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165 results
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MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions.
Lee S, Hormozdiari F, Alkan C, Brudno M. Lee S, et al. Among authors: brudno m. Nat Methods. 2009 Jul;6(7):473-4. doi: 10.1038/nmeth.f.256. Epub 2009 May 31. Nat Methods. 2009. PMID: 19483690 No abstract available.
Computational methods for discovering structural variation with next-generation sequencing.
Medvedev P, Stanciu M, Brudno M. Medvedev P, et al. Among authors: brudno m. Nat Methods. 2009 Nov;6(11 Suppl):S13-20. doi: 10.1038/nmeth.1374. Nat Methods. 2009. PMID: 19844226 Review.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F; Rat Genome Sequencing Project Consortium. Gibbs RA, et al. Among authors: brudno m. Nature. 2004 Apr 1;428(6982):493-521. doi: 10.1038/nature02426. Nature. 2004. PMID: 15057822
Similarity network fusion for aggregating data types on a genomic scale.
Wang B, Mezlini AM, Demir F, Fiume M, Tu Z, Brudno M, Haibe-Kains B, Goldenberg A. Wang B, et al. Among authors: brudno m. Nat Methods. 2014 Mar;11(3):333-7. doi: 10.1038/nmeth.2810. Epub 2014 Jan 26. Nat Methods. 2014. PMID: 24464287
FRESCO: flexible alignment with rectangle scoring schemes.
Dalca AV, Brudno M. Dalca AV, et al. Among authors: brudno m. Pac Symp Biocomput. 2008:3-14. doi: 10.1142/9789812776136_0002. Pac Symp Biocomput. 2008. PMID: 18229672
NSD1 mutations generate a genome-wide DNA methylation signature.
Choufani S, Cytrynbaum C, Chung BH, Turinsky AL, Grafodatskaya D, Chen YA, Cohen AS, Dupuis L, Butcher DT, Siu MT, Luk HM, Lo IF, Lam ST, Caluseriu O, Stavropoulos DJ, Reardon W, Mendoza-Londono R, Brudno M, Gibson WT, Chitayat D, Weksberg R. Choufani S, et al. Among authors: brudno m. Nat Commun. 2015 Dec 22;6:10207. doi: 10.1038/ncomms10207. Nat Commun. 2015. PMID: 26690673 Free PMC article.
Characterization of evolutionary rates and constraints in three Mammalian genomes.
Cooper GM, Brudno M, Stone EA, Dubchak I, Batzoglou S, Sidow A. Cooper GM, et al. Among authors: brudno m. Genome Res. 2004 Apr;14(4):539-48. doi: 10.1101/gr.2034704. Genome Res. 2004. PMID: 15059994 Free PMC article.
Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes.
Cooper GM, Brudno M; NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A. Cooper GM, et al. Among authors: brudno m. Genome Res. 2003 May;13(5):813-20. doi: 10.1101/gr.1064503. Genome Res. 2003. PMID: 12727901 Free PMC article.
Noninvasive Prenatal Detection of Trisomy 21 by Targeted Semiconductor Sequencing: A Technical Feasibility Study.
Xi Y, Arbabi A, McNaughton AJM, Hamilton A, Hull D, Perras H, Chiu T, Morrison S, Goldsmith C, Creede E, Anger GJ, Honeywell C, Cloutier M, Macchio N, Kiss C, Liu X, Crocker S, Davies GA, Brudno M, Armour CM. Xi Y, et al. Among authors: brudno m. Fetal Diagn Ther. 2017;42(4):302-310. doi: 10.1159/000460248. Epub 2017 May 17. Fetal Diagn Ther. 2017. PMID: 28511174 Clinical Trial.
Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease.
Gonorazky HD, Naumenko S, Ramani AK, Nelakuditi V, Mashouri P, Wang P, Kao D, Ohri K, Viththiyapaskaran S, Tarnopolsky MA, Mathews KD, Moore SA, Osorio AN, Villanova D, Kemaladewi DU, Cohn RD, Brudno M, Dowling JJ. Gonorazky HD, et al. Among authors: brudno m. Am J Hum Genet. 2019 Mar 7;104(3):466-483. doi: 10.1016/j.ajhg.2019.01.012. Epub 2019 Feb 28. Am J Hum Genet. 2019. PMID: 30827497 Free PMC article.
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