Enhanced Differential Evolution Entirely Parallel Method for Biomedical Applications. - Konstantin Kozlov; Nikita Ivanisenko; Vladimir A. Ivanisenko; Nikolay A. Kolchanov; Maria Samsonova; Alexander M. Samsonov (PaCT, 2013)

ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology. - Vladimir A. Ivanisenko; Olga V. Saik; Nikita V. Ivanisenko; Evgeny S. Tiys; Timofey V. Ivanisenko; Pavel S. Demenkov; Nikolay A. Kolchanov (BMC Syst. Biol., 2015)

ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature. - Timofey V. Ivanisenko; Olga V. Saik; Pavel S. Demenkov; Nikita V. Ivanisenko; Alexander N. Savostyanov; Vladimir A. Ivanisenko (BMC Bioinform., 2020)

PROSTATA: a framework for protein stability assessment using transformers. - Dmitriy Umerenkov; Fedor Nikolaev; Tatiana I Shashkova; Pavel V. Strashnov; Maria Sindeeva; Andrey Shevtsov; Nikita V. Ivanisenko; Olga L. Kardymon (Bioinform., 2023)

Diffusion on language model embeddings for protein sequence generation. - Viacheslav Meshchaninov; Pavel V. Strashnov; Andrey Shevtsov; Fedor Nikolaev; Nikita Ivanisenko; Olga L. Kardymon; Dmitry P. Vetrov (CoRR, 2024)

Reconstruction of the regulatory hypermethylation network controlling hepatocellular carcinoma development during hepatitis C viral infection. - Evgeniya A. Antropova; Tamara M. Khlebodarova; Pavel S. Demenkov; Anastasiia R. Volianskaia; Artur S. Venzel; Nikita V. Ivanisenko; Alexandr D. Gavrilenko; Timofey V. Ivanisenko; Anna V. Adamovskaya; Polina M. Revva; Nikolay A. Kolchanov; Inna N. Lavrik; et al. (J. Integr. Bioinform., 2024)

AFToolkit: a framework for molecular modeling of proteins with AlphaFold-derived representations. - Maria Sindeeva; Alexander Telepov; Nikita Ivanisenko; Tatiana I Shashkova; Kuzma Khrabrov; Artem Tsypin; Artur Kadurin; Olga L. Kardymon (Briefings Bioinform., 2025)