Ethan Cerami

MITI minimum information guidelines for highly multiplexed tissue images.

Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA, Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK.

Nat Methods. 2022 03. 19(3):262-267. PMID: 35277708

ThreadStates: State-based Visual Analysis of Disease Progression.

Wang Q, Mazor T, Harbig TA, Cerami E, Gehlenborg N.

IEEE Trans Vis Comput Graph. 2022 01. 28(1):238-247. PMID: 34587068

OncoThreads: visualization of large-scale longitudinal cancer molecular data.

Harbig TA, Nusrat S, Mazor T, Wang Q, Thomson A, Bitter H, Cerami E, Gehlenborg N.

Bioinformatics. 2021 07 12. 37(Suppl_1):i59-i66. PMID: 34252935

OncoTree: A Cancer Classification System for Precision Oncology.

Kundra R, Zhang H, Sheridan R, Sirintrapun SJ, Wang A, Ochoa A, Wilson M, Gross B, Sun Y, Madupuri R, Satravada BA, Reales D, Vakiani E, Al-Ahmadie HA, Dogan A, Arcila M, Zehir A, Maron S, Berger MF, Viaplana C, Janeway K, Ducar M, Sholl L, Dogan S, Bedard P, Surrey LF, Sanchez IH, Syed A, Rema AB, Chakravarty D, Suehnholz S, Nissan M, Iyer GV, Murali R, Bouvier N, Soslow RA, Hyman D, Younes A, Intlekofer A, Harding JJ, Carvajal RD, Sabbatini PJ, Abou-Alfa GK, Morris L, Janjigian YY, Gallagher MM, Soumerai TA, Mellinghoff IK, Hakimi AA, Fury M, Huse JT, Bagrodia A, Hameed M, Thomas S, Gardos S, Cerami E, Mazor T, Kumari P, Raman P, Shivdasani P, MacFarland S, Newman S, Waanders A, Gao J, Solit D, Schultz N.

JCO Clin Cancer Inform. 2021 02. 5:221-230. PMID: 33625877

Network for Biomarker Immunoprofiling for Cancer Immunotherapy: Cancer Immune Monitoring and Analysis Centers and Cancer Immunologic Data Commons (CIMAC-CIDC).

Chen HX, Song M, Maecker HT, Gnjatic S, Patton D, Lee JJ, Adam SJ, Moravec R, Liu XS, Cerami E, Lindsay J, Tang M, Hodi FS, Wu CJ, Wistuba II, Al-Atrash G, Bernatchez C, Bendall SC, Hewitt SM, Sharon E, Streicher H, Enos RA, Bowman MD, Tatard-Leitman VM, Sanchez-Espiridion B, Ranasinghe S, Pichavant M, Del Valle DM, Yu J, Janssens S, Peterson-Klaus J, Rowe C, Bongers G, Jenq RR, Chang CC, Abrams JS, Mooney M, Doroshow JH, Harris LN, Thurin M.

Clin Cancer Res. 2021 09 15. 27(18):5038-5048. PMID: 33419780

Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network.

Zeng Z, Fu J, Cibulskis C, Jhaveri A, Gumbs C, Das B, Sanchez-Espiridion B, Janssens S, Taing L, Wang J, Lindsay J, Vilimas T, Zhang J, Tokheim C, Sahu A, Jiang P, Yan C, Duose DY, Cerami E, Chen L, Cohen D, Chen Q, Enos R, Huang X, Lee JJ, Liu Y, Neuberg DS, Nguyen C, Patterson C, Sarkar S, Shukla S, Tang M, Tsuji J, Uduman M, Wang X, Weirather JL, Yu J, Yu J, Zhang J, Zhang J, Meerzaman D, Thurin M, Futreal A, Karlovich C, Gabriel SB, Wistuba II, Liu XS, Wu CJ.

Clin Cancer Res. 2021 09 15. 27(18):5049-5061. PMID: 33323402

Genomic Characterization of de novo Metastatic Breast Cancer.

Garrido-Castro AC, Spurr LF, Hughes ME, Li YY, Cherniack AD, Kumari P, Lloyd MR, Bychkovsky B, Barroso-Sousa R, Di Lascio S, Jain E, Files J, Mohammed-Abreu A, Krevalin M, MacKichan C, Barry WT, Guo H, Xia D, Cerami E, Rollins BJ, MacConaill LE, Lindeman NI, Krop IE, Johnson BE, Wagle N, Winer EP, Dillon DA, Lin NU.

Clin Cancer Res. 2021 02 15. 27(4):1105-1118. PMID: 33293374

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.

Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH.

Cell. 2020 04 16. 181(2):236-249. PMID: 32302568

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.

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.

Nat Genet. 2020 04. 52(4):448-457. PMID: 32246132

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data.

Rodchenkov I, Babur O, Luna A, Aksoy BA, Wong JV, Fong D, Franz M, Siper MC, Cheung M, Wrana M, Mistry H, Mosier L, Dlin J, Wen Q, O'Callaghan C, Li W, Elder G, Smith PT, Dallago C, Cerami E, Gross B, Dogrusoz U, Demir E, Bader GD, Sander C.

Nucleic Acids Res. 2020 01 08. 48(D1):D489-D497. PMID: 31647099