• 21667 Citations
  • 27 h-Index
20042019

Research output per year

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Research Output

  • 21667 Citations
  • 27 h-Index
  • 34 Article
  • 2 Comment/debate
  • 1 Chapter
  • 1 Review article
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Article
2004

The ASTRAL Compendium in 2004

Chandonia, J. M., Hon, G., Walker, N. S., Lo Conte, L., Koehl, P., Levitt, M. & Brenner, S. E., Jan 1 2004, In : Nucleic Acids Research. 32, DATABASE ISS.

Research output: Contribution to journalArticle

456 Scopus citations

WebLogo: A sequence logo generator

Crooks, G. E., Hon, G., Chandonia, J. M. & Brenner, S. E., Jun 1 2004, In : Genome Research. 14, 6, p. 1188-1190 3 p.

Research output: Contribution to journalArticle

5992 Scopus citations
2006

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B. J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., Stark, C., Ho, Y., Botstein, D., Andrews, B., Boone, C., Troyanskya, O. G., Ideker, T., Dolinski, K., Batada, N. N. & Tyers, M., Dec 1 2006, In : Journal of Biology. 5, 11.

Research output: Contribution to journalArticle

255 Scopus citations
2007

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., Wang, W., Weng, Z., Green, R. D., Crawford, G. E. & Ren, B., Mar 1 2007, In : Nature Genetics. 39, 3, p. 311-318 8 p.

Research output: Contribution to journalArticle

1947 Scopus citations

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigó, R., Gingeras, T. R., Margulies, E. H., Weng, Z., Snyder, M., Dermitzakis, E. T., Thurman, R. E., Kuehn, M. S., Taylor, C. M., Neph, S., Koch, C. M., Asthana, S., Malhotra, A., Adzhubei, I., Greenbaum, J. A., Andrews, R. M., Flicek, P. & 291 others, Boyle, P. J., Cao, H., Carter, N. P., Clelland, G. K., Davis, S., Day, N., Dhami, P., Dillon, S. C., Dorschner, M. O., Fiegler, H., Giresi, P. G., Goldy, J., Hawrylycz, M., Haydock, A., Humbert, R., James, K. D., Johnson, B. E., Johnson, E. M., Frum, T. T., Rosenzweig, E. R., Karnani, N., Lee, K., Lefebvre, G. C., Navas, P. A., Neri, F., Parker, S. C. J., Sabo, P. J., Sandstrom, R., Shafer, A., Vetrie, D., Weaver, M., Wilcox, S., Yu, M., Collins, F. S., Dekker, J., Lieb, J. D., Tullius, T. D., Crawford, G. E., Sunyaev, S., Noble, W. S., Dunham, I., Denoeud, F., Reymond, A., Kapranov, P., Rozowsky, J., Zheng, D., Castelo, R., Frankish, A., Harrow, J., Ghosh, S., Sandelin, A., Hofacker, I. L., Baertsch, R., Keefe, D., Dike, S., Cheng, J., Hirsch, H. A., Sekinger, E. A., Lagarde, J., Abril, J. F., Shahab, A., Flamm, C., Fried, C., Hackermüller, J., Hertel, J., Lindemeyer, M., Missal, K., Tanzer, A., Washietl, S., Korbel, J., Emanuelsson, O., Pedersen, J. S., Holroyd, N., Taylor, R., Swarbreck, D., Matthews, N., Dickson, M. C., Thomas, D. J., Weirauch, M. T., Gilbert, J., Drenkow, J., Bell, I., Zhao, X., Srinivasan, K. G., Sung, W. K., Ooi, H. S., Chiu, K. P., Foissac, S., Alioto, T., Brent, M., Pachter, L., Tress, M. L., Valencia, A., Choo, S. W., Choo, C. Y., Ucla, C., Manzano, C., Wyss, C., Cheung, E., Clark, T. G., Brown, J. B., Ganesh, M., Patel, S., Tammana, H., Chrast, J., Henrichsen, C. N., Kai, C., Kawai, J., Nagalakshmi, U., Wu, J., Lian, Z., Lian, J., Newburger, P., Zhang, X., Bickel, P., Mattick, J. S., Carninci, P., Hayashizaki, Y., Weissman, S., Hubbard, T., Myers, R. M., Rogers, J., Stadler, P. F., Lowe, T. M., Wei, C. L., Ruan, Y., Struhl, K., Gerstein, M., Antonarakis, S. E., Fu, Y., Green, E. D., Karaöz, U., Siepel, A., Taylor, J., Liefer, L. A., Wetterstrand, K. A., Good, P. J., Feingold, E. A., Guyer, M. S., Cooper, G. M., Asimenos, G., Dewey, C. N., Hou, M., Nikolaev, S., Montoya-Burgos, J. I., Löytynoja, A., Whelan, S., Pardi, F., Massingham, T., Huang, H., Zhang, N. R., Holmes, I., Mullikin, J. C., Ureta-Vidal, A., Paten, B., Seringhaus, M., Church, D., Rosenbloom, K., Kent, W. J., Stone, E. A., Batzoglou, S., Goldman, N., Hardison, R. C., Haussler, D., Miller, W., Sidow, A., Trinklein, N. D., Zhang, Z. D., Barrera, L., Stuart, R., King, D. C., Ameur, A., Enroth, S., Bieda, M. C., Kim, J., Bhinge, A. A., Jiang, N., Liu, J., Yao, F., Vega, V. B., Lee, C. W. H., Ng, P., Yang, A., Moqtaderi, Z., Zhu, Z., Xu, X., Squazzo, S., Oberley, M. J., Inman, D., Singer, M. A., Richmond, T. A., Munn, K. J., Rada-Iglesias, A., Wallerman, O., Komorowski, J., Fowler, J. C., Couttet, P., Bruce, A. W., Dovey, O. M., Ellis, P. D., Langford, C. F., Nix, D. A., Euskirchen, G., Hartman, S., Urban, A. E., Kraus, P., Van Calcar, S., Heintzman, N., Hoon Kim, T., Wang, K., Qu, C., Hon, G., Luna, R., Glass, C. K., Rosenfeld, M. G., Aldred, S. F., Cooper, S. J., Halees, A., Lin, J. M., Shulha, H. P., Zhang, X., Xu, M., Haidar, J. N. S., Yu, Y., Iyer, V. R., Green, R. D., Wadelius, C., Farnham, P. J., Ren, B., Harte, R. A., Hinrichs, A. S., Trumbower, H., Clawson, H., Hillman-Jackson, J., Zweig, A. S., Smith, K., Thakkapallayil, A., Barber, G., Kuhn, R. M., Karolchik, D., Armengol, L., Bird, C. P., De Bakker, P. I. W., Kern, A. D., Lopez-Bigas, N., Martin, J. D., Stranger, B. E., Woodroffe, A., Davydov, E., Dimas, A., Eyras, E., Hallgrímsdóttir, I. B., Huppert, J., Zody, M. C., Abecasis, G. R., Estivill, X., Bouffard, G. G., Guan, X., Hansen, N. F., Idol, J. R., Maduro, V. V. B., Maskeri, B., McDowell, J. C., Park, M., Thomas, P. J., Young, A. C., Blakesley, R. W., Muzny, D. M., Sodergren, E., Wheeler, D. A., Worley, K. C., Jiang, H., Weinstock, G. M., Gibbs, R. A., Graves, T., Fulton, R., Mardis, E. R., Wilson, R. K., Clamp, M., Cuff, J., Gnerre, S., Jaffe, D. B., Chang, J. L., Lindblad-Toh, K., Lander, E. S., Koriabine, M., Nefedov, M., Osoegawa, K., Yoshinaga, Y., Zhu, B. & De Jong, P. J., Jun 14 2007, In : Nature. 447, 7146, p. 799-816 18 p.

Research output: Contribution to journalArticle

3568 Scopus citations
2008

ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome

Hon, G., Ren, B. & Wang, W., Oct 1 2008, In : PLoS Computational Biology. 4, 10, e1000201.

Research output: Contribution to journalArticle

106 Scopus citations
2009

Discovery and annotation of functional chromatin signatures in the human genome

Hon, G., Wang, W. & Ren, B., Nov 1 2009, In : PLoS Computational Biology. 5, 11, e1000566.

Research output: Contribution to journalArticle

125 Scopus citations

Histone modifications at human enhancers reflect global cell-type-specific gene expression

Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., Ching, K. A., Antosiewicz-Bourget, J. E., Liu, H., Zhang, X., Green, R. D., Lobanenkov, V. V., Stewart, R., Thomson, J. A., Crawford, G. E., Kellis, M. & 1 others, Ren, B., May 7 2009, In : Nature. 459, 7243, p. 108-112 5 p.

Research output: Contribution to journalArticle

1466 Scopus citations

Human DNA methylomes at base resolution show widespread epigenomic differences

Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q. M., Edsall, L., Antosiewicz-Bourget, J., Stewart, R., Ruotti, V., Millar, A. H., Thomson, J. A., Ren, B. & Ecker, J. R., Nov 19 2009, In : Nature. 462, 7271, p. 315-322 8 p.

Research output: Contribution to journalArticle

2705 Scopus citations

Predictive chromatin signatures in the mammalian genome

Hon, G. C., Hawkins, R. D. & Ren, B., Oct 15 2009, In : Human Molecular Genetics. 18, R2

Research output: Contribution to journalArticle

153 Scopus citations
2010

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells

Hawkins, R. D., Hon, G. C., Lee, L. K., Ngo, Q., Lister, R., Pelizzola, M., Edsall, L. E., Kuan, S., Luu, Y., Klugman, S., Antosiewicz-Bourget, J., Ye, Z., Espinoza, C., Agarwahl, S., Shen, L., Ruotti, V., Wang, W., Stewart, R., Thomson, J. A., Ecker, J. R. & 1 others, Ren, B., May 7 2010, In : Cell Stem Cell. 6, 5, p. 479-491 13 p.

Research output: Contribution to journalArticle

508 Scopus citations
2011

Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency

Hawkins, R. D., Hon, G. C., Yang, C., Antosiewicz-Bourget, J. E., Lee, L. K., Ngo, Q. M., Klugman, S., Ching, K. A., Edsall, L. E., Ye, Z., Kuan, S., Yu, P., Liu, H., Zhang, X., Green, R. D., Lobanenkov, V. V., Stewart, R., Thomson, J. A. & Ren, B., Oct 1 2011, In : Cell Research. 21, 10, p. 1393-1409 17 p.

Research output: Contribution to journalArticle

69 Scopus citations

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

Lister, R., Pelizzola, M., Kida, Y. S., Hawkins, R. D., Nery, J. R., Hon, G., Antosiewicz-Bourget, J., Ogmalley, R., Castanon, R., Klugman, S., Downes, M., Yu, R., Stewart, R., Ren, B., Thomson, J. A., Evans, R. M. & Ecker, J. R., Mar 3 2011, In : Nature. 471, 7336, p. 68-73 6 p.

Research output: Contribution to journalArticle

1052 Scopus citations
2012

Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome

Yu, M., Hon, G. C., Szulwach, K. E., Song, C. X., Zhang, L., Kim, A., Li, X., Dai, Q., Shen, Y., Park, B., Min, J. H., Jin, P., Ren, B. & He, C., Jun 8 2012, In : Cell. 149, 6, p. 1368-1380 13 p.

Research output: Contribution to journalArticle

632 Scopus citations

CBX3 regulates efficient RNA processing genome-wide

Smallwood, A., Hon, G. C., Jin, F., Henry, R. E., Espinosa, J. M. & Ren, B., Aug 1 2012, In : Genome Research. 22, 8, p. 1426-1436 11 p.

Research output: Contribution to journalArticle

51 Scopus citations

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

Hon, G. C., Hawkins, R. D., Caballero, O. L., Lo, C., Lister, R., Pelizzola, M., Valsesia, A., Ye, Z., Kuan, S., Edsall, L. E., Camargo, A. A., Stevenson, B. J., Ecker, J. R., Bafna, V., Strausberg, R. L., Simpson, A. J. & Ren, B., Feb 1 2012, In : Genome Research. 22, 2, p. 246-258 13 p.

Research output: Contribution to journalArticle

299 Scopus citations

Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine

Yu, M., Hon, G. C., Szulwach, K. E., Song, C. X., Jin, P., Ren, B. & He, C., Dec 1 2012, In : Nature Protocols. 7, 12, p. 2159-2170 12 p.

Research output: Contribution to journalArticle

140 Scopus citations
2013

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

Hon, G. C., Rajagopal, N., Shen, Y., McCleary, D. F., Yue, F., Dang, M. D. & Ren, B., Oct 1 2013, In : Nature Genetics. 45, 10, p. 1198-1206 9 p.

Research output: Contribution to journalArticle

241 Scopus citations

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis

Chang, K. N., Zhong, S., Weirauch, M. T., Hon, G., Pelizzola, M., Li, H., Carol Huang, S. S., Schmitz, R. J., Urich, M. A., Kuo, D., Nery, J. R., Qiao, H., Yang, A., Jamali, A., Chen, H., Ideker, T., Ren, B., Bar-Joseph, Z., Hughes, T. R. & Ecker, J. R., Jun 11 2013, In : eLife. 2013, 2, e00675.

Research output: Contribution to journalArticle

167 Scopus citations

Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing

Zhang, L., Szulwach, K. E., Hon, G. C., Song, C. X., Park, B., Yu, M., Lu, X., Dai, Q., Wang, X., Street, C. R., Tan, H., Min, J. H., Ren, B., Jin, P. & He, C., Mar 11 2013, In : Nature Communications. 4, 1517.

Research output: Contribution to journalArticle

34 Scopus citations
2014

5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation

Hon, G. C., Song, C. X., Du, T., Jin, F., Selvaraj, S., Lee, A. Y., Yen, C. A., Ye, Z., Mao, S. Q., Wang, B. A., Kuan, S., Edsall, L. E., Zhao, B. S., Xu, G. L., He, C. & Ren, B., Jan 1 2014, In : Molecular Cell. 56, 2, p. 286-297 12 p.

Research output: Contribution to journalArticle

143 Scopus citations

N 6-methyladenosine-dependent regulation of messenger RNA stability

Wang, X., Lu, Z., Gomez, A., Hon, G. C., Yue, Y., Han, D., Fu, Y., Parisien, M., Dai, Q., Jia, G., Ren, B., Pan, T. & He, C., Jan 1 2014, In : Nature. 505, 7481, p. 117-120 4 p.

Research output: Contribution to journalArticle

799 Scopus citations
2015

EGFR Mutation Promotes Glioblastoma through Epigenome and Transcription Factor Network Remodeling

Liu, F., Hon, G. C., Villa, G. R., Turner, K. M., Ikegami, S., Yang, H., Ye, Z., Li, B., Kuan, S., Lee, A. Y., Zanca, C., Wei, B., Lucey, G., Jenkins, D., Zhang, W., Barr, C. L., Furnari, F. B., Cloughesy, T. F., Yong, W. H., Gahman, T. C. & 4 others, Shiau, A. K., Cavenee, W. K., Ren, B. & Mischel, P. S., Oct 15 2015, In : Molecular Cell. 60, 2, p. 307-318 12 p.

Research output: Contribution to journalArticle

73 Scopus citations
2016

An LXR-Cholesterol Axis Creates a Metabolic Co-Dependency for Brain Cancers

Villa, G. R., Hulce, J. J., Zanca, C., Bi, J., Ikegami, S., Cahill, G. L., Gu, Y., Lum, K. M., Masui, K., Yang, H., Rong, X., Hong, C., Turner, K. M., Liu, F., Hon, G. C., Jenkins, D., Martini, M., Armando, A. M., Quehenberger, O., Cloughesy, T. F. & 7 others, Furnari, F. B., Cavenee, W. K., Tontonoz, P., Gahman, T. C., Shiau, A. K., Cravatt, B. F. & Mischel, P. S., Nov 14 2016, In : Cancer Cell. 30, 5, p. 683-693 11 p.

Research output: Contribution to journalArticle

70 Scopus citations
2017

Heme enables proper positioning of Drosha and DGCR8 on primary microRNAs

Partin, A. C., Ngo, T. D., Herrell, E., Jeong, B. C., Hon, G. & Nam, Y., Dec 1 2017, In : Nature Communications. 8, 1, 1737.

Research output: Contribution to journalArticle

13 Scopus citations

In Situ Capture of Chromatin Interactions by Biotinylated dCas9

Liu, X., Zhang, Y., Chen, Y., Li, M., Zhou, F., Li, K., Cao, H., Ni, M., Liu, Y., Gu, Z., Dickerson, K. E., Xie, S., Hon, G. C., Xuan, Z., Zhang, M. Q., Shao, Z. & Xu, J., Aug 24 2017, In : Cell. 170, 5, p. 1028-1043.e19

Research output: Contribution to journalArticle

64 Scopus citations

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells

Xie, S., Duan, J., Li, B., Zhou, P. & Hon, G. C., Apr 20 2017, In : Molecular Cell. 66, 2, p. 285-299.e5

Research output: Contribution to journalArticle

61 Scopus citations
2018

A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra

Henry, G. H., Malewska, A., Joseph, D. B., Malladi, V. S., Lee, J., Torrealba, J. R., Mauck, R., Gahan, J., Raj, G., Roehrborn, C., Hon, G., MacConmara, M. P., Reese, J. C., Hutchinson, R. C., Vezina, C. M. & Strand, D. W., Dec 18 2018, In : Cell Reports. 25, 12, p. 3530-3542.e5

Research output: Contribution to journalArticle

8 Scopus citations

Frequent sgRNA-barcode recombination in single-cell perturbation assays

Xie, S., Cooley, A., Armendariz, D., Zhou, P. & Hon, G. C., Jun 1 2018, In : PLoS One. 13, 6, e0198635.

Research output: Contribution to journalArticle

11 Scopus citations

Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult mice

Hepler, C., Shan, B., Zhang, Q., Henry, G. H., Shao, M., Vishvanath, L., Ghaben, A. L., Mobley, A. B., Strand, D. W., Hon, G. & Gupta, R. K., Sep 28 2018, In : eLife. 7

Research output: Contribution to journalArticle

23 Scopus citations
2019

Experimental and Computational Approaches for Single-Cell Enhancer Perturbation Assay

Xie, S. & Hon, G., Jan 1 2019, In : Methods in molecular biology (Clifton, N.J.). 1935, p. 203-221 19 p.

Research output: Contribution to journalArticle

1 Scopus citations

Rational Reprogramming of Cellular States by Combinatorial Perturbation

Duan, J., Li, B., Bhakta, M., Xie, S., Zhou, P., Munshi, N. V. & Hon, G., Jun 18 2019, In : Cell Reports. 27, 12, p. 3486-3499.e6

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Scina: Semi-supervised analysis of single cells in silico

Zhang, Z., Luo, D., Zhong, X., Choi, J. H., Ma, Y., Wang, S., Mahrt, E., Guo, W., Stawiski, E. W., Modrusan, Z., Seshagiri, S., Kapur, P., Hon, G. C., Brugarolas, J. & Wang, T., Jul 1 2019, In : Genes. 10, 7, 531.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Using Gjd3-CreEGFP mice to examine atrioventricular node morphology and composition

Bhattacharyya, S., Duan, J., Wang, L., Li, B., Bhakta, M., Fernandez-Perez, A., Hon, G. & Munshi, N. V., Dec 1 2019, In : Scientific Reports. 9, 1, 2106.

Research output: Contribution to journalArticle