Group: iSEEM - library 396 articles Export

	Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome [My Copy] Appl. Environ. Microbiol., Vol. 75, No. 7. (1 April 2009), pp. 2221-2229. by Erin J. Biers, Shulei Sun, Erinn C. Howard posted to otu metagenomics gos 16s by skembel to the group iSEEM on 2009-11-18 22:17:14 as along with 2 people Thaverkamp EKotlarska
	The effect of sequencing errors on metagenomic gene prediction. [My Copy] BMC genomics, Vol. 10, No. 1. (12 November 2009), 520. by Katharina J. Hoff posted to sequencing metagenomics gene_prediction by skembel to the group iSEEM on 2009-11-18 21:40:20 as along with 2 people and 1 group jsatkosk ppgardne Journal picks
	Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine [My Copy] PLoS ONE, Vol. 4, No. 8. (20 August 2009), e6669. by Marcus J. Claesson, Orla O'Sullivan, Qiong Wang, et al.Janne Nikkilä, Julian R. Marchesi, Hauke Smidt, Willem M. de Vos, R. Paul Ross, Paul W. O'Toole posted to pyrosequencing phylogenetics metagenomics bootstrap by skembel to the group iSEEM on 2009-11-15 18:23:10 as along with 2 people nnnagara neils
	Field theory for biogeography: a spatially explicit model for predicting patterns of biodiversity [My Copy] Ecology Letters, Vol. 9999, No. 9999. (2009) by James P. O'Dwyer, Jessica L. Green posted to theory ecology community by djkt to the group iSEEM on 2009-11-11 17:27:08 as along with 1 person timothee-poisot
	Characterizing the D2 Statistic: Word Matches in Biological Sequences [My Copy] SAGMB, Vol. 8 by Sylvain Forêt, Susan R. Wilson, Conrad J. Burden posted to testing kmer distribution conservation by djkt to the group iSEEM on 2009-11-10 19:56:54 as
	Species–area relationships explained by the joint effects of dispersal limitation and habitat heterogeneity [My Copy] Ecology, Vol. 90, No. 11. (2009), pp. 3033-3041. by Guochun Shen, Mingjian Yu, Xin-Sheng Hu, et al.Xiangcheng Mi, Haibao Ren, I-Fang Sun, Keping Ma posted to ecology community by djkt to the group iSEEM on 2009-11-09 18:42:07 as
	Bacterial Community Variation in Human Body Habitats Across Space and Time [My Copy] Science (5 November 2009), 1177486. by Elizabeth K. Costello, Christian L. Lauber, Micah Hamady, Noah Fierer, Jeffrey I. Gordon, Rob Knight posted to temporal_variability microflora microbiota microbiome human community_composition community_assembly biogeography bacterial_communities by sharpton to the group iSEEM on 2009-11-06 16:32:29 as along with 3 people kostanik74 djkt skembel
	Distributions of Tree Comparison Metrics--Some New Results [My Copy] Syst Biol, Vol. 42, No. 2. (1 June 1993), pp. 126-141. by Mike A. Steel, David Penny posted to phylogenetics methods by skembel to the group iSEEM on 2009-11-04 19:13:37 as
	De novo computational prediction of non-coding RNA genes in prokaryotic genomes [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 2897-2905. by Thao T. Tran, Fengfeng Zhou, Sarah Marshburn, Mark Stead, Sidney R. Kushner, Ying Xu posted to rna microbes annotation by djkt to the group iSEEM on 2009-11-04 17:41:30 as along with 4 people and 1 group TRHvidsten jmcq ppgardne druvus Journal picks
	Statistical methods in spatial genetics [My Copy] Molecular Ecology, Vol. 9999, No. 9999. (2009) by T. Gilles Guillo, S. Raphaël Lebloi, N. Aurélie Coulo, Alain C. Frantz posted to review popgen ecology by djkt to the group iSEEM on 2009-11-04 16:21:33 as
	Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations [My Copy] Genome Biology, Vol. 10, No. 10. (22 October 2009), R118. by Tom Conrad, Andrew Joyce, M. Kenyon Applebee, et al.Christian Barrett, Bin Xie, Yuan Gao, Bernhard Palsson posted to mutation evolution bacteria by djkt to the group iSEEM on 2009-11-03 01:39:46 as along with 5 people Asclepius venancio nzm operon druvus
	Genomic DNA k-mer spectra: models and modalities [My Copy] Genome Biology, Vol. 10, No. 10. (2009), R108. by Benny Chor, David Horn, Yaron Levy, Nick Goldman, Tim Massingham posted to mutation kmer genome cpg by djkt to the group iSEEM on 2009-11-03 01:38:20 as along with 3 people TRHvidsten medic0747 gjuggler
	A Novel Mechanism of Transposon-Mediated Gene Activation [My Copy] PLoS Genet, Vol. 5, No. 10. (16 October 2009), e1000689. by Zhongge Zhang, Milton H. Saier posted to repeats expression by djkt to the group iSEEM on 2009-11-02 19:02:57 as along with 1 person maren
	Windshield splatter analysis with the Galaxy metagenomic pipeline [My Copy] Genome Research, Vol. 19, No. 11. (9 November 2009), pp. 2144-2153. by Sergei Kosakovsky Pond, Samir Wadhawan, Francesca Chiaromonte, et al.Guruprasad Ananda, Wen-Yu Chung, James Taylor, Anton Nekrutenko posted to workflow metagenomics eukaryotes db by djkt to the group iSEEM on 2009-11-02 18:13:32 as along with 8 people and 1 group jmeppley seb1 Katje operon neils idonaldson jgill kshameer microbiology_nijmegen
	Genome-scale approaches to resolving incongruence in molecular phylogenies [My Copy] Nature, Vol. 425, No. 6960. (23 October 2003), pp. 798-804. by Antonis Rokas, Barry L. Williams, Nicole King, Sean B. Carroll posted to phylogenetics incongruence genomes by skembel to the group iSEEM on 2009-10-28 20:32:38 as along with 7 people biomcgary nlapalu druvus knaseanka aprasad AaronDarling srfairclough
	What is microbial community ecology\|[quest]\| [My Copy] The ISME Journal, Vol. 3, No. 11. (06 August 2009), pp. 1223-1230. by Allan Konopka posted to review microbes metagenomics ecology community by djkt to the group iSEEM on 2009-10-22 22:42:13 as along with 2 people pyilmaz skembel
	Characterizing natural variation using next-generation sequencing technologies [My Copy] Trends in Genetics, Vol. 25, No. 10. (02 October 2009), pp. 463-471. by Yoav Gilad, Jonathan K. Pritchard, Kevin Thornton posted to sequencing review popgen by djkt to the group iSEEM on 2009-10-21 18:55:43 as along with 5 people operon jwfoley skembel n00c natstreet
	Different gene regulation strategies revealed by analysis of binding motifs [My Copy] Trends in Genetics, Vol. 25, No. 10. (06 October 2009), pp. 434-440. by Zeba Wunderlich, Leonid A. Mirny posted to tf motif expression by djkt to the group iSEEM on 2009-10-21 18:50:54 as along with 2 people francemirko behindtherabbit
	Genome evolution and adaptation in a long-term experiment with Escherichia coli. [My Copy] Nature, Vol. 461, No. 7268. (29 October 2009), pp. 1243-1247. by Jeffrey E. Barrick, Dong Su S. Yu, Sung Ho H. Yoon, et al.Haeyoung Jeong, Tae Kwang K. Oh, Dominique Schneider, Richard E. Lenski, Jihyun F. Kim posted to selection evolution bacteria by djkt to the group iSEEM on 2009-10-21 18:18:30 as along with 31 people and 4 groups pmalkus dokky samubernard ilyashl biomcgary kintoki zwang jasontsai aaltenburger sawasthi nurban josepe tjandra venancio maren qayub Garamonfok yyfwuhan Asclepius dbikard nzm jjray treangen lp2 codonusage operon diamantis michaelbarton druvus DrRichardBadge richardfranzese ronbun_2009au Pedro Martinez EvoDevo lab Barcelona Journal picks BergmanLab
	Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia [My Copy] Science, Vol. 326, No. 5951. (16 October 2009), pp. 422-426. by Anne E. Dekas, Rachel S. Poretsky, Victoria J. Orphan posted to microbes environment community by djkt to the group iSEEM on 2009-10-16 06:27:37 as
	Temporal Constraints on the Incorporation of Regulatory Mutants in Evolutionary Pathways [My Copy] Mol Biol Evol, Vol. 26, No. 11. (1 November 2009), pp. 2455-2462. by Kyle M. Brown, Mark A. DePristo, Daniel M. Weinreich, Daniel L. Hartl posted to selection proteins evolution enzymes bacteria by djkt to the group iSEEM on 2009-10-12 17:58:59 as along with 1 person JustinCrocker
	ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2737-2738. by Erik Kristiansson, Philip Hugenholtz, Daniel Dalevi posted to sysbio metagenomics environment annotation by djkt to the group iSEEM on 2009-10-09 16:40:27 as along with 4 people operon jmeppley dswan skembel
	Inference of Microbial Recombination Rates from Metagenomic Data [My Copy] PLoS Genet, Vol. 5, No. 10. (2 October 2009), e1000674. by Philip L. F. Johnson, Montgomery Slatkin posted to recombination microbes metagenomics by djkt to the group iSEEM on 2009-10-08 16:16:52 as along with 3 people druvus kinestetika maren
	Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus [My Copy] Genome Biol Evol, Vol. 2009, No. 0. (23 September 2009), pp. 325-339. by Olga Zhaxybayeva, W. Ford Doolittle, R. Thane Papke, J. Peter Gogarten posted to phylogenetics microbes ecology by djkt to the group iSEEM on 2009-10-01 00:13:13 as along with 1 person skembel
	Bayesian Phylogeography Finds Its Roots [My Copy] PLoS Comput Biol, Vol. 5, No. 9. (25 September 2009), e1000520. by Philippe Lemey, Andrew Rambaut, Alexei J. Drummond, Marc A. Suchard posted to virus phylogenetics model geography bayesian by djkt to the group iSEEM on 2009-09-25 19:55:42 as along with 2 people scmelton nuin
	Worlds within worlds: evolution of the vertebrate gut microbiota [My Copy] Nature Reviews Microbiology, Vol. 6, No. 10. (01 October 2008), pp. 776-788. by Ruth E. Ley, Catherine A. Lozupone, Micah Hamady, Rob Knight, Jeffrey I. Gordon posted to symbiosis by jlgreen to the group iSEEM on 2009-09-23 19:04:31 as along with 3 people skembel guhjy Zephyrus
	XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (07 October 2008), 420. by Daniel Frank posted to no-tag by jlgreen to the group iSEEM on 2009-09-23 17:52:39 as along with 5 people and 2 groups vaulot Thaverkamp treangen ojabado nuin Papers recommended by the Roscoff Plankton Group Microbial-Ecology
	Human gut microbiome adopts an alternative state following small bowel transplantation [My Copy] Proceedings of the National Academy of Sciences (17 September 2009) by Amber L. Hartman, Denver M. Lough, Dinesh K. Barupal, et al.Oliver Fiehn, Thomas Fishbein, Michael Zasloff, Jonathan A. Eisen posted to microbiome microbes community by djkt to the group iSEEM on 2009-09-22 23:32:15 as along with 2 people jgill skembel
	Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection [My Copy] Genome Biol Evol, Vol. 2009, No. 0. (4 September 2009), pp. 308-319. by Jochen B. W. Wolf, Axel Kunstner, Kiwoong Nam, Mattias Jakobsson, Hans Ellegren posted to variation selection positive genomics comparative by sharpton to the group iSEEM on 2009-09-14 18:27:10 as along with 5 people and 2 groups avilella operon stajich gwallau gjuggler Ensembl Compara citations Mycology
	SIZE-CORRECTION AND PRINCIPAL COMPONENTS FOR INTERSPECIFIC COMPARATIVE STUDIES [My Copy] Evolution, Vol. 9999, No. 9999. (2009) by Liam J. Revell posted to statistics species_data species phylogenetic by sharpton to the group iSEEM on 2009-09-14 18:24:49 as
	Species Tree Inference by Minimizing Deep Coalescences [My Copy] PLoS Comput Biol, Vol. 5, No. 9. (11 September 2009), e1000501. by Cuong Than, Luay Nakhleh posted to phylogenetics by djkt to the group iSEEM on 2009-09-11 16:30:16 as along with 6 people and 1 group parnell qcjones gdb gjuggler ppgardne druvus Journal picks
	Fast mapping of short sequences with mismatches, insertions and deletions using index structures. [My Copy] PLoS computational biology, Vol. 5, No. 9. (11 September 2009), e1000502. by Steve Hoffmann, Christian Otto, Stefan Kurtz, et al.Cynthia M. Sharma, Philipp Khaitovich, Jörg Vogel, Peter F. Stadler, Jörg Hackermüller posted to sequencing indel alignment by djkt to the group iSEEM on 2009-09-11 16:28:11 as along with 19 people and 3 groups cthachuk hzoltan darian nuin fenghezi behindtherabbit jandot walshtp torfinnnome stubrown dswan polivares orzenil natstreet jmcq n00c heliopais ppgardne druvus Bioinformatics BergmanLab Journal picks
	Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates [My Copy] Environmental Microbiology, Vol. 9999, No. 9999. (2009) by Victor Kunin, Anna Engelbrektson, Howard Ochman, Philip Hugenholtz posted to pyrosequencing methods diversity by skembel to the group iSEEM on 2009-09-03 20:05:56 as along with 2 people jgill jmeppley
	Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora [My Copy] Science, Vol. 325, No. 5944. (28 August 2009), pp. 1128-1131. by Morten O. A. Sommer, Gautam Dantas, George M. Church posted to pathogen microbiome microbes metagenomics evolution disease by djkt to the group iSEEM on 2009-09-03 18:03:10 as along with 5 people skembel jgill pkm chriswillmott rpatward
	Community-wide analysis of microbial genome sequence signatures [My Copy] Genome Biology, Vol. 10, No. 8. (2009), R85. by Gregory Dick, Anders Andersson, Brett Baker, et al.Sheri Simmons, Brian Thomas, A. Pepper Yelton, Jillian Banfield posted to otu microbes metagenomics community by djkt to the group iSEEM on 2009-09-02 23:52:48 as along with 7 people and 1 group dakelley druvus bdessailly skembel jonilaserson neils barriot Orengo Group Journal Picks
	Evolutionary Triplet Models of Structured RNA [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000483. by Robert K. Bradley, Ian Holmes posted to structure rna phylogenetics alignment by djkt to the group iSEEM on 2009-08-31 19:26:10 as along with 1 person and 1 group ppgardne Journal picks
	Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models [My Copy] Nature Methods, Vol. 6, No. 9. (02 August 2009), pp. 673-676. by Arthur Brady, Steven L. Salzberg posted to otu metagenomics imm classification binning by sharpton to the group iSEEM on 2009-08-25 22:59:51 as along with 7 people and 3 groups azazello robertrentzsch dakelley skembel Thaverkamp jbhiatt stajich Orengo Group Journal Picks Journal picks Mycology
	Redefining chronic viral infection. [My Copy] Cell, Vol. 138, No. 1. (10 July 2009), pp. 30-50. by Herbert W. Virgin, E. John Wherry, Rafi Ahmed posted to virus virome microbiome metagenome human by sharpton to the group iSEEM on 2009-08-24 17:01:49 as along with 1 person rpsimmonsin
	Accurate determination of microbial diversity from 454 pyrosequencing data. [My Copy] Nature methods, Vol. 6, No. 9. (09 September 2009), pp. 639-641. by Christopher Quince, Anders Lanzén, Thomas P. Curtis, et al.Russell J. Davenport, Neil Hall, Ian M. Head, L. Fiona Read, William T. Sloan posted to otu diversity 454 by skembel to the group iSEEM on 2009-08-21 22:29:55 as along with 7 people and 1 group halinat kinestetika jgill jonilaserson druvus orzenil danmaclean Bioinformatics
	On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (21 August 2009), e1000472. by Wilfred Ndifon, Joshua B. Plotkin, Jonathan Dushoff posted to sysbio evolution bacteria by djkt to the group iSEEM on 2009-08-21 16:34:18 as along with 2 people zwang biomcgary
	Does Gene Translocation Accelerate the Evolution of Laterally Transferred Genes? [My Copy] Genetics, Vol. 182, No. 4. (1 August 2009), pp. 1365-1375. by Weilong Hao, G. Brian Golding posted to gene-transfer evolution acceleration by djkt to the group iSEEM on 2009-08-21 01:13:05 as along with 2 people biomcgary operon
	PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating [My Copy] Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2286-2288. by Nicolas Lartillot, Thomas Lepage, Samuel Blanquart posted to phylogenetics molclock bayesian by djkt to the group iSEEM on 2009-08-20 18:55:41 as along with 6 people nesnidal leemond31 operon nuin grahamc phoenixzxl
	Evidence for an early prokaryotic endosymbiosis. [My Copy] Nature, Vol. 460, No. 7258. (20 August 2009), pp. 967-971. by James A. Lake posted to symbiosis evolution bacteria by djkt to the group iSEEM on 2009-08-19 20:22:06 as along with 5 people cmzmasek cambray robfsouza neils behindtherabbit
	A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (14 August 2009), e1000465. by Yuzhen Ye, Thomas G. Doak posted to sysbio metagenomics by djkt to the group iSEEM on 2009-08-14 16:29:25 as along with 6 people mstumpf ptrobajo barriot rdiaz michaelbarton kshameer
	Local Adaptation of Bacteriophages to Their Bacterial Hosts in Soil [My Copy] Science, Vol. 325, No. 5942. (14 August 2009), 833. by Michiel Vos, Philip J. Birkett, Elizabeth Birch, Robert I. Griffiths, Angus Buckling posted to soil selection phage microbes ecology bacteria by djkt to the group iSEEM on 2009-08-14 16:06:51 as along with 3 people maren timothee-poisot michaelbarton
	A Machine-Learning Approach Reveals That Alignment Properties Alone Can Accurately Predict Inference of Lateral Gene Transfer from Discordant Phylogenies [My Copy] Mol Biol Evol, Vol. 26, No. 9. (1 September 2009), pp. 1931-1939. by Mayo Roettger, William Martin, Tal Dagan posted to phylogenetics gene-transfer alignment by djkt to the group iSEEM on 2009-08-13 22:57:54 as along with 3 people and 1 group gwallau stajich operon Mycology
	Systematic artifacts in metagenomes from complex microbial communities [My Copy] ISME (July 2009) by V. Gomez-Alvarez, T. K. Teal, Schmidt Tm posted to bias metagenomics sequencing by djkt to the group iSEEM on 2009-08-07 21:44:22 as
	Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 16. (15 August 2009), pp. 2074-2075. by Kathryn E. Holt, Yik Y. Teo, Heng Li, et al.Satheesh Nair, Gordon Dougan, John Wain, Julian Parkhill posted to metagenomics popgen snps by djkt to the group iSEEM on 2009-08-07 17:57:58 as along with 7 people and 1 group jsatkosk jandot stajich guhjy farhat sandfire druvus Mycology
	Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (7 August 2009), e1000455. by Jing Tang, William P. Hanage, Christophe Fraser, Jukka Corander posted to metagenomics phylogenetics popgen by djkt to the group iSEEM on 2009-08-07 17:16:25 as along with 3 people jjray operon skembel
	Temporal variation of Synechococcus clades at a coastal Pacific Ocean monitoring site [My Copy] ISME J, Vol. 3, No. 8. (9 April 2009), pp. 903-915. by Vera Tai, Brian Palenik posted to clades marine microbiology population temoporal by sharpton to the group iSEEM on 2009-08-06 22:54:40 as

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diversity	78
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ploscb08	74
metagenomic	52
metagenomics	50
microbes	48
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16s	28
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