Peter V. Kharchenko, Ph.D. - Publications

Affiliations: 
2005 Harvard University, Cambridge, MA, United States 
Area:
Computational Genetics

90 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Girskis KM, Stergachis AB, DeGennaro EM, Doan RN, Qian X, Johnson MB, Wang PP, Sejourne GM, Nagy MA, Pollina EA, Sousa AMM, Shin T, Kenny CJ, Scotellaro JL, Debo BM, ... ... Kharchenko PV, et al. Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions. Neuron. PMID 34478631 DOI: 10.1016/j.neuron.2021.08.005  1
2021 Seplyarskiy VB, Soldatov RA, Koch E, McGinty RJ, Goldmann JM, Hernandez RD, Barnes K, Correa A, Burchard EG, Ellinor PT, McGarvey ST, Mitchell BD, Vasan RS, Redline S, Silverman E, ... ... Kharchenko PV, et al. Population sequencing data reveal a compendium of mutational processes in the human germ line. Science (New York, N.Y.). PMID 34385354 DOI: 10.1126/science.aba7408  1
2021 Kharchenko PV. Publisher Correction: The triumphs and limitations of computational methods for scRNA-seq. Nature Methods. 18: 835. PMID 34194051 DOI: 10.1038/s41592-021-01223-2  0.01
2021 Kharchenko PV. The triumphs and limitations of computational methods for scRNA-seq. Nature Methods. PMID 34155396 DOI: 10.1038/s41592-021-01171-x  0.01
2021 Kameneva P, V Artemov A, Kastriti ME, Sundström E, Kharchenko PV, Adameyko I. Evolutionary switch in expression of key markers between mouse and human leads to mis-assignment of cell types in developing adrenal medulla. Cancer Cell. PMID 33930313 DOI: 10.1016/j.ccell.2021.04.009  1
2021 Kameneva P, Artemov AV, Kastriti ME, Faure L, Olsen TK, Otte J, Erickson A, Semsch B, Andersson ER, Ratz M, Frisén J, Tischler AS, de Krijger RR, Bouderlique T, Akkuratova N, ... ... Kharchenko PV, et al. Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin. Nature Genetics. PMID 33833454 DOI: 10.1038/s41588-021-00818-x  1
2021 Kupari J, Usoskin D, Parisien M, Lou D, Hu Y, Fatt M, Lönnerberg P, Spångberg M, Eriksson B, Barkas N, Kharchenko PV, Loré K, Khoury S, Diatchenko L, Ernfors P. Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain. Nature Communications. 12: 1510. PMID 33686078 DOI: 10.1038/s41467-021-21725-z  1
2021 Specht H, Emmott E, Petelski AA, Huffman RG, Perlman DH, Serra M, Kharchenko P, Koller A, Slavov N. Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. Genome Biology. 22: 50. PMID 33504367 DOI: 10.1186/s13059-021-02267-5  0.04
2020 Pfisterer U, Petukhov V, Demharter S, Meichsner J, Thompson JJ, Batiuk MY, Asenjo-Martinez A, Vasistha NA, Thakur A, Mikkelsen J, Adorjan I, Pinborg LH, Pers TH, von Engelhardt J, Kharchenko PV, et al. Author Correction: Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis. Nature Communications. 11: 5988. PMID 33214565 DOI: 10.1038/s41467-020-19869-5  1
2020 Pfisterer U, Petukhov V, Demharter S, Meichsner J, Thompson JJ, Batiuk MY, Martinez AA, Vasistha NA, Thakur A, Mikkelsen J, Adorjan I, Pinborg LH, Pers TH, von Engelhardt J, Kharchenko PV, et al. Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis. Nature Communications. 11: 5038. PMID 33028830 DOI: 10.1038/s41467-020-18752-7  1
2020 Krivanek J, Soldatov RA, Kastriti ME, Chontorotzea T, Herdina AN, Petersen J, Szarowska B, Landova M, Matejova VK, Holla LI, Kuchler U, Zdrilic IV, Vijaykumar A, Balic A, Marangoni P, ... ... Kharchenko PV, et al. Dental cell type atlas reveals stem and differentiated cell types in mouse and human teeth. Nature Communications. 11: 4816. PMID 32968047 DOI: 10.1038/s41467-020-18512-7  1
2020 Bachireddy P, Ennis C, Nguyen VN, Gohil SH, Clement K, Shukla SA, Forman J, Barkas N, Freeman S, Bavli N, Elagina L, Leshchiner I, Mohammad AW, Mathewson ND, Keskin DB, ... ... Kharchenko PV, et al. Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect. Science Translational Medicine. 12. PMID 32938797 DOI: 10.1126/Scitranslmed.Abb7661  1
2020 Kagan J, Moritz RL, Mazurchuck R, Lee JH, Kharchenko PV, Rozenblatt-Rosen O, Ruppin E, Edfors F, Ginty F, Goltsev Y, Wells JA, LaCava J, Riesterer JL, Germain RN, Shi T, et al. NCI Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions. Journal of Proteome Research. PMID 32163288 DOI: 10.1021/Acs.Jproteome.0C00021  0.12
2020 Manz T, Gold I, McCallum C, Keller M, Kharchenko P, Gehlenborg N. Modular Visualization of Spatial Single-Cell Omics Data F1000research. 9. DOI: 10.7490/F1000Research.1118295.1  0.2
2020 Hirz T, Mei S, Kfoury Y, Wu C, Dahl DM, Saylor P, Kharchenko P, Baryawno N, Sykes D. Abstract 3446: High-resolution mapping of human prostate tumors- guiding better risk stratification and therapeutic approaches Cancer Research. 80: 3446-3446. DOI: 10.1158/1538-7445.Am2020-3446  1
2019 Barkas N, Petukhov V, Nikolaeva D, Lozinsky Y, Demharter S, Khodosevich K, Kharchenko PV. Joint analysis of heterogeneous single-cell RNA-seq dataset collections. Nature Methods. PMID 31308548 DOI: 10.1038/S41592-019-0466-Z  1
2019 Soldatov R, Kaucka M, Kastriti ME, Petersen J, Chontorotzea T, Englmaier L, Akkuratova N, Yang Y, Häring M, Dyachuk V, Bock C, Farlik M, Piacentino ML, Boismoreau F, Hilscher MM, ... ... Kharchenko PV, et al. Spatiotemporal structure of cell fate decisions in murine neural crest. Science (New York, N.Y.). 364. PMID 31171666 DOI: 10.1126/Science.Aas9536  1
2019 Stankiewicz AJ, Mortazavi F, Kharchenko PV, McGowan EM, Kharchenko V, Zhdanova IV. Cell kinetics in the adult neurogenic niche and impact of diet-induced accelerated aging. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. PMID 30737307 DOI: 10.1523/Jneurosci.2730-18.2019  1
2018 La Manno G, Soldatov R, Zeisel A, Braun E, Hochgerner H, Petukhov V, Lidschreiber K, Kastriti ME, Lönnerberg P, Furlan A, Fan J, Borm LE, Liu Z, van Bruggen D, Guo J, ... ... Kharchenko PV, et al. RNA velocity of single cells. Nature. PMID 30089906 DOI: 10.1038/S41586-018-0414-6  1
2018 Petukhov V, Guo J, Baryawno N, Severe N, Scadden DT, Samsonova MG, Kharchenko PV. dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments. Genome Biology. 19: 78. PMID 29921301 DOI: 10.1186/S13059-018-1449-6  1
2018 Fan J, Lee HO, Lee S, Ryu DE, Lee S, Xue C, Kim SJ, Kim K, Barkas N, Park PJ, Park WY, Kharchenko PV. Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data. Genome Research. PMID 29898899 DOI: 10.1101/Gr.228080.117  1
2017 Lake BB, Chen S, Sos BC, Fan J, Kaeser GE, Yung YC, Duong TE, Gao D, Chun J, Kharchenko PV, Zhang K. Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. Nature Biotechnology. PMID 29227469 DOI: 10.1038/Nbt.4038  1
2017 Hoggatt J, Singh P, Tate TA, Chou BK, Datari SR, Fukuda S, Liu L, Kharchenko PV, Schajnovitz A, Baryawno N, Mercier FE, Boyer J, Gardner J, Morrow DM, Scadden DT, et al. Rapid Mobilization Reveals a Highly Engraftable Hematopoietic Stem Cell. Cell. PMID 29224778 DOI: 10.1016/J.Cell.2017.11.003  1
2017 Lake BB, Codeluppi S, Yung YC, Gao D, Chun J, Kharchenko PV, Linnarsson S, Zhang K. A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA. Scientific Reports. 7: 6031. PMID 28729663 DOI: 10.1038/S41598-017-04426-W  1
2017 Furlan A, Dyachuk V, Kastriti ME, Calvo-Enrique L, Abdo H, Hadjab S, Chontorotzea T, Akkuratova N, Usoskin D, Kamenev D, Petersen J, Sunadome K, Memic F, Marklund U, Fried K, ... ... Kharchenko PV, et al. Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla. Science (New York, N.Y.). 357. PMID 28684471 DOI: 10.1126/Science.Aal3753  1
2017 Wang L, Fan J, Francis JM, Georghiou G, Hergert S, Li S, Gambe R, Zhou CW, Yang C, Xiao S, Cin PD, Bowden M, Kotliar D, Shukla SA, Brown JR, ... ... Kharchenko PV, et al. Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia. Genome Research. PMID 28679620 DOI: 10.1101/Gr.217331.116  1
2017 Alekseyenko AA, Walsh EM, Zee BM, Pakozdi T, Hsi P, Lemieux ME, Dal Cin P, Ince TA, Kharchenko PV, Kuroda MI, French CA. Ectopic protein interactions within BRD4-chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma. Proceedings of the National Academy of Sciences of the United States of America. PMID 28484033 DOI: 10.1073/Pnas.1702086114  1
2017 Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I. Challenges and emerging directions in single-cell analysis. Genome Biology. 18: 84. PMID 28482897 DOI: 10.1186/S13059-017-1218-Y  0.24
2017 Yu VW, Yusuf RZ, Oki T, Wu J, Saez B, Wang X, Cook C, Baryawno N, Ziller MJ, Lee E, Gu H, Meissner A, Lin CP, Kharchenko PV, Scadden DT. Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells. Cell. 168: 944-945. PMID 28235203 DOI: 10.1016/J.Cell.2017.02.010  1
2017 Akle V, Stankiewicz AJ, Kharchenko V, Yu L, Kharchenko PV, Zhdanova IV. Circadian Kinetics of Cell Cycle Progression in Adult Neurogenic Niches of a Diurnal Vertebrate. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. PMID 28087763 DOI: 10.1523/Jneurosci.3222-16.2017  1
2017 Fan J, Wang L, Francis JM, Georghiou G, Hergert S, Li S, Gambe R, Zhou CW, Yang C, Xiao S, Chin PD, Bowden M, Kotliar D, Shukla SA, Brown JR, ... ... Kharchenko PV, et al. Abstract 27: Integrated analysis of targeted single-cell genetic and transcriptional heterogeneity suggests novel drivers of chronic lymphocytic leukemia Clinical Cancer Research. 23: 27-27. DOI: 10.1158/1557-3265.Hemmal17-27  1
2016 Yu VW, Yusuf RZ, Oki T, Wu J, Saez B, Wang X, Cook C, Baryawno N, Ziller MJ, Lee E, Gu H, Meissner A, Lin CP, Kharchenko PV, Scadden DT. Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells. Cell. 167: 1310-1322.e17. PMID 27863245 DOI: 10.1016/j.cell.2016.10.045  1
2016 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, ... ... Kharchenko PV, et al. Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia. Cancer Cell. PMID 27818134 DOI: 10.1016/J.Ccell.2016.10.005  1
2016 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-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex. Cell. 166: 1147-1162.e15. PMID 27565344 DOI: 10.1016/J.Cell.2016.07.025  1
2016 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, et al. Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators. Cell Stem Cell. PMID 27524439 DOI: 10.1016/J.Stem.2016.07.004  1
2016 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, ... ... Kharchenko PV, et al. Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin. Science (New York, N.Y.). 351: 285-9. PMID 26816381 DOI: 10.1126/Science.Aad3312  1
2016 Fan J, Salathia N, Liu R, Kaeser GE, Yung YC, Herman JL, Kaper F, Fan JB, Zhang K, Chun J, Kharchenko PV. Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nature Methods. PMID 26780092 DOI: 10.1038/Nmeth.3734  1
2016 Wang L, Gambe R, Fan J, Brooks AN, Sun J, Neuberg D, Kharchenko P, Meyerson M, Fleming MD, Ebert BL, Carrasco R, Wu CJ. Abstract 669: Compound heterozygous Sf3b1-K700E mutation and Atm deletion in B cells leads to CLL in mice Cancer Research. 76: 669-669. DOI: 10.1158/1538-7445.Am2016-669  1
2016 Kuroda MI, Alekseyenko AA, Walsh EM, Wang X, Grayson A, Hsi PT, Kharchenko PV, French CA. Abstract 2655: Oncogenic chromatin factors drive cell type-specific transcription within megadomains in NUT midline carcinoma Cancer Research. 76: 2655-2655. DOI: 10.1158/1538-7445.Am2016-2655  1
2015 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. Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer. Proceedings of the National Academy of Sciences of the United States of America. PMID 26575630 DOI: 10.1073/Pnas.1518008112  1
2015 Alekseyenko AA, Walsh EM, Wang X, Grayson AR, Hsi PT, Kharchenko PV, Kuroda MI, French CA. The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains. Genes & Development. 29: 1507-23. PMID 26220994 DOI: 10.1101/Gad.267583.115  1
2015 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, et al. DAZL regulates Tet1 translation in murine embryonic stem cells. Embo Reports. PMID 26077710 DOI: 10.15252/Embr.201540538  1
2015 Zhou H, Schmidt SC, Jiang S, Willox B, Bernhardt K, Liang J, Johannsen EC, Kharchenko P, Gewurz BE, Kieff E, Zhao B. Epstein-Barr virus oncoprotein super-enhancers control B cell growth. Cell Host & Microbe. 17: 205-16. PMID 25639793 DOI: 10.1016/J.Chom.2014.12.013  1
2015 Alekseyenko AA, McElroy KA, Kang H, Zee BM, Kharchenko PV, Kuroda MI. BioTAP-XL: Cross-linking/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. 109: 21.30.1-21.30.32. PMID 25559106 DOI: 10.1002/0471142727.Mb2130S109  1
2015 Schmidt SC, Jiang S, Zhou H, Willox B, Holthaus AM, Kharchenko PV, Johannsen EC, Kieff E, Zhao B. Epstein-Barr virus nuclear antigen 3A partially coincides with EBNA3C genome-wide and is tethered to DNA through BATF complexes. Proceedings of the National Academy of Sciences of the United States of America. 112: 554-9. PMID 25540416 DOI: 10.1073/Pnas.1422580112  1
2015 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. Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. Nature Neuroscience. 18: 145-53. PMID 25420068 DOI: 10.1038/Nn.3881  1
2015 Masuda T, Wang X, Maeda M, Canver MC, Sher F, Funnell APW, Fisher C, Suciu M, Martyn GE, Norton LJ, Zhu R, Kurita R, Nakamura Y, Xu J, Higgs DR, ... ... Kharchenko PV, et al. The LRF/ZBTB7A Transcription Factor Is a BCL11A-Independent Repressor of Fetal Hemoglobin Blood. 126: 2-2. DOI: 10.1182/Blood.V126.23.2.2  1
2014 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, ... ... Kharchenko PV, et al. Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell. 26: 813-25. PMID 25490447 DOI: 10.1016/J.Ccell.2014.10.012  1
2014 Alekseyenko AA, Gorchakov AA, Zee BM, Fuchs SM, Kharchenko PV, Kuroda MI. Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs. Genes & Development. 28: 1445-60. PMID 24990964 DOI: 10.1101/Gad.241950.114  1
2014 Kharchenko PV, Silberstein L, Scadden DT. Bayesian approach to single-cell differential expression analysis. Nature Methods. 11: 740-2. PMID 24836921 DOI: 10.1038/Nmeth.2967  1
2014 Alekseyenko AA, Gorchakov AA, Kharchenko PV, Kuroda MI. Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification. Proceedings of the National Academy of Sciences of the United States of America. 111: 2488-93. PMID 24550272 DOI: 10.1073/Pnas.1400648111  1
2014 Jiang S, Willox B, Zhou H, Holthaus AM, Wang A, Shi TT, Maruo S, Kharchenko PV, Johannsen EC, Kieff E, Zhao B. Epstein-Barr virus nuclear antigen 3C binds to BATF/IRF4 or SPI1/IRF4 composite sites and recruits Sin3A to repress CDKN2A. Proceedings of the National Academy of Sciences of the United States of America. 111: 421-6. PMID 24344258 DOI: 10.1073/Pnas.1321704111  1
2013 Ferrari F, Plachetka A, Alekseyenko AA, Jung YL, Ozsolak F, Kharchenko PV, Park PJ, Kuroda MI. "Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts. Cell Reports. 5: 629-36. PMID 24183666 DOI: 10.1016/J.Celrep.2013.09.037  1
2013 Portal D, Zhou H, Zhao B, Kharchenko PV, Lowry E, Wong L, Quackenbush J, Holloway D, Jiang S, Lu Y, Kieff E. Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2. Proceedings of the National Academy of Sciences of the United States of America. 110: 18537-42. PMID 24167291 DOI: 10.1073/Pnas.1317608110  1
2013 Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE. Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters. Molecular and Cellular Biology. 33: 3274-85. PMID 23775117 DOI: 10.1128/Mcb.00275-13  1
2013 Apostolou E, Ferrari F, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML, Kharchenko PV, Park PJ, Hochedlinger K. Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell. 12: 699-712. PMID 23665121 DOI: 10.1016/J.Stem.2013.04.013  1
2013 Ferrari F, Jung YL, Kharchenko PV, Plachetka A, Alekseyenko AA, Kuroda MI, Park PJ. Comment on "Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters". Science (New York, N.Y.). 340: 273. PMID 23599463 DOI: 10.1126/Science.1231815  1
2013 Wang CI, Alekseyenko AA, LeRoy G, Elia AE, Gorchakov AA, Britton LM, Elledge SJ, Kharchenko PV, Garcia BA, Kuroda MI. Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. Nature Structural & Molecular Biology. 20: 202-9. PMID 23295261 DOI: 10.1038/Nsmb.2477  1
2012 Riddle NC, Jung YL, Gu T, Alekseyenko AA, Asker D, Gui H, Kharchenko PV, Minoda A, Plachetka A, Schwartz YB, Tolstorukov MY, Kuroda MI, Pirrotta V, Karpen GH, Park PJ, et al. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. Plos Genetics. 8: e1002954. PMID 23028361 DOI: 10.1371/Journal.Pgen.1002954  1
2012 Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, ... ... Kharchenko PV, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/Gr.136184.111  1
2012 Schwartz YB, Linder-Basso D, Kharchenko PV, Tolstorukov MY, Kim M, Li HB, Gorchakov AA, Minoda A, Shanower G, Alekseyenko AA, Riddle NC, Jung YL, Gu T, Plachetka A, Elgin SC, et al. Nature and function of insulator protein binding sites in the Drosophila genome. Genome Research. 22: 2188-98. PMID 22767387 DOI: 10.1101/Gr.138156.112  1
2012 Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, et al. Landscape of somatic retrotransposition in human cancers. Science (New York, N.Y.). 337: 967-71. PMID 22745252 DOI: 10.1126/Science.1222077  1
2012 Alekseyenko AA, Ho JW, Peng S, Gelbart M, Tolstorukov MY, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E, Gu T, Minoda A, Riddle NC, Schwartz YB, Elgin SC, et al. Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. Plos Genetics. 8: e1002646. PMID 22570616 DOI: 10.1371/Journal.Pgen.1002646  1
2012 Seplyarskiy VB, Kharchenko P, Kondrashov AS, Bazykin GA. Heterogeneity of the transition/transversion ratio in Drosophila and Hominidae genomes. Molecular Biology and Evolution. 29: 1943-55. PMID 22337862 DOI: 10.1093/Molbev/Mss071  0.12
2011 Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, Borowsky ML, Kuroda MI, Kingston RE. The genomic binding sites of a noncoding RNA. Proceedings of the National Academy of Sciences of the United States of America. 108: 20497-502. PMID 22143764 DOI: 10.1073/Pnas.1113536108  1
2011 Kharchenko PV, Xi R, Park PJ. Evidence for dosage compensation between the X chromosome and autosomes in mammals. Nature Genetics. 43: 1167-9; author reply. PMID 22120048 DOI: 10.1038/Ng.991  1
2011 Larschan E, Bishop EP, Kharchenko PV, Core LJ, Lis JT, Park PJ, Kuroda MI. X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature. 471: 115-8. PMID 21368835 DOI: 10.1038/Nature09757  1
2011 Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 471: 480-5. PMID 21179089 DOI: 10.1038/Nature09725  1
2011 Eaton ML, Prinz JA, MacAlpine HK, Tretyakov G, Kharchenko PV, MacAlpine DM. Chromatin signatures of the Drosophila replication program. Genome Research. 21: 164-74. PMID 21177973 DOI: 10.1101/Gr.116038.110  1
2011 Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, et al. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Research. 21: 147-63. PMID 21177972 DOI: 10.1101/Gr.110098.110  1
2011 Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, et al. An assessment of histone-modification antibody quality. Nature Structural & Molecular Biology. 18: 91-3. PMID 21131980 DOI: 10.1038/Nsmb.1972  1
2010 Tolstorukov MY, Kharchenko PV, Park PJ. Analysis of primary structure of chromatin with next-generation sequencing. Epigenomics. 2: 187-197. PMID 22022339 DOI: 10.2217/Epi.09.48  1
2010 Gorchakov AA, Alekseenko AA, Kharchenko PV, Park P, Kuroda M. [Dosage compensation in drosophila: sequence-specific initiation and sequence-independent spreading of MSL complex to the active genes on the male X chromosome]. Genetika. 46: 1430-4. PMID 21254570  1
2010 Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374  1
2010 Day DS, Luquette LJ, Park PJ, Kharchenko PV. Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biology. 11: R69. PMID 20584328 DOI: 10.1186/Gb-2010-11-6-R69  1
2010 Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE. A region of the human HOXD cluster that confers polycomb-group responsiveness. Cell. 140: 99-110. PMID 20085705 DOI: 10.1016/J.Cell.2009.12.022  1
2010 Gorchakov AA, Alekseyenko AA, Kharchenko PV, Park PJ, Kuroda MI. Dosage compensation in drosophila: Sequence-specific initiation and sequence-independent spreading of MSL complex to the active genes on the male X chromosome Russian Journal of Genetics. 46: 1263-1266. DOI: 10.1134/S1022795410100303  1
2009 Gorchakov AA, Alekseyenko AA, Kharchenko P, Park PJ, Kuroda MI. Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X. Genes & Development. 23: 2266-71. PMID 19797766 DOI: 10.1101/Gad.1840409  1
2009 Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ. Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Research. 19: 967-77. PMID 19246569 DOI: 10.1101/Gr.084830.108  1
2008 Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nature Biotechnology. 26: 1351-9. PMID 19029915 DOI: 10.1038/Nbt.1508  1
2008 Alekseyenko AA, Peng S, Larschan E, Gorchakov AA, Lee OK, Kharchenko P, McGrath SD, Wang CI, Mardis ER, Park PJ, Kuroda MI. A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell. 134: 599-609. PMID 18724933 DOI: 10.1016/J.Cell.2008.06.033  1
2008 Kharchenko PV, Woo CJ, Tolstorukov MY, Kingston RE, Park PJ. Nucleosome positioning in human HOX gene clusters. Genome Research. 18: 1554-61. PMID 18723689 DOI: 10.1101/Gr.075952.107  1
2008 Orford K, Kharchenko P, Lai W, Dao MC, Worhunsky DJ, Ferro A, Janzen V, Park PJ, Scadden DT. Differential H3K4 methylation identifies developmentally poised hematopoietic genes. Developmental Cell. 14: 798-809. PMID 18477461 DOI: 10.1016/J.Devcel.2008.04.002  1
2007 Wright MA, Kharchenko P, Church GM, Segrè D. Chromosomal periodicity of evolutionarily conserved gene pairs. Proceedings of the National Academy of Sciences of the United States of America. 104: 10559-64. PMID 17563360 DOI: 10.1073/Pnas.0610776104  1
2006 Vitkup D, Kharchenko P, Wagner A. Influence of metabolic network structure and function on enzyme evolution. Genome Biology. 7: R39. PMID 16684370 DOI: 10.1186/Gb-2006-7-5-R39  1
2006 Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM. Identifying metabolic enzymes with multiple types of association evidence. Bmc Bioinformatics. 7: 177. PMID 16571130 DOI: 10.1186/1471-2105-7-177  1
2005 Kharchenko P, Church GM, Vitkup D. Expression dynamics of a cellular metabolic network. Molecular Systems Biology. 1: 2005.0016. PMID 16729051 DOI: 10.1038/Msb4100023  1
2005 Petrov SB, Kharchenko PV. [Diagnosis of localized cancer of the prostate]. Urologii͡a (Moscow, Russia : 1999). 19-22. PMID 15776826  0.01
2004 Kharchenko P, Vitkup D, Church GM. Filling gaps in a metabolic network using expression information. Bioinformatics (Oxford, England). 20: i178-85. PMID 15262797 DOI: 10.1093/bioinformatics/bth930  1
2003 Segrè D, Zucker J, Katz J, Lin X, D'haeseleer P, Rindone WP, Kharchenko P, Nguyen DH, Wright MA, Church GM. From annotated genomes to metabolic flux models and kinetic parameter fitting. Omics : a Journal of Integrative Biology. 7: 301-16. PMID 14583118 DOI: 10.1089/153623103322452413  1
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