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Gary C. Hon, Ph.D. - Publications

Affiliations: 
2009 Bioinformatics University of California, San Diego, La Jolla, CA 
Area:
Inference of gene regulatory networks and determination of protein specificity
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35/61 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  0.503
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  0.477
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  0.392
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  0.76
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  0.441
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  0.58
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  0.504
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  0.574
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  0.439
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  0.727
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  0.568
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  0.621
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  0.717
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  0.617
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  0.682
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  0.593
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  0.636
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  0.699
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
Low-probability matches (unlikely to be authored by this person)
2022 Bhattacharyya S, Kollipara RK, Orquera-Tornakian G, Goetsch S, Zhang M, Perry C, Li B, Shelton JM, Bhakta M, Duan J, Xie Y, Xiao G, Evers BM, Hon GC, Kittler R, et al. Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm. The Journal of Clinical Investigation. PMID 36454649 DOI: 10.1172/JCI153635  0.298
2004 Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A sequence logo generator Genome Research. 14: 1188-1190. PMID 15173120 DOI: 10.1101/Gr.849004  0.287
2019 Bhattacharyya S, Duan J, Wang L, Li B, Bhakta M, Fernandez-Perez A, Hon GC, Munshi NV. Using Gjd3-CreEGFP mice to examine atrioventricular node morphology and composition. Scientific Reports. 9: 2106. PMID 30765799 DOI: 10.1038/S41598-019-38683-8  0.279
2018 Henry GH, Malewska A, Joseph DB, Malladi VS, Lee J, Torrealba J, Mauck RJ, Gahan JC, Raj GV, Roehrborn CG, Hon GC, MacConmara MP, Reese JC, Hutchinson RC, Vezina CM, et al. A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra. Cell Reports. 25: 3530-3542.e5. PMID 30566875 DOI: 10.1016/J.Celrep.2018.11.086  0.271
2004 Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. The ASTRAL Compendium in 2004. Nucleic Acids Research. 32: D189-92. PMID 14681391 DOI: 10.1093/Nar/Gkh034  0.27
2018 Hepler C, Shan B, Zhang Q, Henry GH, Shao M, Vishvanath L, Ghaben AL, Mobley AB, Strand D, Hon GC, Gupta RK. Author response: Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult mice Elife. DOI: 10.7554/Elife.39636.032  0.247
2023 Liu L, Oura S, Markham Z, Hamilton JN, Skory RM, Li L, Sakurai M, Wang L, Pinzon-Arteaga CA, Plachta N, Hon GC, Wu J. Modeling post-implantation stages of human development into early organogenesis with stem-cell-derived peri-gastruloids. Cell. PMID 37478861 DOI: 10.1016/j.cell.2023.07.018  0.245
2023 Armendariz DA, Goetsch SC, Sundarrajan A, Sivakumar S, Wang Y, Xie S, Munshi NV, Hon GC. CHD-associated enhancers shape human cardiomyocyte lineage commitment. Elife. 12. PMID 37096669 DOI: 10.7554/eLife.86206  0.243
2016 Villa GR, Hulce JJ, Zanca C, Bi J, Ikegami S, Cahill GL, Gu Y, Lum KM, Masui K, Yang H, Rong X, Hong C, Turner KM, Liu F, Hon GC, et al. An LXR-Cholesterol Axis Creates a Metabolic Co-Dependency for Brain Cancers. Cancer Cell. PMID 27746144 DOI: 10.1016/J.Ccell.2016.09.008  0.243
2017 Partin AC, Ngo TD, Herrell E, Jeong BC, Hon G, Nam Y. Heme enables proper positioning of Drosha and DGCR8 on primary microRNAs. Nature Communications. 8: 1737. PMID 29170488 DOI: 10.1038/S41467-017-01713-Y  0.229
2021 Yu L, Wei Y, Duan J, Schmitz DA, Sakurai M, Wang L, Wang K, Zhao S, Hon GC, Wu J. Blastocyst-like structures generated from human pluripotent stem cells. Nature. PMID 33731924 DOI: 10.1038/s41586-021-03356-y  0.227
2023 Armendariz DA, Sundarrajan A, Hon GC. Breaking enhancers to gain insights into developmental defects. Elife. 12. PMID 37497775 DOI: 10.7554/eLife.88187  0.224
2023 Yu L, Logsdon D, Pinzon-Arteaga CA, Duan J, Ezashi T, Wei Y, Ribeiro Orsi AE, Oura S, Liu L, Wang L, Liu K, Ding X, Zhan L, Zhang J, Nahar A, ... ... Hon GC, et al. Large-scale production of human blastoids amenable to modeling blastocyst development and maternal-fetal cross talk. Cell Stem Cell. 30: 1246-1261.e9. PMID 37683605 DOI: 10.1016/j.stem.2023.08.002  0.222
2021 Li B, Hon GC. Single-Cell Genomics: Catalyst for Cell Fate Engineering. Frontiers in Bioengineering and Biotechnology. 9: 748942. PMID 34733831 DOI: 10.3389/fbioe.2021.748942  0.22
2019 Zhang Z, Luo D, Zhong X, Choi JH, Ma Y, Wang S, Mahrt E, Guo W, Stawiski EW, Modrusan Z, Seshagiri S, Kapur P, Hon GC, Brugarolas J, Wang T. SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples. Genes. 10. PMID 31336988 DOI: 10.3390/Genes10070531  0.218
2022 Wang Y, Xie S, Armendariz D, Hon GC. Computational identification of clonal cells in single-cell CRISPR screens. Bmc Genomics. 23: 135. PMID 35168568 DOI: 10.1186/s12864-022-08359-1  0.217
2023 Wang Y, Armendariz D, Wang L, Zhao H, Xie S, Hon GC. Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes. Biorxiv : the Preprint Server For Biology. PMID 38045327 DOI: 10.1101/2023.11.20.567880  0.213
2018 Partin AC, Ngo TD, Herrell E, Jeong BC, Hon G, Nam Y. Publisher Correction: Heme enables proper positioning of Drosha and DGCR8 on primary microRNAs. Nature Communications. 9: 3852. PMID 30228298 DOI: 10.1038/S41467-018-06426-4  0.206
2020 Bhattacharyya S, Duan J, Wang L, Li B, Bhakta M, Fernandez-Perez A, Hon GC, Munshi NV. Author Correction: Using Gjd3-CreEGFP mice to examine atrioventricular node morphology and composition. Scientific Reports. 10: 4069. PMID 32107454 DOI: 10.1038/S41598-020-60915-5  0.193
2023 Madhukaran S, Hon GC, Mahendroo M. Protocol to dissociate epithelia from non-pregnant and pregnant mouse cervical tissue for single-cell RNA-sequencing. Star Protocols. 4: 102631. PMID 37897730 DOI: 10.1016/j.xpro.2023.102631  0.192
2021 Yu L, Wei Y, Duan J, Schmitz DA, Sakurai M, Wang L, Wang K, Zhao S, Hon GC, Wu J. Author Correction: Blastocyst-like structures generated from human pluripotent stem cells. Nature. PMID 34341538 DOI: 10.1038/s41586-021-03635-8  0.181
2022 Zhang Y, Li B, Cananzi S, Han C, Wang LL, Zou Y, Fu YX, Hon GC, Zhang CL. A single factor elicits multilineage reprogramming of astrocytes in the adult mouse striatum. Proceedings of the National Academy of Sciences of the United States of America. 119: e2107339119. PMID 35254903 DOI: 10.1073/pnas.2107339119  0.175
2022 Bhattacharyya S, Duan J, Vela RJ, Bhakta M, Bajona P, Mammen PPA, Hon GC, Munshi NV. Accurate Classification of Cardiomyopathy Diagnosis by Chromatin Accessibility. Circulation. 146: 878-881. PMID 36095061 DOI: 10.1161/CIRCULATIONAHA.122.059659  0.138
2023 Cooley A, Madhukaran S, Stroebele E, Colon Caraballo M, Wang L, Akgul Y, Hon GC, Mahendroo M. Dynamic states of cervical epithelia during pregnancy and epithelial barrier disruption. Iscience. 26: 105953. PMID 36718364 DOI: 10.1016/j.isci.2023.105953  0.136
2021 Duan J, Hon G. FBA: feature barcoding analysis for single cell RNA-Seq. Bioinformatics (Oxford, England). PMID 33999185 DOI: 10.1093/bioinformatics/btab375  0.12
1995 Hon G, Vaziri ND, Kaupke CJ, Tehranzadeh A, Barton C. Lack of a fast-acting effect of erythropoietin on arterial blood pressure and endothelin level. Artificial Organs. 19: 188-91. PMID 7763199 DOI: 10.1111/j.1525-1594.1995.tb02309.x  0.039
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