Oncology Division

Obi L. Griffith, PhD

Associate Professor
Department of Medicine
Oncology Division
Stem Cell Biology
Department of Genetics
McDonnell Genome Institute

Research Interests

  • Cancer informatics
  • Clinical statistics
  • Breast cancer


Peer-reviewed Manuscripts

  • A Spontaneous Aggressive ERalpha+ Mammary Tumor Model Is Driven by Kras Activation
    Campbell KM, O'Leary KA, Rugowski DE, Mulligan WA, Barnell EK, Skidmore ZL, Krysiak K, Griffith M, Schuler LA, Griffith OL
    Cell Rep 2019 Aug 6;28(6):1526-1537e4
  • Noninvasive Detection of High-Risk Adenomas Using Stool-Derived Eukaryotic RNA Sequences as Biomarkers
    Barnell E, Kang Y, Wurtzler E, Griffith M, Chaudhuri AA*, Griffith OL* (*corresponding author)
    Gastroenterology 2019 May 30; [Epub ahead of print]
  • Accounting for Proximal Variants Improves Neoantigen Prediction
    Hundal J, Kiwala S, Feng YY, Liu CJ, Govindan R, Chapman WC, Uppaluri R, Swamidass SJ, Griffith OL, Mardis ER, Griffith M
    Nat Genet 2019 Jan;51(1):175-179
  • Standard Operating Procedure for Somatic Variant Refinement of Sequencing Data With Paired Tumor and Normal Samples
    Barnell EK, Ronning P, Campbell KM, Krysiak K, Ainscough BJ, Sheta LM, Pema SP, Schmidt AD, Richters M, Cotto KC, Danos AM, Ramirez C, Skidmore ZL, Spies NC, Hundal J, Sediqzad MS, Kunisaki J, Gomez F, Trani L, Matlock M, Wagner AH, Swamidass SJ, Griffith M*, Griffith OL* (*corresponding author)
    Genet Med 2019 Apr;21(4):972-981
  • A Deep Learning Approach to Automate Refinement of Somatic Variant Calling From Cancer Sequencing Data
    Ainscough BJ, Barnell EK, Ronning P, Campbell KM, Wagner AH, Fehniger TA, Dunn GP, Uppaluri R, Govindan R, Rohan TE, Griffith M, Mardis ER, Swamidass SJ*, Griffith OL* (*corresponding author)
    Nat Genet 2018 Dec;50(12):1735-1743
  • Adapting Crowdsourced Clinical Cancer Curation in CIViC to the ClinGen Minimum Variant Level Data Community-Driven Standards
    Danos AM, Ritter DI, Wagner AH, Krysiak K, Sonkin D, Micheel C, McCoy M, Rao S, Raca G, Boca SM, Roy A, Barnell EK, McMichael JF, Kiwala S, Coffman AC, Kujan L, Kulkarni S*, Griffith M*, Madhavan S*, Griffith OL* (*corresponding author)
    Hum Mutat 2018 Nov;39(11):1721-1732
  • Recurrent WNT Pathway Alterations Are Frequent in Relapsed Small Cell Lung Cancer
    Wagner AH, Devarakonda S, Skidmore ZL, Krysiak K, Ramu A, Trani L, Kunisaki J, Masood A, Waqar SN, Spies NC, Morgensztern D, Waligorski J, Ponce J, Fulton RS, Maggi LB Jr, Weber JD, Watson MA, O'Conor CJ, Ritter JH, Olsen RR, Cheng H, Mukhopadhyay A, Can I, Cessna MH, Oliver TG, Mardis ER, Wilson RK, Griffith M*, Griffith OL*, Govindan R* (*corresponding author)
    Nat Commun 2018 Sep 17;9(1):3787
  • Oral Cavity Squamous Cell Carcinoma Xenografts Retain Complex Genotypes and Intertumor Molecular Heterogeneity
    Campbell KM, Lin T, Zolkind P, Barnell EK, Skidmore ZL, Winkler AE, Law JH, Mardis ER, Wartman LD, Adkins DR, Chernock RD, Griffith M, Uppaluri R, Griffith OL* (*corresponding author)
    Cell Rep 2018 Aug 21;24(8):2167-2178
  • The Prognostic Effects of Somatic Mutations in ER-Positive Breast Cancer
    Griffith OL, Spies NC, Anurag M, Griffith M, Luo J, Tu D, Yeo B, Kunisaki J, Miller CA, Krysiak K, Hundal J, Ainscough BJ, Skidmore ZL, Campbell K, Kumar R, Fronick C, Cook L, Snider JE, Davies S, Kavuri SM, Chang EC, Magrini V, Larson DE, Fulton RS, Liu S, Leung S, Voduc D, Bose R, Dowsett M, Wilson RK, Nielsen TO, Mardis ER, Ellis MJ
    Nat Commun 2018 Sep 4;9(1):3476
  • A Case of Acute Myeloid Leukemia With Promyelocytic Features Characterized by Expression of a Novel RARG-CPSF6 Fusion
    Miller CA, Tricarico C, Skidmore ZL, Uy GL, Lee YS, Hassan A, O'Laughlin MD, Schmidt H, Tian L, Duncavage EJ, Griffith M, Griffith OL, Welch JS, Wartman LD
    Blood Adv 2018 Jun 12;2(11):1295-1299
  • Single-Agent Ibrutinib in Relapsed or Refractory Follicular Lymphoma: A Phase 2 Consortium Trial
    Bartlett NL, Costello BA, LaPlant BR, Ansell SM, Kuruvilla JG, Reeder CB, Thye LS, Anderson DM, Krysiak K, Ramirez C, Qi J, Siegel BA, Griffith M, Griffith OL, Gomez F, Fehniger TA
    Blood 2018 Jan 11;131(2):182-190
  • DGIdb 3.0: A Redesign and Expansion of the Drug-Gene Interaction Database
    Cotto KC, Wagner AH, Feng YY, Kiwala S, Coffman AC, Spies G, Wollam A, Spies NC, Griffith OL*, Griffith M* (*corresponding author)
    Nucleic Acids Res 2018 Jan 4;46(D1):D1068-D1073
  • Standardizing and Democratizing Access to Cancer Molecular Diagnostic Test Data From Patients to Drive Translational Research
    Madhavan S, Ritter D, Micheel C, Rao S, Roy A, Sonkin D, Mccoy M, Griffith M, Griffith OL, Mcgarvey P, Kulkarni S
    AMIA Jt Summits Transl Sci Proc 2018 May 18;2017:152-159
  • ClinGen Cancer Somatic Working Group - Standardizing and Democratizing Access to Cancer Molecular Diagnostic Data to Drive Translational Research
    Madhavan S, Ritter D, Micheel C, Rao S, Roy A, Sonkin D, Mccoy M, Griffith M, Griffith OL, Mcgarvey P, Kulkarni S
    Pac Symp Biocomput 2018;23:247-258
  • A Phase II Trial of Neoadjuvant MK-2206, an AKT Inhibitor, With Anastrozole in Clinical Stage II or III PIK3CA-Mutant ER-Positive and HER2-Negative Breast Cancer
    Ma CX, Suman V, Goetz MP, Northfelt D, Burkard ME, Ademuyiwa F, Naughton M, Margenthaler J, Aft R, Gray R, Tevaarwerk A, Wilke L, Haddad T, Moynihan T, Loprinzi C, Hieken T, Barnell EK, Skidmore ZL, Feng YY, Krysiak K, Hoog J, Guo Z, Nehring L, Wisinski KB, Mardis E, Hagemann IS, Vij K, Sanati S, Al-Kateb H, Griffith OL, Griffith M, Doyle L, Erlichman C, Ellis MJ
    Clin Cancer Res 2017 Nov 15;23(22):6823-6832
  • Comprehensive Discovery of Noncoding RNAs in Acute Myeloid Leukemia Cell Transcriptomes
    Zhang J, Griffith M, Miller CA, Griffith OL, Spencer DH, Walker JR, Magrini V, McGrath SD, Ly A, Helton NM, Trissal M, Link DC, Dang HX, Larson DE, Kulkarni S, Cordes MG, Fronick CC, Fulton RS, Klco JM, Mardis ER, Ley TJ, Wilson RK, Maher CA
    Exp Hematol 2017 Nov;55:19-33
  • Melorheostosis: Exome Sequencing of an Associated Dermatosis Implicates Postzygotic Mosaicism of Mutated KRAS
    Whyte MP, Griffith M, Trani L, Mumm S, Gottesman GS, McAlister WH, Krysiak K, Lesurf R, Skidmore ZL, Campbell KM, Rosman IS, Bayliss S, Bijanki VN, Nenninger A, Van Tine BA, Griffith OL, Mardis ER
    Bone 2017 Aug;101:145-155
  • NeoPalAna: Neoadjuvant Palbociclib, a Cyclin-Dependent Kinase 4/6 Inhibitor, and Anastrozole for Clinical Stage 2 or 3 Estrogen Receptor-Positive Breast Cancer
    Ma CX, Gao F, Luo J, Northfelt DW, Goetz M, Forero A, Hoog J, Naughton M, Ademuyiwa F, Suresh R, Anderson KS, Margenthaler J, Aft R, Hobday T, Moynihan T, Gillanders W, Cyr A, Eberlein TJ, Hieken T, Krontiras H, Guo Z, Lee MV, Spies NC, Skidmore ZL, Griffith OL, Griffith M, Thomas S, Bumb C, Vij K, Bartlett CH, Koehler M, Al-Kateb H, Sanati S, Ellis MJ
    Clin Cancer Res 2017 Aug 1;23(15):4055-4065
  • Genomic Characterization of HER2-Positive Breast Cancer and Response to Neoadjuvant Trastuzumab and Chemotherapy-Results From the ACOSOG Z1041 (Alliance) Trial
    Lesurf R, Griffith OL, Griffith M, Hundal J, Trani L, Watson MA, Aft R, Ellis MJ, Ota D, Suman VJ, Meric-Bernstam F, Leitch AM, Boughey JC, Unzeitig G, Buzdar AU, Hunt KK, Mardis ER
    Ann Oncol 2017 May 1;28(5):1070-1077
  • CIViC Is a Community Knowledgebase for Expert Crowdsourcing the Clinical Interpretation of Variants in Cancer
    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 YY, 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 AA, Tamborero D, Lopez-Bigas N, Jones SJ, Bose R, Spencer DH, Wartman LD, Wilson RK, Mardis ER, Griffith OL* (*corresponding author)
    Nat Genet 2017 Jan 31;49(2):170-174
  • Recurrent Somatic Mutations Affecting B-Cell Receptor Signaling Pathway Genes in Follicular Lymphoma
    Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M*, Griffith OL*, Fehniger TA* (*corresponding author)
    Blood 2017 Jan 26;129(4):473-483
  • Neoantigens in Immunotherapy and Personalized Vaccines: Implications for Head and Neck Squamous Cell Carcinoma
    Zolkind P, Dunn GP, Lin T, Griffith M, Griffith OL, Uppaluri R
    Oral Oncol 2017 Aug;71:169-176
  • FOXA1 Overexpression Mediates Endocrine Resistance by Altering the ER Transcriptome and IL-8 Expression in ER-Positive Breast Cancer
    Fu X, Jeselsohn R, Pereira R, Hollingsworth EF, Creighton CJ, Li F, Shea M, Nardone A, De Angelis C, Heiser LM, Anur P, Wang N, Grasso CS, Spellman PT, Griffith OL, Tsimelzon A, Gutierrez C, Huang S, Edwards DP, Trivedi MV, Rimawi MF, Lopez-Terrada D, Hilsenbeck SG, Gray JW, Brown M, Osborne CK, Schiff R
    Proc Natl Acad Sci U S A 2016 Oct 25;113(43):E6600-E6609
  • Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas
    Griffith OL, Chan SR, Griffith M, Krysiak K, Skidmore ZL, Hundal J, Allen JA, Arthur CD, Runci D, Bugatti M, Miceli AP, Schmidt H, Trani L, Kanchi KL, Miller CA, Larson DE, Fulton RS, Vermi W, Wilson RK, Schreiber RD, Mardis ER
    Cell Rep 2016 Sep 27;17(1):249-60
  • DoCM: A Database of Curated Mutations in Cancer
    Ainscough BJ, Griffith M, Coffman AC, Wagner AH, Kunisaki J, Choudhary MN, McMichael JF, Fulton RS, Wilson RK, Griffith OL*, Mardis ER (*corresponding author)
    Nat Methods 2016 Sep 29;13(10):806-7
  • Aromatase Inhibition Remodels the Clonal Architecture of Estrogen-Receptor-Positive Breast Cancers
    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
    Nat Commun 2016 Aug 9;7:12498
  • GenVisR: Genomic Visualizations in R
    Skidmore ZL, Wagner AH, Lesurf R, Campbell KM, Kunisaki J, Griffith OL*, Griffith M* (*corresponding author)
    Bioinformatics 2016 Oct 1;32(19):3012-4
  • Comprehensive Genomic Analysis Reveals FLT3 Activation and a Therapeutic Strategy for a Patient With Relapsed Adult B-Lymphoblastic Leukemia
    Griffith M*, Griffith OL*, Krysiak K, Skidmore ZL, Christopher MJ, Klco JM, Ramu A, Lamprecht TL, Wagner AH, Campbell KM, Lesurf R, Hundal J, Zhang J, Spies NC, Ainscough BJ, Larson DE, Heath SE, Fronick C, O'Laughlin S, Fulton RS, Magrini V, McGrath S, Smith SM, Miller CA, Maher CA, Payton JE, Walker JR, Eldred JM, Walter MJ, Link DC, Graubert TA, Westervelt P, Kulkarni S, DiPersio JF, Mardis ER, Wilson RK, Ley TJ (*these authors contributed equally)
    Exp Hematol 2016 Jul;44(7):603-13
  • High-Performance Web Services for Querying Gene and Variant Annotation
    Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C
    Genome Biol 2016 May 6;17(1):91
  • The ErbB2DeltaEx16 Splice Variant Is a Major Oncogenic Driver in Breast Cancer That Promotes a Pro-Metastatic Tumor Microenvironment
    Turpin J, Ling C, Crosby EJ, Hartman ZC, Simond AM, Chodosh LA, Rennhack JP, Andrechek ER, Ozcelik J, Hallett M, Mills GB, Cardiff RD, Gray JW, Griffith OL, Muller WJ
    Oncogene 2016 Nov 24;35(47):6053-6064
  • A Genomic Case Study of Mixed Fibrolamellar Hepatocellular Carcinoma
    Griffith OL*^, Griffith M*, Krysiak K*, Magrini V, Ramu A, Skidmore ZL, Kunisaki J, Austin R, McGrath S, Zhang J, Demeter R, Graves T, Eldred JM, Walker J, Larson DE, Maher CA, Lin Y, Chapman W, Mahadevan A, Miksad R, Nasser I, Hanto DW^, Mardis ER^ (*contributed equally; ^corresponding author)
    Ann Oncol 2016 Jun;27(6):1148-54
  • A Genomic Analysis of Philadelphia Chromosome-Negative AML Arising in Patients With CML
    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, Griffith OL
    Blood Cancer J 2016 Apr 8;6:e413
  • A Common Founding Clone With TP53 and PTEN Mutations Gives Rise to a Concurrent Germ Cell Tumor and Acute Megakaryoblastic Leukemia
    Lu C, Riedell P, Miller CA, Hagemann IS, Westervelt P, Ozenberger BA, O'Laughlin M, Magrini V, Demeter RT, Duncavage EJ, Griffith M, Griffith OL, Wartman LD
    Cold Spring Harb Mol Case Stud 2016 Jan;2(1):a000687
  • PVAC-Seq: A Genome-Guided in Silico Approach to Identifying Tumor Neoantigens
    Hundal J, Carreno BM, Petti AA, Linette GP, Griffith OL, Mardis ER, Griffith M
    Genome Med 2016 Jan 29;8(1):11
  • ORegAnno 3.0: A Community-Driven Resource for Curated Regulatory Annotation
    Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB, Griffith OL
    Open Regulatory Annotation Consortium

    Nucleic Acids Res 2016 Jan 4;44(D1):D126-32
  • DGIdb 2.0: Mining Clinically Relevant Drug-Gene Interactions
    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* (*corresponding author)
    Nucleic Acids Res 2016 Jan 4;44(D1):D1036-44
  • A Phase I Trial of BKM120 (Buparlisib) in Combination With Fulvestrant in Postmenopausal Women With Estrogen Receptor-Positive Metastatic Breast Cancer
    Ma CX, Luo J, Naughton M, Ademuyiwa F, Suresh R, Griffith M, Griffith OL, Skidmore ZL, Spies NC, Ramu A, Trani L, Pluard T, Nagaraj G, Thomas S, Guo Z, Hoog J, Han J, Mardis E, Lockhart AC, Ellis MJ
    Clin Cancer Res 2016 Apr 1;22(7):1583-91
  • RNA Sequencing of Tumor-Associated Microglia Reveals Ccl5 as a Stromal Chemokine Critical for Neurofibromatosis-1 Glioma Growth
    Solga AC, Pong WW, Kim KY, Cimino PJ, Toonen JA, Walker J, Wylie T, Magrini V, Griffith M, Griffith OL, Ly A, Ellisman MH, Mardis ER, Gutmann DH
    Neoplasia 2015 Oct;17(10):776-88
  • Optimizing Cancer Genome Sequencing and Analysis
    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
    Cell Syst 2015 Sep 23;1(3):210-223
  • Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia
    Klco JM, Miller CA, Griffith M, Petti A, Spencer DH, Ketkar-Kulkarni S, Wartman LD, Christopher M, Lamprecht TL, Helton NM, Duncavage EJ, Payton JE, Baty J, Heath SE, Griffith OL, Shen D, Hundal J, Chang GS, Fulton R, O'Laughlin M, Fronick C, Magrini V, Demeter RT, Larson DE, Kulkarni S, Ozenberger BA, Welch JS, Walter MJ, Graubert TA, Westervelt P, Radich JP, Link DC, Mardis ER, DiPersio JF, Wilson RK, Ley TJ
    JAMA 2015 Aug 25;314(8):811-822
  • Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud
    Griffith M*, Walker JR, Spies NC, Ainscough BJ, Griffith OL* (*corresponding author)
    PLoS Comput Biol 2015 Aug 6;11(8):e1004393
  • Statistically Identifying Tumor Suppressors and Oncogenes From Pan-Cancer Genome-Sequencing Data
    Kumar RD, Searleman AC, Swamidass SJ, Griffith OL, Bose R
    Bioinformatics 2015 Nov 15;31(22):3561-8
  • Decoupling of the PI3K Pathway Via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer
    Korkola JE, Collisson EA, Heiser L, Oates C, Bayani N, Itani S, Esch A, Thompson W, Griffith OL, Wang NJ, Kuo WL, Cooper B, Billig J, Ziyad S, Hung JL, Jakkula L, Feiler H, Lu Y, Mills GB, Spellman PT, Tomlin C, Mukherjee S, Gray JW
    PLoS One 2015 Jul 16;10(7):e0133219
  • Genome Modeling System: A Knowledge Management Platform for Genomics
    Griffith M*^, Griffith OL*^, Scott M. Smith*, 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 (*contributed equally; ^corresponding author)
    PLoS Comput Biol 2015 Jul 9;11(7):e1004274
  • Convergent Loss of PTEN Leads to Clinical Resistance to a PI(3)Kalpha Inhibitor
    Juric D, Castel P, Griffith M, Griffith OL, Won HH, Ellis H, Ebbesen SH, Ainscough BJ, Ramu A, Iyer G, Shah RH, Huynh T, Mino-Kenudson M, Sgroi D, Isakoff S, Thabet A, Elamine L, Solit DB, Lowe SW, Quadt C, Peters M, Derti A, Schegel R, Huang A, Mardis ER, Berger MF, Baselga J, Scaltriti M
    Nature 2015 Feb 12;518(7538):240-4
  • RNA-Sequencing Reveals Oligodendrocyte and Neuronal Transcripts in Microglia Relevant to Central Nervous System Disease
    Solga AC, Pong WW, Walker J, Wylie T, Magrini V, Apicelli AJ, Griffith M, Griffith OL, Kohsaka S, Wu GF, Brody DL, Mardis ER, Gutmann DH
    Glia 2015 Apr;63(4):531-48
  • Clonal Architectures and Driver Mutations in Metastatic Melanomas
    Ding L, Kim M, Kanchi KL, Dees ND, Lu C, Griffith M, Fenstermacher D, Sung H, Miller CA, Goetz B, Wendl MC, Griffith O, Cornelius LA, Linette GP, McMichael JF, Sondak VK, Fields RC, Ley TJ, Mule JJ, Wilson RK, Weber JS
    PLoS One 2014 Nov 13;9(11):e111153
  • Identification of Gene Regulation Patterns Underlying Both Oestrogen- And Tamoxifen-Stimulated Cell Growth Through Global Gene Expression Profiling in Breast Cancer Cells
    Fan P, Cunliffe HE, Griffith OL, Agboke FA, Ramos P, Gray JW, Jordan VC
    Eur J Cancer 2014 Nov;50(16):2877-86
  • Organizing Knowledge to Enable Personalization of Medicine in Cancer
    Good BM, Ainscough BJ, McMichael JF, Su AI*, Griffith OL* (*corresponding author)
    Genome Biol 2014 Aug 27;15(8):438
  • SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution
    Miller CA, White BS, Dees ND, Griffith M, Welch JS, Griffith OL, Vij R, Tomasson MH, Graubert TA, Walter MJ, Ellis MJ, Schierding W, DiPersio JF, Ley TJ, Mardis ER, Wilson RK, Ding L
    PLoS Comput Biol 2014 Aug 7;10(8):e1003665
  • The Cure: Design and Evaluation of a Crowdsourcing Game for Gene Selection for Breast Cancer Survival Prediction
    Good BM, Loguercio S, Griffith OL, Nanis M, Wu C, Su AI
    JMIR Serious Games 2014 Jul 29;2(2):e7
  • cDNA Hybrid Capture Improves Transcriptome Analysis on Low-Input and Archived Samples
    Cabanski CR, Magrini V, Griffith M, Griffith OL, McGrath S, Zhang J, Walker J, Ly A, Demeter R, Fulton RS, Pong WW, Gutmann DH, Govindan R, Mardis ER, Maher CA
    J Mol Diagn 2014 Jul;16(4):440-51
  • F11R Is a Novel Monocyte Prognostic Biomarker for Malignant Glioma
    Pong WW, Walker J, Wylie T, Magrini V, Luo J, Emnett RJ, Choi J, Cooper ML, Griffith M, Griffith OL, Rubin JB, Fuller GN, Piwnica-Worms D, Feng X, Hambardzumyan D, DiPersio JF, Mardis ER, Gutmann DH
    PLoS One 2013 Oct 11;8(10):e77571
  • DGIdb: Mining the Druggable Genome
    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, Walker JR, Larson DE, Dooling DJ, Smith SM, Ley TJ, Mardis ER, Wilson RK (*contributed equally/corresponding author)
    Nat Methods 2013 Dec;10(12):1209-10
  • Modeling Precision Treatment of Breast Cancer
    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 EA, van't Veer LJ, Spellman PT, Gray JW (*contributed equally/corresponding author)
    Genome Biol 2013;14(10):R110
  • A Robust Prognostic Signature for Hormone-Positive Node-Negative Breast Cancer
    Griffith OL*, Pepin F, Enache OM, Heiser LM, Collisson EA, Spellman PT, Gray JW (*corresponding author)
    Genome Med 2013 Oct 11;5(10):92
  • Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts
    Li S, Shen D, Shao J, Crowder R, Liu W, Prat A, He X, Liu S, Hoog J, Lu C, Ding L, Griffith OL, Miller C, Larson D, Fulton RS, Harrison M, Mooney T, McMichael JF, Luo J, Tao Y, Goncalves R, Schlosberg C, Hiken JF, Saied L, Sanchez C, Giuntoli T, Bumb C, Cooper C, Kitchens RT, Lin A, Phommaly C, Davies SR, Zhang J, Kavuri MS, McEachern D, Dong YY, Ma C, Pluard T, Naughton M, Bose R, Suresh R, McDowell R, Michel L, Aft R, Gillanders W, Deschryver K, Wilson RK, Wang S, Mills GB, Gonzalez-Angulo A, Edwards JR, Maher C, Perou CM, Mardis ER, Ellis MJ
    Cell Rep 2013 Sep 26;4(6):1116-30
  • c-Src Modulates Estrogen-Induced Stress and Apoptosis in Estrogen-Deprived Breast Cancer Cells
    Fan P, Griffith OL, Agboke FA, Anur P, Zou X, McDaniel RE, Creswell K, Kim SH, Katzenellenbogen JA, Gray JW, Jordan VC
    Cancer Res 2013 Jul 15;73(14):4510-20
  • Novel mRNA Isoforms and Mutations of Uridine Monophosphate Synthetase and 5-Fluorouracil Resistance in Colorectal Cancer
    Griffith M, Mwenifumbo JC, Cheung PY, Paul JE, Pugh TJ, Tang MJ, Chittaranjan S, Morin RD, Asano JK, Ally AA, Miao L, Lee A, Chan SY, Taylor G, Severson T, Hou YC, Griffith OL, Cheng GS, Novik K, Moore R, Luk M, Owen D, Brown CJ, Morin GB, Gill S, Tai IT, Marra MA
    Pharmacogenomics J 2013 Apr;13(2):148-58
  • Cross-Platform Pathway-Based Analysis Identifies Markers of Response to the PARP Inhibitor Olaparib
    Daemen A, Wolf DM, Korkola JE, Griffith OL, Frankum JR, Brough R, Jakkula LR, Wang NJ, Natrajan R, Reis-Filho JS, Lord CJ, Ashworth A, Spellman PT, Gray JW, van't Veer LJ
    Breast Cancer Res Treat 2012 Sep;135(2):505-17
  • Loss of Cell-Surface Laminin Anchoring Promotes Tumor Growth and Is Associated With Poor Clinical Outcomes
    Akhavan A, Griffith OL, Soroceanu L, Leonoudakis D, Luciani-Torres MG, Daemen A, Gray JW, Muschler JL
    Cancer Res 2012 May 15;72(10):2578-88
  • Identification of PADI2 as a Potential Breast Cancer Biomarker and Therapeutic Target
    McElwee JL, Mohanan S, Griffith OL, Breuer HC, Anguish LJ, Cherrington BD, Palmer AM, Howe LR, Subramanian V, Causey CP, Thompson PR, Gray JW, Coonrod SA
    BMC Cancer 2012 Oct 30;12(1):500
  • Lectin Chromatography/Mass Spectrometry Discovery Workflow Identifies Putative Biomarkers of Aggressive Breast Cancers
    Drake PM, Schilling B, Niles RK, Prakobphol A, Li B, Jung K, Cho W, Braten M, Inerowicz HD, Williams K, Albertolle M, Held JM, Iacovides D, Sorensen DJ, Griffith OL, Johansen E, Zawadzka AM, Cusack MP, Allen S, Gormley M, Hall SC, Witkowska HE, Gray JW, Regnier F, Gibson BW, Fisher SJ
    J Proteome Res 2012 Apr 6;11(4):2508-20
  • The Transcription Factor ZNF217 Is a Prognostic Biomarker and Therapeutic Target During Breast Cancer Progression
    Littlepage LE, Adler AS, Kouros-Mehr H, Huang G, Chou J, Krig SR, Griffith OL, Korkola JE, Qu K, Lawson DA, Xue Q, Sternlicht MD, Dijkgraaf GJ, Yaswen P, Rugo HS, Sweeney CA, Collins CC, Gray JW, Chang HY, Werb Z
    Cancer Discov 2012 Jul;2(7):638-51
  • Lrig1 Is an Estrogen-Regulated Growth Suppressor and Correlates With Longer Relapse-Free Survival in ERalpha-Positive Breast Cancer
    Krig SR, Frietze S, Simion C, Miller JK, Fry WH, Rafidi H, Kotelawala L, Qi L, Griffith OL, Gray JW, Carraway KL 3rd, Sweeney C
    Mol Cancer Res 2011 Oct;9(10):1406-17
  • Immunophenotyping of Thyroid Tumors Identifies Molecular Markers Altered During Transformation of Differentiated Into Anaplastic Carcinoma
    Wiseman SM, Griffith OL, Gown A, Walker B, Jones SJ
    Am J Surg 2011 May;201(5):580-6
  • Detection and Management of Hypothyroidism Following Thyroid Lobectomy: Evaluation of a Clinical Algorithm
    Johner A, Griffith OL, Walker B, Wood L, Piper H, Wilkins G, Baliski C, Jones SJ, Wiseman SM
    Ann Surg Oncol 2011 Sep;18(9):2548-54
  • Alternative Expression Analysis by RNA Sequencing
    Griffith M, Griffith OL, Mwenifumbo J, Goya R, Morrissy AS, Morin RD, Corbett R, Tang MJ, Hou YC, 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 SJ, Tai IT, Marra MA
    Nat Methods 2010 Oct;7(10):843-7
  • Evolution of an Adenocarcinoma in Response to Selection by Targeted Kinase Inhibitors
    Jones SJ, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes AP, 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
    Genome Biol 2010;11(8):R82
  • On the Deep Order-Preserving Submatrix Problem: A Best-Effort Approach
    Gao B, Griffith OL, Ester M, Xiong H, Zhao Q, Jones S
    IEEE Transactions on Knowledge and Data Engineering 19 Nov 2010 IEEE computer Society Digital Library IEEE Computer Society
  • Somatic Mutations Altering EZH2 (Tyr641) in Follicular and Diffuse Large B-Cell Lymphomas of Germinal-Center Origin
    Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Goya R, Paul JE, Boyle M, Woolcock BW, Kuchenbauer F, Yap D, Humphries RK, Griffith OL, Shah S, Zhu H, Kimbara M, Shashkin P, Charlot JF, Tcherpakov M, Corbett R, Tam A, Varhol R, Smailus D, Moksa M, Zhao Y, Delaney A, Qian H, Birol I, Schein J, Moore R, Holt R, Horsman DE, Connors JM, Jones S, Aparicio S, Hirst M, Gascoyne RD, Marra MA
    Nat Genet 2010 Feb;42(2):181-5 doi: 101038/ng518
  • Anaplastic Thyroid Carcinoma Exhibits Intratumoral Molecular Homogeneity for a Therapeutic Target Panel
    Deen S, Griffith OL, Masoudi H, Gown A, Jones SJ, Wiseman SM
    Anticancer Res 2009 Jul;29(7):2437-44
  • KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis
    Griffith OL, Gao B, Bilenky M, Prychyna Y, Ester M, Jones S
    In: Proceedings of the 3rd International Conference on Bioinformatics and Biomedical Engineering (Beijing, China, June 11 - 13, 2009) iCBBE 2009 Institute of Electrical and Electronics Engineers, Inc Los Alamitos, CA, USA, pp 1-9
  • Improving Preoperative Diagnosis of Thyroid Cancer: A Molecular Perspective
    Wiseman S, Melck A, Masoudi H, Ghaidi F, Goldstein L, Gown A, Jones SJM, Griffith OL
    Journal of Japan Surgical Society 2008;109(2):194
  • Phosphorylated Caveolin-1 Regulates Rho/ROCK-Dependent Focal Adhesion Dynamics and Tumor Cell Migration and Invasion
    Joshi B, Strugnell SS, Goetz JG, Kojic LD, Cox ME, Griffith OL, Chan SK, Jones SJ, Leung SP, Masoudi H, Leung S, Wiseman SM, Nabi IR
    Cancer Res 2008 Oct 15;68(20):8210-20
  • Molecular Phenotyping of Thyroid Tumors Identifies a Marker Panel for Differentiated Thyroid Cancer Diagnosis
    Wiseman SM, Melck A, Masoudi H, Ghaidi F, Goldstein L, Gown A, Jones SJ, Griffith OL
    Ann Surg Oncol 2008 Oct;15(10):2811-26
  • Evaluation of Type 1 Growth Factor Receptor Family Expression in Benign and Malignant Thyroid Lesions
    Wiseman SM, Griffith OL, Melck A, Masoudi H, Gown A, Nabi IR, Jones SJ
    Am J Surg 2008 May;195(5):667-73; discussion 673
  • Clinical Utility of Type 1 Growth Factor Receptor Expression in Colon Cancer
    Leung SP, Griffith OL, Masoudi H, Gown A, Jones S, Phang T, Wiseman SM
    Am J Surg 2008 May;195(5):604-10
  • Meta-Analysis of Colorectal Cancer Gene Expression Profiling Studies Identifies Consistently Reported Candidate Biomarkers
    Chan SK, Griffith OL, Tai IT, Jones SJ
    Cancer Epidemiol Biomarkers Prev 2008 Mar;17(3):543-52
  • Text-Mining Assisted Regulatory Annotation
    Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM
    Genome Biol 2008;9(2):R31
  • ALEXA: A Microarray Design Platform for Alternative Expression Analysis
    Griffith M, Tang MJ, Griffith OL, Morin RD, Chan SY, Asano JK, Zeng T, Flibotte S, Ally A, Baross A, Hirst M, Jones SJ, Morin GB, Tai IT, Marra MA
    Nat Methods 2008 Feb;5(2):118
  • ORegAnno: An Open-Access Community-Driven Resource for Regulatory Annotation
    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 (*contributed equally/corresponding author)
    Nucleic Acids Res 2008 Jan;36(Database issue):D107-13
  • Cell Cycle Regulators Show Diagnostic and Prognostic Utility for Differentiated Thyroid Cancer
    Melck A, Masoudi H, Griffith OL, Rajput A, Wilkins G, Bugis S, Jones SJ, Wiseman SM
    Ann Surg Oncol 2007 Dec;14(12):3403-11
  • Identification of Molecular Markers Altered During Transformation of Differentiated Into Anaplastic Thyroid Carcinoma
    Wiseman SM, Griffith OL, Deen S, Rajput A, Masoudi H, Gilks B, Goldstein L, Gown A, Jones SJ
    Arch Surg 2007 Aug;142(8):717-27; discussion 727-9
  • Genome-Wide Profiles of STAT1 DNA Association Using Chromatin Immunoprecipitation and Massively Parallel Sequencing
    Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S
    Nat Methods 2007 Aug;4(8):651-7
  • A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms
    Montgomery SB, Griffith OL, Schuetz JM, Brooks-Wilson A, Jones SJ
    PLoS Comput Biol 2007 Jun;3(6):e106
  • Meta-Analysis and Meta-Review of Thyroid Cancer Gene Expression Profiling Studies Identifies Important Diagnostic Biomarkers
    Griffith OL, Melck A, Jones SJ, Wiseman SM
    J Clin Oncol 2006 Nov 1;24(31):5043-51
  • Discovering Significant OPSM Subspace Clusters in Massive Gene Expression Data
    Gao BJ, Griffith OL, Ester M, Jones SJ
    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, pp 922-8
  • Sequence Biases in Large Scale Gene Expression Profiling Data
    Siddiqui AS, Delaney AD, Schnerch A, Griffith OL, Jones SJ, Marra MA
    Nucleic Acids Res 2006 Jul 13;34(12):e83
  • ORegAnno: An Open Access Database and Curation System for Literature-Derived Promoters, Transcription Factor Binding Sites and Regulatory Variation
    Montgomery SB*, Griffith OL*, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ (*contributed equally)
    Bioinformatics 2006 Mar 1;22(5):637-40
  • CisRED: A Database System for Genome-Scale Computational Discovery of Regulatory Elements
    Robertson G, Bilenky M, Lin K, He A, Yuen W, Dagpinar M, Varhol R, Teague K, Griffith OL, Zhang X, Pan Y, Hassel M, Sleumer MC, Pan W, Pleasance ED, Chuang M, Hao H, Li YY, Robertson N, Fjell C, Li B, Montgomery SB, Astakhova T, Zhou J, Sander J, Siddiqui AS, Jones SJ
    Nucleic Acids Res 2006 Jan 1;34(Database issue):D68-73
  • Assessment and Integration of Publicly Available SAGE, cDNA Microarray, and Oligonucleotide Microarray Expression Data for Global Coexpression Analyses
    Griffith OL, Pleasance ED, Fulton DL, Oveisi M, Ester M, Siddiqui AS, Jones SJ
    Genomics 2005 Oct;86(4):476-88
  • The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)
    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, Morin 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
    Genome Res 2004 Oct;14(10B):2121-7
  • Systematic Recovery and Analysis of Full-ORF Human cDNA Clones
    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, Marra MA
    Genome Res 2004 Oct;14(10B):2083-92
  • Reply to Gregory's Letter to the Editor: Genome Size and Its Correlation With Longevity in Fishes
    Civetta A, Griffith OL, Moodie GE
    Exp Gerontol 2004;39(5):861-2
  • The Genome Sequence of the SARS-Associated Coronavirus
    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
    Science 2003 May 30;300(5624):1399-404
  • Genome Size and Longevity in Fish
    Griffith OL, Moodie GE, Civetta A
    Exp Gerontol 2003 Mar;38(3):333-7