BiologicalNetworks 2.0 - an integrative view of genome biology data. - Sergey Kozhenkov; Yulia Dubinina; Mayya Sedova; Amarnath Gupta; Julia V. Ponomarenko; Michael Baitaluk (BMC Bioinform., 2010)

BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies. - Sergey Kozhenkov; Mayya Sedova; Yulia Dubinina; Amarnath Gupta; Animesh Ray; Julia V. Ponomarenko; Michael Baitaluk (BMC Syst. Biol., 2011)

Continuous Analysis: Evolution of Software Engineering and Reproducibility for Science. - Venkat S. Malladi; Maria Yazykova; Olesya Melnichenko; Yulia Dubinina (CoRR, 2024)

BioAgents: Democratizing Bioinformatics Analysis with Multi-Agent Systems. - Nikita Mehandru; Amanda K. Hall; Olesya Melnichenko; Yulia Dubinina; Daniel Tsirulnikov; David Bamman; Ahmed M. Alaa; T. Scott Saponas; Venkat S. Malladi (CoRR, 2025)