Publications:
  • Yan KK and Gerstein M. MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions. bioRxiv doi: https://doi.org/10.1101/097345.
  • Yan KK, Galip Gürkan Yardımcı, William S Noble and Gerstein M. HiC-Spector: a matrix library for spectral analysis and reproducibility of Hi-C contact maps. bioRxiv doi: 10.1101/088922.
  • Yan KK, Wang D, Sethi A, Muir P, Kitchen R, Cheng C, Gerstein M. Matchmaking between hairballs – insights from cross-disciplinary network comparison. Cell Systems 2016 Mar 23; 2(3):147-157.
  • Wang D, Yan KK, Rozowsky J, Pan E, Gerstein M. Temporal dynamics of collaborative networks driven by large scientific consortia. Trends in Genetics 2016 May;32(5):251-3.
  • Cheng C, Andrews E, Yan KK, Ung M, Wang D, Gerstein M. An Approach for Determining and Measuring Network Hierarchy: Application to Comparing the Phosphorylome and the Regulome. Genome Biol. 16:63.
  • Wang D, Yan KK, Cheng C, Rozowsky J, Gerstein M. Loregic – A method to characterize the cooperative logic of regulatory factors. PLoS Comput Biol. 2015 Apr 17; 11(4):e1004132.
  • Yan KK*, Wang D*, Rozowsky J, Zheng H, Cheng C, and Gerstein M. (2014). OrthoClust: an orthology-based network framework for clustering data across multiple species. Genome Biol. 15, R100.
  • Gerstein M*, Rozowsky J*, Yan KK*, Wang D*, Cheng C*, Brown JB*, Davis, C.A., Hillier, L., Sisu, C., Li, J.J., et al. (2014). Comparative analysis of the transcriptome across distant species. Nature 512, 445–448.
  • Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier L, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, 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, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M and the modENCODE and ENCODE Consortia. (2014). Comparative analysis of regulatory information and circuits across distant species. Nature 512, 453–456.
  • Talbert-Slagle K, Atkins KE, Yan KK, Khurana E, Gerstein M, Bradley EH, Berg D, Galvani AP, and Townsend JP (2014). Cellular Superspreaders: An Epidemiological Perspective on HIV Infection inside the Body. PLoS Pathog 10, e1004092.
  • Gerstein M*, Kundaje A*, Hariharan M*, Landt S*, 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, Euskirche. G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P,Kasowski M, Lacroute P, Leng J, 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. (2012). Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91–100.   
  • 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 (2012). Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res. 2012 Sep; 22(9): 1658-67.
  • ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6; 489(7414): 57-74.
  • Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M (2011) Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PLoS Comput Biol. 2011 Nov 7; (11): e1002190.
  • Yan KK, Gerstein M (2011) The spread of scientific information: insights from the web usage statistics in PLoS article-level metrics. PLoS One. 2011; 6(5): e19917
  • ENCODE Project Consortium (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4): e1001046.
  • Cheng C, Yan KK, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M (2011) A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biol. 2011; 12(2): R15.
  • Shou C, Bhardwaj N, Lam HY, Yan KK, Kim PM, Snyder M, Gerstein M (2011) Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol. 2011 Jan 6; 7(1): e1001050.
  • 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. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010 Dec 24; 330(6012): 1775-87.
  • Bhardwaj N, Carson MB, Abyzov A, Yan KK, Lu H, Gerstein M (2010) Analysis of combinatorial regulation: scaling of partnership between regulators with the number of governed targets. PLoS Comput Biol. 2010 May 27; 6(5): e1000755.
  • Yan KK, Fang G, Bhardwaj N, Alexander RP, Gerstein M (2010) Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Proc Natl Acad Sci USA. 2010 May 18; 107(20): 9186-91.
  • Bhardwaj N, Yan KK, Gerstein M (2010) Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels. Proc Natl Acad Sci USA. 2010 Apr 13; 107(15): 6841-6.
  • Yip KY, Alexander RP, Yan KK, Gerstein M (2010) Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data. PLoS One. 2010 Jan 26; 6(1): e8121.
  • Yan KK, Walker D, Maslov S (2008) Fluctuations in mass-action equilibrium of protein binding networks. Phys. Rev. Lett. 2008 Dec 31; 101 (26): 2681902.
  • Axelsen JP, Yan KK, Maslov S (2007) Parameters of the proteome evolution from the histogram of sequence identities of paralogous proteins. Biol Direct. 2007 Nov 26; 2-32.
  • Walker D, Xie H, Yan KK, Maslov S (2007) Ranking scientific publications using a model of network traffic. Journal of Statistical Mechanics: Theory and Experiment 2007: P06010.
  • Xie H, Yan KK, Maslov S (2007) Optimal ranking in networks with community structure. Physica A 373, 831.
  • Maslov S, Sneppen K, Eriksen KA, Yan KK (2004) Upstream Plasticity and Downstream Robustness in Evolution of Molecular Networks. BMC Evol Biol. 2004 Mar 8; 4:9.
  • Chau HF, Xu H, Lee KM, Siu LW Yan KK (2002) Finding the Sign of a Function Value by Binary Cellular Automation. International Journal of Modern Physics C: Physics and Computers, 2002, v. 13 p. 1347-1364.
  • Chau HF, Siu LW, Yan KK (1999) One Dimensional Nary Density Classification Using Two Cellular Automaton Rules. International Journal of Modern Physics C: Physics and Computers, 1999, v. 10 p. 883-889.
  • Chau HF, Yan KK, Wan KY, Siu LW (1998) Classifying Rational Densities using Two One-Dimensional Cellular Automata. Phys. Rev. E 57, 1367.
  • Chau HF, Wan KY, Yan KK (1998) An Improved Upper Bound for the Critical Car Density of the Two-Dimensional Biham-Middleton-Levine Traffic Model. Physica A 254, 117-121.
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