Network-dosage compensation topologies as recurrent network motifs in natural gene networks. - Ruijie Song; Ping Liu; Murat Acar (BMC Syst. Biol., 2014)

A cell size- and cell cycle-aware stochastic model for predicting time-dynamic gene network activity in individual cells. - Ruijie Song; Weilin Peng; Ping Liu; Murat Acar (BMC Syst. Biol., 2015)

Multi-component gene network design as a survival strategy in diverse environments. - Xinyue Luo; Ruijie Song; Murat Acar (BMC Syst. Biol., 2018)

Stochastic modeling of aging cells reveals how damage accumulation, repair, and cell-division asymmetry affect clonal senescence and population fitness. - Ruijie Song; Murat Acar (BMC Bioinform., 2019)

Analyzing the Impact of Automated User Assistance Systems: A Systematic Review. - Murat Acar; Bedir Tekinerdogan (CoRR, 2020)

scGraPhT: Merging Transformers and Graph Neural Networks for Single-Cell Annotation. - Emirhan Koç; Emre Kulkul; Gülara Kaynar; Tolga Çukur; Murat Acar; Aykut Koç (IEEE Trans. Signal Inf. Process. over Networks, 2025)