PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. - Vladimir A. Ivanisenko; Sergey S. Pintus; Dmitry A. Grigorovich; Nikolay A. Kolchanov (Nucleic Acids Res., 2004)

WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families. - Vladimir A. Ivanisenko; Alexey M. Eroshkin; Nikolay A. Kolchanov (Nucleic Acids Res., 2005)

PDBSite: a database of the 3D structure of protein functional sites. - Vladimir A. Ivanisenko; Sergey S. Pintus; Dmitry A. Grigorovich; Nikolay A. Kolchanov (Nucleic Acids Res., 2005)

Analysis of Protein Functional Site Distribution on Gene Structure. - Irina Medvedeva; Pavel Demenkov; Vladimir A. Ivanisenko; Nikolay A. Kolchanov (BIOCOMP, 2007)

Phylogenetic Analysis of the p53 and p63/p73 Gene Families. - Sergey S. Pintus; Eduard S. Fomin; Ivan S. Oshurkov; Vladimir A. Ivanisenko (Silico Biol., 2007)

Mathematical Model for Suppression of Subgenomic Hepatitis C Virus RNA Replication in Cell Culture. - Elena L. Mishchenko; Kirill D. Bezmaternykh; Vitali A. Likhoshvai; Alexander V. Ratushny; Tamara M. Khlebodarova; Natalia Yu. Sournina; Vladimir A. Ivanisenko; Nikolay A. Kolchanov (J. Bioinform. Comput. Biol., 2007)

Visualization and Analysis of a Cardio Vascular Disease- and MUPP1-related Biological Network combining Text Mining and Data Warehouse Approaches. - Björn Sommer 001; Evgeny S. Tiys; Benjamin Kormeier; Klaus Hippe; Sebastian Janowski; Timofey V. Ivanisenko; Anatoly O. Bragin; Patrizio Arrigo; Pavel Demenkov; Alexey V. Kochetov; Vladimir A. Ivanisenko; Nikolay A. Kolchanov; et al. (J. Integr. Bioinform., 2010)

Finding biomarkers in non-model species: literature mining of transcription factors involved in bovine embryo development. - Nicolas Turenne; Evgeny S. Tiys; Vladimir A. Ivanisenko; Nikolay Yudin; Elena Ignatieva; Damien Valour; Séverine A. Degrelle; Isabelle Hue (BioData Min., 2012)

ANDVisio: A new tool for graphic visualization and analysis of literature mined associative gene networks in the ANDSystem. - Pavel Demenkov; Timofey V. Ivanisenko; Nikolay A. Kolchanov; Vladimir A. Ivanisenko (Silico Biol., 2012)

SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes. - Irina V. Medvedeva 001; Pavel Demenkov; Nikolay A. Kolchanov; Vladimir A. Ivanisenko (Nucleic Acids Res., 2012)

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)

Subcellular Localization Charts: a New Visual Methodology for the Semi-Automatic Localization of protein-Related Data Sets. - Björn Sommer 001; Benjamin Kormeier; Pavel Demenkov; Patrizio Arrigo; Klaus Hippe; Özgür Ates; Alexey V. Kochetov; Vladimir A. Ivanisenko; Nikolay A. Kolchanov; Ralf Hofestädt (J. Bioinform. Comput. Biol., 2013)

Text Mining on PubMed. - Timofey V. Ivanisenko; Pavel S. Demenkov; Vladimir A. Ivanisenko (Approaches in Integrative Bioinformatics, 2014)

Molecular association of pathogenetic contributors to pre-eclampsia (pre-eclampsia associome). - Andrey S. Glotov; Evgeny S. Tiys; Elena S. Vashukova; Vladimir S. Pakin; Pavel S. Demenkov; Olga V. Saik; Timofey V. Ivanisenko; Olga N. Arzhanova; Elena V. Mozgovaya; Marina S. Zainulina; Nikolay A. Kolchanov; Vladislav S. Baranov; et al. (BMC Syst. Biol., 2015)

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)

Permanent proteins in the urine of healthy humans during the Mars-500 experiment. - Irina M. Larina; Lyudmila Kh. Pastushkova; Evgeny S. Tiys; Kirill S. Kireev; Alexey S. Kononikhin; Natalia L. Starodubtseva; Igor A. Popov; Marc-Antoine Custaud; Igor V. Dobrokhotov; Evgeny N. Nikolaev; Nikolay A. Kolchanov; Vladimir A. Ivanisenko (J. Bioinform. Comput. Biol., 2015)

SITEX 2.0: Projections of protein functional sites on eukaryotic genes. Extension with orthologous genes. - Irina V. Medvedeva 001; Pavel S. Demenkov; Vladimir A. Ivanisenko (J. Bioinform. Comput. Biol., 2017)

A study of structural properties of gene network graphs for mathematical modeling of integrated mosaic gene networks. - Olga V. Petrovskaya; Evgeny D. Petrovskiy; Inna N. Lavrik; Vladimir A. Ivanisenko (J. Bioinform. Comput. Biol., 2017)

Molecular Relationships between Bronchial Asthma and Hypertension as Comorbid Diseases. - Elena Yu. Bragina; Irina A. Goncharova; Anna F. Garaeva; Evgeniy V. Nemerov; Anastasija A. Babovskaya; Andrey B. Karpov; Yulia V. Semenova; Irina Z. Zhalsanova; Densema E. Gomboeva; Olga V. Saik; Olga I. Zolotareva; Vladimir A. Ivanisenko; et al. (J. Integr. Bioinform., 2018)

shRNA-Induced Knockdown of a Bioinformatically Predicted Target IL10 Influences Functional Parameters in Spontaneously Hypertensive Rats with Asthma. - Tatiana Drevytska; Roman Morhachov; Lesya Tumanovska; Georgiy Portnichenko; Vasyl Nagibin; Oleksiy Boldyriev; Tatiana Lapikova-Bryhinska; Veronika Gurianova; Borys Dons'koi; Maxim B. Freidin; Vladimir A. Ivanisenko; Elena Yu. Bragina; et al. (J. Integr. Bioinform., 2018)

Integrative Analysis of Co-Morbid Multifactorial Diseases. - Ralf Hofestädt; Vladimir A. Ivanisenko (J. Integr. Bioinform., 2018)

Search for New Candidate Genes Involved in the Comorbidity of Asthma and Hypertension Based on Automatic Analysis of Scientific Literature. - Olga V. Saik; Pavel S. Demenkov; Timofey V. Ivanisenko; Elena Yu. Bragina; Maxim B. Freidin; Victor E. Dosenko; Olga I. Zolotareva; Evgeniy L. Choynzonov; Ralf Hofestädt; Vladimir A. Ivanisenko (J. Integr. Bioinform., 2018)

GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks. - Alban Shoshi; Ralf Hofestädt; Olga I. Zolotareva; Marcel Friedrichs; Alex Maier; Vladimir A. Ivanisenko; Victor E. Dosenko; Elena Yu. Bragina (J. Integr. Bioinform., 2018)

A new version of the ANDSystem tool for automatic extraction of knowledge from scientific publications with expanded functionality for reconstruction of associative gene networks by considering tissue-specific gene expression. - Vladimir A. Ivanisenko; Pavel S. Demenkov; Timofey V. Ivanisenko; Elena L. Mishchenko; Olga V. Saik (BMC Bioinform., 2019)

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)

Integrating omics databases for enhanced crop breeding. - Haoyu Chao; Shilong Zhang; Yueming Hu; Qingyang Ni; Saige Xin; Liang Zhao; Vladimir A. Ivanisenko; Yuriy L. Orlov; Ming Chen 005 (J. Integr. Bioinform., 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)

Accurate noise-robust classification of Bacillus species from MALDI-TOF MS spectra using a denoising autoencoder. - Yulia E. Uvarova; Pavel S. Demenkov; Irina N. Kuzmicheva; Artur S. Venzel; Elena L. Mischenko; Timofey V. Ivanisenko; Vadim M. Efimov; Svetlana V. Bannikova; Asya R. Vasilieva; Vladimir A. Ivanisenko; Sergey E. Peltek (J. Integr. Bioinform., 2024)