PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem. - Erfan Sadeqi Azer; Farid Rashidi Mehrabadi; Salem Malikic; Xuan Cindy Li; Osnat Bartok; Kevin Litchfield; Ronen Levy; Yardena Samuels; Alejandro A. Schäffer; E. Michael Gertz; Chi-Ping Day; Eva Pérez-Guijarro; et al. (Bioinform., 2020)

Fast intratumor heterogeneity inference from single-cell sequencing data. - Can Kizilkale; Farid Rashidi Mehrabadi; Erfan Sadeqi Azer; Eva Pérez-Guijarro; Kerrie Marie; Maxwell P. Lee; Chi-Ping Day; Glenn Merlino; Funda Ergün; Aydin Buluç; Süleyman Cenk Sahinalp; Salem Malikic (Nat. Comput. Sci., 2022)

Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression. - Bayarbaatar Amgalan; Chi-Ping Day; Teresa M. Przytycka (PLoS Comput. Biol., 2023)

GeneAgent: Self-verification Language Agent for Gene Set Knowledge Discovery using Domain Databases. - Zhizheng Wang; Qiao Jin 001; Chih-Hsuan Wei; Shubo Tian; Po-Ting Lai; Qingqing Zhu; Chi-Ping Day; Christina Ross; Zhiyong Lu (CoRR, 2024)

A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data. - Farid Rashidi Mehrabadi; Erfan Sadeqi Azer; John D. Bridgers; Eva Pérez-Guijarro; Kerrie Marie; Howard H. Yang; Charli Gruen; Chih Hao Wu; Welles Robinson; Huaitian Liu; Can Kizilkale; Michael C. Kelly; et al. (RECOMB, 2025)

Knowledge-guided Contextual Gene Set Analysis Using Large Language Models. - Zhizheng Wang; Chi-Ping Day; Chih-Hsuan Wei; Qiao Jin 001; Robert Leaman; Yifan Yang 006; Shubo Tian; Aodong Qiu; Yin Fang; Qingqing Zhu; Xinghua Lu 001; Zhiyong Lu (CoRR, 2025)