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.

BioTAP-XL: Cross-linking/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes.
Authors: Alekseyenko AA, McElroy KA, Kang H, Zee BM, Kharchenko PV, Kuroda MI.
Curr Protoc Mol Biol
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Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing.
Authors: Usoskin D, Furlan A, Islam S, Abdo H, Lönnerberg P, Lou D, Hjerling-Leffler J, Haeggström J, Kharchenko O, Kharchenko PV, Linnarsson S, Ernfors P.
Nat Neurosci
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Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia.
Authors: Landau DA, Clement K, Ziller MJ, Boyle P, Fan J, Gu H, Stevenson K, Sougnez C, Wang L, Li S, Kotliar D, Zhang W, Ghandi M, Garraway L, Fernandes SM, Livak KJ, Gabriel S, Gnirke A, Lander ES, Brown JR, Neuberg D, Kharchenko PV, Hacohen N, Getz G, Meissner A, Wu CJ.
Cancer Cell
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Comparative analysis of metazoan chromatin organization.
Authors: Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ.
Nature
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Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs.
Authors: Alekseyenko AA, Gorchakov AA, Zee BM, Fuchs SM, Kharchenko PV, Kuroda MI.
Genes Dev
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Bayesian approach to single-cell differential expression analysis.
Authors: Kharchenko PV, Silberstein L, Scadden DT.
Nat Methods
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Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification.
Authors: Alekseyenko AA, Gorchakov AA, Kharchenko PV, Kuroda MI.
Proc Natl Acad Sci U S A
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Epstein-Barr virus nuclear antigen 3C binds to BATF/IRF4 or SPI1/IRF4 composite sites and recruits Sin3A to repress CDKN2A.
Authors: Jiang S, Willox B, Zhou H, Holthaus AM, Wang A, Shi TT, Maruo S, Kharchenko PV, Johannsen EC, Kieff E, Zhao B.
Proc Natl Acad Sci U S A
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"Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts.
Authors: Ferrari F, Plachetka A, Alekseyenko AA, Jung YL, Ozsolak F, Kharchenko PV, Park PJ, Kuroda MI.
Cell Rep
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Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2.
Authors: Portal D, Zhou H, Zhao B, Kharchenko PV, Lowry E, Wong L, Quackenbush J, Holloway D, Jiang S, Lu Y, Kieff E.
Proc Natl Acad Sci U S A
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