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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

Is Cited by the Following 47 Articles in this Archive:

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
Gene-Wei Li, Eugene Oh, Jonathan S. Weissman
Nature. Author manuscript; available in PMC 2012 October 26.
Published in final edited form as: Nature. 2012 March 28; 484(7395): 538–541. doi: 10.1038/nature10965
PMCID:
PMC3338875
Free in PMC on 2012/10/26
Comparative Analysis of Gene Content Evolution in Phytoplasmas and Mycoplasmas
Ling-Ling Chen, Wan-Chia Chung, Chan-Pin Lin, Chih-Horng Kuo
PLoS One. 2012; 7(3): e34407. Published online 2012 March 27. doi: 10.1371/journal.pone.0034407
PMCID:
PMC3313985
Abstract Full Text PDF–453K Supplementary Material
Genomes-based phylogeny of the genus Xanthomonas
Luis M Rodriguez-R, Alejandro Grajales, Mario L Arrieta-Ortiz, Camilo Salazar, Silvia Restrepo, Adriana Bernal
BMC Microbiol. 2012; 12: 43. Published online 2012 March 23. doi: 10.1186/1471-2180-12-43
PMCID:
PMC3359215
Abstract Full Text PDF–928K Supplementary Material
Comparative genomics reveals evidence of marine adaptation in Salinispora species
Kevin Penn, Paul R Jensen
BMC Genomics. 2012; 13: 86. Published online 2012 March 8. doi: 10.1186/1471-2164-13-86
PMCID:
PMC3314556
Abstract Full Text PDF–3.7M Supplementary Material
A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity
Michiel Vos, Christopher Quince, Agata S. Pijl, Mattias de Hollander, George A. Kowalchuk
PLoS One. 2012; 7(2): e30600. Published online 2012 February 15. doi: 10.1371/journal.pone.0030600
PMCID:
PMC3280256
Abstract Full Text PDF–583K Supplementary Material
Isolation and Characterization of the Prochlorococcus Carboxysome Reveal the Presence of the Novel Shell Protein CsoS1D
Evan W. Roberts, Fei Cai, Cheryl A. Kerfeld, Gordon C. Cannon, Sabine Heinhorst
J Bacteriol. 2012 February; 194(4): 787–795. doi: 10.1128/JB.06444-11
PMCID:
PMC3272956
Free in PMC on 2012/08/01
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
Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp.
Adam J. Bogdanove, Ralf Koebnik, Hong Lu, Ayako Furutani, Samuel V. Angiuoli, Prabhu B. Patil, Marie-Anne Van Sluys, Robert P. Ryan, Damien F. Meyer, Sang-Wook Han, Gudlur Aparna, Misha Rajaram, Arthur L. Delcher, Adam M. Phillippy, Daniela Puiu, Michael C. Schatz, Martin Shumway, Daniel D. Sommer, Cole Trapnell, Faiza Benahmed, George Dimitrov, Ramana Madupu, Diana Radune, Steven Sullivan, Gopaljee Jha, Hiromichi Ishihara, Sang-Won Lee, Alok Pandey, Vikas Sharma, Malinee Sriariyanun, Boris Szurek, Casiana M. Vera-Cruz, Karin S. Dorman, Pamela C. Ronald, Valérie Verdier, J. Maxwell Dow, Ramesh V. Sonti, Seiji Tsuge, Volker P. Brendel, Pablo D. Rabinowicz, Jan E. Leach, Frank F. White, Steven L. Salzberg
J Bacteriol. 2011 October; 193(19): 5450–5464. doi: 10.1128/JB.05262-11
PMCID:
PMC3187462
Abstract Full Text PDF–3.5M Supplementary Material
Identification of Nicotinamide Mononucleotide Deamidase of the Bacterial Pyridine Nucleotide Cycle Reveals a Novel Broadly Conserved Amidohydrolase Family
Luca Galeazzi, Paola Bocci, Adolfo Amici, Lucia Brunetti, Silverio Ruggieri, Margaret Romine, Samantha Reed, Andrei L. Osterman, Dmitry A. Rodionov, Leonardo Sorci, Nadia Raffaelli
J Biol Chem. 2011 November 18; 286(46): 40365–40375. Published online 2011 September 27. doi: 10.1074/jbc.M111.275818
PMCID:
PMC3220592
Free in PMC on 2012/11/18
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
The genome of Th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment
Andrew Sczesnak, Nicola Segata, Xiang Qin, Dirk Gevers, Joseph F. Petrosino, Curtis Huttenhower, Dan R. Littman, Ivaylo I. Ivanov
Cell Host Microbe. Author manuscript; available in PMC 2012 September 15.
Published in final edited form as: Cell Host Microbe. 2011 September 15; 10(3): 260–272. doi: 10.1016/j.chom.2011.08.005
PMCID:
PMC3209701
Free in PMC on 2012/09/15
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
De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities
Priya Narasingarao, Sheila Podell, Juan A Ugalde, Céline Brochier-Armanet, Joanne B Emerson, Jochen J Brocks, Karla B Heidelberg, Jillian F Banfield, Eric E Allen
ISME J. 2012 January; 6(1): 81–93. Published online 2011 June 30. doi: 10.1038/ismej.2011.78
PMCID:
PMC3246234
Free in PMC on 2013/01/01
Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential
Christian G Klatt, Jason M Wood, Douglas B Rusch, Mary M Bateson, Natsuko Hamamura, John F Heidelberg, Arthur R Grossman, Devaki Bhaya, Frederick M Cohan, Michael Kühl, Donald A Bryant, David M Ward
ISME J. 2011 August; 5(8): 1262–1278. Published online 2011 June 23. doi: 10.1038/ismej.2011.73
PMCID:
PMC3146275
Free in PMC on 2012/08/01
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
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