☰

Howard Y. Chang - Publications

Affiliations: 
2014- Dermatology Stanford University, Palo Alto, CA 
Tree Info Similar researchers PubMed Report error

313 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
2023 Rose JC, Wong IT, Daniel B, Jones MG, Yost KE, Hung KL, Curtis EJ, Mischel PS, Chang HY. Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair. Biorxiv : the Preprint Server For Biology. PMID 37961138 DOI: 10.1101/2023.10.22.563489  0.753
2023 Chapman OS, Luebeck J, Sridhar S, Wong IT, Dixit D, Wang S, Prasad G, Rajkumar U, Pagadala MS, Larson JD, He BJ, Hung KL, Lange JT, Dehkordi SR, Chandran S, ... ... Chang HY, et al. Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma. Nature Genetics. PMID 37945900 DOI: 10.1038/s41588-023-01551-3  0.758
2023 Yu M, Nie Y, Yang J, Yang S, Li R, Rao V, Hu X, Fang C, Li S, Song D, Guo F, Snyder MP, Chang HY, Kuo CJ, Xu J, et al. Integrative multi-omic profiling of adult mouse brain endothelial cells and potential implications in Alzheimer's disease. Cell Reports. 42: 113392. PMID 37925638 DOI: 10.1016/j.celrep.2023.113392  0.407
2023 Li Z, Amaya L, Pi R, Wang SK, Ranjan A, Waymouth RM, Blish CA, Chang HY, Wender PA. Charge-altering releasable transporters enhance mRNA delivery in vitro and exhibit in vivo tropism. Nature Communications. 14: 6983. PMID 37914693 DOI: 10.1038/s41467-023-42672-x  0.63
2023 Berson E, Sreenivas A, Phongpreecha T, Perna A, Grandi FC, Xue L, Ravindra NG, Payrovnaziri N, Mataraso S, Kim Y, Espinosa C, Chang AL, Becker M, Montine KS, Fox EJ, ... Chang HY, et al. Whole genome deconvolution unveils Alzheimer's resilient epigenetic signature. Nature Communications. 14: 4947. PMID 37587197 DOI: 10.1038/s41467-023-40611-4  0.769
2023 Hung KL, Jones MG, Wong IT, Lange JT, Luebeck J, Scanu E, He BJ, Brückner L, Li R, González RC, Schmargon R, Dörr JR, Belk JA, Bafna V, Werner B, ... ... Chang HY, et al. Coordinated inheritance of extrachromosomal DNA species in human cancer cells. Biorxiv : the Preprint Server For Biology. PMID 37503111 DOI: 10.1101/2023.07.18.549597  0.783
2023 Chamorro González R, Conrad T, Stöber MC, Xu R, Giurgiu M, Rodriguez-Fos E, Kasack K, Brückner L, van Leen E, Helmsauer K, Dorado Garcia H, Stefanova ME, Hung KL, Bei Y, Schmelz K, ... ... Chang HY, et al. Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells. Nature Genetics. 55: 880-890. PMID 37142849 DOI: 10.1038/s41588-023-01386-y  0.798
2023 Gonzalez-Sandoval A, Pekrun K, Tsuji S, Zhang F, Hung KL, Chang HY, Kay MA. The AAV capsid can influence the epigenetic marking of rAAV delivered episomal genomes in a species dependent manner. Nature Communications. 14: 2448. PMID 37117181 DOI: 10.1038/s41467-023-38106-3  0.777
2023 Chang HY, Qi LS. Reversing the Central Dogma: RNA-guided control of DNA in epigenetics and genome editing. Molecular Cell. 83: 442-451. PMID 36736311 DOI: 10.1016/j.molcel.2023.01.010  0.325
2023 Chen LL, Bindereif A, Bozzoni I, Chang HY, Matera AG, Gorospe M, Hansen TB, Kjems J, Ma XK, Pek JW, Rajewsky N, Salzman J, Wilusz JE, Yang L, Zhao F. A guide to naming eukaryotic circular RNAs. Nature Cell Biology. PMID 36658223 DOI: 10.1038/s41556-022-01066-9  0.588
2023 Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, et al. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature Reviews. Molecular Cell Biology. PMID 36596869 DOI: 10.1038/s41580-022-00566-8  0.754
2022 Haddad Derafshi B, Danko T, Chanda S, Batista PJ, Litzenburger U, Lee QY, Ng YH, Sebin A, Chang HY, Südhof TC, Wernig M. The autism risk factor CHD8 is a chromatin activator in human neurons and functionally dependent on the ERK-MAPK pathway effector ELK1. Scientific Reports. 12: 22425. PMID 36575212 DOI: 10.1038/s41598-022-23614-x  0.69
2022 Wang SK, Nair S, Li R, Kraft K, Pampari A, Patel A, Kang JB, Luong C, Kundaje A, Chang HY. Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases. Cell Genomics. 2. PMID 36277849 DOI: 10.1016/j.xgen.2022.100164  0.743
2022 Hung KL, Luebeck J, Dehkordi SR, Colón CI, Li R, Wong IT, Coruh C, Dharanipragada P, Lomeli SH, Weiser NE, Moriceau G, Zhang X, Bailey C, Houlahan KE, Yang W, ... ... Chang HY, et al. Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH. Nature Genetics. PMID 36253572 DOI: 10.1038/s41588-022-01190-0  0.77
2022 Lange JT, Rose JC, Chen CY, Pichugin Y, Xie L, Tang J, Hung KL, Yost KE, Shi Q, Erb ML, Rajkumar U, Wu S, Taschner-Mandl S, Bernkopf M, Swanton C, ... ... Chang HY, et al. The evolutionary dynamics of extrachromosomal DNA in human cancers. Nature Genetics. PMID 36123406 DOI: 10.1038/s41588-022-01177-x  0.769
2022 Moonen JR, Chappell J, Shi M, Shinohara T, Li D, Mumbach MR, Zhang F, Nair RV, Nasser J, Mai DH, Taylor S, Wang L, Metzger RJ, Chang HY, Engreitz JM, et al. KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress. Nature Communications. 13: 4941. PMID 35999210 DOI: 10.1038/s41467-022-32566-9  0.401
2022 Chen R, Wang SK, Belk JA, Amaya L, Li Z, Cardenas A, Abe BT, Chen CK, Wender PA, Chang HY. Author Correction: Engineering circular RNA for enhanced protein production. Nature Biotechnology. PMID 35978134 DOI: 10.1038/s41587-022-01472-2  0.658
2022 Hung KL, Mischel PS, Chang HY. Gene regulation on extrachromosomal DNA. Nature Structural & Molecular Biology. 29: 736-744. PMID 35948767 DOI: 10.1038/s41594-022-00806-7  0.785
2022 Chen R, Wang SK, Belk JA, Amaya L, Li Z, Cardenas A, Abe BT, Chen CK, Wender PA, Chang HY. Engineering circular RNA for enhanced protein production. Nature Biotechnology. PMID 35851375 DOI: 10.1038/s41587-022-01393-0  0.703
2022 Kraft K, Yost KE, Murphy SE, Magg A, Long Y, Corces MR, Granja JM, Wittler L, Mundlos S, Cech TR, Boettiger AN, Chang HY. Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation. Proceedings of the National Academy of Sciences of the United States of America. 119: e2201883119. PMID 35617427 DOI: 10.1073/pnas.2201883119  0.675
2022 Raj N, Wang M, Seoane JA, Zhao RL, Kaiser AM, Moonie NA, Demeter J, Boutelle AM, Kerr CH, Mulligan AS, Moffatt C, Zeng SX, Lu H, Barna M, Curtis C, ... Chang HY, et al. The Mettl3 epitranscriptomic writer amplifies p53 stress responses. Molecular Cell. PMID 35512709 DOI: 10.1016/j.molcel.2022.04.010  0.502
2022 Xie L, Dong P, Qi Y, Hsieh TS, English BP, Jung S, Chen X, De Marzio M, Casellas R, Chang HY, Zhang B, Tjian R, Liu Z. BRD2 compartmentalizes the accessible genome. Nature Genetics. 54: 481-491. PMID 35410381 DOI: 10.1038/s41588-022-01044-9  0.689
2022 Weiser NE, Hung KL, Chang HY. Oncogene Convergence in Extrachromosomal DNA Hubs. Cancer Discovery. 12: 1195-1198. PMID 35398879 DOI: 10.1158/2159-8290.CD-22-0076  0.756
2022 Abe BT, Wesselhoeft RA, Chen R, Anderson DG, Chang HY. Circular RNA migration in agarose gel electrophoresis. Molecular Cell. PMID 35358469 DOI: 10.1016/j.molcel.2022.03.008  0.302
2022 Bailey AS, Batista PJ, Chang HY, Fuller MT. Identification of Protein-RNA Interactions in Mouse Testis Tissue Using fRIP. Bio-Protocol. 12: e4286. PMID 35118177 DOI: 10.21769/BioProtoc.4286  0.725
2022 Meijer M, Agirre E, Kabbe M, van Tuijn CA, Heskol A, Zheng C, Mendanha Falcão A, Bartosovic M, Kirby L, Calini D, Johnson MR, Corces MR, Montine TJ, Chen X, Chang HY, et al. Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility. Neuron. PMID 35093191 DOI: 10.1016/j.neuron.2021.12.034  0.715
2021 Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro González R, Weiser NE, Chen C, Valieva ME, Wong IT, Wu S, Dehkordi SR, ... ... Chang HY, et al. ecDNA hubs drive cooperative intermolecular oncogene expression. Nature. PMID 34819668 DOI: 10.1038/s41586-021-04116-8  0.81
2021 Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, ... ... Chang HY, et al. Noncoding RNAs: biology and applications-a Keystone Symposia report. Annals of the New York Academy of Sciences. PMID 34791665 DOI: 10.1111/nyas.14713  0.614
2021 Richards RM, Zhao F, Freitas KA, Parker KR, Xu P, Fan A, Sotillo E, Daugaard M, Oo HZ, Liu J, Hong WJ, Sorensen PH, Chang HY, Satpathy AT, Majzner RG, et al. NOT-Gated CD93 CAR T Cells Effectively Target AML with Minimized Endothelial Cross-Reactivity. Blood Cancer Discovery. 2: 648-665. PMID 34778803 DOI: 10.1158/2643-3230.BCD-20-0208  0.503
2021 Kim DS, Risca VI, Reynolds DL, Chappell J, Rubin AJ, Jung N, Donohue LKH, Lopez-Pajares V, Kathiria A, Shi M, Zhao Z, Deep H, Sharmin M, Rao D, Lin S, ... Chang HY, et al. The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation. Nature Genetics. PMID 34650237 DOI: 10.1038/s41588-021-00947-3  0.392
2021 Sanghi A, Gruber JJ, Metwally A, Jiang L, Reynolds W, Sunwoo J, Orloff L, Chang HY, Kasowski M, Snyder MP. Chromatin accessibility associates with protein-RNA correlation in human cancer. Nature Communications. 12: 5732. PMID 34593797 DOI: 10.1038/s41467-021-25872-1  0.503
2021 Chen CK, Cheng R, Demeter J, Chen J, Weingarten-Gabbay S, Jiang L, Snyder MP, Weissman JS, Segal E, Jackson PK, Chang HY. Structured elements drive extensive circular RNA translation. Molecular Cell. PMID 34437836 DOI: 10.1016/j.molcel.2021.07.042  0.644
2021 Chen L, Chang HY, Artandi SE. Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE. Star Protocols. 2: 100477. PMID 33997809 DOI: 10.1016/j.xpro.2021.100477  0.318
2021 Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, et al. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell. PMID 33838111 DOI: 10.1016/j.cell.2021.03.025  0.799
2021 Yu B, Qi Y, Li R, Shi Q, Satpathy AT, Chang HY. B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells. Cell. PMID 33735607 DOI: 10.1016/j.cell.2021.02.015  0.303
2020 Lu Z, Guo JK, Wei Y, Dou DR, Zarnegar B, Ma Q, Li R, Zhao Y, Liu F, Choudhry H, Khavari PA, Chang HY. Structural modularity of the XIST ribonucleoprotein complex. Nature Communications. 11: 6163. PMID 33268787 DOI: 10.1038/s41467-020-20040-3  0.523
2020 Corley M, Flynn RA, Lee B, Blue SM, Chang HY, Yeo GW. Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces. Molecular Cell. PMID 33242392 DOI: 10.1016/j.molcel.2020.11.014  0.332
2020 Corces MR, Shcherbina A, Kundu S, Gloudemans MJ, Frésard L, Granja JM, Louie BH, Eulalio T, Shams S, Bagdatli ST, Mumbach MR, Liu B, Montine KS, Greenleaf WJ, Kundaje A, ... ... Chang HY, et al. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases. Nature Genetics. PMID 33106633 DOI: 10.1038/s41588-020-00721-x  0.404
2020 Parker KR, Migliorini D, Perkey E, Yost KE, Bhaduri A, Bagga P, Haris M, Wilson NE, Liu F, Gabunia K, Scholler J, Montine TJ, Bhoj VG, Reddy R, Mohan S, ... ... Chang HY, et al. Single-Cell Analyses Identify Brain Mural Cells Expressing CD19 as Potential Off-Tumor Targets for CAR-T Immunotherapies. Cell. PMID 32961131 DOI: 10.1016/J.Cell.2020.08.022  0.479
2020 Kim H, Nguyen NP, Turner K, Wu S, Gujar AD, Luebeck J, Liu J, Deshpande V, Rajkumar U, Namburi S, Amin SB, Yi E, Menghi F, Schulte JH, Henssen AG, ... Chang HY, et al. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nature Genetics. PMID 32807987 DOI: 10.1038/S41588-020-0678-2  0.333
2020 Wilson KD, Ameen M, Guo H, Abilez OJ, Tian L, Mumbach MR, Diecke S, Qin X, Liu Y, Yang H, Ma N, Gaddam S, Cunningham NJ, Gu M, Neofytou E, ... ... Chang HY, et al. Endogenous Retrovirus-Derived lncRNA BANCR Promotes Cardiomyocyte Migration in Humans and Non-human Primates. Developmental Cell. PMID 32763147 DOI: 10.1016/J.Devcel.2020.07.006  0.417
2020 Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, ... ... Chang H, et al. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Research. PMID 32718982 DOI: 10.1101/Gr.254219.119  0.467
2020 Wu KE, Fazal FM, Parker KR, Zou J, Chang HY. RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus. Cell Systems. PMID 32673562 DOI: 10.1016/J.Cels.2020.06.008  0.8
2020 Rinn JL, Chang HY. Long Noncoding RNAs: Molecular Modalities to Organismal Functions. Annual Review of Biochemistry. 89: 283-308. PMID 32569523 DOI: 10.1146/Annurev-Biochem-062917-012708  0.649
2020 Ang CE, Trevino AE, Chang HY. Diverse lncRNA mechanisms in brain development and disease. Current Opinion in Genetics & Development. 65: 42-46. PMID 32554106 DOI: 10.1016/J.Gde.2020.05.006  0.452
2020 Nasrallah R, Imianowski CJ, Bossini-Castillo L, Grant FM, Dogan M, Placek L, Kozhaya L, Kuo P, Sadiyah F, Whiteside SK, Mumbach MR, Glinos D, Vardaka P, Whyte CE, Lozano T, ... ... Chang HY, et al. A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by T cells. Nature. PMID 32499651 DOI: 10.1038/S41586-020-2296-7  0.35
2020 Fazal FM, Chang HY. Subcellular Spatial Transcriptomes: Emerging Frontier for Understanding Gene Regulation. Cold Spring Harbor Symposia On Quantitative Biology. PMID 32482897 DOI: 10.1101/Sqb.2019.84.040352  0.819
2020 Carter AC, Xu J, Nakamoto MY, Wei Y, Zarnegar BJ, Shi Q, Broughton JP, Ransom RC, Salhotra A, Nagaraja SD, Li R, Dou DR, Yost KE, Cho SW, Mistry A, ... ... Chang HY, et al. Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation. Elife. 9. PMID 32379046 DOI: 10.7554/Elife.54508  0.455
2020 Paik DT, Cho S, Tian L, Chang HY, Wu JC. Single-cell RNA sequencing in cardiovascular development, disease and medicine. Nature Reviews. Cardiology. PMID 32231331 DOI: 10.1038/S41569-020-0359-Y  0.379
2020 Lee QY, Mall M, Chanda S, Zhou B, Sharma KS, Schaukowitch K, Adrian-Segarra JM, Grieder SD, Kareta MS, Wapinski OL, Ang CE, Li R, Südhof TC, Chang HY, Wernig M. Pro-neuronal activity of Myod1 due to promiscuous binding to neuronal genes. Nature Cell Biology. PMID 32231311 DOI: 10.1038/S41556-020-0490-3  0.312
2020 Wu KE, Parker KR, Fazal FM, Chang H, Zou J. RNA-GPS predicts high-resolution RNA subcellular localization and highlights the role of splicing. Rna (New York, N.Y.). PMID 32220894 DOI: 10.1261/Rna.074161.119  0.804
2020 Xie L, Dong P, Chen X, Hsieh TS, Banala S, De Marzio M, English BP, Qi Y, Jung SK, Kieffer-Kwon KR, Legant WR, Hansen AS, Schulmann A, Casellas R, Zhang B, ... ... Chang HY, et al. 3D ATAC-PALM: super-resolution imaging of the accessible genome. Nature Methods. PMID 32203384 DOI: 10.1038/S41592-020-0775-2  0.714
2020 Horlbeck MA, Liu SJ, Chang HY, Lim DA, Weissman JS. Fitness effects of CRISPR/Cas9-targeting of long noncoding RNA genes. Nature Biotechnology. PMID 32094656 DOI: 10.1038/S41587-020-0428-0  0.412
2020 Wasson CW, Abignano G, Hermes H, Malaab M, Ross RL, Jimenez SA, Chang HY, Feghali-Bostwick CA, Del Galdo F. Long non-coding RNA HOTAIR drives EZH2-dependent myofibroblast activation in systemic sclerosis through miRNA 34a-dependent activation of NOTCH. Annals of the Rheumatic Diseases. PMID 32041748 DOI: 10.1136/Annrheumdis-2019-216542  0.321
2020 Li Y, Gruber JJ, Litzenburger UM, Zhou Y, Miao YR, LaGory EL, Li AM, Hu Z, Yip M, Hart LS, Maris JM, Chang HY, Giaccia AJ, Ye J. Acetate supplementation restores chromatin accessibility and promotes tumor cell differentiation under hypoxia. Cell Death & Disease. 11: 102. PMID 32029721 DOI: 10.1038/S41419-020-2303-9  0.335
2020 Stadtmauer EA, Fraietta JA, Davis MM, Cohen AD, Weber KL, Lancaster E, Mangan PA, Kulikovskaya I, Gupta M, Chen F, Tian L, Gonzalez VE, Xu J, Jung IY, Melenhorst JJ, ... ... Chang HY, et al. CRISPR-engineered T cells in patients with refractory cancer. Science (New York, N.Y.). PMID 32029687 DOI: 10.1126/Science.Aba7365  0.34
2020 Trevino AE, Sinnott-Armstrong N, Andersen J, Yoon SJ, Huber N, Pritchard JK, Chang HY, Greenleaf WJ, Pașca SP. Chromatin accessibility dynamics in a model of human forebrain development. Science (New York, N.Y.). 367. PMID 31974223 DOI: 10.1126/Science.Aay1645  0.344
2020 Carter AC, Xu J, Nakamoto MY, Wei Y, Zarnegar BJ, Shi Q, Broughton JP, Ransom RC, Salhotra A, Nagaraja SD, Li R, Dou DR, Yost KE, Cho S, Mistry A, ... ... Chang HY, et al. Author response: Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation Elife. DOI: 10.7554/Elife.54508.Sa2  0.356
2020 Chang HY. Abstract PL01-01: Personal regulome navigation of cancer Cancer Research. 80. DOI: 10.1158/1538-7445.Am2020-Pl01-01  0.366
2020 Ramilowski JA, Yip CW, Agrawal S, Chang J, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, ... ... Chang H, et al. Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping Genome Research. 30: 1377-1-1377-1. DOI: 10.1101/Gr.270330.120  0.41
2019 Fang J, Ma Q, Chu C, Huang B, Li L, Cai P, Batista PJ, Tolentino KEM, Xu J, Li R, Du P, Qu K, Chang HY. PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications. Genome Biology. 20: 292. PMID 31862000 DOI: 10.1186/S13059-019-1880-3  0.74
2019 Yost KE, Chang HY, Satpathy AT. Tracking the immune response with single-cell genomics. Vaccine. PMID 31859202 DOI: 10.1016/J.Vaccine.2019.11.035  0.306
2019 Esfahani MS, Lee LJ, Jeon YJ, Flynn RA, Stehr H, Hui AB, Ishisoko N, Kildebeck E, Newman AM, Bratman SV, Porteus MH, Chang HY, Alizadeh AA, Diehn M. Functional significance of U2AF1 S34F mutations in lung adenocarcinomas. Nature Communications. 10: 5712. PMID 31836708 DOI: 10.1038/S41467-019-13392-Y  0.66
2019 Lynn RC, Weber EW, Sotillo E, Gennert D, Xu P, Good Z, Anbunathan H, Lattin J, Jones R, Tieu V, Nagaraja S, Granja J, de Bourcy CFA, Majzner R, Satpathy AT, ... ... Chang HY, et al. c-Jun overexpression in CAR T cells induces exhaustion resistance. Nature. PMID 31802004 DOI: 10.1038/S41586-019-1805-Z  0.313
2019 Granja JM, Klemm S, McGinnis LM, Kathiria AS, Mezger A, Corces MR, Parks B, Gars E, Liedtke M, Zheng GXY, Chang HY, Majeti R, Greenleaf WJ. Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nature Biotechnology. PMID 31792411 DOI: 10.1038/S41587-019-0332-7  0.791
2019 Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, ... ... Chang HY, et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. PMID 31748743 DOI: 10.1038/S41586-019-1763-5  0.74
2019 López-Isac E, Acosta-Herrera M, Kerick M, Assassi S, Satpathy AT, Granja J, Mumbach MR, Beretta L, Simeón CP, Carreira P, Ortego-Centeno N, Castellvi I, Bossini-Castillo L, Carmona FD, Orozco G, ... ... Chang HY, et al. GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways. Nature Communications. 10: 4955. PMID 31672989 DOI: 10.1038/S41467-019-12760-Y  0.304
2019 Chen YG, Chen R, Ahmad S, Verma R, Kasturi SP, Amaya L, Broughton JP, Kim J, Cadena C, Pulendran B, Hur S, Chang HY. N6-Methyladenosine Modification Controls Circular RNA Immunity. Molecular Cell. PMID 31474572 DOI: 10.1016/J.Molcel.2019.07.016  0.372
2019 Bousard A, Raposo AC, Żylicz JJ, Picard C, Pires VB, Qi Y, Gil C, Syx L, Chang HY, Heard E, da Rocha ST. The role of Xist-mediated Polycomb recruitment in the initiation of X-chromosome inactivation. Embo Reports. e48019. PMID 31456285 DOI: 10.15252/Embr.201948019  0.43
2019 Durai V, Bagadia P, Granja JM, Satpathy AT, Kulkarni DH, Davidson JT, Wu R, Patel SJ, Iwata A, Liu TT, Huang X, Briseño CG, Grajales-Reyes GE, Wöhner M, Tagoh H, ... ... Chang HY, et al. Cryptic activation of an Irf8 enhancer governs cDC1 fate specification. Nature Immunology. PMID 31406378 DOI: 10.1038/S41590-019-0450-X  0.364
2019 Bagadia P, Huang X, Liu TT, Durai V, Grajales-Reyes GE, Nitschké M, Modrusan Z, Granja JM, Satpathy AT, Briseño CG, Gargaro M, Iwata A, Kim S, Chang HY, Shaw AS, et al. An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development. Nature Immunology. PMID 31406377 DOI: 10.1038/S41590-019-0449-3  0.391
2019 Satpathy AT, Granja JM, Yost KE, Qi Y, Meschi F, McDermott GP, Olsen BN, Mumbach MR, Pierce SE, Corces MR, Shah P, Bell JC, Jhutty D, Nemec CM, Wang J, ... ... Chang HY, et al. Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nature Biotechnology. 37: 925-936. PMID 31375813 DOI: 10.1038/S41587-019-0206-Z  0.798
2019 Ghosh RP, Shi Q, Yang L, Reddick MP, Nikitina T, Zhurkin VB, Fordyce P, Stasevich TJ, Chang HY, Greenleaf WJ, Liphardt JT. Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions. Nature Communications. 10: 3221. PMID 31324780 DOI: 10.1038/S41467-019-11118-8  0.306
2019 Lee J, Termglinchan V, Diecke S, Itzhaki I, Lam CK, Garg P, Lau E, Greenhaw M, Seeger T, Wu H, Zhang JZ, Chen X, Gil IP, Ameen M, Sallam K, ... ... Chang HY, et al. Activation of PDGF pathway links LMNA mutation to dilated cardiomyopathy. Nature. PMID 31316208 DOI: 10.1038/S41586-019-1406-X  0.717
2019 Fazal FM, Han S, Parker KR, Kaewsapsak P, Xu J, Boettiger AN, Chang HY, Ting AY. Atlas of Subcellular RNA Localization Revealed by APEX-Seq. Cell. PMID 31230715 DOI: 10.1016/J.Cell.2019.05.027  0.809
2019 Mumbach MR, Granja JM, Flynn RA, Roake CM, Satpathy AT, Rubin AJ, Qi Y, Jiang Z, Shams S, Louie BH, Guo JK, Gennert DG, Corces MR, Khavari PA, Atianand MK, ... ... Chang HY, et al. HiChIRP reveals RNA-associated chromosome conformation. Nature Methods. PMID 31133759 DOI: 10.1038/S41592-019-0407-X  0.457
2019 Xu J, Nuno K, Litzenburger UM, Qi Y, Corces MR, Majeti R, Chang HY. Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA. Elife. 8. PMID 30958261 DOI: 10.7554/Elife.45105  0.572
2019 Sun L, Fazal FM, Li P, Broughton JP, Lee B, Tang L, Huang W, Kool ET, Chang HY, Zhang QC. RNA structure maps across mammalian cellular compartments. Nature Structural & Molecular Biology. PMID 30886404 DOI: 10.1038/S41594-019-0200-7  0.825
2019 Van Gool F, Nguyen MLT, Mumbach MR, Satpathy AT, Rosenthal WL, Giacometti S, Le DT, Liu W, Brusko TM, Anderson MS, Rudensky AY, Marson A, Chang HY, Bluestone JA. A Mutation in the Transcription Factor Foxp3 Drives T Helper 2 Effector Function in Regulatory T Cells. Immunity. PMID 30709738 DOI: 10.1016/J.Immuni.2018.12.016  0.36
2019 Li L, Wang Y, Torkelson JL, Shankar G, Pattison JM, Zhen HH, Fang F, Duren Z, Xin J, Gaddam S, Melo SP, Piekos SN, Li J, Liaw EJ, Chen L, ... ... Chang HY, et al. TFAP2C- and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment. Cell Stem Cell. PMID 30686763 DOI: 10.1016/J.Stem.2018.12.012  0.347
2019 Luo C, Lee QY, Wapinski O, Castanon R, Nery JR, Mall M, Kareta MS, Cullen SM, Goodell MA, Chang HY, Wernig M, Ecker JR. Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons. Elife. 8. PMID 30644360 DOI: 10.7554/Elife.40197  0.314
2019 Ang CE, Ma Q, Wapinski OL, Fan S, Flynn RA, Lee QY, Coe B, Onoguchi M, Olmos VH, Do BT, Dukes-Rimsky L, Xu J, Tanabe K, Wang L, Elling U, ... ... Chang HY, et al. The novel lncRNA is pro-neurogenic and mutated in human neurodevelopmental disorders. Elife. 8. PMID 30628890 DOI: 10.7554/Elife.41770  0.401
2019 Xu J, Nuno K, Litzenburger UM, Qi Y, Corces MR, Majeti R, Chang HY. Author response: Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA Elife. DOI: 10.7554/Elife.45105.033  0.542
2019 Mumbach M, Granja J, Flynn R, Roake C, Satpathy A, Rubin A, Qi Y, Jiang Z, Shams S, Louie B, Guo J, Gennert D, Corces MR, Khavari P, Atianand M, ... ... Chang H, et al. HiChIRP: RNA-centric chromatin conformation Protocol Exchange. DOI: 10.1038/Protex.2019.032  0.408
2019 Ramanathan M, Rubin A, Parker K, Satpathy A, Greenleaf W, Chang H, Khavari P. 366 Unraveling keratinocyte gene regulatory networks with single-cell cripsr screening and epigenomic profiling Journal of Investigative Dermatology. 139: S63. DOI: 10.1016/J.Jid.2019.03.442  0.302
2019 Simonetta F, Maas-Bauer K, Hirai T, Wenokur A, Fazal FM, Kambham N, Ribado J, Mavers M, Baker J, Bhatt AS, Chang HY, Negrin RS. Distinct Immune Regulatory Potential of Invariant Natural Killer T (iNKT) Cell Subsets: iNKT2 and iNKT17, but Not iNKT1, Protect from Graft-Versus-Host-Disease Biology of Blood and Marrow Transplantation. 25. DOI: 10.1016/J.Bbmt.2018.12.683  0.767
2018 Rubin AJ, Parker KR, Satpathy AT, Qi Y, Wu B, Ong AJ, Mumbach MR, Ji AL, Kim DS, Cho SW, Zarnegar BJ, Greenleaf WJ, Chang HY, Khavari PA. Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks. Cell. PMID 30580963 DOI: 10.1016/J.Cell.2018.11.022  0.45
2018 Lu Z, Chang HY. The RNA Base-Pairing Problem and Base-Pairing Solutions. Cold Spring Harbor Perspectives in Biology. 10. PMID 30510063 DOI: 10.1101/Cshperspect.A034926  0.565
2018 Pattison JM, Melo SP, Piekos SN, Torkelson JL, Bashkirova E, Mumbach MR, Rajasingh C, Zhen HH, Li L, Liaw E, Alber D, Rubin AJ, Shankar G, Bao X, Chang HY, et al. Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment. Nature Genetics. PMID 30397335 DOI: 10.1038/S41588-018-0263-0  0.348
2018 Chen X, Litzenburger UM, Wei Y, Schep AN, LaGory EL, Choudhry H, Giaccia AJ, Greenleaf WJ, Chang HY. Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity. Nature Communications. 9: 4590. PMID 30389926 DOI: 10.1038/S41467-018-07115-Y  0.72
2018 Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, ... ... Chang HY, et al. The chromatin accessibility landscape of primary human cancers. Science (New York, N.Y.). 362. PMID 30361341 DOI: 10.1126/Science.Aav1898  0.545
2018 Ransom RC, Carter AC, Salhotra A, Leavitt T, Marecic O, Murphy MP, Lopez ML, Wei Y, Marshall CD, Shen EZ, Jones RE, Sharir A, Klein OD, Chan CKF, Wan DC, ... Chang HY, et al. Mechanoresponsive stem cells acquire neural crest fate in jaw regeneration. Nature. PMID 30356216 DOI: 10.1038/S41586-018-0650-9  0.329
2018 Jeng MY, Mumbach MR, Granja JM, Satpathy AT, Chang HY, Chang ALS. Enhancer connectome nominates target genes of inherited risk variants from inflammatory skin disorders. The Journal of Investigative Dermatology. PMID 30315781 DOI: 10.1016/J.Jid.2018.09.011  0.367
2018 Chan CKF, Gulati GS, Sinha R, Tompkins JV, Lopez M, Carter AC, Ransom RC, Reinisch A, Wearda T, Murphy M, Brewer RE, Koepke LS, Marecic O, Manjunath A, Seo EY, ... ... Chang HY, et al. Identification of the Human Skeletal Stem Cell. Cell. 175: 43-56.e21. PMID 30241615 DOI: 10.1016/J.Cell.2018.07.029  0.578
2018 Chu C, Chang HY. ChIRP-MS: RNA-Directed Proteomic Discovery. Methods in Molecular Biology (Clifton, N.J.). 1861: 37-45. PMID 30218357 DOI: 10.1007/978-1-4939-8766-5_3  0.399
2018 Arda HE, Tsai J, Rosli YR, Giresi P, Bottino R, Greenleaf WJ, Chang HY, Kim SK. A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas. Cell Systems. PMID 30145115 DOI: 10.1016/J.Cels.2018.07.007  0.351
2018 Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang SC, Durand NC, Feng T, ... ... Chang HY, et al. Genetic determinants of co-accessible chromatin regions in activated T cells across humans. Nature Genetics. PMID 29988122 DOI: 10.1038/S41588-018-0156-2  0.381
2018 Duren Z, Chen X, Zamanighomi M, Zeng W, Satpathy AT, Chang HY, Wang Y, Wong WH. Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations. Proceedings of the National Academy of Sciences of the United States of America. PMID 29987051 DOI: 10.1073/Pnas.1805681115  0.347
2018 Chen L, Roake CM, Freund A, Batista PJ, Tian S, Yin YA, Gajera CR, Lin S, Lee B, Pech MF, Venteicher AS, Das R, Chang HY, Artandi SE. An Activity Switch in Human Telomerase Based on RNA Conformation and Shaped by TCAB1. Cell. PMID 29804836 DOI: 10.1016/J.Cell.2018.04.039  0.727
2018 Satpathy AT, Brown RA, Gomulia E, Briseño CG, Mumbach MR, Pan Z, Murphy KM, Natkunam Y, Chang HY, Kim J. Expression of the transcription factor ZBTB46 distinguishes human histiocytic disorders of classical dendritic cell origin. Modern Pathology : An Official Journal of the United States and Canadian Academy of Pathology, Inc. PMID 29743654 DOI: 10.1038/S41379-018-0052-4  0.331
2018 Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He J, Nevins SA, Chin SF, Caldas C, Liu SJ, Horlbeck MA, Lim DA, ... ... Chang HY, et al. Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. Cell. PMID 29731168 DOI: 10.1016/J.Cell.2018.03.068  0.405
2018 Buenrostro JD, Corces MR, Lareau CA, Wu B, Schep AN, Aryee MJ, Majeti R, Chang HY, Greenleaf WJ. Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation. Cell. PMID 29706549 DOI: 10.1016/J.Cell.2018.03.074  0.636
2018 Wang KC, Chang HY. Epigenomics: Technologies and Applications. Circulation Research. 122: 1191-1199. PMID 29700067 DOI: 10.1161/Circresaha.118.310998  0.506
2018 Satpathy AT, Saligrama N, Buenrostro JD, Wei Y, Wu B, Rubin AJ, Granja JM, Lareau CA, Li R, Qi Y, Parker KR, Mumbach MR, Serratelli WS, Gennert DG, Schep AN, ... ... Chang HY, et al. Transcript-indexed ATAC-seq for precision immune profiling. Nature Medicine. PMID 29686426 DOI: 10.1038/S41591-018-0008-8  0.303
2018 Calo E, Gu B, Bowen ME, Aryan F, Zalc A, Liang J, Flynn RA, Swigut T, Chang HY, Attardi LD, Wysocka J. Tissue-selective effects of nucleolar stress and rDNA damage in developmental disorders. Nature. PMID 29364875 DOI: 10.1038/Nature25449  0.427
2018 Koh AS, Miller EL, Buenrostro JD, Moskowitz DM, Wang J, Greenleaf WJ, Chang HY, Crabtree GR. Rapid chromatin repression by Aire provides precise control of immune tolerance. Nature Immunology. PMID 29335648 DOI: 10.1038/S41590-017-0032-8  0.334
2018 Maas-Bauer K, Simonetta F, Hirai T, Wenokur A, Fazal F, Kambham N, Ribado J, Mavers M, Baker J, Bhatt AS, Chang HY, Negrin RS. Invariant Natural Killer T Cell Subsets Have Diverse Functions: iNKT2 and iNKT17 Protect from Graft-Versus-Host-Disease, Whereas iNKT1 Have Antitumor Potential Blood. 132: 475-475. DOI: 10.1182/Blood-2018-99-113673  0.771
2018 Lynn RC, Weber EW, Gennert D, Sotillo E, Jones R, Xu P, Satpathy A, Chang HY, Mackall CL. Abstract LB-112: Engineering AP1 to combat CAR T cell exhaustion Cancer Research. 78. DOI: 10.1158/1538-7445.Am2018-Lb-112  0.326
2018 Chang HY. Abstract PL05-01: Personal regulome navigation Molecular Cancer Therapeutics. 17. DOI: 10.1158/1535-7163.Targ-17-Pl05-01  0.409
2018 Kim D, Risca V, Chappell J, Shi M, Zhao Z, Jung N, Chang H, Snyder M, Greenleaf W, Kundaje A, Khavari P. 795 Decoding regulatory sequence across skin differentiation with deep learning Journal of Investigative Dermatology. 138: S135. DOI: 10.1016/J.Jid.2018.03.805  0.394
2018 Lee MY, Chen X, Gustavsson A, Chang HY, Moerner W. In Situ Imaging of Spatial Organization of Accessible Chromatin at the Nanoscale with ATAC-see and Single-Molecule Super-Resolution Fluorescence Microscopy Biophysical Journal. 114: 539a. DOI: 10.1016/J.Bpj.2017.11.2944  0.664
2017 Chen YG, Chang HY. LncRNA Seduction of GOT2 Goes Viral. Immunity. 47: 1021-1023. PMID 29262346 DOI: 10.1016/J.Immuni.2017.12.006  0.347
2017 Carter AC, Chang HY, Church G, Dombkowski A, Ecker JR, Gil E, Giresi PG, Greely H, Greenleaf WJ, Hacohen N, He C, Hill D, Ko J, Kohane I, Kundaje A, et al. Challenges and recommendations for epigenomics in precision health. Nature Biotechnology. 35: 1128-1132. PMID 29220033 DOI: 10.1038/Nbt.4030  0.346
2017 Corces MR, Chang HY, Majeti R. Preleukemic Hematopoietic Stem Cells in Human Acute Myeloid Leukemia. Frontiers in Oncology. 7: 263. PMID 29164062 DOI: 10.3389/Fonc.2017.00263  0.562
2017 Bailey AS, Batista PJ, Gold RS, Chen YG, de Rooij DG, Chang HY, Fuller MT. The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline. Elife. 6. PMID 29087293 DOI: 10.7554/Elife.26116  0.742
2017 Wapinski OL, Lee QY, Chen AC, Li R, Corces MR, Ang CE, Treutlein B, Xiang C, Baubet V, Suchy FP, Sankar V, Sim S, Quake SR, Dahmane N, Wernig M, ... Chang HY, et al. Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons. Cell Reports. 20: 3236-3247. PMID 28954238 DOI: 10.1016/J.Celrep.2017.09.011  0.337
2017 Lu Z, Carter AC, Chang HY. Mechanistic insights in X-chromosome inactivation. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 372. PMID 28947655 DOI: 10.1098/Rstb.2016.0356  0.526
2017 Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, ... ... Chang HY, et al. Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nature Genetics. PMID 28945252 DOI: 10.1038/Ng.3963  0.378
2017 Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, ... ... Chang HY, et al. Discovery of stimulation-responsive immune enhancers with CRISPR activation. Nature. PMID 28854172 DOI: 10.1038/Nature23875  0.388
2017 Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, ... ... Chang HY, et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature Methods. PMID 28846090 DOI: 10.1038/Nmeth.4396  0.46
2017 Chen YG, Satpathy AT, Chang HY. Gene regulation in the immune system by long noncoding RNAs. Nature Immunology. 18: 962-972. PMID 28829444 DOI: 10.1038/Ni.3771  0.464
2017 Rubin AJ, Barajas BC, Furlan-Magaril M, Lopez-Pajares V, Mumbach MR, Howard I, Kim DS, Boxer LD, Cairns J, Spivakov M, Wingett SW, Shi M, Zhao Z, Greenleaf WJ, Kundaje A, ... ... Chang HY, et al. Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nature Genetics. PMID 28805829 DOI: 10.1038/Ng.3935  0.496
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, ... Chang HY, 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  0.692
2017 Liu Q, Jiang C, Xu J, Zhao M, Van Bortle K, Cheng X, Wang G, Chang HY, Wu JC, Snyder MP. Genome-Wide Temporal Profiling of Transcriptome and Open-Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs. Circulation Research. PMID 28663367 DOI: 10.1161/Circresaha.116.310456  0.513
2017 Wang KC, Chang HY. Transcription coactivator and lncRNA duet evoke Hox genes. Plos Genetics. 13: e1006797. PMID 28662057 DOI: 10.1371/Journal.Pgen.1006797  0.558
2017 Chen YG, Kim MV, Chen X, Batista PJ, Aoyama S, Wilusz JE, Iwasaki A, Chang HY. Sensing Self and Foreign Circular RNAs by Intron Identity. Molecular Cell. PMID 28625551 DOI: 10.1016/J.Molcel.2017.05.022  0.818
2017 Qu K, Zaba LC, Satpathy AT, Giresi PG, Li R, Jin Y, Armstrong R, Jin C, Schmitt N, Rahbar Z, Ueno H, Greenleaf WJ, Kim YH, Chang HY. Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors. Cancer Cell. PMID 28625481 DOI: 10.1016/J.Ccell.2017.05.008  0.33
2017 Simsek D, Tiu GC, Flynn RA, Byeon GW, Leppek K, Xu AF, Chang HY, Barna M. The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity. Cell. 169: 1051-1065.e18. PMID 28575669 DOI: 10.1016/J.Cell.2017.05.022  0.385
2017 Chang J, Mancuso MR, Maier C, Liang X, Yuki K, Yang L, Kwong JW, Wang J, Rao V, Vallon M, Kosinski C, Zhang JJ, Mah AT, Xu L, Li L, ... ... Chang HY, et al. Gpr124 is essential for blood-brain barrier integrity in central nervous system disease. Nature Medicine. PMID 28288111 DOI: 10.1038/Nm.4309  0.395
2017 Schmitt AM, Chang HY. Long Noncoding RNAs: At the Intersection of Cancer and Chromatin Biology. Cold Spring Harbor Perspectives in Medicine. PMID 28193769 DOI: 10.1101/Cshperspect.A026492  0.738
2017 Litzenburger UM, Buenrostro JD, Wu B, Shen Y, Sheffield NC, Kathiria A, Greenleaf WJ, Chang HY. Single-cell epigenomic variability reveals functional cancer heterogeneity. Genome Biology. 18: 15. PMID 28118844 DOI: 10.1186/S13059-016-1133-7  0.318
2017 Xu J, Carter AC, Gendrel AV, Attia M, Loftus J, Greenleaf WJ, Tibshirani R, Heard E, Chang HY. Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells. Nature Genetics. PMID 28112738 DOI: 10.1038/Ng.3769  0.368
2017 Bailey AS, Batista PJ, Gold RS, Chen YG, Rooij DGd, Chang HY, Fuller MT. Author response: The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline Elife. DOI: 10.7554/Elife.26116.050  0.725
2017 Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, ... ... Chang HY, et al. Omni-ATAC-seq: Improved ATAC-seq protocol Protocol Exchange. DOI: 10.1038/Protex.2017.096  0.435
2017 Lopez-Pajares V, Rubin A, Barajas B, Furlan-Magaril M, Mumbach M, Greenleaf W, Kundaje A, Snyder M, Chang H, Fraser P, Khavari P. 464 Dynamic and stable enhancer-promoter contacts regulate epidermal terminal differentiation Journal of Investigative Dermatology. 137: S80. DOI: 10.1016/J.Jid.2017.02.483  0.423
2017 Moore AL, Marshall CD, Litzenburger U, Barnes L, Ransom RC, Hu M, Leavitt T, Chang HY, Longaker MT. Epigenetic Analysis of Scar Forming Fibroblasts Reveals Key Differences in Genes Associated with Fibrosis Journal of the American College of Surgeons. 225: S200-S201. DOI: 10.1016/J.Jamcollsurg.2017.07.460  0.318
2016 Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, Attenello FJ, Villalta JE, Cho MY, Chen Y, Mandegar MA, Olvera MP, Gilbert LA, Conklin BR, Chang HY, et al. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science (New York, N.Y.). PMID 27980086 DOI: 10.1126/Science.Aah7111  0.458
2016 Lee B, Flynn RA, Kadina A, Guo JK, Kool ET, Chang HY. Comparison of SHAPE Reagents for Mapping RNA Structures Inside Living Cells. Rna (New York, N.Y.). PMID 27879433 DOI: 10.1261/Rna.058784.116  0.392
2016 Xu J, Spitale RC, Guan L, Flynn RA, Torre EA, Li R, Raber I, Qu K, Kern D, Knaggs HE, Chang HY, Chang AL. Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing. Plos One. 11: e0165913. PMID 27829007 DOI: 10.1371/Journal.Pone.0165913  0.616
2016 Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna JA, Greenleaf WJ, Liphardt JT, Chang HY. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nature Methods. PMID 27749837 DOI: 10.1038/Nmeth.4031  0.721
2016 Fazal FM, Chang HY. lncRNA Structure: Message to the Heart. Molecular Cell. 64: 1-2. PMID 27716479 DOI: 10.1016/J.Molcel.2016.09.030  0.776
2016 Schmitt AM, Garcia JT, Hung T, Flynn RA, Shen Y, Qu K, Payumo AY, Peres-da-Silva A, Broz DK, Baum R, Guo S, Chen JK, Attardi LD, Chang HY. An inducible long noncoding RNA amplifies DNA damage signaling. Nature Genetics. PMID 27668660 DOI: 10.1038/Ng.3673  0.702
2016 Chu C, Chang HY. Understanding RNA-Chromatin Interactions Using Chromatin Isolation by RNA Purification (ChIRP). Methods in Molecular Biology (Clifton, N.J.). 1480: 115-23. PMID 27659979 DOI: 10.1007/978-1-4939-6380-5_10  0.437
2016 Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nature Genetics. PMID 27526324 DOI: 10.1038/Ng.3646  0.674
2016 Wang K, Lee CS, Marinkovich MP, Chang HY, Oro AE, Khavari PA. Factors That May Promote an Effective Local Research Environment. The Journal of Investigative Dermatology. 136: 1529-31. PMID 27450496 DOI: 10.1016/J.Jid.2016.04.015  0.457
2016 Giorgetti L, Lajoie BR, Carter AC, Attia M, Zhan Y, Xu J, Chen CJ, Kaplan N, Chang HY, Heard E, Dekker J. Structural organization of the inactive X chromosome in the mouse. Nature. PMID 27437574 DOI: 10.1038/Nature18589  0.364
2016 Atianand MK, Hu W, Satpathy AT, Shen Y, Ricci EP, Alvarez-Dominguez JR, Bhatta A, Schattgen SA, McGowan JD, Blin J, Braun JE, Gandhi P, Moore MJ, Chang HY, Lodish HF, et al. A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation. Cell. 165: 1672-85. PMID 27315481 DOI: 10.1016/J.Cell.2016.05.075  0.408
2016 Sadik H, Korangath P, Nguyen N, Győrffy B, Kumar R, Hedayati M, Teo WW, Park S, Panday H, Gonzalez Munoz T, Menyhart O, Shah N, Pandita RK, Chang JC, DeWeese TL, ... Chang HY, et al. HOXC10 expression supports the development of chemotherapy resistance by fine tuning DNA repair in breast cancer cells. Cancer Research. PMID 27302171 DOI: 10.1158/0008-5472.Can-16-0774  0.333
2016 Lu Z, Zhang QC, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech TR, Chang HY. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. PMID 27180905 DOI: 10.1016/J.Cell.2016.04.028  0.709
2016 Arda HE, Li L, Tsai J, Torre EA, Rosli Y, Peiris H, Spitale RC, Dai C, Gu X, Qu K, Wang P, Wang J, Grompe M, Scharfmann R, Snyder MS, ... ... Chang HY, et al. Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function. Cell Metabolism. PMID 27133132 DOI: 10.1016/J.Cmet.2016.04.002  0.681
2016 Zarnegar BJ, Flynn RA, Shen Y, Do BT, Chang HY, Khavari PA. irCLIP platform for efficient characterization of protein-RNA interactions. Nature Methods. PMID 27111506 DOI: 10.1038/Nmeth.3840  0.394
2016 Ma Q, Chang HY. Single-cell profiling of lncRNAs in the developing human brain. Genome Biology. 17: 68. PMID 27079200 DOI: 10.1186/S13059-016-0933-0  0.403
2016 Schmitt AM, Chang HY. Long Noncoding RNAs in Cancer Pathways. Cancer Cell. 29: 452-63. PMID 27070700 DOI: 10.1016/J.Ccell.2016.03.010  0.733
2016 Tan JL, Fogley RD, Flynn RA, Ablain J, Yang S, Saint-André V, Fan ZP, Do BT, Laga AC, Fujinaga K, Santoriello C, Greer CB, Kim YJ, Clohessy JG, Bothmer A, ... ... Chang HY, et al. Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma. Molecular Cell. 62: 34-46. PMID 27058786 DOI: 10.1016/J.Molcel.2016.03.013  0.42
2016 Oh S, Flynn RA, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DT, Northcott PA, Risch T, ... ... Chang HY, et al. Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. Oncotarget. 7: 28169-82. PMID 27058758 DOI: 10.18632/Oncotarget.8612  0.43
2016 Lu Z, Chang HY. Decoding the RNA structurome. Current Opinion in Structural Biology. 36: 142-148. PMID 26923056 DOI: 10.1016/J.Sbi.2016.01.007  0.573
2016 He C, Hu H, Wilson KD, Wu H, Feng J, Xia S, Churko J, Qu K, Chang HY, Wu JC. Systematic Characterization of Long Non-Coding RNAs Reveals the Contrasting Coordination of Cis- and Trans- Molecular Regulation in Human Fetal and Adult Heart. Circulation. Cardiovascular Genetics. PMID 26896382 DOI: 10.1161/Circgenetics.115.001264  0.413
2016 Flynn RA, Do BT, Rubin AJ, Calo E, Lee B, Kuchelmeister H, Rale M, Chu C, Kool ET, Wysocka J, Khavari PA, Chang HY. 7SK-BAF axis controls pervasive transcription at enhancers. Nature Structural & Molecular Biology. PMID 26878240 DOI: 10.1038/Nsmb.3176  0.444
2016 Lee Y, Shin JH, Longmire M, Wang H, Kohrt HE, Chang HY, Sunwoo JB. CD44+ cells in head and neck squamous cell carcinoma suppress T cell-mediated immunity by selective constitutive and inducible expression of PD-L1. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 26864211 DOI: 10.1158/1078-0432.Ccr-15-2665  0.301
2016 Huang W, Thomas B, Flynn RA, Gavzy SJ, Wu L, Kim SV, Hall JA, Miraldi ER, Ng CP, Rigo F, Meadows S, Montoya NR, Herrera NG, Domingos AI, Rastinejad F, ... ... Chang HY, et al. Corrigendum: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions. Nature. PMID 26789242 DOI: 10.1038/Nature16968  0.309
2016 Quinn JJ, Zhang QC, Georgiev P, Ilik IA, Akhtar A, Chang HY. Rapid evolutionary turnover underlies conserved lncRNA-genome interactions. Genes & Development. 30: 191-207. PMID 26773003 DOI: 10.1101/Gad.272187.115  0.638
2016 Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach MR, Chang HY. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nature Protocols. 11: 273-90. PMID 26766114 DOI: 10.1038/Nprot.2016.011  0.758
2016 Wan Y, Qu K, Ouyang Z, Chang HY. Genome-Wide Probing of RNA Structures In Vitro Using Nucleases and Deep Sequencing. Methods in Molecular Biology (Clifton, N.J.). 1361: 141-60. PMID 26483021 DOI: 10.1007/978-1-4939-3079-1_9  0.658
2016 Chang HY. Abstract IA02: Genome regulation by long noncoding RNAs Cancer Research. 76. DOI: 10.1158/1538-7445.Nonrna15-Ia02  0.472
2016 Liu S, Horlbeck M, Cho SW, Birk H, Malatesta M, He D, Villalta J, Cho M, Chen Y, Mandegar M, Olvera M, Conklin B, Chang H, Weissman J, Lim D. GENT-49. SYSTEMATIC IDENTIFICATION OF ESSENTIAL LONG NON-CODING RNA GENES IN GLIOBLASTOMA Neuro-Oncology. 18: vi84-vi85. DOI: 10.1093/Neuonc/Now212.354  0.411
2015 Bao X, Rubin AJ, Qu K, Zhang J, Giresi PG, Chang HY, Khavari PA. A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63. Genome Biology. 16: 284. PMID 26683334 DOI: 10.1186/S13059-015-0840-9  0.334
2015 Huang W, Thomas B, Flynn RA, Gavzy SJ, Wu L, Kim SV, Hall JA, Miraldi ER, Ng CP, Rigo FW, Meadows S, Montoya NR, Herrera NG, Domingos AI, Rastinejad F, ... ... Chang HY, et al. DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions. Nature. PMID 26675721 DOI: 10.1038/Nature16193  0.454
2015 Quinn JJ, Chang HY. Unique features of long non-coding RNA biogenesis and function. Nature Reviews. Genetics. 17: 47-62. PMID 26666209 DOI: 10.1038/Nrg.2015.10  0.418
2015 Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, ... ... Chang HY, et al. The histone chaperone CAF-1 safeguards somatic cell identity. Nature. 528: 218-224. PMID 26659182 DOI: 10.1038/Nature15749  0.632
2015 Carlson HL, Quinn JJ, Yang YW, Thornburg CK, Chang HY, Stadler HS. LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes. Plos Genetics. 11: e1005680. PMID 26633036 DOI: 10.1371/Journal.Pgen.1005680  0.438
2015 Mazumdar C, Shen Y, Xavy S, Zhao F, Reinisch A, Li R, Corces MR, Flynn RA, Buenrostro JD, Chan SM, Thomas D, Koenig JL, Hong WJ, Chang HY, Majeti R. Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation. Cell Stem Cell. PMID 26607380 DOI: 10.1182/Blood.V126.23.841.841  0.598
2015 Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. Erratum: Structural imprints in vivo decode RNA regulatory mechanisms. Nature. PMID 26416736 DOI: 10.1038/Nature15717  0.785
2015 Qu K, Zaba LC, Giresi PG, Li R, Longmire M, Kim YH, Greenleaf WJ, Chang HY. Individuality and variation of personal regulomes in primary human T cells. Cell Systems. 1: 51-61. PMID 26251845 DOI: 10.1016/J.Cels.2015.06.003  0.352
2015 Roost C, Lynch SR, Batista PJ, Qu K, Chang HY, Kool ET. Correction to "Structure and Thermodynamics of N(6)-Methyladenosine in RNA: A Spring-Loaded Base Modification". Journal of the American Chemical Society. PMID 26087989 DOI: 10.1021/Jacs.5B05858  0.699
2015 Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 523: 486-90. PMID 26083756 DOI: 10.1038/Nature14590  0.505
2015 Satpathy AT, Chang HY. Long noncoding RNA in hematopoiesis and immunity. Immunity. 42: 792-804. PMID 25992856 DOI: 10.1016/J.Immuni.2015.05.004  0.474
2015 Grow EJ, Flynn RA, Chavez SL, Bayless NL, Wossidlo M, Wesche DJ, Martin L, Ware CB, Blish CA, Chang HY, Pera RA, Wysocka J. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature. 522: 221-5. PMID 25896322 DOI: 10.1038/Nature14308  0.369
2015 Chu C, Zhang QC, da Rocha ST, Flynn RA, Bharadwaj M, Calabrese JM, Magnuson T, Heard E, Chang HY. Systematic discovery of Xist RNA binding proteins. Cell. 161: 404-16. PMID 25843628 DOI: 10.1016/J.Cell.2015.03.025  0.642
2015 Chang H, Replogle JM, Vather N, Tsao-Wu M, Mistry R, Liu JM. A cis-regulatory antisense RNA represses translation in Vibrio cholerae through extensive complementarity and proximity to the target locus. Rna Biology. 12: 136-48. PMID 25826566 DOI: 10.1080/15476286.2015.1017203  0.382
2015 Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. Structural imprints in vivo decode RNA regulatory mechanisms. Nature. 519: 486-90. PMID 25799993 DOI: 10.1038/Nature14263  0.829
2015 Cho SW, Chang HY. Genomics: CRISPR engineering turns on genes. Nature. 517: 560-2. PMID 25631441 DOI: 10.1038/517560A  0.371
2015 Corley M, Solem A, Qu K, Chang HY, Laederach A. Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark. Nucleic Acids Research. 43: 1859-68. PMID 25618847 DOI: 10.1093/Nar/Gkv010  0.391
2015 Roost C, Lynch SR, Batista PJ, Qu K, Chang HY, Kool ET. Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification. Journal of the American Chemical Society. 137: 2107-15. PMID 25611135 DOI: 10.1021/Ja513080V  0.719
2015 Chu C, Spitale RC, Chang HY. Technologies to probe functions and mechanisms of long noncoding RNAs. Nature Structural & Molecular Biology. 22: 29-35. PMID 25565030 DOI: 10.1038/Nsmb.2921  0.673
2015 Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. 109: 21.29.1-9. PMID 25559105 DOI: 10.1002/0471142727.Mb2129S109  0.315
2015 Quinn JJ, Chang HY. In situ dissection of RNA functional subunits by domain-specific chromatin isolation by RNA purification (dChIRP). Methods in Molecular Biology (Clifton, N.J.). 1262: 199-213. PMID 25555583 DOI: 10.1007/978-1-4939-2253-6_12  0.417
2015 Calo E, Flynn RA, Martin L, Spitale RC, Chang HY, Wysocka J. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature. 518: 249-53. PMID 25470060 DOI: 10.1038/Nature13923  0.701
2015 Flynn RA, Martin L, Spitale RC, Do BT, Sagan SM, Zarnegar B, Qu K, Khavari PA, Quake SR, Sarnow P, Chang HY. Dissecting noncoding and pathogen RNA-protein interactomes. Rna (New York, N.Y.). 21: 135-43. PMID 25411354 DOI: 10.1261/Rna.047803.114  0.681
2014 Paik KJ, Qu K, Hsueh B, Torre EA, Flynn RA, Chung MT, Spencley A, Wang KC, Wu JC, Longaker MT, Chang HY, Wan DC. Abstract 158: Identification of BMP-Responsive Long Noncoding RNAs in Pluripotent Cells. Plastic and Reconstructive Surgery. 133: 174. PMID 25942268 DOI: 10.1097/01.Prs.0000444987.90678.B2  0.596
2014 Batista PJ, Molinie B, Wang J, Qu K, Zhang J, Li L, Bouley DM, Lujan E, Haddad B, Daneshvar K, Carter AC, Flynn RA, Zhou C, Lim KS, Dedon P, ... ... Chang HY, et al. m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell. 15: 707-19. PMID 25456834 DOI: 10.1016/J.Stem.2014.09.019  0.723
2014 Benitez CM, Qu K, Sugiyama T, Pauerstein PT, Liu Y, Tsai J, Gu X, Ghodasara A, Arda HE, Zhang J, Dekker JD, Tucker HO, Chang HY, Kim SK. An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development. Plos Genetics. 10: e1004645. PMID 25330008 DOI: 10.1371/Journal.Pgen.1004645  0.398
2014 Quinn JJ, Chang HY. RNA switch at enhancers. Nature Genetics. 46: 929-31. PMID 25162802 DOI: 10.1038/Ng.3074  0.416
2014 Spitale RC, Flynn RA, Torre EA, Kool ET, Chang HY. RNA structural analysis by evolving SHAPE chemistry. Wiley Interdisciplinary Reviews. Rna. 5: 867-81. PMID 25132067 DOI: 10.1002/Wrna.1253  0.687
2014 Li L, Chang HY. Physiological roles of long noncoding RNAs: insight from knockout mice. Trends in Cell Biology. 24: 594-602. PMID 25022466 DOI: 10.1016/J.Tcb.2014.06.003  0.462
2014 Quinn JJ, Ilik IA, Qu K, Georgiev P, Chu C, Akhtar A, Chang HY. Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Nature Biotechnology. 32: 933-40. PMID 24997788 DOI: 10.1038/Nbt.2943  0.436
2014 Zheng GX, Do BT, Webster DE, Khavari PA, Chang HY. Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs. Nature Structural & Molecular Biology. 21: 585-90. PMID 24929436 DOI: 10.1038/Nsmb.2842  0.767
2014 Flynn RA, Chang HY. Long noncoding RNAs in cell-fate programming and reprogramming. Cell Stem Cell. 14: 752-61. PMID 24905165 DOI: 10.1016/J.Stem.2014.05.014  0.445
2014 Buenrostro JD, Araya CL, Chircus LM, Layton CJ, Chang HY, Snyder MP, Greenleaf WJ. Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. Nature Biotechnology. 32: 562-8. PMID 24727714 DOI: 10.1038/Nbt.2880  0.55
2014 Yang YW, Flynn RA, Chen Y, Qu K, Wan B, Wang KC, Lei M, Chang HY. Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency. Elife. 3: e02046. PMID 24521543 DOI: 10.7554/Elife.02046  0.534
2014 Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY. Landscape and variation of RNA secondary structure across the human transcriptome. Nature. 505: 706-9. PMID 24476892 DOI: 10.1038/Nature12946  0.826
2014 Mazumdar C, Li R, Buenrostro J, Chang HY, Majeti R. Cohesin Complex Mutations Impair Differentiation of Human Hematopoietic Stem and Progenitor Cells Blood. 124: 4785-4785. DOI: 10.1182/Blood.V124.21.4785.4785  0.343
2014 Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of Native Chromatin for Fast and Sensitive Mulitmodal Analysis of Chromatin Architecture Biophysical Journal. 106: 77a. DOI: 10.1016/J.Bpj.2013.11.503  0.393
2013 Harcourt EM, Ehrenschwender T, Batista PJ, Chang HY, Kool ET. Identification of a selective polymerase enables detection of N(6)-methyladenosine in RNA. Journal of the American Chemical Society. 135: 19079-82. PMID 24328136 DOI: 10.1021/Ja4105792  0.712
2013 Wapinski OL, Vierbuchen T, Qu K, Lee QY, Chanda S, Fuentes DR, Giresi PG, Ng YH, Marro S, Neff NF, Drechsel D, Martynoga B, Castro DS, Webb AE, Südhof TC, ... ... Chang HY, et al. Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons. Cell. 155: 621-35. PMID 24243019 DOI: 10.1016/J.Cell.2013.09.028  0.368
2013 Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature Methods. 10: 1213-8. PMID 24097267 DOI: 10.1038/Nmeth.2688  0.345
2013 Li L, Liu B, Wapinski OL, Tsai MC, Qu K, Zhang J, Carlson JC, Lin M, Fang F, Gupta RA, Helms JA, Chang HY. Targeted disruption of Hotair leads to homeotic transformation and gene derepression. Cell Reports. 5: 3-12. PMID 24075995 DOI: 10.1016/J.Celrep.2013.09.003  0.42
2013 Schmitt AM, Chang HY. Gene regulation: Long RNAs wire up cancer growth. Nature. 500: 536-7. PMID 23945584 DOI: 10.1038/Nature12548  0.703
2013 Rapicavoli NA, Qu K, Zhang J, Mikhail M, Laberge RM, Chang HY. A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. Elife. 2: e00762. PMID 23898399 DOI: 10.7554/Elife.00762  0.331
2013 Ilik IA, Quinn JJ, Georgiev P, Tavares-Cadete F, Maticzka D, Toscano S, Wan Y, Spitale RC, Luscombe N, Backofen R, Chang HY, Akhtar A. Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. Molecular Cell. 51: 156-73. PMID 23870142 DOI: 10.1016/J.Molcel.2013.07.001  0.761
2013 Shah N, Jin K, Cruz LA, Park S, Sadik H, Cho S, Goswami CP, Nakshatri H, Gupta R, Chang HY, Zhang Z, Cimino-Mathews A, Cope L, Umbricht C, Sukumar S. HOXB13 mediates tamoxifen resistance and invasiveness in human breast cancer by suppressing ERα and inducing IL-6 expression. Cancer Research. 73: 5449-58. PMID 23832664 DOI: 10.1158/0008-5472.Can-13-1178  0.325
2013 Wan Y, Qu K, Ouyang Z, Chang HY. Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nature Protocols. 8: 849-69. PMID 23558785 DOI: 10.1038/Nprot.2013.045  0.657
2013 Batista PJ, Chang HY. Long noncoding RNAs: cellular address codes in development and disease. Cell. 152: 1298-307. PMID 23498938 DOI: 10.1016/J.Cell.2013.02.012  0.726
2013 Gomez JA, Wapinski OL, Yang YW, Bureau JF, Gopinath S, Monack DM, Chang HY, Brahic M, Kirkegaard K. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus. Cell. 152: 743-54. PMID 23415224 DOI: 10.1016/J.Cell.2013.01.015  0.671
2013 Batista PJ, Chang HY. Cytotopic localization by long noncoding RNAs. Current Opinion in Cell Biology. 25: 195-9. PMID 23279909 DOI: 10.1016/J.Ceb.2012.12.001  0.75
2013 Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GX, ... ... Chang HY, et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 493: 231-5. PMID 23201690 DOI: 10.1038/Nature11661  0.823
2013 Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET, Chang HY. RNA SHAPE analysis in living cells. Nature Chemical Biology. 9: 18-20. PMID 23178934 DOI: 10.1038/Nchembio.1131  0.699
2013 Ouyang Z, Snyder MP, Chang HY. SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data. Genome Research. 23: 377-87. PMID 23064747 DOI: 10.1101/Gr.138545.112  0.54
2013 Chang AL, Bitter PH, Qu K, Lin M, Rapicavoli NA, Chang HY. Rejuvenation of gene expression pattern of aged human skin by broadband light treatment: a pilot study. The Journal of Investigative Dermatology. 133: 394-402. PMID 22931923 DOI: 10.1038/Jid.2012.287  0.336
2013 Yang YW, Flynn RA, Chen Y, Qu K, Wan B, Wang KC, Lei M, Chang HY. Author response: Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency Elife. DOI: 10.7554/Elife.02046.013  0.533
2013 Chang HY. Abstract SY31-03: Genome regulation by long noncoding RNAs. Cancer Research. 73. DOI: 10.1158/1538-7445.Am2013-Sy31-03  0.488
2013 Abignano G, Hermes H, Esteves F, Gillespie J, Chang HY, Jimenez SA, Emery P, Galdo FD. SAT0022 Palmoplantar specific long NCRNA hotair drives myofibroblasts specific signature in systemic sclerosis Annals of the Rheumatic Diseases. 71: 478-478. DOI: 10.1136/Annrheumdis-2012-Eular.2970  0.363
2013 Schmitt A, Hung T, Flynn R, Payumo A, Peres-da-Silva A, Kenzelmann Broz D, Attardi L, Chen J, Chang H. Regulation of the DNA Damage Response by an Inducible Long Noncoding RNA International Journal of Radiation Oncology*Biology*Physics. 87: S19. DOI: 10.1016/J.Ijrobp.2013.06.055  0.704
2012 Siprashvili Z, Webster DE, Kretz M, Johnston D, Rinn JL, Chang HY, Khavari PA. Identification of proteins binding coding and non-coding human RNAs using protein microarrays. Bmc Genomics. 13: 633. PMID 23157412 DOI: 10.1186/1471-2164-13-633  0.64
2012 Martin L, Meier M, Lyons SM, Sit RV, Marzluff WF, Quake SR, Chang HY. Systematic reconstruction of RNA functional motifs with high-throughput microfluidics Nature Methods. 9: 1192-1194. PMID 23142872 DOI: 10.1038/Nmeth.2225  0.428
2012 Chisholm KM, Wan Y, Li R, Montgomery KD, Chang HY, West RB. Detection of long non-coding RNA in archival tissue: correlation with polycomb protein expression in primary and metastatic breast carcinoma. Plos One. 7: e47998. PMID 23133536 DOI: 10.1371/Journal.Pone.0047998  0.647
2012 Wan Y, Qu K, Ouyang Z, Kertesz M, Li J, Tibshirani R, Makino DL, Nutter RC, Segal E, Chang HY. Genome-wide measurement of RNA folding energies. Molecular Cell. 48: 169-81. PMID 22981864 DOI: 10.1016/J.Molcel.2012.08.008  0.667
2012 Lee CS, Ungewickell A, Bhaduri A, Qu K, Webster DE, Armstrong R, Weng WK, Aros CJ, Mah A, Chen RO, Lin M, Sundram U, Chang HY, Kretz M, Kim YH, et al. Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts. Blood. 120: 3288-97. PMID 22936659 DOI: 10.1182/Blood-2012-04-423061  0.45
2012 Brunner AL, Beck AH, Edris B, Sweeney RT, Zhu SX, Li R, Montgomery K, Varma S, Gilks T, Guo X, Foley JW, Witten DM, Giacomini CP, Flynn RA, Pollack JR, ... ... Chang HY, et al. Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers. Genome Biology. 13: R75. PMID 22929540 DOI: 10.1186/Gb-2012-13-8-R75  0.431
2012 Littlepage LE, Adler AS, Kouros-Mehr H, Huang G, Chou J, Krig SR, Griffith OL, Korkola JE, Qu K, Lawson DA, Xue Q, Sternlicht MD, Dijkgraaf GJ, Yaswen P, Rugo HS, ... ... Chang HY, et al. The transcription factor ZNF217 is a prognostic biomarker and therapeutic target during breast cancer progression. Cancer Discovery. 2: 638-51. PMID 22728437 DOI: 10.1158/2159-8290.Cd-12-0093  0.642
2012 Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annual Review of Biochemistry. 81: 145-66. PMID 22663078 DOI: 10.1182/Blood.V122.21.Sci-29.Sci-29  0.677
2012 Martin L, Chang HY. Uncovering the role of genomic "dark matter" in human disease. The Journal of Clinical Investigation. 122: 1589-95. PMID 22546862 DOI: 10.1172/Jci60020  0.408
2012 Chu C, Quinn J, Chang HY. Chromatin isolation by RNA purification (ChIRP). Journal of Visualized Experiments : Jove. PMID 22472705 DOI: 10.3791/3912  0.493
2012 Kretz M, Webster DE, Flockhart RJ, Lee CS, Zehnder A, Lopez-Pajares V, Qu K, Zheng GX, Chow J, Kim GE, Rinn JL, Chang HY, Siprashvili Z, Khavari PA. Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes & Development. 26: 338-43. PMID 22302877 DOI: 10.1101/Gad.182121.111  0.811
2012 Wang P, McKnight KD, Wong DJ, Rodriguez RT, Sugiyama T, Gu X, Ghodasara A, Qu K, Chang HY, Kim SK. A molecular signature for purified definitive endoderm guides differentiation and isolation of endoderm from mouse and human embryonic stem cells. Stem Cells and Development. 21: 2273-87. PMID 22236333 DOI: 10.1089/Scd.2011.0416  0.352
2012 Flynn RA, Chang HY. Active chromatin and noncoding RNAs: an intimate relationship. Current Opinion in Genetics & Development. 22: 172-8. PMID 22154525 DOI: 10.1016/J.Gde.2011.11.002  0.443
2012 Marques M, Nieves B, Chen R, Vaka D, Chan C, Zheng G, Chang H, Weissman I, Sweet-Cordero A. Abstract 1427: Signal rewiring induced by EWS/FLI-1 in mouse and human mesenchymal stem cells Cancer Research. 72: 1427-1427. DOI: 10.1158/1538-7445.Am2012-1427  0.756
2011 Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Molecular Cell. 44: 667-78. PMID 21963238 DOI: 10.1016/J.Molcel.2011.08.027  0.47
2011 Marro S, Pang ZP, Yang N, Tsai MC, Qu K, Chang HY, Südhof TC, Wernig M. Direct lineage conversion of terminally differentiated hepatocytes to functional neurons. Cell Stem Cell. 9: 374-82. PMID 21962918 DOI: 10.1016/J.Stem.2011.09.002  0.359
2011 Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Molecular Cell. 43: 904-14. PMID 21925379 DOI: 10.1016/J.Molcel.2011.08.018  0.576
2011 Wan Y, Kertesz M, Spitale RC, Segal E, Chang HY. Understanding the transcriptome through RNA structure. Nature Reviews. Genetics. 12: 641-55. PMID 21850044 DOI: 10.1038/Nrg3049  0.771
2011 Alastalo TP, Li M, De Jesus Perez V, Pham D, Sawada H, Wang JK, Koskenvuo M, Wang L, Freeman BA, Chang HY, Rabinovitch M. Disruption of PPARγ/β-catenin-mediated regulation of apelin impairs BMP-induced mouse and human pulmonary arterial EC survival Journal of Clinical Investigation. 121: 3735-3746. PMID 21821917 DOI: 10.1172/Jci43382  0.317
2011 Kawahara TLA, Rapicavoli NA, Wu AR, Qu K, Quake SR, Chang HY. Dynamic chromatin localization of sirt6 shapes stress- and aging-related transcriptional networks Plos Genetics. 7. PMID 21738489 DOI: 10.1371/Journal.Pgen.1002153  0.351
2011 Chen Y, Wan B, Wang KC, Cao F, Yang Y, Protacio A, Dou Y, Chang HY, Lei M. Crystal structure of the N-terminal region of human Ash2L shows a winged-helix motif involved in DNA binding. Embo Reports. 12: 797-803. PMID 21660059 DOI: 10.1038/Embor.2011.101  0.508
2011 Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, Horlings HM, Shah N, Umbricht C, Wang P, Wang Y, Kong B, Langerød A, Børresen-Dale AL, Kim SK, ... ... Chang HY, et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nature Genetics. 43: 621-9. PMID 21642992 DOI: 10.1038/Ng.848  0.486
2011 Wapinski O, Chang HY. Long noncoding RNAs and human disease. Trends in Cell Biology. 21: 354-61. PMID 21550244 DOI: 10.1016/J.Tcb.2011.04.001  0.43
2011 Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 472: 120-4. PMID 21423168 DOI: 10.1038/Nature09819  0.607
2011 Spitale RC, Tsai MC, Chang HY. RNA templating the epigenome: long noncoding RNAs as molecular scaffolds. Epigenetics : Official Journal of the Dna Methylation Society. 6: 539-43. PMID 21393997 DOI: 10.4161/Epi.6.5.15221  0.685
2011 Tsai MC, Spitale RC, Chang HY. Long intergenic noncoding RNAs: new links in cancer progression. Cancer Research. 71: 3-7. PMID 21199792 DOI: 10.1158/0008-5472.Can-10-2483  0.69
2011 Wapinski O, Chang HY. Corrigendum: Long noncoding RNAs and human disease. [Trends in Cell Biology 21 (2011), 354-361] Trends in Cell Biology. 21: 561. DOI: 10.1016/J.Tcb.2011.08.004  0.351
2010 Ouyang Z, Zheng GX, Chang HY. Noncoding RNA landmarks of pluripotency and reprogramming. Cell Stem Cell. 7: 649-50. PMID 21112559 DOI: 10.1016/J.Stem.2010.11.018  0.761
2010 Wirt SE, Adler AS, Gebala V, Weimann JM, Schaffer BE, Saddic LA, Viatour P, Vogel H, Chang HY, Meissner A, Sage J. G1 arrest and differentiation can occur independently of Rb family function. The Journal of Cell Biology. 191: 809-25. PMID 21059851 DOI: 10.1083/Jcb.201003048  0.634
2010 Hung T, Chang HY. Long noncoding RNA in genome regulation: prospects and mechanisms. Rna Biology. 7: 582-5. PMID 20930520 DOI: 10.4161/Rna.7.5.13216  0.502
2010 Wan Y, Chang HY. HOTAIR: Flight of noncoding RNAs in cancer metastasis. Cell Cycle (Georgetown, Tex.). 9: 3391-2. PMID 20864820 DOI: 10.4161/Cc.9.17.13122  0.677
2010 Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E. Genome-wide measurement of RNA secondary structure in yeast. Nature. 467: 103-7. PMID 20811459 DOI: 10.1038/Nature09322  0.743
2010 Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes. Science (New York, N.Y.). 329: 689-93. PMID 20616235 DOI: 10.1126/Science.1192002  0.624
2010 Tsai MC, Wang JK, Chang HY. Tumor suppression by the histone demethylase UTX. Cell Cycle (Georgetown, Tex.). 9: 2043-4. PMID 20505331 DOI: 10.4161/Cc.9.11.11845  0.427
2010 Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, ... ... Chang HY, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 464: 1071-6. PMID 20393566 DOI: 10.1038/Nature08975  0.712
2010 Wang JK, Tsai MC, Poulin G, Adler AS, Chen S, Liu H, Shi Y, Chang HY. The histone demethylase UTX enables RB-dependent cell fate control. Genes & Development. 24: 327-32. PMID 20123895 DOI: 10.1101/Gad.1882610  0.687
2010 Sargent JL, Milano A, Bhattacharyya S, Varga J, Connolly MK, Chang HY, Whitfield ML. A TGFbeta-responsive gene signature is associated with a subset of diffuse scleroderma with increased disease severity. The Journal of Investigative Dermatology. 130: 694-705. PMID 19812599 DOI: 10.1038/Jid.2009.318  0.307
2010 Kertesz M, Wan Y, Mazor E, Rinn J, Nutter R, Chang H, Segal E. Probing RNA structure genome-wide using high throughput sequencing Nature Protocols. DOI: 10.1038/Nprot.2010.152  0.725
2009 Chang HY. Anatomic demarcation of cells: genes to patterns. Science (New York, N.Y.). 326: 1206-7. PMID 19965461 DOI: 10.1126/Science.1175686  0.377
2009 Chan KS, Espinosa I, Chao M, Wong D, Ailles L, Diehn M, Gill H, Presti J, Chang HY, van de Rijn M, Shortliffe L, Weissman IL. Identification, molecular characterization, clinical prognosis, and therapeutic targeting of human bladder tumor-initiating cells. Proceedings of the National Academy of Sciences of the United States of America. 106: 14016-21. PMID 19666525 DOI: 10.1073/Pnas.0906549106  0.511
2009 Mace KA, Restivo TE, Rinn JL, Paquet AC, Chang HY, Young DM, Boudreau NJ. HOXA3 modulates injury-induced mobilization and recruitment of bone marrow-derived cells. Stem Cells (Dayton, Ohio). 27: 1654-65. PMID 19544454 DOI: 10.1002/Stem.90  0.567
2009 Chang HY, Cuvier O, Dekker J. Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization. Embo Reports. 10: 689-93. PMID 19525922 DOI: 10.1038/Embor.2009.136  0.343
2009 Reuter JA, Ortiz-Urda S, Kretz M, Garcia J, Scholl FA, Pasmooij AM, Cassarino D, Chang HY, Khavari PA. Modeling inducible human tissue neoplasia identifies an extracellular matrix interaction network involved in cancer progression. Cancer Cell. 15: 477-88. PMID 19477427 DOI: 10.1016/J.Ccr.2009.04.002  0.33
2009 Wang KC, Helms JA, Chang HY. Regeneration, repair and remembering identity: the three Rs of Hox gene expression. Trends in Cell Biology. 19: 268-75. PMID 19428253 DOI: 10.1016/J.Tcb.2009.03.007  0.599
2009 Rando OJ, Chang HY. Genome-wide views of chromatin structure. Annual Review of Biochemistry. 78: 245-71. PMID 19317649 DOI: 10.1146/Annurev.Biochem.78.071107.134639  0.369
2009 Somervaille TC, Matheny CJ, Spencer GJ, Iwasaki M, Rinn JL, Witten DM, Chang HY, Shurtleff SA, Downing JR, Cleary ML. Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells. Cell Stem Cell. 4: 129-40. PMID 19200802 DOI: 10.1016/J.Stem.2008.11.015  0.586
2009 Hung T, Binda O, Champagne KS, Kuo AJ, Johnson K, Chang HY, Simon MD, Kutateladze TG, Gozani O. ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation. Molecular Cell. 33: 248-56. PMID 19187765 DOI: 10.1016/J.Molcel.2008.12.016  0.303
2009 Chung L, Fiorentino DF, Benbarak MJ, Adler AS, Mariano MM, Paniagua RT, Milano A, Connolly MK, Ratiner BD, Wiskocil RL, Whitfield ML, Chang HY, Robinson WH. Molecular framework for response to imatinib mesylate in systemic sclerosis. Arthritis and Rheumatism. 60: 584-91. PMID 19180499 DOI: 10.1002/Art.24221  0.619
2009 Kawahara TL, Michishita E, Adler AS, Damian M, Berber E, Lin M, McCord RA, Ongaigui KC, Boxer LD, Chang HY, Chua KF. SIRT6 links histone H3 lysine 9 deacetylation to NF-kappaB-dependent gene expression and organismal life span. Cell. 136: 62-74. PMID 19135889 DOI: 10.1016/J.Cell.2008.10.052  0.639
2008 Sääf AM, Tengvall-Linder M, Chang HY, Adler AS, Wahlgren CF, Scheynius A, Nordenskjöld M, Bradley M. Global expression profiling in atopic eczema reveals reciprocal expression of inflammatory and lipid genes. Plos One. 3: e4017. PMID 19107207 DOI: 10.1371/Journal.Pone.0004017  0.657
2008 Wong DJ, Segal E, Chang HY. Stemness, cancer and cancer stem cells. Cell Cycle (Georgetown, Tex.). 7: 3622-4. PMID 19029796 DOI: 10.4161/Cc.7.23.7104  0.345
2008 Gardner JM, Devoss JJ, Friedman RS, Wong DJ, Tan YX, Zhou X, Johannes KP, Su MA, Chang HY, Krummel MF, Anderson MS. Deletional tolerance mediated by extrathymic Aire-expressing cells. Science (New York, N.Y.). 321: 843-7. PMID 18687966 DOI: 10.1126/Science.1159407  0.318
2008 Sen GL, Webster DE, Barragan DI, Chang HY, Khavari PA. Control of differentiation in a self-renewing mammalian tissue by the histone demethylase JMJD3. Genes & Development. 22: 1865-70. PMID 18628393 DOI: 10.1101/Gad.1673508  0.333
2008 Su MA, Giang K, Zumer K, Jiang H, Oven I, Rinn JL, Devoss JJ, Johannes KP, Lu W, Gardner J, Chang A, Bubulya P, Chang HY, Peterlin BM, Anderson MS. Mechanisms of an autoimmunity syndrome in mice caused by a dominant mutation in Aire. The Journal of Clinical Investigation. 118: 1712-26. PMID 18414681 DOI: 10.1172/Jci34523  0.55
2008 Wong DJ, Liu H, Ridky TW, Cassarino D, Segal E, Chang HY. Module map of stem cell genes guides creation of epithelial cancer stem cells. Cell Stem Cell. 2: 333-44. PMID 18397753 DOI: 10.1016/J.Stem.2008.02.009  0.363
2008 Michishita E, McCord RA, Berber E, Kioi M, Padilla-Nash H, Damian M, Cheung P, Kusumoto R, Kawahara TL, Barrett JC, Chang HY, Bohr VA, Ried T, Gozani O, Chua KF. SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin. Nature. 452: 492-6. PMID 18337721 DOI: 10.1038/Nature06736  0.319
2008 Rinn JL, Wang JK, Liu H, Montgomery K, van de Rijn M, Chang HY. A systems biology approach to anatomic diversity of skin. The Journal of Investigative Dermatology. 128: 776-82. PMID 18337710 DOI: 10.1038/Sj.Jid.5700986  0.605
2008 Adler AS, Kawahara TL, Segal E, Chang HY. Reversal of aging by NFkappaB blockade. Cell Cycle (Georgetown, Tex.). 7: 556-9. PMID 18256548 DOI: 10.4161/Cc.7.5.5490  0.64
2008 Sinha S, Adler AS, Field Y, Chang HY, Segal E. Systematic functional characterization of cis-regulatory motifs in human core promoters. Genome Research. 18: 477-88. PMID 18256240 DOI: 10.1101/Gr.6828808  0.674
2008 Rinn JL, Wang JK, Allen N, Brugmann SA, Mikels AJ, Liu H, Ridky TW, Stadler HS, Nusse R, Helms JA, Chang HY. A dermal HOX transcriptional program regulates site-specific epidermal fate. Genes & Development. 22: 303-7. PMID 18245445 DOI: 10.1101/gad.1610508  0.549
2008 Adler AS, Littlepage LE, Lin M, Kawahara TL, Wong DJ, Werb Z, Chang HY. CSN5 isopeptidase activity links COP9 signalosome activation to breast cancer progression. Cancer Research. 68: 506-15. PMID 18199546 DOI: 10.1158/0008-5472.Can-07-3060  0.628
2008 Wong DJ, Nuyten DS, Regev A, Lin M, Adler AS, Segal E, van de Vijver MJ, Chang HY. Revealing targeted therapy for human cancer by gene module maps. Cancer Research. 68: 369-78. PMID 18199530 DOI: 10.1158/0008-5472.Can-07-0382  0.665
2007 Adler AS, Sinha S, Kawahara TL, Zhang JY, Segal E, Chang HY. Motif module map reveals enforcement of aging by continual NF-kappaB activity. Genes & Development. 21: 3244-57. PMID 18055696 DOI: 10.1101/Gad.1588507  0.642
2007 Lan F, Bayliss PE, Rinn JL, Whetstine JR, Wang JK, Chen S, Iwase S, Alpatov R, Issaeva I, Canaani E, Roberts TM, Chang HY, Shi Y. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature. 449: 689-94. PMID 17851529 DOI: 10.1038/Nature06192  0.627
2007 Chang HY, Cotsarelis G. Turning skin into embryonic stem cells. Nature Medicine. 13: 783-4. PMID 17618266 DOI: 10.1038/Nm0707-783  0.322
2007 Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 129: 1311-23. PMID 17604720 DOI: 10.1016/J.Cell.2007.05.022  0.662
2007 Liu H, Adler AS, Segal E, Chang HY. A transcriptional program mediating entry into cellular quiescence. Plos Genetics. 3: e91. PMID 17559306 DOI: 10.1371/Journal.Pgen.0030091  0.678
2007 O'Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ. Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. Plos Genetics. 3: e89. PMID 17542650 DOI: 10.1371/Journal.Pgen.0030089  0.623
2007 Segal E, Sirlin CB, Ooi C, Adler AS, Gollub J, Chen X, Chan BK, Matcuk GR, Barry CT, Chang HY, Kuo MD. Decoding global gene expression programs in liver cancer by noninvasive imaging. Nature Biotechnology. 25: 675-80. PMID 17515910 DOI: 10.1038/Nbt1306  0.643
2006 Chang HY, Thomson JA, Chen X. Microarray analysis of stem cells and differentiation. Methods in Enzymology. 420: 225-54. PMID 17161699 DOI: 10.1016/S0076-6879(06)20010-7  0.393
2006 DeVoss J, Hou Y, Johannes K, Lu W, Liou GI, Rinn J, Chang H, Caspi RR, Caspi R, Fong L, Anderson MS. Spontaneous autoimmunity prevented by thymic expression of a single self-antigen. The Journal of Experimental Medicine. 203: 2727-35. PMID 17116738 DOI: 10.1084/Jem.20061864  0.541
2006 Nuyten DS, Kreike B, Hart AA, Chi JT, Sneddon JB, Wessels LF, Peterse HJ, Bartelink H, Brown PO, Chang HY, van de Vijver MJ. Predicting a local recurrence after breast-conserving therapy by gene expression profiling. Breast Cancer Research : Bcr. 8: R62. PMID 17069664 DOI: 10.1186/Bcr1614  0.744
2006 Sneddon JB, Zhen HH, Montgomery K, van de Rijn M, Tward AD, West R, Gladstone H, Chang HY, Morganroth GS, Oro AE, Brown PO. Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation. Proceedings of the National Academy of Sciences of the United States of America. 103: 14842-7. PMID 17003113 DOI: 10.1073/Pnas.0606857103  0.777
2006 Rinn JL, Bondre C, Gladstone HB, Brown PO, Chang HY. Anatomic demarcation by positional variation in fibroblast gene expression programs. Plos Genetics. 2: e119. PMID 16895450 DOI: 10.1371/Journal.Pgen.0020119  0.677
2006 Ray S, Atkuri KR, Deb-Basu D, Adler AS, Chang HY, Herzenberg LA, Felsher DW. MYC can induce DNA breaks in vivo and in vitro independent of reactive oxygen species. Cancer Research. 66: 6598-605. PMID 16818632 DOI: 10.1158/0008-5472.Can-05-3115  0.633
2006 Adler AS, Chang HY. From description to causality: mechanisms of gene expression signatures in cancer. Cell Cycle (Georgetown, Tex.). 5: 1148-51. PMID 16721055 DOI: 10.4161/Cc.5.11.2798  0.67
2006 Adler AS, Lin M, Horlings H, Nuyten DS, van de Vijver MJ, Chang HY. Genetic regulators of large-scale transcriptional signatures in cancer. Nature Genetics. 38: 421-30. PMID 16518402 DOI: 10.1038/Ng1752  0.666
2006 DeVoss J, Hou Y, Johannes K, Lu W, Liou GI, Rinn J, Chang H, Caspi RR, Fong L, Anderson MS. CORRECTION Journal of Experimental Medicine. 204: 203-203. DOI: 10.1084/Jem.20061864121306C  0.478
2005 Wong DJ, Chang HY. Learning more from microarrays: insights from modules and networks. The Journal of Investigative Dermatology. 125: 175-82. PMID 16098025 DOI: 10.1111/J.0022-202X.2005.23827.X  0.351
2005 Tang J, Chang HY, Yang X. The death domain-associated protein modulates activity of the transcription co-factor Skip/NcoA62. Febs Letters. 579: 2883-90. PMID 15878163 DOI: 10.1016/J.Febslet.2005.04.029  0.334
2005 Chang HY, Nuyten DS, Sneddon JB, Hastie T, Tibshirani R, Sørlie T, Dai H, He YD, van't Veer LJ, Bartelink H, van de Rijn M, Brown PO, van de Vijver MJ. Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proceedings of the National Academy of Sciences of the United States of America. 102: 3738-43. PMID 15701700 DOI: 10.1073/Pnas.0409462102  0.753
2005 Nuyten D, Chang H, Brown P, Vijver MVd. Reproducibility of molecular portraits in early stage breast cancer Breast Cancer Research. 7: 1-2. DOI: 10.1186/Bcr1156  0.434
2004 Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi JT, van de Rijn M, Botstein D, Brown PO. Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. Plos Biology. 2: E7. PMID 14737219 DOI: 10.1371/Journal.Pbio.0020007  0.79
2003 Chi JT, Chang HY, Haraldsen G, Jahnsen FL, Troyanskaya OG, Chang DS, Wang Z, Rockson SG, van de Rijn M, Botstein D, Brown PO. Endothelial cell diversity revealed by global expression profiling. Proceedings of the National Academy of Sciences of the United States of America. 100: 10623-8. PMID 12963823 DOI: 10.1073/Pnas.1434429100  0.504
2003 Chi JT, Chang HY, Wang NN, Chang DS, Dunphy N, Brown PO. Genomewide view of gene silencing by small interfering RNAs. Proceedings of the National Academy of Sciences of the United States of America. 100: 6343-6. PMID 12730368 DOI: 10.1073/Pnas.1037853100  0.618
2002 Chang HY, Chi JT, Dudoit S, Bondre C, van de Rijn M, Botstein D, Brown PO. Diversity, topographic differentiation, and positional memory in human fibroblasts. Proceedings of the National Academy of Sciences of the United States of America. 99: 12877-82. PMID 12297622 DOI: 10.1073/Pnas.162488599  0.545
1999 Chang HY, Yang X, Baltimore D. Dissecting Fas signaling with an altered-specificity death-domain mutant: requirement of FADD binding for apoptosis but not Jun N-terminal kinase activation. Proceedings of the National Academy of Sciences of the United States of America. 96: 1252-6. PMID 9990010 DOI: 10.1073/Pnas.96.4.1252  0.434
1998 Chang HY, Nishitoh H, Yang X, Ichijo H, Baltimore D. Activation of apoptosis signal-regulating kinase 1 (ASK1) by the adapter protein Daxx. Science (New York, N.Y.). 281: 1860-3. PMID 9743501 DOI: 10.1126/Science.281.5384.1860  0.423
1998 Yang X, Chang HY, Baltimore D. Essential role of CED-4 oligomerization in CED-3 activation and apoptosis. Science (New York, N.Y.). 281: 1355-7. PMID 9721101 DOI: 10.1126/Science.281.5381.1355  0.451
1998 Yang X, Chang HY, Baltimore D. Autoproteolytic activation of pro-caspases by oligomerization. Molecular Cell. 1: 319-25. PMID 9659928 DOI: 10.1016/S1097-2765(00)80032-5  0.41
1997 Yang X, Khosravi-Far R, Chang HY, Baltimore D. Daxx, a novel Fas-binding protein that activates JNK and apoptosis. Cell. 89: 1067-76. PMID 9215629 DOI: 10.1016/S0092-8674(00)80294-9  0.423
Show low-probability matches.