Ranking Scientific Publications Using a Simple Model of Network Traffic - Dylan Walker; Huafeng Xie; Koon-Kiu Yan; Sergei Maslov (CoRR, 2006)

Hierarchical analysis of regulatory networks and cross-disciplinary comparison with the Linux call graph. - Koon-Kiu Yan; Mark Gerstein (GENSiPS, 2010)

Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets. - Nitin Bhardwaj; Matthew B. Carson; Alexej Abyzov; Koon-Kiu Yan; Hui Lu 004; Mark B. Gerstein (PLoS Comput. Biol., 2010)

Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data. - Chao Cheng; Koon-Kiu Yan; Woochang Hwang; Jiang Qian; Nitin Bhardwaj; Joel S. Rozowsky; Zhi John Lu; Wei Niu; Pedro Alves; Masaomi Kato; Michael Snyder 001; Mark Gerstein (PLoS Comput. Biol., 2011)

Measuring the Evolutionary Rewiring of Biological Networks. - Chong Shou; Nitin Bhardwaj; Hugo Y. K. Lam; Koon-Kiu Yan; Philip M. Kim; Michael Snyder 001; Mark B. Gerstein (PLoS Comput. Biol., 2011)

Comparative analysis of regulatory information and circuits across distant species Open. - Alan P. Boyle; Carlos L. Araya; Cathleen Brdlik; Philip Cayting; Chao Cheng; Yong Cheng; Kathryn Gardner; LaDeana W. Hillier; Judith Janette; Lixia Jiang; Dionna Kasper; Trupti Kawli; et al. (Nat., 2014)

Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors. - Daifeng Wang; Koon-Kiu Yan; Cristina Sisu; Chao Cheng; Joel S. Rozowsky; William Meyerson; Mark B. Gerstein (PLoS Comput. Biol., 2015)

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps. - Koon-Kiu Yan; Galip Gürkan Yardimci; Chengfei Yan; William S. Noble; Mark Gerstein (Bioinform., 2017)

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions. - Koon-Kiu Yan; Shaoke Lou; Mark Gerstein (PLoS Comput. Biol., 2017)

The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data. - Cheng Ye; Alberto Paccanaro; Mark Gerstein; Koon-Kiu Yan (BMC Bioinform., 2020)