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A simple, fast, and accurate method of phylogenomic inference
Martin Wu, Jonathan A Eisen
Genome Biol. 2008; 9(10): R151. Published online 2008 October 13. doi: 10.1186/gb-2008-9-10-r151
PMCID:
PMC2760878
Abstract Full Text PDF–497K Supplementary Material
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 Is Cited by the Following 36 Articles in this Archive:
A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem
Hideto Takami, Hideki Noguchi, Yoshihiro Takaki, Ikuo Uchiyama, Atsushi Toyoda, Shinro Nishi, Gab-Joo Chee, Wataru Arai, Takuro Nunoura, Takehiko Itoh, Masahira Hattori, Ken Takai
PLoS One. 2012; 7(1): e30559. Published online 2012 January 27. doi: 10.1371/journal.pone.0030559
PMCID:
PMC3267732
Abstract Full Text PDF–1.2M Supplementary Material
Accounting For Alignment Uncertainty in Phylogenomics
Martin Wu, Sourav Chatterji, Jonathan A. Eisen
PLoS One. 2012; 7(1): e30288. Published online 2012 January 17. doi: 10.1371/journal.pone.0030288
PMCID:
PMC3260272
Abstract Full Text PDF–493K Supplementary Material
Genomic insights into an obligate epibiotic bacterial predator: Micavibrio aeruginosavorus ARL-13
Zhang Wang, Daniel E Kadouri, Martin Wu
BMC Genomics. 2011; 12: 453. Published online 2011 September 21. doi: 10.1186/1471-2164-12-453
PMCID:
PMC3189940
Abstract Full Text PDF–2.6M Supplementary Material
Toward an Efficient Method of Identifying Core Genes for Evolutionary and Functional Microbial Phylogenies
Nicola Segata, Curtis Huttenhower
PLoS One. 2011; 6(9): e24704. Published online 2011 September 12. doi: 10.1371/journal.pone.0024704
PMCID:
PMC3171473
Abstract Full Text PDF–1.7M Supplementary Material
Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development
Jason W. Holder, Jil C. Ulrich, Anthony C. DeBono, Paul A. Godfrey, Christopher A. Desjardins, Jeremy Zucker, Qiandong Zeng, Alex L. B. Leach, Ion Ghiviriga, Christine Dancel, Thomas Abeel, Dirk Gevers, Chinnappa D. Kodira, Brian Desany, Jason P. Affourtit, Bruce W. Birren, Anthony J. Sinskey
PLoS Genet. 2011 September; 7(9): e1002219. Published online 2011 September 8. doi: 10.1371/journal.pgen.1002219
PMCID:
PMC3169528
Abstract Full Text PDF–1.4M Supplementary Material
The Phylogenetic Diversity of Metagenomes
Steven W. Kembel, Jonathan A. Eisen, Katherine S. Pollard, Jessica L. Green
PLoS One. 2011; 6(8): e23214. Published online 2011 August 31. doi: 10.1371/journal.pone.0023214
PMCID:
PMC3166145
Abstract Full Text PDF–560K Supplementary Material
Phylogenomics-Based Reconstruction of Protozoan Species Tree
Kary A.C.S. Ocaña, Alberto M.R. Dávila
Evol Bioinform Online. 2011; 7: 107–121. Published online 2011 July 31. doi: 10.4137/EBO.S6861
PMCID:
PMC3153122
Abstract Full Text PDF–1.0M Supplementary Material
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
Bo Liu, Theodore Gibbons, Mohammad Ghodsi, Todd Treangen, Mihai Pop
BMC Genomics. 2011; 12(Suppl 2): S4. Published online 2011 July 27. doi: 10.1186/1471-2164-12-S2-S4
PMCID:
PMC3194235
Abstract Full Text PDF–1.7M
Evolutionary transitions in bacterial symbiosis
Joel L. Sachs, Ryan G. Skophammer, John U. Regus
Proc Natl Acad Sci U S A. 2011 June 28; 108(Supplement_2): 10800–10807. Published online 2011 June 20. doi: 10.1073/pnas.1100304108
PMCID:
PMC3131820
Abstract Full Text PDF–923K Supplementary Material
Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data
Miguel Pignatelli, Andrés Moya
PLoS One. 2011; 6(5): e19984. Published online 2011 May 23. doi: 10.1371/journal.pone.0019984
PMCID:
PMC3100316
Abstract Full Text PDF–442K Supplementary Material
Mixture models for analysis of the taxonomic composition of metagenomes
Peter Meinicke, Kathrin Petra Aßhauer, Thomas Lingner
Bioinformatics. 2011 June 15; 27(12): 1618–1624. Published online 2011 May 5. doi: 10.1093/bioinformatics/btr266
PMCID:
PMC3106201
Abstract Full Text PDF–259K Supplementary Material
CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis
Brandon Chisham, Ben Wright, Trung Le, Tran Cao Son, Enrico Pontelli
BMC Bioinformatics. 2011; 12: 98. Published online 2011 April 15. doi: 10.1186/1471-2105-12-98
PMCID:
PMC3101187
Abstract Full Text PDF–1.7M
Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees
Dongying Wu, Martin Wu, Aaron Halpern, Douglas B. Rusch, Shibu Yooseph, Marvin Frazier, J. Craig Venter, Jonathan A. Eisen
PLoS One. 2011; 6(3): e18011. Published online 2011 March 18. doi: 10.1371/journal.pone.0018011
PMCID:
PMC3060911
Abstract Full Text PDF–775K
A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-tuples
Yu-Wei Wu, Yuzhen Ye
J Comput Biol. 2011 March; 18(3): 523–534. doi: 10.1089/cmb.2010.0245
PMCID:
PMC3123841
Abstract Full Text PDF–318K Supplementary Material
Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment
Yuzhen Ye
Proceedings (IEEE Int Conf Bioinformatics Biomed) Author manuscript; available in PMC 2011 November 16.
Published in final edited form as: Proceedings (IEEE Int Conf Bioinformatics Biomed). 2011 February 4; 2010: 153–157. doi: 10.1109/BIBM.2010.5706555
PMCID:
PMC3217275
Abstract Full Text PDF–476K
RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles
Ozkan U Nalbantoglu, Samuel F Way, Steven H Hinrichs, Khalid Sayood
BMC Bioinformatics. 2011; 12: 41. Published online 2011 January 31. doi: 10.1186/1471-2105-12-41
PMCID:
PMC3038895
Abstract Full Text PDF–628K Supplementary Material
PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data
Thomas J. Sharpton, Samantha J. Riesenfeld, Steven W. Kembel, Joshua Ladau, James P. O'Dwyer, Jessica L. Green, Jonathan A. Eisen, Katherine S. Pollard
PLoS Comput Biol. 2011 January; 7(1): e1001061. Published online 2011 January 20. doi: 10.1371/journal.pcbi.1001061
PMCID:
PMC3024254
Abstract Full Text PDF–777K Supplementary Material
Genomic fluidity: an integrative view of gene diversity within microbial populations
Andrey O Kislyuk, Bart Haegeman, Nicholas H Bergman, Joshua S Weitz
BMC Genomics. 2011; 12: 32. Published online 2011 January 13. doi: 10.1186/1471-2164-12-32
PMCID:
PMC3030549
Abstract Full Text PDF–644K Supplementary Material
Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing
G. Xie, P.S.G. Chain, C. Lo, K-L. Liu, J. Gans, J. Merritt, F. Qi
Mol Oral Microbiol. Author manuscript; available in PMC 2011 December 1.
Published in final edited form as: Mol Oral Microbiol. 2010 December; 25(6): 391–405. doi: 10.1111/j.2041-1014.2010.00587.x
PMCID:
PMC2975940
Abstract Full Text PDF–827K Supplementary Material
Assembling networks of microbial genomes using linear programming
Catherine Holloway, Robert G Beiko
BMC Evol Biol. 2010; 10: 360. Published online 2010 November 20. doi: 10.1186/1471-2148-10-360
PMCID:
PMC3224671
Abstract Full Text PDF–2.7M Supplementary Material
Clustering metagenomic sequences with interpolated Markov models
David R Kelley, Steven L Salzberg
BMC Bioinformatics. 2010; 11: 544. Published online 2010 November 2. doi: 10.1186/1471-2105-11-544
PMCID:
PMC3098094
Abstract Full Text PDF–754K
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
Frederick A Matsen, Robin B Kodner, E Virginia Armbrust
BMC Bioinformatics. 2010; 11: 538. Published online 2010 October 30. doi: 10.1186/1471-2105-11-538
PMCID:
PMC3098090
Abstract Full Text PDF–1.7M Supplementary Material
Legionella pneumophila Strain 130b Possesses a Unique Combination of Type IV Secretion Systems and Novel Dot/Icm Secretion System Effector Proteins
Gunnar N. Schroeder, Nicola K. Petty, Aurélie Mousnier, Clare R. Harding, Adam J. Vogrin, Bryan Wee, Norman K. Fry, Timothy G. Harrison, Hayley J. Newton, Nicholas R. Thomson, Scott A. Beatson, Gordon Dougan, Elizabeth L. Hartland, Gad Frankel
J Bacteriol. 2010 November; 192(22): 6001–6016. Published online 2010 September 10. doi: 10.1128/JB.00778-10
PMCID:
PMC2976443
Abstract Full Text PDF–1.6M Supplementary Material
MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies
Manuel Stark, Simon A Berger, Alexandros Stamatakis, Christian von Mering
BMC Genomics. 2010; 11: 461. Published online 2010 August 5. doi: 10.1186/1471-2164-11-461
PMCID:
PMC3091657
Abstract Full Text PDF–3.6M
Some considerations for analyzing biodiversity using integrative metagenomics and gene networks
Lucie Bittner, Sébastien Halary, Claude Payri, Corinne Cruaud, Bruno de Reviers, Philippe Lopez, Eric Bapteste
Biol Direct. 2010; 5: 47. Published online 2010 July 30. doi: 10.1186/1745-6150-5-47
PMCID:
PMC2921367
Abstract Full Text PDF–2.0M Supplementary Material
Phylogeny of Gammaproteobacteria
Kelly P. Williams, Joseph J. Gillespie, Bruno W. S. Sobral, Eric K. Nordberg, Eric E. Snyder, Joshua M. Shallom, Allan W. Dickerman
J Bacteriol. 2010 May; 192(9): 2305–2314. Published online 2010 March 5. doi: 10.1128/JB.01480-09
PMCID:
PMC2863478
Abstract Full Text PDF–1.9M Supplementary Material
Standard operating procedure for computing pangenome trees
Lars Snipen, David W. Ussery
Stand Genomic Sci. 2010 February 28; 2(1): 135–141. Published online 2010 January 28. doi: 10.4056/sigs.38923
PMCID:
PMC3035256
Abstract Full Text PDF–876K
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function
Jeremy D Selengut, Douglas B Rusch, Daniel H Haft
BMC Bioinformatics. 2010; 11: 52. Published online 2010 January 26. doi: 10.1186/1471-2105-11-52
PMCID:
PMC3098086
Abstract Full Text PDF–4.6M
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
Dongying Wu, Philip Hugenholtz, Konstantinos Mavromatis, Rüdiger Pukall, Eileen Dalin, Natalia N. Ivanova, Victor Kunin, Lynne Goodwin, Martin Wu, Brian J. Tindall, Sean D. Hooper, Amrita Pati, Athanasios Lykidis, Stefan Spring, Iain J. Anderson, Patrik D’haeseleer, Adam Zemla, Mitchell Singer, Alla Lapidus, Matt Nolan, Alex Copeland, Cliff Han, Feng Chen, Jan-Fang Cheng, Susan Lucas, Cheryl Kerfeld, Elke Lang, Sabine Gronow, Patrick Chain, David Bruce, Edward M. Rubin, Nikos C. Kyrpides, Hans-Peter Klenk, Jonathan A. Eisen
Nature. Author manuscript; available in PMC 2011 April 9.
Published in final edited form as: Nature. 2009 December 24; 462(7276): 1056–1060. doi: 10.1038/nature08656
PMCID:
PMC3073058
Abstract Full Text PDF–442K Supplementary Material
Cohesion Group Approach for Evolutionary Analysis of Aspartokinase, an Enzyme That Feeds a Branched Network of Many Biochemical Pathways
Chien-Chi Lo, Carol A. Bonner, Gary Xie, Mark D'Souza, Roy A. Jensen
Microbiol Mol Biol Rev. 2009 December; 73(4): 594–651. doi: 10.1128/MMBR.00024-09
PMCID:
PMC2786584
Abstract Full Text PDF–12M
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