 | 2008 |
|---|
| 67 |       | 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:
TRRD: Technology for extraction, storage, and use of knowledge about the structural-functional organization of the transcriptional regulatory regions in the eukaryotic genes.
Intell. Data Anal. 12(5): 443-461 (2008) |
| 66 | | Victor G. Levitsky,
Elena V. Ignatieva,
Eugenia Aman,
Tatyana I. Merkulova,
Nikolay A. Kolchanov,
T. Charles Hodgman:
Genetic algorithm and optimized weight matrix application for peroxisome proliferator response elements recognition: Prerequisites of accuracy growth for wide genome research.
Intell. Data Anal. 12(5): 513-526 (2008) |
| 2007 |
|---|
| 65 |  | Irina Medvedeva,
Pavel Demenkov,
Vladimir A. Ivanisenko,
Nikolay A. Kolchanov:
Analysis of Protein Functional Site Distribution on Gene Structure.
BIOCOMP 2007: 452-455 |
| 64 | | Alexey V. Kochetov,
Andrey Palyanov,
Igor I. Titov,
Dmitry A. Grigorovich,
Akinori Sarai,
Nikolay A. Kolchanov:
AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site.
BMC Bioinformatics 8: (2007) |
| 63 | | Victor G. Levitsky,
Elena V. Ignatieva,
Elena A. Ananko,
Igor I. Turnaev,
Tatyana I. Merkulova,
Nikolay A. Kolchanov,
T. Charles Hodgman:
Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions.
BMC Bioinformatics 8: (2007) |
| 62 | | Elena A. Ananko,
Yury V. Kondrakhin,
Tatyana I. Merkulova,
Nikolay A. Kolchanov:
Recognition of interferon-inducible sites, promoters, and enhancers.
BMC Bioinformatics 8: (2007) |
| 61 | | 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:
Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes.
Briefings in Bioinformatics 8(4): 266-274 (2007) |
| 60 | | Konstantin V. Gunbin,
Leonid V. Omelyanchuk,
Vladislav V. Kogai,
Stanislav I. Fadeev,
Nikolay A. Kolchanov:
Model of the reception of Hedgehog morphogen concentration Gradient: Comparison with an Extended Range of Experimental Data.
J. Bioinformatics and Computational Biology 5(2b): 491-506 (2007) |
| 59 | | Tamara M. Khlebodarova,
Nina V. Tikunova,
Alla V. Kachko,
Irina L. Stepanenko,
Nikolay L. Podkolodny,
Nikolay A. Kolchanov:
Application of Bioinformatics Resources for Genosensor Design.
J. Bioinformatics and Computational Biology 5(2b): 507-520 (2007) |
| 58 | | Elena L. Mishchenko,
Kirill D. Bezmaternykh,
Vitali A. Likhoshvai,
Alexander V. Ratushny,
Tamara M. Khlebodarova,
Natalia Yu. Sournina,
Vladimir A. Ivanisenko,
Nikolay A. Kolchanov:
Mathematical Model for Suppression of Subgenomic Hepatitis C Virus RNA Replication in Cell Culture.
J. Bioinformatics and Computational Biology 5(2b): 593-609 (2007) |
| 57 | | Ilya R. Akberdin,
Evgeniy A. Ozonov,
Victoria V. Mironova,
Nadezda A. Omelyanchuk,
Vitali A. Likhoshvai,
Dmytry N. Gorpinchenko,
Nikolay A. Kolchanov:
A Cellular Automaton to Model the Development of Primary Shoot Meristems of Arabidopsis thaliana.
J. Bioinformatics and Computational Biology 5(2b): 641-650 (2007) |
| 2005 |
|---|
| 56 | | Vladimir A. Ivanisenko,
Sergey S. Pintus,
Dmitry A. Grigorovich,
Nikolay A. Kolchanov:
PDBSite: a database of the 3D structure of protein functional sites.
Nucleic Acids Research 33(Database-Issue): 183-187 (2005) |
| 55 | | 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.
Nucleic Acids Research 33(Database-Issue): 425-427 (2005) |
| 54 | | Victor G. Levitsky,
Aleksey V. Katokhin,
Olga A. Podkolodnaya,
Dagmara P. Furman,
Nikolay A. Kolchanov:
NPRD: Nucleosome Positioning Region Database.
Nucleic Acids Research 33(Database-Issue): 67-70 (2005) |
| 53 | | Oleg V. Vishnevsky,
Nikolay A. Kolchanov:
ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters.
Nucleic Acids Research 33(Web-Server-Issue): 417-422 (2005) |
| 52 | | Vladimir A. Ivanisenko,
Alexey M. Eroshkin,
Nikolay A. Kolchanov:
WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families.
Nucleic Acids Research 33(Web-Server-Issue): 99-104 (2005) |
| 2004 |
|---|
| 51 | | 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.
Nucleic Acids Research 32(Web-Server-Issue): 549-554 (2004) |
| 50 | | Dmitry A. Afonnikov,
Nikolay A. Kolchanov:
CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences.
Nucleic Acids Research 32(Web-Server-Issue): 64-68 (2004) |
| 2003 |
|---|
| 49 | | Nikolay A. Kolchanov,
Ralf Hofestädt:
The 3rd International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002) - Preface.
In Silico Biology 3: 1 (2003) |
| 2002 |
|---|
| 48 | | 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.
Gene Regulations and Metabolism 2002: 149-179 |
| 47 | | Yuri L. Orlov,
V. P. Filippov,
V. N. Potapov,
Nikolay A. Kolchanov:
Construction of stochastic context trees for genetical texts.
In Silico Biology 2: 22 (2002) |
| 46 | | Eugenii E. Vityaev,
Yuri L. Orlov,
Oleg V. Vishnevsky,
Mikhail A. Pozdnyakov,
Nikolay A. Kolchanov:
Computer system "Gene Discovery" for promoter structure analysis.
In Silico Biology 2: 24 (2002) |
| 45 | | Ralf Hofestädt,
Nikolay A. Kolchanov,
John Reinitz:
Information and simulation systems for the analysis of gene regulation and metabolic pathways (Preface).
In Silico Biology 2: 4 (2002) |
| 44 | | 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.
In Silico Biology 2: 9 (2002) |
| 43 | | 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.
Nucleic Acids Research 30(1): 200-202 (2002) |
| 42 | | 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.
Nucleic Acids Research 30(1): 312-317 (2002) |
| 41 | | 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.
Nucleic Acids Research 30(1): 398-401 (2002) |
| 2001 |
|---|
| 40 | | Yuri L. Orlov,
V. P. Filippov,
V. N. Potapov,
Nikolay A. Kolchanov:
Construction of stochastic context trees for genetical texts.
German Conference on Bioinformatics 2001: 212-215 |
| 39 | | 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.
German Conference on Bioinformatics 2001: 215-217 |
| 38 | | Dmitry A. Afonnikov,
Dmitry Yu. Oshchepkov,
Nikolay A. Kolchanov:
Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions.
Bioinformatics 17(11): 1035-1046 (2001) |
| 37 | | Victor G. Levitsky,
Olga A. Podkolodnaya,
Nikolay A. Kolchanov,
Nikolay L. Podkolodny:
Nucleosome formation potential of exons, introns, and Alu repeats.
Bioinformatics 17(11): 1062-1064 (2001) |
| 36 | | Nikolay A. Kolchanov,
Charlie Hodgman:
The 2nd international conference on the Bioinformatics of Genome Regulation and Structure (BGRS-2000), Novosibirsk, August 2000.
Bioinformatics 17(11): 997 (2001) |
| 35 | | Victor G. Levitsky,
Olga A. Podkolodnaya,
Nikolay A. Kolchanov,
Nikolay L. Podkolodny:
Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis.
Bioinformatics 17(11): 998-1010 (2001) |
| 34 | | 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.
Nucleic Acids Research 29(1): 284-287 (2001) |
| 2000 |
|---|
| 33 | | 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.
Nucleic Acids Research 28(1): 205-208 (2000) |
| 32 | | 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.
Nucleic Acids Research 28(1): 298-301 (2000) |
| 31 | | 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.
Nucleic Acids Research 28(1): 311-315 (2000) |
| 1999 |
|---|
| 30 | | Victor G. Levitsky,
Mikhail P. Ponomarenko,
Julia V. Ponomarenko,
Anatoly S. Frolov,
Nikolay A. Kolchanov:
Nucleosomal DNA property database.
Bioinformatics 15(7): 582-592 (1999) |
| 29 | | 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.
Bioinformatics 15(7): 631-643 (1999) |
| 28 | | 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.
Bioinformatics 15(7): 654-668 (1999) |
| 27 | | 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.
Bioinformatics 15(7): 669-686 (1999) |
| 26 | | 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.
Bioinformatics 15(7): 687-703 (1999) |
| 25 | | Alexey V. Kochetov,
Mikhail P. Ponomarenko,
Anatoly S. Frolov,
L. L. Kisselev,
Nikolay A. Kolchanov:
Prediction of eukaryotic mRNA translational properties.
Bioinformatics 15(7): 704-712 (1999) |
| 24 | | 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.
Nucleic Acids Research 27(1): 303-306 (1999) |
| 1998 |
|---|
| 23 | | Alexander E. Kel,
Olga V. Kel-Margoulis,
Vladimir N. Babenko,
Nikolay A. Kolchanov,
Edgar Wingender:
Combinatorial identification of promoters induced upon immune cell activation.
German Conference on Bioinformatics 1998 |
| 22 | | 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.
ISMB 1998: 95-104 |
| 21 | | F. A. Kolpakov,
Elena A. Ananko,
G. B. Kolesov,
Nikolay A. Kolchanov:
GeneNet: a gene network database and its automated visualization.
Bioinformatics 14(6): 529-537 (1998) |
| 20 | | 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.
Nucleic Acids Research 26(1): 362-367 (1998) |
| 1997 |
|---|
| 19 | | Elena V. Ignatieva,
Alexander E. Kel,
Nikolay A. Kolchanov:
Lipid Metabolism Transcription Regulatory Regions Database (LM-TRRD).
German Conference on Bioinformatics 1997: 153-154 |
| 18 | | 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.
German Conference on Bioinformatics 1997: 171 |
| 17 | | Dmitry A. Afonnikov,
Y. V. Kondrakhin,
Igor I. Titov,
Nikolay A. Kolchanov:
Detecting direct correlations between positions in multiple alignments of amino acid sequences.
German Conference on Bioinformatics 1997: 87-98 |
| 16 | | Mikhail P. Ponomarenko,
A. N. Kolchanova,
Nikolay A. Kolchanov:
Generating Programs for Predicting the Activity of Functional Sites.
Journal of Computational Biology 4(1): 83- (1997) |
| 15 | | 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.
Nucleic Acids Research 25(1): 265-268 (1997) |
| 1996 |
|---|
| 14 | | 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.
German Conference on Bioinformatics 1996: 113-117 |
| 13 | | 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.
German Conference on Bioinformatics 1996: 124-129 |
| 12 | | Elena A. Ananko,
Elena V. Ignatieva,
Alexander E. Kel,
Nikolay A. Kolchanov:
WWWTRRD: Hypertext Information System an Transcription Regulation.
German Conference on Bioinformatics 1996: 153-155 |
| 11 | | 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.
German Conference on Bioinformatics 1996: 238-240 |
| 10 | | 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.
German Conference on Bioinformatics 1996: 247-250 |
| 9 | | 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.
German Conference on Bioinformatics - Selected Papers 1996: 99-105 |
| 8 | | Igor B. Rogozin,
Luciano Milanesi,
Nikolay A. Kolchanov:
Gene structure prediction using information on homologous protein sequence.
Computer Applications in the Biosciences 12(3): 161-170 (1996) |
| 1995 |
|---|
| 7 | | 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.
HICSS (5) 1995: 42-51 |
| 6 | | 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.
ISMB 1995: 197-205 |
| 5 | | 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.
ISMB 1995: 206-214 |
| 4 | | Y. V. Kondrakhin,
Alexander E. Kel,
Nikolay A. Kolchanov,
Aida G. Romashchenko,
Luciano Milanesi:
Eukaryotic promoter recognition by binding sites for transcription factors.
Computer Applications in the Biosciences 11(5): 477-488 (1995) |
| 1994 |
|---|
| 3 | | 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.
Computer Applications in the Biosciences 10(6): 597-603 (1994) |
| 1993 |
|---|
| 2 | | 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.
Computer Applications in the Biosciences 9(6): 617-627 (1993) |
| 1992 |
|---|
| 1 | | 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.
Computer Applications in the Biosciences 8(6): 529-534 (1992) |
