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"COMPUTATIONAL
SYSTEMS BIOLOGY:
from analysis to synthesis"
Проект "Системная биология"

Колчанов Николай Александрович



Директор ИЦиГ СО РАН,
Зав. Отделом системной биологии ИЦиГ СО РАН,
Академик РАН, проф. КОЛЧАНОВ Николай Александрович



Степень, звание: академик РАН, доктор биологических наук, профессор
Должность в НГУ: заведующий кафедрой информационной биологии ФЕН, профессор кафедр информационной биологии, цитологии и генетики
Должность по месту работы:директор Института цитологии и генетики СО РАН, заведующий Отделом системной биологии ИЦиГ СО РАН
Адрес: Новосибирск-90, пр. акад. Коптюга 2, ИЦиГ;
Телефон: +7 (383) 333-34-68
E-mail: kol@bionet.nsc.ru

Основные научные интересы: информационная биология, молекулярная биология, молекулярная генетика, компьютерный анализ структурно-функциональной организации и эволюции геномов, генетических макромолекул - ДНК, РНК и белков и молекулярно-генетических систем геномов.
Основные научные результаты. Созданы программно-информационные комплексы для решения задач биоинформатики и системной компьютерной биологии: интеграции, хранения и анализа экспериментальных данных по структурно-функциональной организации молекулярно-генетических систем; анализа и компьютерной аннотации геномных последовательностей, высокоточного распознавания сайтов связывания транскрипционных факторов; предсказания структуры и функции белков, поиска в них фармакологических мишеней; реконструкции и моделирования генных сетей, контролирующих процессы метаболизма в клетке и процессы морфогенеза растений; исследованы молекулярные механизмы функционирования и эволюции регуляторных генетических систем и мутационного процесса; разработаны компьютерно-экспериментальные подходы к конструированию геносенсоров, позиционируемых в микро/нанофлюидных системах, создаваемых на основе лигатехнологий с использованием синхротронного излучения. Исследовано применение терагерцового излучения для перехода ДНК и белков в форме наночастиц в аэрозольную фазу.
Публикации: Автор и соавтор более чем 480 публикаций в отечественной и зарубежной печати, в том числе - 9 монографий, 4 учебных пособий, 12 авторских свидетельств и 1 патента.

Н.А.Колчанов входит в состав:

  • Научного совета РАН по молекулярной биологии и генетике,

  • рабочей группы "Стратегия развития наноиндустрии" при Правительственном совете по нанотехнологиям,

  • Совета СО РАН по супервычислениям,

  • Бюро Объединенного ученого совета по наукам о жизни СО РАН,

  • редакционных коллегий журналов "In Silico Biology", "Сибирского журнала вычислительной математики" и "Сибирского экологического журнала" СО РАН, "Информационный Вестник ВОГИС"

Также он является

  • членом совета Российского фонда фундаментальных исследований (РФФИ),

  • членом Президиума СО РАН,

  • вице-президентом ВОГИС,

  • председателем Научного совета СО РАН по биоинформатике,

  • председателем Ученого совета ИЦиГ СО РАН,

  • заместителем председателя Научного совета РАН по генетике и селекции.

Web Resources:

GeneNet
a system designed for formalized description and automated visualization of gene networks.
http://wwwmgs.bionet.nsc.ru/mgs/systems/genenet/

TRRD
Transcription Regulatory Regions Database.
http://www.bionet.nsc.ru/trrd/

SITECON
a program package for revealing and analysis of conservative conformational and physicochemical properties in transcription factor binding sites sets.
http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/

CompoSITECON
a program package for searching potential composite binding sites in genomic sequences proposed by user
http://wwwmgs.bionet.nsc.ru/mgs/programs/compositecon/

EnPDB
search system for query implementation to the PDB (Protein Data Bank)
http://wwwmgs.bionet.nsc.ru/mgs/gnw/enpdb/

PDBSITE
a database on protein active sites and their spatial environment.
http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsite/

ASPD
(Artificial Selected Peptides/Proteins Database)
a curated database on proteins and peptides selected by in vitro directed evolution methods (phage display, ribosome display, SIP etc.) from randomized pools.
http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/

CRASP
a program package for revealing and analysis of co-adaptive amino acid substitutions in pairs of positions based on multiple sequence alignment in families of related proteins.
http://wwwmgs.bionet.nsc.ru/mgs/gnw/crasp/

PDBSiteScan
a Tool for Search for Functional Sites in Protein Tertiary Structures.
http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsitescan/

AGNS
Arabidopsis GeneNet Supplementary DataBase.
http://wwwmgs.bionet.nsc.ru/agns/

Recon program
a program to recognize nucleosome formation sites.
http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/

SiteGA
Transcription Factor Binding Sites recognition by Genetic Algorithm.
http://wwwmgs.bionet.nsc.ru/mgs/programs/sitega

ARGOViewer
Recognition of promoters of functionally important gene groups.
http://wwwmgs.bionet.nsc.ru/mgs/programs/argo/argo_viewer.html

GenSensor and ConSensor
databases containing information about the sensitivities of prokaryotic genes to external stimuli.
http://wwwmgs.bionet.nsc.ru/mgs/dbases/gensensor/index.html

Bibliography:

The following main publications:

Monographs:

Computational system biology (Eds. N. Kolchanov, S.S. Goncharov, V.A. Likhoshvai, V.A. Ivanisenko), Siberian Branch of the Russian Academy of Science, Novosibirsk, 2008, 650 pp.

Biosphere origin and evolution. Ed. By N.Dobretsov, N.Kolchanov, A.Rozanov, G.Zavarzin. Springer 2007, 430 pp.

Biodiversity and dynamic of ecosystems: Computational approaches and modeling. Ed. by V.K. Shumny, Yu.I.Shokin, N.A.Kolchanov, A.M.Fedotov. Siberian Branch of the Russian Academy of Science, Novosibirsk, 2006, 648 pp.

Bioinformatics of Genome Regulation and Structure II. (Eds. N.Kolchanov, R. Hofestaedt ,L.Milanesi), Springer Science+Business Media, Inc., New York, 2006,556 pp.

Bioinformatics of genome regulation and structure. (Eds. N.Kolchanov and R. Hofestaedt), Kluwer Academic Publishers, Boston/Dordrecht/London, 2004,373 pp.

Ratner V.A., Zharkikh A.A., Kolchanov N.A., Rodin S.N., Solovyov V.V., Antonov A.S. Molecular Evolution (Biomathematics: v. 24), Springer-Verlag, Berlin Heidelberg New York ,1996, 433 pp.

Computer Analysis of Genetic Macromolecules: Structure, Function and Evolution, (Eds. N.A. Kolchanov, H.A. Lim), World Scientific Pub. co., Singapore, New Jersey, London, Hong Kong, 1994, 556 pp. Author (co-editor with H.A. Lim)

Modelling and computer methods in molecular biology and genetics. (Novosibirsk, August 28- September,1990). (Eds V.A. Ratner and N.A. Kolchanov), Nova science Publishers, Inc., 1992, 508 pp.

Ratner V.A.,Zharkikh A.A,Kolchanov N.A.,Rodin S.N.,Solovyev V.V. Shamin V.V. Problems of the theory of molecular evolution. (Ed.R.I. Salganik) "Science",Siberian Branch of the USSR Academy of Science, Novosibirsk, (Russ) 1985,259 pp.

Educational books for university students:

Educational books for university students: Solovyev V.V., Kell A.E., Rogozin I.B., Kolchanov N.A. The application of computers in Molecular Biology. The theory of genetic texts. Novosibirsk State University (Russ), 1987, 90 pp.

Kolchanov N.A.,Solovyev V.V.,Shindyalov I.N.,Strelets V.B. The application of computers in Molecular Biology. The structural organization of globular proteins. Novosibirsk State University (Russ),1986, 90 pp.

Kell A.E., Kolchanov N.A.,Solovyev V.V.The mathematical modeling in the molecular biology and genetics. The theory of the mutational process: deletions and duplications. Novosibirsk State University ,1989, 86 pp.

Information biology and bioinformatics. Introduction. Eds. N.A.Kolchanov, O.V.Vishnevsky, N.A.Popova, D.P.Furman. Novosibirsk State University. 2008. 6 volumes, 1500 pp Selected Articles:

Ivanisenko V.A., Afonnikov D.A., Kolchanov N.A. Web-based computational tools for the prediction and analysis of posttranslational modifications of proteins. In: the 2nd ed. "Posttranslational Modifications of Proteins: Tools for Functional Proteomics", Series: "Methods in Molecular Biology". Vol. 446 Ed. by C. Kannicht, Humana Press, USA, 2nd ed., 2008, (415 pages) pp 359-376. (ISBN: 978-1-58829-719-8).

Ananko E.A., Kondrakhin Y.V., Merkulova T.I., Kolchanov N.A. Recognition of interferon-inducible sites, promoters, and enhancers. BMC Bioinformatics, 2007, 8:56.

Kochetov A.V., Palyanov A., Titov I.I., Grigorovich D., Sarai A., Kolchanov N.A. AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site. BMC Bioinformatics, 2007, 8(1):318 (Epub ahead of print)

Kolchanov N.A., Merkulova T.I., Ignatieva E.V., Ananko E.A., Oshchepkov D.Y., Levitsky V.G., Vasiliev G.V., Klimova N.V., Merkulov V.M., Hodgman T.C. Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes. Brief Bioinform, 2007, 8(4): 266-274, doi: 10.1093/bib/bbm027

Lashin S.A., Suslov V.V., Kolchanov N.A., Matushkin Yu.G.. Simulation of coevolution in community by using the "Evolutionary Constructor" program. In Silico Biology (Special Issue: 5th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2006)), 2007, 7: 0042.

Gunbin K.V., Afonnikov D.A., Kolchanov N.A. The evolution of the Hh-signaling pathway genes: a computer-assisted study. In Silico Biol., 2007, 7:0047

Khlebodarova T.M., Tikunova N.V., Kachko A.V., Stepanenko I.L., Podkolodny N.L., Kolchanov N.A. Application of bioinformatics resources for genosensor design. J Bioinform Comput Biol, 2007, 5(2b):507-520.

Akberdin I.R., Ozonov E.A., Mironova V.V., Omelyanchuk N.A., Likhoshvai V.A., Gorpinchenko D.N., Kolchanov N.A. A cellular automaton to model the development of primary shoot meristems of Arabidopsis thaliana. J Bioinform Comput Biol, 2007, 5(2b):641-50.

Mishchenko E.L., Bezmaternykh K.D., Likhoshvai V.A., Ratushny A.V., Khlebodarova T.M., Sournina N. Yu., Ivanisenko V.A., Kolchanov N.A. Mathematical model for suppression of subgenomic hepatitis C virus RNA replication in cell culture. J Bioinform Comput Biol, 2007, 5(2b):593-609.

Gunbin K.V., Omelyanchuk L.V., Kogai V.V., Fadeev S.I., Kolchanov N.A. Model of the reception of hedgehog morphogen concentration gradient: comparison with an extended range of experimental data. J Bioinform Comput Biol, 2007, 5(2b):491-506.

Ignatieva E. V., Klimova N. V., Oshchepkov D. Yu., Vasiliev G. V., Merkulova T. I., Corresponding Member of RAS Kolchanov N. A. Search for new binding sites for transcription factor SF-1 by the SITECON method:experimental verification and analysis of regulatory regions of orthologous genes. Dokl Akad Nauk, 2007, 415(1):120-4.

Gunbin K.V., Suslov V.V., Kolchanov N.A. Aromorphoses and the adaptive molecular evolution. The Herald Vavilov Soc Genet Breed Sci , 2007, 11(2):373-400 (In Russian).

Lashin S.A., Suslov V.V., Kolchanov N.A., Matushkin Yu.G. "Evolutionary constructor" - methodic for simulation of coevolution in community. Proceedeings of the Third International Moscow Conference on Computational Molecular Biology (MCCMB'07), Moscow, Russia, July 27-31 2007, 174-176.

Akberdin I.R., Ozonov E.A., Mironova V.V., Gorpinchenko D.N.,Omelyanchuk N.A., Likhoshvai V.A., Miginsky D.S., Kolchanov N.A. 2d modelling and analysis of spatially distributed cells types of primary shoot apical meristem (SAM) of Arabidopsis thaliana. Proceedeings of the Third International Moscow Conference on Computational Molecular Biology (MCCMB'07), Moscow, Russia, July 27-31 2007, 25-26.

Kochetov A.V., Ivanisenko V.A., Titov I.I., Kolchanov N.A., Sarai A. Signals influencing general translation efficiency of eukaryotic mRNAs. Proceedeings of the Third International Moscow Conference on Computational Molecular Biology (MCCMB'07), Moscow, Russia, July 27-31 2007, 152-153.

Lavreha V.V., Nikolaev S.V., Kolchanov N.A., Penenko A.V. Computer system for analysis and modeling 2D plant tissue. Proceedeings of the Third International Moscow Conference on Computational Molecular Biology (MCCMB'07), Moscow, Russia, July 27-31 2007, 177-178.

Nikolaev S., Fadeev S., Mjolsness E., Kolchanov N. Significance of molecular mechanisms of morphogen detection for pattern formation modeling. Proceedeings of the Third International Moscow Conference on Computational Molecular Biology (MCCMB'07), Moscow, Russia, July 27-31 2007, 226-227.

Zubairova U.S., Nikolaev S.V., Kolchanov N.A. An using of DL-systems to model of the renewable zone size control in growing tissue. . Proceedeings of the Third International Moscow Conference on Computational Molecular Biology (MCCMB'07), Moscow, Russia, July 27-31 2007, 328-329.

Gunbin K.V., Afonnikov D.A., Omelyanchuk L.V., Kolchanov N.A. The Hedgehog Signaling Cascade System: Evolution and Functional Dynamics. Proceedeings of the Third International Moscow Conference on Computational Molecular Biology (MCCMB'07), Moscow, Russia, July 27-31 2007, 114-116.

Kolchanov N.A., Suslov V.V., Gunbin K.V. Gene networks and evolution of regulatory genetic system. Current Evolutionary Thinking in Biology, Medicine and Sociology. International Conference Dedicated to 90 Anniversary of Prof. Dmitry K. Belyaev. Novosibirsk, Russia, August 7-9 2007. http://www.bionet.nsc.ru/meeting/Belyaev_2007/

Akberdin I.R., Ozonov E.A., Mironova V.V., Omelyanchuk N.A., Likhoshvai V.A., Gorpinchenko D.N., Kolchanov N.A. Mathematical model of the Arabidopsis thaliana L. morphogenesis in a cellular automaton terms. FEBS Journal, 2007, Vol. 274, S1, Abstracts of the 32nd FEBS Congress, Jul 2007, 134.

Akberdin I.R., Ozonov E.A., Mironova V.V., Gorpinchenko D.N., Omelyanchuk N.A., Likhoshvai V.A., Kolchanov N.A. Modelling and analysis of spatially distributed systems regulation in apical meristem of Arabidopsis thaliana. Proceedings of the 3-rd International Conference "Basic Science for Medicine", Novosibirsk, Russia, September 2-8 2007, 95.

Ivanisenko V.A., Demenkov P.S., Aman E.E., Pintus S.S., Kolchanov N.A. Associative network and protein structure discovery: a software complex for facilitating search of targets for drugs, drug design, and evaluation of molecular toxicity. Proceedings of the 3-rd International Сonference "Basic Science for Medicine", Novosibirsk, Russia, September 2-8 2007, 92.

Mazzarelli J.M., White P., Gorski R., Brestelli J., Pinney D.F., Arsenlis A., Katokhin A., Belova O., Bogdanova V., Elisafenko E., Gubina M., Nizolenko L., Perelman P., Puzakov M., Shilov A., Trifonoff V., Vorobjeva N., Kolchanov N., Kaestner K.H., Stoeckert CJ. Jr. Novel genes identified by manual annotation and microarray expression analysis in the pancreas. Genomics, 2006, 88(6):752-61.

Omelyanchuk N., Mironova V., Poplavsky A., Podkoldny N., Kolchanov N., Mjolsness E., Meyerowitz E. AGNS, a database on expression of Arabidopsis genes. In: Bioinformatics of Genome Regulation and Structure II. (Eds. Kolchanov N., Hofestaedt R., Milanesi L.) Springer Science+Business Media, Inc., New York, 2006, 433-442.

Ananko E., Oshchepkov D., Nedosekina E., Levitsky V., Lokhova I., Smirnova O., Likhoshvai V., Kolchanov N. Study of the interactions between viral and human genomes during transformation of B cells with Epstein-Barr virus. In: Bioinformatics of Genome Regulation and Structure II. (Eds. Kolchanov N., Hofestaedt R., Milanesi L.) Springer Science+Business Media, Inc., New York, 2006, 443-450.

Kolchanov N., Ignatieva E., Podkolodnaya O., Ananko E., Stepanenko I., Merkulova T., Khlebodarova T., Merkulov V., Podkolodny N., Grigorovich D., Poplavsky A., Romashchenko A. Transcription Regulatory Regions Database (TRRD): a source of experimentally confirmed data on transcription regulatory regions of eukaryotic genes. In: Bioinformatics of Genome Regulation and Structure II. (Eds. Kolchanov N., Hofestaedt R., Milanesi L.) Springer Science+Business Media, Inc., New York, 2006, 43-53.

Levitsky V., Ignatieva E., Vasiliev G., Limova N., Busygina T., Merkulova T., Kolchanov N. The SiteGA tool for recognition and context analysis of transcription factor binding sites: significant dinucleotide features besides the canonical consensus exemplified by SF-1 binding site. In: Bioinformatics of Genome Regulation and Structure II. (Eds. Kolchanov N., Hofestaedt R., Milanesi L.) Springer Science+Business Media, Inc., New York, 2006, 31-41.

Orlov Yu.L., Levitsky V.G., Smirnova O.G., Podkolodnaya O.A., Khlebodarova T.M., Kolchanov N.A. VMM: a variable memory Markov model prediction of nucleosome formation sites. In: Bioinformatics of Genome Regulation and Structure II. (Eds. Kolchanov N., Hofestaedt R., Milanesi L.) Springer Science+Business Media, Inc., New York, 2006, 85-95.

Levitsky V.G., Katokhin A.V., Podkolodnaya O.A., Furman D.P., Kolchanov N.A. NPRD: Nucleosome Positioning Region Database. Nucleic Acids Res, 2005, 33(Database issue):D67-70.

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 Res, 2005, 33(Database issue):D425-7.

Vishnevsky O.V., Kolchanov N.A. ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters. Nucleic Acids Res, 2005, 33(Web Server issue):W417-22.

Ivanisenko V.A., Eroshkin A.M., Kolchanov N.A. WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families. Nucleic Acids Res, 2005, 33(Web Server issue):W99-104.

Ivanisenko V.A., Pintus S.S., Grigorovich D.A., Kolchanov N.A. PDBSite: a database of the 3D structure of protein functional sites. Nucleic Acids Res, 2005, 33(Database issue):D183-7.

Kochetov A.V., Sarai A., Rogozin I.B., Shumny V.K., Kolchanov N.A. The role of alternative translation start sites in the generation of human protein diversity. Mol Genet Genomics, 2005, 273(6):491-6.

Oshchepkov D.Yu., Bugreev D.V., Kolchanov N.A., Nevinsky G.A. Computer analysis of the conformational and physico-chemical properties of DNA Topoisomerase I cleavage sites. Mol. Biol (Mosk), 2005, 39(3):488-496.

Orlov Yu.L., Levitsky V.G., Podkolodnaya O.A., Khlebodarova T.M., Kolchanov N.A. Prediction of nucleosome formation sites in gene regulatory regions. Proceedings of the International Moscow Conference on Computational Molecular Biology (MCCMB'05), Moscow State University, 2005, 270-271.

Kochetov A.V., Kolchanov N.A., Sarai A. The role of alternative translation start sites in generation of human protein diversity. Proceedings of the International Moscow Conference on Computational Molecular Biology (MCCMB'05), Moscow State University, 2005, 177-178.

Pintus S., Ivanisenko V.A., Kolchanov N.A. Computer analysis of structure and evolution of functional sites of the DNA-binding domain of human P53 protein. Proceedings of the International Moscow Conference on Computational Molecular Biology (MCCMB'05), Moscow State University, 2005, 297-298.

Nedosekina E.A., Ananko E.A., Likhoshvai V.A., Oshchepkov D.Yu., Kolchanov N.A. Modelling of signal transduction and gene expression regulation in immune system cells. In: Proceedings of the Conference on Modeling and Simulation in Biology, Medicine and Biomedical Engineering. Linkoping, Sweden, 2005, May 26-27, 125-128.

Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Stepanenko I.L., Khlebodarova T.M., Merkulova T.I., Pozdnyakov M.A., Proscura A.L., Grigorovich D.A., Podkolodny N.L., Naumochkin A.N., Romashchenko A.G., Kolchanov N.A. Transcription Regulatory Regions Database (TRRD): description of transcription regulation and the main capabilities of the database. In: Bioinformatics of Genome Regulation and Structure. (Eds. Kolchanov N., Hofestaedt R.) Kluwer Academic Publishers, Boston/Dordrecht/London, 2004, 81-92.

Oshchepkov D.Yu., Turnaev I.I., Pozdnyakov M.A., Milanesi L., Vityaev E.E., Kolchanov N.A. Sitecon - a tool for analysis of DNA physicochemical and conformational properties: E2F/DP transcription factor binding site analysis and recognition. In: Bioinformatics of Genome Regulation and Structure. (Eds. Kolchanov N., Hofestaedt R.) Kluwer Academic Publishers, Boston/Dordrecht/London, 2004, 93-102.

Pichueva A.G., Kochetov A.V., Milanesi L., Kondrakhin Yu.V., Kolchanov N.A. Correlations between sequence features of yeast genes functional regions and the level of expression. In: Bioinformatics of Genome Regulation and Structure. (Eds. Kolchanov N., Hofestaedt R.) Kluwer Academic Publishers, Boston/Dordrecht/London, 2004, 125-132.

Kondrakhin Yu.V., Podkolodnaya O.A., Kochetov A.V., Erokhin G.N., Kolchanov N.A. Statistical analysis of microarray data: identification and classification of yeast cell cycle genes. In: Bioinformatics of Genome Regulation and Structure. (Eds. Kolchanov N., Hofestaedt R.) Kluwer Academic Publishers, Boston/Dordrecht/London, 2004, 331-342.

Nedosekina E.A., Ananko E.A., Milanesi L., Likhoshvai V.A., Kolchanov N.A. Mathematical simulation of dynamics of macrophage gene network activated by lipopolysaccharides and/or interferon-gamma. In: Bioinformatics of Genome Regulation and Structure. (Eds. Kolchanov N., Hofestaedt R.) Kluwer Academic Publishers, Boston/Dordrecht/London, 2004, 283-292.

Ivanisenko V.A., Pintus S.S., Grigorovich D.A., Kolchanov N.A. PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res, 2004, 32(Web Server issue):W549-54.

Afonnikov D.A., Kolchanov N.A. CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences. Nucleic Acids Res, 2004, 32(Web Server issue):W64-8.

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. Mol Biol (Mosk), 2004, 38(1):69-81.

Kolchanov N.A., Latypov A.F., Likhoshvai V.A., Matushkin Yu.G., Nikulichev Yu.V., Ratushny A.V. Problems of optimal control in gene network dynamics and methods for their solving. Izvestiya RAS. Theory and systems of control (Rus). 2004, 6:36-45.

Suslov V.V., Gunbin K.V., Kolchanov N.A., Omelyanchuk N.A. Genetic mechanisms of morphological evolution, part 1. Siberian Journal of Ecology (Rus) 2004, 11(5):599-610.

Suslov V.V., Gunbin K.V., Kolchanov N.A., Omelyanchuk N.A. Genetic mechanisms of morphological evolution, part 2. Siberian Journal of Ecology (Rus) 2004, 11(5):611-621.

Suslov V.V., Gunbin K.V., Kolchanov N.A. Genetic mechanisms of biological complexity encoding. Ecological genetics (Rus). 2004, 2(1):13-26.

Likhoshvai V.A., Fadeev S.I., Matushkin Yu.G., Demidenko G.V, Kolchanov N.A. Mathematical modeling of regulatory circuits of gene networks. J Computational Mathematics and Mathematical Physics (Rus). 2004, 44(10):1921-1940.

Omelianchuk N.A., Mironova V.V., Poplavsky A.S., Kukeeva Yu.A., Podkolodny N.L., Kolchanov N.A. AGNS: Arabidopsis GeneNet Supplementary Database. Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2004), 2004, 2:121-124.

Kochetov A.V., Sarai A., Kolchanov N.A. Translational polymorphism as a potential source of eukaryotic proteins variety. Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2004), 2004, 1:107-109.

Ratushny A.V., Likhoshvai V.A., Ignatieva E.V., Kolchanov N.A. Robustness of key components of homeostatic gene networks to a wide range of mutations. The 12th International Conference on Intelligent Systems for Molecular Biology (ISMB 2004) and 3rd the European Conference on Computational Biology (ECCB 2004), Conference programme, 2004, p. 219.

Ratushny A.V., Likhoshvai V.A., Ignatieva E.V., Kolchanov N.A. Robustness of homeostatic gene networks target products to a wide range of mutations and perturbations in the cell. ISMB 2004 and ECCB 2004 Satellite Meeting, Special Interest Group in Simulations and Modelling, Book of abstracts, 2004, p. 29.

Kolchanov N.A., Pozdnyakov M.A., Orlov Y.L., Vishnevsky O.V., Podkolodny N.L., Vityaev E.E., Kovalerchuk B. Computer system "Gene Discovery" for promoter structure analysis. In: Artificial Intelligence and Heuristic Methods in Bioinformatics. (Eds.: Frasconi and R. Shamir) IOS Press, 2003, 173-192.

Stepanenko I., Kolchanov N. Apoptosis gene network: description in the GeneNet and TRRD databases. Ann N Y Acad Sci, 2003, 1010:16-8.

Kochetov A.V., Kolchanov N.A., Sarai A. Interrelations between the efficiency of translation start sites and other sequence features of yeast mRNAs. Mol Genet Genomics, 2003, 270(5):442-7.

Ratushny A.V., Likhoshvai V.A., Ignatieva E.V., Kolchanov N.A. Resilience of cholesterol concentration to a wide range of mutations in the cell. Complexus, 2003, 1:142-148.

Zagoruiko N.G., Kolchanov N.A., Pichueva A.G., Kutnenko O.A., Borisova I.A., Kochetov A.V., Ivanisenko V.A., Nikolaev S.V., Likhoshvai V.A., Ratushnyi A.V. Data mining techniques in bioinformatics. Pattern Recognition and Image Analysis, 2003. 13(4):550-555.

Kolchanov N.A., Hofestaedt R. The 3rd International conference on bioinformatics of genome regulation and structure (BGRS'2002). Preface. In Silico Biology 2003, 3(1-2):1-2.

Kolchanov N.A., Likhoshvai V.A., Ananko E.A., Stepanenko I.L.,Podkolodnaya O.A., Ignatieva E.V., Ratushny A.V., Nedosekina E.A., Podkolodny N.L. GeneNet Discovery: gene networks reconstruction,analysis and modeling. Proceedeings of the First International Moscow Conference on Computational Molecular Biology (MCCMB'03), Moscow, Russia, 2003, 109-111.

Pichueva A.G., Kochetov A.V., Kondrakhin Yu.V., Kolchanov N.A Relationship between the contextual features of yeast core promoter and the level of gene expression. Proceedeings of the First International Moscow Conference on Computational Molecular Biology (MCCMB'03), Moscow, Russia, 2003, 187.

Proscura A.L., Levitsky V.G., Oshchepkov D.Yu., Pozdnyakov M.A., Ignatieva E.V., Kolchanov N.A. Expression of lipid metabolism genes: description in TRRD database and computer-assisted analysis. Proceedeings of the First International Moscow Conference on Computational Molecular Biology (MCCMB'03), Moscow, Russia, 2003, 194-195.

Afonnikov,D.A., Nikolaev,S.V., Ivanisenko,V.A., Kolchanov,N.A. Сlassification of local spatial environment of amino acid residues by physicochemical characteristics in transcription factor DNA-binding domains. Proceedeings of the First International Moscow Conference on Computational Molecular Biology (MCCMB'03), Moscow, Russia, 2003, 17-18.

Ratushny A.V., Likhoshvai V.A., Matushkin Y.G., Kolchanov N.A., Borisova I.A., Zagoruiko N.G. Computer analysis of mutations and evolution of gene networks. Proceedeings of the First International Moscow Conference on Computational Molecular Biology (MCCMB'03), Moscow, Russia, 2003, 198-199.

Ratushnyi A.V., Likhoshvai V.A., Ignat'eva E.V., Matushkin Y.G., Goryanin, II, Kolchanov N.A. A computer model of the gene network of the cholesterol biosynthesis regulation in the cell: analysis of the effect of mutations. Dokl Biochem Biophys, 2003, 389:90-93.

Kochetov A.V., Pichueva A.G., Kondrakhin Yu.V., Titov S.E., Kolchanov N.A. The contextual features of higher plant mRNA 5'-untranslated regions as related to the translation initiation mechanisms. Biofizika. 2003, 48(1):76-80.

Kolchanov N.A., Suslov V.V., Shumnyi V.K. Molecular evolution of genetic systems Paleontological Journal, 2003, N6:58-71.

Kolchanov N.A., Ananko E.A., Likhoshvani V.A., Podkolodnaya O.A., Ignatieva E.V., Ratushny A.V., Matushkin Yu.G. Gene networks description and modeling in the GeneNet system, Chapter 5. In "Gene Regulation and Metabolism". (Eds. Julio Collado-Vides and Ralf Hofestadt) The MIT Press, Cambridge, Massachusetts, 2002, 149-180.

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 Res, 2002, 30(1):398-401.

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 Res, 2002, 30(1):312-7.

Valuev V.P., Afonnikov D.A., Ponomarenko M.P., Milanesi L., Kolchanov N.A. ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro. Nucleic Acids Res, 2002, 30(1):200-202.

Kutsenko A.S., Gizatullin R.Z., Al-Amin A.N., Wang F., Kvasha S.M., Podowski R.M., Matushkin Y.G., Gyanchandani A., Muravenko O.V., Levitsky V.G., Kolchanov N.A., Protopopov A.I., Kashuba V.I., Kisselev L.L., Wasserman W., Wahlestedt C., Zabarovsky E.R. Not I flanking sequences: a tool for gene discovery and verification of the human genome. Nucleic Acids Res, 2002, 30(14):3163-70.

Kolchanov N.A., Nedosekina E.A., Ananko E.A., Likhoshvai V.A., Podkolodny N.L., Ratushny A.V., Stepanenko I.L., Podkolodnaya O.A., Ignatieva E.V., Matushkin Y.G. GeneNet database: description and modeling of gene networks. In Silico Biol, 2002, 2(2):97-110.

Orlov Y.L., Filippov V.P., Potapov V.N., Kolchanov N.A. Construction of stochastic context trees for genetic texts. In Silico Biol, 2002, 2(3):233-47.

Vityaev E.E., Orlov Y.L., Vishnevsky O.V., Pozdnyakov M.A., Kolchanov N.A. Computer system "Gene Discovery" for promoter structure analysis. In Silico Biol, 2002, 2(3):257-62.

Hofestadt R, Kolchanov N,Reinitz J. Information and simulation systems for the analysis of gene regulation and metabolic pathways. In Silico Biology, 2002, 2:35-36.

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. Mol Biol (Mosk), 2002, 36(6):1026-34.

Ananko E.A., Podkolodny N.L., Ignatieva E.V., Podkolodnaya O.A., Stepanenko I.L., Kolchanov N.A. GeneNet system: its status in, 2002. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 2:70-73.

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., Kolchanov N.A. Transcription Regulatory Regions Database (TRRD): its status in 2002. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 1:10-13.

Borisova I.A., Zagoruiko N.G., Likhoshvai V.A., Ratushny A.V., Kolchanov N.A. Diagnostics of mutations based on analysis of gene networks. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 2:163-165.

Ivanisenko V.A., Grigorovich D.A., Kolchanov N.A. PDBSITE: A database on protein active sites and their environmen. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:145-148.

Ivanisenko V.A., Debelov V.A., Pintus S.S., Matsokin A.M., Nikolaev S.V., Grigorovich D.A., Kolchanov N.A. PDBSiteScan: A tool for search for the best-matching superposition in the database PDBSite. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:149-152.

Kolchanov N.A., Podkolodny N.L., Likhoshvai V.A., Loktev K.A., Ananko E.A., Ignatieva E.V., Podkolodnaya O.A., Stepanenko I.L., Nedosekina E.A., Matushkin Yu.G., Ratushny A.V., Tkachev Yu.A., Borisova I.A., Zagoruiko N.G., Dobrynin A.A., Makarov L.I., Fadeev S.I., Gainova I.A., Latypov A.F., Nikulichev Yu.V. Computer systemic biology: informational and software toolsfor complex molecular biological systems. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 2:140-142.

Kolchanov N.A., Podkolodny N.L., Ananko E.A., Ignatieva E.V., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Lavryushev S.V., Grigorovich D.A., Kochetov A.V., Orlova G.V., Titov I.I., Vishnevsky O.V., Orlov Yu.L., Ivanisenko V.A., Vorobiev D.G., Oschepkov D.Yu., Omel'yanchuk N.A., Pozdnyakov M.A., Afonnikov D.A., Matushkin Yu.G., Likhoshvai V.A., Ratushny A.V., Katokhin A.V., Turnaev I.I., Proskura A.L., Suslov V.V., Nedosekina E.A. GeneExpress - 2002: an integrated system on gene expression regulation. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:232-234.

Latypov A.F., Nikulichev Yu.V., Likhoshvai V.A., Ratushny A.V., Matushkin Yu.G., Kolchanov N.A. Problems of control of gene networks in a space of stable states. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 2:195-198.

Latypov A.F., Nikulichev Yu.V., Likhoshvai V.A., Ratushny A.V., Matushkin Yu.G., Kolchanov N.A. A method of solving problems of optimal control in dinamics of gene networks. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 2:199-202.

Likhoshvai V.A., Kochetov A.V., Matushkin Yu.G., Kolchanov N.A. Structural features of mRNA region at the translation start site. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:55-57.

Ratushny A.V., Likhoshvai V.A., Matushkin Yu.G., Kolchanov N.A. Evolution of diploid gene network of cholesterol biosynthesis regulation in a cell. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 2:160-162.

Ratushny A.V., Likhoshvai V.A., Kolchanov N.A. Analysis of mutational portraits of gene networks. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 2:157-159.

Stepanenko I.L., Podkolodnaya O.A., Kolchanov N.A. Gene networks: principles of organization and mechanisms of operation and integration. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 2:109-113.

Matushkin Yu.G., Levitsky V.G., Likhoshvai V.A., Vishnevsky O.V., Kutsenko A.S., Protopopov A.I., Zabarovsky E.R., Kolchanov N.A. Analysis of the secondary structure and nucleosomal potential of Not I sites of the human genome. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:235-239.

Kochetov A.V., Kolchanov N.A., Sarai A. Unoptimal translation start site correlates with increased content of in-frame downstream AUG codons at the beginning of CDS of eukaryotic mRNAs. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:52-54.

Titov I.I., Kochetov A.V., Kolchanov N.A., Sarai A. Computer analysis of mRNA untranslated regions of hypoxia-induced corn genes. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:46-48.

Kochetov A.V., Sarai A., Grigorovich D.A., Kolchanov N.A. Database on mRNA-located eucariotic translational signals. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:40-42.

Pozdnyakov M.A., Vityaev E.E., Ananko E.A., Busygina T.V., Ignatieva E.V., Proskura A.L., Podkolodnaya O.A., Podkolodny N.L., Merkulova T.I., Kolchanov N.A. Detection of the core structure of transcription factor binding sites. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:251-254.

Afonnikov D.A., Ivanisenko V.A., Grigorovich D.A., Valuev V.P., Nikolaev S.V., Kolchanov N.A. Resources for the analysis of protein sequences and structures in the GeneExpress system. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:138-140.

Nikolaev S.V., Afonnikov D.A., Ivanisenko V.A., Bazhan S.I., Kolchanov N.A. Comparison of methods for predicting proteasome cleavage motifs. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:108-111.

Nikolaev S.V., Ivanisenko V.A., Afonnikov D.A., Bazhan S.I., Kolchanov N.A. An index for estimating the efficiency of antigenic epitope generation during proteasomal proteolysis. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:112-114.

Vishnevsky O.V., Avdeeva I.V., Kolchanov N.A. Study of the specific contextual features of translation initiation and termination regions in eukaryotes. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:72-76.

Vityaev E.E, Kostin V.S., Podkolodny N.L., Kolchanov N.A. Natural classification of nucleotide sequences. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:197-199.

Vityaev E.E., Pozdnyakov M.A., Orlov Yu.L., Vishnevsky O.V., Podkolodny N.L., Kolchanov N.A. Gene Discovery computer system for analysis of regulatory regions. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:257-259.

Zagoruiko N.G., Pichueva A.G., Kutnenko O.A., Borisova I.A., Kochetov A.V., Ivanisenko V.A., Nikolaev S.V., Likhochvai V.A., Ratushny A.V., Kolchanov N.A. Application of the method of intellectual data analysis to solving the problems of bioinformatics. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3;204-207.

Kolchanov N.A., Valishev A.I., Popova N.A. On specialization "BIOINFORMATICS" in the Novosibirsk State University and High College of informatics of Novosibirsk State University. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3;220-221.

Brunk B., Crabtree J., Diskin S., Mazzarelli J., Zigouras N., Alkalaeva E., Bogdanova V., Trifonoff V., Vorobjeva N., Katokhin A., Kolchanov N., Stoeckert C. Manual annotation of the human and mouse gene index: www.allgenes.org. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 1:182-184.

Vityaev E.E., Orlov Yu.L., Pozdnyakov M.A., Vishnevsky O.V., Kolchanov N.A., Kovalerchuk B.K. Knowledge discovery for promoter structure analysis. Proceedings of the International Conference on Imaging Science, Systems, and Technology, Eds.: Hamid R. Arabnia, Youngsong Mun, Las Vegas, Nevada, USA, June 24-27, 2002, CSREA Press, v.1:122-128.

Vityaev E.E., OrlovYu.L., Vishnevsky O.V., Kovalerchuk B.Ya., Belenok A.S., Podkolodnii N.L., Kolchanov N.A. Knowledge discovery for gene regulatory regions analysis. In: Knowledge-Based Intelligent Information Engineering Systems and Allied Technologies, KES, 2002. (Eds. E.Damiani, R. Howlett, L.Jain, N. Ichalkaranje) IOS Press, Amsterdam, 2002, part 1, 487-491.

Ratushny A.V., Likhoshvai V.A., Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Matushkin Y.G., Kolchanov N.A. Computer dynamic modeling of gene networks and the analysis of the action of mutations. 10th Intern. Conf. on Intelligent Systems for Molecular Biology, Conf. program, 2002, 107.

Kolchanov N.A Bioinformatics of genomic regulation and structure. Mol Biol (Mosk). 2001,35(6):931-3.

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. Mol Biol (Mosk), 2001, 35(6):934-42.

Kochetov A.V., Grigorovich D.A., Titov, II, Vorob'ev D.G., Syrnik O.A., Vishnevskii O.V., Sarai A., Kolchanov N.A. mRNA-FAST (mRNA-Function, Activity, STructure) computer system. Mol Biol (Mosk), 2001, 35(6):1039-47.

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. Mol Biol (Mosk), 2001, 35(6):961-9.

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. Mol Biol (Mosk), 2001, 35(6):952-960.

Afonnikov D.A., Kolchanov N.A. The conserved characteristics of DNA-binding domains belonging to the homeodomain class that are associated with coadaptive substitutions of amino acid residues. Dokl Biochem Biophys, 2001, 380:352-355.

Kolchanov N.A., Hodgman C. The 2nd international conference on the Bioinformatics of Genome Regulation and Structure (BGRS-2000), Novosibirsk, August 2000. Bioinformatics, 2001, 17:997.

Levitsky V.G., Podkolodnaya O.A., Kolchanov N.A., Podkolodny N.L. Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis. Bioinformatics, 2001, 17(11):998-1010.

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, 2001, 17(11):1035-46.

Levitsky V.G., Podkolodnaya O.A., Kolchanov N.A., Podkolodny N.L. Nucleosome formation potential of exons, introns, and Alu repeats. Bioinformatics, 2001, 17(11):1062-4.

Valuev V.P., Afonnikov D.A., Ponomarenko M.P., Kolchanov N.A. ASPD (Artificial Selected Proteins/Peptides Database) - a tool for proteomic studies. European Journal of Biochemistry, 2001, 268(Suppl. 1):44.

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 Res, 2001, 29(1):284-7.

Ponomarenko J., Ponomarenko M., Orlova G., Kolchanov N., Sarai A. Conformational B-helix DNA properties specific to DNA free energy of protein binding to DNA with point mutation focused on SNP-analysis. Proceedings of the Pacific Symposium on Biocomputing (PSB '2001), January 3-7, 2001, Hawaii, USA, (Eds. Altman R.S., et al.), Singapore: World Scientific, p. 118.

Kochetov A., Grigorovich D., Sarai A., Kolchanov N. Database on mRNA-located eukaryotic expression signals influencing translation efficiency and specificity. Proc. Int. Conf. "RNA as therapeutic and genomics target'2001" Novosibirsk, Russia. 2001, 64.

Vityaev E.E., Orlov Yu.L., Vishnevsky O.V., Kovalerchuk B.K., Belenok A.S., Podkolodnii N.L., Kolchanov N.A. Computer system "Gene Discovery" for functional annotation of DNA sequences. In: ECML'2001 Workshop Machine Learning as Philosophy of Science. (Eds. Korb K.B., Bensusan H.) Freiburg, Sept., 2001, 1-11.

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 Res, 2000, 28(1):311-5.

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 Res, 2000, 28(1):298-301.

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 Res, 2000, 28(1):205-8.

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. Mol Biol (Mosk), 2000, 34(4):533-44. 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. Mol Biol (Mosk), 2000, 34(2):214-22.

Ivanisenko V.A., Grigorovich D.A., Kolchanov N.A. PDBSite: a database on biologically active sites and their spatial surroundings in proteins with known tertiary structure. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 2:171-174.

Ananko E.A., Kolpakov F.A., Kolchanov N.A. GeneNet database: a technology for a formalized description of gene networks. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 1:174-177.

Titov I.I., Kolchanov N.A., Schroder H.C. Model of phosphate high-affinity transport in bacteria. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 3:62-64.

Ignatieva E.V., Podkolodny N.L., Kolchanov N.A. Informational support of ontology for transcription regulation (ISOTR). Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 3: 99-102.

Kel-Margoulis O.V., Romashchenko A.G., Deineko I.V., Kolchanov N.A., Wingender E. Kel A.E. Database on composite regulatory elements in eukaryotic genes (COMPEL). Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 1:45-48.

Kolchanov N.A., Podkolodny N.L., Ponomarenko M.P., Ananko E.A., Ignatieva E.V., Kolpakov F.A., Levitsky V.G., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Vorobiev D.G., Lavryushev S.V., Grigorovich D.A., Ponomarenko J.V., Kochetov A.V., Orlova G.V., Kondrakhin Y.V., Titov I.I., Vishnevsky O.V., Orlov Yu.L, Valuev V.P., Ivanisenko V.A, Oschepkov D.Yu., Omel'yanchuk N.A., Pozdnyakov M.A., Kosarev P.S., Goryachkovskaya T. N., Fokin O.N., Kalinichenko L.A., Kotlyarov Yu.V. Integrated system on gene expression regulation GeneExpress - 2000. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 1:12-17.

Kolchanov N.A. Regulatory genomic sequences: coding, organization, and function. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 1:168-172.

Levitsky V.G., Kolchanov N.A. Nucleosome organization of chromatin in eukaryotic genes and structure-functional genome regions. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 1:90-93.

Ananko E.A., Podkolodnaya O.A., Ignatieva E.V., Kel-Margoulis O.V., Kel A.E., Merkulova T.I., Stepanenko I.L., Goryachkovskaya T. N., Podkolodny N.L., Grigorovich D.A., Naumochkin A.N., Korostishevskaya I.M., Lokhova I.V., Romashchenko A.G., Kolchanov N.A. Transcription Regulatory Regions Database (TRRD). Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 1:18-21.

Kochetov A.V., Vorobiev D.G., Sirinko.A., Kisselev L.L., Kolchanov N.A. Contextual features of yeast mRNA 5'UTRs potentially important for their translational activity. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 1:67-70.

Kochetov A.V., Sirnik O.A., Komarova M.L., Trifonova E.A., Kolchanov N.A., Shumny V.K. Translational features of 5'UTR-located miniORFs. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 1:74-77.

Kondrakhin Y.V., Milanesi L., Lavryushev S.V., Schug J., Kolchanov N.A. Recognition groups: a new method for description and prediction of transcription factor binding sites. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 1:62-65.

Titov I.I., Vorobiev D.G., Kolchanov N.A. Mass analysis of RNA secondary structures using a genetic algorithm. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 2:138-142.

Vorobiev D.G., Titov I.I., Kochetov A.V., Kolchanov N.A. Structural features of mRNA 5'UTRs of eukaryotic genes expressed at high and low levels. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 2:135-137.

Grigorovich D.A., Ivanisenko V.A., Kolchanov N.A. Structure and format of the EnPDB database accumulating spatial structures of DNA, RNA and proteins. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 2:119-121.

Levashova Z.B., Kaledin V.I., Ponomarenko M.P., Kobzev V.F., Vasiliev G.V., Ponomarenko J.V., Podkolodnaya O.A., Merkulova T.I., Kolchanov N.A. Single nucleotide polymorphism in the region of 288-296 bp of intron 2 of the k-ras gene, related to lung tumor susceptibility, causes alteration in the set of proteins binding to this region. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 1:164-167.

Merkulova T.I., Vasiliev G.V., Ponomarenko M.P., Kobzev V.F., Podkolodnaya O.A., Ponomarenko Yu.V., Kolchanov N.A. Analysis of the region of intron 6 of the human TDO2 gene in that point mutations associated with psychiatric disorders are located with the aid of computer and experimental approaches. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 1:134-137.

Vityaev E.E., Podkolodny N.L., Vishnevsky O.V., Kosarev P.S., Ananko E.A., Ignatieva E.V., Podkolodnaya O.A., Kolchanov N.A. Detecting patterns of structure-function organization of regulatory genomic sequences in a first order logic. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 1:150-152.

Valishev A.I., Kolchanov N.A., Podkolodny N.L., Melnikov V.N., Alsynbayeva L.G., Yaroslavtseva R.G., Haans W.J.A. Bioinformatics: novel profile of vocational education. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2000), 2000, 2:232-234.

Levitsky V.G., Katokhin A.V., Kolchanov N.A. Inherent modular promoter structure and its application for recognition tools development. Computational Technologies, 2000, 5(Special Issue):41-47.

Afonnikov D.A., Oshchepkov D.Yu., Kolchanov N.A. A method of estimation of variances and covariances of protein physico-chemical characteristics in families of homologous sequences. Computational Technologies, 2000, 5(Special Issue):79-86.

Kolchanov N.A., Podkolodny N.L., Ananko E.A., Podkolodnaia O.A., Ignatieva E.V., Merkulova T.I., Goryachkovsky T.N., Stepanenko I.L., Kel-Margoulis O.V., Kel A.E., Naumochkin I.M., Grigorovich D.A., Lokhova I.V., Romashchenko A.G. Transcription Regulatory Regions Database (TRRD): new possibilities. Computational Technologies, 2000, 5(Special Issue):32-40.

Titov I.I., Ivanisenko V.A., Kolchanov N.A. Fitness - a WWW-resource for RNA folding simulation based on genetic algorithm with local minimization. Computational Technologies, 2000, 5(Special Issue):48-56.

Vishnevsky O.V., Katokhin A.V., Babenko V.N., Overton G.C., Kolchanov N.A. Open reading frame reconstruction by using EST multiple alignment and dynamic programming. Computational Technologies, 2000, 5(Special Issue):16-25.

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):628-631.

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):649-654.

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.

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., et al. WWWMGS: an integrated server for molecular-genetic studies. Biofizika, 1999, 44(5):832-836.

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., et al. 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.

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.

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 Res, 1999, 27(1):303-6.

Levitsky V.G., Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Kolchanov N.A. Nucleosomal DNA property database. Bioinformatics, 1999, 15(7-8):582-92.

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, 1999, 15(7-8):631-643.

Kochetov A.V., Ponomarenko M.P., Frolov A.S., Kisselev L.L., Kolchanov N.A. Prediction of eukaryotic mRNA translational properties. Bioinformatics, 1999, 15(7-8):704-12.

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, 1999, 15(7-8):654-68.

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, 1999, 15(7-8):669-86.

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, 1999, 15(7-8):687-703.

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 Lett, 1999, 462(1-2):85-8.

Kolchanov N.A., Frolov A.S., Lavryushev S.V., Grigorovich D.A., Kolpakov F.A., Ananko E.A., Podkolodny N.L., Overton G.C., Ptitcyn A.A. WWWMGS: an integrative server for molecular genetic studies. In: Proceedings of the international conference "Advances in Systemics, Signals, Control and Computers, SSCC'99, Durban, South Africa" (Ed. Bajic V.B.), IAAMSAD and SAB ANS, 1999, 2:316-320.

Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Merkulova T.I., Podkolodny N.L., Frolov A.S., Kolchanov N.A. The genes regulated by PPARs: the presentation in the TRRD database. E2: Keystone Symposia on Molecular and Cellular Biology. The PPARs: Transcriptional Links to Obesity, Diabetes and Cardiovascular Disease. Keystone, Colorado, April 28 - May 2, 1999, Abstract #126, p.34.

Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Podkolodnaya O.A., Vorobyev D.V., Kolchanov N.A., Overton G.C. Mean-recognition: a systematic approach increasing the accuracy of the functional site recognition for the genomic DNA annotation. Proceedings of the World Multiconference on Systemics, Cybernetics and Informatics, SCI'98,(Ed. N. Callaos, L. Holmes), Orlando, Florida, July 12-16, 1998, 4:224-230.

Kolchanov N.A., Matushkin Yu.G., Frolov A.S. Regulation mechanisms in biological systems. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 1:111-114.

Ananko E.A., Kolpakov F.A., Kolesov G.B., Kolchanov N.A. Gene networks: a database and its automated visualization through the internet in the GeneNet computing system. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 1:82-85.

Kel-Margoulis O.V., Kel A.E., Frisch M., Romashchenko A.G., Kolchanov N.A., Wingender E. COMPEL: a database on composite regulatory elements. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 1:54-57.

Kolesov G.B., Kolpakov F.A., Kolchanov N.A. New method for the study of the modular structure of transcription regulatory regions. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 2:430-433.

Kolchanov N.A., Ignatieva E.V., Kel-Margoulis O.V., Kel A.E., Ananko E.A., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Goryachkovsky T.N., Kolpakov F.A., Podkolodny N.L., Lavryushev S.V., Grigorovich D.A., Frolov A.S., Romashchenko A.G. Transcription Regulatory Regions Database (TRRD): new possibilities provided by release 4.0. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 1:25-28.

Kochetov A.V., Ponomarenko M.P., Vorobiev D.G., Frolov A.S., Kisselev L.L.1, Kolchanov N.A. Eukaryotic mRNAs encoding abundant and scarce proteins are dissimilar in many structural features of 5'-untranslated leaders. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 1:214-217.

Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Vorobiev D.G., Levitsky V.G., Podkolodnaya O.A., Overton G.C.&, Kolchanov N.A. B-DNA-VIDEO:an active database for the significant B-DNA features of transcription factor binding sites. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 1:66-70.

Kolchanov N.A., Ponomarenko M.P., Kondrakhin Y.V., Frolov A.S., Kolpakov F.A., Kel A.E., Kel-Margoulis O.V., Ananko E.A., Ignatieva E.V., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Babenko V.N., Vorobiev D.G., Lavryushev S.V., Grigorovich D.A., Ponomarenko J.V., Kochetov A.V., Kolesov G.B., Podkolodny N.L., Wingender E., Hainemeier T., Milanesi L., Solovyev V.V., Overton G.C. GeneExpress system:description, analysis, and recognition of regulatory sequences in eukaryotic genomes. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 1:71-76.

Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Podkolodnaya O.A., Vorobiev D.G., Kolchanov N.A., Overton G.C. Recognition accuracy of DNA functional sites can be increased by averaging partial recognitions. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 1:158-162.

Ponomarenko M.P., Kolchanov N.A., Shindyalov I., Bourne P. Likeness: a system searching for and aligning similar protein conformations. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 2:370-374.

Likhacheva E., Ponomarenko M.P., Bogachev S., Kokoza E., Fisher P., Ponomarenko J.V., Vorobiev D.G., Kolesov G.B., Kolchanov N.A. The structural analysis of the DNA fragments associated with the nuclear lamins in Drosophila melanogaster. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 2:247-248.

Ponomarenko M.P., Kolchanov N.A., Ponomarenko J.V., Frolov A.S., Podkolodnaya O.A., Vorobiev D.G., Podkolodny N.L., Overton G.C. Revealing the conformational and physico-chemical DNA properties applicable for predicting the activity of DNA functional sites. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 1:186-190.

Ponomarenko M.P., Vorobiev D.G., Ponomarenko J.V., Kuzin F.E., Gruzdev A.D., Kolchanov N.A. Significant B-DNA conformational and physico-chemical properties of the DNA topoisomerase I sites. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 2:446-447.

Savinkova L.K., Sokolenko A.A., Rau V.A., Kobzev V.F., Ponomarenko M.P., Ponomarenko J.V., Kolchanov N.A. Quantitative computer-assisted analysis of the TATA-binding protein affinity for complementary duplexes of synthetic oligodeoxyribonucleotides. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 1:165-169.

Ponomarenko M.P., Ishchenko I.V., Frolov A.S., Ponomarenko J.V., Kolchanov N.A., Mikhailov Yu.I., Minina A.V., Ivashin S.A. Bioinformatics for humanitarians. Proceedings of the First Iternational Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1998, 2:417-418.

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 Res, 1998, 26(1):362-7.

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 Lett, 1998, 440(3):351-355.

Kolpakov F.A., Ananko E.A., Kolesov G.B., Kolchanov N.A. GeneNet: a gene network database and its automated visualization. Bioinformatics, 1998, 14(6):529-37.

Kolchanov N.A., Kel A.E., Podkolodnaya O.A., Kel O.V., Romaschenko A.G., Wingender E., Overton G.C. TRRD, GERD and COMPEL: Databases on Gene-Expression Regulation as a Tool for Analysis of Functional Genomic Sequences. DOE Human Genome Program Report, U.S. Gov. Print. Office. 1998, 2:35-36.

Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Podkolodnaya O.A., Vorobyev D.V., Kolchanov N.A., Overton G.C. Mean-recognition: a systematic approach increasing the accuracy of the functional site recognition for the genomic DNA annotation. Proceedings of the World Multiconference on Systemics, Cybernetics and Informatics, SCI'98, July 12-16, 1998, Orlando, Florida. (Eds. N. Callaos, L. Holmes) 4:224-230.

Kolchanov N.A., Ponomarenko M.P., Kel A.E., Kondrakhin Yu V., 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 Yu V., 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. Proc Int Conf Intell Syst Mol Biol, 1998, 6:95-104.

Ponomarenko, Kolchanov N., Kel A., Kondrakhin Y., Frolov A., Kolpakov F., Kel O., Ananko E., Ignatieva E., Podkolodnaya O., Stepanenko I., Merkulova T., Babenko V., Vorobiev D., Lavryushev S., Ponomarenko J., Kochetov A., Kolesov G., Podkolodny N. (Russia), L. Milanesi (Italy), E. Wingender (Germany), T. Heinemeyer (Germany), and V. Solovyev (United Kingdom). GeneExpress: a computer system for investigating molecular mechanisms of gene expression. Abstracts XVIIIth International Congress of Genetics, August 10-15, 1998, Beijing, China, p. 62, 4S24.

Ponomarenko M.P., Ponomarenko Iu V., Titov, II, Kolchanov N.A., Mazin A.V., Kowalczykowski S.C. Preference of RecA-filament to the DNA sequences correlates with genetic code. Dokl Akad Nauk 1998, 363(1):122-5.

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. Mol Biol (Mosk), 1998, 32(2):255-67.

Wingender E., Kel A.E., Kel O.V., Karas H., Heinemeyer T., Dietze P., Knuppel R., Romaschenko A.G., Kolchanov N.A. TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. Nucleic Acids Res 1997, 25(1):265-8.

Ponomarenko M.P., Savinkova L.K., Kel A.E., Kolchanov N.A. Computer modeling of TATA-box sequences of eukaryotic promoters. Dokl Akad Nauk 1997, 355(4):557-61.

Pozdniakov M.A., Rogozin I.B., Babenko V.N., Kolchanov N.A. Neighboring base effect on emergence of spontaneous mutations in human pseudogenes. Dokl Akad Nauk 1997, 356(4):566-8.

Kolpakov F.A., Kel A.E., Ponomarenko M.P., Kolchanov N.A. High heterogeneity of higher eukaryotic gene promoters, transcribed by RNA polymerase II. Dokl Akad Nauk 1997, 357(5):693-5.

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. Pac Symp Biocomput 1997:340-51.

Afonnikov D.A., Kondrakhin Yu.V., Titov I.I., Kolchanov N.A. Detecting direct correlations between positions in multiple aligment of amino acid sequences. Computer science and biology. Genome informatics: Function, structure, phylogeny. Proc. of the German Conference on Bioinformatics GCB'97, (Eds. Mewes H.W., Frishman D),Kloster Irsee, Bavaria, Sept. 22-24, 1997, 87-98.

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. Mol Biol (Mosk) 1997, 31(4):733-40.

Ponomarenko M.P., Savinkova L.K., Ponomarenko Iu V., Kel A.E., Titov, II, Kolchanov N.A. Modeling TATA-box sequences in eukaryotic genes`. Mol Biol (Mosk) 1997, 31(4):726-32.

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. Mol Biol (Mosk) 1997, 31(4):637-46.

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. Mol Biol (Mosk) 1997, 31(4):626-36.

Kel O.V., Kel A.E., Romashchenko A.G., Wingender E., Kolchanov N.A. Composite regulatory elements: classification and description in the COMPEL database. Mol Biol (Mosk) 1997, 31(4):601-15.

Kolchanov N.A. Transcriptional regulation of eukaryotic genes: data bases and computer analysis. Mol Biol (Mosk) 1997, 31(4):581-3.

Ponomarenko M.P., Kolchanova A.N., Kolchanov N.A. Generating programs for predicting the activity of functional sites. J Comput Biol 1997, 4(1):83-90.

Kolchanov N.A., Matushkin Yu.G. A Biological self-reproducing systems: principles of organization and evolution. Russian Journal of Genetics, 1997, 33(8):889-897.

Kolchanov N.A., Babenko V.N., Vishnevskii O.V., Kel A.E. Oligonucleotide vocabularies of isofunctional families of genes that code proteins. Dokl Akad Nauk 1996, 348(5):696-9.

Ponomarenko M.P., Kel A.E., Kolchanova A.N., Kolchanov N.A. Contextual signals and antisignals of the intron td-homing site. Dokl Akad Nauk 1996, 348(3):424-7.

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. Mol Biol (Mosk) 1996, 30(2):432-41. Rogozin I.B., Milanesi L., Kolchanov N.A. Gene structure prediction using information on homologous protein sequence. Comput Appl Biosci 1996, 12(3):161-70.

Rogozin I.B., Sredneva N.E., Kolchanov N.A. Somatic hypermutagenesis in immunoglobulin genes. III. Somatic mutations in the chicken light chain locus. Biochim Biophys Acta 1996, 1306(2-3):171-8.

Kolchanov N.A., Titov, II, Vlassova I.E., Vlassov V.V. Chemical and computer probing of RNA structure. Prog Nucleic Acid Res Mol Biol 1996, 53:131-96.

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 Res 1995, 23(20):4097-103.

Kel A.E., Kondrakhin Y.V., Kolpakov Ph A., Kel O.V., Romashenko A.G., Wingender E., Milanesi L., Kolchanov N.A. Computer tool FUNSITE for analysis of eukaryotic regulatory genomic sequences. Proc Int Conf Intell Syst Mol Biol 1995, 3:197-205.

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. Proc Int Conf Intell Syst Mol Biol 1995, 3:206-14.

Ponomarenko M.P., Savinkova L.K., Kolchanova A.N., Kel A.E., Kolchanov N.A. Quantitative analysis of dissociation constant of transcription factor TFIID complex with synthetic ssDNA 15-mers. Notes of Gene-Finding and Gene Structure Prediction Workshop, Penn Tower Hotel, Philadelphia, October 13-14, 1995, 1-5.

Kel O.V., Romachenko A.G., Kel A.E., Naumochkin A.N., Kolchanov N.A. Data representation in the TRRD - a database of transcription regulatory regions of the eukaryotic genomes.

Proceedings of the 28th Annual Hawaii International Conference on System Scienses [HICSS]. v.5, Biotechnology Computing, IEE Computer Society Press, Los Alamitos, California, 1995, 42-51.

Kondrakhin Y.V., Kel A.E., Kolchanov N.A., Romashchenko A.G., Milanesi L. Eukaryotic promoter recognition by binding sites for transcription factors. Comput Appl Biosci 1995, 11(5):477-88.

Kondrakhin Yu V., Shamin V.V., Kolchanov N.A. Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3'-terminal processing sites. Comput Appl Biosci 1994, 10(6):597-603.

Shindyalov I.N., Kolchanov N.A., Sander C. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng 1994, 7(3):349-58.

Ptitsyn A.A., Strelets V.B., Rogozin I.B., Kel A.E., Milanesi L., Kolchanov N.A. The AutoGene v1.0: a computer system for automatic molecular genetic analysis, Novosibirsk, 1994, 47 pp.

Milanesi L., Kolchanov N.A., Rogozin I.B., Kel A.E. Titov I.I. Sequence Functional Inference. Guide to Human Genome Computing (Eds.Martin J., Bishop.), Academic press, 1994, 249-312.

Kel A.E., Ponomarenko M.P., Likhachev E.A., Orlov Yu L., Ischenko I.V., Milanesi L., Kolchanov N.A. SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. Comput Appl Biosci 1993, 9(6):617-27.

Kolchanov N.A., Kel A.E., Ponomarenko M.P., Romachenko A.G., Likchachev J., Milanesi L., Lim H.A. Patterns of oligonucleotides distribution within DNA and RNA functional sites. Proceedings of the Second International Conference on Bioinformatic, Supercomputing and Complex Genome Analysis (Eds.C.R.Cantor & H.A.Lim), Jun 1992, St. Petersburg, Florida, USA, 1993, 445-464.

Rogozin I.B., Kolchanov N.A. Somatic hypermutagenesis in immunoglobulin genes. II. Influence of neighbouring base sequences on mutagenesis. Biochim Biophys Acta 1992, 1171(1):11-8.

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. Comput Appl Biosci 1992, 8(6):529-34.

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. Biochim Biophys Acta 1991, 1089(2):175-82.

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.

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.

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. Mol Biol (Mosk) 1989, 23(1):184-92.

Kolchanov N.A., Rogozin I.B., Solov'ev V.V. Theoretical analysis of mechanisms of spontaneous and induced mutations in DNA based on repeated sequences. Genetika 1989, 25(9):1690-8.

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. 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.

Kapitonov V.V., Shakhmuradov I.A., Kolchanov N.A. Evolution of Alu repeats: imitation model. Genetika 1989, 25(6):1111-8.

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.

Kiseleva E.V., Kapitonov V.V., Ovchinnikova L.P., Khristoliubova N.B., Kolchanov N.A. Detection of paired transcription complexes in bacterial chromatin. Dokl Akad Nauk SSSR 1989, 305(5):1235-8.

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. Mol Biol (Mosk) 1989, 23(2):537-44.

Kolchanov N.A., Kel A.E., Solov'ev V.V. Statistical evidence for the correlation of DNA deletions in prokaryotic genomes with direct repeats. Mol Biol (Mosk) 1989, 23(1):175-83. 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. Mol Biol (Mosk) 1989, 23(4):1130-7.

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. Mol Biol (Mosk) 1989, 23(2):526-36.

Solov'ev V.V., Rogozin I.V., Kolchanov N.A. Somatic hypermutagenesis in immunoglobulin genes. I. Connection of somatic mutations with repeats. A statistical weighting method. Mol Biol (Mosk) 1989, 23(3):783-94.

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. Zh Obshch Biol 1989, 50(1):116-22.

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. J Mol Evol 1988, 27(2):154-62.

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.

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. Zh Obshch Biol 1988, 49(3):343-54.

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. Zh Obshch Biol 1988, 49(6):723-8.

Kolchanov N.A., Shakhmuradov I.A., Kapitonov V.V., Omel'ianchuk L.V. Various aspects of evolution of Alu repeats in mammals. Mol Biol (Mosk) 1988, 22(5):1335-44.

Potapov V.A., Sosnovtsev S.V., Solovyev V.V., Ivanov S.V., Romashenko A.G., Kolchanov V.A. Structure of complex repeats in fox precentromere geterochromatin: regulatory elements of replication, recombination, and gene expression. Dokl Akad Nauk SSSR 1988, 299(5):1250-1255.

Omel'ianchuk L.V., Kolchanov N.A. Evolutionary study of genomes based on an analysis of primary tRNA structures. Zh Obshch Biol 1987, 48(2):156-66.

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):2112-2119.

Kolchanov N.A., Solovyov V.V., Rogozin I.B. Peculiarities of immunoglobulin gene structures as a basis for somatic mutation emergence. FEBS Lett 1987, 214(1):87-91.

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.

Merkulova T.I., Solov'ev V.V., Kolchanov N.A., Plisov S., Salganik R.I. Identification of the nucleotide sequences specific for the 5'-flanking regions of the genes regulated by glucocorticoids by a computer analysis method. Biull Eksp Biol Med 1986, 101(4):466-8.

Shindyalov I.N., Kolchanov N.A. Analysis of the factors and implications of an empirical method for estimating the stability of mutant human haemoglobins. J Theor Biol 1985, 117(1):19-46.

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.

Kolchanov N.A., Solov'ev V.V., Rogozin I.B. Molecular mechanism of somatic hypermutagenesis in immunoglobulin genes. Dokl Akad Nauk SSSR 1985, 281(4):994-999.

Solov'ev V.V., Kolchanov N.A. Exon-intron structure of eukaryotic genes can be due to the nucleosome organization of chromatin and to its related characteristics of gene expression regulation. Dokl Akad Nauk SSSR 1985, 284(1):232-237.

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. Mol Biol (Mosk) 1985, 19(2):524-536.

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. Mol Biol (Mosk) 1985, 19(3):597-609.

Shindialov I.N., Kolchanov N.A. Factors determining the instability of the conformation of human mutant hemoglobins. A method for evaluating the instability. Mol Biol (Mosk) 1985, 19(6):1501-13.

Ratner V.A., Omel'ianchuk L.V., Zharkikh A.A., Kolchanov N.A. Theoretical analysis of the structural characteristics and evolution of transfer RNAs. Zh Obshch Biol 1985, 46(6):732-42.

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 Lett 1984, 165(1):72-8.

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. J Theor Biol 1984, 110(1):67-91.

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. J Mol Evol 1984, 21(1):42-53.

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 Lett 1983, 161(1):65-70.

Kolchanov N.A., Solov'ev V.V., Zharkikh A.A. High saturation by direct copies in RNA-polymerase genes based on context analysis data. Dokl Akad Nauk SSSR 1983, 273(3):741-4.

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. Dokl Akad Nauk SSSR 1983, 273(5):1256-61.

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. Zh Obshch Biol 1983, 44(6):790-801.

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.

Solovyov V.V., Kolchanov N.A. Single amino acid substitutions can lead to the complete distortion of a normal tertiary structure of globular proteins. Genetika 1982, 18(10):1573-80.

Kolchanov N.A., Omelyanchuk L.V. Estimation of the tRNA and 5S RNA secondary structures based upon their polynucleotide chains. Studia Biophysic, 1982, 87(2/3):115-116.

Solovyov V.V., Kolchanov N.A. The method of calculation of low-energy conformations of alpha-helical pairs of globular proteins. Mol Biol (Mosk) 1981, 15(1):323-35.

Kolpakov M.G., Kolchanov N.A., Matveev P.A., Poliak M.G., Protsenko M.I. Feedback mechanisms in the renin-angiotensin system. Izv Akad Nauk SSSR Biol 1977, 1:113-9.

Poliak M.G., Kolchanov N.A. Mathematical modelling of the distribution and metabolism of angiotensin II. Nauchnye Doki Vyss Shkoly Biol Nauki 1975(8):41-6.

Zhegalina L.V., Kolchanov N.A., Poliak M.G. Presence of a renin inhibitor in the plasma of intact dogs. Biull Eksp Biol Med 1975, 80(10):48-51.

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