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SHRiMP: accurate mapping of short color-space reads.
Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M. Rumble SM, et al. Among authors: brudno m. PLoS Comput Biol. 2009 May;5(5):e1000386. doi: 10.1371/journal.pcbi.1000386. Epub 2009 May 22. PLoS Comput Biol. 2009. PMID: 19461883 Free PMC article.
Savant: genome browser for high-throughput sequencing data.
Fiume M, Williams V, Brook A, Brudno M. Fiume M, et al. Among authors: brudno m. Bioinformatics. 2010 Aug 15;26(16):1938-44. doi: 10.1093/bioinformatics/btq332. Epub 2010 Jun 20. Bioinformatics. 2010. PMID: 20562449 Free PMC article.
Detecting copy number variation with mated short reads.
Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M. Medvedev P, et al. Among authors: brudno m. Genome Res. 2010 Nov;20(11):1613-22. doi: 10.1101/gr.106344.110. Epub 2010 Aug 30. Genome Res. 2010. PMID: 20805290 Free PMC article.
Mixture model for sub-phenotyping in GWAS.
Warde-Farley D, Brudno M, Morris Q, Goldenberg A. Warde-Farley D, et al. Among authors: brudno m. Pac Symp Biocomput. 2012:363-74. Pac Symp Biocomput. 2012. PMID: 22174291 Free article.
Savant Genome Browser 2: visualization and analysis for population-scale genomics.
Fiume M, Smith EJ, Brook A, Strbenac D, Turner B, Mezlini AM, Robinson MD, Wodak SJ, Brudno M. Fiume M, et al. Among authors: brudno m. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W615-21. doi: 10.1093/nar/gks427. Epub 2012 May 25. Nucleic Acids Res. 2012. PMID: 22638571 Free PMC article.
PhenoTips: patient phenotyping software for clinical and research use.
Girdea M, Dumitriu S, Fiume M, Bowdin S, Boycott KM, Chénier S, Chitayat D, Faghfoury H, Meyn MS, Ray PN, So J, Stavropoulos DJ, Brudno M. Girdea M, et al. Among authors: brudno m. Hum Mutat. 2013 Aug;34(8):1057-65. doi: 10.1002/humu.22347. Epub 2013 May 24. Hum Mutat. 2013. PMID: 23636887
Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations.
Buczkowicz P, Hoeman C, Rakopoulos P, Pajovic S, Letourneau L, Dzamba M, Morrison A, Lewis P, Bouffet E, Bartels U, Zuccaro J, Agnihotri S, Ryall S, Barszczyk M, Chornenkyy Y, Bourgey M, Bourque G, Montpetit A, Cordero F, Castelo-Branco P, Mangerel J, Tabori U, Ho KC, Huang A, Taylor KR, Mackay A, Bendel AE, Nazarian J, Fangusaro JR, Karajannis MA, Zagzag D, Foreman NK, Donson A, Hegert JV, Smith A, Chan J, Lafay-Cousin L, Dunn S, Hukin J, Dunham C, Scheinemann K, Michaud J, Zelcer S, Ramsay D, Cain J, Brennan C, Souweidane MM, Jones C, Allis CD, Brudno M, Becher O, Hawkins C. Buczkowicz P, et al. Among authors: brudno m. Nat Genet. 2014 May;46(5):451-6. doi: 10.1038/ng.2936. Epub 2014 Apr 6. Nat Genet. 2014. PMID: 24705254 Free PMC article.
211 results