Javed  Khan, M.D.

Javed Khan, M.D.

  • Center for Cancer Research
  • National Cancer Institute
Genetics Branch


The mission of the Oncogenomics Section is to harness the power of high throughput genomics, proteomics, machine learning and bioinfomratics to improve the outcome of children with high-risk metastatic, refractory and recurrent cancers. The research goals are to integrate the data, decipher the biology of these cancers and to identify and validate biomarkers and novel therapeutic targets and to rapidly translate our findings to the clinic.

Areas of Expertise

Convolutional neural network and machine learning
Oncogenomics and Proteomics


Selected Key Publications

Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma

Gryder BE, Pomella S, Sayers C, Wu XS, Song Y, Chiarella AM, Bagchi S, Chou HC, Sinniah RS, Walton A, Wen X, Rota R, Hathaway NA, Zhao K, Chen J, Vakoc CR, Shern JF, Stanton BZ, Khan J.
Nature Genetics. 51(12): 1714-1722, 2019. [ Journal Article ]

Chemical genomics reveals histone deacetylases are required for core regulatory transcription

Gryder BE, Wu L, Woldemichael GM, Pomella S, Quinn TR, Park PMC, Cleveland A, Stanton BZ, Song Y, Rota R, Wiest O, Yohe ME, Shern JF, Qi J, Khan J.
Nat Commun. 10(1): 3004, 2019. [ Journal Article ]

PAX3-FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability

Gryder BE, Yohe ME, Chou H-C, Zhang X, Marques J, Wachtel M, Schaefer B, Sen N, Song Y, Gualtieri A, Pomella S, Rota R, Cleveland A, Wen X, Sindiri S, Wei JS, Barr FG, Das S, Andresson T, Guha R, Lal-Nag M, Ferrer M, Shern JF, Zhao K, Thomas CJ, Khan J.
Cancer Discov. 7(8): 884-899, 2017. [ Journal Article ]

MultiDimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research

Chang W, Brohl AS, Patidar R, Sindiri S, Shern JF, Wei JS, Song YK, Yohe ME, Gryder B, Zhang S, Calzone KA, Shivaprasad N, Wen X, Badgett TC, Miettinen M, Hartman KR, League-Pascual JC, Trahair TN, Widemann BC, Merchant MS, Kaplan RN, Lin JC, Khan J.
Clin Cancer Res. 22(15): 810-20, 2016. [ Journal Article ]

Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors

Shern JF, Chen L, Chmielecki J, Wei JS, Patidar R, Rosenberg M, Ambrogio L, Auclair D, Wang J, Song YK, Tolman C, Hurd L, Liao H, Zhang S, Bogen D, Brohl AS, Sindiri S, Catchpoole D, Badgett T, Getz G, Mora J, Anderson JR, Skapek SX, Barr FG, Meyerson M, Hawkins DS, Khan J.
Cancer Discov. 4: 216-31, 2014. [ Journal Article ]

Job Vacancies

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Bioinformatics Analyst (Contr.)
Hsien-Chao Chou, Ph.D.
Vineela Gangalapudi
Research Collaborator
Robert G. Hawley, Ph.D.
Clinical Fellow
Yong Kim, M.D., Ph.D.
Special Volunteer
Katherine Masih, B.S.
Staff Scientist
David E. Milewski, Ph.D.
Young Song, Ph.D.
Postdoctoral Fellow (Visiting)
Meijie Tian, Ph.D.
Chaoyu Wang, M.S.
Xinyu Wen, M.S.
Postdoctoral Fellow (Visiting)
Arwa I. Fallatah, Ph.D.
Prebaccalaureate Fellow (CRTA)
Benjamin J. Somerville
Special Volunteer
Abdelrahman Rahmy, B.S.
Postbaccalaureate Fellow
Eleanor Pope
Joseph Toker
Program Support Specialist
Kristen Martin
Research Fellow
Zhongmei Zhang
Special Volunteer
Zahin Islam
Special Volunteer
Jerry Wu