Selected Publications

Xia H, McMichael J, Becker-Hapak M, Onyeador OC, Buchli R, McClain E, Pence P, Supabphol S, Richters MM, Basu A, Ramirez CA, Puig-Saus C, Cotto KC, Freshour SL, Hundal J, Kiwala S, Goedegebuure SP, Johanns TM, Dunn GP, Ribas A, Miller CA, Gillanders WE, Fehniger TA, Griffith OL, Griffith M. Computational prediction of MHC anchor locations guides neoantigen identification and prioritization. Science Immunology. 2023 Apr.
pmid: 37027480; doi: 10.1126/sciimmunol.abg2200

Cotto KC*, Feng YY*, Ramu A, Richters M, Freshour SL, Skidmore ZL, Xia H, McMichael JF, Kunisaki J, Campbell KM, Chen TH, Rozycki EB, Adkins D, Devarakonda S, Sankararaman S, Lin Y, Chapman WC, Maher CA, Arora V, Dunn GP, Uppaluri R, Govindan R, Griffith OL, Griffith M. Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer. Nature Communications. 2023 Mar.
pmid: 36949070; doi: 10.1038/s41467-023-37266-6

Puig-Saus C, Sennino B, Peng S, Wang CL, Pan Z, Yuen B, Purandare B, An D, Quach BB, Nguyen D, Xia H, Jilani S, Shao K, McHugh C, Greer J, Peabody P, Nayak S, Hoover J, Said S, Jacoby K, Dalmas O, Foy SP, Conroy A, Yi MC, Shieh C, Lu W, Heeringa K, Ma Y, Chizari S, Pilling MJ, Ting M, Tunuguntla R, Sandoval S, Moot R, Hunter T, Zhao S, Saco JD, Perez-Garcilazo I, Medina E, Vega-Crespo A, Baselga-Carretero I, Abril-Rodriguez G, Cherry G, Wong DJ, Hundal J, Chmielowski B, Speiser DE, Bethune MT, Bao XR, Gros A, Griffith OL, Griffith M, Heath JR, Franzusoff A, Mandl SJ, Ribas A. Neoantigen-targeted CD8+ T cell responses with PD-1 blockade therapy. Nature. 2023 Mar.
pmid: 36890230; doi: 10.1038/s41586-023-05787-1

Krysiak K, Danos AM, Saliba J, McMichael JF, Coffman AC, Kiwala S, Barnell EK, Sheta L, Grisdale CJ, Kujan L, Pema S, Lever J, Ridd S, Spies NC, Andric V, Chiorean A, Rieke DT, Clark KA, Reisle C, Venigalla AC, Evan M, Jani P, Takahashi H, Suda A, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Kesserwan C, Lamping M, Shen H, Marr AR, Hoan MH, Singhal K, Khanfar M, Li BV, Lin W, Terraf P, Corson LB, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, King I, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca Gordana, Rao S, Madhavan S, Wagner AH, Griffith M, Griffith OL. CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase . Nucleic Acids Research. 2022 Nov.
pmid: 36373660; doi: 10.1093/nar/gkac979

Yoon CJ, Kim SY, Nam CH, Lee J, Park JW, Mun J, Park S, Lee S, Yi B, Min KI, Wiley B, Bolton KL, Lee JH, Kim E, Yoo HJ, Jun JK, Choi JS, Griffith M, Griffith OL, Ju YS.. Estimation of intrafamilial DNA contamination in family trio genome sequencing using deviation from Mendelian inheritance. Genome Research. 2022 Dec.
pmid: 36617634; doi: 10.1101/gr.276794.122

Barnell EK, Fisk B, Skidmore ZL, Cotto KC, Spies NC, Basu A, Anand A, Richters MM, Luo J, Fronick C, Anurag M, Fulton R, Ellis MJ, Griffith OL, Griffith M, Ademuyiwa FO. Personalized ctDNA micro-panels can monitor and predict clinical outcomes for patients with triple-negative breast cancer. Scientific Reports. 2022 Oct.
pmid: 36273232; doi: 10.1038/s41598-022-20928-8

Barnell EK, Skidmore ZL, Newcomer KF, Chavez M, Campbell KM, Cotto KC, Spies NC, Ruzinova MB, Wang T, Abro B, Kreisel F, Parikh BA, Duncavage EJ, Frater JL, Lee Y, Hassan A, King JA, Kohnen DR, Fiala MA, Welch JS, Uy GL, Vij K, Vij R, Griffith M, Griffith OL, Wartman LD. Distinct clonal identities of B-ALLs arising after lenolidomide therapy for multiple myeloma. Blood Advances. 2022 Oct.
pmid: 36251745; doi: 10.1182/bloodadvances.2022007496

Saliba J, Church AJ, Rao S, Danos A, Furtado LV, Laetsch T, Zhang L, Nardi V, Lin WH, Ritter DI, Madhavan S, Li MM, Griffith OL, Griffith M, Raca G, Roy A. Standardized evidence-based approach for assessment of oncogenic and clinical significance of NTRK fusions. Cancer Genetics. 2022 Jun.
pmid: 35366592; doi: 10.1016/j.cancergen.2022.03.001

Krysiak K, Danos AM, Kiwala S, McMichael JF, Coffman AC, Barnell EK, Sheta L, Saliba J, Grisdale CJ, Kujan L, Pema S, Lever J, Spies NC, Chiorean A, Rieke DT, Clark KA, Jani P, Takahashi H, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Lamping M, Marr AR, Li BV, Lin W, Terraf P, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca Gordana, Rao S, Madhavan S, Wagner AH, Griffith M, Griffith OL. A community approach to the cancer-variant-interpretation bottleneck. Nature Cancer. 2022 Jun.
pmid: 35624339; doi: 10.1038/s43018-022-00379-w

Skidmore ZL, Kunisaki J, Lin Y, Cotto KC, Barnell EK, Hundal J, Krysiak K, Magrini V, Trani L, Walker JR, Fulton R, Brunt EM, Miller CA, Wilson RK, Mardis ER, Griffith M, Chapman W, Griffith OL. Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers. Cancer Genetics. 2022 Jun.
pmid: 35568002; doi: 10.1016/j.cancergen.2022.04.002

Chiorean A, Farncombe KM, Delong S, Andric V, Ansar S, Chan C, Clark K, Danos AM, Gao Y, Giles RH, Goldenberg A, Jani P, Krysiak K, Kujan L, Macpherson S, Maher ER, McCoy LG, Salama Y, Saliba J, Sheta L, Griffith M, Griffith OL, Erdman L, Ramani A, Kim RH.. Large scale genotype- and phenotype-driven machine learning in Von Hippel-Lindau disease. Human Mutation. 2022 Apr.
pmid: 35475554; doi: 10.1002/humu.24392

Wahle BM, Zolkind P, Ramirez RJ, Skidmore ZL, Anderson SR, Mazul A, Hayes DN, Sandulache VC, Thorstad WL, Adkins D, Griffith OL, Griffith M, Zevallos JP. Integrative genomic analysis reveals low T-cell infiltration as the primary feature of tobacco use in HPV-positive oropharyngeal cancer. iScience. 2022 Apr.
pmid: 35494251; doi: 10.1016/j.isci.2022.104216

Berrien-Elliott MM, Foltz JA, Russler-Germain DA, Neal CC, Tran J, Gang M, Wong P, Fisk B, Cubitt CC, Marin ND, Zhou AY, Jacobs MT, Foster M, Schappe T, McClain E, Kersting-Schadek S, Desai S, Pence P, Becker-Hapak M, Eisele J, Mosior M, Marsala L, Griffith OL, Griffith M, Khan SM, Spencer DH, DiPersio JF, Romee R, Uy GL, Abboud CN, Ghobadi A, Westervelt P, Stockerl-Goldstein K, Schroeder MA, Wan F, Lie WR, Soon-Shiong P, Petti AA, Cashen AF, Fehniger TA. Hematopoietic cell transplantation donor-derived memory-like NK cells functionally persist after transfer into patients with leukemia. Science Translational Medicine. 2022 Feb.
pmid: 35196021; doi: 10.1126/scitranslmed.abm1375

Horak P, Griffith M, Danos AM, Pitel BA, Madhavan S, Liu X, Chow C, Williams H, Carmody L, Barrow-Laing L, Rieke D, Kreutzfeldt S, Stenzinger A, Tambrero D, Benary M, Rajagopal PS, Ida CM, Lesmana H, Satgunaseelan L, Merker JD, Tolstorukov MY, Campregher PV, Warner JL, Rao S, Natesan M, Shen H, Venstrom J, Roy S, Tao K, Kanagal-Shamanna R, Xu X, Ritter DI, Pagel K, Krysiak K, Dubuc A, Akkari YM, Li XS, Lee J, King I, Raca G, Wagner AH, Li MM, Plon SE, Kulkarni S, Griffith OL, Chakravarty D, Sonkin D. Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC). Genetics in Medicine. 2022 Jan.
pmid: 35101336; doi: 10.1016/j.gim.2022.01.001

Zhou L, Zeng Z, Egloff AM, Zhang F, Guo F, Campbell KM, Du P, Fu J, Zolkind P, Ma X, Zhang Z, Zhang Y, Wang X, Gu S, Riley R, Nakahori Y, Keegan J, Haddad R, Schoenfeld JD, Griffith O, Manguso RT, Lederer JA, Liu XS, Uppaluri R. Checkpoint blockade-induced CD8+ T cell differentiation in head and neck cancer responders.. Journal of Immunotherapy in Cancer. 2022 Jan.
pmid: 35058328; doi: 10.1136/jitc-2021-004034

Schaettler MO, Richters MM, Wang AZ, Skidmore ZL, Fisk B, Miller KE, Vickery TL, Kim AH, Chicoine MR, Osbun JW, Leuthardt EC, Downling JL, Zipfel GJ, Dacey RG, Lu H, Johanns TM, Griffith OL, Mardis ER, Griffith M, Dunn GP. Characterization of the Genomic and Immunologic Diversity of Malignant Brain Tumors through Multisector Analysis. Cancer Discovery. 2022 Jan.
pmid: 34610950; doi: 10.1158/2159-8290.CD-21-0291

Rockwell NC, Yang W, Warrington NM, Staller MV, Griffith M, Griffith OL, Gurnett CA, Cohen BA, Baldridge D, Rubin JB. Sex-and Mutation-Specific p53 Gain-of-Function Activity in Gliomagenesis. Cancer Research Communications. 2021 Dec.
pmid: 34957471; doi: 10.1158/2767-9764.CRC-21-0026

Bednarski JJ, Zimmerman C, Berrien-Elliott MM, Foltz JA, Becker-Hapak M, Neal CC, Foster M, Schappe T, McClain E, Pence PP, Desai S, Kersting-Schadek S, Wong P, Russler-Germain DA, Fisk B, Lie W, Eisele J, Hyde S, Bhatt ST, Griffith OL, Griffith M, Petti AA, Cashen AF, Fehniger TA. Donor Memory-like NK cells Persist and Induce Remissions in Pediatric Patients with Relapsed AML after Transplant. Blood. 2021 Nov.
pmid: 34871371; doi: 10.1182/blood.2021013972

Ward J, Berrien-Elliott MM, Gomez F, Luo J, Becker-Hapak M, Cashen AF, Wagner-Johnston ND, Maddocks K, Mosior M, Foster M, Krysiak K, Schmidt A, Skidmore ZL, Desai S, Watkins MP, Fischer A, Griffith M, Griffith OL, Fehniger TA, Bartlett NL. Phase I/Dose Expansion Trial of Brentuximab vedotin/Lenalidomide in Relapsed or Refractory Diffuse Large B-cell Lymphoma. Blood. 2022 Nov.
pmid: 34780623; doi: 10.1182/blood.2021011894

James CA, Ronning P, Cullinan D, Cotto KC, Barnell EK, Campbell KM, Skidmore ZL, Sanford DE, Goedegebuure SP, Gillanders WE, Griffith OL, Hawkins WG, Griffith M. In Silico Epitope Prediction Analyses Highlight the Potential for Distracting Antigen Immunodominance with Allogeneic Cancer Vaccines. Cancer Research Communications. 2021 Nov.
pmid: 35611186; doi: 10.1158/2767-9764.CRC-21-0029

Skidmore ZL, Campbell KM, Cotto KC, Griffith M, Griffith OL. Exploring the Genomic Landscape of Cancer Patient Cohorts with GenVisR. Curr Protoc. 2021 Sept 10.
pmid: 34506690; doi: 10.1002/cpz1.252

Ademuyiwa FO, Chen I, Luo J, Rimawi MF, Hagemann IS, Fisk B, Jeffers G, Skidmore ZL, Basu A, Richters M, Ma CX, Weilbaecher K, Davis J, Suresh R, Peterson LL, Bose R, Bagegni N, Rigden CE, Frith A, Rearden TP, Hernandez-Aya LF, Roshal A, Clifton K, Opyrchal M, Akintola-Ogunremi O, Lee BH, Ferrando-Martinez S, Church SE, Anurag M, Ellis MJ, Gao F, Gillanders W, Griffith OL, Griffith M. Immunogenomic profiling and pathological response results from a clinical trial of docetaxel and carboplatin in triple-negative breast cancer. Breast Cancer Research and Treatment. 2021 Aug.
pmid: 34173924; doi: 10.1007/s10549-021-06307-3

Barnell EK, Kang Y, Barnell AR, Kruse KR, Fiske J, Pittz ZR, Khan AR, Huebner TA, Holmes FL, Griffith M, Griffith OL, Chauduri AA, Wurtzler EM. Multitarget Stool RNA Test for Noninvasive Detection of Colorectal Neoplasias in a Multicenter, Prospective, and Retrospective Cohort. Clinical Translational Gastroenterology. 2021 May 24.
pmid: 34029233; doi: 10.14309/ctg.0000000000000360

Cheng X, Joseph A, Castro V, Chen-Liaw A, Skidmore ZL, Ueno T, Fujisawa J, Rauch DA, Challen GA, Martinez MP, Green P, Griffith M, Payton JE, Edwards JR, Ratner L. Epigenomic regulation of human T-cell leukemia virus by chromatin-insulator CTCF. PLoS Pathogens. 2021 May 21.
pmid: 34019588; doi: 10.1371/journal.ppat.1009577

Mudianto T, Campbell KM, Webb J, Zolkind, Skidmore ZL, Riley R, Barnell EK, Oxgenc I, Giri T, Dunn GP, Adkins DR, Griffith M, Egloff AN, Griffith OL, Uppaluri R. Yap1 Mediates Trametinib Resistance in Head and Neck Squamous Cell Carcinomas. Clinical Cancer Research. 2021 Apr 15.
pmid: 33547198; doi: 10.1158/1078-0432.CCR-19-4179

Gomez F, Griffith M, Griffith OL. Genetic Ancestry Correlations with Driver Mutations Suggest Complex Interactions between Somatic and Germline Variation in Cancer. Cancer Discovery. 2021 Mar 11.
pmid: 33653917; doi: 10.1158/2159-8290.CD-21-0092

Chu S, Skidmore ZL, Kunisaki J, Walker JR, Griffith M, Griffith OL, Bryan JN. Unraveling the chaotic genomic landscape of primary and metastatic canine appendicular osteosarcoma with current sequencing technologies and bioinformatic approaches. PLoS One. 2021 Feb 8.
pmid: 33556121; doi: 10.1371/journal.pone.0246443

Barnell EK, Newcomer NF, Skidmore ZL, Krysiak K, Anderson SR, Wartman LD, Oh ST, Welch JS, Stockerl-Goldstein KE, Vij R, Cashen AF, Pusic I, Westervelt P, Abboud CN, Ghobadi A, Uy GL, Schroeder MA, Dipersio JF, Politi MC, Spencer DH, Duncavage EJ, Ley TJ, Griffith M, Jacoby MA, Griffith OL. Impact of a 40-Gene Targeted Panel Test on Physician Decision Making for Patients With Acute Myeloid Leukemia. JCO Precision Oncology. 2021 Jan 14.
pmid: 34036230; doi: 10.1200/PO.20.00182

Freshour SL, Kiwala S*, Cotto KC*, Coffman AC, McMichael FJ, Song JJ, Griffith M+, Griffith OL+, Wagner AH+. Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts. Nucleic Acids Research. 2021 Jan 8.
pmid: 33237278; doi: 10.1093/nar/gkaa1084

Uppaluri R, Campbell KM, Egloff AM, Zolkind P, Skidmore ZL, Nussenbaum B, Paniello RC, Rich JT, Jackson R, Pipkorn P, Michel LS, Ley J, Oppelt P, Dunn GP, Barnell EK, Spies NC, Lin T, Li T, Mulder D, Hanna Y, Cirlan I, Pugh TJ, Mudianto T, Riley R, Zhou L, Jo VY, Stachler MD, Hanna GJ, Kass JI, Haddad RI, Schoenfeld JD, Gjini E, Lako A, Thorstad WL, Gay HA, Daly M, Rodig S, Hagemann IS, Kallogjeri D, Piccirillo JF, Chernock RD, Griffith M, Griffith OL, Adkins DR. Neoadjuvant and Adjuvant Pembrolizumab in Resectable Locally Advanced, Human Papillomavirus-Unrelated Head and Neck Cancer: A Multicenter, Phase 2 Trial. Clinical Cancer Research. 2020 Jul 14..
pmid: 32665297; doi: 10.1158/1078-0432.CCR-20-1695

Rao S, Pitel B, Wagner AH, Boca SM, McCoy M, King I, Gupta S, Park BH, Warner JL, Chen J, Rogan PK, Chakravarty D, Griffith M, Griffith OL, Madhavan S. Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices. JCO Clinical Cancer Informatics. 2020 Jul;4:602-613.
pmid: 32644817; doi: 10.1200/CCI.19.00169

De Mattos-Arruda L, Vazquez M, Finotello F, Lepore R, Porta E, Hundal J, Amengual-Rigo P, Ng CKY, Valencia A, Carrillo J, Chan TA, Guallar V, McGranahan N, Blanco J, Griffith M. Neoantigen prediction and computational perspectives towards clinical benefit: Recommendations from the ESMO Precision Medicine Working Group. Annals of Oncology. 2020 Aug;31(8):978-990..
pmid: 32610166; doi: 10.1016/j.annonc.2020.05.008

Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M+, Griffith OL+, Margolin AA; Variant Interpretation for Cancer Consortium. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nature Genetics. 2020 Apr;52(4):448-457.
pmid: 32246132; doi: 10.1038/s41588-020-0603-8

Wagner AH, Kiwala S, Coffman AC, McMichael JF, Cotto KC, Mooney TB, Barnell EK, Krysiak K, Danos AM, Walker J, Griffith M+, Griffith OL+. CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase. JCO Clinical Cancer Informatics. 2020 Mar 19; 4, 245-253.
pmid: 32191543; doi: 10.1200/CCI.19.00127

Hundal J, Kiwala S, McMichael J, Miller CA, Xia H, Wollam AT, Liu CJ, Zhao S, Feng YY, Graubert AP, Wollam AZ, Neichin J, Neveau M, Walker J, Gillanders WE, Mardis ER, Griffith OL+, Griffith M+. pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens. Cancer Immunol Research. 2020 Mar;8(3):409-420.
pmid: 31907209; doi: 10.1158/2326-6066.CIR-19-0401

Chu S, Wylie TN, Wylie KM, Johnson GC, Skidmore ZL, Fleer M, Griffith OL, Bryan JN. A virome sequencing approach to feline oral squamous cell carcinoma to evaluate viral causative factors. Veterinary Microbiology. 2020 Jan;240:108491..
pmid: 31902496; doi: 10.1016/j.vetmic.2019.108491

Lever J, Jones MR, Danos AM, Krysiak K, Bonakdar M, Grewal JK, Culibrk L, Griffith OL+, Griffith M+, Jones SJM+. Text-mining clinically relevant cancer biomarkers for curation into the CIViC database. Genome Medicine. 2019 Dec 03;11(1):78.
pmid: 31796060; doi: 10.1186/s13073-019-0686-y

Danos AM, Krysiak K, Barnell EK, Coffman AC, McMichael JF, Kiwala S, Spies NC, Sheta LM, Pema SP, Kujan L, Clark KA, Wollam AZ, Rao S, Ritter DI, Sonkin Dmitriy, Raca G, Lin W, Grisdale CJ, Kim RH, Wagner AH, Madhavan S, Griffith M+, Griffith OL+. Standard operating procedure for curation and clinical interpretation of variants in cancer. Genome Medicine. 2019 Nov 29;11, 76.
pmid: 31779674; doi: 10.1186/s13073-019-0687-x

Linette GP, Becker-Hapak M, Skidmore ZL, Baroja ML, Xu C, Hundal J, Spencer DH, Fu W, Cummins C, Robnett M, Kaabinejadian S, Hildebrand WH, Magrini V, Demeter R, Krupnick AS, Griffith OL, Griffith M, Mardis ER, Carreno BM. Immunological ignorance is an enabling feature of the oligo-clonal T cell response to melanoma neoantigens. Proc Natl Acad Sci U S A. 2019 Nov 19;116(47):23662-23670..
pmid: 31685621; doi: 10.1073/pnas.1906026116

Barnell EK, Waalkes A, Mosior MC, Penewit K, Cotto KC, Danos AM, Sheta LM, Campbell KM, Krysiak K, Rieke D, Spies NC, Skidmore ZL, Pritchard CC, Fehniger TA, Uppaluri R, Govindan R, Griffith M+, Salipante SJ+, Griffith OL+. Open-Sourced CIViC Annotation Pipeline to Identify and Annotate Clinically Relevant Variants Using Single-Molecule Molecular Inversion Probes. JCO Clinical Cancer Informatics. 2019 Oct 16;3, 1-12.
pmid: 31618044; doi: 10.1200/CCI.19.00077

Richters MM, Xia H, Campbell KM, Gillanders WE, Griffith OL+, Griffith M+. Best practices for bioinformatic characterization of neoantigens for clinical utility. Genome Medicine. 2019 Aug 28;11(1):56.
pmid: 31462330; doi: 10.1186/s13073-019-0666-2

Campbell KM, O'Leary KA, Rugowski DE, Mulligan WA, Barnell EK, Skidmore ZL, Krysiak K, Griffith M, Schuler LA+, Griffith OL+. A Spontaneous Aggressive ERα+ Mammary Tumor Model Is Driven by Kras Activation. Cell Reports. 2019 Aug 6;28(6):1526-1537.e4.
pmid: 31390566; doi: 10.1016/j.celrep.2019.06.098

Barnell E, Kang Y, Wurtzler E, Griffith M, Chaudhuri AA+, Griffith OL+; Geneoscopy Scientists. Noninvasive Detection of High-Risk Adenomas Using Stool-Derived Eukaryotic RNA Sequences as Biomarkers. Gastroenterology. 2019 May 30. pii: S0016-5085(19)40976-1. [Epub ahead of print].
pmid: 31154021; doi: 10.1053/j.gastro.2019.05.058

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+. Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples. Genetics in Medicine. 2019 Apr;21(4):972-981.
pmid: 30287923; doi: 10.1038/s41436-018-0278-z

Hundal J, Kiwala S, Feng YY, Liu CJ, Govindan R, Chapman WC, Uppaluri R, Swamidass SJ, Griffith OL, Mardis ER, Griffith M. Accounting for proximal variants improves neoantigen prediction. Nature Genetics. 2019 Jan;51(1):175-179.
pmid: 30510237; doi: 10.1038/s41588-018-0283-9

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+. A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data. Nature Genetics. 2018 Dec;50(12):1735-1743.
pmid: 30397337; doi: 10.1038/s41588-018-0257-y

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+. Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards. Human Mutation. 2018 Nov;39(11):1721-1732.
pmid: 30311370; doi: 10.1002/humu.23651

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+. Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer. Nature Communication. 2018 Sep 17;9(1):3787.
pmid: 30224629; doi: 10.1038/s41467-018-06162-9

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+. The prognostic effects of somatic mutations in ER-positive breast cancer. Nature Communication. 2018 Sep 4;9(1):3476.
pmid: 30181556; doi: 10.1038/s41467-018-05914-x

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+. Oral Cavity Squamous Cell Carcinoma Xenografts Retain Complex Genotypes and Intertumor Molecular Heterogeneity. Cell Reports. 2018 Aug 21;24(8):2167-2178.
pmid: 30134176; doi: 10.1016/j.celrep.2018.07.058

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. A case of acute myeloid leukemia with promyelocytic features characterized by expression of a novel RARG-CPSF6 fusion. Blood Advances. 2018 Jun 12;2(11):1295-1299.
pmid: 29891591; doi: 10.1182/bloodadvances.2017014183

Madhavan S, Ritter D, Micheel C, Rao S, Roy A, Sonkin D, Mccoy M, Griffith M, Griffith OL, Mcgarvey P, Kulkarni S. Standardizing And Democratizing Access To Cancer Molecular Diagnostic Test Data From Patients To Drive Translational Research. AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:152-159. eCollection 2018.
pmid: 29888062;

Madhavan S, Ritter D, Micheel C, Rao S, Roy A, Sonkin D, Mccoy M, Griffith M, Griffith OL, Mcgarvey P, Kulkarni S. ClinGen Cancer Somatic Working Group - standardizing and democratizing access to cancer molecular diagnostic data to drive translational research. Pacific Symposium of Biocomputing. 2018;23:247-258.
pmid: 29218886; doi: 10.1142/9789813235533_0023

Cotto KC*, Wagner AH*+, Feng YY, Kiwala S, Coffman AC, Spies G, Wollam A, Spies NC, Griffith OL+, Griffith M+. DGIdb 3.0: a redesign and expansion of the drug-gene interaction database. Nucleic Acids Res. 2018 Jan 4;46(D1):D1068-D1073.
pmid: 29156001; doi: 10.1093/nar/gkx1143

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*. Single-Agent Ibrutinib in Relapsed or Refractory Follicular Lymphoma: A Phase 2 Consortium Trial. Blood. 2018 Jan 11;131(2):182-190.
pmid: 29074501; doi: 10.1182/blood-2017-09-804641

Ma CX, Suman V, Goetz MP, Northfelt DW, Burkard ME, Ademuyiwa F, Naughton MJ, Margenthaler J, Aft R, Gray RJ, Tevaarwerk AJ, Wilke LG, Haddad TC, Moynihan T, Loprenzi C, Hieken T, Barnell EK, Skidmore ZL, Feng YY, Krysiak K, Hoog J, Guo Z, Nehring L, Wisinski KB, Mardis ER, Hagemann IS, Vij K, Sanati S, Al-Kateb H, Griffith OL, Griffith M, Doyle A, Erlichman C, Ellis MJ. A Phase II trial of neoadjuvant MK2206, an AKT inhibitor, with anastrozole in clinical stage 2 or 3 PIK3CA mutant ER positive and HER2 negative breast cancer. Clinical Cancer Research. 2017 Nov 15;23(22):6823-6832.
pmid: 28874413; doi: 10.1158/1078-0432.CCR-17-1260

Feng YY, Griffith OL+, Griffith M+. Clinical implications of neoepitope landscapes for adult and pediatric cancers. Genome Medicine. 2017 Aug 31;9(1):77.
pmid: 28854952; doi: 10.1186/s13073-017-0470-9

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. NeoPalAna: Neoadjuvant Palbociclib, a Cyclin-Dependent Kinase 4/6 Inhibitor, and Anastrozole for Clinical Stage 2 or 3 Estrogen Receptor-Positive Breast Cancer. Clinical Cancer Research. 2017 Aug 1;23(15):4055-4065.
pmid: 28270497; doi: 10.1158/1078-0432.CCR-16-3206

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. Melorheostosis: Exome sequencing of an associated dermatosis implicates postzygotic mosaicism of mutated KRAS. Bone. 2017 Aug;101:145-155.
pmid: 28434888; doi: 10.1016/j.bone.2017.04.010

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. Genomic characterization of HER2-positive breast cancer and response to neoadjuvant trastuzumab and chemotherapy-results from the ACOSOG Z1041 (Alliance) trial. Annals of Oncology. 2017 May 1;28(5):1070-1077.
pmid: 28453704; doi: 10.1093/annonc/mdx048

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+. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nature Genetics. 2017 Jan 31;49(2):170-174.
pmid: 28138153; doi: 10.1038/ng.3774

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+. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473-483.
pmid: 28064239; doi: 10.1182/blood-2016-07-729954

Zolkind P, Dunn GP, Lin T, Griffith M, Griffith OL, Uppaluri R. Neoantigens in immunotherapy and personalized vaccines: Implications for head and neck squamous cell carcinoma. Oral Oncology. 2017 Aug;71:169-176.
pmid: 27751760; doi: 10.1016/j.oraloncology.2016.09.010

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. 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. 2016 113(43):E6600-E6609.
pmid: 27791031; doi: 10.1073/pnas.1612835113

Skidmore ZL, Wagner AH, Lesurf R, Campbell KM, Kunisaki J, Griffith OL+, Griffith M+. GenVisR: Genomic Visualizations in R. Bioinformatics. 2016 Oct 1;32(19):3012-4.
pmid: 27288499; doi: 10.1093/bioinformatics/btw325

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. MyGene.info and MyVariant.info: Gene and Variant Annotation Query Services. Genome Biology. 2016 17(1):91.
pmid: 27154141; doi: 10.1186/s13059-016-0953-9

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. The ErbB2ΔEx16 splice variant is a major oncogenic driver in breast cancer that promotes a pro-metastatic tumor microenvironment. Oncogene. 2016 35(47):6053-6064.
pmid: 27157621; doi: 10.1038/onc.2016.129

Ainscough BJ, Griffith M+, Coffman AC, Wagner AH, Kunisaki J, Choudhary MN, McMichael JF, Fulton RS, Wilson RK, Griffith OL+, Mardis ER. DoCM: a database of curated mutations in cancer. Nature Methods. 2016 Sep 29;13(10):806-7.
pmid: 27684579; doi: 10.1038/nmeth.4000

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+. Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas. Cell Reports. 2016 Sep 27;17(1):249-60.
pmid: 27681435; doi: 10.1016/j.celrep.2016.08.076

Miller CA, Gindin Y, Lu C, Griffith OL, Griffith M, Shen D, Hoog J, Li T, Larson DE, Watson M, Davies SR, Hunt K, Suman VJ, Snider J, Walsh T, Colditz GA, DeSchryver K, Wilson RK, Mardis ER, Ellis MJ. Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers. Nature Communications. 2016 Aug 9;7:12498.
pmid: 27502118; doi: 10.1038/ncomms12498

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 R, 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+. Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia. Experimental Hematology. 2016 Jul;44(7):603-13.
pmid: 27181063; doi: 10.1016/j.exphem.2016.04.011

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+. A genomic analysis of Philadelphia chromosome-negative AML arising in patients with CML. Blood Cancer Journal. 2016 Apr 8;6:e413.
pmid: 27058228; doi: 10.1038/bcj.2016.18

Ma CX, Luo J, Naughton M, Ademuyiwa FO, Suresh R, Griffith M, Griffith OL, Skidmore Z, Spies NC, Ramu A, Trani L, Pluard T, Nagaraj G, Thomas SN, Guo Z, Hoog J, Han J, Mardis ER, Lockhart AC, Ellis MJ. A phase 1 trial of BKM120 (Buparlisib) in combination with fulvestrant in postmenopausal women with estrogen receptor positive metastatic breast cancer. Clinical Cancer Research. 2015 Nov 12. pii: clincanres.1745.2015.
pmid: 26563128; doi: 10.1158/1078-0432.CCR-15-1745

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. A genomic case study of mixed fibrolamellar hepatocellular carcinoma. Annals of Oncology. 2016 Mar 30. pii: mdw135.
pmid: 27029710; doi: 10.1093/annonc/mdw135

Hundal J, Carreno BM, Petti AA, Linette GP, Griffith OL, Mardis ER, Griffith M. pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Medicine. 2016 Jan 29;8(1):11.
pmid: 26825632; doi: 10.1186/s13073-016-0264-5

Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB+, Griffith OL+; Open Regulatory Annotation Consortium. ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Research. 2016 Jan 4;44(D1):D126-32.
pmid: 26578589; doi: 10.1093/nar/gkv1203

Wagner AH, Coffman AC, Ainscough BJ, Spies NC, Skidmore ZL, Campbell KM, Krysiak K, Pan D, McMichael JF, Eldred JM, Walker JR, Wilson RK, Mardis ER, Griffith M+, Griffith OL+. DGIdb 2.0: mining clinically relevant drug-gene interactions. Nucleic Acids Research. 2016 Jan 4;44(D1):D1036-44.
pmid: 26531824; doi: 10.1093/nar/gkv1165

Lu C, Riedell P, Miller CA, Hagemann IS, Westervelt P, Ozenberger BA, OLaughlin M, Magrini V, Demeter RT, Duncavage EJ, Griffith M, Griffith OL, Wartman LD. A common founding clone with TP53 and PTEN mutations gives rise to a concurrent germ cell tumor and acute megakaryoblastic leukemia. Cold Spring Harbor Molecular Case Studies. 2016 Jan;2(1):a000687.
pmid: 27148581; doi: 10.1101/mcs.a000687

Griffith M*, Miller CA*, Griffith OL, Krysiak KC, 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. Optimizing cancer genome sequencing and analysis. Cell Systems. 2015 Sep 23;1(3):210-223.
pmid: 26645048; doi: 10.1016/j.cels.2015.08.015

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. Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia. Journal of the American Medical Association (JAMA). 2015 Aug 25;314(8):811-22.
pmid: 26305651; doi: 10.1001/jama.2015.9643

Griffith M, Walker JR, Spies NC, Ainscough BJ, Griffith OL. Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud. PLoS Computational Biology. 2015 Aug 6;11(8):e1004393.
pmid: 26248053; doi: 10.1371/journal.pcbi.1004393

Griffith M*, Griffith OL*, Smith SM*, Ramu A, Callaway MB, Brummett AM, Kiwala MJ, Coffman AC, Regier AA, Oberkfell BJ, Sanderson GE, Mooney TP, Nutter NG, Belter EA, Du F, Long RL, Abbott TE, Ferguson IT, Morton DL, Burnett MM, Weible JV, Peck JB, Dukes A, McMichael JF, Lolofie JT, Derickson BR, Hundal J, Skidmore ZL, Ainscough BJ, Dees ND, Schierding WS, Kandoth C, Kim KH, Lu C, Harris CC, Maher N, Maher CA, Magrini VJ, Abbott BS, Chen K, Clark E, Das I, Fan X, Hawkins AE, Hepler TG, Wylie TN, Leonard SM, Schroeder WE, Shi X, Carmichael LK, Weil MR, Wohlstadter RW, Stiehr G, McLellan MD, Pohl CS, Miller CA, Koboldt DC, Walker JR, Eldred JM, Larson DE, Dooling DJ, Ding L, Mardis ER, Wilson RK. Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Computational Biology. 2015 Jul 9;11(7):e1004274.
pmid: 26158448; doi: 10.1371/journal.pcbi.1004274