Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data. - Ridvan Eksi; Hongdong Li; Rajasree Menon; Yuchen Wen; Gilbert S. Omenn; Matthias Kretzler; Yuanfang Guan (PLoS Comput. Biol., 2013)

Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation. - Fan Zhu; Lihong Shi; Hongdong Li; Ridvan Eksi; James Douglas Engel; Yuanfang Guan (Bioinform., 2014)

Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms. - Hongyang Li; Ridvan Eksi; Daiyao Yi; Bradley Godfrey; Lisa R. Mathew; Christopher L. O'Connor; Markus Bitzer; Matthias Kretzler; Rajasree Menon; Yuanfang Guan (PLoS Comput. Biol., 2022)

PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis. - Yan Wu; Esther Wershof; Sebastian M. Schmon; Marcel Nassar; Blazej Osinski; Ridvan Eksi; Kun Zhang; Thore Graepel (CoRR, 2024)