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Selection of models for the analysis of risk-factor trees: leveraging biological knowledge to mine large sets of risk factors with application to microbiome data.
Zhang Q, Abel H, Wells A, Lenzini P, Gomez F, Province MA, Templeton AA, Weinstock GM, Salzman NH, Borecki IB. Zhang Q, et al. Among authors: weinstock gm. Bioinformatics. 2015 May 15;31(10):1607-13. doi: 10.1093/bioinformatics/btu855. Epub 2015 Jan 6. Bioinformatics. 2015. PMID: 25568281 Free PMC article.
Somatic mutations affect key pathways in lung adenocarcinoma.
Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK. Ding L, et al. Among authors: weinstock gm. Nature. 2008 Oct 23;455(7216):1069-75. doi: 10.1038/nature07423. Nature. 2008. PMID: 18948947 Free PMC article.
Enteric defensins are essential regulators of intestinal microbial ecology.
Salzman NH, Hung K, Haribhai D, Chu H, Karlsson-Sjöberg J, Amir E, Teggatz P, Barman M, Hayward M, Eastwood D, Stoel M, Zhou Y, Sodergren E, Weinstock GM, Bevins CL, Williams CB, Bos NA. Salzman NH, et al. Among authors: weinstock gm. Nat Immunol. 2010 Jan;11(1):76-83. doi: 10.1038/ni.1825. Epub 2009 Oct 22. Nat Immunol. 2010. PMID: 19855381 Free PMC article.
MSC: a metagenomic sequence classification algorithm.
Saha S, Johnson J, Pal S, Weinstock GM, Rajasekaran S. Saha S, et al. Among authors: weinstock gm. Bioinformatics. 2019 Sep 1;35(17):2932-2940. doi: 10.1093/bioinformatics/bty1071. Bioinformatics. 2019. PMID: 30649204 Free PMC article.
Microbiome Signatures Associated With Steatohepatitis and Moderate to Severe Fibrosis in Children With Nonalcoholic Fatty Liver Disease.
Schwimmer JB, Johnson JS, Angeles JE, Behling C, Belt PH, Borecki I, Bross C, Durelle J, Goyal NP, Hamilton G, Holtz ML, Lavine JE, Mitreva M, Newton KP, Pan A, Simpson PM, Sirlin CB, Sodergren E, Tyagi R, Yates KP, Weinstock GM, Salzman NH. Schwimmer JB, et al. Among authors: weinstock gm. Gastroenterology. 2019 Oct;157(4):1109-1122. doi: 10.1053/j.gastro.2019.06.028. Epub 2019 Jun 27. Gastroenterology. 2019. PMID: 31255652 Free PMC article.
Characterizing the cancer genome in lung adenocarcinoma.
Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, Lin WM, Province MA, Kraja A, Johnson LA, Shah K, Sato M, Thomas RK, Barletta JA, Borecki IB, Broderick S, Chang AC, Chiang DY, Chirieac LR, Cho J, Fujii Y, Gazdar AF, Giordano T, Greulich H, Hanna M, Johnson BE, Kris MG, Lash A, Lin L, Lindeman N, Mardis ER, McPherson JD, Minna JD, Morgan MB, Nadel M, Orringer MB, Osborne JR, Ozenberger B, Ramos AH, Robinson J, Roth JA, Rusch V, Sasaki H, Shepherd F, Sougnez C, Spitz MR, Tsao MS, Twomey D, Verhaak RG, Weinstock GM, Wheeler DA, Winckler W, Yoshizawa A, Yu S, Zakowski MF, Zhang Q, Beer DG, Wistuba II, Watson MA, Garraway LA, Ladanyi M, Travis WD, Pao W, Rubin MA, Gabriel SB, Gibbs RA, Varmus HE, Wilson RK, Lander ES, Meyerson M. Weir BA, et al. Among authors: weinstock gm. Nature. 2007 Dec 6;450(7171):893-8. doi: 10.1038/nature06358. Epub 2007 Nov 4. Nature. 2007. PMID: 17982442 Free PMC article.
The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. Danecek P, et al. Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. Bioinformatics. 2011. PMID: 21653522 Free PMC article.
Graph accordance of next-generation sequence assemblies.
Yao G, Ye L, Gao H, Minx P, Warren WC, Weinstock GM. Yao G, et al. Among authors: weinstock gm. Bioinformatics. 2012 Jan 1;28(1):13-6. doi: 10.1093/bioinformatics/btr588. Epub 2011 Oct 23. Bioinformatics. 2012. PMID: 22025481 Free PMC article.
Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci.
Leslie EJ, Taub MA, Liu H, Steinberg KM, Koboldt DC, Zhang Q, Carlson JC, Hetmanski JB, Wang H, Larson DE, Fulton RS, Kousa YA, Fakhouri WD, Naji A, Ruczinski I, Begum F, Parker MM, Busch T, Standley J, Rigdon J, Hecht JT, Scott AF, Wehby GL, Christensen K, Czeizel AE, Deleyiannis FW, Schutte BC, Wilson RK, Cornell RA, Lidral AC, Weinstock GM, Beaty TH, Marazita ML, Murray JC. Leslie EJ, et al. Among authors: weinstock gm. Am J Hum Genet. 2015 Mar 5;96(3):397-411. doi: 10.1016/j.ajhg.2015.01.004. Epub 2015 Feb 19. Am J Hum Genet. 2015. PMID: 25704602 Free PMC article.
366 results