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Publications and Academic Activities The following sections list selected publications, invited presentations, patents, posters, etc. Publications (reverse chronological order) Griffith M, Paul JE, Pugh TJ, Tang MJ, Morin RD, Asano JK, Ally AA, Miao L, Cheung P, Lee A, Chan SY, Taylor G, Severson T, Hou YC, Griffith OL, Cheng GSW, Novik K, Moore R, Luk M, Owen D, Brown CJ, Morin GB, Gill S, Tai IT & Marra MA. Novel mRNA isoforms and mutations of uridine monophosphate synthetase are associated with fluorouracil resistance in colorectal cancer. Under revision (Pharmacogenomics).
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, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27.
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 Short-read Transcriptome Sequence Data. Nature Methods. 2010 Nov;7(11):909-12. Epub 2010 Oct 10.
McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, Huntsman D, Shah SP. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol. 2011 May;7(5):e1001138. Epub 2011 May 19.
Morrissy AS, Griffith M, Marra MA. Extensive relationship between antisense transcription and alternative splicing in the human genome. Genome Research. 2011 Aug;21(8):1203-12. Epub 2011 Jun 30.
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. 2010 Oct;7(10):843-847.
Jones SJM, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes A, Griffith M, Yee J, Martin M, Mayo M, Melnyk N, Morin RD, Pugh TJ, Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T, Zhao Y, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA and Marra MA. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biology. 2010, 11:R82.
MGC Project Team, Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, Misquitta L, Schaefer CF, Buetow KH, Bonner TI, Yankie L, Ward M, Phan L, Astashyn A, Brown G, Farrell C, Hart J, Landrum M, Maidak BL, Murphy M, Murphy T, Rajput B, Riddick L, Webb D, Weber J, Wu W, Pruitt KD, Maglott D, Siepel A, Brejova B, Diekhans M, Harte R, Baertsch R, Kent J, Haussler D, Brent M, Langton L, Comstock CL, Stevens M, Wei C, van Baren MJ, Salehi-Ashtiani K, Murray RR, Ghamsari L, Mello E, Lin C, Pennacchio C, Schreiber K, Shapiro N, Marsh A, Pardes E, Moore T, Lebeau A, Muratet M, Simmons B, Kloske D, Sieja S, Hudson J, Sethupathy P, Brownstein M, Bhat N, Lazar J, Jacob H, Gruber CE, Smith MR, McPherson J, Garcia AM, Gunaratne PH, Wu J, Muzny D, Gibbs RA, Young AC, Bouffard GG, Blakesley RW, Mullikin J, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJ, Holt RA, Marra MA, Lu S, Yang S, Hartigan J, Graf M, Wagner R, Letovksy S, Pulido JC, Robison K, Esposito D, Hartley J, Wall VE, Hopkins RF, Ohara O, Wiemann S. The completion of the Mammalian Gene Collection (MGC). Genome Research 2009 Dec;19(12):2324-33.
Kuchenbauer F, Morin RD, Argiropoulos B, Griffith M, Heuser M, Yung E, Piper J, Delaney A, Prabhu A, Zhao Y, McDonald H, Zeng T, Hirst M, Marra MA and Humphries RK. In depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Research 2008 Nov;18(11):1787-97. Epub 2008 Oct 10.
Pugh TJ, Delaney AD, Farnoud N, Flibotte S, Griffith M, Li HI, Farinha P, Gascoyne RD, Marra MA. Impact of whole genome amplification on analysis of copy number variants. Nucleic Acids Research. 2008. Aug. 36(13):e80.
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 Feb. 5(2):118.
Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu A, Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ and Marra MA. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Research. 2008. Apr; 18(4):610-21.
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. 36:D107-13.
Griffith M and Marra MA. Alternative expression analysis: experimental and bioinformatic approaches for the analysis of transcript diversity. 2007. Chapter 12. Genes Genomes and Genomics, Volume 2. p201-242. Regency Publications. New Delhi.
Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delany A, Griffith M, Hickenbotham M, Magrini V, Mardis ER, Sadar MD, Siddiqui AS, Marra MA, and Jones SJM. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics. 2006 Sep 29;7(1):246.
Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, Babakaiff R, Dickson MC, Matsuo C, Wong D, Yang GS, Smailus DE, Wetherby KD, Kwong PN, Grimwood J, Brinkley III CP, Brown-John M, Reddix-Dugue ND, Mayo M, Schmutz J, Beland J, Park M, Gibson S, Olson T, Bouffard GG, Tsai M, Featherstone R, Chand S, Siddiqui AS, Jang W, Lee E, Steven L. Klein SL, Blakesley RW, Zeeberg BR, Narasimhan S, Weinstein JN, Pennacchio CP, Myers RM, Green ED, Wagner L, Gerhard DS, Marra MA, Jones SJM, and Holt RA. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis. Genome Research. 2006 Jun;16(6):796-803.
Hirst M, Astell CR, Griffith M, Coughlin SM, Moksa M, Zeng T, Smailus DE, Holt RA, Jones S, Marra MA, Petric M, Krajden M, Lawrence D, Mak A, Chow R, Skowronski DM, Tweed SA, Goh S, Brunham RC, Robinson J, Bowes V, Sojonky K, Byrne SK, Li Y, Kobasa D, Booth T, and Paetzel M. Novel avian influenza H7N3 strain outbreak, British Columbia. Emerging Infectious Diseases. 2004 Dec;10(12):2192-5.
Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morrin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J; MGC Project Team. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Research. 2004 Oct;14(10B):2121-7.
Baross A, Butterfield YS, Coughlin SM, Zeng T, Griffith M, Griffith OL, Petrescu AS, Smailus DE, Khattra J, McDonald HL, McKay SJ, Moksa M, Holt RA, and Marra MA. Systematic recovery and analysis of full-ORF human cDNA clones. Genome Research. 2004 Oct;14(10B):2083-92.
Griffith M and Gietz RD. Escherichia coli endA deletion strain for use in two-hybrid shuttle vector selection. Biotechniques. 2003 Aug;35(2):272-4, 276, 278.
Invited talks Griffith M. Novel methods for transcript variant discovery and alternative expression analysis - application to the study of fluorouracil resistance in colorectal cancer. Invited talk (50 minutes). BCCA Research Seminar Series. Lloyd Skarsgard memorial lecture (presentation given by the recipient of BCCA Graduate Student Research Excellence Prize). Vancouver, BC, Canada. 28 September 2009.
Griffith M. A candidate marker of 5-FU resistance in colorectal cancer – from basic science observation to clinical validation. Invited talk (20 minutes). Bridging the Gulf between BC Cancer Clinicians and Scientists. Gastrointestinal Cancers Session. Squamish, BC, Canada. 4 April 2009.
Griffith M. Transcriptome sequencing reveals alternative splicing events in chemotherapy resistant colon cancer cells. Invited talk (20 minutes). Advances in Genomics and Biology Technology. Marco Island, Florida, USA. 5 February 2009.
Griffith M. ALEXA – a microarray design platform for alternative expression analysis. Invited talk (15 minutes). Vancouver Bioinformatics User Group. Vancouver, BC, Canada. 10 April 2008.
Griffith M. A microarray strategy to identify alternative splicing events specific to cancer cells. Invited talk (15 minutes). BC Cancer Conference. Vancouver, BC, Canada. 29 November 2007.
Griffith M. Chair’s opening address. Invited to chair session ‘Emerging Technologies and Arrays’. Discovery2Diagnostics Conference. Philadelphia, PA, USA. 19 September 2007. Griffith M. ALEXA – a platform for alternative expression analysis. Invited talk (30 minutes). Discovery2Diagnostics Conference. Philadelphia, PA, USA. 19 September 2007.
Griffith M. Microarray analysis of alternative transcription. Invited talk (15 minutes). Genome Sciences Centre – Science Retreat. Vancouver, BC, Canada. 2 November 2006.
Patents US patent application. UMPS Isoforms as Novel Predictive Markers and Therapeutic Targets for 5-FU resistance. Inventors: Marco A Marra, Isabella T Tai and Malachi Griffith. Filed by BC Cancer Agency technology development office. US patent application. Compositions and Methods for Improving Response of Cancer Patients to Chemotherapy. Inventors: Marco A Marra, Isabella T Tai and Malachi Griffith. Filed by BC Cancer Agency technology development office. Poster presentations (first author only; reverse chronological order) Griffith M, Goya R, Morin R, Pleasance E, Shah S, Huntsman D, Aparicio S, Marra MA. RNA sequencing and exon junction profiling for isoform specific biomarker discovery. Advances in Genome Biology and Technology. Marco Island, FL, USA. Feb 2011.
Griffith M, Griffith OL, Morin RD, Tang MJ, Hou YJ, Pugh TJ, Ally A, Asana JK, Chan SY, Li HI, McDonald H, Teague K, Zhao Y, Zeng T, Delaney A, Hirst M, Morin GB, Jones SJM, Tai IT, Marra MA. Alternative expression analysis by RNA sequencing. Advances in Genome Biology and Technology. Marco Island, FL, USA. Feb 2011.
Griffith M, Griffith OL, Morin RD, Tang MJ, Hou YJ, Pugh TJ, Ally A, Asana JK, Chan SY, Li HI, McDonald H, Teague K, Zhao Y, Zeng T, Delaney A, Hirst M, Morin GB, Jones SJM, Tai IT, Marra MA. Alternative expression analysis by RNA sequencing. British Columbia Cancer Agency Research Day. Vancouver, BC, Canada. September 2010.
Griffith M, Tang MJ, Chan S, Asano J, Ally A, Pugh T, Tai IT and Marra MA. Identification of differentially expressed alternative mRNA isoforms associated with chemotherapy resistance in colon cancer cell lines. Medical Genetics Research Day. Vancouver, BC, Canada. November 2008.
Griffith M, Tang MJ, Chan S, Asano J, Ally A, Pugh T, Tai IT and Marra MA. Identification of differentially expressed alternative mRNA isoforms associated with chemotherapy resistance in colon cancer cell lines. RiboWest. Lethbridge, AB, Canada. June 2008. Poster presented by Gregg Morin.
Griffith M, Tang MJ, Chan S, Asano J, Ally A, Pugh T, Tai IT and Marra MA. Identification of differentially expressed alternative mRNA isoforms associated with chemotherapy resistance in colon cancer cell lines. Digestive Disease Week. San Diego, CA, USA. May 2008. NOTE: This poster was identified as a ‘Poster of Distinction’ (top 10% of submissions).
Griffith M, Tang M, Griffith O, Morin R, Chan S, Asano J, Zeng T, Flibotte S, Ally A, Baross A, Hirst M, Jones S, Morin G, Tai I and Marra MA. ALEXA, A microarray design platform for alternative expression analysis. Pacific Symposium of Biocomputing. Kohala Coast, HI, USA. January 2008.
Griffith M, Tang M, Griffith O, Morin R, Chan S, Asano J, Zeng T, Flibotte S, Ally A, Baross A, Hirst M, Jones S, Morin G, Tai I and Marra MA. ALEXA, A microarray design platform for alternative expression analysis. BC Cancer Conference. Vancouver, BC, Canada. November 2007.
Griffith M, Tang M, Griffith O, Morin R, Chan S, Asano J, Zeng T, Flibotte S, Ally A, Baross A, Hirst M, Jones S, Morin G, Tai I and Marra MA. ALEXA, A microarray design platform for alternative expression analysis. Medical Genetics Research Day. Vancouver, BC, Canada. November 2007.
Griffith M, Tang M, Chan S, Asano J, Griffith O, Zeng T, Flibotte S, Baross A, Hirst M, Tai I and Marra MA. ALEXA, A computational platform for alternative expression analysis. Advances in Genome Biology and Technology. Marco Island, FL, USA. February 2007.
Griffith M, Tang M, Chan S, Asano J, Griffith O, Zeng T, Flibotte S, Baross A, Hirst M, Tai I and Marra MA. Identification of Differentially Expressed Isoforms Associated with Chemotherapy Resistance in Colon Cancer Cell Lines. Medical Genetics Research Day. Vancouver, BC, Canada. December 2006.
Griffith M, Tang M, Chan S, Asano J, Griffith O, Zeng T, Flibotte S, Baross A, Hirst M, Tai I and Marra MA. Identification of Differentially Expressed Isoforms Associated with Chemotherapy Resistance in Colon Cancer Cell Lines. BC Cancer Conference. Vancouver, BC, Canada. November 2006.
Griffith M, Flibotte S, Zheng T, Hirst M and Marra M. Characterization of alternative splicing events in the druggable genome using splicing microarrays. CIHR Student Health Research Forum. Winnipeg, MB, Canada. June 2006.
Griffith M, Flibotte S, Zheng T, Hirst M and Marra M. Characterization of alternative splicing events in the druggable genome using splicing microarrays. The Biology of Genomes. Cold Spring Harbor Laboratory, NY, USA. May 2006.
Griffith M, Flibotte S, Zheng T, Hirst M and Marra M. Characterization of alternative splicing events in the druggable genome using splicing microarrays. World Microarray Congress. Vancouver, BC, Canada. March 2006.
Griffith M, Hirst M, Morin R, Flibotte S, Connors J, Marra M. Development of a Method for the Study of Alternative Splicing in Cancer. Pacific Symposium on Biocomputing. Wailea, HI, USA. January 2006.
Griffith M, Hirst M, Morin R, Flibotte S, Connors J, Marra M. Development of a Method for the Study of Alternative Splicing in Cancer. BC Cancer Conference. Vancouver, BC, Canada. November 2005.
Griffith M, Baross A, Butterfield YSN, Coughlin SM, Zeng T, Griffith OL, Petrescu AS, Smailus DE, Khattra J, McDonald HL, McKay SJ, Moksa M, Holt RA, Marra MA. Targeted large scale generation and analysis of full-ORF human cDNA clones. The Biology of Genomes. Cold Spring Harbor Laboratory, NY, USA. May 2004. Griffith M, Baross A, Butterfield Y, Coughlin S, Zeng T, Griffith O, Petrescu A, Smailus D, Khattra J, McDonald H, McKay S, Moksa M, Holt R, Marra M. Targeted large scale generation and analysis of full-orf human cDNA clones. Genomics Forum: Genomics and the Science of Life. Vancouver, BC, Canada. Mar 2004. |
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