Peter Kharchenko

Peter Kharchenko, PhD

Research Collaborator
Former Associate Professor of Biomedical Informatics
Altos Labs San Diego Institute of Science

Peter Kharchenko received a PhD in biophysics at Harvard University, studying gene regulation and metabolic networks under the advisement of George Church. He then completed a four-year postdoctoral fellowship in computational biology and genomics in the laboratory of DBMI's Peter Park. As a former Gilbert S. Omenn Associate Professor of Biomedical Informatics, he studied the epigenetic mechanisms that regulate the growth and maintenance of normal tissues as well as the disruptions of the epigenetic state that contribute to a variety of disorders.

Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia.
Authors: Wang L, Brooks AN, Fan J, Wan Y, Gambe R, Li S, Hergert S, Yin S, Freeman SS, Levin JZ, Fan L, Seiler M, Buonamici S, Smith PG, Chau KF, Cibulskis CL, Zhang W, Rassenti LZ, Ghia EM, Kipps TJ, Fernandes S, Bloch DB, Kotliar D, Landau DA, Shukla SA, Aster JC, Reed R, DeLuca DS, Brown JR, Neuberg D, Getz G, Livak KJ, Meyerson MM, Kharchenko PV, Wu CJ.
Cancer Cell
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Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators.
Authors: Silberstein L, Goncalves KA, Kharchenko PV, Turcotte R, Kfoury Y, Mercier F, Baryawno N, Severe N, Bachand J, Spencer JA, Papazian A, Lee D, Chitteti BR, Srour EF, Hoggatt J, Tate T, Lo Celso C, Ono N, Nutt S, Heino J, Sipilä K, Shioda T, Osawa M, Lin CP, Hu GF, Scadden DT.
Cell Stem Cell
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Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex.
Authors: Zhang X, Chen MH, Wu X, Kodani A, Fan J, Doan R, Ozawa M, Ma J, Yoshida N, Reiter JF, Black DL, Kharchenko PV, Sharp PA, Walsh CA.
Cell
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Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis.
Authors: Fan J, Salathia N, Liu R, Kaeser GE, Yung YC, Herman JL, Kaper F, Fan JB, Zhang K, Chun J, Kharchenko PV.
Nat Methods
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Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin.
Authors: Masuda T, Wang X, Maeda M, Canver MC, Sher F, Funnell AP, Fisher C, Suciu M, Martyn GE, Norton LJ, Zhu C, Kurita R, Nakamura Y, Xu J, Higgs DR, Crossley M, Bauer DE, Orkin SH, Kharchenko PV, Maeda T.
Science
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Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer.
Authors: Bersani F, Lee E, Kharchenko PV, Xu AW, Liu M, Xega K, MacKenzie OC, Brannigan BW, Wittner BS, Jung H, Ramaswamy S, Park PJ, Maheswaran S, Ting DT, Haber DA.
Proc Natl Acad Sci U S A
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The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains.
Authors: Alekseyenko AA, Walsh EM, Wang X, Grayson AR, Hsi PT, Kharchenko PV, Kuroda MI, French CA.
Genes Dev
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DAZL regulates Tet1 translation in murine embryonic stem cells.
Authors: Welling M, Chen HH, Muñoz J, Musheev MU, Kester L, Junker JP, Mischerikow N, Arbab M, Kuijk E, Silberstein L, Kharchenko PV, Geens M, Niehrs C, van de Velde H, van Oudenaarden A, Heck AJ, Geijsen N.
EMBO Rep
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Epstein-Barr virus oncoprotein super-enhancers control B cell growth.
Authors: Zhou H, Schmidt SC, Jiang S, Willox B, Bernhardt K, Liang J, Johannsen EC, Kharchenko P, Gewurz BE, Kieff E, Zhao B.
Cell Host Microbe
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Epstein-Barr virus nuclear antigen 3A partially coincides with EBNA3C genome-wide and is tethered to DNA through BATF complexes.
Authors: Schmidt SC, Jiang S, Zhou H, Willox B, Holthaus AM, Kharchenko PV, Johannsen EC, Kieff E, Zhao B.
Proc Natl Acad Sci U S A
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