Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types. - Ke Chen; Amitesh Anand; Connor A. Olson; Troy E. Sandberg; Ye Gao 005; Nathan Mih; Bernhard O. Palsson (PLoS Comput. Biol., 2021)

proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. - Katherine Decker; Ye Gao 005; Kevin Rychel; Tahani Al Bulushi; Siddharth M. Chauhan; Donghyuk Kim; Byung-Kwan Cho; Bernhard O. Palsson (Nucleic Acids Res., 2022)

Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling. - Ina Bang; Sang-Mok Lee; Seojoung Park; Joon Young Park; Linh Khanh Nong; Ye Gao 005; Bernhard O. Palsson; Donghyuk Kim (Briefings Bioinform., 2023)