Yong Cheng, Ph.D. - Publications

Affiliations: 
2009 Pennsylvania State University, State College, PA, United States 
Area:
Genetics, Conservation Biology

38 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
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  0.318
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  0.414
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  0.567
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  0.571
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  0.398
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  0.342
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  0.775
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  0.783
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  0.656
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  0.671
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  0.845
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  0.782
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  0.524
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  0.507
2013 Zou X, Tan X, Hu C, Zeng L, Lu G, Fu G, Cheng Y, Zhang X. The Transcriptome of Brassica napus L. Roots under Waterlogging at the Seedling Stage. International Journal of Molecular Sciences. 14: 2637-51. PMID 23358252 DOI: 10.3390/ijms14022637  0.3
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  0.349
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  0.532
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  0.45
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  0.507
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  0.752
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  0.689
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  0.349
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  0.369
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  0.791
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  0.668
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  0.671
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  0.674
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  0.848
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  0.799
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  0.655
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  0.764
2008 Wan LB, Pan H, Hannenhalli S, Cheng Y, Ma J, Fedoriw A, Lobanenkov V, Latham KE, Schultz RM, Bartolomei MS. Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development Development. 135: 2729-2738. PMID 18614575 DOI: 10.1242/Dev.024539  0.313
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  0.766
2007 Cheng Y, Buffone MG, Kouadio M, Goodheart M, Page DC, Gerton GL, Davidson I, Wang PJ. Abnormal sperm in mice lacking the Taf7l gene. Molecular and Cellular Biology. 27: 2582-9. PMID 17242199 DOI: 10.1128/Mcb.01722-06  0.312
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  0.727
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  0.77
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  0.823
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  0.356
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