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Nikolay A. Kolchanov :
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Nikolay A. Kolchanov , Elena A. Ananko , Vitali A. Likhoshvai , Olga A. Podkolodnaya , Elena V. Ignatieva , Alexander V. Ratushny , Yuri G. Matushkin Gene Networks Description and Modeling in the GeneNet System. [Citation Graph (0, 0)][DBLP ] Gene Regulations and Metabolism, 2002, pp:149-179 [Conf ] Dmitry A. Afonnikov , Y. V. Kondrakhin , I. I. Titov , Nikolay A. Kolchanov Detecting direct correlations between positions in multiple alignments of amino acid sequences. [Citation Graph (0, 0)][DBLP ] German Conference on Bioinformatics, 1997, pp:87-98 [Conf ] Elena A. Ananko , Elena V. Ignatieva , Alexander E. Kel , Nikolay A. Kolchanov WWWTRRD: Hypertext Information System an Transcription Regulation. [Citation Graph (0, 0)][DBLP ] German Conference on Bioinformatics, 1996, pp:153-155 [Conf ] I. V. Ischenko , Alexey V. Kochetov , Alexander E. Kel , Nikolay A. Kolchanov , L. L. Kisselev Comparative Analysis of the Secondary Structure of mRNA Encoded by High- and Low-Expression Eukaryotic Genes. [Citation Graph (0, 0)][DBLP ] German Conference on Bioinformatics, 1996, pp:124-129 [Conf ] Alexander E. Kel , Olga V. Kel-Margoulis , Vladimir N. Babenko , Nikolay A. Kolchanov , Edgar Wingender Combinatorial identification of promoters induced upon immune cell activation. [Citation Graph (0, 0)][DBLP ] German Conference on Bioinformatics, 1998, pp:- [Conf ] Alexander E. Kel , O. V. Kel , I. V. Ischenko , Nikolay A. Kolchanov , Holger Karas , Edgar Wingender , Heinz Sklenar TRRD and COMPEL Databases an Transcription Linked to TRANSFAC as Tools for Analysis and Recognition of Regulatory Sequences. [Citation Graph (0, 0)][DBLP ] German Conference on Bioinformatics, 1996, pp:113-117 [Conf ] Alexander E. Kel , O. V. Kel , Oleg V. Vishnevsky , Mikhail P. Ponomarenko , I. V. Ischenko , Holger Karas , Edgar Wingender , Nikolay A. Kolchanov , Heinz Sklenar TRRD and COMPEL Databases on Transcription Linked to TRANSFAC as Tools for Analysis and Recognition of Regulatory Sequences. [Citation Graph (0, 0)][DBLP ] German Conference on Bioinformatics - Selected Papers, 1996, pp:99-105 [Conf ] Alexander E. Kel , M. Philipenko , Vladimir N. Babenko , Nikolay A. Kolchanov Genetic Algorithm for Selection of Oligonucleotides for Identification by Hybridisation of Genomic DNA Fragments Possessing Gene Potential. [Citation Graph (0, 0)][DBLP ] German Conference on Bioinformatics, 1996, pp:238-240 [Conf ] Y. V. Kondrakhin , F. A. Kolpakov , Alexander E. Kel , Nikolay A. Kolchanov , Luciano Milanesi Computer Analysis and Recognition of the Transcription Regulatory Elements in Eukaryotic Genomes. [Citation Graph (0, 0)][DBLP ] German Conference on Bioinformatics, 1996, pp:247-250 [Conf ] Elena V. Ignatieva , Alexander E. Kel , Nikolay A. Kolchanov Lipid Metabolism Transcription Regulatory Regions Database (LM-TRRD). [Citation Graph (0, 0)][DBLP ] German Conference on Bioinformatics, 1997, pp:153-154 [Conf ] Yuri L. Orlov , V. P. Filippov , V. N. Potapov , Nikolay A. Kolchanov Construction of stochastic context trees for genetical texts. [Citation Graph (0, 0)][DBLP ] German Conference on Bioinformatics, 2001, pp:212-215 [Conf ] Yuri L. Orlov , Eugenii E. Vityaev , Oleg V. Vishnevsky , A. S. Belenok , Boris Kovalerchuk , Mikhail A. Pozdnyakov , Nikolay A. Kolchanov Program "Gene Discovery" for Pattern Matching in Promoter Sequences. [Citation Graph (0, 0)][DBLP ] German Conference on Bioinformatics, 2001, pp:215-217 [Conf ] Mikhail P. Ponomarenko , Julia V. Ponomarenko , Alexander E. Kel , Nikolay A. Kolchanov , N. Karas , Edgar Wingender , Heinz Sklenar Identification of the significant conformational features of functional sites in B-DNA. [Citation Graph (0, 0)][DBLP ] German Conference on Bioinformatics, 1997, pp:171- [Conf ] O. V. Kel , A. G. Romachenko , Alexander E. Kel , Andrey N. Naumochkin , Nikolay A. Kolchanov Data representation in the TRRD-a database of transcription regulatory regions of the eukaryotic genomes. [Citation Graph (0, 0)][DBLP ] HICSS (5), 1995, pp:42-51 [Conf ] Alexander E. Kel , Y. V. Kondrakhin , Ph. A. Kolpakov , O. V. Kel , Aida G. Romashchenko , Edgar Wingender , Luciano Milanesi , Nikolay A. Kolchanov Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences. [Citation Graph (0, 0)][DBLP ] ISMB, 1995, pp:197-205 [Conf ] Nikolay A. Kolchanov , Mikhail P. Ponomarenko , Alexander E. Kel , Y. V. Kondrakhin , Anatoly S. Frolov , F. A. Kolpakov , T. N. Goryachkovskaya , O. V. Kel , Elena A. Ananko , Elena V. Ignatieva , Olga A. Podkolodnaya , Vladimir N. Babenko , Irina L. Stepanenko , Aida G. Romashchenko , Tatyana I. Merkulova , Denis G. Vorobiev , Sergey V. Lavryushev , Y. V. Ponomarenko , Alexey V. Kochetov , G. B. Kolesov , Victor V. Solovyev , Luciano Milanesi , Nikolay L. Podkolodny , Edgar Wingender , T. Heinemeyer GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome. [Citation Graph (0, 0)][DBLP ] ISMB, 1998, pp:95-104 [Conf ] Nikolay A. Kolchanov , Oleg V. Vishnevsky , Vladimir N. Babenko , Alexander E. Kel , Ilya N. Shindyalov Identification of CDNA Sequences by Specific Oligonucleotide Sets - A Computer Tool and Application. [Citation Graph (0, 0)][DBLP ] ISMB, 1995, pp:206-214 [Conf ] Dmitry A. Afonnikov , D. Yu. Oshchepkov , Nikolay A. Kolchanov Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions. [Citation Graph (0, 0)][DBLP ] Bioinformatics, 2001, v:17, n:11, pp:1035-1046 [Journal ] Nikolay A. Kolchanov , Mikhail P. Ponomarenko , Anatoly S. Frolov , Elena A. Ananko , F. A. Kolpakov , Elena V. Ignatieva , Olga A. Podkolodnaya , T. N. Goryachkovskaya , Irina L. Stepanenko , Tatyana I. Merkulova , V. V. Babenko , Y. V. Ponomarenko , Alexey V. Kochetov , Nikolay L. Podkolodny , Denis G. Vorobiev , Sergey V. Lavryushev , Dmitry A. Grigorovich , Y. V. Kondrakhin , Luciano Milanesi , Edgar Wingender , Victor V. Solovyev , G. Christian Overton Integrated databases and computer systems for studying eukaryotic gene expression. [Citation Graph (0, 0)][DBLP ] Bioinformatics, 1999, v:15, n:7, pp:669-686 [Journal ] Alexander E. Kel , Mikhail P. Ponomarenko , E. A. Likhachev , Yuri L. Orlov , I. V. Ischenko , Luciano Milanesi , Nikolay A. Kolchanov SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. [Citation Graph (0, 0)][DBLP ] Computer Applications in the Biosciences, 1993, v:9, n:6, pp:617-627 [Journal ] Alexey V. Kochetov , Mikhail P. Ponomarenko , Anatoly S. Frolov , L. L. Kisselev , Nikolay A. Kolchanov Prediction of eukaryotic mRNA translational properties. [Citation Graph (0, 0)][DBLP ] Bioinformatics, 1999, v:15, n:7, pp:704-712 [Journal ] Nikolay A. Kolchanov , Charlie Hodgman The 2nd international conference on the Bioinformatics of Genome Regulation and Structure (BGRS-2000), Novosibirsk, August 2000. [Citation Graph (0, 0)][DBLP ] Bioinformatics, 2001, v:17, n:11, pp:997- [Journal ] F. A. Kolpakov , Elena A. Ananko , G. B. Kolesov , Nikolay A. Kolchanov GeneNet: a gene network database and its automated visualization. [Citation Graph (0, 0)][DBLP ] Bioinformatics, 1998, v:14, n:6, pp:529-537 [Journal ] Y. V. Kondrakhin , Alexander E. Kel , Nikolay A. Kolchanov , Aida G. Romashchenko , Luciano Milanesi Eukaryotic promoter recognition by binding sites for transcription factors. [Citation Graph (0, 0)][DBLP ] Computer Applications in the Biosciences, 1995, v:11, n:5, pp:477-488 [Journal ] Y. V. Kondrakhin , V. V. Shamin , Nikolay A. Kolchanov Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3'-terminal processing sites. [Citation Graph (0, 0)][DBLP ] Computer Applications in the Biosciences, 1994, v:10, n:6, pp:597-603 [Journal ] Victor G. Levitsky , Olga A. Podkolodnaya , Nikolay A. Kolchanov , Nikolay L. Podkolodny Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis. [Citation Graph (0, 0)][DBLP ] Bioinformatics, 2001, v:17, n:11, pp:998-1010 [Journal ] Victor G. Levitsky , Olga A. Podkolodnaya , Nikolay A. Kolchanov , Nikolay L. Podkolodny Nucleosome formation potential of exons, introns, and Alu repeats. [Citation Graph (0, 0)][DBLP ] Bioinformatics, 2001, v:17, n:11, pp:1062-1064 [Journal ] Victor G. Levitsky , Mikhail P. Ponomarenko , Julia V. Ponomarenko , Anatoly S. Frolov , Nikolay A. Kolchanov Nucleosomal DNA property database. [Citation Graph (0, 0)][DBLP ] Bioinformatics, 1999, v:15, n:7, pp:582-592 [Journal ] Mikhail P. Ponomarenko , Julia V. Ponomarenko , Anatoly S. Frolov , Nikolay L. Podkolodny , L. K. Savinkova , Nikolay A. Kolchanov , G. Christian Overton Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins. [Citation Graph (0, 0)][DBLP ] Bioinformatics, 1999, v:15, n:7, pp:687-703 [Journal ] Mikhail P. Ponomarenko , Julia V. Ponomarenko , Anatoly S. Frolov , Olga A. Podkolodnaya , Denis G. Vorobiev , Nikolay A. Kolchanov , G. Christian Overton Oligonucleotide frequency matrices addressed to recognizing functional DNA sites. [Citation Graph (0, 0)][DBLP ] Bioinformatics, 1999, v:15, n:7, pp:631-643 [Journal ] Julia V. Ponomarenko , Mikhail P. Ponomarenko , Anatoly S. Frolov , Denis G. Vorobiev , G. Christian Overton , Nikolay A. Kolchanov Conformational and physicochemical DNA features specific for transcription factor binding sites. [Citation Graph (0, 0)][DBLP ] Bioinformatics, 1999, v:15, n:7, pp:654-668 [Journal ] Igor B. Rogozin , Luciano Milanesi , Nikolay A. Kolchanov Gene structure prediction using information on homologous protein sequence. [Citation Graph (0, 0)][DBLP ] Computer Applications in the Biosciences, 1996, v:12, n:3, pp:161-170 [Journal ] Victor B. Strelets , Ilya N. Shindyalov , Nikolay A. Kolchanov , Luciano Milanesi Fast, statistically based alignment of amino acid sequences on the base of diagonal fragments of DOT-matrices. [Citation Graph (0, 0)][DBLP ] Computer Applications in the Biosciences, 1992, v:8, n:6, pp:529-534 [Journal ] Nikolay A. Kolchanov , Ralf Hofestädt The 3rd International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002) - Preface. [Citation Graph (0, 0)][DBLP ] In Silico Biology, 2003, v:3, n:, pp:1- [Journal ] 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 GeneNet database: description and modeling of gene networks. [Citation Graph (0, 0)][DBLP ] In Silico Biology, 2002, v:2, n:, pp:9- [Journal ] Yuri L. Orlov , V. P. Filippov , V. N. Potapov , Nikolay A. Kolchanov Construction of stochastic context trees for genetical texts. [Citation Graph (0, 0)][DBLP ] In Silico Biology, 2002, v:2, n:, pp:22- [Journal ] Ralf Hofestädt , Nikolay A. Kolchanov , John Reinitz Information and simulation systems for the analysis of gene regulation and metabolic pathways (Preface). [Citation Graph (0, 0)][DBLP ] In Silico Biology, 2002, v:2, n:, pp:4- [Journal ] Eugenii E. Vityaev , Yuri L. Orlov , Oleg V. Vishnevsky , Mikhail A. Pozdnyakov , Nikolay A. Kolchanov Computer system "Gene Discovery" for promoter structure analysis. [Citation Graph (0, 0)][DBLP ] In Silico Biology, 2002, v:2, n:, pp:24- [Journal ] Mikhail P. Ponomarenko , A. N. Kolchanova , Nikolay A. Kolchanov Generating Programs for Predicting the Activity of Functional Sites. [Citation Graph (0, 0)][DBLP ] Journal of Computational Biology, 1997, v:4, n:1, pp:83-0 [Journal ] Dmitry A. Afonnikov , Nikolay A. Kolchanov CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2004, v:32, n:Web-Server-Issue, pp:64-68 [Journal ] Elena A. Ananko , Nikolay L. Podkolodny , Irina L. Stepanenko , Elena V. Ignatieva , Olga A. Podkolodnaya , Nikolay A. Kolchanov GeneNet: a database on structure and functional organisation of gene networks. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2002, v:30, n:1, pp:398-401 [Journal ] T. Heinemeyer , Edgar Wingender , Ingmar Reuter , Henning Hermjakob , Alexander E. Kel , Olga V. Kel-Margoulis , Elena V. Ignatieva , Elena A. Ananko , Olga A. Podkolodnaya , F. A. Kolpakov , Nikolay L. Podkolodny , Nikolay A. Kolchanov Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 1998, v:26, n:1, pp:362-367 [Journal ] Vladimir A. Ivanisenko , Sergey S. Pintus , Dmitry A. Grigorovich , Nikolay A. Kolchanov PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2004, v:32, n:Web-Server-Issue, pp:549-554 [Journal ] Olga V. Kel-Margoulis , Aida G. Romashchenko , Nikolay A. Kolchanov , Edgar Wingender , Alexander E. Kel COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2000, v:28, n:1, pp:311-315 [Journal ] 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 , F. A. Kolpakov , Nikolay L. Podkolodny , Andrey N. Naumochkin , Aida G. Romashchenko Transcription Regulatory Regions Database (TRRD): its status in 1999. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 1999, v:27, n:1, pp:303-306 [Journal ] 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 Transcription Regulatory Regions Database (TRRD): its status in 2002. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2002, v:30, n:1, pp:312-317 [Journal ] 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 , F. A. Kolpakov , Nikolay L. Podkolodny , Andrey N. Naumochkin , I. M. Korostishevskaya , Aida G. Romashchenko , G. Christian Overton Transcription Regulatory Regions Database (TRRD): its status in 2000. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2000, v:28, n:1, pp:298-301 [Journal ] Julia V. Ponomarenko , Dagmara P. Furman , Anatoly S. Frolov , Nikolay L. Podkolodny , Galina Orlova , Mikhail P. Ponomarenko , Nikolay A. Kolchanov , Akinori Sarai ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2001, v:29, n:1, pp:284-287 [Journal ] Julia V. Ponomarenko , Galina Orlova , Mikhail P. Ponomarenko , Sergey V. Lavryushev , Anatoly S. Frolov , Svetlana V. Zybova , Nikolay A. Kolchanov SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2000, v:28, n:1, pp:205-208 [Journal ] Vadim P. Valuev , Dmitry A. Afonnikov , Mikhail P. Ponomarenko , Luciano Milanesi , Nikolay A. Kolchanov ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2002, v:30, n:1, pp:200-202 [Journal ] Edgar Wingender , Alexander E. Kel , Olga V. Kel-Margoulis , Holger Karas , T. Heinemeyer , P. Dietze , R. Knüppel , Aida G. Romashchenko , Nikolay A. Kolchanov TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 1997, v:25, n:1, pp:265-268 [Journal ] Vladimir A. Ivanisenko , Sergey S. Pintus , Dmitry A. Grigorovich , Nikolay A. Kolchanov PDBSite: a database of the 3D structure of protein functional sites. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:183-187 [Journal ] Victor G. Levitsky , Aleksey V. Katokhin , Olga A. Podkolodnaya , Dagmara P. Furman , Nikolay A. Kolchanov NPRD: Nucleosome Positioning Region Database. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:67-70 [Journal ] Elena A. Ananko , Nikolay L. Podkolodny , Irina L. Stepanenko , Olga A. Podkolodnaya , D. A. Rasskazov , D. S. Miginsky , Vitali A. Likhoshvai , Alexander V. Ratushny , N. N. Podkolodnaya , Nikolay A. Kolchanov GeneNet in 2005. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:425-427 [Journal ] Oleg V. Vishnevsky , Nikolay A. Kolchanov ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2005, v:33, n:Web-Server-Issue, pp:417-422 [Journal ] Vladimir A. Ivanisenko , Alexey M. Eroshkin , Nikolay A. Kolchanov WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families. [Citation Graph (0, 0)][DBLP ] Nucleic Acids Research, 2005, v:33, n:Web-Server-Issue, pp:99-104 [Journal ] Analysis of Protein Functional Site Distribution on Gene Structure. [Citation Graph (, )][DBLP ] Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes. [Citation Graph (, )][DBLP ] Recognition of interferon-inducible sites, promoters, and enhancers. [Citation Graph (, )][DBLP ] AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site. [Citation Graph (, )][DBLP ] Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions. [Citation Graph (, )][DBLP ] Search in 0.005secs, Finished in 0.608secs