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PyCogent: a toolkit for making sense from sequence
Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, J Gregory Caporaso, Brett C Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymond Sammut, Sandra Smit, Matthew J Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua Ying, Gavin A Huttley
Genome Biol. 2007; 8(8): R171. Published online 2007 August 21. doi: 10.1186/gb-2007-8-8-r171
PMCID:
PMC2375001
Abstract Full Text PDF–955K Supplementary Material
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 Is Cited by the Following 33 Articles in this Archive:
Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution
Robert K. Bradley, Jason Merkin, Nicole J. Lambert, Christopher B. Burge
PLoS Biol. 2012 January; 10(1): e1001229. Published online 2012 January 3. doi: 10.1371/journal.pbio.1001229
PMCID:
PMC3250501
Abstract Full Text PDF–1.0M Supplementary Material
Patterns of Positive Selection and Neutral Evolution in the Protein-Coding Genes of Tetraodon and Takifugu
Juan I. Montoya-Burgos
PLoS One. 2011; 6(9): e24800. Published online 2011 September 13. doi: 10.1371/journal.pone.0024800
PMCID:
PMC3172292
Abstract Full Text PDF–190K 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
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata
Meg Pirrung, Ryan Kennedy, J. Gregory Caporaso, Jesse Stombaugh, Doug Wendel, Rob Knight
Bioinformatics. 2011 November 1; 27(21): 3067–3069. Published online 2011 September 8. doi: 10.1093/bioinformatics/btr517
PMCID:
PMC3198578
Abstract Full Text PDF–263K
Boulder ALignment Editor (ALE): a web-based RNA alignment tool
Jesse Stombaugh, Jeremy Widmann, Daniel McDonald, Rob Knight
Bioinformatics. 2011 June 15; 27(12): 1706–1707. Published online 2011 May 5. doi: 10.1093/bioinformatics/btr258
PMCID:
PMC3106197
Abstract Full Text PDF–156K
Exploiting CpG Hypermutability to Identify Phenotypically Significant Variation Within Human Protein-Coding Genes
Hua Ying, Gavin Huttley
Genome Biol Evol. 2011; 3: 938–949. Published online 2011 March 11. doi: 10.1093/gbe/evr021
PMCID:
PMC3184784
Abstract Full Text PDF–329K
Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition
J. Gregory Caporaso, Rob Knight, Scott T. Kelley
PLoS One. 2011; 6(2): e16900. Published online 2011 February 24. doi: 10.1371/journal.pone.0016900
PMCID:
PMC3044705
Abstract Full Text PDF–354K Supplementary Material
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
William A. Walters, J. Gregory Caporaso, Christian L. Lauber, Donna Berg-Lyons, Noah Fierer, Rob Knight
Bioinformatics. 2011 April 15; 27(8): 1159–1161. Published online 2011 February 23. doi: 10.1093/bioinformatics/btr087
PMCID:
PMC3072552
Abstract Full Text PDF–564K Supplementary Material
ModeRNA: a tool for comparative modeling of RNA 3D structure
Magdalena Rother, Kristian Rother, Tomasz Puton, Janusz M. Bujnicki
Nucleic Acids Res. 2011 May; 39(10): 4007–4022. Published online 2011 February 7. doi: 10.1093/nar/gkq1320
PMCID:
PMC3105415
Abstract Full Text PDF–12M Supplementary Material
An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators
Laurent Gautier
BMC Bioinformatics. 2010; 11(Suppl 12): S11. Published online 2010 December 21. doi: 10.1186/1471-2105-11-S12-S11
PMCID:
PMC3040525
Abstract Full Text PDF–627K
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
Justin Kuczynski, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Noah Fierer, Rob Knight
Nat Methods. Author manuscript; available in PMC 2011 April 1.
Published in final edited form as: Nat Methods. 2010 October; 7(10): 813–819. Published online 2010 September 5. doi: 10.1038/nmeth.1499
PMCID:
PMC2948603
Abstract Full Text PDF–1.4M Supplementary Material
Stable tRNA-based phylogenies using only 76 nucleotides
Jeremy Widmann, J. Kirk Harris, Catherine Lozupone, Alexey Wolfson, Rob Knight
RNA. 2010 August; 16(8): 1469–1477. doi: 10.1261/rna.726010
PMCID:
PMC2905747
Abstract Full Text PDF–1.3M
QIIME allows analysis of high-throughput community sequencing data
J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Peña, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld, Rob Knight
Nat Methods. Author manuscript; available in PMC 2011 August 16.
Published in final edited form as: Nat Methods. 2010 May; 7(5): 335–336. Published online 2010 April 11. doi: 10.1038/nmeth.f.303
PMCID:
PMC3156573
Full Text PDF–217K Supplementary Material
Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives
Jesse R. Zaneveld, Catherine Lozupone, Jeffrey I. Gordon, Rob Knight
Nucleic Acids Res. 2010 July; 38(12): 3869–3879. Published online 2010 March 2. doi: 10.1093/nar/gkq066
PMCID:
PMC2896507
Abstract Full Text PDF–5.3M Supplementary Material
A Primer on Metagenomics
John C. Wooley, Adam Godzik, Iddo Friedberg
PLoS Comput Biol. 2010 February; 6(2): e1000667. Published online 2010 February 26. doi: 10.1371/journal.pcbi.1000667
PMCID:
PMC2829047
Abstract Full Text PDF–360K
Positive Selection Differs between Protein Secondary Structure Elements in Drosophila
Kate E. Ridout, Christopher J. Dixon, Dmitry A. Filatov
Genome Biol Evol. 2010; 2: 166–179. Published online 2010 February 25. doi: 10.1093/gbe/evq008
PMCID:
PMC2997536
Abstract Full Text PDF–341K
Natural and artificial RNAs occupy the same restricted region of sequence space
Ryan Kennedy, Manuel E. Lladser, Zhiyuan Wu, Chen Zhang, Michael Yarus, Hans De Sterck, Rob Knight
RNA. 2010 February; 16(2): 280–289. doi: 10.1261/rna.1923210
PMCID:
PMC2811657
Abstract Full Text PDF–1.1M
ETE: a python Environment for Tree Exploration
Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón
BMC Bioinformatics. 2010; 11: 24. Published online 2010 January 13. doi: 10.1186/1471-2105-11-24
PMCID:
PMC2820433
Abstract Full Text PDF–623K
PyNAST: a flexible tool for aligning sequences to a template alignment
J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, Rob Knight
Bioinformatics. 2010 January 15; 26(2): 266–267. Published online 2009 November 13. doi: 10.1093/bioinformatics/btp636
PMCID:
PMC2804299
Abstract Full Text PDF–180K
Evidence that Localized Variation in Primate Sequence Divergence Arises from an Influence of Nucleosome Placement on DNA Repair
Hua Ying, Julian Epps, Rohan Williams, Gavin Huttley
Mol Biol Evol. 2010 March; 27(3): 637–649. Published online 2009 October 20. doi: 10.1093/molbev/msp253
PMCID:
PMC2822288
Abstract Full Text PDF–526K Supplementary Material
Estimates of the Effect of Natural Selection on Protein-Coding Content
Von Bing Yap, Helen Lindsay, Simon Easteal, Gavin Huttley
Mol Biol Evol. 2010 March; 27(3): 726–734. Published online 2009 October 8. doi: 10.1093/molbev/msp232
PMCID:
PMC2822286
Abstract Full Text PDF–445K Supplementary Material
Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
Micah Hamady, Catherine Lozupone, Rob Knight
ISME J. Author manuscript; available in PMC 2010 July 1.
Published in final edited form as: ISME J. 2010 January; 4(1): 17–27. Published online 2009 August 27. doi: 10.1038/ismej.2009.97
PMCID:
PMC2797552
Abstract Full Text PDF–1.7M Supplementary Material
CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes
Micah Hamady, Stephanie A. Wilson, Jesse Zaneveld, Noboru Sueoka, Rob Knight
Bioinformatics. 2009 May 15; 25(10): 1331–1332. Published online 2009 March 11. doi: 10.1093/bioinformatics/btp141
PMCID:
PMC2677738
Abstract Full Text PDF–189K
Pathological rate matrices: from primates to pathogens
Harold W Schranz, Von Bing Yap, Simon Easteal, Rob Knight, Gavin A Huttley
BMC Bioinformatics. 2008; 9: 550. Published online 2008 December 19. doi: 10.1186/1471-2105-9-550
PMCID:
PMC2639438
Abstract Full Text PDF–595K Supplementary Material
Pitfalls of the most commonly used models of context dependent substitution
Helen Lindsay, Von Bing Yap, Hua Ying, Gavin A Huttley
Biol Direct. 2008; 3: 52. Published online 2008 December 16. doi: 10.1186/1745-6150-3-52
Correction in:
Biol Direct. 2009; 4: 10.
PMCID:
PMC2628887
Abstract Full Text PDF–1.4M Supplementary Material Correction
Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics
J Gregory Caporaso, Sandra Smit, Brett C Easton, Lawrence Hunter, Gavin A Huttley, Rob Knight
BMC Evol Biol. 2008; 8: 327. Published online 2008 December 3. doi: 10.1186/1471-2148-8-327
PMCID:
PMC2637866
Abstract Full Text PDF–2.0M Supplementary Material
Comparison of methods for estimating the nucleotide substitution matrix
Maribeth Oscamou, Daniel McDonald, Von Bing Yap, Gavin A Huttley, Manuel E Lladser, Rob Knight
BMC Bioinformatics. 2008; 9: 511. Published online 2008 December 1. doi: 10.1186/1471-2105-9-511
PMCID:
PMC2655096
Abstract Full Text PDF–415K
A core gut microbiome in obese and lean twins
Peter J. Turnbaugh, Micah Hamady, Tanya Yatsunenko, Brandi L. Cantarel, Alexis Duncan, Ruth E. Ley, Mitchell L. Sogin, William J. Jones, Bruce A. Roe, Jason P. Affourtit, Michael Egholm, Bernard Henrissat, Andrew C. Heath, Rob Knight, Jeffrey I. Gordon
Nature. Author manuscript; available in PMC 2009 July 22.
Published in final edited form as: Nature. 2009 January 22; 457(7228): 480–484. Published online 2008 November 30. doi: 10.1038/nature07540
PMCID:
PMC2677729
Abstract Full Text PDF–964K Supplementary Material
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
Zongzhi Liu, Todd Z. DeSantis, Gary L. Andersen, Rob Knight
Nucleic Acids Res. 2008 October; 36(18): e120. Published online 2008 October. doi: 10.1093/nar/gkn491
PMCID:
PMC2566877
Abstract Full Text PDF–1.1M
Worlds within worlds: evolution of the vertebrate gut microbiota
Ruth E. Ley, Catherine A. Lozupone, Micah Hamady, Rob Knight, Jeffrey I. Gordon
Nat Rev Microbiol. Author manuscript; available in PMC 2009 April 1.
Published in final edited form as: Nat Rev Microbiol. 2008 October; 6(10): 776–788. doi: 10.1038/nrmicro1978
PMCID:
PMC2664199
Abstract Full Text PDF–4.3M Supplementary Material
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