Gary C. Hon, Ph.D. - Publications

2009 Bioinformatics University of California, San Diego, La Jolla, CA 
Inference of gene regulatory networks and determination of protein specificity

35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 England AR, Chaney CP, Das A, Patel M, Malewska A, Armendariz D, Hon GC, Strand DW, Drake KA, Carroll TJ. Identification and characterization of cellular heterogeneity within the developing renal interstitium. Development (Cambridge, England). PMID 32586976 DOI: 10.1242/Dev.190108  0.318
2019 Xie S, Armendariz D, Zhou P, Duan J, Hon GC. Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules. Cell Reports. 29: 2570-2578.e5. PMID 31775028 DOI: 10.1016/J.Celrep.2019.10.073  0.441
2019 Duan J, Li B, Bhakta M, Xie S, Zhou P, Munshi NV, Hon GC. Rational Reprogramming of Cellular States by Combinatorial Perturbation. Cell Reports. 27: 3486-3499.e6. PMID 31216470 DOI: 10.1016/J.Celrep.2019.05.079  0.378
2019 Xie S, Hon GC. Experimental and Computational Approaches for Single-Cell Enhancer Perturbation Assay. Methods in Molecular Biology (Clifton, N.J.). 1935: 203-221. PMID 30758829 DOI: 10.1007/978-1-4939-9057-3_14  0.465
2018 Hepler C, Shan B, Zhang Q, Henry GH, Shao M, Vishvanath L, Ghaben AL, Mobley AB, Strand D, Hon GC, Gupta RK. Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult mice. Elife. 7. PMID 30265241 DOI: 10.7554/Elife.39636  0.347
2018 Xie S, Cooley A, Armendariz D, Zhou P, Hon GC. Frequent sgRNA-barcode recombination in single-cell perturbation assays. Plos One. 13: e0198635. PMID 29874289 DOI: 10.1371/Journal.Pone.0198635  0.357
2018 Yu M, Han D, Hon GC, He C. Tet-Assisted Bisulfite Sequencing (TAB-seq). Methods in Molecular Biology (Clifton, N.J.). 1708: 645-663. PMID 29224168 DOI: 10.1007/978-1-4939-7481-8_33  0.504
2017 Liu X, Zhang Y, Chen Y, Li M, Zhou F, Li K, Cao H, Ni M, Liu Y, Gu Z, Dickerson KE, Xie S, Hon GC, Xuan Z, Zhang MQ, et al. In Situ Capture of Chromatin Interactions by Biotinylated dCas9. Cell. 170: 1028-1043.e19. PMID 28841410 DOI: 10.1016/J.Cell.2017.08.003  0.478
2017 Xie S, Duan J, Li B, Zhou P, Hon GC. Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells. Molecular Cell. PMID 28416141 DOI: 10.1016/J.Molcel.2017.03.007  0.391
2015 Liu F, Hon GC, Villa GR, Turner KM, Ikegami S, Yang H, Ye Z, Li B, Kuan S, Lee AY, Zanca C, Wei B, Lucey G, Jenkins D, Zhang W, et al. EGFR Mutation Promotes Glioblastoma through Epigenome and Transcription Factor Network Remodeling. Molecular Cell. PMID 26455392 DOI: 10.1016/J.Molcel.2015.09.002  0.495
2014 Hon GC, Song CX, Du T, Jin F, Selvaraj S, Lee AY, Yen CA, Ye Z, Mao SQ, Wang BA, Kuan S, Edsall LE, Zhao BS, Xu GL, He C, et al. 5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation. Molecular Cell. 56: 286-97. PMID 25263596 DOI: 10.1016/J.Molcel.2014.08.026  0.761
2014 Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M, Dai Q, Jia G, Ren B, Pan T, He C. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 505: 117-20. PMID 24284625 DOI: 10.1038/Nature12730  0.442
2014 Hon G, Song C, Jin F, Selvaraj S, Lee AY, Yen C, Ye Z, Mao S, Wang B, Kuan S, Edsall L, Zhao BS, Xu G, He C, Ren B. Abstract 460: Base resolution epigenomic analysis reveals a role for Tet2 in modulating enhancer activity Molecular and Cellular Biology. 74: 460-460. DOI: 10.1158/1538-7445.Am2014-460  0.783
2014 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, et al. Corrigendum: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells Nature. 514: 126. DOI: 10.1038/Nature13843  0.581
2013 Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nature Genetics. 45: 1198-206. PMID 23995138 DOI: 10.1038/Ng.2746  0.766
2013 Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, et al. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2: e00675. PMID 23795294 DOI: 10.7554/Elife.00675  0.505
2013 Zhang L, Szulwach KE, Hon GC, Song CX, Park B, Yu M, Lu X, Dai Q, Wang X, Street CR, Tan H, Min JH, Ren B, Jin P, He C. Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. Nature Communications. 4: 1517. PMID 23443545 DOI: 10.1038/Ncomms2527  0.575
2013 Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SC, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, et al. Author response: Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis Elife. DOI: 10.7554/Elife.00675.022  0.44
2013 Hon GC, Shen Y, McCleary DF, Edsall L, Kuan S, Ren B. Abstract 1111: Whole genome bisulfite sequencing reveals tissue-specific DNA methylation in a normal mouse. Cancer Research. 73: 1111-1111. DOI: 10.1158/1538-7445.Am2013-1111  0.728
2012 Yu M, Hon GC, Szulwach KE, Song CX, Jin P, Ren B, He C. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nature Protocols. 7: 2159-70. PMID 23196972 DOI: 10.1038/Nprot.2012.137  0.569
2012 Smallwood A, Hon GC, Jin F, Henry RE, Espinosa JM, Ren B. CBX3 regulates efficient RNA processing genome-wide. Genome Research. 22: 1426-36. PMID 22684280 DOI: 10.1101/Gr.124818.111  0.732
2012 Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, Min JH, Jin P, Ren B, He C. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell. 149: 1368-80. PMID 22608086 DOI: 10.1016/J.Cell.2012.04.027  0.676
2012 Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Research. 22: 246-58. PMID 22156296 DOI: 10.1101/Gr.125872.111  0.661
2011 Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z, Kuan S, Yu P, Liu H, Zhang X, Green RD, et al. Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Research. 21: 1393-409. PMID 21876557 DOI: 10.1038/Cr.2011.146  0.694
2011 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 471: 68-73. PMID 21289626 DOI: 10.1038/Nature09798  0.693
2010 Hawkins RD, Hon GC, Ren B. Next-generation genomics: An integrative approach Nature Reviews Genetics. 11: 476-486. PMID 20531367 DOI: 10.1038/Nrg2795  0.622
2010 Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 6: 479-91. PMID 20452322 DOI: 10.1016/J.Stem.2010.03.018  0.718
2009 Hon G, Wang W, Ren B. Discovery and annotation of functional chromatin signatures in the human genome. Plos Computational Biology. 5: e1000566. PMID 19918365 DOI: 10.1371/Journal.Pcbi.1000566  0.62
2009 Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 462: 315-22. PMID 19829295 DOI: 10.1038/Nature08514  0.728
2009 Hon GC, Hawkins RD, Ren B. Predictive chromatin signatures in the mammalian genome Human Molecular Genetics. 18: R195-R201. PMID 19808796 DOI: 10.1093/Hmg/Ddp409  0.683
2009 Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 459: 108-12. PMID 19295514 DOI: 10.1038/Nature07829  0.684
2008 Hon G, Ren B, Wang W. ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome Plos Computational Biology. 4. PMID 18927605 DOI: 10.1371/Journal.Pcbi.1000201  0.596
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Hon G, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.656
2007 Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Nature Genetics. 39: 311-318. PMID 17277777 DOI: 10.1038/Ng1966  0.701
2006 Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, et al. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. Journal of Biology. 5: 11. PMID 16762047 DOI: 10.1186/Jbiol36  0.46
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