| Year |
Citation |
Score |
| 2023 |
Brown AP, Parameswaran S, Cai L, Elston S, Pham C, Barski A, Weirauch MT, Ji H. TET1 regulates responses to house dust mite by altering chromatin accessibility, DNA methylation, and gene expression in airway epithelial cells. Research Square. PMID 38168374 DOI: 10.21203/rs.3.rs-3726852/v1 |
0.367 |
|
| 2023 |
Maezawa S, Yukawa M, Hasegawa K, Sugiyama R, Iizuka M, Hu M, Sakashita A, Vidal M, Koseki H, Barski A, DeFalco T, Namekawa SH. PRC1 suppresses a female gene regulatory network to ensure testicular differentiation. Cell Death & Disease. 14: 501. PMID 37542070 DOI: 10.1038/s41419-023-05996-6 |
0.308 |
|
| 2023 |
Stefan K, Barski A. Cis-regulatory atlas of primary human CD4+ T cells. Bmc Genomics. 24: 253. PMID 37170195 DOI: 10.1186/s12864-023-09288-3 |
0.335 |
|
| 2023 |
Cazares TA, Rizvi FW, Iyer B, Chen X, Kotliar M, Bejjani AT, Wayman JA, Donmez O, Wronowski B, Parameswaran S, Kottyan LC, Barski A, Weirauch MT, Prasath VBS, Miraldi ER. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. Plos Computational Biology. 19: e1010863. PMID 36719906 DOI: 10.1371/journal.pcbi.1010863 |
0.316 |
|
| 2021 |
Felton JM, Bouffi C, Schwartz JT, Schollaert KL, Malik A, Vallabh S, Wronowski B, Magier AZ, Merlin L, Barski A, Weirauch MT, Fulkerson PC, Rothenberg ME. Aiolos regulates eosinophil migration into tissues. Mucosal Immunology. PMID 34341502 DOI: 10.1038/s41385-021-00416-4 |
0.301 |
|
| 2021 |
Felton JM, Vallabh S, Parameswaran S, Edsall LE, Ernst K, Wronowski B, Malik A, Kotliar M, Weirauch MT, Barski A, Fulkerson PC, Rothenberg ME. Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. Journal of Immunology (Baltimore, Md. : 1950). PMID 34330753 DOI: 10.4049/jimmunol.2000207 |
0.455 |
|
| 2021 |
Milewski D, Shukla S, Gryder BE, Pradhan A, Donovan J, Sudha P, Vallabh S, Pyros A, Xu Y, Barski A, Szabo S, Turpin B, Pressey JG, Millay DP, Khan J, et al. FOXF1 is required for the oncogenic properties of PAX3-FOXO1 in rhabdomyosarcoma. Oncogene. PMID 33627785 DOI: 10.1038/s41388-021-01694-9 |
0.393 |
|
| 2020 |
Maezawa S, Sakashita A, Yukawa M, Chen X, Takahashi K, Alavattam KG, Nakata I, Weirauch MT, Barski A, Namekawa SH. Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition. Nature Structural & Molecular Biology. PMID 32895557 DOI: 10.1038/S41594-020-0488-3 |
0.482 |
|
| 2020 |
Sakashita A, Maezawa S, Takahashi K, Alavattam KG, Yukawa M, Hu YC, Kojima S, Parrish NF, Barski A, Pavlicev M, Namekawa SH. Endogenous retroviruses drive species-specific germline transcriptomes in mammals. Nature Structural & Molecular Biology. PMID 32895553 DOI: 10.1038/S41594-020-0487-4 |
0.423 |
|
| 2020 |
Lavery WJ, Barski A, Wiley S, Schorry EK, Lindsley AW. KMT2C/D COMPASS complex-associated diseases [KCOM-ADs]: an emerging class of congenital regulopathies. Clinical Epigenetics. 12: 10. PMID 31924266 DOI: 10.1186/S13148-019-0802-2 |
0.384 |
|
| 2020 |
Felton J, Vallabh S, Parameswaran S, Ernst K, Malik A, Weirauch M, BARSKI A, Rothenberg M, Fulkerson P. Mapping the epigenetic landscape of murine eosinophils Journal of Allergy and Clinical Immunology. 145: AB154. DOI: 10.1016/J.Jaci.2019.12.400 |
0.306 |
|
| 2019 |
Yukawa M, Jagannathan S, Vallabh S, Kartashov AV, Chen X, Weirauch MT, Barski A. AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation. The Journal of Experimental Medicine. PMID 31653690 DOI: 10.1084/Jem.20182009 |
0.427 |
|
| 2019 |
Alavattam KG, Maezawa S, Sakashita A, Khoury H, Barski A, Kaplan N, Namekawa SH. Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development. Nature Structural & Molecular Biology. PMID 30778237 DOI: 10.1038/S41594-019-0189-Y |
0.353 |
|
| 2019 |
Miller DE, Forney C, Rochman M, Cranert S, Habel J, Rymer J, Lynch A, Schroeder C, Lee J, Sauder A, Smith Q, Chawla M, Trimarchi MP, Lu X, Fjellman E, ... ... Barski A, et al. Genetic, Inflammatory, and Epithelial Cell Differentiation Factors Control Expression of Human Calpain-14. G3 (Bethesda, Md.). PMID 30626591 DOI: 10.1534/G3.118.200901 |
0.342 |
|
| 2018 |
Kelly D, Kotliar M, Woo V, Jagannathan S, Whitt J, Moncivaiz J, Aronow BJ, Dubinsky MC, Hyams JS, Markowitz JF, Baldassano RN, Stephens MC, Walters TD, Kugathasan S, Haberman Y, ... ... Barski A, et al. Microbiota-sensitive epigenetic signature predicts inflammation in Crohn's disease. Jci Insight. 3. PMID 30232290 DOI: 10.1172/Jci.Insight.122104 |
0.419 |
|
| 2018 |
Maezawa S, Alavattam KG, Tatara M, Nagai R, Barski A, Namekawa SH. A rapidly evolved domain, the SCML2 DNA-binding (SDB) repeats, contributes to chromatin binding of mouse SCML2. Biology of Reproduction. PMID 30137219 DOI: 10.1093/Biolre/Ioy181 |
0.387 |
|
| 2018 |
Maezawa S, Hasegawa K, Alavattam KG, Funakoshi M, Sato T, Barski A, Namekawa SH. SCML2 promotes heterochromatin organization in late spermatogenesis. Journal of Cell Science. PMID 30097555 DOI: 10.1242/Jcs.217125 |
0.485 |
|
| 2018 |
Bouffi C, Barski A, Fulkerson PC. Chromatin Preparation from Murine Eosinophils for Genome-Wide Analyses. Methods in Molecular Biology (Clifton, N.J.). 1799: 265-274. PMID 29956158 DOI: 10.1007/978-1-4939-7896-0_20 |
0.514 |
|
| 2018 |
Vallabh S, Kartashov AV, Barski A. Analysis of ChIP-Seq and RNA-Seq Data with BioWardrobe. Methods in Molecular Biology (Clifton, N.J.). 1783: 343-360. PMID 29767371 DOI: 10.1007/978-1-4939-7834-2_17 |
0.321 |
|
| 2018 |
Grace JO, Malik A, Reichman H, Munitz A, Barski A, Fulkerson PC. Reuse of public, genome-wide, murine eosinophil expression data for hypotheses development. Journal of Leukocyte Biology. PMID 29758095 DOI: 10.1002/Jlb.1Ma1117-444R |
0.37 |
|
| 2018 |
Maezawa S, Hasegawa K, Yukawa M, Kubo N, Sakashita A, Alavattam KG, Sin HS, Kartashov AV, Sasaki H, Barski A, Namekawa SH. Polycomb protein SCML2 facilitates H3K27me3 to establish bivalent domains in the male germline. Proceedings of the National Academy of Sciences of the United States of America. PMID 29686098 DOI: 10.1073/Pnas.1804512115 |
0.371 |
|
| 2018 |
Harley JB, Chen X, Pujato M, Miller D, Maddox A, Forney C, Magnusen AF, Lynch A, Chetal K, Yukawa M, Barski A, Salomonis N, Kaufman KM, Kottyan LC, Weirauch MT. Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nature Genetics. PMID 29662164 DOI: 10.1038/S41588-018-0102-3 |
0.361 |
|
| 2018 |
Rochman Y, Dienger-Stambaugh K, Richgels PK, Lewkowich IP, Kartashov AV, Barski A, Khurana Hershey GK, Leonard WJ, Singh H. TSLP signaling in CD4T cells programs a pathogenic T helper 2 cell state. Science Signaling. 11. PMID 29535264 DOI: 10.1126/Scisignal.Aam8858 |
0.302 |
|
| 2018 |
Adams SR, Maezawa S, Alavattam KG, Abe H, Sakashita A, Shroder M, Broering TJ, Sroga Rios J, Thomas MA, Lin X, Price CM, Barski A, Andreassen PR, Namekawa SH. RNF8 and SCML2 cooperate to regulate ubiquitination and H3K27 acetylation for escape gene activation on the sex chromosomes. Plos Genetics. 14: e1007233. PMID 29462142 DOI: 10.1371/Journal.Pgen.1007233 |
0.462 |
|
| 2018 |
Harley J, Chen X, Pujato M, Miller D, Maddox A, Forney C, Magnusen A, Lynch A, Chetal K, Yukawa M, Barski A, Salomonis N, Kaufman K, Kottyan L, Weirauch M. GG-09 A role for EBNA2 in mechanisms that are responsible for lupus and other autoimmune diseases Lupus Science & Medicine. 5. DOI: 10.1136/Lupus-2018-Lsm.96 |
0.313 |
|
| 2017 |
Maezawa S, Yukawa M, Alavattam KG, Barski A, Namekawa SH. Dynamic reorganization of open chromatin underlies diverse transcriptomes during spermatogenesis. Nucleic Acids Research. PMID 29126117 DOI: 10.1093/Nar/Gkx1052 |
0.467 |
|
| 2017 |
Maezawa S, Hasegawa K, Yukawa M, Sakashita A, Alavattam KG, Andreassen PR, Vidal M, Koseki H, Barski A, Namekawa SH. Polycomb directs timely activation of germline genes in spermatogenesis. Genes & Development. PMID 28924034 DOI: 10.1101/Gad.302000.117 |
0.438 |
|
| 2017 |
Bolte C, Flood HM, Ren X, Jagannathan S, Barski A, Kalin TV, Kalinichenko VV. FOXF1 transcription factor promotes lung regeneration after partial pneumonectomy. Scientific Reports. 7: 10690. PMID 28878348 DOI: 10.1038/S41598-017-11175-3 |
0.352 |
|
| 2017 |
Yue M, Ogawa A, Yamada N, Charles Richard JL, Barski A, Ogawa Y. Xist RNA repeat E is essential for ASH2L recruitment to the inactive X and regulates histone modifications and escape gene expression. Plos Genetics. 13: e1006890. PMID 28686623 DOI: 10.1371/Journal.Pgen.1006890 |
0.428 |
|
| 2017 |
Stevens ML, Chaturvedi P, Rankin SA, Macdonald M, Jagannathan S, Yukawa M, Barski A, Zorn AM. Genomic integration of Wnt/β-catenin and BMP/Smad1 signaling coordinates foregut and hindgut transcriptional program. Development (Cambridge, England). PMID 28219948 DOI: 10.1242/Dev.145789 |
0.389 |
|
| 2017 |
Barski A, Cuddapah S, Kartashov AV, Liu C, Imamichi H, Yang W, Peng W, Lane HC, Zhao K. Rapid Recall Ability of Memory T cells is Encoded in their Epigenome. Scientific Reports. 7: 39785. PMID 28054639 DOI: 10.1038/Srep39785 |
0.753 |
|
| 2016 |
Bian F, Gao F, Kartashov AV, Jegga AG, Barski A, Das SK. Polycomb repressive complex 1 controls uterine decidualization. Scientific Reports. 6: 26061. PMID 27181215 DOI: 10.1038/Srep26061 |
0.505 |
|
| 2015 |
Jagannathan L, Jose CC, Arita A, Kluz T, Sun H, Zhang X, Yao Y, Kartashov AV, Barski A, Costa M, Cuddapah S. Nuclear Factor κB1/RelA Mediates Inflammation in Human Lung Epithelial Cells at Atmospheric Oxygen Levels. Journal of Cellular Physiology. PMID 26588041 DOI: 10.1002/Jcp.25262 |
0.668 |
|
| 2015 |
Bouffi C, Kartashov AV, Schollaert KL, Chen X, Bacon WC, Weirauch MT, Barski A, Fulkerson PC. Transcription Factor Repertoire of Homeostatic Eosinophilopoiesis. Journal of Immunology (Baltimore, Md. : 1950). 195: 2683-95. PMID 26268651 DOI: 10.4049/Jimmunol.1500510 |
0.539 |
|
| 2015 |
Kartashov AV, Barski A. BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data. Genome Biology. 16: 158. PMID 26248465 DOI: 10.1186/S13059-015-0720-3 |
0.338 |
|
| 2015 |
Sin HS, Kartashov AV, Hasegawa K, Barski A, Namekawa SH. Poised chromatin and bivalent domains facilitate the mitosis-to-meiosis transition in the male germline. Bmc Biology. 13: 53. PMID 26198001 DOI: 10.1186/S12915-015-0159-8 |
0.42 |
|
| 2015 |
Rochman Y, Yukawa M, Kartashov AV, Barski A. Functional characterization of human T cell hyporesponsiveness induced by CTLA4-Ig. Plos One. 10: e0122198. PMID 25860138 DOI: 10.1371/Journal.Pone.0122198 |
0.342 |
|
| 2015 |
Hasegawa K, Sin HS, Maezawa S, Broering TJ, Kartashov AV, Alavattam KG, Ichijima Y, Zhang F, Bacon WC, Greis KD, Andreassen PR, Barski A, Namekawa SH. SCML2 establishes the male germline epigenome through regulation of histone H2A ubiquitination. Developmental Cell. 32: 574-88. PMID 25703348 DOI: 10.1016/J.Devcel.2015.01.014 |
0.463 |
|
| 2015 |
Rochman M, Kartashov AV, Caldwell JM, Collins MH, Stucke EM, Kc K, Sherrill JD, Herren J, Barski A, Rothenberg ME. Neurotrophic tyrosine kinase receptor 1 is a direct transcriptional and epigenetic target of IL-13 involved in allergic inflammation. Mucosal Immunology. 8: 785-98. PMID 25389033 DOI: 10.1038/Mi.2014.109 |
0.363 |
|
| 2015 |
Bouffi C, Schollaert KL, Kartashov AV, Barski A, Fulkerson PC. Global Expression and Epigenetic Analyses of Eosinophil Development Reveal Potential Novel Regulators Journal of Allergy and Clinical Immunology. 135: AB161. DOI: 10.1016/J.Jaci.2014.12.1465 |
0.388 |
|
| 2014 |
Barski A, Cuddapah S, Kartashov AV, Imamichi H, Yang W, Peng W, Lane H, Zhao K. Epigenetic regulation of gene expression and cellular differentiation Molecular Pain. 10: O20. DOI: 10.1186/1744-8069-10-S1-O20 |
0.812 |
|
| 2013 |
Byeon B, Wang W, Barski A, Ranallo RT, Bao K, Schones DE, Zhao K, Wu C, Wu WH. The ATP-dependent chromatin remodeling enzyme Fun30 represses transcription by sliding promoter-proximal nucleosomes. The Journal of Biological Chemistry. 288: 23182-93. PMID 23779104 DOI: 10.1074/Jbc.M113.471979 |
0.808 |
|
| 2012 |
Sin HS, Barski A, Zhang F, Kartashov AV, Nussenzweig A, Chen J, Andreassen PR, Namekawa SH. RNF8 regulates active epigenetic modifications and escape gene activation from inactive sex chromosomes in post-meiotic spermatids. Genes & Development. 26: 2737-48. PMID 23249736 DOI: 10.1101/Gad.202713.112 |
0.465 |
|
| 2011 |
Cuddapah S, Schones DE, Cui K, Roh TY, Barski A, Wei G, Rochman M, Bustin M, Zhao K. Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions. Molecular and Cellular Biology. 31: 700-9. PMID 21173166 DOI: 10.1128/Mcb.00740-10 |
0.8 |
|
| 2010 |
Barski A, Chepelev I, Liko D, Cuddapah S, Fleming AB, Birch J, Cui K, White RJ, Zhao K. Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes. Nature Structural & Molecular Biology. 17: 629-34. PMID 20418881 DOI: 10.1038/Nsmb.1806 |
0.788 |
|
| 2010 |
Cuddapah S, Barski A, Zhao K. Epigenomics of T cell activation, differentiation, and memory. Current Opinion in Immunology. 22: 341-7. PMID 20226645 DOI: 10.1016/J.Coi.2010.02.007 |
0.762 |
|
| 2009 |
Cuddapah S, Barski A, Cui K, Schones DE, Wang Z, Wei G, Zhao K. Native chromatin preparation and Illumina/Solexa library construction. Cold Spring Harbor Protocols. 2009: pdb.prot5237. PMID 20147195 DOI: 10.1101/Pdb.Prot5237 |
0.768 |
|
| 2009 |
Barski A, Jothi R, Cuddapah S, Cui K, Roh TY, Schones DE, Zhao K. Chromatin poises miRNA- and protein-coding genes for expression. Genome Research. 19: 1742-51. PMID 19713549 DOI: 10.1101/Gr.090951.109 |
0.805 |
|
| 2009 |
Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell. 138: 1019-31. PMID 19698979 DOI: 10.1016/J.Cell.2009.06.049 |
0.835 |
|
| 2009 |
Barski A, Zhao K. Genomic location analysis by ChIP-Seq. Journal of Cellular Biochemistry. 107: 11-8. PMID 19173299 DOI: 10.1002/Jcb.22077 |
0.659 |
|
| 2008 |
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Research. 36: 5221-31. PMID 18684996 DOI: 10.1093/Nar/Gkn488 |
0.756 |
|
| 2008 |
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genetics. 40: 897-903. PMID 18552846 DOI: 10.1038/Ng.154 |
0.802 |
|
| 2008 |
Barski A, Pregizer S, Frenkel B. Identification of transcription factor target genes by ChIP display. Methods in Molecular Biology (Clifton, N.J.). 455: 177-90. PMID 18463820 DOI: 10.1007/978-1-59745-104-8_14 |
0.807 |
|
| 2008 |
Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. Dynamic regulation of nucleosome positioning in the human genome. Cell. 132: 887-98. PMID 18329373 DOI: 10.1016/J.Cell.2008.02.022 |
0.802 |
|
| 2007 |
Prescott J, Jariwala U, Jia L, Cogan JP, Barski A, Pregizer S, Shen HC, Arasheben A, Neilson JJ, Frenkel B, Coetzee GA. Androgen receptor-mediated repression of novel target genes. The Prostate. 67: 1371-83. PMID 17624924 DOI: 10.1002/Pros.20623 |
0.774 |
|
| 2007 |
Jariwala U, Prescott J, Jia L, Barski A, Pregizer S, Cogan JP, Arasheben A, Tilley WD, Scher HI, Gerald WL, Buchanan G, Coetzee GA, Frenkel B. Identification of novel androgen receptor target genes in prostate cancer. Molecular Cancer. 6: 39. PMID 17553165 DOI: 10.1186/1476-4598-6-39 |
0.762 |
|
| 2007 |
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-Resolution Profiling of Histone Methylations in the Human Genome Cell. 129: 823-837. PMID 17512414 DOI: 10.1016/J.Cell.2007.05.009 |
0.8 |
|
| 2007 |
Pregizer S, Barski A, Gersbach CA, García AJ, Frenkel B. Identification of novel Runx2 targets in osteoblasts: cell type-specific BMP-dependent regulation of Tram2. Journal of Cellular Biochemistry. 102: 1458-71. PMID 17486635 DOI: 10.1002/Jcb.21366 |
0.805 |
|
| 2007 |
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. Response: Mapping Nucleosome Positions Using ChIP-Seq Data Cell. 131: 832-833. DOI: 10.1016/J.Cell.2007.11.018 |
0.816 |
|
| 2004 |
Barski A, Frenkel B. ChIP Display: novel method for identification of genomic targets of transcription factors. Nucleic Acids Research. 32: e104. PMID 15252151 DOI: 10.1093/Nar/Gnh097 |
0.714 |
|
| 2003 |
Luppen CA, Leclerc N, Noh T, Barski A, Khokhar A, Boskey AL, Smith E, Frenkel B. Brief bone morphogenetic protein 2 treatment of glucocorticoid-inhibited MC3T3-E1 osteoblasts rescues commitment-associated cell cycle and mineralization without alteration of Runx2. The Journal of Biological Chemistry. 278: 44995-5003. PMID 12933820 DOI: 10.1074/Jbc.M306730200 |
0.744 |
|
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