Obi Griffith, Ph.D.,  The Genome Institute

Dr. Obi Griffith is Assistant Professor of Medicine and Assistant Director at The Genome Institute. Dr. Griffith's research is focused on the development of personalized medicine strategies for cancer using genomic technologies with a particular focus on gene regulatory changes associated with breast cancer. He develops and uses bioinformatics and statistical methods for the analysis of high throughput sequence data and identification of biomarkers for diagnostic, prognostic and drug response prediction.

Dr. Griffith has developed and instructs a workshop on RNA sequence analysis for Cold Spring Harbor Laboratories and is a regular instructor for the Canadian Bioinformatics Workshops series. He was recently awarded an NCI K22 Transition Career Development Award. In the past, he has received numerous other awards from Atomic Energy of Canada Ltd., Natural Sciences and Engineering Research Council, University of Winnipeg, University of British Columbia, Canadian Institutes of Health Research (CIHR) and British Columbia Cancer Agency. He was a Junior and Senior Trainee of the Michael Smith Foundation for Health Research and received both doctoral and post-doctoral fellowship awards from CIHR. He was profiled in Maclean’s magazine as one of Canada’s 25 ‘Best and Brightest’ for his contribution to the sequencing of the SARS genome. He has also been profiled as an 'up and coming investigator' by Genome Technology Magazine and as an emerging talent in Wired Magazine's Annual 'Smart List'.

Before coming to Washington University, Dr. Griffith completed bioinformatics post-doctoral fellowships at Lawrence Berkeley National Laboratory in Berkeley, California and at the BC Cancer Agency Genome Sciences Centre in Vancouver, British Columbia. He received his Ph.D. (Medical Genetics, 2008) from the University of British Columbia and B.S. (Biochemistry and Biology with Honors, 2002) from the University of Winnipeg.

Selected Publications

List of publications (PubMed)

Solga A, Pong W, Walker J, Wylie T, Magrini V, Apicelli A, Griffith M, Griffith OL, Kohsaka S, Wu G, Brody D, Mardis E, Gutmann D. 2014. RNA-sequencing reveals oligodendrocyte and neuronal transcripts in microglia relevant to central nervous system disease. GLIA. Accepted.

Juric D*, Castel P*, Griffith M, Griffith OL, Won HH, Ellis H, Ebbesen S, Ainscough BJ, Ramu A, Iyer G, Shah RH, Huynh T, Mino-Kenudson M, Sgroi D, Isakoff S, Thabet A, Elamine L, Quadt C, Peters M, Huang A, Mardis ER, Solit D, Lowe S, Berger MF, Baselga J, Scaltriti M. 2014. Convergent loss of PTEN leads to clinical resistance to a PI3Kalpha inhibitor. Nature. Accepted. *These authors contributed equally to this work.

Fan P, Cunliffe HE, Griffith OL, Agboke FA, Ramos P, Gray JW, Jordan VC. 2014. A molecular model for the mechanism of acquired tamoxifen resistance in breast cancer. European Journal of Cancer. Accepted.

Good BM, Ainscough BJ, McMichael JF, Su AI†, Griffith OL†. 2014. Organizing knowledge to personalize medicine in cancer. Genome Biology. 15(8):438. †Corresponding author

Good BM, Loguercio S, Griffith OL, Nanis M, Wu C, Su AI. 2014. The Cure: Design and Evaluation of a Crowdsourcing Game for Gene Selection for Breast Cancer Survival Prediction. Journal of Medical Internet Research. 2(2):e7.

Griffith OL, Griffith M. 2013. Nucleic Acid Databases in Concise Encyclopaedia of Bioinformatics and Computational Biology. Hancock JM, Zvelebil MJ, editors. John Wiley & Sons. Hoboken, NJ.

Griffith M*, Griffith OL*, Coffman AC, Weible JV, McMichael JF, Spies NC, Koval J, Das I, Callaway MB, Eldred JM, Miller CA, Subramanian J, Govindan R, Kumar RD, Bose R, Ding L, Larson DE, Dooling DJ, Smith SM, Ley TJ, Mardis ER, Wilson RK. 2013. DGIdb – Mining the druggable genome for personalized medicine. Nature Methods. Advance online publication. *These authors contributed equally to this work.

Daemen A*, Griffith OL*, Heiser LM, Wang NJ, Enache OM, Sanborn Z, Pepin F, Durinck S, Korkola JE, Griffith M, Hur JS, Huh N, Chung J, Cope L, Fackler MJ, Umbricht C, Sukumar S, Seth P, Sukhatme VP, Jakkula LR, Lu Y, Mills GB, Cho RJ, Collisson E, van’t Veer LJ, Spellman PT, Gray JW. 2013. Modeling precision treatment of breast cancer. Genome Biology. 14:R110. *These authors contributed equally.

Griffith OL, Pepin F, Enache OM, Heiser LM, Collisson EA, Spellman PT, Gray JW. 2013. A robust prognostic signature for hormone-positive node-negative breast cancer. Genome Medicine. 5(10):92.

Fan P, Griffith OL, Agboke FA, Anur P, Zou X, McDaniel RE, Creswell K, Kim SH, Katzenellenbogen JA, Gray JW, Jordan VC. 2013. c-Src Modulates Estrogen-Induced Stress and Apoptosis in Estrogen-Deprived Breast Cancer Cells. Cancer Research. 73(14):4510-20.

Akhavan A, Griffith OL, Soroceanu L, Leonoudakis D, Luciani-Torres MG, Daemen A, Gray JW, Muschler JL. 2012. Loss of cell-surface laminin anchoring promotes tumor growth and is associated with poor clinical outcomes. Cancer Research. 72(10):2578-88.

Griffith OL, Gray JW. 2011. Omic approaches to preventing or managing metastatic breast cancer. Breast Cancer Research. 13(6):230.

Wiseman SM, Griffith OL, Gown A, Walker B, Jones SJM. 2011. Immunophenotyping Of Thyroid Tumors Identifies Molecular Markers Altered During Transformation Of Differentiated Into Anaplastic Carcinoma. American Journal of Surgery. 201(5):580-586.

Johner A, Griffith OL, Wood L, Piper H, Wilkins G, Walker B, Baliski C, Bugis S, Jones SJM, Wiseman SM. 2011. Detection and Management of Hypothyroidism Following Thyroid Lobectomy: Evaluation of a Clinical Algorithm. Annals of Surgical Oncology. 18(9):2548-2554.

Griffith M, Griffith OL, Mwenifumbo J, Morin RD, Goya R, Tang MJ, Hou Y, Pugh TJ, Robertson G, Chittaranjan S, Ally A, Asano 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. 2010. Alternative expression analysis by RNA sequencing. Nature Methods. 7(10):843-7.

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, Marra MA. 2010. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biology. 11:R82.

Montgomery SB, Kasaian K, Jones SJM, Griffith OL. 2010. Annotating the regulatory genome. Methods Mol Biol. 674:313-49.

Griffith OL, Melck A, Jones SJM, Wiseman SM. Thyroid Cancer: Identification of Gene Expression Markers for Diagnosis. 2010. In Methods of Cancer Diagnosis, Therapy and Prognosis, 7(3):353-377. Hayat MA, editor. Springer Publishing Company. New York, NY.

Griffith OL, Chiu CG, Gown AM, Jones SJM, Wiseman SM. 2008. Biomarker Panel Diagnosis of Thyroid Cancer: A Critical Review. Expert Review of Anticancer Therapy. 8(9):1399-1413.

Wiseman SM, Melck A, Masoudi H, Ghaidi F, Goldstein L, Gown A, Jones SJM, Griffith OL. 2008. Molecular Phenotyping of Thyroid Tumors Identifies a Marker Panel for Differentiated Thyroid Cancer Diagnosis. Annals of Surgical Oncology. 15(10):2811-26.

Wiseman SM, Griffith OL, Melck A, Masoudi H, Gown A, Nabi IR, Jones SJM. 2008. Evaluation of type 1 growth factor receptor family expression in benign and malignant thyroid lesions. The American Journal of Surgery. 195(5):667-73.

Leung S, Griffith OL, Masoudi H, Gown A, Jones S, Phang T, Wiseman SM. 2008. Clinical utility of type 1 growth factor receptor expression in colon cancer. The American Journal of Surgery. 195(5):604-10.

Chan SK, Griffith OL, Tai IT, Jones SJM. 2008. Meta-analysis of Colorectal Cancer Gene Expression Profiling Studies Identifies Consistently Reported Candidate Biomarkers. Cancer Epidemiology Biomarkers & Prevention. 17(3):543-52.

Aerts S, Haeussler M, Van Vooren S, Griffith OL, Hulpiau P, Jones SJM, Montgomery SB, Bergman CM; Open Regulatory Annotation Consortium. 2008. Text-mining assisted regulatory annotation. Genome Biology. 9(2):R31.1-13.

Griffith M, Tang MJ, Griffith OL, Chan SY, Asano JK, Zeng T, Flibotte S, Ally A, Baross A, Morin RD, Hirst M, Jones SJM, Morin GB, Tai IT and Marra MA. 2008. ALEXA - A microarray design platform for alternative expression analysis. Nature Methods. 5(2):118.

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; Open Regulatory Annotation Consortium. 2008. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research. 36(Database issue):D107-13. *These authors contributed equally to this work.

Wiseman SM, Griffith OL, Deen S, Rajput A, Masoudi H, Gilks B, Goldstein L, Gown A, Jones SJM. 2007. Identification of Molecular Markers Altered During Transformation of Differentiated Into Anaplastic Thyroid Carcinoma. Archives of Surgery. 142(8):717-729.

Montgomery SB, Griffith OL, Schuetz JM, Brooks-Wilson A, Jones SJM. 2007. A survey of genomic properties for the detection of regulatory polymorphisms. PLoS Computational Biology. 3(6): e106.

Griffith OL, Melck A, Jones SJM, Wiseman SM. 2006. A Meta-analysis and Meta-review of Thyroid Cancer Gene Expression Profiling Studies Identifies Important Diagnostic Biomarkers. Journal of Clinical Oncology. 24(31):5043-5051.

Gao BJ, Griffith OL, Ester M, Jones SJ. 2006. Discovering significant OPSM subspace clusters in massive gene expression data. In Proceedings of the 12th ACM SIGKDD international Conference on Knowledge Discovery and Data Mining (Philadelphia, PA, USA, August 20 - 23, 2006). KDD '06. ACM Press, New York, NY, 922-928.

Montgomery SB*, Griffith OL*, Bilenky M, Pleasance ED, Prychyna Y, Sleumer MC, Zhang X, Jones SJM. 2006. ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites, and regulatory variation. Bioinformatics. 22(5):637-640. *These authors contributed equally to this work.

Siddiqui AS, Delaney AD, Schnerch A, Griffith OL, Jones SJM, Marra MA. 2006. Sequence biases in large scale gene expression profiling data. Nucleic Acids Research. 34(12):e83.

Griffith OL, Pleasance ED, Fulton DL, Oveisi M, Ester M, Siddiqui AS, Jones SJM. 2005. Assessment and Integration of Publicly Available SAGE, cDNA Microarray, and Oligonucleotide Microarray Expression Data for Global Coexpression Analyses. Genomics. 86:476-488.

Baross Á, Butterfield YSN, Coughlin SM, Zeng T, Griffith M, Griffith OL, Petrescu AS, Smailus DE, Khattra J, McDonald HL, McKay SJ, Moksa M, Holt RA, Marra MA. 2004. Systematic Recovery and Analysis of Full-ORF Human cDNA Clones. Genome Research. 14(10B):2083-92.

Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YS, Khattra J, Asano JK, Barber SA, Chan SY, Cloutier A, Coughlin SM, Freeman D, Girn N, Griffith OL, Leach SR, Mayo M, McDonald H, Montgomery SB, Pandoh PK, Petrescu AS, Robertson AG, Schein JE, Siddiqui A, Smailus DE, Stott JM, Yang GS, Plummer F, Andonov A, Artsob H, Bastien N, Bernard K, Booth TF, Bowness D, Czub M, Drebot M, Fernando L, Flick R, Garbutt M, Gray M, Grolla A, Jones S, Feldmann H, Meyers A, Kabani A, Li Y, Normand S, Stroher U, Tipples GA, Tyler S, Vogrig R, Ward D, Watson B, Brunham RC, Krajden M, Petric M, Skowronski DM, Upton C, Roper RL. 2003. The Genome sequence of the SARS-associated coronavirus. Science. 300(5624):1399-404.

Griffith OL, Moodie GE, Civetta A. 2003. Genome size and Longevity in Fish. Experimental Gerontology. 38(3):333-337.

 

Publications

title citation publication date
Convergent loss of PTEN leads to clinical resistance to a PI(3)K? inhibitor. Nature. 2014 Nov 17. doi: 10.1038/nature13948. [Epub ahead of print] 2014-11-17
Clonal architectures and driver mutations in metastatic melanomas. PLoS One. 2014 Nov 13;9(11):e111153. doi: 10.1371/journal.pone.0111153. eCollection 2014. 2014-11-13
RNA-sequencing reveals oligodendrocyte and neuronal transcripts in microglia relevant to central nervous system disease. Glia. 2014 Sep 24. doi: 10.1002/glia.22754. [Epub ahead of print] 2014-09-24
Identification of gene regulation patterns underlying both oestrogen- and tamoxifen-stimulated cell growth through global gene expression profiling in breast cancer cells. Eur J Cancer. 2014 Sep 8. pii: S0959-8049(14)00889-2. doi: 10.1016/j.ejca.2014.08.010. [Epub ahead of print] 2014-09-08
Organizing knowledge to enable personalization of medicine in cancer. Genome Biol. 2014 Aug 27;15(8):438. [Epub ahead of print] 2014-08-27
SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution. PLoS Comput Biol. 2014 Aug 7;10(8):e1003665. doi: 10.1371/journal.pcbi.1003665. eCollection 2014. 2014-08-07
cDNA Hybrid Capture Improves Transcriptome Analysis on Low-Input and Archived Samples. J Mol Diagn. 2014 May 8. pii: S1525-1578(14)00072-5. doi: 10.1016/j.jmoldx.2014.03.004. [Epub ahead of print] 2014-05-08
A robust prognostic signature for hormone-positive node-negative breast cancer. Genome Med. 2013 Oct 11;5(10):92. [Epub ahead of print] 2013-10-11
Modeling precision treatment of breast cancer Genome Biol. 2013;14(10):R110. 2013-10-31
F11R Is a Novel Monocyte Prognostic Biomarker for Malignant Glioma. PLoS One. 2013 Oct 11;8(10):e77571. doi: 10.1371/journal.pone.0077571. 2013-10-11
DGIdb: mining the druggable genome. Nat Methods. 2013 Oct 13. doi: 10.1038/nmeth.2689. [Epub ahead of print] 2013-10-13
Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts. Cell Rep. 2013 Sep 18. pii: S2211-1247(13)00463-4. doi: 10.1016/j.celrep.2013.08.022. [Epub ahead of print] 2013-09-18