http://malachig.github.io/

Professional Preparation

Ph.D. in Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada, 2004–2010

B.Sc. (Honours) in Biology and Biochemistry, University of Winnipeg, Winnipeg, MB, Canada, 1996-2002

 
Selected Publications

Griffith M*†, Spies NC*, Krysiak K*, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ,Jones MR, Bilski RL, Lesurf R, Feng Y, Shah NM, Bonakdar M, Trani L, Matlock M, Ramu A, Campbell KM, Spies GC, Graubert AP, Gangavarapu K, Eldred JM, Larson DE, Walker JR, Good BM, Wu C, Su AI, Dienstmann R, Margolin A, Lopez-Bigas N, Jones SJM, Bose R, Spencer DH, Wartman LD, Wilson RK, Mardis ER, Griffith OL†. CIViC: A resource forcrowdsourcing the clinical interpretation of variants in cancer. Accepted for publication in Nature Genetics.

Griffith OL, Chan SR, Griffith M, Krysiak K, Skidmore ZL, Hundal J, Allen JA, Arthur C, Miceli AP, Schmidt H, Trani L, Kanchi K, Miller CA, Larson DE, Fulton RS, Wilson RK,Schreiber RD, Mardis ER. Whole Genome Sequencing of Murine Estrogen Receptor-Alpha Mammary Carcinoma Identifies Prolactin Receptor Mutation that Drives Tumor Development . Accepted for publication in Cell Reports.

Ainscough BJ*, Griffith M†, Coffman AC, Wagner AH, Kunisaki J, Choudhary MNK, McMichael JF, Fulton RS, Wilson RK, Griffith OL†, Mardis ER. A curated knowledgebase rescues clinically impactful cancer mutations. Accepted for publication in Nature Methods.

Miller CA, Gindin Y, Lu C, Griffith OL, Griffith M, Shen D, Hoog J, Li T, Larson DE, Watson M, Davies SR, Hunt K, Suman VJ, Snider J, Walsh T, Colditz GA, DeSchryver K,Wilson RK, Mardis ER, Ellis MJ. Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers. Nat Commun. 2016 Aug 9;7:12498.

Skidmore ZL, Wagner AH, Lesurf R, Campbell KM, Kunisaki J, Griffith OL†, Griffith M†. GenVisR: Genomic Visualizations in R. Bioinformatics. 2016

Krysiak K, Christopher MJ, Skidmore ZL, Demeter RT, Magrini V, Kunisaki J, O'Laughlin M, Duncavage EJ, Miller CA, Ozenberger BA, Griffith M, Wartman LD, and Griffith OL. A genomic analysis of Philadelphia chromosome-negative AML arising in patients with CML.Blood Cancer J. 2016.

Hundal J, Carreno BM, Petti AA, Linette GP, Griffith OL, Mardis ER, Griffith M. pVACSeq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Med.  2016

Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB, Griffith OL; Open Regulatory Annotation Consortium. ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Res. 2016

Wagner AH, Coffman AC, Ainscough BJ, Spies NC, Skidmore ZL, Campbell KM, Krysiak K, Pan D, McMichael JF, Eldred JM, Walker JR, Wilson RK, Mardis ER, Griffith M†, Griffith OL†. DGIdb 2.0: mining clinically relevant drug-gene interactions. Nucleic Acids Res. 2016

Griffith M*, Miller CA*, Griffith OL, Krysiak K, Skidmore ZL, Ramu A, Walker JR, Dang HX, Trani L, Larson DE, Demeter RT, Wendl MC, McMichael JF, Austin RE, Magrini V, McGrath SD, Ly A, Kulkarni S, Cordes MG, Fronick CC, Fulton RS, Maher CA, Ding L, Klco JM, Mardis ER, Ley TJ, Wilson RK. Optimizing cancer genome sequencing and analysis. Cell Syst. 2015.

Griffith M†, Walker JR, Spies NC, Ainscough BJ, Griffith OL†. Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud. PLoS Comput Biol. 2015.

Griffith M*†, Griffith OL*†, Smith SM*, Ramu A, Callaway MB, Brummett AM, Kiwala MJ, Coffman AC, Regier AA, Oberkfell BJ, Sanderson GE, Mooney TP, Nutter NG, Belter EA, Du F, Long RL, Abbott TE, Ferguson IT, Morton DL, Burnett MM, Weible JV, Peck JB, Dukes A, McMichael JF, Lolofie JT, Derickson BR, Hundal J, Skidmore ZL, Ainscough BJ, Dees ND, Schierding WS, Kandoth C, Kim KH, Lu C, Harris CC, Maher N, Maher CA, Magrini VJ, Abbott BS, Chen K, Clark E, Das I, Fan X, Hawkins AE, Hepler TG, Wylie TN, Leonard SM, Schroeder WE, Shi X, Carmichael LK, Weil MR, Wohlstadter RW, Stiehr G, McLellan MD, Pohl CS, Miller CA, Koboldt DC, Walker JR, Eldred JM, Larson DE, Dooling DJ, Ding L, Mardis ER, Wilson RK. Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Comput Biol. 2015.

Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, Delaney A, Tam A, Kamoh B, Cho S, Griffith M, Chu A, Robertson G, Cheung D, Li I, Heravi-Moussavi A, Moksa M, Mingay M, Hussainkhel A, Davis B, Nagarajan RP, Hong C, Echipare L, O'Geen H, Hangauer MJ, Cheng JB, Neel D, Hu D, McManus MT, Moore R, Mungall A, Ma Y, Plettner P, Ziv E, Wang T, Farnham PJ, Jones SJ, Marra MA, Tlsty TD, Costello JF, Hirst M. Epigenetic and transcriptional determinants of the human breast . Nat Commun. 2015

Miller CA, White BS, Dees ND, Griffith M, Griffith OL, Welch JS, Vij R, Tomasson MH, Graubert TA, Walter MJ, Ellis MJ, Schierding W, DiPersio JF, Ley TJ, Mardis ER, Wilson RK, and Ding L. SciClone: Inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLoS Comput Biol. 2014

Griffith M†, Griffith OL, Coffman AC, Weible JV, Koval J, Das I, McMichael JF, Callaway MB, Eldred J, Subramanian J, Govindan R, Kumar R, Bose R, Ding L, Larson D, Dooling D, Smith S, Ley T, Mardis ER, Wilson RK. DGIdb – Mining the druggable genome for personalized medicine. Nature Methods. 2013

Govindan R, Ding L, Griffith M, Subramanian J, Dees ND, Kanchi KL, Maher C, Fulton R, Fulton L, Wallis J, Chen K, Walker J, McDonald S, Bose R, Ornitz D, Xiong D, You M, Dooling DJ, Watson M, Mardis ER, Wilson RK. Genomic landscape of non-small cell lung cancer . Cell. 2012

Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SW, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S. The clonal and mutational evolution spectrum of primary triple-negativebreast cancers. Nature. 2012

Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, ConnorsJM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011

Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield Y, Newsome R, Chan SK, Varhol R, Kamoh B, Prabhu A, Tam A, Zhao Y, Moore R, Hirst M, Marra MA, Jones SJM, Hoodless PA, Birol I. De novo assembly and analysis of RNA-seq data. Nature Methods. 2010.

Griffith M, Griffith OL, Mwenifumbo J, Morin RD, Goya R, Tang MJ, Hou YC, Pugh TJ, Robertson G, Chittaranjan S, Ally A, Asano JK, Chan SY, Li I, McDonald H, Teague K, Zhao Y, Zeng T, Delaney AD, Hirst M, Morin GB, Jones SJM, Tai IT, Marra MA. Alternative expression analysis by RNA sequencing. Nature Methods.

Griffith M, Tang MJ, Griffith OL, Morin RD, Chan SY, Asano JK, Zeng T, Flibotte S, Ally A, Baross A, Hirst M, Jones SJM, Morin GB, Tai IT and Marra MA. ALEXA – A microarray design platform for alternative expression analysis. Nature Methods. 2008

Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ; The Open Regulatory Annotation Consortium. ORegAnno: an open-access community driven resource for regulatory annotation. Nucleic Acids Research. 2008.