WWWTRRD: Hypertext Information System an Transcription Regulation. - Elena A. Ananko; Elena V. Ignatieva; Alexander E. Kel; Nikolay A. Kolchanov (German Conference on Bioinformatics, 1996)

Lipid Metabolism Transcription Regulatory Regions Database (LM-TRRD). - Elena V. Ignatieva; Alexander E. Kel; Nikolay A. Kolchanov (German Conference on Bioinformatics, 1997)

GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome. - Nikolay A. Kolchanov; Mikhail P. Ponomarenko; Alexander E. Kel; Yury V. Kondrakhin; Anatoly S. Frolov; Fedor A. Kolpakov; T. N. Goryachkovskaya; O. V. Kel; Elena A. Ananko; Elena V. Ignatieva; Olga A. Podkolodnaya; Vladimir N. Babenko; et al. (ISMB, 1998)

Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. - T. Heinemeyer; Edgar Wingender; Ingmar Reuter; Henning Hermjakob; Alexander E. Kel; Olga V. Kel-Margoulis; Elena V. Ignatieva; Elena A. Ananko; Olga A. Podkolodnaya; Fedor A. Kolpakov; Nikolay L. Podkolodny; Nikolay A. Kolchanov (Nucleic Acids Res., 1998)

Integrated databases and computer systems for studying eukaryotic gene expression. - Nikolay A. Kolchanov; Mikhail P. Ponomarenko; Anatoly S. Frolov; Elena A. Ananko; Fedor A. Kolpakov; Elena V. Ignatieva; Olga A. Podkolodnaya; T. N. Goryachkovskaya; Irina L. Stepanenko; Tatyana I. Merkulova; V. V. Babenko; Y. V. Ponomarenko; et al. (Bioinform., 1999)

Transcription Regulatory Regions Database (TRRD): its status in 1999. - Nikolay A. Kolchanov; Elena A. Ananko; Olga A. Podkolodnaya; Elena V. Ignatieva; Irina L. Stepanenko; Olga V. Kel-Margoulis; Alexander E. Kel; Tatyana I. Merkulova; T. N. Goryachkovskaya; T. V. Busygina; Fedor A. Kolpakov; Nikolay L. Podkolodny; et al. (Nucleic Acids Res., 1999)

Transcription Regulatory Regions Database (TRRD): its status in 2000. - Nikolay A. Kolchanov; Olga A. Podkolodnaya; Elena A. Ananko; Elena V. Ignatieva; Irina L. Stepanenko; Olga V. Kel-Margoulis; Alexander E. Kel; Tatyana I. Merkulova; T. N. Goryachkovskaya; T. V. Busygina; Fedor A. Kolpakov; Nikolay L. Podkolodny; et al. (Nucleic Acids Res., 2000)

Gene Networks Description and Modeling in the GeneNet System. - Nikolay A. Kolchanov; Elena A. Ananko; Vitali A. Likhoshvai; Olga A. Podkolodnaya; Elena V. Ignatieva; Alexander V. Ratushny; Yuri G. Matushkin (Gene Regulations and Metabolism, 2002)

GeneNet database: description and modeling of gene networks. - Nikolay A. Kolchanov; Eugenia A. Nedosekina; Elena A. Ananko; Vitali A. Likhoshvai; Nikolay L. Podkolodny; Alexander V. Ratushny; Irina L. Stepanenko; Olga A. Podkolodnaya; Elena V. Ignatieva; Yuri G. Matushkin (Silico Biol., 2002)

GeneNet: a database on structure and functional organisation of gene networks. - Elena A. Ananko; Nikolay L. Podkolodny; Irina L. Stepanenko; Elena V. Ignatieva; Olga A. Podkolodnaya; Nikolay A. Kolchanov (Nucleic Acids Res., 2002)

Transcription Regulatory Regions Database (TRRD): its status in 2002. - Nikolay A. Kolchanov; Elena V. Ignatieva; Elena A. Ananko; Olga A. Podkolodnaya; Irina L. Stepanenko; Tatyana I. Merkulova; Mikhail A. Pozdnyakov; Nikolay L. Podkolodny; Andrey N. Naumochkin; Aida G. Romashchenko (Nucleic Acids Res., 2002)

SITECON: a tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition. - Dmitry Yu. Oshchepkov; Evgenii E. Vityaev 001; Dmitry A. Grigorovich; Elena V. Ignatieva; Tamara M. Khlebodarova (Nucleic Acids Res., 2004)

Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes. - Nikolay A. Kolchanov; Tatyana I. Merkulova; Elena V. Ignatieva; Elena A. Ananko; Dmitry Yu. Oshchepkov; Victor G. Levitsky; Gennady V. Vasiliev; Nataly V. Klimova; Vasily M. Merkulov; T. Charles Hodgman (Briefings Bioinform., 2007)

Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions. - Victor G. Levitsky; Elena V. Ignatieva; Elena A. Ananko; Igor I. Turnaev; Tatyana I. Merkulova; Nikolay A. Kolchanov; T. Charles Hodgman (BMC Bioinform., 2007)

TRRD: Technology for extraction, storage, and use of knowledge about the structural-functional organization of the transcriptional regulatory regions in the eukaryotic genes. - Nikolay A. Kolchanov; Elena V. Ignatieva; Olga A. Podkolodnaya; Elena A. Ananko; Tamara M. Khlebodarova; Irina L. Stepanenko; Tatyana I. Merkulova; Vasily M. Merkulov; Nikolay L. Podkolodny; Aida G. Romashchenko (Intell. Data Anal., 2008)

Genetic algorithm and optimized weight matrix application for peroxisome proliferator response elements recognition: Prerequisites of accuracy growth for wide genome research. - Victor G. Levitsky; Elena V. Ignatieva; Eugenia Aman; Tatyana I. Merkulova; Nikolay A. Kolchanov; T. Charles Hodgman (Intell. Data Anal., 2008)

ExpertDiscovery and UGENE integrated system for intelligent analysis of regulatory regions of genes. - Y. Y. Vaskin; I. V. Khomicheva; Elena V. Ignatieva; Evgenii E. Vityaev 001 (Silico Biol., 2012)

Hidden heterogeneity of transcription factor binding sites: A case study of SF-1. - Victor G. Levitsky; Dmitry Yu. Oshchepkov; Nataly V. Klimova; Elena V. Ignatieva; Gennady V. Vasiliev; Vasily M. Merkulov; Tatyana I. Merkulova (Comput. Biol. Chem., 2016)