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Yuval Kluger - Publications

Affiliations: 
Program in Computational Biology New York University, New York, NY, United States 
Area:
Bioinformatics
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55 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
2020 Marczyk M, Patwardhan GA, Zhao J, Qu R, Li X, Wali VB, Gupta AK, Pillai MM, Kluger Y, Yan Q, Hatzis C, Pusztai L, Gunasekharan V. Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells. Cancers. 12. PMID 32911681 DOI: 10.3390/Cancers12092551  0.334
2020 Roulis M, Kaklamanos A, Schernthanner M, Bielecki P, Zhao J, Kaffe E, Frommelt LS, Qu R, Knapp MS, Henriques A, Chalkidi N, Koliaraki V, Jiao J, Brewer JR, Bacher M, ... ... Kluger Y, et al. Paracrine orchestration of intestinal tumorigenesis by a mesenchymal niche. Nature. 580: 524-529. PMID 32322056 DOI: 10.1038/S41586-020-2166-3  0.329
2020 Marczyk M, Gunasekharan V, Zhao J, Qu R, Li X, Patwardhan GA, Wali VB, Gupta AK, Pillai MM, Kluger Y, Hatzis C, Pusztai L. Abstract 6333: Genomic, transcriptomic, and epigenetic profiling of triple-negative breast cancer cells after Navitoclax treatment Cancer Research. 80: 6333-6333. DOI: 10.1158/1538-7445.Am2020-6333  0.373
2019 Bailis W, Shyer JA, Zhao J, Canaveras JCG, Al Khazal FJ, Qu R, Steach HR, Bielecki P, Khan O, Jackson R, Kluger Y, Maher LJ, Rabinowitz J, Craft J, Flavell RA. Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function. Nature. PMID 31217581 DOI: 10.1038/S41586-019-1311-3  0.332
2018 Gupta K, Levinsohn J, Linderman G, Chen D, Sun TY, Dong D, Taketo MM, Bosenberg M, Kluger Y, Choate K, Myung P. Single-Cell Analysis Reveals a Hair Follicle Dermal Niche Molecular Differentiation Trajectory that Begins Prior to Morphogenesis. Developmental Cell. PMID 30595533 DOI: 10.1016/J.Devcel.2018.11.032  0.324
2018 Wang Z, Gearhart MD, Lee YW, Kumar I, Ramazanov B, Zhang Y, Hernandez C, Lu AY, Neuenkirchen N, Deng J, Jin J, Kluger Y, Neubert TA, Bardwell VJ, Ivanova NB. A Non-canonical BCOR-PRC1.1 Complex Represses Differentiation Programs in Human ESCs. Cell Stem Cell. PMID 29337181 DOI: 10.1016/J.Stem.2017.12.002  0.323
2018 Carvajal-Hausdorf D, Stanton K, Patsenker J, Villarroel-Espindola F, Esch A, Montgomery R, Psyrri A, Kalogeras K, Kotoula V, Fountzilas G, Schalper K, Kluger Y, Rimm D. Abstract P2-09-18: Multiplexed (18-Plex) measurement of protein targets in trastuzumab-treated patients using imaging mass cytometry Cancer Research. 78. DOI: 10.1158/1538-7445.Sabcs17-P2-09-18  0.324
2017 Stanton KP, Jin J, Lederman RR, Weissman SM, Kluger Y. Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling. Nucleic Acids Research. PMID 28981893 DOI: 10.1093/Nar/Gkx799  0.324
2017 Li HB, Tong J, Zhu S, Batista PJ, Duffy EE, Zhao J, Bailis W, Cao G, Kroehling L, Chen Y, Wang G, Broughton JP, Chen YG, Kluger Y, Simon MD, et al. m(6)A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways. Nature. PMID 28792938 DOI: 10.1038/Nature23450  0.315
2016 Yang J, Tanaka Y, Seay M, Li Z, Jin J, Garmire LX, Zhu X, Taylor A, Li W, Euskirchen G, Halene S, Kluger Y, Snyder MP, Park IH, Pan X, et al. Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors. Nucleic Acids Research. PMID 28003475 DOI: 10.1093/Nar/Gkw1214  0.351
2016 Jiang T, Raviram R, Snetkova V, Rocha PP, Proudhon C, Badri S, Bonneau R, Skok JA, Kluger Y. Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions. Nucleic Acids Research. PMID 27439714 DOI: 10.1093/Nar/Gkw568  0.319
2016 Proudhon C, Snetkova V, Raviram R, Lobry C, Badri S, Jiang T, Hao B, Trimarchi T, Kluger Y, Aifantis I, Bonneau R, Skok JA. Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation. Cell Reports. PMID 27239026 DOI: 10.1016/J.Celrep.2016.04.087  0.326
2015 Jeon YJ, Khelifa S, Ratnikov B, Scott DA, Feng Y, Parisi F, Ruller C, Lau E, Kim H, Brill LM, Jiang T, Rimm DL, Cardiff RD, Mills GB, Smith JW, ... ... Kluger Y, et al. Regulation of glutamine carrier proteins by RNF5 determines breast cancer response to ER stress-inducing chemotherapies. Cancer Cell. 27: 354-69. PMID 25759021 DOI: 10.1016/J.Ccell.2015.02.006  0.304
2015 Vassilakopoulou M, Parisi F, Siddiqui S, England AM, Zarella ER, Anagnostou V, Kluger Y, Hicks DG, Rimm DL, Neumeister VM. Preanalytical variables and phosphoepitope expression in FFPE tissue: quantitative epitope assessment after variable cold ischemic time. Laboratory Investigation; a Journal of Technical Methods and Pathology. 95: 334-41. PMID 25418580 DOI: 10.1038/Labinvest.2014.139  0.301
2015 Murtha M, Strino F, Tokcaer-Keskin Z, Sumru Bayin N, Shalabi D, Xi X, Kluger Y, Dailey L. Comparative FAIRE-seq analysis reveals distinguishing features of the chromatin structure of ground state- and primed-pluripotent cells. Stem Cells (Dayton, Ohio). 33: 378-91. PMID 25335464 DOI: 10.1002/Stem.1871  0.36
2014 Jiang T, Shi W, Natowicz R, Ononye SN, Wali VB, Kluger Y, Pusztai L, Hatzis C. Statistical measures of transcriptional diversity capture genomic heterogeneity of cancer. Bmc Genomics. 15: 876. PMID 25294321 DOI: 10.1186/1471-2164-15-876  0.322
2014 Bonasio R, Lecona E, Narendra V, Voigt P, Parisi F, Kluger Y, Reinberg D. Interactions with RNA direct the Polycomb group protein SCML2 to chromatin where it represses target genes. Elife. 3: e02637. PMID 24986859 DOI: 10.7554/Elife.02637  0.339
2014 Murtha M, Tokcaer-Keskin Z, Tang Z, Strino F, Chen X, Wang Y, Xi X, Basilico C, Brown S, Bonneau R, Kluger Y, Dailey L. FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells. Nature Methods. 11: 559-65. PMID 24658142 DOI: 10.1038/Nmeth.2885  0.374
2014 Jeon YJ, Khelifa S, Feng Y, Lau E, Cardiff R, Kim H, Rimm DL, Kluger Y, Ronai Z. Abstract 2440: RNF5 mediates ER stress-induced degradation of SLC1A5 in breast cancer Cancer Research. 74: 2440-2440. DOI: 10.1158/1538-7445.Am2014-2440  0.301
2013 Rocha PP, Micsinai M, Kluger Y, Skok JA. Response to Casellas et al. Molecular Cell. 51: 277-8. PMID 23932710 DOI: 10.1016/J.Molcel.2013.07.019  0.724
2013 Chaumeil J, Micsinai M, Ntziachristos P, Roth DB, Aifantis I, Kluger Y, Deriano L, Skok JA. The RAG2 C-terminus and ATM protect genome integrity by controlling antigen receptor gene cleavage. Nature Communications. 4: 2231. PMID 23900513 DOI: 10.1038/Ncomms3231  0.747
2013 Strino F, Parisi F, Micsinai M, Kluger Y. TrAp: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Research. 41: e165. PMID 23892400 DOI: 10.1093/Nar/Gkt641  0.74
2013 Stanton KP, Parisi F, Strino F, Rabin N, Asp P, Kluger Y. Arpeggio: harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures. Nucleic Acids Research. 41: e161. PMID 23873955 DOI: 10.1093/Nar/Gkt627  0.334
2013 Zhang J, Bonasio R, Strino F, Kluger Y, Holloway JK, Modzelewski AJ, Cohen PE, Reinberg D. SFMBT1 functions with LSD1 to regulate expression of canonical histone genes and chromatin-related factors. Genes & Development. 27: 749-66. PMID 23592795 DOI: 10.1101/Gad.210963.112  0.369
2013 Chaumeil J, Micsinai M, Ntziachristos P, Deriano L, Wang JM, Ji Y, Nora EP, Rodesch MJ, Jeddeloh JA, Aifantis I, Kluger Y, Schatz DG, Skok JA. Higher-order looping and nuclear organization of Tcra facilitate targeted rag cleavage and regulated rearrangement in recombination centers. Cell Reports. 3: 359-70. PMID 23416051 DOI: 10.1016/J.Celrep.2013.01.024  0.751
2013 Jiang T, Szekely B, Szasz AM, Kluger Y, Kulka J, Pusztai L. Genomic alterations in matching primary tumors and metastasis in breast cancer. Journal of Clinical Oncology. 31: 1549-1549. DOI: 10.1200/Jco.2013.31.15_Suppl.1549  0.306
2013 Agarwal S, Hu J, Stanton K, Schalper K, Kluger Y, Zarrella E, Liu X, Schlegel R, Rimm DL. Abstract 1569: Next generation cell line models: conditionally reprogrammed cells. Cancer Research. 73: 1569-1569. DOI: 10.1158/1538-7445.Am2013-1569  0.319
2012 Parisi F, Micsinai M, Strino F, Ariyan S, Narayan D, Bacchiocchi A, Cheng E, Xu F, Li P, Kluger H, Halaban R, Kluger Y. Integrated analysis of tumor samples sheds light on tumor heterogeneity. The Yale Journal of Biology and Medicine. 85: 347-61. PMID 23012583  0.739
2012 Rocha PP, Micsinai M, Kim JR, Hewitt SL, Souza PP, Trimarchi T, Strino F, Parisi F, Kluger Y, Skok JA. Close proximity to Igh is a contributing factor to AID-mediated translocations. Molecular Cell. 47: 873-85. PMID 22864115 DOI: 10.1016/J.Molcel.2012.06.036  0.748
2012 Johnson K, Chaumeil J, Micsinai M, Wang JM, Ramsey LB, Baracho GV, Rickert RC, Strino F, Kluger Y, Farrar MA, Skok JA. IL-7 functionally segregates the pro-B cell stage by regulating transcription of recombination mediators across cell cycle. Journal of Immunology (Baltimore, Md. : 1950). 188: 6084-92. PMID 22581861 DOI: 10.4049/Jimmunol.1200368  0.731
2012 Gao Z, Zhang J, Bonasio R, Strino F, Sawai A, Parisi F, Kluger Y, Reinberg D. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Molecular Cell. 45: 344-56. PMID 22325352 DOI: 10.1016/J.Molcel.2012.01.002  0.321
2012 Micsinai M, Parisi F, Strino F, Asp P, Dynlacht BD, Kluger Y. Picking ChIP-seq peak detectors for analyzing chromatin modification experiments. Nucleic Acids Research. 40: e70. PMID 22307239 DOI: 10.1093/Nar/Gks048  0.723
2011 Parisi F, Ariyan S, Narayan D, Bacchiocchi A, Hoyt K, Cheng E, Xu F, Li P, Halaban R, Kluger Y. Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies. Bmc Genomics. 12: 230. PMID 21569352 DOI: 10.1186/1471-2164-12-230  0.318
2011 Asp P, Blum R, Vethantham V, Parisi F, Micsinai M, Cheng J, Bowman C, Kluger Y, Dynlacht BD. Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proceedings of the National Academy of Sciences of the United States of America. 108: E149-58. PMID 21551099 DOI: 10.1073/Pnas.1102223108  0.751
2011 Collins A, Hewitt SL, Chaumeil J, Sellars M, Micsinai M, Allinne J, Parisi F, Nora EP, Bolland DJ, Corcoran AE, Kluger Y, Bosselut R, Ellmeier W, Chong MM, Littman DR, et al. RUNX transcription factor-mediated association of Cd4 and Cd8 enables coordinate gene regulation. Immunity. 34: 303-14. PMID 21435585 DOI: 10.1016/J.Immuni.2011.03.004  0.717
2010 van Oevelen C, Bowman C, Pellegrino J, Asp P, Cheng J, Parisi F, Micsinai M, Kluger Y, Chu A, Blais A, David G, Dynlacht BD. The mammalian Sin3 proteins are required for muscle development and sarcomere specification. Molecular and Cellular Biology. 30: 5686-97. PMID 20956564 DOI: 10.1128/Mcb.00975-10  0.755
2010 Halaban R, Zhang W, Bacchiocchi A, Cheng E, Parisi F, Ariyan S, Krauthammer M, McCusker JP, Kluger Y, Sznol M. PLX4032, a selective BRAF(V600E) kinase inhibitor, activates the ERK pathway and enhances cell migration and proliferation of BRAF melanoma cells. Pigment Cell & Melanoma Research. 23: 190-200. PMID 20149136 DOI: 10.1111/J.1755-148X.2010.00685.X  0.337
2009 Halaban R, Krauthammer M, Pelizzola M, Cheng E, Kovacs D, Sznol M, Ariyan S, Narayan D, Bacchiocchi A, Molinaro A, Kluger Y, Deng M, Tran N, Zhang W, Picardo M, et al. Integrative analysis of epigenetic modulation in melanoma cell response to decitabine: clinical implications. Plos One. 4: e4563. PMID 19234609 DOI: 10.1371/Journal.Pone.0004563  0.375
2008 van Oevelen C, Wang J, Asp P, Yan Q, Kaelin WG, Kluger Y, Dynlacht BD. A role for mammalian Sin3 in permanent gene silencing. Molecular Cell. 32: 359-70. PMID 18995834 DOI: 10.1016/J.Molcel.2008.10.015  0.358
2007 Acosta-Alvear D, Zhou Y, Blais A, Tsikitis M, Lents NH, Arias C, Lennon CJ, Kluger Y, Dynlacht BD. XBP1 controls diverse cell type- and condition-specific transcriptional regulatory networks. Molecular Cell. 27: 53-66. PMID 17612490 DOI: 10.1016/J.Molcel.2007.06.011  0.388
2006 Tuck DP, Kluger HM, Kluger Y. Characterizing disease states from topological properties of transcriptional regulatory networks. Bmc Bioinformatics. 7: 236. PMID 16670008 DOI: 10.1186/1471-2105-7-236  0.333
2005 Kluger HM, Chelouche Lev D, Kluger Y, McCarthy MM, Kiriakova G, Camp RL, Rimm DL, Price JE. Using a xenograft model of human breast cancer metastasis to find genes associated with clinically aggressive disease. Cancer Research. 65: 5578-87. PMID 15994930 DOI: 10.1158/0008-5472.Can-05-0108  0.316
2005 Blais A, Tsikitis M, Acosta-Alvear D, Sharan R, Kluger Y, Dynlacht BD. An initial blueprint for myogenic differentiation. Genes & Development. 19: 553-69. PMID 15706034 DOI: 10.1101/Gad.1281105  0.359
2004 Kluger Y, Lian Z, Zhang X, Newburger PE, Weissman SM. A panorama of lineage-specific transcription in hematopoiesis. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 26: 1276-87. PMID 15551261 DOI: 10.1002/Bies.20144  0.372
2004 Cam H, Balciunaite E, Blais A, Spektor A, Scarpulla RC, Young R, Kluger Y, Dynlacht BD. A common set of gene regulatory networks links metabolism and growth inhibition. Molecular Cell. 16: 399-411. PMID 15525513 DOI: 10.1016/J.Molcel.2004.09.037  0.376
2004 Kluger Y, Tuck DP, Chang JT, Nakayama Y, Poddar R, Kohya N, Lian Z, Ben Nasr A, Halaban HR, Krause DS, Zhang X, Newburger PE, Weissman SM. Lineage specificity of gene expression patterns. Proceedings of the National Academy of Sciences of the United States of America. 101: 6508-13. PMID 15096607 DOI: 10.1073/Pnas.0401136101  0.379
2004 Kluger HM, Kluger Y, Gilmore-Hebert M, DiVito K, Chang JT, Rodov S, Mironenko O, Kacinski BM, Perkins AS, Sapi E. cDNA microarray analysis of invasive and tumorigenic phenotypes in a breast cancer model. Laboratory Investigation; a Journal of Technical Methods and Pathology. 84: 320-31. PMID 14767486 DOI: 10.1038/Labinvest.3700044  0.355
2004 Zhang X, Kluger Y, Nakayama Y, Poddar R, Whitney C, DeTora A, Weissman SM, Newburger PE. Gene expression in mature neutrophils: early responses to inflammatory stimuli. Journal of Leukocyte Biology. 75: 358-72. PMID 14634056 DOI: 10.1189/Jlb.0903412  0.343
2003 Kluger Y, Yu H, Qian J, Gerstein M. Relationship between gene co-expression and probe localization on microarray slides. Bmc Genomics. 4: 49. PMID 14667251 DOI: 10.1186/1471-2164-4-49  0.301
2003 Qian J, Kluger Y, Yu H, Gerstein M. Identification and correction of spurious spatial correlations in microarray data. Biotechniques. 35: 42-4, 46, 48. PMID 12866403 DOI: 10.2144/03351Bm03  0.35
2003 Kluger Y, Basri R, Chang JT, Gerstein M. Spectral biclustering of microarray data: coclustering genes and conditions. Genome Research. 13: 703-16. PMID 12671006 DOI: 10.1101/Gr.648603  0.343
2002 Lian Z, Kluger Y, Greenbaum DS, Tuck D, Gerstein M, Berliner N, Weissman SM, Newburger PE. Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line. Blood. 100: 3209-20. PMID 12384419 DOI: 10.1182/Blood-2002-03-0850  0.326
2001 Lian Z, Wang L, Yamaga S, Bonds W, Beazer-Barclay Y, Kluger Y, Gerstein M, Newburger PE, Berliner N, Weissman SM. Genomic and proteomic analysis of the myeloid differentiation program. Blood. 98: 513-24. PMID 11468144 DOI: 10.1182/Blood.V98.3.513  0.382
2001 Bertone P, Kluger Y, Lan N, Zheng D, Christendat D, Yee A, Edwards AM, Arrowsmith CH, Montelione GT, Gerstein M. SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. Nucleic Acids Research. 29: 2884-98. PMID 11433035 DOI: 10.1093/Nar/29.13.2884  0.303
2001 Subrahmanyam YV, Yamaga S, Prashar Y, Lee HH, Hoe NP, Kluger Y, Gerstein M, Goguen JD, Newburger PE, Weissman SM. RNA expression patterns change dramatically in human neutrophils exposed to bacteria. Blood. 97: 2457-68. PMID 11290611 DOI: 10.1182/Blood.V97.8.2457  0.318
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