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Items: 36

1.

The Power Decoder Simulator for the Evaluation of Pooled shRNA Screen Performance.

Stombaugh J, Licon A, Strezoska Ž, Stahl J, Anderson SB, Banos M, van Brabant Smith A, Birmingham A, Vermeulen A.

J Biomol Screen. 2015 Sep;20(8):965-75. doi: 10.1177/1087057115576715. Epub 2015 Mar 16.

2.

Meta-analyses of studies of the human microbiota.

Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vázquez-Baeza Y, Jansson JK, Gordon JI, Knight R.

Genome Res. 2013 Oct;23(10):1704-14. doi: 10.1101/gr.151803.112. Epub 2013 Jul 16.

3.

Widespread colonization of the lung by Tropheryma whipplei in HIV infection.

Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, Campbell TB, Flores SC, Ackerman G, Stombaugh J, Ursell L, Beck JM, Curtis JL, Young VB, Lynch SV, Huang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight R, Fontenot AP; Lung HIV Microbiome Project.

Am J Respir Crit Care Med. 2013 May 15;187(10):1110-7. doi: 10.1164/rccm.201211-2145OC.

4.

Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R.

Curr Protoc Microbiol. 2012 Nov;Chapter 1:Unit 1E.5.. doi: 10.1002/9780471729259.mc01e05s27.

5.

Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish.

Semova I, Carten JD, Stombaugh J, Mackey LC, Knight R, Farber SA, Rawls JF.

Cell Host Microbe. 2012 Sep 13;12(3):277-88. doi: 10.1016/j.chom.2012.08.003.

6.

Diversity, stability and resilience of the human gut microbiota.

Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R.

Nature. 2012 Sep 13;489(7415):220-30. doi: 10.1038/nature11550. Review.

7.

Lake microbial communities are resilient after a whole-ecosystem disturbance.

Shade A, Read JS, Youngblut ND, Fierer N, Knight R, Kratz TK, Lottig NR, Roden EE, Stanley EH, Stombaugh J, Whitaker RJ, Wu CH, McMahon KD.

ISME J. 2012 Dec;6(12):2153-67. doi: 10.1038/ismej.2012.56. Epub 2012 Jun 28.

8.

RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs.

Widmann J, Stombaugh J, McDonald D, Chocholousova J, Gardner P, Iyer MK, Liu Z, Lozupone CA, Quinn J, Smit S, Wikman S, Zaneveld JR, Knight R.

RNA. 2012 Jul;18(7):1319-27. doi: 10.1261/rna.032052.111. Epub 2012 May 29.

9.

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.

McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG.

Gigascience. 2012 Jul 12;1(1):7. doi: 10.1186/2047-217X-1-7.

10.

SitePainter: a tool for exploring biogeographical patterns.

Gonzalez A, Stombaugh J, Lauber CL, Fierer N, Knight R.

Bioinformatics. 2012 Feb 1;28(3):436-8. doi: 10.1093/bioinformatics/btr685. Epub 2011 Dec 9.

11.

Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R.

Curr Protoc Bioinformatics. 2011 Dec;Chapter 10:Unit 10.7.. doi: 10.1002/0471250953.bi1007s36.

12.

Microbial biogeography of public restroom surfaces.

Flores GE, Bates ST, Knights D, Lauber CL, Stombaugh J, Knight R, Fierer N.

PLoS One. 2011;6(11):e28132. doi: 10.1371/journal.pone.0028132. Epub 2011 Nov 23.

13.

Comprehensive survey and geometric classification of base triples in RNA structures.

Abu Almakarem AS, Petrov AI, Stombaugh J, Zirbel CL, Leontis NB.

Nucleic Acids Res. 2012 Feb;40(4):1407-23. doi: 10.1093/nar/gkr810. Epub 2011 Nov 3.

14.

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.

Pirrung M, Kennedy R, Caporaso JG, Stombaugh J, Wendel D, Knight R.

Bioinformatics. 2011 Nov 1;27(21):3067-9. doi: 10.1093/bioinformatics/btr517. Epub 2011 Sep 8.

15.

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation.

Zaneveld JR, Parfrey LW, Van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuczynski J, Knight R.

Trends Microbiol. 2011 Oct;19(10):472-82. doi: 10.1016/j.tim.2011.07.006. Epub 2011 Aug 25. Review.

16.

Meeting report of the RNA Ontology Consortium January 8-9, 2011.

Birmingham A, Clemente JC, Desai N, Gilbert J, Gonzalez A, Kyrpides N, Meyer F, Nawrocki E, Sterk P, Stombaugh J, Weinberg Z, Wendel D, Leontis NB, Zirbel C, Knight R, Laederach A.

Stand Genomic Sci. 2011 Apr 29;4(2):252-6. doi: 10.4056/sigs.1724282.

17.

Moving pictures of the human microbiome.

Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, Gordon JI, Knight R.

Genome Biol. 2011;12(5):R50. doi: 10.1186/gb-2011-12-5-r50.

18.

Sharing and archiving nucleic acid structure mapping data.

Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, Zirbel CL, Laederach A.

RNA. 2011 Jul;17(7):1204-12. doi: 10.1261/rna.2753211. Epub 2011 May 24.

19.

Responses of gut microbiota to diet composition and weight loss in lean and obese mice.

Ravussin Y, Koren O, Spor A, LeDuc C, Gutman R, Stombaugh J, Knight R, Ley RE, Leibel RL.

Obesity (Silver Spring). 2012 Apr;20(4):738-47. doi: 10.1038/oby.2011.111. Epub 2011 May 19.

20.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO.

Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823.

21.

Boulder ALignment Editor (ALE): a web-based RNA alignment tool.

Stombaugh J, Widmann J, McDonald D, Knight R.

Bioinformatics. 2011 Jun 15;27(12):1706-7. doi: 10.1093/bioinformatics/btr258. Epub 2011 May 5.

22.

The mind-body-microbial continuum.

Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh PJ, Gordon JI, Knight R.

Dialogues Clin Neurosci. 2011;13(1):55-62.

23.

Technology and data-intensive science in the beginning of the 21st century.

Bernstein PA, Wecker D, Krishnamurthy A, Manocha D, Gardner J, Kolker N, Reschke C, Stombaugh J, Vagata P, Stewart E, Welch D, Kolker E.

OMICS. 2011 Apr;15(4):203-7. doi: 10.1089/omi.2011.0013.

PMID:
21476841
24.

Human oral, gut, and plaque microbiota in patients with atherosclerosis.

Koren O, Spor A, Felin J, Fåk F, Stombaugh J, Tremaroli V, Behre CJ, Knight R, Fagerberg B, Ley RE, Bäckhed F.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4592-8. doi: 10.1073/pnas.1011383107. Epub 2010 Oct 11.

25.

UniFrac: an effective distance metric for microbial community comparison.

Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R.

ISME J. 2011 Feb;5(2):169-72. doi: 10.1038/ismej.2010.133. Epub 2010 Sep 9. No abstract available.

26.

Succession of microbial consortia in the developing infant gut microbiome.

Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4578-85. doi: 10.1073/pnas.1000081107. Epub 2010 Jul 28.

27.

QIIME allows analysis of high-throughput community sequencing data.

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R.

Nat Methods. 2010 May;7(5):335-6. doi: 10.1038/nmeth.f.303. Epub 2010 Apr 11. No abstract available.

28.

The RNA structure alignment ontology.

Brown JW, Birmingham A, Griffiths PE, Jossinet F, Kachouri-Lafond R, Knight R, Lang BF, Leontis N, Steger G, Stombaugh J, Westhof E.

RNA. 2009 Sep;15(9):1623-31. doi: 10.1261/rna.1601409. Epub 2009 Jul 21.

29.

Classification and energetics of the base-phosphate interactions in RNA.

Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB.

Nucleic Acids Res. 2009 Aug;37(15):4898-918. doi: 10.1093/nar/gkp468. Epub 2009 Jun 14.

30.

Frequency and isostericity of RNA base pairs.

Stombaugh J, Zirbel CL, Westhof E, Leontis NB.

Nucleic Acids Res. 2009 Apr;37(7):2294-312. doi: 10.1093/nar/gkp011. Epub 2009 Feb 24.

31.

Time and cardiac risk of surgery after bare-metal stent percutaneous coronary intervention.

Nuttall GA, Brown MJ, Stombaugh JW, Michon PB, Hathaway MF, Lindeen KC, Hanson AC, Schroeder DR, Oliver WC, Holmes DR, Rihal CS.

Anesthesiology. 2008 Oct;109(4):588-95. doi: 10.1097/ALN.0b013e318186ddf8.

PMID:
18813036
32.

FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.

Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB.

J Math Biol. 2008 Jan;56(1-2):215-52. Epub 2007 Aug 11.

33.

Tertiary structure and function of an RNA motif required for plant vascular entry to initiate systemic trafficking.

Zhong X, Tao X, Stombaugh J, Leontis N, Ding B.

EMBO J. 2007 Aug 22;26(16):3836-46. Epub 2007 Jul 26.

34.

Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database.

Fedorov A, Stombaugh J, Harr MW, Yu S, Nasalean L, Shepelev V.

Nucleic Acids Res. 2005 Aug 10;33(14):4578-83. Print 2005.

35.
36.

The non-Watson-Crick base pairs and their associated isostericity matrices.

Leontis NB, Stombaugh J, Westhof E.

Nucleic Acids Res. 2002 Aug 15;30(16):3497-531.

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