Harvard Catalyst Profiles

Contact, publication, and social network information about Harvard faculty and fellows.

Peter Vasili Kharchenko, Ph.D.

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Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. U54HL145608 (ZHANG, KUN) Sep 25, 2018 - Jun 30, 2022
    NIH/NHLBI
    KULMAP: Human Kidney, urinary tract and lung mapping center
    Role: Co-Principal Investigator
  2. R21CA220147 (KHARCHENKO, PETER V) Aug 1, 2017 - Jul 31, 2020
    NIH/NCI
    Single-cell analysis of tumor-microenvironment interactions in follicular lymphoma
    Role: Principal Investigator
  3. R01DK107784 (SCADDEN, DAVID T) Jan 1, 2016 - Dec 31, 2020
    NIH/NIDDK
    Deconvoluting the hematopoietic niche under stress
    Role: Principal Investigator
  4. R01HL131768 (KHARCHENKO, PETER V) Aug 15, 2015 - May 31, 2020
    NIH/NHLBI
    Statistical methods for analysis of single-cell variability
    Role: Principal Investigator
  5. K25AG037596 (KHARCHENKO, PETER) Sep 1, 2010 - Aug 31, 2015
    NIH/NIA
    Age-associated chromatin changes in hematopoiesis
    Role: Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. 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, Yokota C, Qian X, Nilsson M, Bronner ME, Croci L, Hsiao WY, Guertin DA, Brunet JF, Consalez GG, Ernfors P, Fried K, Kharchenko PV, Adameyko I. Spatiotemporal structure of cell fate decisions in murine neural crest. Science. 2019 06 07; 364(6444). PMID: 31171666.
    Citations:    
  2. 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. J Neurosci. 2019 Apr 10; 39(15):2810-2822. PMID: 30737307.
    Citations:    
  3. 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, He X, Barker R, Sundström E, Castelo-Branco G, Cramer P, Adameyko I, Linnarsson S, Kharchenko PV. RNA velocity of single cells. Nature. 2018 08; 560(7719):494-498. PMID: 30089906.
    Citations: 1     Fields:    
  4. 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 Biol. 2018 06 19; 19(1):78. PMID: 29921301.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  5. 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 Res. 2018 08; 28(8):1217-1227. PMID: 29898899.
    Citations:    Fields:    Translation:HumansCells
  6. 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. Nat Biotechnol. 2018 01; 36(1):70-80. PMID: 29227469.
    Citations: 14     Fields:    Translation:HumansCells
  7. 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, Pelus LM. Rapid Mobilization Reveals a Highly Engraftable Hematopoietic Stem Cell. Cell. 2018 01 11; 172(1-2):191-204.e10. PMID: 29224778.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  8. 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. Sci Rep. 2017 07 20; 7(1):6031. PMID: 28729663.
    Citations: 7     Fields:    Translation:AnimalsCells
  9. 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, Topilko P, Lallemend F, Kharchenko PV, Ernfors P, Adameyko I. Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla. Science. 2017 07 07; 357(6346). PMID: 28684471.
    Citations: 7     Fields:    Translation:AnimalsCells
  10. 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, Neuberg D, Alessi DR, Zhang CZ, Kharchenko PV, Livak KJ, Wu CJ. Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia. Genome Res. 2017 08; 27(8):1300-1311. PMID: 28679620.
    Citations: 2     Fields:    Translation:HumansCells
  11. 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. Proc Natl Acad Sci U S A. 2017 05 23; 114(21):E4184-E4192. PMID: 28484033.
    Citations: 4     Fields:    Translation:HumansCells
  12. 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 Biol. 2017 05 08; 18(1):84. PMID: 28482897.
    Citations: 20     Fields:    Translation:HumansAnimals
  13. Yu VWC, 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. 2017 02 23; 168(5):944-945. PMID: 28235203.
    Citations: 5     Fields:    
  14. 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. J Neurosci. 2017 02 15; 37(7):1900-1909. PMID: 28087763.
    Citations: 7     Fields:    Translation:Animals
  15. Yu VWC, 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. 2016 11 17; 167(5):1310-1322.e17. PMID: 27863245.
    Citations: 24     Fields:    Translation:AnimalsCells
  16. 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. Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia. Cancer Cell. 2016 Nov 14; 30(5):750-763. PMID: 27818134.
    Citations: 13     Fields:    Translation:HumansCells
  17. 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. 2016 Aug 25; 166(5):1147-1162.e15. PMID: 27565344.
    Citations: 27     Fields:    Translation:HumansAnimalsCells
  18. 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. Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators. Cell Stem Cell. 2016 10 06; 19(4):530-543. PMID: 27524439.
    Citations: 14     Fields:    Translation:AnimalsCells
  19. 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. Nat Methods. 2016 Mar; 13(3):241-4. PMID: 26780092.
    Citations: 43     Fields:    Translation:AnimalsCells
  20. 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. Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin. Science. 2016 Jan 15; 351(6270):285-9. PMID: 26816381.
    Citations: 27     Fields:    Translation:HumansAnimalsCells
  21. 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. Proc Natl Acad Sci U S A. 2015 Dec 08; 112(49):15148-53. PMID: 26575630.
    Citations: 19     Fields:    Translation:HumansCells
  22. 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 Dev. 2015 Jul 15; 29(14):1507-23. PMID: 26220994.
    Citations: 30     Fields:    Translation:HumansCells
  23. 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. DAZL regulates Tet1 translation in murine embryonic stem cells. EMBO Rep. 2015 Jul; 16(7):791-802. PMID: 26077710.
    Citations: 4     Fields:    Translation:AnimalsCells
  24. 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. 2015 Feb 11; 17(2):205-16. PMID: 25639793.
    Citations: 35     Fields:    Translation:Cells
  25. 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. Curr Protoc Mol Biol. 2015 Jan 05; 109:21.30.1-32. PMID: 25559106.
    Citations: 9     Fields:    Translation:HumansAnimalsCells
  26. 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. Proc Natl Acad Sci U S A. 2015 Jan 13; 112(2):554-9. PMID: 25540416.
    Citations: 14     Fields:    Translation:HumansCells
  27. 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. Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell. 2014 Dec 08; 26(6):813-825. PMID: 25490447.
    Citations: 59     Fields:    Translation:HumansCells
  28. 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. Nat Neurosci. 2015 Jan; 18(1):145-53. PMID: 25420068.
    Citations: 229     Fields:    Translation:AnimalsCells
  29. 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. Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28; 512(7515):449-52. PMID: 25164756.
    Citations: 86     Fields:    Translation:HumansAnimalsCells
  30. 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 Dev. 2014 Jul 01; 28(13):1445-60. PMID: 24990964.
    Citations: 23     Fields:    Translation:AnimalsCells
  31. Kharchenko PV, Silberstein L, Scadden DT. Bayesian approach to single-cell differential expression analysis. Nat Methods. 2014 Jul; 11(7):740-2. PMID: 24836921.
    Citations: 152     Fields:    
  32. 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. Proc Natl Acad Sci U S A. 2014 Feb 18; 111(7):2488-93. PMID: 24550272.
    Citations: 21     Fields:    Translation:HumansCells
  33. 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. Proc Natl Acad Sci U S A. 2014 Jan 07; 111(1):421-6. PMID: 24344258.
    Citations: 30     Fields:    Translation:HumansCells
  34. 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 Rep. 2013 Nov 14; 5(3):629-36. PMID: 24183666.
    Citations: 14     Fields:    Translation:AnimalsCells
  35. 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. Proc Natl Acad Sci U S A. 2013 Nov 12; 110(46):18537-42. PMID: 24167291.
    Citations: 17     Fields:    Translation:AnimalsCells
  36. 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. Mol Cell Biol. 2013 Aug; 33(16):3274-85. PMID: 23775117.
    Citations: 19     Fields:    Translation:HumansAnimalsCells
  37. 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. 2013 Jun 06; 12(6):699-712. PMID: 23665121.
    Citations: 69     Fields:    Translation:HumansAnimalsCells
  38. 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. 2013 Apr 19; 340(6130):273. PMID: 23599463.
    Citations: 11     Fields:    Translation:AnimalsCells
  39. 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. Nat Struct Mol Biol. 2013 Feb; 20(2):202-9. PMID: 23295261.
    Citations: 47     Fields:    Translation:AnimalsCells
  40. 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, Elgin SC. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. PLoS Genet. 2012 Sep; 8(9):e1002954. PMID: 23028361.
    Citations: 18     Fields:    Translation:HumansAnimalsCells
  41. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
    Citations: 3893     Fields:    Translation:HumansAnimalsCells
  42. 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, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep; 22(9):1813-31. PMID: 22955991.
    Citations: 436     Fields:    Translation:HumansAnimals
  43. 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, Kuroda MI, Park PJ, Savitsky M, Karpen GH, Pirrotta V. Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res. 2012 Nov; 22(11):2188-98. PMID: 22767387.
    Citations: 79     Fields:    Translation:AnimalsCells
  44. 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, Park PJ. Landscape of somatic retrotransposition in human cancers. Science. 2012 Aug 24; 337(6097):967-71. PMID: 22745252.
    Citations: 252     Fields:    Translation:HumansCells
  45. 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, Karpen GH, Pirrotta V, Kuroda MI, Park PJ. Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PLoS Genet. 2012; 8(4):e1002646. PMID: 22570616.
    Citations: 25     Fields:    Translation:AnimalsCells
  46. Seplyarskiy VB, Kharchenko P, Kondrashov AS, Bazykin GA. Heterogeneity of the transition/transversion ratio in Drosophila and Hominidae genomes. Mol Biol Evol. 2012 Aug; 29(8):1943-55. PMID: 22337862.
    Citations: 10     Fields:    Translation:HumansAnimals
  47. 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. Proc Natl Acad Sci U S A. 2011 Dec 20; 108(51):20497-502. PMID: 22143764.
    Citations: 119     Fields:    Translation:AnimalsCells
  48. Kharchenko PV, Xi R, Park PJ. Evidence for dosage compensation between the X chromosome and autosomes in mammals. Nat Genet. 2011 Nov 28; 43(12):1167-9; author reply 1171-2. PMID: 22120048.
    Citations: 30     Fields:    Translation:HumansAnimalsCells
  49. 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. 2011 Mar 03; 471(7336):115-8. PMID: 21368835.
    Citations: 88     Fields:    Translation:AnimalsCells
  50. 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, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011 Mar 24; 471(7339):480-5. PMID: 21179089.
    Citations: 339     Fields:    Translation:AnimalsCells
  51. 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, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97. PMID: 21177974.
    Citations: 492     Fields:    Translation:AnimalsCells
  52. Eaton ML, Prinz JA, MacAlpine HK, Tretyakov G, Kharchenko PV, MacAlpine DM. Chromatin signatures of the Drosophila replication program. Genome Res. 2011 Feb; 21(2):164-74. PMID: 21177973.
    Citations: 80     Fields:    Translation:AnimalsCells
  53. 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, Park PJ, Elgin SC, Karpen GH. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res. 2011 Feb; 21(2):147-63. PMID: 21177972.
    Citations: 80     Fields:    Translation:HumansAnimalsCells
  54. 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, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SC, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD. An assessment of histone-modification antibody quality. Nat Struct Mol Biol. 2011 Jan; 18(1):91-3. PMID: 21131980.
    Citations: 145     Fields:    Translation:AnimalsCells
  55. 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. 2010 Oct; 46(10):1430-4. PMID: 21254570.
    Citations:    Fields:    Translation:AnimalsCells
  56. Day DS, Luquette LJ, Park PJ, Kharchenko PV. Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol. 2010; 11(6):R69. PMID: 20584328.
    Citations: 41     Fields:    Translation:HumansAnimalsCells
  57. Tolstorukov MY, Kharchenko PV, Park PJ. Analysis of primary structure of chromatin with next-generation sequencing. Epigenomics. 2010 Apr; 2(2):187-197. PMID: 22022339.
    Citations: 4     Fields:    
  58. Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE. A region of the human HOXD cluster that confers polycomb-group responsiveness. Cell. 2010 Jan 08; 140(1):99-110. PMID: 20085705.
    Citations: 144     Fields:    Translation:HumansCells
  59. 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 Dev. 2009 Oct 01; 23(19):2266-71. PMID: 19797766.
    Citations: 25     Fields:    Translation:AnimalsCells
  60. Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ. Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Res. 2009 Jun; 19(6):967-77. PMID: 19246569.
    Citations: 43     Fields:    Translation:HumansCells
  61. Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008 Dec; 26(12):1351-9. PMID: 19029915.
    Citations: 338     Fields:    Translation:Cells
  62. Kharchenko PV, Woo CJ, Tolstorukov MY, Kingston RE, Park PJ. Nucleosome positioning in human HOX gene clusters. Genome Res. 2008 Oct; 18(10):1554-61. PMID: 18723689.
    Citations: 18     Fields:    Translation:HumansCells
  63. 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. 2008 Aug 22; 134(4):599-609. PMID: 18724933.
    Citations: 119     Fields:    Translation:AnimalsCells
  64. 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. Dev Cell. 2008 May; 14(5):798-809. PMID: 18477461.
    Citations: 51     Fields:    Translation:HumansAnimalsCells
  65. Wright MA, Kharchenko P, Church GM, Segrè D. Chromosomal periodicity of evolutionarily conserved gene pairs. Proc Natl Acad Sci U S A. 2007 Jun 19; 104(25):10559-64. PMID: 17563360.
    Citations: 26     Fields:    Translation:Cells
  66. Vitkup D, Kharchenko P, Wagner A. Influence of metabolic network structure and function on enzyme evolution. Genome Biol. 2006; 7(5):R39. PMID: 16684370.
    Citations: 65     Fields:    Translation:Animals
  67. Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM. Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics. 2006 Mar 29; 7:177. PMID: 16571130.
    Citations: 42     Fields:    
  68. Kharchenko P, Church GM, Vitkup D. Expression dynamics of a cellular metabolic network. Mol Syst Biol. 2005; 1:2005.0016. PMID: 16729051.
    Citations: 37     Fields:    Translation:AnimalsCells
  69. Petrov SB, Kharchenko PV. [Diagnosis of localized cancer of the prostate]. Urologiia. 2005 Jan-Feb; (1):19-22. PMID: 15776826.
    Citations:    Fields:    Translation:Humans
  70. Kharchenko P, Vitkup D, Church GM. Filling gaps in a metabolic network using expression information. Bioinformatics. 2004 Aug 04; 20 Suppl 1:i178-85. PMID: 15262797.
    Citations: 36     Fields:    Translation:Cells
  71. 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. 2003; 7(3):301-16. PMID: 14583118.
    Citations: 23     Fields:    Translation:Cells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.