JianJiong Gao

Assistant Attending

JianJiong Gao

Office Phone


Dr. JianJiong (JJ) Gao is an Assistant Attending Computational Oncologist in the Department of Epidemiology and Biostatistics and the Lead Scientist of Knowledge Systems group in the Marie-Josée and Henry R. Kravis Center for Molecular Oncology. Trained in computer science and bioinformatics, Dr. Gao’s passion lies at the intersection of computational oncology and software engineering. The primary goal of his group is to enable translational and clinical discoveries by building large biomedical data and software infrastructure. The projects his team has been building include cBioPortal (a web resource of the analysis of complex cancer genomics data), OncoKB (a precision oncology knowledge base), and Genome Nexus (a web resource for comprehensive annotation of cancer variants). Dr. Gao has also contributed to a number of collaborative cancer genomics projects including TCGA, AACR Project GENIE, and MSK-IMPACT. By building computational and translational data infrastructure, his goal is to provide researchers and clinicians with the tools for analyzing and interpreting complex genotypic and phenotypic data from cancer patients.


  1. Wu P, …, Gao J. Integration and analysis of CPTAC proteomics data in the context of cancer genomics in the cBioPortal. Mol Cell Proteomics. 2019 Jul 15. pii: mcp.TIR119.001673. doi: 10.1074/mcp.TIR119.001673. [Epub ahead of print] PubMed PMID: 31308250.
  2. Wang J, …, Gao J. G2S: a web-service for annotating genomic variants on 3D protein structures. Bioinformatics. 2018 Jun 1;34(11):1949-1950. doi: 10.1093/bioinformatics/bty047. PubMed PMID: 29385402; PubMed Central PMCID: PMC5972642.
  3. Chakravarty D, Gao J, et al. OncoKB: A Precision Oncology Knowledge Base. JCO Precis Oncol. 2017 Jul;2017. doi: 10.1200/PO.17.00011. Epub 2017 May 16. PubMed PMID: 28890946; PubMed Central PMCID: PMC5586540.
  4. Zehir A, …, Gao J, et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med. 2017 Jun;23(6):703-713. doi: 10.1038/nm.4333. Epub 2017 May 8. Erratum in: Nat Med. 2017 Aug 4;23 (8):1004. PubMed PMID: 28481359; PubMed Central PMCID: PMC5461196.
  5. Gao J, et al. 3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets. Genome Med. 2017 Jan 23;9(1):4. doi: 10.1186/s13073-016-0393-x. PubMed PMID: 28115009; PubMed Central PMCID: PMC5260099.
  6. Gao J, et al. Collection, integration and analysis of cancer genomic profiles: from data to insight. Curr Opin Genet Dev. 2014 Feb;24:92-8. doi: 10.1016/j.gde.2013.12.003. Epub 2014 Feb 27. Review. PubMed PMID: 24584084; PubMed Central PMCID: PMC4084973.
  7. Gao J, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013 Apr 2;6(269):pl1. doi: 10.1126/scisignal.2004088. PubMed PMID: 23550210; PubMed Central PMCID: PMC4160307.
  8. Cerami E, Gao J, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012 May;2(5):401-4. doi: 10.1158/2159-8290.CD-12-0095. Erratum in: Cancer Discov. 2012 Oct;2(10):960. PubMed PMID: 22588877; PubMed Central PMCID: PMC3956037.

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