| Year |
Citation |
Score |
| 2023 |
Wright S, Zhao X, Rosikiewicz W, Mryncza S, Hyle J, Qi W, Liu Z, Yi S, Cheng Y, Xu B, Li C. Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by noncoding CRISPR screens. Nature Communications. 14: 7464. PMID 38016946 DOI: 10.1038/s41467-023-43264-5 |
0.373 |
|
| 2023 |
Xiang G, He X, Giardine BM, Weaver KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, ... ... Cheng Y, et al. Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Biorxiv : the Preprint Server For Biology. PMID 37066352 DOI: 10.1101/2023.04.02.535219 |
0.756 |
|
| 2022 |
Walker M, Li Y, Morales-Hernandez A, Qi Q, Parupalli C, Brown SA, Christian C, Clements WK, Cheng Y, McKinney Freeman SL. An NFIX-mediated regulatory network governs the balance of hematopoietic stem and progenitor cells during hematopoiesis. Blood Advances. PMID 36478187 DOI: 10.1182/bloodadvances.2022007811 |
0.321 |
|
| 2022 |
Shrestha D, Bag A, Wu R, Zhang Y, Tang X, Qi Q, Xing J, Cheng Y. Genomics and epigenetics guided identification of tissue-specific genomic safe harbors. Genome Biology. 23: 199. PMID 36131352 DOI: 10.1186/s13059-022-02770-3 |
0.33 |
|
| 2021 |
Su W, Raza A, Gao A, Jia Z, Zhang Y, Hussain MA, Mehmood SS, Cheng Y, Lv Y, Zou X. Genome-Wide Analysis and Expression Profile of Superoxide Dismutase (SOD) Gene Family in Rapeseed ( L.) under Different Hormones and Abiotic Stress Conditions. Antioxidants (Basel, Switzerland). 10. PMID 34439430 DOI: 10.3390/antiox10081182 |
0.313 |
|
| 2021 |
Doerfler PA, Feng R, Li Y, Palmer LE, Porter SN, Bell HW, Crossley M, Pruett-Miller SM, Cheng Y, Weiss MJ. Activation of γ-globin gene expression by GATA1 and NF-Y in hereditary persistence of fetal hemoglobin. Nature Genetics. PMID 34341563 DOI: 10.1038/s41588-021-00904-0 |
0.386 |
|
| 2021 |
Cheng L, Li Y, Qi Q, Xu P, Feng R, Palmer L, Chen J, Wu R, Yee T, Zhang J, Yao Y, Sharma A, Hardison RC, Weiss MJ, Cheng Y. Single-nucleotide-level mapping of DNA regulatory elements that control fetal hemoglobin expression. Nature Genetics. PMID 33958780 DOI: 10.1038/s41588-021-00861-8 |
0.555 |
|
| 2021 |
Yang Y, Li X, Ma Z, Wang C, Yang Q, Byrne-Steele M, Hong R, Min Q, Zhou G, Cheng Y, Qin G, Youngyunpipatkul JV, Wing JB, Sakaguchi S, Toonstra C, et al. CTLA-4 expression by B-1a B cells is essential for immune tolerance. Nature Communications. 12: 525. PMID 33483505 DOI: 10.1038/s41467-020-20874-x |
0.409 |
|
| 2021 |
McLeod C, Gout AM, Zhou X, Thrasher A, Rahbarinia D, Brady SW, Macias M, Birch K, Finkelstein D, Sunny J, Mudunuri R, Orr BA, Treadway M, Davidson B, Ard TK, ... ... Cheng Y, et al. St. Jude Cloud-a Pediatric Cancer Genomic Data Sharing Ecosystem. Cancer Discovery. PMID 33408242 DOI: 10.1158/2159-8290.CD-20-1230 |
0.336 |
|
| 2020 |
Qi Q, Cheng L, Tang X, He Y, Li Y, Yee T, Shrestha D, Feng R, Xu P, Zhou X, Pruett-Miller SM, Hardison RC, Weiss MJ, Cheng Y. Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis. Blood. PMID 33512425 DOI: 10.1182/blood.2020005780 |
0.606 |
|
| 2020 |
Xu P, Scott DC, Xu B, Yao Y, Feng R, Cheng L, Mayberry K, Bi W, Palmer LE, King MT, Wang H, Li Y, Fan Y, Alpi AF, Li C, ... ... Cheng Y, et al. FBXO11-Mediated Proteolysis of BAHD1 Relieves PRC2-dependent Transcriptional Repression in Erythropoiesis. Blood. PMID 33156908 DOI: 10.1182/blood.2020007809 |
0.356 |
|
| 2020 |
Lazzarotto CR, Malinin NL, Li Y, Zhang R, Yang Y, Lee G, Cowley E, He Y, Lan X, Jividen K, Katta V, Kolmakova NG, Petersen CT, Qi Q, Strelcov E, ... ... Cheng Y, et al. CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity. Nature Biotechnology. PMID 32541958 DOI: 10.1038/S41587-020-0555-7 |
0.364 |
|
| 2020 |
Xiang G, Keller CA, Heuston EF, Giardine BM, An L, Wixom AQ, Miller A, Cockburn A, Sauria MEG, Weaver K, Lichtenberg J, Göttgens B, Li Q, Bodine D, Mahony S, ... ... Cheng Y, et al. An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Genome Research. PMID 32132109 DOI: 10.1101/Gr.255760.119 |
0.777 |
|
| 2015 |
Dogan N, Wu W, Morrissey CS, Chen KB, Stonestrom A, Long M, Keller CA, Cheng Y, Jain D, Visel A, Pennacchio LA, Weiss MJ, Blobel GA, Hardison RC. Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics & Chromatin. 8: 16. PMID 25984238 DOI: 10.1186/S13072-015-0009-5 |
0.794 |
|
| 2015 |
Denas O, Sandstrom R, Cheng Y, Beal K, Herrero J, Hardison RC, Taylor J. Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution. Bmc Genomics. 16: 87. PMID 25765714 DOI: 10.1186/S12864-015-1245-6 |
0.655 |
|
| 2014 |
Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, et al. Topologically associating domains are stable units of replication-timing regulation. Nature. 515: 402-5. PMID 25409831 DOI: 10.1038/Nature13986 |
0.696 |
|
| 2014 |
Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, et al. Principles of regulatory information conservation between mouse and human. Nature. 515: 371-5. PMID 25409826 DOI: 10.1038/Nature13985 |
0.84 |
|
| 2014 |
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992 |
0.795 |
|
| 2014 |
Sundaram V, Cheng Y, Ma Z, Li D, Xing X, Edge P, Snyder MP, Wang T. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Research. 24: 1963-76. PMID 25319995 DOI: 10.1101/Gr.168872.113 |
0.603 |
|
| 2014 |
Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, et al. Comparative analysis of regulatory information and circuits across distant species. Nature. 512: 453-6. PMID 25164757 DOI: 10.1038/Nature13668 |
0.827 |
|
| 2013 |
Cheng Y, Gaughan J, Midic U, Han Z, Liang CG, Patel BG, Latham KE. Systems genetics implicates cytoskeletal genes in oocyte control of cloned embryo quality. Genetics. 193: 877-96. PMID 23307892 DOI: 10.1534/Genetics.112.148866 |
0.326 |
|
| 2012 |
Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Research. 22: 1798-812. PMID 22955990 DOI: 10.1101/Gr.139105.112 |
0.613 |
|
| 2012 |
Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M. Annotation of functional variation in personal genomes using RegulomeDB. Genome Research. 22: 1790-7. PMID 22955989 DOI: 10.1101/Gr.137323.112 |
0.746 |
|
| 2012 |
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, ... ... Cheng Y, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 489: 91-100. PMID 22955619 DOI: 10.1038/Nature11245 |
0.8 |
|
| 2012 |
Kadauke S, Udugama MI, Pawlicki JM, Achtman JC, Jain DP, Cheng Y, Hardison RC, Blobel GA. Tissue-specific mitotic bookmarking by hematopoietic transcription factor GATA1. Cell. 150: 725-37. PMID 22901805 DOI: 10.1016/J.Cell.2012.06.038 |
0.738 |
|
| 2012 |
Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, ... ... Cheng Y, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/Gb-2012-13-8-418 |
0.732 |
|
| 2012 |
Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 148: 1293-307. PMID 22424236 DOI: 10.1016/J.Cell.2012.02.009 |
0.713 |
|
| 2012 |
Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, Na K, Choi EY, Yan F, Zhang F, Zhang Y, Snyder M, Cheng Y, Chen R, et al. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nature Biotechnology. 30: 221-3. PMID 22398612 DOI: 10.1038/Nbt.2152 |
0.551 |
|
| 2011 |
Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Research. 21: 1659-71. PMID 21795386 DOI: 10.1101/Gr.125088.111 |
0.805 |
|
| 2011 |
Lamonica JM, Deng W, Kadauke S, Campbell AE, Gamsjaeger R, Wang H, Cheng Y, Billin AN, Hardison RC, Mackay JP, Blobel GA. Bromodomain protein Brd3 associates with acetylated GATA1 to promote its chromatin occupancy at erythroid target genes. Proceedings of the National Academy of Sciences of the United States of America. 108: E159-68. PMID 21536911 DOI: 10.1073/Pnas.1102140108 |
0.647 |
|
| 2011 |
Kadauke S, Pawlicki JM, Udugama M, Achtman JC, Cheng Y, Hardison RC, Blobel GA. Lineage-Specific Mitotic Bookmarking by Hematopoietic Transcription Factor GATA1 Blood. 118: 547-547. DOI: 10.1182/Blood.V118.21.547.547 |
0.655 |
|
| 2009 |
Yu M, Riva L, Xie H, Schindler Y, Moran TB, Cheng Y, Yu D, Hardison R, Weiss MJ, Orkin SH, Bernstein BE, Fraenkel E, Cantor AB. Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Molecular Cell. 36: 682-95. PMID 19941827 DOI: 10.1016/J.Molcel.2009.11.002 |
0.656 |
|
| 2009 |
Cheng Y, Wu W, Kumar SA, Yu D, Deng W, Tripic T, King DC, Chen KB, Zhang Y, Drautz D, Giardine B, Schuster SC, Miller W, Chiaromonte F, Zhang Y, et al. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Research. 19: 2172-84. PMID 19887574 DOI: 10.1101/Gr.098921.109 |
0.843 |
|
| 2009 |
Zhang Y, Wu W, Cheng Y, King DC, Harris RS, Taylor J, Chiaromonte F, Hardison RC. Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. Nucleic Acids Research. 37: 7024-38. PMID 19767611 DOI: 10.1093/Nar/Gkp747 |
0.782 |
|
| 2009 |
Tripic T, Deng W, Cheng Y, Zhang Y, Vakoc CR, Gregory GD, Hardison RC, Blobel GA. SCL and associated proteins distinguish active from repressive GATA transcription factor complexes. Blood. 113: 2191-201. PMID 19011221 DOI: 10.1182/Blood-2008-07-169417 |
0.635 |
|
| 2008 |
Cheng Y, King DC, Dore LC, Zhang X, Zhou Y, Zhang Y, Dorman C, Abebe D, Kumar SA, Chiaromonte F, Miller W, Green RD, Weiss MJ, Hardison RC. Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Genome Research. 18: 1896-905. PMID 18818370 DOI: 10.1101/Gr.083089.108 |
0.782 |
|
| 2007 |
King DC, Taylor J, Zhang Y, Cheng Y, Lawson HA, Martin J, Chiaromonte F, Miller W, Hardison RC. Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Research. 17: 775-86. PMID 17567996 DOI: 10.1101/Gr.5592107 |
0.765 |
|
| 2007 |
Zhou Y, Cheng Y, Wang H, Zhang Y, King DC, Taylor J, Chiaromonte F, Dorman C, Miller W, Dore LC, Weiss MJ, Hardison RC. Validation of predicted erythroid cis-regulatory modules Blood Cells, Molecules, and Diseases. 38: 190. DOI: 10.1016/J.Bcmd.2006.10.158 |
0.725 |
|
| 2007 |
Hardison RC, King DC, Taylor J, Wang H, Zhang Y, Zhou Y, Cheng Y, Dorman C, Dore LC, Weiss MJ, Chiaromonte F, Miller W. Comparative genomics to find function in noncoding DNA Blood Cells, Molecules, and Diseases. 38: 144-145. DOI: 10.1016/J.Bcmd.2006.10.060 |
0.771 |
|
| 2006 |
Wang H, Zhang Y, Cheng Y, Zhou Y, King DC, Taylor J, Chiaromonte F, Kasturi J, Petrykowska H, Gibb B, Dorman C, Miller W, Dore LC, Welch J, Weiss MJ, et al. Experimental validation of predicted mammalian erythroid cis-regulatory modules. Genome Research. 16: 1480-92. PMID 17038566 DOI: 10.1101/Gr.5353806 |
0.822 |
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| 1989 |
Cheng Y, Kaiser D. dsg, a gene required for Myxococcus development, is necessary for cell viability. Journal of Bacteriology. 171: 3727-31. PMID 2544553 DOI: 10.1128/Jb.171.7.3727-3731.1989 |
0.334 |
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