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Nikolay Kolchanov

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Co-Publications
Name
30
Ponomarenko, Mikhail
15
Merkulova, Tatyana
15
Kel, Alexander
15
Kel', AE
14
Ananko, Elena
14
Podkolodny, Nikolay
13
Frolov, Anatoly
13
Stepanenko, Irina
13
Podkolodnaya, Olga
12
Kochetov, Alex
11
Kolpakov, Fedor
11
Ignatieva, Elena
10
Ignat'eva, EV
10
Wingender, Edgar
8
Rogozin, Igor

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Publications

TOP 3
Turnaev I I; Gunbin K V; Kolchanov N A
The evolution of key cell cycle proteins correlates with an increase in the complexity of eukaryotic organisms.
Gunbin K V; Afonnikov D A; Boldyreva E V; Kolchanov N A
Adaptive evolution of genes of archaea belonging to the genus Pyrococcus associated with adaptation to life under high-pressure conditions.
Savinkova L K; Ponomarenko M P; Ponomarenko P M; Drachkova I A; Lysova M V; Arshinova T V; Kolchanov N A
TATA box polymorphisms in human gene promoters and associated hereditary pathologies.

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All Publications

2009: Turnaev I I; Gunbin K V; Kolchanov N A
The evolution of key cell cycle proteins correlates with an increase in the complexity of eukaryotic organisms.
Doklady. Biochemistry and biophysics 2009;426():147-51.
2009: Gunbin K V; Afonnikov D A; Boldyreva E V; Kolchanov N A
Adaptive evolution of genes of archaea belonging to the genus Pyrococcus associated with adaptation to life under high-pressure conditions.
Doklady. Biochemistry and biophysics 2009;425():91-3.
2009: Savinkova L K; Ponomarenko M P; Ponomarenko P M; Drachkova I A; Lysova M V; Arshinova T V; Kolchanov N A
TATA box polymorphisms in human gene promoters and associated hereditary pathologies.
Biochemistry. Biokhimii?a 2009;74(2):117-29.
2008: Ponomarenko M P; Omel'yanchuk N A; Katokhin A V; Savinskaya S A; Kolchanov N A
The abundance of microRNA in Arabidopsis thaliana correlates with the presence of tetranucleotides WRHW and DRYD in their sequences.
Doklady. Biochemistry and biophysics 2008;420():150-4.
2008: Kochetov Alex V; Ahmad Shandar; Ivanisenko Vladimir; Volkova Oxana A; Kolchanov Nikolay A; Sarai Akinori
uORFs, reinitiation and alternative translation start sites in human mRNAs.
FEBS letters 2008;582(9):1293-7.
2008: Ponomarenko P M; Savinkova L K; Drachkova I A; Lysova M V; Arshinova T V; Ponomarenko M P; Kolchanov N A
A step-by-step model of TBP/TATA box binding allows predicting human hereditary diseases by single nucleotide polymorphism.
Doklady. Biochemistry and biophysics 2008;419():88-92.
2008: Gunbin K V; Suslov V V; Kolchanov N A
Molecular-genetic systems of development: functional dynamics and molecular evolution.
Biochemistry. Biokhimii?a 2008;73(2):219-30.
2008: Ivanisenko Vladimir A; Afonnikov Dmitry A; Kolchanov Nikolay A
Web-based computational tools for the prediction and analysis of post-translational modifications of proteins.
Methods in molecular biology (Clifton, N.J.) 2008;446():363-84.
2007: Tikunova N V; Khlebodarova T M; Kachko A V; Stepanenko I L; Kolchanov N A
A computational-experimental approach to designing a polyfunctional genosensor derived from the Escherichia coli gene yfiA promoter.
Doklady. Biochemistry and biophysics 2007;417():357-61.
2007: Merkulova T I; Oshchepkov D Yu; Ignatieva E V; Ananko E A; Levitsky V G; Vasiliev G V; Klimova N V; Merkulov V M; Kolchanov N A
Bioinformatical and experimental approaches to investigation of transcription factor binding sites in vertebrate genes.
Biochemistry. Biokhimii?a 2007;72(11):1187-93.
2007: Ignat'eva E V; Klimova N V; Oshchepkov D Y; Vasil'ev G V; Merkulova T I; Kolchanov N A
Search for new binding sites for the transcriptional factor SF-1 by the SITECON method: experimental verification and analysis of regulatory regions of orthologous genes.
Doklady. Biochemistry and biophysics 2007;415():165-9.
2007: Kolchanov Nikolay A; Merkulova Tatyana I; Ignatieva Elena V; Ananko Elena A; Oshchepkov Dmitry Yu; Levitsky Viktor G; Vasiliev Gennady V; Klimova Nataly V; Merkulov Vasily M; Charles Hodgman T
Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes.
Briefings in bioinformatics 2007;8(4):266-74.
2007: Akberdin Ilya R; Ozonov Evgeniy A; Mironova Victoria V; Omelyanchuk Nadezda A; Likhoshvai Vitaly A; Gorpinchenko Dmytry N; Kolchanov Nikolai A
A cellular automaton to model the development of primary shoot meristems of Arabidopsis thaliana.
Journal of bioinformatics and computational biology 2007;5(2B):641-50.
2007: Mishchenko Elena L; Bezmaternykh Kirill D; Likhoshvai Vitaly A; Ratushny Alexander V; Khlebodarova Tamara M; Yu Sournina Natalia; Ivanisenko Vladimir A; Kolchanov Nikolai A
Mathematical model for suppression of subgenomic hepatitis C virus RNA replication in cell culture.
Journal of bioinformatics and computational biology 2007;5(2B):593-609.
2007: Khlebodarova Tamara M; Tikunova Nina V; Kachko Alla V; Stepanenko Irina L; Podkolodny Nikolai L; Kolchanov Nikolai A
Application of bioinformatics resources for genosensor design.
Journal of bioinformatics and computational biology 2007;5(2B):507-20.
2007: Gunbin Konstantin V; Omelyanchuk Leonid V; Kogai Vladislav V; Fadeev Stanislav I; Kolchanov Nikolay A
Model of the reception of hedgehog morphogen concentration gradient: comparison with an extended range of experimental data.
Journal of bioinformatics and computational biology 2007;5(2B):491-506.
2007: Gunbin Konstantin V; Afonnikov Dmitrij A; Kolchanov Nikolay A
The evolution of the Hh-signaling pathway genes: a computer-assisted study.
In silico biology 2007;7(3):333-54.
2007: Lashin Sergey A; Suslov Valentin V; Kolchanov Nikolay A; Matushkin Yury G
Simulation of coevolution in community by using the "Evolutionary Constructor" program.
In silico biology 2007;7(3):261-75.
2007: Levitsky Victor G; Ignatieva Elena V; Ananko Elena A; Turnaev Igor I; Merkulova Tatyana I; Kolchanov Nikolay A; Hodgman T C
Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions.
BMC bioinformatics 2007;8():481.
2007: Kochetov Alex V; Palyanov Andrey; Titov Igor I; Grigorovich Dmitry; Sarai Akinori; Kolchanov Nikolay A
AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site.
BMC bioinformatics 2007;8():318.
2007: Ananko Elena A; Kondrakhin Yury V; Merkulova Tatiana I; Kolchanov Nikolay A
Recognition of interferon-inducible sites, promoters, and enhancers.
BMC bioinformatics 2007;8():56.
2006: Mazzarelli Joan M; White Peter; Gorski Regina; Brestelli John; Pinney Deborah F; Arsenlis Athanasios; Katokhin Alexey; Belova Olga; Bogdanova Vera; Elisafenko Eugenij; Gubina Marina; Nizolenko Lilia; Perelman Polina; Puzakov Mikhail; Shilov Alexandre; Trifonoff Vladimir; Vorobjeva Nadezhda; Kolchanov Nikolay; Kaestner Klaus H; Stoeckert Christian J
Novel genes identified by manual annotation and microarray expression analysis in the pancreas.
Genomics 2006;88(6):752-61.
2006: Pintus S S; Fomin E S; Ivanisenko V A; Kolchanov N A
[Phylogenetic analysis of the family of p53]
Biofizika 2006;51(4):640-9.
2006: Levitskii V G; Ignat'eva E V; Anan'ko E A; Merkulova T I; Kolchanov N A; Hodgman T C
[Method SiteGA for the recognition of transcription factor binding sites]
Biofizika 2006;51(4):633-9.
2006: Volkova O A; Kochetov A V; Titov S E; Kolchanov N A
[Potential open reading frames within 5'-untranslated regions of eukaryotic mRNAs]
Biofizika 2006;51(4):615-21.
2006: Orlov Iu L; Levitskii V G; Smirnova O G; Podkolodnaia O A; Khlebodarova T M; Kolchanov N A
[Statistical analysis of nucleosome formation sites]
Biofizika 2006;51(4):608-14.
2006: Vorob'ev N V; Biltueva L S; Orlov Iu L; Grafodatskii A S; Kolchanov N A
[Interstitial telomere repeats as markers of evolutionary changes in the mammalian karyotype: human chromosome 2]
Biofizika 2006;51(4):602-7.
2006: Klimova N V; Levitskii V G; Ignat'eva E V; Vasil'ev G V; Kobzev V F; Busygina T V; Merkulova T I; Kolchanov N A
[Recognition of the potential SF-1 binding sites by SiteGA method, their experimental verification and search for new SF-1 target genes]
Molekuliarnaia biologiia 2006;40(3):512-23.
2005: Ivanisenko Vladimir A; Eroshkin Alexey M; Kolchanov Nickolay A
WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families.
Nucleic acids research 2005;33(Web Server issue):W99-104.
2005: Vishnevsky Oleg V; Kolchanov Nikolay A
ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters.
Nucleic acids research 2005;33(Web Server issue):W417-22.
2005: Kochetov Alex V; Sarai Akinori; Rogozin Igor B; Shumny Vladimir K; Kolchanov Nikolay A
The role of alternative translation start sites in the generation of human protein diversity.
Molecular genetics and genomics : MGG 2005;273(6):491-6.
2005: Levitsky Victor G; Katokhin Aleksey V; Podkolodnaya Olga A; Furman Dagmara P; Kolchanov Nikolay A
NPRD: Nucleosome Positioning Region Database.
Nucleic acids research 2005;33(Database issue):D67-70.
2005: Ananko E A; Podkolodny N L; Stepanenko I L; Podkolodnaya O A; Rasskazov D A; Miginsky D S; Likhoshvai V A; Ratushny A V; Podkolodnaya N N; Kolchanov N A
GeneNet in 2005.
Nucleic acids research 2005;33(Database issue):D425-7.
2005: Ivanisenko Vladimir A; Pintus Sergey S; Grigorovich Dmitry A; Kolchanov Nickolay A
PDBSite: a database of the 3D structure of protein functional sites.
Nucleic acids research 2005;33(Database issue):D183-7.
2004: Ivanisenko Vladimir A; Pintus Sergey S; Grigorovich Dmitry A; Kolchanov Nickolay A
PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins.
Nucleic acids research 2004;32(Web Server issue):W549-54.
2004: Afonnikov Dmitry A; Kolchanov Nikolay A
CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences.
Nucleic acids research 2004;32(Web Server issue):W64-8.
2004: Kolchanov N A; Podkolodnaia O A; Anan'ko E A; Afonnikov D A; Vishnevskii O V; Vorob'ev D G; Ignat'eva E V; Levitskii V G; Likhoshvai V A; Omel'ianchuk N A
[Integrated computer system for regulating eukaryotic gene expression]
Molekuliarnaia biologiia 2004;38(1):69-81.
2003: Stepanenko Irina; Kolchanov Nikolay
Apoptosis gene network: description in the GeneNet and TRRD databases.
Annals of the New York Academy of Sciences 2003;1010():16-8.
2003: Kochetov A V; Kolchanov N A; Sarai A
Interrelations between the efficiency of translation start sites and other sequence features of yeast mRNAs.
Molecular genetics and genomics : MGG 2003;270(5):442-7.
2003: Ratushnyi A V; Likhoshvai V A; Ignat'eva E V; Matushkin Yu G; Goryanin I I; Kolchanov N A
A computer model of the gene network of the cholesterol biosynthesis regulation in the cell: analysis of the effect of mutations.
Doklady. Biochemistry and biophysics 2003;389():90-3.
2002: Kochetov A V; Sarai A; Vorob'ev D G; Kolchanov N A
[The context organization of functional regions in yeast genes with high-level expression]
Molekuliarnaia biologiia 2002;36(6):1026-34.
2002: Kutsenko Alexey S; Gizatullin Rinat Z; Al-Amin Ali N; Wang Fuli; Kvasha Sergei M; Podowski Raf M; Matushkin Yuri G; Gyanchandani Anita; Muravenko Olga V; Levitsky Viktor G; Kolchanov Nikolay A; Protopopov Alexei I; Kashuba Vladimir I; Kisselev Lev L; Wasserman Wyeth; Wahlestedt Claes; Zabarovsky Eugene R
NotI flanking sequences: a tool for gene discovery and verification of the human genome.
Nucleic acids research 2002;30(14):3163-70.
2002: Ananko E A; Podkolodny N L; Stepanenko I L; Ignatieva E V; Podkolodnaya O A; Kolchanov N A
GeneNet: a database on structure and functional organisation of gene networks.
Nucleic acids research 2002;30(1):398-401.
2002: Kolchanov N A; Ignatieva E V; Ananko E A; Podkolodnaya O A; Stepanenko I L; Merkulova T I; Pozdnyakov M A; Podkolodny N L; Naumochkin A N; Romashchenko A G
Transcription Regulatory Regions Database (TRRD): its status in 2002.
Nucleic acids research 2002;30(1):312-7.
2002: Valuev Vadim P; Afonnikov Dmitry A; Ponomarenko Mikhail P; Milanesi Luciano; Kolchanov Nikolay A
ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro.
Nucleic acids research 2002;30(1):200-2.
2002: Vityaev Eugenii E; Orlov Yury L; Vishnevsky Oleg V; Pozdnyakov Mikhail A; Kolchanov Nikolay A
Computer system "gene discovery" for promoter structure analysis.
In silico biology 2002;2(3):257-62.
2002: Orlov Yury L; Filippov Vladimir P; Potapov Vladimir N; Kolchanov Nikolay A
Construction of stochastic context trees for genetic texts.
In silico biology 2002;2(3):233-47.
2002: Kolchanov Nikolay A; Nedosekina Eugenia A; Ananko Elena A; Likhoshvai Vitaly A; Podkolodny Nikolay L; Ratushny Alexander V; Stepanenko Irina L; Podkolodnaya Olga A; Ignatieva Elena V; Matushkin Yury G
GeneNet database: description and modeling of gene networks.
In silico biology 2002;2(2):97-110.
2001: Pozdniakov M A; Vitiaev E E; Anan'ko E A; Ignat'eva E V; Podkolodnaia O A; Podkolodnyi N L; Lavriushev S V; Kolchanov N A
[Comparative analysis of methods for recognizing potential transcription factor binding sites]
Molekuliarnaia biologiia 2001;35(6):961-9.
2001: Vitiaev E E; Orlov Iu L; Vishnevskii O V; Belenok A S; Kolchanov N A
[Computer system "Gene Discovery" for searching for regularities in organization of eukaryotic regulatory sequences]
Molekuliarnaia biologiia 2001;35(6):952-60.
2001: Kolchanov N A; Podkolodnaia O A; Anan'ko E A; Ignat'eva E V; Podkolodnyi N L; Merkulov V M; Stepanenko I L; Pozdniakov M A; Belova O E; Grigorovich D A; Naumochkin A N
[Regulation of eukaryotic gene transcription: description in the TRRD database]
Molekuliarnaia biologiia 2001;35(6):934-42.
2001: Kochetov A V; Grigorovich D A; Titov I I; Vorob'ev D G; Syrnik O A; Vishnevskii O V; Sarai A; Kolchanov N A
[mRNA-FAST (mRNA-Function, Activity, STructure) computer system]
Molekuliarnaia biologiia 2001;35(6):1039-47.
2001: Levitsky V G; Podkolodnaya O A; Kolchanov N A; Podkolodny N L
Nucleosome formation potential of exons, introns, and Alu repeats.
Bioinformatics (Oxford, England) 2001;17(11):1062-4.
2001: Afonnikov D A; Oshchepkov D Y; Kolchanov N A
Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions.
Bioinformatics (Oxford, England) 2001;17(11):1035-46.
2001: Levitsky V G; Podkolodnaya O A; Kolchanov N A; Podkolodny N L
Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis.
Bioinformatics (Oxford, England) 2001;17(11):998-1010.
2001: Ponomarenko J V; Furman D P; Frolov A S; Podkolodny N L; Orlova G V; Ponomarenko M P; Kolchanov N A; Sarai A
ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another.
Nucleic acids research 2001;29(1):284-7.
2000: Kolchanov N A; Anan'ko E A; Kolpakov F A; Podkolodnaia O A; Ignat'eva E V; Goriachkovskaia T N; Stepanenko E L
[Gene networks]
Molekuliarnaia biologiia 2000;34(4):533-44.
2000: Vasil'ev G V; Merkulov V M; Kobzev V F; Merkulova T I; Ponomarenko M P; Podkolodnaia O A; Ponomarenko Iu V; Kolchanov N A
[Point mutations in region 663-666 of intron 6 or the tryptophan oxygenase gene, connected with a series of mental disorders, disrupts the transcription factor YY1 binding site]
Molekuliarnaia biologiia 2000;34(2):214-22.
2000: Kel-Margoulis O V; Romashchenko A G; Kolchanov N A; Wingender E; Kel A E
COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation.
Nucleic acids research 2000;28(1):311-5.
2000: Kolchanov N A; Podkolodnaya O A; Ananko E A; Ignatieva E V; Stepanenko I L; Kel-Margoulis O V; Kel A E; Merkulova T I; Goryachkovskaya T N; Busygina T V; Kolpakov F A; Podkolodny N L; Naumochkin A N; Korostishevskaya I M; Romashchenko A G; Overton G C
Transcription regulatory regions database (TRRD): its status in 2000.
Nucleic acids research 2000;28(1):298-301.
2000: Ponomarenko J V; Orlova G V; Ponomarenko M P; Lavryushev S V; Frolov A S; Zybova S V; Kolchanov N A
SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation.
Nucleic acids research 2000;28(1):205-8.
1999: Vasiliev G V; Merkulov V M; Kobzev V F; Merkulova T I; Ponomarenko M P; Kolchanov N A
Point mutations within 663-666 bp of intron 6 of the human TDO2 gene, associated with a number of psychiatric disorders, damage the YY-1 transcription factor binding site.
FEBS letters 1999;462(1-2):85-8.
1999: Kolchanov N A; Ponomarenko M P; Kel A E; Kondrakhin Iu V; Frolov A S; Kolpakov F A; Goriachkovskaia T N; Kel O V; Anan'ko E A; Ignat'eva E V
[GeneExpress: an integrator for databases and computer systems accessible by the Internet and intended for studying eukaryotic gene expression]
Biofizika 1999;44(5):837-41.
1999: Frolov A S; Lavriushev S V; Grigorovich D A; Kel A E; Ptitsyn A A; Kolchanov N A; Podkolodnyi N L; Solov'ev V V; Milanesi L; Bourne P
[WWWMGS: an integrated server for molecular-genetic studies]
Biofizika 1999;44(5):832-6.
1999: Ponomarkenko M P; Shindialov I; Bourne P; Kolchanov N A
[Likeness: a system for rapid retrieval of similar conformation of proteins and their spatial structures]
Biofizika 1999;44(5):821-31.
1999: Ponomarenko M P; Ponomarenko Iu V; Kolchanov N A
[Contribution of signals and antisignals in the mutational spectrum of the td-intron insertion site]
Biofizika 1999;44(4):655-63.
1999: Ponomarenko M P; Ponomarenko Iu V; Podkolodnaia O A; Frolov A S; Vorob'ev D V; Kolchanov N A; Overton G C
[Averaging results of site recognition can increase the accuracy of annotating the human genome]
Biofizika 1999;44(4):649-54.
1999: Anan'ko E A; Kolpakov F A; Kolesov G B; Kolchanov N A
[Automatic generation of gene network schemes based on their formalized description in the GeneNet database]
Biofizika 1999;44(4):628-31.
1999: Kochetov A V; Ponomarenko M P; Frolov A S; Kisselev L L; Kolchanov N A
Prediction of eukaryotic mRNA translational properties.
Bioinformatics (Oxford, England) 1999;15(7-8):704-12.
1999: Ponomarenko M P; Ponomarenko J V; Frolov A S; Podkolodny N L; Savinkova L K; Kolchanov N A; Overton G C
Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins.
Bioinformatics (Oxford, England) 1999;15(7-8):687-703.
1999: Kolchanov N A; Ponomarenko M P; Frolov A S; Ananko E A; Kolpakov F A; Ignatieva E V; Podkolodnaya O A; Goryachkovskaya T N; Stepanenko I L; Merkulova T I; Babenko V V; Ponomarenko Y V; Kochetov A V; Podkolodny N L; Vorobiev D V; Lavryushev S V; Grigorovich D A; Kondrakhin Y V; Milanesi L; Wingender E; Solovyev V; Overton G C
Integrated databases and computer systems for studying eukaryotic gene expression.
Bioinformatics (Oxford, England) 1999;15(7-8):669-86.
1999: Ponomarenko J V; Ponomarenko M P; Frolov A S; Vorobyev D G; Overton G C; Kolchanov N A
Conformational and physicochemical DNA features specific for transcription factor binding sites.
Bioinformatics (Oxford, England) 1999;15(7-8):654-68.
1999: Ponomarenko M P; Ponomarenko J V; Frolov A S; Podkolodnaya O A; Vorobyev D G; Kolchanov N A; Overton G C
Oligonucleotide frequency matrices addressed to recognizing functional DNA sites.
Bioinformatics (Oxford, England) 1999;15(7-8):631-43.
1999: Levitsky V G; Ponomarenko M P; Ponomarenko J V; Frolov A S; Kolchanov N A
Nucleosomal DNA property database.
Bioinformatics (Oxford, England) 1999;15(7-8):582-92.
1999: Kolchanov N A; Ananko E A; Podkolodnaya O A; Ignatieva E V; Stepanenko I L; Kel-Margoulis O V; Kel A E; Merkulova T I; Goryachkovskaya T N; Busygina T V; Kolpakov F A; Podkolodny N L; Naumochkin A N; Romashchenko A G
Transcription Regulatory Regions Database (TRRD):its status in 1999.
Nucleic acids research 1999;27(1):303-6.
1998: Kochetov A V; Ischenko I V; Vorobiev D G; Kel A E; Babenko V N; Kisselev L L; Kolchanov N A
Eukaryotic mRNAs encoding abundant and scarce proteins are statistically dissimilar in many structural features.
FEBS letters 1998;440(3):351-5.
1998: Ponomarenko M P; Ponomarenko Iu V; Titov I I; Kolchanov N A; Mazin A V; Kowalczykowski S C
[Preference of RecA-filament to the DNA sequences correlates with genetic code]
Doklady Akademii nauk / [Rossiiskaia akademii nauk] 1998;363(1):122-5.
1998: Kolchanov N A; Ponomarenko M P; Ponomarenko Iu V; Podkolodnyi N L; Frolov A S
[Functional sites of pro- and eukaryotic genomes: computer modeling and predicting activity]
Molekuliarnaia biologiia 1998;32(2):255-67.
1998: Heinemeyer T; Wingender E; Reuter I; Hermjakob H; Kel A E; Kel O V; Ignatieva E V; Ananko E A; Podkolodnaya O A; Kolpakov F A; Podkolodny N L; Kolchanov N A
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL.
Nucleic acids research 1998;26(1):362-7.
1998: Kolchanov N A; Ponomarenko M P; Kel A E; Kondrakhin YuV; Frolov A S; Kolpakov F A; Goryachkovsky T N; Kel O V; Ananko E A; Ignatieva E V; Podkolodnaya O A; Babenko V N; Stepanenko I L; Romashchenko A G; Merkulova T I; Vorobiev D G; Lavryushev S V; Ponomarenko YuV; Kochetov A V; Kolesov G B; Solovyev V V; Milanesi L; Podkolodny N L; Wingender E; Heinemeyer T
GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences in eukaryotic genome.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1998;6():95-104.
1998: Kolpakov F A; Ananko E A; Kolesov G B; Kolchanov N A
GeneNet: a gene network database and its automated visualization.
Bioinformatics (Oxford, England) 1998;14(6):529-37.
1997: Kolpakov F A; Kel' A E; Ponomarenko M P; Kolchanov N A
[High heterogeneity of higher eukaryotic gene promoters, transcribed by RNA polymerase II]
Doklady Akademii nauk / [Rossiiskaia akademii nauk] 1997;357(5):693-5.
1997: Pozdniakov M A; Rogozin I B; Babenko V N; Kolchanov N A
[Neighboring base effect on emergence of spontaneous mutations in human pseudogenes]
Doklady Akademii nauk / [Rossiiskaia akademii nauk] 1997;356(4):566-8.
1997: Ponomarenko M P; Savinkova L K; Kel' A E; Kolchanov N A
[Computer modeling of TATA-box sequences of eukaryotic promoters]
Doklady Akademii nauk / [Rossiiskaia akademii nauk] 1997;355(4):557-61.
1997: Ponomarenko M P; Ponomarenko Iu V; Kel' A E; Kolchanov N A; Karas H; Wingender E; Sklenar H
[Computer analysis of conformational features of the eukaryotic TATA-box DNA promotors]
Molekuliarnaia biologiia 1997;31(4):733-40.
1997: Ponomarenko M P; Savinkova L K; Ponomarenko Iu V; Kel' A E; Titov I I; Kolchanov N A
[Modeling TATA-box sequences in eukaryotic genes]
Molekuliarnaia biologiia 1997;31(4):726-32.
1997: Karas H; Kel' E; Kel' O V; Kolchanov N A; Wingender E
[Integrating knowledge on transcriptional regulation of eukaryotic genes based on information from TRANSFAC, TRRD, and COMPEL databases]
Molekuliarnaia biologiia 1997;31(4):637-46.
1997: Kel' A E; Kolchanov N A; Kel' O V; Romashchenko A G; Anan'ko E A; Ignat'eva E V; Merkulova T I; Podkolodnaia O A; Stepanenko I L; Kochetov A V; Kolpakov F A; Podkolodnyi N L; Naumochkin A A
[TRRD: a database of transcription regulatory regions in eukaryotic genes]
Molekuliarnaia biologiia 1997;31(4):626-36.
1997: Kel' O V; Kel' A E; Romashchenko A G; Wingender E; Kolchanov N A
[Composite regulatory elements: classification and description in the COMPEL database]
Molekuliarnaia biologiia 1997;31(4):601-15.
1997: Wingender E; Kel A E; Kel O V; Karas H; Heinemeyer T; Dietze P; Knüppel R; Romaschenko A G; Kolchanov N A
TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation.
Nucleic acids research 1997;25(1):265-8.
1997: Ponomarenko M P; Ponomarenko J V; Kel A E; Kolchanov N A
Search for DNA conformational features for functional sites. Investigation of the TATA box.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1997;():340-51.
1997: Ponomarenko M P; Kolchanova A N; Kolchanov N A
Generating programs for predicting the activity of functional sites.
Journal of computational biology : a journal of computational molecular cell biology 1997;4(1):83-90.
1996: Kolchanov N A; Babenko V N; Vishnevskii O V; Kel' A E
[Oligonucleotide vocabularies of isofunctional families of genes that code proteins]
Doklady Akademii nauk / [Rossiiskaia akademii nauk] 1996;348(5):696-9.
1996: Rogozin I B; Milanesi L; Kolchanov N A
Gene structure prediction using information on homologous protein sequence.
Computer applications in the biosciences : CABIOS 1996;12(3):161-70.
1996: Ponomarenko M P; Kel' A E; Kolchanova A N; Kolchanov N A
[Contextual signals and antisignals of the intron td-homing site]
Doklady Akademii nauk / [Rossiiskaia akademii nauk] 1996;348(3):424-7.
1996: Rogozin I B; Sredneva N E; Kolchanov N A
Somatic hypermutagenesis in immunoglobulin genes. III. Somatic mutations in the chicken light chain locus.
Biochimica et biophysica acta 1996;1306(2-3):171-8.
1996: Ptitsyn A A; Rogozin I B; Grigorovich D A; Strelets V B; Kel' A E; Milanezi L; Kolchanov N A
[Computer system "AutoGene" for automatic analysis of nucleotide sequences]
Molekuliarnaia biologiia 1996;30(2):432-41.
1996: Kolchanov N A; Titov I I; Vlassova I E; Vlassov V V
Chemical and computer probing of RNA structure.
Progress in nucleic acid research and molecular biology 1996;53():131-96.
1995: Kondrakhin Y V; Kel A E; Kolchanov N A; Romashchenko A G; Milanesi L
Eukaryotic promoter recognition by binding sites for transcription factors.
Computer applications in the biosciences : CABIOS 1995;11(5):477-88.
1995: Kel O V; Romaschenko A G; Kel A E; Wingender E; Kolchanov N A
A compilation of composite regulatory elements affecting gene transcription in vertebrates.
Nucleic acids research 1995;23(20):4097-103.
1995: Kolchanov N A; Vishnevsky O V; Babenko V N; Kel A E; Shindyalov I N
Identification of cDNA sequences by specific oligonucleotide sets. Computer tool and application.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1995;3():206-14.
1995: Kel A E; Kondrakhin Y V; Kolpakov PhA; Kel O V; Romashenko A G; Wingender E; Milanesi L; Kolchanov N A
Computer tool FUNSITE for analysis of eukaryotic regulatory genomic sequences.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1995;3():197-205.
1994: Kondrakhin YuV; Shamin V V; Kolchanov N A
Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3'-terminal processing sites.
Computer applications in the biosciences : CABIOS 1994;10(6):597-603.
1994: Shindyalov I N; Kolchanov N A; Sander C
Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
Protein engineering 1994;7(3):349-58.
1993: Kel A E; Ponomarenko M P; Likhachev E A; Orlov YuL; Ischenko I V; Milanesi L; Kolchanov N A
SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites.
Computer applications in the biosciences : CABIOS 1993;9(6):617-27.
1992: Streletc V B; Shindyalov I N; Kolchanov N A; Milanesi L
Fast, statistically based alignment of amino acid sequences on the base of diagonal fragments of DOT-matrices.
Computer applications in the biosciences : CABIOS 1992;8(6):529-34.
1992: Rogozin I B; Kolchanov N A
Somatic hypermutagenesis in immunoglobulin genes. II. Influence of neighbouring base sequences on mutagenesis.
Biochimica et biophysica acta 1992;1171(1):11-8.
1991: Beniukh D N; Ponomarenko M P; Kolchanov N A
[Classification of DNA- (RNA)-interacting proteins based on recognition of structure-function determinants]
Biofizika 1991;36(6):957-67.
1991: Ponomarenko M P; Beniukh D N; Orlov Iu L; Kolchanov N A
[Precise recognition method of structure-function determinants of protein molecules]
Biofizika 1991;36(6):943-56.
1991: Rogozin I B; Solovyov V V; Kolchanov N A
Somatic hypermutagenesis in immunoglobulin genes. I. Correlation between somatic mutations and repeats. Somatic mutation properties and clonal selection.
Biochimica et biophysica acta 1991;1089(2):175-82.
1989: Shakhmuradov I A; Kapitonov V V; Kolchanov N A; Omel'ianchuk L V
[Evolution of Alu repeats: dynamics of distribution in genome]
Genetika 1989;25(9):1682-9.
1989: Ratner V A; Kolchanov N A; Omel'ianchuk L V
[Phylogenetic analysis of genes of the influenza virus. Relationship between adaptability and neutrality]
Genetika 1989;25(8):1499-507.
1989: Omel'ianchuk L V; Kolchanov N A; Ratner V A
[A phylogenetic analysis of genes of the influenza virus. Phylogenetic trees and fixation rates]
Genetika 1989;25(8):1391-401.
1989: Shakhmuradov I A; Kolchanov N A
[tRNA as a possible primer for the initiation of reverse transcription of dispersed repeats Alu, B1, B2 and L1]
Molekuliarnaia biologiia 1989;23(4):1130-7.
1989: Kolchanov N A; Solov'ev V V; Kel' A E
[Theoretical analysis of the DNA duplication mechanisms in the prokaryotic genomes on the basis of repeats]
Molekuliarnaia biologiia 1989;23(2):537-44.
1989: Shakhmuradov I A; Kolchanov N A; Kapitonov V V
[Distribution of Alu repeats along the human genome: formation of clusters and features of insertion regions]
Molekuliarnaia biologiia 1989;23(2):526-36.
1989: Kel' A E; Kolchanov N A; Solov'ev V V
[Theoretical analysis of mechanisms of occurrence of DNA deletions in prokaryotic genomes based on direct repeats]
Molekuliarnaia biologiia 1989;23(1):184-92.
1989: Kolchanov N A; Kel' A E; Solov'ev V V
[Statistical evidence for the correlation of DNA deletions in prokaryotic genomes with direct repeats]
Molekuliarnaia biologiia 1989;23(1):175-83.
1989: Solov'ev V V; Kel' A E; Kolchanov N A
[Convergent origin of repeats in genes coding for globular proteins. An analysis of the factors determining the presence of inverted and symmetrical repeats]
Zhurnal obshchei biologii 1989;50(1):116-22.
1989: Kiseleva E V; Kapitonov V V; Ovchinnikova L P; Khristoliubova N B; Kolchanov N A
[Detection of paired transcription complexes in bacterial chromatin]
Doklady Akademii nauk SSSR 1989;305(5):1235-8.
1988: Kolchanov N A; Kel' A E; Solov'ev V V
[Convergent origin of repeats in the genes coding for globular proteins. The modelling of the convergent origin of direct repeats]
Zhurnal obshchei biologii 1988;49(6):723-8.
1988: Kolchanov N A; Shakhmuradov I A; Kapitonov V V; Omel'ianchuk L V
[Various aspects of evolution of Alu repeats in mammals]
Molekuliarnaia biologiia 1988;22(5):1335-44.
1988: Kapitonov V V; Kolchanov N A
[Evolutionary significance of the presence in mobile genetic elements of regulatory sites reacting to the environment. Regulatory site as a trigger]
Genetika 1988;24(9):1696-703.
1988: Kel' A E; Kolchanov N A; Solov'ev V V
[Convergent origin of the repetitions in genes coding for globular proteins. An analysis of the factors determining the presence of direct repetitions]
Zhurnal obshchei biologii 1988;49(3):343-54.
1988: Kolchanov N A; Shindyalov I N
Single amino acid substitutions producing instability of globular proteins. Calculation of their frequencies in the entire mutational spectra of the alpha- and beta-subunits of human hemoglobin.
Journal of molecular evolution 1988;27(2):154-62.
1987: Kapitonov V V; Kolchanov N A; Shakhmuradov I A; Solov'ev V V
[Presence in the mobile genetic elements of regions homologous to the heat shock regulatory site]
Genetika 1987;23(12):2112-9.
1987: Kolchanov N A; Solovyov V V; Rogozin I B
Peculiarities of immunoglobulin gene structures as a basis for somatic mutation emergence.
FEBS letters 1987;214(1):87-91.
1987: Omel'ianchuk L V; Kolchanov N A
[Evolutionary study of genomes based on an analysis of primary tRNA structures]
Zhurnal obshchei biologii 1987;48(2):156-66.
1986: Shakhmuradov I A; Kolchanov N A; Solov'ev V V; Ratner V A
[Enhancer-like structures in moderately repetitive sequences of eukaryotic genomes]
Genetika 1986;22(3):357-67.
1985: Ratner V A; Omel'ianchuk L V; Zharkikh A A; Kolchanov N A
[Theoretical analysis of the structural characteristics and evolution of transfer RNAs]
Zhurnal obshchei biologii 1985;46(6):732-42.
1985: Shindialov I N; Kolchanov N A
[Factors determining the instability of the conformation of human mutant hemoglobins. A method for evaluating the instability]
Molekuliarnaia biologiia 1985;19(6):1501-13.
1985: Shindyalov I N; Kolchanov N A
Analysis of the factors and implications of an empirical method for estimating the stability of mutant human haemoglobins.
Journal of theoretical biology 1985;117(1):19-46.
1985: Kolchanov N A; Shindialov I N
[Estimation of the frequency of amino acid substitutions causing instability of the spatial structure in an overall mutation spectrum of alpha- and beta-subunits of human hemoglobin]
Genetika 1985;21(10):1740-8.
1985: Zharkikh A A; Solov'ev V V; Kolchanov N A
[The context analysis of polynucleotide sequences. II. Inverted repeats and complementary palindromes in RNA-polymerase genes]
Molekuliarnaia biologiia 1985;19(3):597-609.
1985: Solov'ev V V; Zharkikh A A; Kolchanov N A
[Context analysis of polynucleotide sequences. Methods of detecting non-random repeats. I. Direct repeats in genes of beta-, beta'-, sigma subunits of Escherichia coli RNA-polymerase]
Molekuliarnaia biologiia 1985;19(2):524-36.
1984: Solovyov V V; Kolchanov N A
A simple method for the calculation of low energy packings of alpha-helices--a threshold approximation. I. The use of the method to estimate the effects of amino acid substitutions, deletions and insertions in globins.
Journal of theoretical biology 1984;110(1):67-91.
1984: Solovyov V V; Zharkikh A A; Kolchanov N A; Ratner V A
The template RNAs of RNA polymerases can have compact secondary structure, formed by long double helices with partial violations of the complementarity.
FEBS letters 1984;165(1):72-8.
1984: Zharkikh A A; Solovyov V V; Kolchanov N A
Conformational changes in the globin family during evolution. 1. Analysis of the evolutionary role of insertions and deletions.
Journal of molecular evolution 1984;21(1):42-53.
1983: Zharkikh A A; Solov'ev V V; Kolchanov N A
[Evolutionary and conformational analysis of a family of globins. The evolutionary role of deletions and insertions]
Zhurnal obshchei biologii 1983;44(6):790-801.
1983: Kolchanov N A; Soloviov V V; Zharkikh A A
The effects of mutations, deletions and insertions of single amino acids on the three-dimensional structure of globins.
FEBS letters 1983;161(1):65-70.
1983: Kolchanov N A; Solov'ev V V; Zharkikh A A
[High saturation by direct copies in RNA-polymerase genes based on context analysis data]
Doklady Akademii nauk SSSR 1983;273(3):741-4.
1983: Solov'ev V V; Zharkikh A A; Kolchanov N A
[RNA-polymerase matrix RNAs have a compact secondary structure formed by long double helices with partial mispairing]
Doklady Akademii nauk SSSR 1983;273(5):1256-61.
1982: Omel'ianchuk L V; Kolchanov N A
[Recurrent relationship for the characteristic polynom of a system of enzymatic catalysis of nonbranched monomolecular reactions]
Biofizika 1982;27(3):404-9.

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