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Ethan Cerami, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. 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. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell. 2020 04 16; 181(2):236-249. PMID: 32302568.
    Citations: 2     Fields:    
  2. 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. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nat Genet. 2020 04; 52(4):448-457. PMID: 32246132.
    Citations: 8     Fields:    Translation:Humans
  3. 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. Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Res. 2020 01 08; 48(D1):D489-D497. PMID: 31647099.
    Citations: 4     Fields:    Translation:Humans
  4. Exman P, Garrido-Castro AC, Hughes ME, Freedman RA, Li T, Trippa L, Bychkovsky BL, Barroso-Sousa R, Di Lascio S, Mackichan C, Lloyd MR, Krevalin M, Cerami E, Merrill MS, Santiago R, Crowley L, Kuhnly N, Files J, Lindeman NI, MacConaill LE, Kumari P, Tolaney SM, Krop IE, Bose R, Johnson BE, Ma CX, Dillon DA, Winer EP, Wagle N, Lin NU. Identifying ERBB2 Activating Mutations in HER2-Negative Breast Cancer: Clinical Impact of Institute-Wide Genomic Testing and Enrollment in Matched Therapy Trials. JCO Precis Oncol. 2019; 3. PMID: 32923853.
    Citations:    
  5. Gray SW, Gagan J, Cerami E, Cronin AM, Uno H, Oliver N, Lowenstein C, Lederman R, Revette A, Suarez A, Lee C, Bryan J, Sholl L, Van Allen EM. Interactive or static reports to guide clinical interpretation of cancer genomics. J Am Med Inform Assoc. 2018 05 01; 25(5):458-464. PMID: 29315417.
    Citations: 4     Fields:    Translation:Humans
  6. Sholl LM, Do K, Shivdasani P, Cerami E, Dubuc AM, Kuo FC, Garcia EP, Jia Y, Davineni P, Abo RP, Pugh TJ, van Hummelen P, Thorner AR, Ducar M, Berger AH, Nishino M, Janeway KA, Church A, Harris M, Ritterhouse LL, Campbell JD, Rojas-Rudilla V, Ligon AH, Ramkissoon S, Cleary JM, Matulonis U, Oxnard GR, Chao R, Tassell V, Christensen J, Hahn WC, Kantoff PW, Kwiatkowski DJ, Johnson BE, Meyerson M, Garraway LA, Shapiro GI, Rollins BJ, Lindeman NI, MacConaill LE. Institutional implementation of clinical tumor profiling on an unselected cancer population. JCI Insight. 2016 11 17; 1(19):e87062. PMID: 27882345.
    Citations: 65     Fields:    Translation:Humans
  7. Jones S, Stransky N, McCord CL, Cerami E, Lagowski J, Kelly D, Angiuoli SV, Sausen M, Kann L, Shukla M, Makar R, Wood LD, Diaz LA, Lengauer C, Velculescu VE. Genomic analyses of gynaecologic carcinosarcomas reveal frequent mutations in chromatin remodelling genes. Nat Commun. 2014 Sep 19; 5:5006. PMID: 25233892.
    Citations: 56     Fields:    Translation:HumansCells
  8. Stransky N, Cerami E, Schalm S, Kim JL, Lengauer C. The landscape of kinase fusions in cancer. Nat Commun. 2014 Sep 10; 5:4846. PMID: 25204415.
    Citations: 220     Fields:    Translation:Humans
  9. Aksoy BA, Gao J, Dresdner G, Wang W, Root A, Jing X, Cerami E, Sander C. PiHelper: an open source framework for drug-target and antibody-target data. Bioinformatics. 2013 Aug 15; 29(16):2071-2. PMID: 23766416.
    Citations: 6     Fields:    
  10. Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013 Apr 02; 6(269):pl1. PMID: 23550210.
    Citations: 3221     Fields:    Translation:Humans
  11. Ciriello G, Cerami E, Aksoy BA, Sander C, Schultz N. Using MEMo to discover mutual exclusivity modules in cancer. Curr Protoc Bioinformatics. 2013 Mar; Chapter 8:Unit 8.17. PMID: 23504936.
    Citations: 12     Fields:    Translation:Humans
  12. Garg K, Levine DA, Olvera N, Dao F, Bisogna M, Secord AA, Berchuck A, Cerami E, Schultz N, Soslow RA. BRCA1 immunohistochemistry in a molecularly characterized cohort of ovarian high-grade serous carcinomas. Am J Surg Pathol. 2013 Jan; 37(1):138-46. PMID: 23232854.
    Citations: 19     Fields:    Translation:Humans
  13. Wallace MD, Pfefferle AD, Shen L, McNairn AJ, Cerami EG, Fallon BL, Rinaldi VD, Southard TL, Perou CM, Schimenti JC. Comparative oncogenomics implicates the neurofibromin 1 gene (NF1) as a breast cancer driver. Genetics. 2012 Oct; 192(2):385-96. PMID: 22851646.
    Citations: 30     Fields:    Translation:HumansAnimalsCells
  14. Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012 May; 2(5):401-4. PMID: 22588877.
    Citations: 3618     Fields:    Translation:Humans
  15. Ciriello G, Cerami E, Sander C, Schultz N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Res. 2012 Feb; 22(2):398-406. PMID: 21908773.
    Citations: 224     Fields:    Translation:HumansCells
  16. Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011 Jan; 39(Database issue):D685-90. PMID: 21071392.
    Citations: 371     Fields:    
  17. Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL. Integrative genomic profiling of human prostate cancer. Cancer Cell. 2010 Jul 13; 18(1):11-22. PMID: 20579941.
    Citations: 1415     Fields:    Translation:HumansAnimalsCells
  18. Cerami E, Demir E, Schultz N, Taylor BS, Sander C. Automated network analysis identifies core pathways in glioblastoma. PLoS One. 2010 Feb 12; 5(2):e8918. PMID: 20169195.
    Citations: 155     Fields:    Translation:HumansCells
  19. Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 2007 Oct 09; 5:44. PMID: 17925023.
    Citations: 124     Fields:    
  20. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007; 2(10):2366-82. PMID: 17947979.
    Citations: 960     Fields:    
  21. Cerami EG, Bader GD, Gross BE, Sander C. cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics. 2006 Nov 13; 7:497. PMID: 17101041.
    Citations: 50     Fields:    Translation:HumansCells
  22. Kane DW, Hohman MM, Cerami EG, McCormick MW, Kuhlmman KF, Byrd JA. Agile methods in biomedical software development: a multi-site experience report. BMC Bioinformatics. 2006 May 30; 7:273. PMID: 16734914.
    Citations: 17     Fields:    Translation:Humans
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.