Identification of residues of the archaeal RNA-binding Nip7 proteins specific to environmental conditions. - Kirill E. Medvedev; Nikolay A. Kolchanov; Dmitry A. Afonnikov (J. Bioinform. Comput. Biol., 2017)

Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways. - Kirill E. Medvedev; Lisa N. Kinch; R. Dustin Schaeffer; Nick V. Grishin (PLoS Comput. Biol., 2019)

The Potential of Single Cell RNA-Sequencing Data for the Prediction of Gastric Cancer Serum Biomarkers. - Kirill E. Medvedev; Anna V. Savelyeva; Aditya Bagrodia; Nick V. Grishin (ISMCO, 2020)

DisEnrich: database of enriched regions in human dark proteome. - Kirill E. Medvedev; Jimin Pei; Nick V. Grishin (Bioinform., 2022)

ECOD Classification of AFDB 48 Proteomes. - R. Dustin Schaeffer; Jing Zhang 115; Kirill E. Medvedev; Qian Cong; Nick V. Grishin (Zenodo, 2023)

ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2. - R. Dustin Schaeffer; Jing Zhang; Kirill E. Medvedev; Lisa N. Kinch; Qian Cong; Nick V. Grishin (PLoS Comput. Biol., 2024)

Leveraging AI to explore structural contexts of post-translational modifications in drug binding. - Kirill E. Medvedev; R. Dustin Schaeffer; Nick V. Grishin (J. Cheminformatics, 2025)