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Nikolay A. Kolchanov
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2020 – today
- 2024
- [j72]Evgeniya A. Antropova
, Tamara M. Khlebodarova, Pavel S. Demenkov
Reconstruction of the regulatory hypermethylation network controlling hepatocellular carcinoma development during hepatitis C viral infection. J. Integr. Bioinform. 20(3) (2024) - [j71]Yuriy L. Orlov
BGRS: bioinformatics of genome regulation and data integration. J. Integr. Bioinform. 20(3) (2024)
2010 – 2019
- 2018
- [j70]Oleg V. Vishnevsky
Argo_CUDA: Exhaustive GPU based approach for motif discovery in large DNA datasets. J. Bioinform. Comput. Biol. 16(1): 1740012:1-1740012:23 (2018) - [j69]Yuriy L. Orlov
Introduction to the 9th Young Scientists School on Systems Biology and Bioinformatics (SBB'2017). J. Bioinform. Comput. Biol. 16(1): 1802001:1-1802001:5 (2018) - 2017
- [j68]Kirill E. Medvedev
Identification of residues of the archaeal RNA-binding Nip7 proteins specific to environmental conditions. J. Bioinform. Comput. Biol. 15(2): 1650036:1-1650036:18 (2017) - [j67]Yuriy L. Orlov
Editorial - Bioinformatics development at the BGRS\SB conference series: 10th anniversary. J. Bioinform. Comput. Biol. 15(2): 1702001:1-1702001:5 (2017) - 2016
- [j66]Dmitry S. Ischenko, Dmitry G. Alexeev
Large scale analysis of amino acid substitutions in bacterial proteomics. BMC Bioinform. 17: 450:1-450:10 (2016) - 2015
- [j65]Vladimir A. Ivanisenko
ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology. BMC Syst. Biol. 9(S-2): S2 (2015) - [j64]Andrey S. Glotov
Molecular association of pathogenetic contributors to pre-eclampsia (pre-eclampsia associome). BMC Syst. Biol. 9(S-2): S4 (2015) - [j63]Yuriy L. Orlov
Introductory note for BGRS\SB-2014 special issue. J. Bioinform. Comput. Biol. 13(1): 1502001:1-1502001:3 (2015) - [j62]Irina M. Larina, Lyudmila Kh. Pastushkova, Evgeny S. Tiys
Permanent proteins in the urine of healthy humans during the Mars-500 experiment. J. Bioinform. Comput. Biol. 13(1): 1540001:1-1540001:17 (2015) - 2013
- [j61]Nikolay A. Kolchanov
Introductory Note for Bgrs-2012 Special Issue. J. Bioinform. Comput. Biol. 11(1) (2013) - [j60]Victoria V. Mironova
How Multiple Auxin Responsive Elements May Interact in plant promoters: a Reverse Problem solution. J. Bioinform. Comput. Biol. 11(1) (2013) - [j59]Björn Sommer, Benjamin Kormeier, Pavel Demenkov
Subcellular Localization Charts: a New Visual Methodology for the Semi-Automatic Localization of protein-Related Data Sets. J. Bioinform. Comput. Biol. 11(1) (2013) - [c20]Konstantin Kozlov
Enhanced Differential Evolution Entirely Parallel Method for Biomedical Applications. PaCT 2013: 409-416 - 2012
- [j58]Pavel Demenkov
ANDVisio: A new tool for graphic visualization and analysis of literature mined associative gene networks in the ANDSystem. Silico Biol. 11(3-4): 149-161 (2012) - [j57]Irina V. Medvedeva
SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes. Nucleic Acids Res. 40(Database-Issue): 278-283 (2012) - 2010
- [j56]Victoria V. Mironova
A plausible mechanism for auxin patterning along the developing root. BMC Syst. Biol. 4: 98 (2010) - [j55]Valentin V. Suslov, Petr M. Ponomarenko, Vadim M. Efimov
Snps in the HIV-1 TATA Box and the Aids pandemic. J. Bioinform. Comput. Biol. 8(3): 607-625 (2010) - [j54]Björn Sommer, Evgeny S. Tiys, Benjamin Kormeier, Klaus Hippe, Sebastian Janowski, Timofey V. Ivanisenko
Visualization and Analysis of a Cardio Vascular Disease- and MUPP1-related Biological Network combining Text Mining and Data Warehouse Approaches. J. Integr. Bioinform. 7(1) (2010)
2000 – 2009
- 2008
- [j53]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) - [j52]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
- [j51]Nikolay A. Kolchanov
Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes. Briefings Bioinform. 8(4): 266-274 (2007) - [j50]Elena A. Ananko, Yury V. Kondrakhin, Tatyana I. Merkulova, Nikolay A. Kolchanov
Recognition of interferon-inducible sites, promoters, and enhancers. BMC Bioinform. 8 (2007) - [j49]Alexey V. Kochetov, Andrey Palyanov
AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site. BMC Bioinform. 8 (2007) - [j48]Victor G. Levitsky
Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions. BMC Bioinform. 8 (2007) - [j47]Sergei N. Rodin, Nikolay A. Kolchanov:
Fifth International Conference on Bioinformatics of Genome Regulation and Structure-BGRS'2006. Silico Biol. 7(3): 239-240 (2007) - [j46]Sergey A. Lashin, Valentin V. Suslov, Nikolay A. Kolchanov, Yuri G. Matushkin:
Simulation of Coevolution in Community by Using the "Evolutionary Constructor" Program. Silico Biol. 7(3): 261-275 (2007) - [j45]Konstantin V. Gunbin, Dmitry A. Afonnikov, Nikolay A. Kolchanov:
The Evolution of the Hh-Signaling Pathway Genes: A Computer-Assisted Study. Silico Biol. 7(3): 333-354 (2007) - [j44]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. Bioinform. Comput. Biol. 5(2b): 491-506 (2007) - [j43]Tamara M. Khlebodarova, Nina V. Tikunova, Alla V. Kachko, Irina L. Stepanenko, Nikolay L. Podkolodny
Application of Bioinformatics Resources for Genosensor Design. J. Bioinform. Comput. Biol. 5(2b): 507-520 (2007) - [j42]Elena L. Mishchenko, Kirill D. Bezmaternykh, Vitali A. Likhoshvai, Alexander V. Ratushny, Tamara M. Khlebodarova, Natalia Yu. Sournina, Vladimir A. Ivanisenko
Mathematical Model for Suppression of Subgenomic Hepatitis C Virus RNA Replication in Cell Culture. J. Bioinform. Comput. Biol. 5(2b): 593-609 (2007) - [j41]Ilya R. Akberdin
A Cellular Automaton to Model the Development of Primary Shoot Meristems of Arabidopsis thaliana. J. Bioinform. Comput. Biol. 5(2b): 641-650 (2007) - [c19]Irina Medvedeva, Pavel Demenkov, Vladimir A. Ivanisenko, Nikolay A. Kolchanov:
Analysis of Protein Functional Site Distribution on Gene Structure. BIOCOMP 2007: 452-455 - [c18]Denis K. Ponomaryov, Nadezhda Omelianchuk, Victoria V. Mironova
From Published Expression and Phenotype Data to Structured Knowledge: The Arabidopsis Gene Net Supplementary Database and Its Applications. KONT/KPP 2007: 101-120 - 2005
- [j40]Victor G. Levitsky
NPRD: Nucleosome Positioning Region Database. Nucleic Acids Res. 33(Database-Issue): 67-70 (2005) - [j39]Vladimir A. Ivanisenko
PDBSite: a database of the 3D structure of protein functional sites. Nucleic Acids Res. 33(Database-Issue): 183-187 (2005) - [j38]Elena A. Ananko, Nikolay L. Podkolodny
GeneNet in 2005. Nucleic Acids Res. 33(Database-Issue): 425-427 (2005) - [j37]Vladimir A. Ivanisenko
WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families. Nucleic Acids Res. 33(Web-Server-Issue): 99-104 (2005) - [j36]Oleg V. Vishnevsky
ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters. Nucleic Acids Res. 33(Web-Server-Issue): 417-422 (2005) - 2004
- [j35]Dmitry A. Afonnikov
CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences. Nucleic Acids Res. 32(Web-Server-Issue): 64-68 (2004) - [j34]Vladimir A. Ivanisenko
PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res. 32(Web-Server-Issue): 549-554 (2004) - 2003
- [j33]Nikolay A. Kolchanov, Ralf Hofestädt:
The 3rd International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002) - Preface. Silico Biol. 3(1-2): 1-2 (2003) - 2002
- [j32]Ralf Hofestädt, Nikolay A. Kolchanov, John Reinitz:
Information and simulation systems for the analysis of gene regulation and metabolic pathways (Preface). Silico Biol. 2(2): 35-36 (2002) - [j31]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. Silico Biol. 2(2): 97-110 (2002) - [j30]Yuri L. Orlov, V. P. Filippov, Vladimir N. Potapov, Nikolay A. Kolchanov:
Construction of stochastic context trees for genetical texts. Silico Biol. 2(3): 233-247 (2002) - [j29]Evgenii E. Vityaev, Yuri L. Orlov, Oleg V. Vishnevsky, Mikhail A. Pozdnyakov, Nikolay A. Kolchanov:
Computer system "Gene Discovery" for promoter structure analysis. Silico Biol. 2(3): 257-262 (2002) - [j28]Vadim P. Valuev, Dmitry A. Afonnikov
ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro. Nucleic Acids Res. 30(1): 200-202 (2002) - [j27]Nikolay A. Kolchanov, Elena V. Ignatieva, Elena A. Ananko, Olga A. Podkolodnaya, Irina L. Stepanenko, Tatyana I. Merkulova, Mikhail A. Pozdnyakov, Nikolay L. Podkolodny
Transcription Regulatory Regions Database (TRRD): its status in 2002. Nucleic Acids Res. 30(1): 312-317 (2002) - [j26]Elena A. Ananko, Nikolay L. Podkolodny
GeneNet: a database on structure and functional organisation of gene networks. Nucleic Acids Res. 30(1): 398-401 (2002) - [c17]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 - 2001
- [j25]Nikolay A. Kolchanov, Charlie Hodgman:
The 2nd international conference on the Bioinformatics of Genome Regulation and Structure (BGRS-2000), Novosibirsk, August 2000. Bioinform. 17(11): 997 (2001) - [j24]Victor G. Levitsky
Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis. Bioinform. 17(11): 998-1010 (2001) - [j23]Dmitry A. Afonnikov
Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions. Bioinform. 17(11): 1035-1046 (2001) - [j22]Victor G. Levitsky
Nucleosome formation potential of exons, introns, and Alu repeats. Bioinform. 17(11): 1062-1064 (2001) - [j21]Julia V. Ponomarenko
ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. Nucleic Acids Res. 29(1): 284-287 (2001) - [c16]Yuri L. Orlov, V. P. Filippov, Vladimir N. Potapov, Nikolay A. Kolchanov:
Construction of stochastic context trees for genetical texts. German Conference on Bioinformatics 2001: 212-215 - [c15]Yuri L. Orlov, Evgenii 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 - 2000
- [j20]Julia V. Ponomarenko
SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation. Nucleic Acids Res. 28(1): 205-208 (2000) - [j19]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
Transcription Regulatory Regions Database (TRRD): its status in 2000. Nucleic Acids Res. 28(1): 298-301 (2000) - [j18]Olga V. Kel-Margoulis, Aida G. Romashchenko, Nikolay A. Kolchanov, Edgar Wingender
COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation. Nucleic Acids Res. 28(1): 311-315 (2000) - [j17]Fedor A. Kolpakov
Methods for integration of heterogeneous information resources in molecular biology in the digital library GeneExpress. Program. Comput. Softw. 26(3): 170-176 (2000)
1990 – 1999
- 1999
- [j16]Victor G. Levitsky
Nucleosomal DNA property database. Bioinform. 15(7): 582-592 (1999) - [j15]Mikhail P. Ponomarenko, Julia V. Ponomarenko
Oligonucleotide frequency matrices addressed to recognizing functional DNA sites. Bioinform. 15(7): 631-643 (1999) - [j14]Julia V. Ponomarenko
Conformational and physicochemical DNA features specific for transcription factor binding sites. Bioinform. 15(7): 654-668 (1999) - [j13]Nikolay A. Kolchanov, Mikhail P. Ponomarenko, Anatoly S. Frolov, Elena A. Ananko, Fedor A. Kolpakov
Integrated databases and computer systems for studying eukaryotic gene expression. Bioinform. 15(7): 669-686 (1999) - [j12]Mikhail P. Ponomarenko, Julia V. Ponomarenko
Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins. Bioinform. 15(7): 687-703 (1999) - [j11]Alexey V. Kochetov, Mikhail P. Ponomarenko, Anatoly S. Frolov, L. L. Kisselev, Nikolay A. Kolchanov:
Prediction of eukaryotic mRNA translational properties. Bioinform. 15(7): 704-712 (1999) - [j10]Nikolay A. Kolchanov
Transcription Regulatory Regions Database (TRRD): its status in 1999. Nucleic Acids Res. 27(1): 303-306 (1999) - 1998
- [j9]Fedor A. Kolpakov
GeneNet: a gene network database and its automated visualization. Bioinform. 14(6): 529-537 (1998) - [j8]T. Heinemeyer, Edgar Wingender
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res. 26(1): 362-367 (1998) - [c14]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 - [c13]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, 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 - 1997
- [j7]Mikhail P. Ponomarenko, A. N. Kolchanova, Nikolay A. Kolchanov:
Generating Programs for Predicting the Activity of Functional Sites. J. Comput. Biol. 4(1): 83-90 (1997) - [j6]Edgar Wingender
TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. Nucleic Acids Res. 25(1): 265-268 (1997) - [c12]Dmitry A. Afonnikov, Yury 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 - [c11]Elena V. Ignatieva, Alexander E. Kel, Nikolay A. Kolchanov:
Lipid Metabolism Transcription Regulatory Regions Database (LM-TRRD). German Conference on Bioinformatics 1997: 153-154 - [c10]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 - 1996
- [j5]Igor B. Rogozin, Luciano Milanesi, Nikolay A. Kolchanov:
Gene structure prediction using information on homologous protein sequence. Comput. Appl. Biosci. 12(3): 161-170 (1996) - [c9]Alexander E. Kel, O. V. Kel, Oleg V. Vishnevsky
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 - [c8]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 - [c7]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 - [c6]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 - [c5]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 - [c4]Yury V. Kondrakhin, Fedor 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 - 1995
- [j4]Yury V. Kondrakhin, Alexander E. Kel, Nikolay A. Kolchanov
Eukaryotic promoter recognition by binding sites for transcription factors. Comput. Appl. Biosci. 11(5): 477-488 (1995) - [c3]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 - [c2]Alexander E. Kel, Yury 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 - [c1]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 - 1994
- [j3]Yury V. Kondrakhin, V. V. Shamin, Nikolay A. Kolchanov
Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3'-terminal processing sites. Comput. Appl. Biosci. 10(6): 597-603 (1994) - 1993
- [j2]Alexander E. Kel, Mikhail P. Ponomarenko
SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. Comput. Appl. Biosci. 9(6): 617-627 (1993) - 1992
- [j1]Victor B. Strelets, Ilya N. Shindyalov, Nikolay A. Kolchanov
Fast, statistically based alignment of amino acid sequences on the base of diagonal fragments of DOT-matrices. Comput. Appl. Biosci. 8(6): 529-534 (1992)
Coauthor Index
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