| Year |
Citation |
Score |
| 2025 |
Embaie BT, Sarkar H, Alchahin AM, Otte J, Olsen TK, Tümmler C, Kameneva P, Artemov AV, Akkuratova N, Adameyko I, Stukenborg JB, Wickström M, Kogner P, Johnsen JI, Mei S, ... Kharchenko PV, et al. Comparative Single-Cell Transcriptomics of Human Neuroblastoma and Preclinical Models Reveals Conservation of an Adrenergic Cell State. Cancer Research. PMID 39808065 DOI: 10.1158/0008-5472.CAN-24-1507 |
0.32 |
|
| 2024 |
Mitchel J, Gordon MG, Perez RK, Biederstedt E, Bueno R, Ye CJ, Kharchenko PV. Coordinated, multicellular patterns of transcriptional variation that stratify patient cohorts are revealed by tensor decomposition. Nature Biotechnology. PMID 39313646 DOI: 10.1038/s41587-024-02411-z |
0.351 |
|
| 2024 |
Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer CR, Yuan Y, Zhang Y, Li X, Song J, Knoten A, Lake BB, Gaut JP, Keene CD, ... ... Kharchenko PV, et al. Mapping human tissues with highly multiplexed RNA in situ hybridization. Nature Communications. 15: 2511. PMID 38509069 DOI: 10.1038/s41467-024-46437-y |
0.399 |
|
| 2024 |
Zhang Y, Petukhov V, Biederstedt E, Que R, Zhang K, Kharchenko PV. Gene panel selection for targeted spatial transcriptomics. Genome Biology. 25: 35. PMID 38273415 DOI: 10.1186/s13059-024-03174-1 |
0.36 |
|
| 2023 |
Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer C, Yuan Y, Zhang Y, Song J, Knoten A, Lake BB, Gaut JP, Keene D, Lein E, ... Kharchenko PV, et al. Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization. Biorxiv : the Preprint Server For Biology. PMID 37645998 DOI: 10.1101/2023.08.16.553610 |
0.412 |
|
| 2023 |
Lake BB, Menon R, Winfree S, Hu Q, Ferreira RM, Kalhor K, Barwinska D, Otto EA, Ferkowicz M, Diep D, Plongthongkum N, Knoten A, Urata S, Mariani LH, Naik AS, ... ... Kharchenko PV, et al. An atlas of healthy and injured cell states and niches in the human kidney. Nature. 619: 585-594. PMID 37468583 DOI: 10.1038/s41586-023-05769-3 |
0.397 |
|
| 2023 |
Zhang Y, Petukhov V, Biederstedt E, Que R, Zhang K, Kharchenko PV. Gene panel selection for targeted spatial transcriptomics. Biorxiv : the Preprint Server For Biology. PMID 36993340 DOI: 10.1101/2023.02.03.527053 |
0.363 |
|
| 2022 |
Haase C, Gustafsson K, Mei S, Yeh SC, Richter D, Milosevic J, Turcotte R, Kharchenko PV, Sykes DB, Scadden DT, Lin CP. Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging. Nature Methods. 19: 1622-1633. PMID 36424441 DOI: 10.1038/s41592-022-01673-2 |
0.309 |
|
| 2022 |
Faure L, Soldatov R, Kharchenko PV, Adameyko I. scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single cell data. Bioinformatics (Oxford, England). PMID 36394263 DOI: 10.1093/bioinformatics/btac746 |
0.776 |
|
| 2022 |
Gao T, Soldatov R, Sarkar H, Kurkiewicz A, Biederstedt E, Loh PR, Kharchenko PV. Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes. Nature Biotechnology. PMID 36163550 DOI: 10.1038/s41587-022-01468-y |
0.771 |
|
| 2022 |
Verhoeven BM, Mei S, Olsen TK, Gustafsson K, Valind A, Lindström A, Gisselsson D, Fard SS, Hagerling C, Kharchenko PV, Kogner P, Johnsen JI, Baryawno N. The immune cell atlas of human neuroblastoma. Cell Reports. Medicine. 3: 100657. PMID 35688160 DOI: 10.1016/j.xcrm.2022.100657 |
0.325 |
|
| 2022 |
Purroy Zuriguel N, Tong YE, Lemvigh CK, Cieri N, Li S, Parry EM, Zhang W, Rassenti LZ, Kipps TJ, Slager SL, Kay NE, Lesnick C, Shanafelt TD, Ghia P, Scarfò L, ... ... Kharchenko PV, et al. Single cell analysis reveals immune dysfunction from the earliest stages of CLL that can be reversed by ibrutinib. Blood. PMID 35020831 DOI: 10.1182/blood.2021013926 |
0.68 |
|
| 2021 |
Petukhov V, Xu RJ, Soldatov RA, Cadinu P, Khodosevich K, Moffitt JR, Kharchenko PV. Cell segmentation in imaging-based spatial transcriptomics. Nature Biotechnology. PMID 34650268 DOI: 10.1038/s41587-021-01044-w |
0.765 |
|
| 2021 |
Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, ... ... Kharchenko PV, et al. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature. 598: 103-110. PMID 34616066 DOI: 10.1038/s41586-021-03500-8 |
0.305 |
|
| 2021 |
Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, ... ... Kharchenko PV, et al. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. 598: 111-119. PMID 34616062 DOI: 10.1038/s41586-021-03465-8 |
0.428 |
|
| 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 |
0.709 |
|
| 2021 |
Tasdemir-Yilmaz OE, Druckenbrod NR, Olukoya OO, Dong W, Yung AR, Bastille I, Pazyra-Murphy MF, Sitko AA, Hale EB, Vigneau S, Gimelbrant AA, Kharchenko PV, Goodrich LV, Segal RA. Diversity of developing peripheral glia revealed by single-cell RNA sequencing. Developmental Cell. PMID 34469751 DOI: 10.1016/j.devcel.2021.08.005 |
0.3 |
|
| 2021 |
Bergen V, Soldatov RA, Kharchenko PV, Theis FJ. RNA velocity-current challenges and future perspectives. Molecular Systems Biology. 17: e10282. PMID 34435732 DOI: 10.15252/msb.202110282 |
0.757 |
|
| 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 |
0.75 |
|
| 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 |
0.313 |
|
| 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 |
0.769 |
|
| 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 |
0.389 |
|
| 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 |
0.409 |
|
| 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 |
0.305 |
|
| 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 |
0.337 |
|
| 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 |
0.421 |
|
| 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 |
0.77 |
|
| 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 |
0.413 |
|
| 2019 |
Bachireddy P, Ennis C, Nguyen VN, Barkas N, Shukla S, Clement K, Freeman S, Gohil SH, Bavli N, Elagina L, Leshchiner I, Brown JR, Getz G, Ho VT, Neuberg DS, ... ... Kharchenko P, et al. Distinct Evolutionary Patterns in Chronic Lymphocytic Leukemia (CLL) during Resistance to Graft-Versus-Leukemia (GvL) Blood. 134: 516-516. DOI: 10.1182/Blood-2019-129520 |
0.406 |
|
| 2019 |
Gustafsson K, Barkas N, Baryawno N, Scadden EW, Severe N, Spencer JA, Gessessew H, Kooshesh K, Guo J, Lin C, Kharchenko P, Scadden DT. Thymus Regeneration Is Dependent on Distinct Mesenchymal Stromal Cell Populations Blood. 134: 586-586. DOI: 10.1182/Blood-2019-126708 |
0.388 |
|
| 2019 |
Parry E, Lemvigh CK, Anandappa AJ, Li S, Werner L, Lako A, Purroy N, Gohil SH, Oliveira G, Bachireddy P, Huang T, Leshchiner I, Martinez AZ, Olsen LR, Livak K, ... ... Kharchenko P, et al. T Cell Determinants of Response and Resistance to PD-1 Blockade in Richter's Transformation Blood. 134: 680-680. DOI: 10.1182/Blood-2019-125904 |
0.32 |
|
| 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 |
0.765 |
|
| 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 |
0.428 |
|
| 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 |
0.752 |
|
| 2018 |
Bachireddy P, Barkas N, Shukla SA, Freeman S, Elagina L, Nguyen VN, Clement K, Leshchiner I, Brown JR, Neuberg DS, Ho VT, Soiffer RJ, Ritz J, Getz G, Alyea EP, ... Kharchenko P, et al. Clonal and Single Cell Dynamics of Resistance to Graft-Versus-Leukemia (GvL) in Chronic Lymphocytic Leukemia (CLL) Blood. 132: 820-820. DOI: 10.1182/Blood-2018-99-116681 |
0.442 |
|
| 2018 |
Purroy N, Fan J, Li S, Rassenti LZ, Lederer JA, Neuberg DS, Kipps TJ, Kharchenko P, Wu CJ. Single Cell Transcriptomic Characterization of the Immune Microenvironment in Naturally Progressing Chronic Lymphocytic Leukemia (CLL) Blood. 132: 3112-3112. DOI: 10.1182/Blood-2018-99-110931 |
0.376 |
|
| 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 |
0.758 |
|
| 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 |
0.335 |
|
| 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 |
0.55 |
|
| 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 |
0.417 |
|
| 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 |
0.757 |
|
| 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 |
0.371 |
|
| 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 |
0.446 |
|
| 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 |
0.381 |
|
| 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 |
0.33 |
|
| 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 |
0.48 |
|
| 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 |
0.333 |
|
| 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 |
0.721 |
|
| 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 |
0.713 |
|
| 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 |
0.431 |
|
| 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 |
0.386 |
|
| 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 |
0.767 |
|
| 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 |
0.389 |
|
| 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 |
0.418 |
|
| 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 |
0.418 |
|
| 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 |
0.461 |
|
| 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 |
0.386 |
|
| 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 |
0.361 |
|
| 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 |
0.386 |
|
| 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 |
0.389 |
|
| 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 |
0.352 |
|
| 2015 |
Silberstein L, Kharchenko PV, Kfoury YS, Mercier F, Turcotte R, Lin CP, Baryawno N, Severe N, Tate T, Hoggatt J, Scadden DT. Embigin Regulates HSPC Homing and Quiescence and Acts As a Cell Surface Marker for a Niche Factor-Enriched Subset of Osteolineage Cells Blood. 126: 663-663. DOI: 10.1182/Blood.V126.23.663.663 |
0.421 |
|
| 2015 |
Fan J, Wang L, Brooks AN, Wan Y, Neuberg DS, Rassenti LZ, Ghia EM, Kipps TJ, Brown JR, Li S, Livak KJ, Meyerson MM, Kharchenko PV, Wu CJ. Comprehensive Bulk and Single Cell Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia Blood. 126: 2906-2906. DOI: 10.1182/Blood.V126.23.2906.2906 |
0.427 |
|
| 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 |
0.44 |
|
| 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 |
0.708 |
|
| 2014 |
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, ... ... Kharchenko PV, et al. Comparative analysis of metazoan chromatin organization. Nature. 512: 449-52. PMID 25164756 DOI: 10.1038/Nature13415 |
0.362 |
|
| 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 |
0.394 |
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| 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 |
0.425 |
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| 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 |
0.316 |
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| 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 |
0.307 |
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| 2014 |
Silberstein L, Kharchenko P, Kfoury Y, Mercier F, Osawa M, Hoggatt J, Tate T, Lin C, Scadden DT. Proximity-Based Single Cell Analysis of the Bone Marrow Niche Identifies Interleukin-18 As a Quiescence Regulator of Early Hematopoietic Progenitors Blood. 124: 773-773. DOI: 10.1182/Blood.V124.21.773.773 |
0.303 |
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| 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 |
0.364 |
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| 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 |
0.305 |
|
| 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 |
0.35 |
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| 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 |
0.405 |
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| 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 |
0.306 |
|
| 2013 |
Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE. Identification of regions in the HOX cluster that can confer repression in a Polycomb-dependent manner Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-P86 |
0.346 |
|
| 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 |
0.373 |
|
| 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 |
0.318 |
|
| 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 |
0.335 |
|
| 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 |
0.373 |
|
| 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 |
0.349 |
|
| 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. Analysis of somatic retrotransposition in human cancers Bmc Proceedings. 6. DOI: 10.1186/1753-6561-6-S6-O23 |
0.345 |
|
| 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 |
0.372 |
|
| 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 |
0.345 |
|
| 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 |
0.392 |
|
| 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 |
0.385 |
|
| 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 |
0.612 |
|
| 2011 |
Silberstein L, Osawa M, Lin C, Kharchenko P, Celso CL, Aribeana C, Scadden DT. Real-Time RT-PCR Analysis of Individual Osteolineage Cells within the Hematopoietic Stem Cell Niche Blood. 118: 2389-2389. DOI: 10.1182/Blood.V118.21.2389.2389 |
0.467 |
|
| 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 |
0.33 |
|
| 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 |
0.405 |
|
| 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 |
0.338 |
|
| 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 |
0.341 |
|
| 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 |
0.325 |
|
| 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 |
0.326 |
|
| 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 |
0.31 |
|
| 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 |
0.327 |
|
| 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 |
0.324 |
|
| 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 |
0.386 |
|
| 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 |
0.384 |
|
| 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 |
0.671 |
|
| 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 |
0.48 |
|
| 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 |
0.448 |
|
| 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 |
0.36 |
|
| 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 |
0.652 |
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