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)

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)

Mining Genome Variation to Associate Disease with Transcription Factor Binding Site Alteration. - Julia V. Ponomarenko; Tatyana I. Merkulova; Galina Orlova; Elena Gorshkova; Oleg N. Fokin; Mikhail P. Ponomarenko (BIBE, 2001)

Mining SNPs for Associating Disease Penetration with Transcription Factor Binding Site Alterations. - Julia V. Ponomarenko; Tatyana I. Merkulova; Galina Orlova; Oleg N. Fokin; Elena Gorshkova; Mikhail P. Ponomarenko (German Conference on Bioinformatics, 2001)

rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations. - Julia V. Ponomarenko; Tatyana I. Merkulova; Gennady V. Vasiliev; Zoya B. Levashova; Galina Orlova; Sergey V. Lavryushev; Oleg N. Fokin; Mikhail P. Ponomarenko; Anatoly S. Frolov; Akinori Sarai (Nucleic Acids Res., 2001)

Mining DNA sequences to predict sites which mutations cause genetic diseases. - Julia V. Ponomarenko; Tatyana I. Merkulova; Galina Orlova; Oleg N. Fokin; Elena Gorshkova; Mikhail P. Ponomarenko (Knowl. Based Syst., 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)

rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation. - Julia V. Ponomarenko; Tatyana I. Merkulova; Galina Orlova; Oleg N. Fokin; Elena Gorshkova; Anatoly S. Frolov; Vadim P. Valuev; Mikhail P. Ponomarenko (Nucleic Acids Res., 2003)

Mining Genome Variation to Associate Genetic Disease with Mutation Alterations and Ortho/Paralogous Polimorphysms in Transcription Factor Binding Site. - Julia V. Ponomarenko; Galina Orlova; Tatyana I. Merkulova; Gennady V. Vasiliev; Mikhail P. Ponomarenko (Int. J. Artif. Intell. Tools, 2005)

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)

Recognition of interferon-inducible sites, promoters, and enhancers. - Elena A. Ananko; Yury V. Kondrakhin; Tatyana I. Merkulova; Nikolay A. Kolchanov (BMC 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)

Analysis and recognition of the GAGA transcription factor binding sites in Drosophila genes. - E. S. Omelina; E. M. Baricheva; Dmitry Yu. Oshchepkov; Tatyana I. Merkulova (Comput. Biol. Chem., 2011)

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)