obigriffith.org

Publications (Pubmed | Google Scholar | Research Gate)

I periodically update this page with my publications. For the most current results, please use the links above.

Griffith M*,†, Spies NC*, Krysiak K*, Coffman AC, McMichael JF, Ainscough BJ, Rieke DT, Danos AM, Kujan L, Ramirez CA, Wagner AH, Skidmore ZL, Liu CJ, Jones MR, Bilski RL, Lesurf R, Barnell EK, 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, Jones SJM, Bose R, Spencer DH, Wartman LD, Wilson RK, Mardis ER, Griffith OL†. 2017. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nature Genetics. 49(2):170-4. *These authors contributed equally to this work. †Corresponding author.
abstract | full text

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†. 2017. Recurrent Somatic Mutations Affecting B-Cell Receptor Signaling Pathway Genes in Follicular Lymphoma. Blood. 129(4):473-483. †Corresponding author.
abstract | full text | commentary

Zolkind P, Dunn GP, Lin T, Griffith M, Griffith OL, Uppaluri R. 2016. Neoantigens in immunotherapy and personalized vaccines: Implications for head and neck squamous cell carcinoma. Oral Oncology. pii: S1368-8375(16)30175-0. [Epub ahead of print].
abstract | full text

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 P, 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. 2016. FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer. Proceedings of the National Academy of Sciences. 113(43):E6600-E6609.
abstract | full text

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. 2016. Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas. Cell Reports. 17(1):249-60. *These authors contributed equally to this work.
abstract | full text

Ainscough BJ, Griffith M†, Coffman AC, Wagner AH, Kunisaki J, Choudhary MNK, McMichael JF, Fulton RS, Wilson RK, Griffith OL†, Mardis ER. 2016. DoCM: a database of curated mutations in cancer. Nature Methods. 13(10):806-7. †Corresponding author.
abstract | full text

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 V, Snider J, Walsh T, Colditz GA, Katherine DeSchryver K, Wilson RK, Mardis ER, Ellis MJ. 2016. Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers.. Nature Communications. 7:12498.
abstract | full text

Skidmore ZL, Wagner AH, Lesurf R, Campbell KM, Kunisaki J, Griffith OL†, Griffith M†. 2016. GenVisR: Genomic Visualizations in R. Bioinformatics. pii: btw325. [Epub ahead of print]. †Corresponding author.
abstract | full text

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, Larson DE, Heath S, Fronick C, O'Laughlin S, Fulton RS, Magrini V, McGrath S, Smith SM, Miller CA, Maher CA, Payton JE, Walter MJ, Link DC, Graubert TA, Westervelt P, Kulkarni S, DiPersio JF, Mardis ER, Wilson RK, Ley TJ. 2016. Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia. Experimental Hematology. 44(7):603-13. *These authors contributed equally to this work.
abstract | full text

Xin J, Mark A, Afrasiabi1 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. 2016. MyGene.info and MyVariant.info: Gene and Variant Annotation Query Services. Genome Biology. 17(1):91.
abstract | full text

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. 2016. The ErbB2ΔEx16 splice variant is a major oncogenic driver in breast cancer that promotes a pro-metastatic tumor microenvironment. Oncogene. doi: 10.1038/onc.2016.129. [Epub ahead of print].
abstract | full text

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†. 2016. A genomic case study of mixed fibrolamellar hepatocellular carcinoma. Annals of Oncology. 27(6):1148-54. *These authors contributed equally to this work. †Corresponding author.
abstract | full text

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†. 2016. Philadelphia Chromosome-Negative AML Arising In Patients With CML Is Clonally Distinct. Blood Cancer Journal. 6:e413. †Corresponding author.
abstract | full text

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. 2016. A common founding clone with TP53 and PTEN mutations gives rise to a concurrent germ cell tumor and acute megakaryoblastic leukemia. Molecular Case Studies. 2(1):a000687.
abstract | full text

Hundal J, Carreno BM, Petti AA, Linette GP, Griffith OL, Mardis ER, Griffith M. 2016. pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Medicine. 8(1):11.
abstract | full text

Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJM, Montgomery SB†, Griffith OL†. 2016. ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Research. 44(D1):D126-32. †Corresponding author.
abstract | full text

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†. 2016. DGIdb 2.0: mining clinically relevant drug-gene interactions.. Nucleic Acids Research. 44(D1):D1036-44. †Corresponding author.
abstract | full text

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 C, Ellis MJ. 2015. A phase 1 trial of BKM120 (Buparlisib) in combination with fulvestrant in postmenopausal women with estrogen receptor positive metastatic breast cancer. Clinical Cancer Research. 22(7):1583-91.
abstract | full text

Solga AC, Pong WW, Kim KY, Cimino PJ, Walker J, Wylie T, Magrini V, Griffith M, Griffith OL, Ly A, Gianino SM, Ellisman MH, Mardis ER, Gutmann DH. 2015. RNA-sequencing of tumor-associated microglia reveals Ccl5 as a stromal chemokine critical for neurofibromatosis-1 glioma growth. Neoplasia. 17(10):776-88.
abstract | full text

Griffith M*, Miller CA*, Griffith OL, Krysiak K, Skidmore ZL, Ramu A, Walker JR, Dang H, Trani L, Larson DE, Demeter RT, Wendl MC, McMichael JF, Austin R, Magrini V, McGrath S, Ly A, Kulkarni S, Cordes M, Fronick CC, Fulton RS, Maher CA, Ding L, Klco JM, Mardis ER, Ley TJ, Wilson RK. 2015. Optimizing cancer genome sequencing and analysis. Cell Systems. 1(3):210-223. *These authors contributed equally to this work. Featured article with commentary.
abstract | full text

Klco JM, Miller CA, Griffith M, Petti A, Spencer DH, Ketkar-Kulkarni S, Wartman LD, Christopher M, Lamprecht TL, Helton NM, Wong TN, Young AL, 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. 2015. Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia. The Journal of the American Medical Association. 314(8):811-22.
abstract | full text

Griffith M†, Walker JR, Spies N, Ainscough BJ, Griffith OL†. 2015. Informatics for RNA-seq: A web resource for analysis on the cloud. PLoS Computational Biology. 11(8):e1004393. †Corresponding author.
abstract | full text

Kumar RD, Searleman AC, Swamidass SJ, Griffith OL, Bose R. 2015. Statistically Identifying Tumor Suppressors and Oncogenes from Pan-Cancer Genome Sequence Data. Bioinformatics. 31(22):3561-8.
abstract | full text

Korkola JE, Collisson EA, Heiser L, Oates C, Bayani N, Itani S, Esch A, Thompson W, Griffith OL, Wang NJ, Kuo W, Cooper B, Billig J, Ziyad S, Hung JL, Jakkula L, Lu Y, Mills G, Spellman PT, Tomlin C, Mukherjee S, Gray JW. 2015. Decoupling of the PI3K pathway via mutation necessitates combinatorial treatment in HER2+ breast cancer. PLoS One. 10(7):e0133219.
abstract | full text

Griffith M*,†, Griffith OL*,†, Smith SM*, Ramu A, Callaway MB, Brummett AM, Kiwala M, Coffmann AC, Regier AA, Oberkfell BJ, Sanderson GE, Mooney TP, Nutter N, Belter EA, Du F, Long RL, Abbott TE, Ferguson I, Morton D, Burnett M, Weible JV, Peck JB, Dukes A, McMichael JF, Lolofie JT, Derickson BR, Hundall J, Skidmore ZL, Ainscough BJ, Dees ND, Schierding WS, Kandoth C, Kim K, 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 S, Schroeder WE, Shi X, Carmichael KL, Weil M, Wohldstadter 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. 2015. Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Computational Biology. 11(7): e1004274. *These authors contributed equally to this work and are listed in alphabetical order. †Corresponding author.
abstract | full text

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 PI3Kα inhibitor. Nature. [Epub ahead of print]. *These authors contributed equally to this work.
abstract | full text | doi

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. [Epub ahead of print]
abstract | full text | doi

Ding L, Kim M, Dees ND, Kanchi KL, Lu C, Griffith M, Fenstermacher D, Sung H, Miller CA, McMichael JF, Goetz B, Wendl MC, Griffith OL, Cornelius LA, Linette GP, Sondak VK, Fields RC, Mulé JJ, Wilson RK, and Weber JS. 2014. Clonal Architectures and Driver Mutations in Metastatic Melanomas. PLoS One. 9(11):e111153.
abstract | full text | doi

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. S0959-8049(14)00889-2.
abstract | full text | pdf

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
abstract | full text | pdf

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, Ding L. 2014. SciClone: Inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLoS Computational Biology. 10(8):e1003665.
abstract | full text | pdf

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.
full text | pdf

Cabanski CR, Magrini V, Griffith M, Griffith OL, McGrath S, Walker J, Ly A, Demeter R, Pong WW, Gutmann DH, Govindan R, Mardis ER, Maher CA. 2014. cDNA Hybrid Capture Improves Transcriptome Analysis on Low-input and Archived Samples. The Journal of Molecular Diagnostics. 16(4):440-51.
abstract | full text | pdf

Griffith OL, Griffith M. 2014. Nucleic Acid Databases in Concise Encyclopaedia of Bioinformatics and Computational Biology, 2nd Edition. Hancock JM, Zvelebil MJ, editors. Wiley-Blackwell. Hoboken, NJ. 822p.
order (Wiley)

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. [Epub ahead of print]. *These authors contributed equally to this work.
abstract | full text | pdf

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 to this work.
abstract | full text | pdf | research highlight

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.
abstract | full text | pdf

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, Kavuri MS, McEachern D, Dong YY, Ma C, Pluard T, Naughton M, Bose R, Suresh R, McDowell R, Michel L, Aft R, DeSchryver K, Wilson RK, Wang S, Mills GB, Gonzalez-Angulo A, Edwards JR, Maher C, Perou CM, Mardis ER, Ellis MJ. 2013. Endocrine-Therapy-Resistant ESR1 Variants revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts. Cell Reports. 4(6):1116-30.
abstract | full text | pdf | doi

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.
abstract | full text | pdf

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 Y, Griffith OL, Cheng GSW, Novik K, Moore R, Luk M, Owen D, Brown CJ, Morin GB, Gill S, Tai IT, Marra MA. 2013. Novel mRNA isoforms and mutations of uridine monophosphate synthetase and 5-fluorouracil resistance in colorectal cancer. The Pharmacogenomics Journal. 13(2):148-58.
abstract | full text | pdf | suppl. materials | doi

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. 2012. Cross-platform pathway-based analysis identifies markers of response to the PARP inhibitor olaparib. Breast Cancer Research and Treatment. 135(2):505-17.
abstract | full text | pdf

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.
abstract | full text | pdf

McElwee JL, Mohanan S, Griffith OL, Cherrington BD, Anguish LJ, Breuer HC, Thompson PR, Gray JW, Coonrod SA. 2012. Identification of PADI2 as a potential breast cancer biomarker and therapeutic target. BMC Cancer. 12(1):500.
abstract | full text | pdf

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, Allen S, Gormley M, Hall SC, Witkowska HE, Gray JW, Regnier F, Gibson BW, Fisher SJ. 2012. Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers. Journal of Proteome Research. 11(4):2508-20.
abstract | full text | pdf

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 GJP, Yaswen P, Rugo HS, Sweeney CA, Collins CC, Gray JW, Chang HY, Werb Z. 2012. The transcription factor ZNF217 is a prognostic biomarker and therapeutic target during breast cancer progression. Cancer Discovery. 2(7):638-51.
abstract | full text

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

Krig SR, Frietze S, Simion C, Miller JK, Fry WH, Rafidi H, Kotelawala L, Qi L, Griffith OL, Gray JW, Carraway KL, Sweeney C. 2011. Lrig1 is an ER-alpha target gene and correlates with longer relapse free survival in ER-positive breast cancer. Molecular Cancer Research. 9(10):1406-1417.
abstract | full text | pdf | doi

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.
abstract | full text | doi

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.
abstract | full text | pdf | doi

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. (Made "Top Ten" list)
abstract | full text | pdf | suppl. materials (News and Views)

Jones SJM, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Chuah E, Corbett R, Fejes A, Chan S, Liao N, Kasaian K, 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. Personalized oncogenomics. Genome Biology. 11(Suppl 1):I5

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. (Nominated for BioMed Central’s Annual Research Awards Biology Prize)
abstract | full text | pdf

Gao B, Griffith OL, Ester M, Xiong H, Zhao Q, Jones S. 2010. On The Deep Order-preserving Submatrix Problem: A Best-Effort Approach. IEEE Transactions on Knowledge and Data Engineering. 19 Nov. 2010. IEEE computer Society Digital Library. IEEE Computer Society.
abstract

Chiu CG, Strugnell SS, Griffith OL, Jones SJM, Gown AM, Walker B, Nabi IR, and Wiseman SM. 2010. Diagnostic Utility of Galectin-3 in Thyroid Cancer. The American Journal of Pathology.176(5):2067-2081.
abstract | full text | pdf

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. 2010. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nature Genetics. 42(2):181-5.
abstract | full text | pdf (News and Views)

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

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.
abstract | full text | pdf

Deen S, Griffith OL, Masoudi H, Gown A, Jones SJM, Wiseman SM. 2009. Anaplastic Thyroid Carcinoma Exhibits Intratumoral Molecular Homogeneity for a Therapeutic Target Panel. Anticancer Res. 29(7):2437-2444.
abstract | full text | pdf

Griffith OL, Gao B, Bilenky M, Prychyna Y, Ester M, Jones S. 2009. KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis. Accepted for publication. 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. p. 1-9.
abstract | pdf

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. 2008. Phosphorylated caveolin-1 regulates Rho/ROCK-dependent focal adhesion dynamics and tumor cell migration and invasion. Cancer Research. 68(20):8210-20.
abstract | full text | pdf

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.
abstract | full text | pdf

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.
abstract | full text | pdf

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.
abstract | full text

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.
abstract | full text

Griffith OL. 2008. Identification of gene expression changes in human cancer using bioinformatic approaches. Ph.D. dissertation. University of British Columbia, Vancouver, BC, Canada.
abstract | pdf

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.
abstract | full text | pdf

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.
abstract | full text | pdf

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.
abstract | full text | pdf | suppl. materials

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.
abstract | full text | pdf

Melck AL, Masoudi H, Griffith OL, Rajput A, Wilkins GE, Bugis S, Jones S, Wiseman SM. 2007. Cell Cycle Regulators Show Diagnostic and Prognostic Utility for Differentiated Thyroid Cancer. Annals of Surgical Oncology. 14(12):3403–3411.
abstract | full text | pdf

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.
abstract | full text | pdf

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 and Jones S. 2007. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods. 4(8):651-7.
abstract | full text | pdf (News and Views)

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.
abstract | full text | pdf

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.
abstract | full text | pdf | suppl. webpage

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.
abstract | pdf

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
abstract | full text | pdf

Montgomery SB*, Griffith OL*, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, 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):637-40. *These authors contributed equally to this work.
abstract | full text | pdf

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 SJM. 2006. cisRED: A database system for genome scale computational discovery of regulatory elements. Nucleic Acids Research. 34(Database issue):D68-73.
abstract | full text | pdf

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.
abstract | full text | suppl. webpage

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. 2004. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Research. 14(10B):2121-7.
abstract | full text | pdf

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.
abstract | full text | pdf

Civetta A, Griffith OL, Moodie GEE. 2004. Reply to Gregory's Letter to the Editor: Genome size and its correlation with longevity in fishes. Experimental Gerontology. 39(5):861-862.
full text

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.
abstract | full text | pdf

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

Griffith OL. 2001. The Effect of Mating on the Pheromone System of the Yellow Mealworm Beetle, Tenebrio molitor. B.Sc. Honours thesis. University of Winnipeg. Winnipeg, MB, Canada.
pdf

Haveman SA, Stroes-Gascoyne S, Hamon CJ, Griffith OL, Messerer CL. 1996. Microbial Analysis of Water Collected from Privately Owned Wells and a Beaver Pond. AECL Technical Report (TR-757).