Detecting direct correlations between positions in multiple alignments of amino acid sequences. - Dmitry A. Afonnikov; Yury V. Kondrakhin; Igor I. Titov; Nikolay A. Kolchanov (German Conference on Bioinformatics, 1997)

Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions. - Dmitry A. Afonnikov; Dmitry Yu. Oshchepkov; Nikolay A. Kolchanov (Bioinform., 2001)

ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro. - Vadim P. Valuev; Dmitry A. Afonnikov; Mikhail P. Ponomarenko; Luciano Milanesi; Nikolay A. Kolchanov (Nucleic Acids Res., 2002)

CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences. - Dmitry A. Afonnikov; Nikolay A. Kolchanov (Nucleic Acids Res., 2004)

The Location of the Gene Regions Under Selective Pressure: Plato Algorithm Parallelization. - Yuri Vyatkin; Konstantin V. Gunbin; Alexey V. Snytnikov; Dmitry A. Afonnikov (PaCT, 2007)

The Evolution of the Hh-Signaling Pathway Genes: A Computer-Assisted Study. - Konstantin V. Gunbin; Dmitry A. Afonnikov; Nikolay A. Kolchanov (Silico Biol., 2007)

Computer System for Analysis of Molecular Evolution Modes (SAMEM): Analysis of molecular evolution modes at deep inner branches of the phylogenetic tree. - Konstantin V. Gunbin; Valentin V. Suslov; Mikhail A. Genaev; Dmitry A. Afonnikov (Silico Biol., 2012)

Computer and Statistical Analysis of Transcription Factor Binding and Chromatin Modifications by ChIP-seq data in Embryonic Stem Cell. - Yuriy L. Orlov; Han Xu; Dmitry A. Afonnikov; Bing Lim; Jian-Chien Heng; Ping Yuan; Ming Chen 005; Junli Yan; Neil D. Clarke; Nina Orlova; Mikael Huss; Konstantin V. Gunbin; et al. (J. Integr. Bioinform., 2012)

Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles. - Zakhar S. Mustafin; Sergey A. Lashin; Yury G. Matushkin; Konstantin V. Gunbin; Dmitry A. Afonnikov (BMC Bioinform., 2017)

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)