Finding steady states of large scale regulatory networks through partitioning. - Ferhat Ay; Günhan Gülsoy; Tamer Kahveci (GENSiPS, 2010)

Topology aware coloring of gene regulatory networks. - Günhan Gülsoy; Bhavik Gandhi; Tamer Kahveci (BCB, 2011)

RINQ: Reference-based Indexing for Network Queries. - Günhan Gülsoy; Tamer Kahveci (Bioinform., 2011)

Inferring gene functions from metabolic reactions. - Günhan Gülsoy; Tamer Kahveci (GENSiPS, 2012)

HIDEN: Hierarchical decomposition of regulatory networks. - Günhan Gülsoy; Nirmalya Bandyopadhyay; Tamer Kahveci (BMC Bioinform., 2012)

Topac: Alignment of gene Regulatory Networks Using Topology-Aware Coloring. - Günhan Gülsoy; Bhavik Gandhi; Tamer Kahveci (J. Bioinform. Comput. Biol., 2012)

Topologically associating domains are stable units of replication-timing regulation Open. - Benjamin D. Pope; Tyrone Ryba; Vishnu Dileep; Feng Yue; Wei-Sheng Wu; Olgert Denas; Daniel L. Vera; Yanli Wang; R. Scott Hansen; Theresa K. Canfield; Robert E. Thurman; Yong Cheng; et al. (Nat., 2014)