. 1. (2008), pp. 375-401.
    by Ainslie EF Little, Courtney J Robinson, Brook S Peterson, Kenneth F Raffa, Jo Handelsman
    posted to review evolution ecology community biogeography by jladau to the group iSEEM on 2008-11-19 20:22:59 as read along with 1 person skembel
  • A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
    Nucl. Acids Res. (5 August 2008), gkn496.
    by Chaysavanh Manichanh, Charles E Chapple, Lionel Frangeul, Karine Gloux, Roderic Guigo, Joel Dore
    posted to methods metagenomics diversity by skembel to the group iSEEM on 2008-11-19 19:17:16 as ** along with 1 person druvus
  • Microbial biogeography: putting microorganisms on the map
    Nature Reviews Microbiology, Vol. 4, No. 2., pp. 102-112.
    by Jennifer, Brendan JM Bohannan, James H Brown, Robert K Colwell, Jed A Fuhrman, Jessica L Green, Claire M Horner-Devine, Matthew Kane, Jennifer A Krumins, Cheryl R Kuske, Peter J Morin, Shahid Naeem, Lise Øvreås, Anna-Louise Reysenbach, Val H Smith, James T Staley
    posted to biogeography by jlgreen to the group iSEEM on 2008-11-19 18:26:33 as ** along with 2 people cajita kwinset
  • Weights for data related by a tree.
    J. Mol. Biol., Vol. 207, No. 4. (20 June 1989), pp. 647-653.
    by SF Altschul, RJ Carroll, DJ Lipman
    posted to no-tag by souravc to the group iSEEM on 2008-11-19 00:03:43 as ** along with 2 people nuke2005 newton1234
  • The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing
    PLoS Biology, Vol. 6, No. 11. (1 November 2008), e280.
    by Les Dethlefsen, Sue Huse, Mitchell L Sogin, David A Relman
    posted to microbes metagenomics human 16s by djkt to the group iSEEM on 2008-11-18 23:47:20 as **
  • Measurement of biological information with applications from genes to landscapes
    Molecular Ecology, Vol. 15, No. 10. (September 2006), pp. 2857-2869.
    by William B Sherwin, Franck Jabot, Rebecca Rush, Maurizio Rossetto
    posted to entropy diversity by skembel to the group iSEEM on 2008-11-18 23:05:40 as **
  • Diversity and dissimilarity coefficients: A unified approach
    Theoretical Population Biology, Vol. 21, No. 1. (February 1982), pp. 24-43.
    by C Rao
    posted to phylodiversity functionaldiversity entropy diversity by skembel to the group iSEEM on 2008-11-18 20:48:54 as **
  • Bridging the gap between ecological diversity indices and measures of biodiversity with Shannon's entropy: comment to Izsák and Papp
    Ecological Modelling, Vol. 152, No. 1. (15 June 2002), pp. 1-3.
    by C Ricotta
    posted to phylodiversity entropy diversity by skembel to the group iSEEM on 2008-11-18 20:48:08 as **
  • Alignment networks and electrical networks
    Discrete Appl. Math., Vol. 71, No. 1-3. (1996), pp. 297-309.
    by Martin Vingron, Michael S Waterman
    posted to no-tag by souravc to the group iSEEM on 2008-11-18 19:55:59 as read
  • http://www.citeulike.org/user/souravc/article/3575691
    American Naturalist, Vol. 125, No. 1. (1985), pp. 1-15.
    by J Felsenstein
    posted to no-tag by souravc to the group iSEEM on 2008-11-18 19:47:57 as read
  • Predicting functional gene links from phylogenetic-statistical analyses of whole genomes.
    PLoS Comput Biol, Vol. 1, No. 1. (June 2005)
    by D Barker, M Pagel
    posted to phylogenetics methods comparativemethods by skembel to the group iSEEM on 2008-11-14 22:35:57 as ** along with 8 people Robinder rw294 balajis maryee arunyan bartleby pradiptaray rvosa
  • Coined quantum walks lift the cospectrality of graphs and trees
    Pattern Recognition (06 November 2008)
    by D Emms, S Severini, R Wilson, E Hancock
    posted to phylogenetics by djkt to the group iSEEM on 2008-11-14 22:03:45 as **
  • The rate and pattern of cladogenesis in microbes.
    Evolution; international journal of organic evolution, Vol. 58, No. 5. (May 2004), pp. 946-955.
    by AP Martin, EK Costello, AF Meyer, DR Nemergut, SK Schmidt
    posted to microbial comparativemethods by skembel to the group iSEEM on 2008-11-14 00:05:11 as **
  • Pattern Classification of Phylogeny Signals
    Statistical Applications in Genetics and Molecular Biology, Vol. 7, No. 1., article 30.
    by Xiaofei, Hong, Chris
    posted to proteins phylogenetics clustering by djkt to the group iSEEM on 2008-11-12 00:15:26 as **
  • Global patterns in bacterial diversity
    Proceedings of the National Academy of Sciences, Vol. 104, No. 27. (3 July 2007), pp. 11436-11440.
    by Catherine A Lozupone, Rob Knight
    posted to microbial diversity by skembel to the group iSEEM on 2008-11-10 01:33:42 as **
  • Using pyrosequencing to shed light on deep mine microbial ecology.
    BMC Genomics, Vol. 7 (2006)
    by RA Edwards, B Rodriguez-Brito, L Wegley, M Haynes, M Breitbart, DM Peterson, MO Saar, S Alexander, EC Alexander, F Rohwer
    posted to pyrosequencing metagenomics by skembel to the group iSEEM on 2008-11-10 01:32:03 as ** along with 7 people jmeppley balicea rabu xingxu mcox darioacha werwiesel
  • Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes
    PLoS Comput Biol, Vol. 4, No. 11. (7 November 2008), e1000214.
    by Osnat Penn, Adi Stern, Nimrod D Rubinstein, Julien Dutheil, Eran Bacharach, Nicolas Galtier, Tal Pupko
    posted to hiv evolution acceleration by djkt to the group iSEEM on 2008-11-08 19:06:29 as ** along with 1 person skembel
  • Population Genetic Inference from Resequencing Data
    Genetics (3 November 2008), genetics.107.080630.
    by Rong Jiang, Simon Tavare, Paul Marjoram
    posted to sequencing popgen by djkt to the group iSEEM on 2008-11-08 18:38:29 as ** along with 4 people and 1 group natstreet abizar druvus stajich Berkeley Mycology
  • Probabilistic Phylogenetic Inference with Insertions and Deletions
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000172.
    by Elena Rivas, Sean R Eddy
    posted to phylogenetics indel evolution by djkt to the group iSEEM on 2008-11-06 18:14:53 as ** along with 8 people pradiptaray zwang nuin timflutre druvus aprasad gjuggler emptyhb
  • Profile Comparer (PRC): a program for scoring and aligning profile hidden Markov models.
    Bioinformatics (Oxford, England) (9 October 2008)
    by Martin Madera
    posted to proteins msa hmm alignment by djkt to the group iSEEM on 2008-11-05 16:15:23 as ** along with 2 people j3xucite nuin
  • Phylogenetic distances are encoded in networks of interacting pathways
    Bioinformatics (26 September 2008), btn503.
    by Aurelien Mazurie, Danail Bonchev, Benno Schwikowski, Gregory A Buck
    posted to sysbio phylogenetics evolution by djkt to the group iSEEM on 2008-11-05 16:07:48 as ** along with 4 people behindtherabbit markchen nuin renatomilani
  • MetaMine - A tool to detect and analyse gene patterns in their environmental context
    BMC Bioinformatics, Vol. 9 (28 October 2008), 459.
    by Uta Bohnebeck, Thierry Lombardot, Renzo Kottmann, Frank O Glockner
    posted to proteins metagenomics db by djkt to the group iSEEM on 2008-11-04 03:28:46 as ** along with 3 people and 1 group jyuh stajich druvus Berkeley Mycology
  • Factors affecting the concordance between orthologous gene trees and species tree in bacteria
    BMC Evolutionary Biology, Vol. 8 (30 October 2008), 300.
    by Santiago Castillo-Ramirez, Victor Gonzalez
    posted to proteins phylogenetics by djkt to the group iSEEM on 2008-11-03 19:43:57 as ** along with 1 person nklee
  • Horizontal versus familial transmission of Helicobacter pylori.
    PLoS pathogens, Vol. 4, No. 10. (October 2008)
    by S Schwarz, G Morelli, B Kusecek, A Manica, F Balloux, RJ Owen, DY Graham, S van der Merwe, M Achtman, S Suerbaum
    posted to popgen microbes genographic biogeography by djkt to the group iSEEM on 2008-10-28 18:08:05 as ***
  • Fusion and Fission of Genes Define a Metric between Fungal Genomes
    PLoS Comput Biol, Vol. 4, No. 10. (24 October 2008), e1000200.
    by Pascal Durrens, Macha Nikolski, David Sherman
    posted to yeast proteins phylogenetics duplication by djkt to the group iSEEM on 2008-10-24 19:25:52 as ** along with 2 people and 1 group taguchi stajich Berkeley Mycology
  • Truncated xpt gene present in invasive Streptococcus pneumoniae may have implications for MLST schemes.
    Journal of medical microbiology, Vol. 54, No. Pt 10. (October 2005), pp. 909-912.
    by MA Diggle, SC Clarke
    posted to mlst by djkt to the group iSEEM on 2008-10-23 22:06:37 as **
  • mlstdbNet - distributed multi-locus sequence typing (MLST) databases.
    BMC bioinformatics, Vol. 5 (1 July 2004)
    by KA Jolley, MS Chan, MC Maiden
    posted to otu mlst database by djkt to the group iSEEM on 2008-10-23 22:05:34 as **
  • Nucleotide sequence-based typing of bacteria and the impact of automation.
    BioEssays : news and reviews in molecular, cellular and developmental biology, Vol. 24, No. 9. (September 2002), pp. 858-862.
    by SC Clarke
    posted to otu mlst database by djkt to the group iSEEM on 2008-10-23 22:04:12 as **
  • Database-driven multi locus sequence typing (MLST) of bacterial pathogens.
    Bioinformatics (Oxford, England), Vol. 17, No. 11. (November 2001), pp. 1077-1083.
    by MS Chan, MC Maiden, BG Spratt
    posted to phylogenetics otu mlst database by djkt to the group iSEEM on 2008-10-23 22:02:44 as **
  • Rapid quantitative profiling of complex microbial populations
    Nucleic Acids Research, Vol. 34, No. 1. (2006), pp. e5-e5.
    by Chana Palmer, Elisabeth M Bik, Michael B Eisen, Paul B Eckburg, Theodore R Sana, Paul K Wolber, David A Relman, Patrick O Brown
    posted to microbes metagenomics arrays by djkt to the group iSEEM on 2008-10-23 22:00:29 as **
  • An African origin for the intimate association between humans and Helicobacter pylori
    Nature
    by Bodo Linz, François Balloux, Yoshan Moodley, Andrea Manica, Hua Liu, Philippe Roumagnac, Daniel Falush, Christiana Stamer, Franck Prugnolle, Schalk W van der Merwe, Yoshio Yamaoka, David Y Graham, Emilio Perez-Trallero, Torkel Wadstrom, Sebastian Suerbaum, Mark Achtman
    posted to microbes human genographic biogeography by djkt to the group iSEEM on 2008-10-23 21:50:01 as ** along with 5 people and 1 group jyuh oamg brembs xingxu Xavier Glimcher_Lab
  • Phylogenetic clustering and overdispersion in bacterial communities.
    Ecology, Vol. 87, No. 7 Suppl. (July 2006)
    by MC Horner-Devine, BJ Bohannan
    posted to phylogenetics microbes community by djkt to the group iSEEM on 2008-10-23 00:31:17 as **
  • Innate immunity and intestinal microbiota in the development of Type 1 diabetes
    Nature (21 September 2008)
    by Li Wen, Ruth E Ley, Pavel, Peter B Stranges, Lia Avanesyan, Austin C Stonebraker, Changyun Hu, Susan F Wong, Gregory L Szot, Jeffrey A Bluestone, Jeffrey I Gordon, Alexander V Chervonsky
    posted to microbes immunity human by djkt to the group iSEEM on 2008-10-22 19:53:06 as ** along with 3 people vplagnol Zephyrus jdbowes
  • A simple, fast, and accurate method of phylogenomic inference
    Genome Biology, Vol. 9 (13 October 2008), R151.
    by Martin Wu, Jonathan A Eisen
    posted to proteins phylogenomic phylogenetics microbes by djkt to the group iSEEM on 2008-10-21 21:10:44 as ** along with 7 people and 1 group treangen Katje operon ellakat scryrps aramata druvus microbiology_nijmegen
  • ADZE: a rarefaction approach for counting alleles private to combinations of populations
    Bioinformatics, Vol. 24, No. 21. (1 November 2008), pp. 2498-2504.
    by Zachary A Szpiech, Mattias Jakobsson, Noah A Rosenberg
    posted to rarefaction private_alleles popgen by djkt to the group iSEEM on 2008-10-20 18:17:51 as ** along with 1 person druvus
  • Estimation of Phylogenetic Inconsistencies in the Three Domains of Life
    Mol Biol Evol (12 August 2008), msn176.
    by Victor Soria-Carrasco, Jose Castresana
    posted to phylogenetics microbe by djkt to the group iSEEM on 2008-10-16 18:48:12 as ** along with 1 person alpae
  • Intragenomic Variation of Fungal Ribosomal Genes Is Higher than Previously Thought
    Mol Biol Evol, Vol. 25, No. 11. (1 November 2008), pp. 2251-2254.
    by Uwe K Simon, Michael Weiss
    posted to variation rna ribosome phylogenetics evolution eukaryote by djkt to the group iSEEM on 2008-10-16 18:35:23 as **
  • Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
    Nucl. Acids Res., Vol. 36, No. 18. (1 October 2008), e120.
    by Zongzhi Liu, Todd Z Desantis, Gary L Andersen, Rob Knight
    posted to taxonomy 454 16s by jlgreen to the group iSEEM on 2008-10-16 17:28:20 as ** along with 2 people and 2 groups ojabado vaulot Papers recommended by the Roscoff Plankton Group Microbial-Ecology
  • 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 8 people and 3 groups lflorez skembel claymans vaulot Katje dinnes neils kinestetika Papers recommended by the Roscoff Plankton Group Microbial-Ecology 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 7 people and 3 groups natstreet antonkratz 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 phylogenetics metabolic by djkt to the group iSEEM on 2008-09-17 18:52:21 as **
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