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Items: 23

1.

Measuring the reproducibility and quality of Hi-C data.

Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, Taylor J, Yue F, Dekker J, Noble WS.

Genome Biol. 2019 Mar 19;20(1):57. doi: 10.1186/s13059-019-1658-7.

2.

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors.

Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, Jameel N, Kadaba M, Patton J, Terrell R, Corson M, Durham TJ, Park S, Samanta S, Han M, Xu J, Yan KK, Celniker SE, White KP, Ma L, Gerstein M, Reinke V, Waterston RH.

Genetics. 2018 Mar;208(3):937-949. doi: 10.1534/genetics.117.300657. Epub 2017 Dec 28.

3.

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.

Yan KK, Lou S, Gerstein M.

PLoS Comput Biol. 2017 Jul 24;13(7):e1005647. doi: 10.1371/journal.pcbi.1005647. eCollection 2017 Jul.

4.

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.

Yan KK, Yardimci GG, Yan C, Noble WS, Gerstein M.

Bioinformatics. 2017 Jul 15;33(14):2199-2201. doi: 10.1093/bioinformatics/btx152.

5.

Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs.

Yan KK, Wang D, Sethi A, Muir P, Kitchen R, Cheng C, Gerstein M.

Cell Syst. 2016 Mar 23;2(3):147-157.

6.

Temporal Dynamics of Collaborative Networks in Large Scientific Consortia.

Wang D, Yan KK, Rozowsky J, Pan E, Gerstein M.

Trends Genet. 2016 May;32(5):251-253. doi: 10.1016/j.tig.2016.02.006. Epub 2016 Mar 20.

PMID:
27005445
7.

Loregic: a method to characterize the cooperative logic of regulatory factors.

Wang D, Yan KK, Sisu C, Cheng C, Rozowsky J, Meyerson W, Gerstein MB.

PLoS Comput Biol. 2015 Apr 17;11(4):e1004132. doi: 10.1371/journal.pcbi.1004132. eCollection 2015 Apr.

8.

An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome.

Cheng C, Andrews E, Yan KK, Ung M, Wang D, Gerstein M.

Genome Biol. 2015 Mar 31;16:63. doi: 10.1186/s13059-015-0624-2.

9.

OrthoClust: an orthology-based network framework for clustering data across multiple species.

Yan KK, Wang D, Rozowsky J, Zheng H, Cheng C, Gerstein M.

Genome Biol. 2014 Aug 28;15(8):R100. doi: 10.1186/gb-2014-15-8-r100.

10.

Comparative analysis of regulatory information and circuits across distant species.

Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M.

Nature. 2014 Aug 28;512(7515):453-6. doi: 10.1038/nature13668.

11.

Comparative analysis of the transcriptome across distant species.

Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R.

Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424.

12.

Cellular superspreaders: an epidemiological perspective on HIV infection inside the body.

Talbert-Slagle K, Atkins KE, Yan KK, Khurana E, Gerstein M, Bradley EH, Berg D, Galvani AP, Townsend JP.

PLoS Pathog. 2014 May 8;10(5):e1004092. doi: 10.1371/journal.ppat.1004092. eCollection 2014 May. No abstract available.

13.

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M.

Genome Res. 2012 Sep;22(9):1658-67. doi: 10.1101/gr.136838.111.

14.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

15.

Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data.

Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M.

PLoS Comput Biol. 2011 Nov;7(11):e1002190. doi: 10.1371/journal.pcbi.1002190. Epub 2011 Nov 17.

16.

The spread of scientific information: insights from the web usage statistics in PLoS article-level metrics.

Yan KK, Gerstein M.

PLoS One. 2011;6(5):e19917. doi: 10.1371/journal.pone.0019917. Epub 2011 May 16.

17.

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets.

Cheng C, Yan KK, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M.

Genome Biol. 2011;12(2):R15. doi: 10.1186/gb-2011-12-2-r15. Epub 2011 Feb 16.

18.

Measuring the evolutionary rewiring of biological networks.

Shou C, Bhardwaj N, Lam HY, Yan KK, Kim PM, Snyder M, Gerstein MB.

PLoS Comput Biol. 2011 Jan 6;7(1):e1001050. doi: 10.1371/journal.pcbi.1001050.

19.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X; modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH.

Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22. Erratum in: Science. 2011 Jan 7;331(6013):30.

20.

Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets.

Bhardwaj N, Carson MB, Abyzov A, Yan KK, Lu H, Gerstein MB.

PLoS Comput Biol. 2010 May 27;6(5):e1000755. doi: 10.1371/journal.pcbi.1000755.

21.

Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks.

Yan KK, Fang G, Bhardwaj N, Alexander RP, Gerstein M.

Proc Natl Acad Sci U S A. 2010 May 18;107(20):9186-91. doi: 10.1073/pnas.0914771107. Epub 2010 May 3.

22.

Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels.

Bhardwaj N, Yan KK, Gerstein MB.

Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6841-6. doi: 10.1073/pnas.0910867107. Epub 2010 Mar 29.

23.

Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data.

Yip KY, Alexander RP, Yan KK, Gerstein M.

PLoS One. 2010 Jan 26;5(1):e8121. doi: 10.1371/journal.pone.0008121.

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