Essential Laboratory 6 publications since year 2000

2000

Articles

• A.G. Vitreshchak, M.S. Gel"fand “Computer analysis of control signals in bacterial genomes. Attenuators of operons of aromatic amino acids metabolism”, Molecular Biology (Moscow), 2000, Vol. 34, No. 4, P. 461–67, URL: http://www.springerlink.com/content/rn126571v2w17765/?p=7f037f93bed342e1950dae9eeaa6ee32, DOI: 10.1007/BF02759555
• А.В. Зарелуа, В.А. Любецкий «Предисловие редакторов к 1-му тому», в книге А. Маллиос «Геометрия векторных пучков», Мир, 2000, 460 стр.
• V.G. Kanovei, M. Reeken “On Ulam"s Problem of Stability of Non-exact Homomorphisms”, Proceedings of the Steklov Institute of Mathematics, 2000, Vol. 231, P. 238–270, URL: http://mi.mathnet.ru/eng/tm/v231/p249
• K.Yu. Gorbunov, V.A. Lyubetsky “On an algorithm of detecting regulatory signal in sequence data”, Logic research, Iss. 7, Moscow, Nauka, 2000, P. 159–163, in Russian
• N.K. Vereschagin, V.A. Lyubetsky “An algorithm of inferring RNA secondary structure”, Proceedings of scientific workshop of the Logic Center of RAS, Iss. 14, Moscow, RAS, 2000, P. 99–109, in Russian

Books

• V.A. Lyubetsky, M.J.A. Larijani “Topics in Classical and Intuitionistic Model Theory”, Gardariki, Moscow, 2000, 390 pages

Abstracts

• N.A. Kusnetsov, V.A. Lyubetsky, A.V. Chernavsky “On the concept of informational interaction, 1: pre-psychic bioinformatics”, Proceedings of II international conference of the RAS “Issues in control and modeling in complex systems”, Samara, Russia, RAS Press, 2000, P. 8–20, in Russian
• A.G. Vitreschak, А.К. Bansal, M.S. Gelfand “Comparative approach to analysis of regulation in complete genomes: attenuators of aromatic amino acid operons of gamma-proteobacteria”, Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS’2000), Novosibirsk, Russia, August 7–11 2000, Vol. 2, P. 57–58, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/pages/bgrs2000.html
• А.Г. Витрещак, М.С. Гельфанд «Сравнительный подход к анализу регуляции в полных геномах: аттенюаторы ароматических аминокислотных оперонов гамма-протеобактерий», Материалы школы-конференции «Горизонты физико-химической биологии», Пущино, Май 2000, стр. 231
• A.G. Vitreschak, А.А. Mironov, M.S. Gelfand “Comparative approach of regulation in complete genomes: attenuators of aromatic amino acid operons of gamma-proteobacteria”, Proceedings of the second International Conference "ComplexSystems: Control and modeling problems", Samara, Russia, June 2000, P. 141–142
• V.V. V"yugin, K.Yu. Gorbunov, V.A. Lyubetsky “Algorithms of detecting regulatory signal and constructing evolutionary trees”, Proceedings of II international conference of the RAS “Issues in control and modeling in complex systems”, Samara, Russia, RAS Press, 2000, P. 130–137, in Russian

2001

Articles

• E.M. Panina, A.G. Vitreschak, A.A. Mironov, M.S. Gelfand “Regulation of Aromatic Amino Acid Biosynthesis in Gamma-Proteobacteria”, Journal of Molecular Microbiology and Biotechnology (JMMB), Vol. 3, No. 4, Oct 2001, P. 529–543, URL: http://www.horizonpress.com/jmmb/tocs/v3n4toc.html, PMID: 11545272
• А.В. Зарелуа, В.А. Любецкий «Предисловие редакторов ко 2-му тому», в книге А. Маллиос «Геометрия векторных пучков», Мир, 2001, 442 стр.
• V.G. Kanovei “Nonstandard Set Theory in Э-Language”, Mathematical Notes, 2001, Vol. 70, No. 1-2, P. 42–45, URL: http://www.springerlink.com/content/m73167239788104t/, DOI: 10.1023/A:1010265716574
• L.V. Danilova, K.Yu. Gorbunov, M.S. Gelfand, V. A. Lyubetskii “Algorithm of Regulatory Signal Recognition in DNA Sequences”, Molecular Biology (Moscow), Vol. 35, No. 6, 2001, P. 841–848, URL: http://www.springerlink.com/content/un4v052738h0634u/, PMID: 11771146

Preprints

• L.V. Danilova, K.Yu. Gorbunov, M.S. Gelfand, V.A. Lyubetsky “An algorithm to detect regulatory signals in DNA sequence data”, Information processes, Vol. 1, No. 1, 2001, P. 56–63, in Russian
• M.S. Gelfand, V.V. V"yugin, V.A. Lyubetsky “An approach to infer evolutionary species tree from multiple gene data”, Information processes, Vol. 1, No. 1, 2001, P. 64–77, in Russian
• V.V. V"yugin, V.A. Lyubetsky “An algorithm to detect horizontal gene transfer events with multiple gene trees”, Information processes, Vol. 1, No. 2, 2001, P. 167–177, in Russian
• K.Yu. Gorbunov, E.V. Lyubetskaya, V.A. Lyubetsky “On two algorithms of searching for alternative RNA structures”, Information processes, Vol. 1, No. 2, 2001, P. 178–187, in Russian

Abstracts

• N.A. Kusnetsov, V.A. Lyubetsky, A.V. Chernavsky “On the concept of informational interaction, 2: pre-speech intellect”, Proceedings of III international conference of the RAS “Issues in control and modeling in complex systems”, Samara, Russia, RAS, 2001, P. 25–42, in Russian
• A.G. Vitreschak, А.А. Mironov, M.S. Gelfand “Computer prediction of RNA secondary structure. The RNApattern program: searching for RNA secondary structure by the pattern rule”, Proceedings of the third International Conference "ComplexSystems: Control and modeling problems", Samara, Russia, June 2001, P. 623–625
• A.G. Vitreschak “Computer analysis of regulation of genes, encoding aminoacyl-tRNA synthetases and amino acid biosynthetic proteins in Gram positive bacteria: T-box RNA regulatory element. Prediction of regulation of new genes, including amino acid transporters”, Abstracts of International School “Artifical Intelligence and Heuristic Methods for Bioinformatics”, Italy, San-Miniato, October 1–11 2001, P. 63
• M.S. Gelfand, O.N. Laikova, А.А. Mironov, P.S. Novichkov, E.M. Panina, D.A. Rodionov, A.G. Vitreschak “Comparative analysis of bacterial patterns”, Abstracts of Meeting of HHMI International Research Scholars, Vancouver, Canada, June 20–23 2001, P. 75
• V.A. Lyubetsky, A.V. Seliverstov “A probabilistic algorithm of solving an NP-complete problem”, Proceedings of III international conference “Smirnov readings” of RAS, Moscow, 2001, P. 47–49, in Russian
• V.A. Lyubetsky “First projective sets, AE-prefix and quantifiers elimination”, Abstracts of International conference on Mathematical Logic, Algebra and Set theory dedicated to the 100-th anniversary of P.S. Novikov, Steklov Mathematical Institute RAS, Moscow, August 27–31 2001, P. 27
• L.V. Danilova, V.A. Lyubetsky “An algorithm to detect regulatory signal: testing and biological applications”, Proceedings of III international conference of the RAS “Issues in control and modeling in complex systems”, Samara, Russia, RAS, 2001, P. 632–634, in Russian

2002

Articles

• A.G. Vitreschak, D.A. Rodionov, A.A. Mironov, M.S. Gelfand “Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation”, Nucleic Acids Research, Vol. 30, No. 14, July 15 2002, P. 3141–3151, Oxford University Press, URL: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12136096, PMID: 12136096
• D.A. Rodionov, A.G. Vitreschak, A.A. Mironov, M.S. Gelfand “Comparative Genomics of Thiamin Biosynthesis in Procaryotes. New Genes and Regulatory Mechanisms”, The Journal of Biological Chemistry, Vol. 277, No. 50, Dec 13 2002, P. 48949–48959, URL: http://www.jbc.org/content/277/50/48949, PMID: 12376536
• V.V. V"yugin, M.S. Gelfand and V.A. Lyubetsky “Tree Reconciliation: Reconstruction of Species Phylogeny by Phylogenetic Gene Trees”, Molecular Biology (Moscow), Vol. 36, No. 5, 2002, P. 650–658, URL: http://www.springerlink.com/content/x351018pr2pm3w68/, DOI: 10.1023/A:1020667228952, PMID: 12391844

Preprints

• А.Г. Витрещак «Компьютерное предсказание регуляторных сайтов мРНК. Анализ регуляции экспрессии генов биосинтеза аминокислот и генов, кодирующих тРНК-синтетазы в грам-положительных бактериях», Информационные процессы, том 2, № 1, 2002, стр. 91–95, URL: http://www.jip.ru/2002/2-1-2002.htm
• K.Yu. Gorbunov, V.A. Lyubetsky “An algorithm to search for conservative RNA secondary structures in a database of RNA fragments”, Information processes, Vol. 2, No. 1, 2002, P. 55–58, in Russian
• L.A. Leont"yev, E.V. Lyubetskaya, V.A. Lyubetsky “Description and performance of a modified algorithm to search for alternative RNA secondary structures”, Information processes, Vol. 2, No. 1, 2002, P. 100–105, in Russian
• V.V. V"yugin, V.A. Lyubetsky “Some approaches to detect HGTs with phylogenetic data”, “Information processes”, Vol. 2, No. 1, 2002, P. 120–140, in Russian

Abstracts

• N.A. Kusnetsov, V.A. Lyubetsky, A.V. Chernavsky “On the concept of informational interaction, 3: speech intellect”, Proceedings of IV international conference of the RAS “Issues in control and modeling in complex systems”, Samara, Russia, RAS, 2002, P. 7–17, in Russian
• L.V. Danilova, M.S. Gelfand “Search for regulatory signals in groups of orthologous genes of gamma-proteobacteria”, Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2002), Novosibirsk, Russia, July 14–20 2002, Vol. 2, P. 21–22, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/pages/bgrs2002.html
• E.M. Panina, A.G. Vitreschak, A.A. Mironov, M.S. Gelfand “Bioinformatics approach to analysis of regulation of aromatic amino acids biosynthesis in Bacillus/Clostridium group”, Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2002), Novosibirsk, Russia, July 14–20 2002, Vol. 2, P. 32–34, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/pages/bgrs2002.html
• A.G. Vitreschak, D.A. Rodionov, A.A. Mironov, M.S. Gelfand “Regulation of bacterial riboflavin genes by a conserved RNA structural element”, Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2002), Novosibirsk, Russia, July 14–20 2002, Vol. 2, P. 44–46, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/pages/bgrs2002.html
• A.G. Vitreschak, E.M. Panina, D.A. Rodionov, A.A. Mironov, M.S. Gelfand “Comparative analysis of RNA regulation in bacterial genomes”, Proceedings of the Meeting of International Research Scholars of the Howard Hughes Medical Institute, Palm Cove, Australia, June 25–28 2002
• A.G. Vitreschak “Computer analysis of regulation of genes, encoding aminoacyl-tRNA synthetases and amino acid biosynthetic proteins in Gram positive bacteria: T-box RNA regulatory element. Prediction of regulation of new genes, including amino acid transporters”, Proceedings of the International Summer School "From Genome to Life: Structural, Functional and Evolutionary Approaches", Cargese, Corsica, France, July 15–27 2002, P. 57–58
• V.A. Lyubetsky, L.I. Rubanov “Parallel algorithm for searching regulatory signal in bacterial genome”, Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2002), Novosibirsk, Russia, July 14–20 2002, Vol. 1, P. 24–27, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/pages/bgrs2002.html
• V.A. Lyubetsky, V.V. V"yugin “Method of horizontal gene transfer determination using phylogenetic data”, Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2002), Novosibirsk, Russia, July 14–20 2002, Vol. 2, P. 61–63, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/pages/bgrs2002.html
• E.V. Lyubetsky, V.A. Lyubetsky “Algorithm for searching for alternative secondary RNA structures”, Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2002), Novosibirsk, Russia, July 14–20 2002, Vol. 3, P. 14–16, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/pages/bgrs2002.html
• K.Yu. Gorbunov, V.A. Lyubetsky “An algorithm for searching for common secondary structures in a set of RNA sequences”, Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2002), Novosibirsk, Russia, July 14–20 2002, Vol. 3, P. 20–22, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/pages/bgrs2002.html

2003

Articles

• L.V. Danilova, M.S. Gelfand, V.A. Lyubetsky, O.N. Laikova “Computer-Assisted Analysis of Regulation of the Glycerol-3-Phosphate Metabolism in Genomes of Proteobacteria”, Molecular Biology (Moscow), Vol. 37, No. 5, 2003, P. 716–722, URL: http://www.springerlink.com/content/t2016v0w73r38312/, PMID: 14593921
• M.S. Gelfand, V.A. Lyubetsky “DNA: from molecules toward genomes, from biochemical breakthroughs toward algorithmic analysis”, Proceedings of the RAS (Vestnik RAN), No. 11, 2003, P. 963–970, in Russian
• E.V. Lyubetskaya, L.A. Leont"ev, M.S. Gelfand, V.A. Lyubetsky “Search for Alternative RNA Secondary Structures Regulating Expression of Bacterial Genes”, Molecular Biology (Moscow), Vol. 37, No. 5, 2003, P. 707–715, URL: http://www.springerlink.com/content/p45t6p6614l76811/, PMID: 14593920
• A.G. Vitreschak, D.A. Rodionov, А.А. Mironov, M.S. Gelfand “Regulation of the vitamin B₁₂ metabolism and transport in bacteria by a conserved RNA structural element”, RNA, Vol. 9, No. 9, Sep 2003, P. 1084–1097, URL: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12923257, PMID: 12923257
• D.A. Rodionov, A.G. Vitreschak, А.А. Mironov, M.S. Gelfand “Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?”, Nucleic Acids Research, Vol. 31, No. 23, Dec 1 2003, P. 6748–6757, URL: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=14627808, PMID: 14627808
• D.A. Rodionov, A.G. Vitreschak, А.А. Mironov, M.S. Gelfand “Comparative genomics of the vitamin B₁₂ metabolism and regulation in prokaryotes”, The Journal of Biological Chemistry, Vol. 278, No. 42, Oct 17 2003, P. 41148–41159, URL: http://www.jbc.org/cgi/content/full/278/42/41148, PMID: 12869542
• E.M. Panina, A.G. Vitreschak, A.A. Mironov, M.S. Gelfand “Regulation of biosynthesis and transport of aromatic amino acids in low-GC Gram-positive bacteria”, FEMS Microbiology Letters, Vol. 222, Iss. 2, May 28 2003, P. 211–220, URL: http://www.sciencedirect.com/science/article/pii/S0378109703003033, PMID: 12770710
• Z. Zhang, J.N. Feige, A.B. Chang, I.J. Anderson, V.M. Brodianski, A.G. Vitreschak, M.S. Gelfand, M.H. Saier “A transporter of Escherichia coli specific for l- and d-methionine is the prototype for a new family within the ABC superfamily”, Archives of microbiology, Vol. 180, No. 2, Aug 2003, P. 88–100, URL: http://www.springerlink.com/content/ylj23b9fp53be09d/, DOI: 10.1007/s00203-003-0561-4, PMID: 12819857
• P.V. Golubtsov, V.A. Lyubetsky “Stochastic Dynamic Games with Various Types of Information”, Problems of Information Transmission, Vol. 39, Iss. 3, 2003, P. 266–293, URL: http://www.springerlink.com/content/qwpk022273302137/, DOI: 10.1023/A:1026114615609
• V.G. Kanovei, V.A. Lyubetsky “On some classical problems of descriptive set theory”, Russian mathematical surveys, Vol. 58, Iss. 5, 2003, P. 839–927, DOI: 10.1070/RM2003v058n05ABEH000666
• P.V. Golubtsov, V.A. Lyubetsky “Informational structure of dynamic games and the information content available to players”, Logic research, Iss. 10, 2003, P. 39–49, in Russian
• K.Yu. Gorbunov “A Generalization of the Hilbert Basis Theorem”, Mathematical Notes, Vol. 74, No. 3-4, P. 483–490, URL: http://www.springerlink.com/content/p2q4470144076567/, DOI: 10.1023/A:1026187625738
• V.A. Lyubetsky, V.V. V"yugin “Methods of horizontal gene transfer determination using phylogenetic data”, In Silico Biology, IOS Press, Vol. 3, No. 1,2, 2003, P. 17–31, URL: http://www.bioinfo.de/isb/2003/03/0003, PMID: 12762843
• L.V. Danilova, V.A. Lyubetsky, M.S. Gelfand “An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation”, In Silico Biology, Vol. 3, No. 1,2, 2003, P. 33–47, URL: http://www.bioinfo.de/isb/2003/03/0004, PMID: 12762844
• V.V. V"yugin, M.S. Gelfand, V.A. Lyubetsky “Identification of Horizontal Gene Transfer from Phylogenetic Gene Trees”, Molecular Biology (Moscow), Vol. 37, No. 4, 2003, P. 571–584, URL: http://www.springerlink.com/content/w22575448864j5mu/, PMID: 12942641
• K.Yu. Gorbunov, A.A. Mironov, V.A. Lyubetsky “Search for Conserved Secondary Structures of RNA”, Molecular Biology (Moscow), Vol. 37, No. 5, 2003, P. 723–732, URL: http://www.springerlink.com/content/rmh22j17lg457487/, PMID: 14593922

Preprints

• N.A. Kusnetsov, V.A. Lyubetsky, A.V. Chernavsky “On the concept of informational interaction, 1: pre-psychic level”, Information processes, Vol. 3, No. 1, 2003, P. 1–22, in Russian
• E.V. Lyubetskaya, L.A. Leont"yev, V.A. Lyubetsky “Searching for alternative RNA secondary structures in gamma-proteobacteria”, Information processes, Vol. 3, No. 1, 2003, P. 23–38, in Russian
• V.A. Lyubetsky, K.Yu. Gorbunov “Searching for alternative RNA secondary structures”, Information processes, Vol. 3, No. 1, 2003, P. 47–60, in Russian
• N.A. Kusnetsov, V.A. Lyubetsky, A.V. Chernavsky “On the concept of informational interaction, 2: pre-psychic level”, Information processes, Vol. 3, No. 2, 2003, P. 154–172, in Russian
• V.A. Lyubetsky, A.V. Seliverstov “Some algorithms related to finite groups”, Information processes, Vol. 3, No. 1, 2003, P. 39–46, in Russian

Abstracts

• L.V. Danilova, V.A. Lyubetsky, O.N. Laikova “Computer detecting of glycerol-3-phosphate metabolism regulation in proteobacterial genomes”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’03, Moscow, Russia, July 22–25 2003, P. 52–53
• K.Yu. Gorbunov, V.A. Lyubetsky “Detecting common secondary structures in a set of RNA sequences and its testing”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’03, Moscow, Russia, July 22–25 2003, P. 83–85
• V.A. Lyubetsky, V.V. V"yugin “Complex phylogenetic analysis of evolutionary history for prokaryotes families”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’03, Moscow, Russia, July 22–25 2003, P. 146–147
• A.G. Vitreschak “Identification of RNA 5’ UTR regulatory elements and prediction of RNA riboswitch mechanism of regulation of vitamin biosynthetic and transport genes in bacteria”, Proceedings of the International Moscow Conference on Computational Molecular Biology, Moscow, Russia, July 22–25 2003, P. 233
• P.V. Golubtsov, V.A. Lyubetsky “The result of an information process depends on the nature and content of information available to its participants”, International conference of RAS, Samara, Russia, 2003, P. 445–453, in Russian
• V.G. Kanovey, V.A. Lyubetsky “Classic problems of descriptive set theory”, Proceedings of IV international Smirnov conference, RAS, Moscow, 2003, P. 32–34, in Russian
• В.Г. Кановей, В.А. Любецкий «On the existence of regular non-definable sets of reals», Труды конференции «Колмогоров и современная математика (100 лет Колмогорову)», Москва, 2003, стр. 690
• V.G. Kanovei, M. Reeken “Some new results on Borel irreducibility of equivalence relations”, Izvestiya: Mathematics, 2003, Vol. 67, No. 1, P. 55–76, URL: http://iopscience.iop.org/1064-5632/67/1/A04/, DOI: 10.1070/IM2003v067n01ABEH000418
• E.V. Lyubetskaya, L.A. Leont"yev, V.A. Lyubetsky “Algorithm for detecting alternative secondary RNA structures and mass analysis attenuator regulation in proteobacteria”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’03, Moscow, Russia, July 22–25 2003, P. 144–145

2004

Articles

• L.Yu. Rusin, M.B. Sevryuk, J.P. Toennies “Simulation of the reactive scattering of F+D2 on a model family of potential energy surfaces with various topographies: the correlation approach”, The Journal of chemical physics, Vol. 120, No. 2, Jan 8 2004, P. 800–812, PMID: 15267916
• A. Kalinin, O. Kornilov, L.Yu. Rusin , J.P. Toennies “Evidence for a bound HeH2 halo molecule by diffraction from a transmission grating”, The Journal of chemical physics, Vol. 121, No. 2, July 8 2004, P. 625–627, PMID: 15260586
• A.G. Vitreschak, D.A. Rodionov, A.A. Mironov, M.S. Gelfand “Riboswitches: the oldest mechanism for the regulation of gene expression?”, Trends in Genetics, Vol. 20, Iss. 1, Jan 2004, P. 44–50, URL: http://www.sciencedirect.com/science/article/pii/S0168952503003238, PMID: 14698618
• D.A. Rodionov, A.G. Vitreschak, A.A. Mironov, M.S. Gelfand “Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems”, Nucleic Acids Research, Vol. 32, No. 11, June 23 2004, P. 3340–3353, URL: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15215334, PMID: 15215334
• V.G. Kanovey, V.A. Lyubetsky “On the set of constructive real numbers”, Proceedings of the Steklov Mathematical Institute, Vol. 247, 2004, P. 83–114
• V.A. Lyubetsky, A.V. Seliverstov “Note on Cliques and Alignments”, Information Processes, Vol. 4, No. 3, 2004, P. 241–246, URL: http://www.jip.ru/2004/4-3-2004.htm
• A.G. Vitreschak, E.V. Lyubetskaya, M.A. Shirshin, M.S. Gelfand, V.A. Lyubetsky “Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis”, FEMS Microbiological Letters, Vol. 234, Iss. 2, May 15 2004, P. 357–370, URL: http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2004.tb09555.x/full, DOI: 10.1016/j.femsle.2004.04.005, PMID: 15135544
• K.Yu. Gorbunov, V.A. Lyubetsky “New approach for detecting common secondary structures in a set of RNA sequences”, Biophysics (Moscow), 2004, Vol. 48, Suppl. 1 (2003), P. 56–67, URL: http://www.maik.ru/contents/biophyss/biophyss1_3v48cont.pdf
• V.A. Lyubetsky, V.V. V"yugin “Complex phylogenetic analysis of the evolutionary history for some prokaryotes family”, Biophysics (Moscow), 2004, Vol. 48, Suppl. 1 (2003), P. 97–106, URL: http://www.maik.ru/contents/biophyss/biophyss1_3v48cont.pdf

Books

• V.A. Lyubetsky “Basic notions of elementary mathematics”, (university text book), Iris-press, 2004, 625 pages, in Russian
• V.G. Kanovei, M. Reeken “Nonstandard Analysis, Axiomatically”, Series: Springer Monographs in Mathematics, 2004, XVI+408 pages, ISBN: 978-3-540-22243-9, URL: http://www.springer.com/math/analysis/book/978-3-540-22243-9

Preprints

• N.A. Kusnetsov, V.A. Lyubetsky, A.V. Chernavsky “On the concept of informational interaction, 3: speech intellect”, Information Processes, Vol. 4, No. 2, 2004, P. 117–126, in Russian
• A.V. Seliverstov, V.A. Lyubetsky “Properties of cysteine synthesis in Corynebacterium, Mycobacterium and Propionibacterium”, Information Processes, Vol. 4, No. 3, 2004, P. 247–250, in Russian
• V.A. Lyubetsky, A.V. Seliverstov “Multifraction graphs with two vertices per fraction”, Information processes, Vol. 4, No. 2, 2004, P. 127–132, in Russian

Abstracts

• L.A. Leont"yev, M.A. Shirshin, V.A Lyubetsky “Detection of classical attenuation in bacterial genomes”, Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2004), Novosibirsk, Russia, July 25–30 2004, Vol. 1, P. 116–118, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/pages/bgrs2004.html
• V.A. Lyubetsky, A.V. Seliverstov “Amino acid biosynthesis attenuation in bacteria”, Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2004), Novosibirsk, Russia, July 25–30 2004, Vol. 1, P. 307–310, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/pages/bgrs2004.html
• A. Vitreschak, L. Noe, G. Kucherov “Computer analysis of multiple repeats in bacteria”, Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2004), Novosibirsk, Russia, July 25–30 2004, Vol. 2, P. 297–299, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/pages/bgrs2004.html
• N.A. Kusnetsov, M.S. Gelfand, V.A. Lyubetsky “Bioinformatics of Bacteria: central issues and model types”, International conference “Issues of control and modeling in complex systems”, June 14–17 2004, RAS, P. 5–11, in Russian
• V.A. Lyubetsky, K.Yu. Gorbunov, V.V. V"yugin “Inferring evolutionary events, quality of COGs, measuring the dissimilarity between gene and species trees”, Presentation abstracts of the EMBO World Phylogenetic Course 2004, Rio de Janeiro, Brazil, Nov 1–7 2004, (устное сообщение)
• A.G. Vitreschak “Detection of multiple repeats in bacteria”, Conference “Indexation de texte et decouverte de motifs. Algorithmique des sequences”, Lille, France, Dec 9–10 2004
• K.Yu. Gorbunov, V.A. Lyubetsky “A model of tryptophan biosynthesis regulation”, Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2004), Novosibirsk, Russia, July 25–30 2004, Vol. 2, P. 53–55, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/pages/bgrs2004.html
• V.A. Lyubetsky, V.V. V"yugin “Measuring the dissimilarity between gene and species trees, the quality of a COG”, Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2004), Novosibirsk, Russia, July 25–30 2004, Vol. 2, P. 281–284, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/pages/bgrs2004.html
• K.Yu. Gorbunov, V.A. Lyubetsky “A model of biosynthesis regulation”, Proceedings of VI International conference “Issues of control and modeling in complex systems”, June 14–17 2004, RAS, P. 151–153, in Russian
• V.A. Lyubetsky, A.V. Seliverstov “A geometric method of searching for clique in the graph and its application to signal detection”, International conference “Issues of control and modeling in complex systems”, June 14–17 2004, RAS, P. 154–157, in Russian
• E.V. Lyubetskaya, L.A. Leont"yev, M.A. Shirshin, V.A. Lyubetsky “An algorithm to search for complex signals”, International conference “Issues of control and modeling in complex systems”, June 14–17 2004, RAS, P. 158–162, in Russian

2005

Articles

• A.V. Seliverstov, H. Putzer, M.S Gelfand, V.A. Lyubetsky “Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria”, BMC Microbiology, Vol. 5, No. 1, Oct 3 2005, P. 54, URL: http://www.biomedcentral.com/1471-2180/5/54, PMID: 16202131
• V.A. Lyubetsky, A.V. Seliverstov “Expression Regulation of the Amino Acid Biosynthesis and Aminoacyl-tRNA Synthase Genes in Actinobacteria”, Molecular Biology (Moscow), Vol. 39, No. 6, 2005, P. 942–945, URL: http://www.springerlink.com/content/y03333415852r117/, PMID: 16358745
• V.M. Azriel, L.Yu. Rusin, M.B. Sevryuk “The complete T-->V,R energy conversion in three-body collisions within the hard sphere model”, The Journal of chemical physics, Feb 15 2005, Vol. 122, No. 7, 074322, PMID: 15743247
• L.Yu. Rusin, M.B. Sevryuk, J.P. Toennies “Comparison of experimental time-of-flight spectra of the HF products from the F+H2 reaction with exact quantum mechanical calculations”, The Journal of chemical physics, Apr 1 2005, Vol. 122, No. 13, 134314, PMID: 15847472
• V.G. Kanovei, V.A. Lyubetsky “Perfect subsets of invariant CA-sets”, Mathematical Notes, Vol. 77, No. 3-4, 2005, P. 307–310, URL: http://www.springerlink.com/content/hx77t845227524g5/, DOI: 10.1007/s11006-005-0031-1
• K.Yu. Gorbunov, V.A. Lyubetsky “Identification of Ancestral Genes That Introduce Incongruence between Protein- and Species Trees”, Molecular Biology (Moscow), Vol. 39, No. 5, 2005, P. 741–751, URL: http://www.springerlink.com/content/f540517833324746/, PMID: 16240718
• L.A. Leontiev, A.V. Seliverstov, V.A. Lyubetsky “Algorithm for a Large-Scale Search for T-Box Transcription Regulation in Bacteria”, Molecular Biology (Moscow), Vol. 39, No. 6, 2005, P. 946–948, URL: http://www.springerlink.com/content/f501777352360411/, PMID: 16358746

Preprints

• A.V. Seliverstov, V.A. Lyubetsky “Translation regulation in chloroplasts”, Information Processes, Vol. 5, No. 5, 2005, P. 400–404, in Russian
• V.A. Lyubetsky, A.V. Seliverstov “Searching for conservative motifs in leader regions of genes on a fixed species tree”, Information Processes, Vol. 5, No. 4, 2005, P. 265–270, in Russian
• V.A. Lyubetsky, K.Yu. Gorbunov, S.A. Pirogov, L.I. Rubanov, A.V. Seliverstov “An algorithm and search results for a model of gene expression regulation with RNA secondary structures in bacteria”, Information Processes, Vol. 5, No. 5, 2005, P. 337–366, in Russian
• V.A. Lyubetsky, K.Yu. Gorbunov, V.V. V"yugin, L.Yu. Rusin “Removing noise in protein multiple alignment”, Information Processes, Vol. 5, No. 5, 2005, P. 380–391, in Russian

Abstracts

• V.A. Lyubetsky, A.V. Seliverstov “RNA regulatory structures in Actinobacteria and Cyanobacteria”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’05, Moscow, Russia, July 18–21 2005, P. 351–353
• A. Vitreschak, G. Kucherov “Computer prediction of H-NS regulon in E. coli. Comparative analysis of regulation of rrn operons in proteobacteria”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’05, Moscow, Russia, July 18–21 2005, P. 403–405
• V.A. Lyubetsky, A.V. Seliverstov “Translation regulation in Actinobacteria and Cyano-bacteria based on mRNA secondary structures”, Proceedings of the RAS conference “Issues of control and modeling in complex systems, VII International conference”, Samara, Russia, June 27 – July 1 2005, P. 216–221, in Russian
• L.A. Leont"yev, A.V. Seliverstov, V.A. Lyubetsky “Transcription regulation with T-boxes”, Proceedings of the RAS conference “Issues of control and modeling in complex systems, VII International conference”, Samara, Russia, June 27 – July 1 2005, P. 222–224, in Russian
• V.G. Kanovey, V.A. Lyubetsky “A cofinal family of equivalence relations generated by Borel ideals”, Logic Colloquium "05, A.S.L. European Summer Meeting, Athens, Greece, July 28 – August 3 2005, P. 83, URL: http://www.math.uoa.gr/lc2005/
• L.A. Leont"yev, A.V. Seliverstov, V.A. Lyubetsky “An algorithm for mass searching of T-box structures in bacteria”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’05, Moscow, Russia, July 18–21 2005, P. 202–206
• V.A. Lyubetsky, S.A. Pirogov “A model for bacterial gene expression regulation with secondary RNA structures”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’05, Moscow, Russia, July 18–21 2005, P. 214–216
• V.A. Lyubetsky, V.V. V"yugin “A model for evolutionary event reconstruction”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’05, Moscow, Russia, July 18–21 2005, P. 217–219
• K.Yu. Gorbunov, V.A. Lyubetsky “Algorithms to reconstruct ancestral gene evolution events”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’05, Moscow, Russia, July 18–21 2005, P. 128–129
• L.Yu. Rusin, V.V. V"yugin, V.A. Lyubetsky “Enhancing phylogenetic inference: concentration of the signal in sequence data”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’05, July 18–21 2005, P. 342–346
• V.A. Lyubetsky, S.A. Pirogov “A model of attenuator regulation in bacteria”, Proceedings of the RAS conference “Issues of control and modeling in complex systems, VII International conference”, Samara, Russia, June 27 – July 1 2005, P. 205–209, in Russian
• S.A. Pirogov, K.Yu. Gorbunov, V.A. Lyubetsky “Macro- and microconditions in a model of attenuator regulation of gene expression in bacteria”, Proceedings of the RAS conference “Issues of control and modeling in complex systems, VII International conference”, Samara, Russia, June 27 – July 1 2005, P. 210–215, in Russian
• V.A. Lyubetsky “Mathematic models of evolution and gene expression regulation”, Proceedings of the RAS conference “Issues of control and modeling in complex systems, VII International conference”, Samara, Russia, June 27 – July 1 2005, P. 366–368, in Russian

2006

Articles

• A.V. Seliverstov, V.A. Lyubetsky “Translation regulation of intron containing genes in chloroplasts”, Journal of Bioinformatics and Computational Biology, 2006, Vol. 4, No. 4, P. 783–793, PMID: 17007067
• A.V. Seliverstov, O.A. Zverkov, V. A. Lyubetsky “Translation of some chloroplast genes is checked to allow for splicing and editing”, Biophysics (Moscow), 2006, Vol. 51, Supplement 1, P. 18–22, Pleiades Publishing, Inc., (The supplement is published only in English), URL: http://www.springerlink.com/content/p7517k3187230111/, DOI: 10.1134/S0006350906070049
• M.S. Gelfand, A.V. Gerasimova, E.A. Kotelnikova, O.N. Laikova, V.Y. Makeev, A.A. Mironov, E.M. Panina, D.A. Ravcheev, D.A. Rodionov, A.G. Vitreschak “Comparative Genomics and Evolution of Bacterial Regulatory Systems”, Article in the book Bioinformatics of Genome Regulation and Structure II, Springer US, 2006, Part 1, P. 111–119, URL: http://www.springerlink.com/content/tt37j13rjp6j43m6/, DOI: 10.1007/0-387-29455-4_12
• V.G. Kanovei, V.A. Lyubetsky “A Cofinal Family of Equivalence Relations and Borel Ideals Generating Them”, Proceedings of the Steklov Institute of Mathematics, 2006, Vol. 252, No. 1, P. 85–103, Pleiades Publishing, Inc., URL: http://www.springerlink.com/content/lt2ww22633g71042/, DOI: 10.1134/S008154380601010X
• V.A. Lyubetsky, K.Yu. Gorbunov, L.Yu. Rusin, V.V. V’yugin “Algorithms to reconstruct evolutionary events at molecular level and infer species phylogeny”, Article in the book Bioinformatics of Genome Regulation and Structure II, Springer US, 2006, Part 1, P. 189–204, URL: http://www.springerlink.com/content/q67568k37g687647/, DOI: 10.1007/0-387-29455-4_20
• A.V. Lyubetskaya, L.I. Rubanov, M.S.Gelfand “Use of the flux model of amino acid metabolism of Escherichia coli”, Biochemistry (Moscow), 2006, Vol. 71, No. 11, P. 1256–1260, PMID: 17140387
• V.A. Lyubetsky, L.I. Rubanov, A.V. Seliverstov, S.A. Pirogov “Model of gene expression regulation in bacteria via formation of RNA secondary structures”, Molecular Biology (Moscow), Vol. 40, No. 3, 2006, P. 440–453, URL: http://www.springerlink.com/content/v781354463x18q2v/, PMID: 16813169

Preprints

• L.A. Leont"yev, V.A. Lyubetsky “Mass detection of conserved T-box containing regulatory structures: search results”, Information Processes, Vol. 6, No. 1, 2006, P. 20–23, in Russian
• V.A. Lyubetsky, A.V. Seliverstov “Computation of regulation efficiency of tryptophan biosynthesis in bacteria based on a model of classic attenuation”, Information Processes, Vol. 6, No. 1, 2006, P. 55–57, in Russian
• L.A. Leont"yev, V.A. Lyubetsky “An algorithm of searching for proteins coherent with a given phylogenetic profile”, Information Processes, Vol. 6, No. 1, 2006, P. 24–32, in Russian
• A.V. Seliverstov, V.A. Lyubetsky “An algorithm for detecting conserved motifs in nucleotide sequences”, Information processes, Vol. 6, No. 1, 2006, P. 33–36, in Russian
• Е.В. Любецкая, Л.И. Рубанов, А.В. Селиверстов, В.А. Любецкий «Алгоритм поиска мощных вторичных структур в нуклеотидной последовательности и его применение для подсчета числа таких структур в разных областях геномов», Информационные процессы, том 6, № 3, 2006, стр. 258–263, URL: http://www.jip.ru/2006/6-3-2006.htm

Abstracts

• E.V. Lyubetskaya, A.V. Seliverstov, V.A. Lyubetsky “Detecting hairpins in 3"-untranslated regions of highly expressed genes in Actinobacteria”, Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2006), Novosibirsk, Russia, July 16–22 2006, Vol. 1, P. 99–101, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/
• A.V. Seliverstov, V.A. Lyubetsky “Translation regulation in chloroplasts”, Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2006), Novosibirsk, Russia, July 16–22 2006, Vol. 1, P. 146–149, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/
• K.Yu. Gorbunov, V.A. Lyubetsky “Inferring regulatory signal profiles and evolution events”, Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2006), Novosibirsk, Russia, July 16–22 2006, Vol. 3, P. 151–154, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/
• A.G. Vitreschak, V.A. Lyubetsky, M.S. Gelfand “Evolutional and functional analysis of T-box regulon in bacteria: identification of new genes involved in amino acid metabolism”, Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2006), Novosibirsk, Russia, July 16–22 2006, Vol. 3, P. 236–240, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/
• А.Г. Витрещак «Регуляторные РНК-переключатели», Международная школа «биоинформатика, геномика и протеоимка», Алматы, 11–16 апреля 2006, (доклад)
• V.A. Lyubetsky, A.V. Seliverstov “Modeling classic attenuation regulation of gene expression in bacteria”, Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2006), Novosibirsk, Russia, July 16–22 2006, Vol. 1, P. 102–105, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/
• L.Yu. Rusin, V.A. Lyubetsky “Refinement of phylogenetic signal in multiple sequence aliment: results of simulation study”, Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2006), Novosibirsk, Russia, July 16–22 2006, Vol. 3, P. 222–224, URL: http://www.bionet.nsc.ru/meeting/bgrs_proceedings/
• L.Yu. Rusin, V.A. Lyubetsky, O.A. Zverkov, K.Yu. Gorbunov, V.V. V"yugin “Signal concentration in multiple sequence alignment: empirical and simulation studies”, Society for Molecular Biology and Evolution Meeting 2006: Genomes, Evolution and Bioinformatics (GEB2006) conference, Tempe, Arizona, USA, May 24–28 2006, (poster presentation), URL: http://www.smbe.org/geb/

2007

Articles

• A.V. Seliverstov, V.A. Lyubetsky “Regulation of proline biosynthesis in proteobacteria”, Molecular Biology (Moscow), Vol. 41, No. 3, 2007, P. 513–515, URL: http://www.springerlink.com/content/324t192150m27u72/, PMID: 17685234
• E.V. Lyubetskaya, A.V. Seliverstov, V.A. Lyubetsky “The number of long hairpins in intergenic trailer regions of actinobacteria is far greater than in other genomic regions”, Molecular Biology (Moscow), Vol. 41, No. 4, 2007, P. 670–673, URL: http://www.springerlink.com/content/51l03u1138062028/, PMID: 17936997
• C. Peth, A. Kalinin, F Barkusky, K Mann, J.P. Toennies, L.Yu. Rusin “XUV laser-plasma source based on solid Ar filament”, The Review of scientific instruments, Oct 2007, Vol. 78, No. 10, 103509, PMID: 17979421
• M.D. Kazanov, A.G. Vitreschak, M.S. Gelfand “Abundance and functional diversity of riboswitches in microbial communities”, BMC Genomics, 2007, Vol. 8, P. 347, URL: http://www.biomedcentral.com/1471-2164/8/347, DOI: 10.1186/1471-2164-8-347, PMID: 17908319
• V.A. Lyubetskii, S.A. Pirogov “Nonstandard representations of locally compact groups”, Mathematical Notes, Vol. 82, Iss. 3-4, 2007, P. 341–346, MAIK Nauka/Interperiodica distributed exclusively by Springer Science+Business Media LLC., URL: http://www.springerlink.com/content/bj210202g2448945/, DOI: 10.1134/S0001434607090064
• V.G. Kanovei, V.A. Lyubetskii, M. Reeken “Reducibility of monadic equivalence relations”, Mathematical Notes, Vol. 81, Iss. 5-6, 2007, P. 757–766, MAIK Nauka/Interperiodica distributed exclusively by Springer Science+Business Media LLC., URL: http://www.springerlink.com/content/n35u046784852j64/, DOI: 10.1134/S0001434607050239
• V.G. Kanovei, V.A. Lyubetskii “Problems of set-theoretic non-standard analysis”, Russian Mathematical Surveys, Vol. 62, Iss. 1, Jan-Feb 2007, P. 45–111, URL: http://www.turpion.org/php/paper.phtml?journal_id=rm&paper_id=4381, DOI: 10.1070/RM2007v062n01ABEH004381
• K.Yu. Gorbunov “Bound on the cardinality of a covering of an arbitrary randomness test by frequency tests”, Problems of Information Transmission, Vol. 43, Iss. 1, 2007, P. 48–56, URL: http://www.springerlink.com/content/l72100vr38908422/, DOI: 10.1134/S0032946007010061
• V.A. Lyubetsky, S.A. Pirogov, L.V. Rubanov, A.V. Seliverstov “Modeling classic attenuation regulation of gene expression in bacteria”, Journal of Bioinformatics and Computational Biology, Vol. 5, Iss. 1, 2007, P. 155–180, URL: http://www.worldscinet.com/jbcb/05/0501/S0219720007002576.html, DOI: 10.1142/S0219720007002576, PMID: 17477496
• K.Yu. Gorbunov, V.A. Lyubetsky “Reconstruction of ancestral regulatory signals along a transcription factor tree”, Molecular Biology (Moscow), 2007, Vol. 41, No. 5, P. 836–842, URL: http://www.springerlink.com/content/y777j5145r5l0508/, PMID: 18240574
• E. Asarin, Th. Cachat, A. Seliverstov, T. Touili, V. Lyubetsky “Attenuation regulation as a term rewriting system”, Article in the book Algebraic Biology, Lecture Notes in Computer Science, Vol. 4545, Springer Berlin / Heidelberg, P. 81–94, Proceedings of the 2nd international conference on Algebraic biology: AB"07, Castle of Hagenberg, Austria, July 2–4 2007, URL: http://www.springerlink.com/content/e6854048p7r65w73/, DOI: 10.1007/978-3-540-73433-8_7
• L.I. Rubanov, V.A. Lyubetsky “RNAmodel Web Server: Modeling Classic Attenuation in Bacteria”, In Silico Biology, Vol. 7, No. 3, 2007, P. 285–308, URL: http://www.bioinfo.de/isb/2007/07/0044/, PMID: 18415978

Books

• V.G. Kanovei, V.A. Lyubetsky “Contemporary set theory: basics of descriptive dynamics”, Nauka, 2007, 231 pages, (Monograph)

Preprints

• А.В. Селиверстов, В.А. Любецкий «Структура РНК перед геном 2-изопропилмалат синтазы у некоторых протеобактерий», Информационные процессы, том 7, № 1, 2007, стр. 113–115, URL: http://www.jip.ru/2007/7-1-2007.htm
• В.Г. Кановей, В.А. Любецкий «Борелевская сводимость сохраняется при счетном дизъюнктном объединении борелевских множеств», Препринт Петербургского отделения Математического института РАН, 2007, URL: http://www.pdmi.ras.ru/preprint/2007/07-16.html
• Л.Ю. Русин, Л.И. Рубанов, В.А. Любецкий «Данные для построения эволюционного дерева высших Metazoa», Информационные процессы, том 7, № 3, 2007, стр. 199–213, URL: http://www.jip.ru/2007/7-3-2007.htm

Abstracts

• V.A. Lyubetsky, A.V. Seliverstov “Long helices in mRNA processing”, Proceedings of the 3-rd Moscow Conference on Computational Molecular Biology (МССМВ’07), Moscow, Russia, July 27–31 2007, P. 189–191
• V.A. Lyubetsky, A.V. Seliverstov, O.A. Zverkov “RNA Structures upstream leuA Genes in α-proteobacteria”, Proceedings of the 3-rd Moscow Conference on Computational Molecular Biology (МССМВ’07), Moscow, Russia, July 27–31 2007, P. 191–192
• L.Yu. Rusin, V.A. Lyubetsky “Phylogenomics of Metazoa: Constructing the Gene Set”, Proceedings of the 3-rd Moscow Conference on Computational Molecular Biology (МССМВ’07), Moscow, Russia, July 27–31 2007, P. 267–268
• A.G. Vitreschak, A.A. Mironov, V.A. Lyubetsky, M.S. Gelfand “Function and evolutionary analysis of the T-box regulon in bacteria”, Proceedings of the 3-rd Moscow Conference on Computational Molecular Biology (МССМВ’07), Moscow, Russia, July 27–31 2007, P. 309–310
• A.G. Vitreschak, V.A. Lyubetsky, M.S. Gelfand “Analysis of evolution of T-box regulatory elements prediction of amino acid transporters and other amino acid related genes”, Proceedings of the international scientific conference “Computational Phylogenetics and Molecular Systematics, CPMS’2007”, Moscow, November 16–19 2007, KMK Scientific Press, P. 30–37
• A.V. Seliverstov, E.A. Lysenko, V.A. Lyubetsky “Rapid evolution of promoters in Magnoliophyta chloroplasts”, Proceedings of the international scientific conference “Computational Phylogenetics and Molecular Systematics, CPMS’2007”, Moscow, November 16–19 2007, KMK Scientific Press, P. 286–292
• А.Г. Витрещак, А.А. Миронов, В.А. Любецкий, М.С. Гельфанд «Компьютерный анализ, функциональная аннотация и изучение эволюции Т-бокс регулона в бактериях», Труды 30-й конференции «Информационные технологии и системы» (ИТиС’07), Звенигород, 18–21 сентября 2007, стр. 220–221
• И. Глотова, Л.И. Рубанов, А.В. Селиверстов, В.А. Любецкий «Псевдоузлы и РНК-триплексы в модели классической аттенюаторной регуляции», Труды 30-й конференции «Информационные технологии и системы» (ИТиС’07), Звенигород, 18–21 сентября 2007, стр. 222–227
• А.В. Селиверстов, В.А. Любецкий «Кластеризация и поиск промоторов у хлоропластов», Труды 30-й конференции «Информационные технологии и системы» (ИТиС’07), Звенигород, 18–21 сентября 2007, стр. 321–323
• K.Yu. Gorbunov, D. Radionov, O.N. Laikova, M.S. Gelfand, V.A. Lyubetsky “Reconstruction of ancestral regulatory signal along a phylogeny”, Proceedings of the 3-rd Moscow Conference on Computational Molecular Biology (МССМВ’07), Moscow, Russia, July 27–31 2007, P. 111–113
• K.Yu. Gorbunov, V.A. Lyubetsky “Modeling evolution of the nucleotide sequence with secondary structure”, Proceedings of the international scientific conference “Computational Phylogenetics and Molecular Systematics, CPMS’2007”, Moscow, November 16–19 2007, KMK Scientific Press, P. 68–75
• V.A. Lyubetsky, A.V. Seliverstov, K.Yu. Gorbunov, “Models of gene expression regulation and evolution of regulatory elements”, Proceedings of the international scientific conference “Computational Phylogenetics and Molecular Systematics, CPMS’2007”, Moscow, November 16–19 2007, KMK Scientific Press, P. 158–165
• L.Yu. Rusin, V.A. Lyubetsky “Algorithms to model gene evolution events and reconstruct multigene phylogenetics of species”, Proceedings of the international scientific conference “Computational Phylogenetics and Molecular Systematics, CPMS’2007”, Moscow, November 16–19 2007, KMK Scientific Press, P. 274–277
• В.А. Любецкий, Е.А. Жижина, К.Ю. Горбунов, А.В. Селиверстов «Модель эволюции нуклеотидной последовательности», Труды конференции «Математические методы распознавания образов», 2007, стр. 605–609

2008

Articles

• A.G. Vitreschak, A.A. Mironov, V.A. Lyubetsky, M.S. Gelfand “Comparative genomic analysis of T-box regulatory systems in bacteria”, RNA, Cambridge University Press, Vol. 14, No. 4, Apr 2008, P. 717–735, URL: http://rnajournal.cshlp.org/content/14/4/717.full, DOI: 10.1261/rna.81930, PMID: 18359782
• V.G. Kanovei, T. Linton, V.A. Uspensky “Lebesgue measure and gambling”, Sbornik: Mathematics, 2008, Vol. 199, No. 11, P. 1597–1619, URL: http://iopscience.iop.org/1064-5616/199/11/A02/, DOI: 10.1070/SM2008v199n11ABEH003974
• V.A. Lyubetsky, E.A. Zhizhina, L.I. Rubanov “Gibbs field approach for evolutionary analysis of regulatory signal of gene expression”, Problems of Information Transmission, Vol. 44, Iss. 4, 2008, P. 333–351, URL: http://www.springerlink.com/content/c8161517p0477366/

Books

• V.G. Kanovei “Borel equivalence relations: structure and classification”, University Lectures series of the AMS, Vol. 44, 2008, 240 pages, ISBN-10: 0-8218-4453-9, ISBN-13: 978-0-8218-4453-3, URL: http://www.ams.org/bookstore-getitem/item=ulect-44

Preprints

• А.В. Селиверстов, В.А. Любецкий «О квадратичных формах, равных единице на большом множестве вершин n-мерного куба», Информационные процессы, том 8, № 4, 2008, стр. 201–204, URL: http://www.jip.ru/2008/8-4-2008.htm

Abstracts

• I. Glotova, V.A. Lyubetsky “Classical attenuation regulation model”, Abstracts of The Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2008), Novosibirsk, Russia, June 22–28 2008, P. 85, URL: http://www.bionet.nsc.ru/meeting/bgrs2008/index.html
• K.V. Lopatovskaya, A.V. Seliverstov, V.A. Lyubetsky “RNA structures upstream the 2-isopropylmalate synthase encoding gene in alfa-proteobacteria and actinobacteria”, Abstracts of The Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2008), Novosibirsk, Russia, June 22–28 2008, P. 144, URL: http://www.bionet.nsc.ru/meeting/bgrs2008/index.html
• E.A. Lysenko, A.V. Seliverstov, V.A. Lyubetsky “Analysis of Sig3, Sig4 and Sig6 evolution on new genomic data”, Abstracts of The Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2008), Novosibirsk, Russia, June 22–28 2008, P. 147, URL: http://www.bionet.nsc.ru/meeting/bgrs2008/index.html
• V.A. Lyubetsky, A.V. Seliverstov “On evolution of promoters in plastomes”, Abstracts of The Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2008), Novosibirsk, Russia, June 22–28 2008, P. 217, URL: http://www.bionet.nsc.ru/meeting/bgrs2008/index.html
• V.G. Kanovey, V.A. Lyubetsky “Borel reducibility as an additive property of domains”, Article in the book Studies in constructive mathematics and mathematical logic. Part XI, Zapiski Nauchnyh Seminarov POMI, Vol. 358, 2008, St.Petersburg, POMI, P. 189–198, URL: http://mi.mathnet.ru/eng/znsl/v358/p189
• Sy-D. Friedman, V.G Kanovei, V.A Lyubetsky “On ROD reducibility of equivalence relations in Solovay model”, Article in the book Proceedings of the International Conference “Methods of Logic in Mathematics V”, Saint-Petersburg, Russia, June 1–7 2008, P. 6
• А.В. Селиверстов, В.А. Любецкий «О квадратичных формах ранга n-2, равных единице на большом множестве вершин n-мерного куба», Труды 51-й научной конференции МФТИ, Москва, 2008, стр. 150–153
• В.А. Любецкий, Л.И. Рубанов, А.В. Селиверстов «Выравнивание последовательностей на основе дерева», Труды 9-й Международной конференции РАН «Распознавание образов и анализ изображений: новые информационные технологии», Нижний Новгород, 15–20 сентября 2008, стр. 137–140
• V.A Lyubetsky “Models of gene expression regulation and evolution of regulatory elements”, Proceedings of the Fifth International Conference of Applied Mathematics and Computing, Plovdiv, Bulgaria, August 12–18 2008, P. 17–19
• K.Yu. Gorbunov, V.G. Kanovei, V.A. Lyubetsky “Inferring optimal scenario of gene evolution along a species tree”, Abstracts of The Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2008), Novosibirsk, Russia, June 22–28 2008, P. 90, URL: http://www.bionet.nsc.ru/meeting/bgrs2008/index.html
• V.A. Lyubetsky, E.A. Zhizhina, L.I. Rubanov “A model of regulatory signal evolution”, Abstracts of The Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2008), Novosibirsk, Russia, June 22–28 2008, P. 148, URL: http://www.bionet.nsc.ru/meeting/bgrs2008/index.html
• L.I. Rubanov, A.V. Seliverstov, V.A. Lyubetsky “Multiple alignment based on species tree”, Abstracts of The Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2008), Novosibirsk, Russia, June 22–28 2008, P. 212, URL: http://www.bionet.nsc.ru/meeting/bgrs2008/index.html
• О.А. Зверков «Программный комплекс для согласования набора эволюционных деревьев и выявления эволюционных событий», Труды 51-й научной конференции МФТИ, Москва, 2008, стр. 133–136
• К.В. Лопатовская, А.В. Селиверстов, В.А. Любецкий «Об одном подходе к поиску регуляции в дискретных последовательностях», Труды 51-й научной конференции МФТИ, Москва, 2008, стр. 141–143
• Е.В. Любецкая, К.Ю. Горбунов «Алгоритмы реконструкции эволюции регуляторных сигналов», Труды 51-й научной конференции МФТИ, Москва, 2008, стр. 144–146
• А.В. Селиверстов, В.А. Любецкий «Алгоритмы для поиска многобоксовых сигналов и их применения», Труды 51-й научной конференции МФТИ, Москва, 2008, стр. 147–149

2009

Articles

• A.V. Seliverstov, V.A. Lyubetsky “Mechanism of manganese transport regulation in Brucella involving a long RNA helix”, Biophysics (Moscow), Vol. 54, No. 2, 2009, P. 152–155, URL: http://www.springerlink.com/content/d16u8046685x0j57/, DOI: 10.1134/S0006350909020055, PMID: 19402531
• A.V. Seliverstov, E.A. Lysenko, V.A. Lyubetsky “Rapid evolution of promoters for the plastome gene ndhF in flowering plants”, Russian Journal of Plant Physiology, Vol. 56, No. 6, 2009, P. 838–845, URL: http://www.springerlink.com/content/6987k34161278v52/
• K.V. Mikhailov, A.V. Konstantinova, M.A. Nikitin, P.V. Troshin, L.Yu. Rusin, V.A. Lyubetsky, Yu.V. Panchin, A.P. Mylnikov, L.L. Moroz, S. Kumar, V.V. Aleoshin “The origin of Metazoa: a transition from temporal to spatial cell differentiation”, BioEssays, Vol. 31, Iss. 7, July 2009, P. 758–768, URL: http://onlinelibrary.wiley.com/doi/10.1002/bies.200800214/full, DOI: 10.1002/bies.200800214, PMID: 19472368
• M.S. Gelfand, A.E. Kazakov, Yu.D. Korostelev, O.N. Laikova, A.A. Mironov, A.B. Rakhmaninova, D.A. Ravcheev, D.A. Rodionov, A.G. Vitreschak “Evolution of Regulatory Systems in Bacteria (Invited Keynote Talk)”, Article in the book Bioinformatics Research and Applications, Lecture Notes in Computer Science, Vol. 5542, Proceedings of the 5th International Symposium, ISBRA 2009, Fort Lauderdale, FL, USA, May 13–16 2009, P. 1–4, URL: http://dblp.uni-trier.de/db/conf/isbra/isbra2009.html, DOI: 10.1007/978-3-642-01551-9_1
• T.A. Sadovskaya, A.V. Seliverstov “Analysis of the 5"-Leader Regions of Several Plastid Genes in Protozoa of the Phylum Apicomplexa and Red Algae”, Molecular Biology (Moscow), Vol. 43, No. 4, 2009, P. 552–556
• A.V. Seliverstov, V.A. Lyubetsky “On symmetric matrices with indeterminate leading diagonals”, Problems of Information Transmission, Vol. 45, No. 3, 2009, P. 258–263, URL: http://www.springerlink.com/content/y4m17878w8j65551/, DOI: 10.1134/S0032946009030065
• V.G. Kanovei, V.A. Lyubetsky “Borel reducibility as an additive property of domains”, Journal of Mathematical Sciences, Vol. 158, No. 5, 2009, P. 708–712, URL: http://www.springerlink.com/content/t61n117p753548n1/, DOI: 10.1007/s10958-009-9406-2
• V.G. Kanovei, V.A. Lyubetsky “Reasonable non-Radon-Nikodym ideals”, Topology and its Applications, Vol. 156, No. 5, 2009, P. 911–914
• V.G. Kanovei “On Hausdorff ordered structures”, Izvestiya: Mathematics, 2009, Vol. 73, No. 5, P. 939–958, URL: http://iopscience.iop.org/1064-5632/73/5/A04/, DOI: 10.1070/IM2009v073n05ABEH002469
• K.Yu. Gorbunov, E.V. Lyubetskaya, E.A. Asarin V.A. Lyubetsky “Modeling evolution of the bacterial regulatory signals involving secondary structure”, Molecular Biology (Moscow), Vol. 43, No. 3, 2009, P. 485–499, URL: http://www.springerlink.com/content/m864583474537mvr/, PMID: 19548539
• K.Yu. Gorbunov, V.A. Lyubetsky “Reconstructing the evolution of genes along the species tree”, Molecular Biology (Moscow), Vol. 43, No. 5, 2009, P. 881–893, URL: http://www.springerlink.com/content/g376625187q212w9/, PMID: 19899641

Preprints

• А.В. Селиверстов, В.А. Любецкий «Совместная регуляция белков, гомологичных рубредоксину, у диатомовых водорослей и паразитов Piroplasmida», Информационные процессы, том 9, № 1, 2009, стр. 30–33, URL: http://www.jip.ru/2009/9-1-2009.htm

Abstracts

• V.A. Lyubetsky, A.V. Seliverstov “Protein expression regulation in plastids of parasites, algae and plants”, Proceedings of V Bioinformatics Congress, Moscow, 2009, P. 387–388
• V.A. Lyubetsky, L.I. Rubanov, A.V. Seliverstov “RNA polymerase competition at complementary DNA strands”, Proceedings of the Genetics and Selection Meeting and V Congress of the Vavilov Genetics and Selection Society, Moscow, June 21–27 2009, Part II, P. 68
• K.V. Lopatovskaya, A.V. Seliverstov, V.A. Lyubetsky “Chlorophyll synthesis regulation in plant chloroplasts”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’09, Moscow, Russia, July 20–23 2009, P. 217–218
• V.A. Lyubetsky, K.V. Lopatovskaya “Comparative genomic analysis of the attenuation regulation of amino acid and amino acyl-tRNA biosynthesis operons in bacteria”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’09, Moscow, Russia, July 20–23 2009, P. 219–220
• К.В. Лопатовская, О.А. Зверков, А.В. Селиверстов, В.А. Любецкий «Транскрипция генов синтеза пролина у бактерий родов Marinobacter, Pseudomonas и Shewanella регулируется белком семейства tetR», Труды 32-й конференции «Информационные технологии и системы» (ИТиС’09), пос. д/о Бекасово, 15–18 декабря 2009, стр. 278–281, URL: http://www.iitp.ru/ru/conferences/539.htm
• О.А. Зверков, А.В. Селиверстов, Л.И. Рубанов, В.А. Любецкий «Моделирование конкуренции РНК-полимераз: влияние нокаута сигма субъединицы и температуры на экспрессию генов», Труды 32-й конференции «Информационные технологии и системы» (ИТиС’09), пос. д/о Бекасово, 15–18 декабря 2009, стр. 328–331, URL: http://www.iitp.ru/ru/conferences/539.htm
• К.Ю. Горбунов, Е.В. Любецкая «Реконструкция эволюции белковых семейств», Труды 32-й конференции «Информационные технологии и системы» (ИТиС’09), пос. д/о Бекасово, 15–18 декабря 2009, стр. 332–334, URL: http://www.iitp.ru/ru/conferences/539.htm
• В.А. Любецкий, А.В. Селиверстов «Прямые повторы в некодирующих областях хлоропластов у семенных растений», Труды 52-й научной конференции МФТИ «Современные проблемы фундаментальных и прикладных наук», Часть I. Радиотехника и кибернетика, том 1, М.: МФТИ, 2009, стр. 116–117, URL: http://mipt.ru/nauka/conf_mipt/52conf/materialy.html
• V.G. Kanovei, V.A. Lyubetsky, M. Reeken “Nonstandard class and superset theories”, Logic and Mathematics, Department of Mathematics, The University of York, August 3–7 2009, P. 21
• А.В. Селиверстов, В.А. Любецкий «Об эллипсоидах, внутри которых нет целых точек», Труды 52-й научной конференции МФТИ «Современные проблемы фундаментальных и прикладных наук», Часть I. Радиотехника и кибернетика, том 1, М.: МФТИ, 2009, стр. 128–130, URL: http://mipt.ru/nauka/conf_mipt/52conf/materialy.html
• V.A. Lyubetsky, E.A. Zhizhina, L.I. Rubanov “Gibbs Field for Evolutionary Analysis of Regulatory Signal of Gene Expression under Constraints on Secondary Structure”, The 18th IMACS World Congress on Computational and Applied Mathematics & Applications in Science and Engineering, August 3–5 2009, The University of Georgia, Athens, GA 30602-7404, USA, P. 54
• K.Yu. Gorbunov, V.A. Lyubetsky “Inferring gene evolution along a species tree”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’09, Moscow, Russia, July 20–23 2009, P. 120–121

2010

Articles

• K.V. Lopatovskaya, K.Yu. Gorbunov, L.Yu. Rusin, A.V. Seliverstov, V.A. Lyubetsky “The evolution of proline synthesis transcriptional regulation in gammaproteobacteria”, Moscow University Biological Sciences Bulletin, Vol. 65, No. 4, 2010, P. 211–212, URL: http://www.springerlink.com/content/47u7051060653157/
• K.V. Lopatovskaya, A.V. Seliverstov, V.A. Lyubetsky “Attenuation Regulation of the Amino Acid and Aminoacyl-tRNA Biosynthesis Operons in Bacteria: A Comparative Genomic Analysis”, Molecular Biology (Moscow), Vol. 44, No. 1, 2010, P. 128–139, URL: http://www.springerlink.com/content/e76550k718277364/, PMID: 20198868
• K.Yu. Gorbunov, O.N. Laikova, D.A. Rodionov, M.S. Gelfand, V.A. Lyubetsky “Evolution of regulatory motifs of bacterial transcription factors”, In Silico Biology, Vol. 10, 0012, 2010, URL: http://www.bioinfo.de/isb/2010/10/0012/
• J.-Ph. Doyon, C. Scornavacca, K.Yu. Gorbunov, G.J. Szollosi, V. Ranwez, V. Berry “An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers”, Article in the book Comparative Genomics, Lecture Notes in Computer Science, Springer-Verlag Berlin Heidelberg, 2010, Vol. 6398, P. 93–108, URL: http://www.springerlink.com/content/d8h78633p3n31268/, DOI: 10.1007/978-3-642-16181-0_9
• V.A. Lyubetsky, L.I. Rubanov, A.V. Seliverstov “Lack of conservation of bacterial type promoters in plastids of Streptophyta”, Biology Direct, 2010, Vol. 5, No. 1, 34, URL: http://www.biology-direct.com/content/5/1/34, DOI: 10.1186/1745-6150-5-34, PMID: 20459727

Books

• V.G. Kanovei, V.A. Lyubetsky “Modern Set Theory: Borel and projective sets”, Published by Independent Moscow university, 2010, 320 pages, (Monograph)

Preprints

• А.В. Селиверстов, В.А. Любецкий «О вещественных точках на многообразии четвёртой степени, ближайших к данной точке», Информационные процессы, том 10, № 3, 2010, стр. 245–246, URL: http://www.jip.ru/2010/10-3-2010.htm
• К.Ю. Горбунов, В.А. Любецкий «Об одном алгоритме согласования деревьев генов и видов с учетом дупликаций, потерь и горизонтальных переносов генов», Информационные процессы, том 10, № 2, 2010, стр. 140–144, URL: http://www.jip.ru/2010/10-2-2010.htm

Abstracts

• V.A. Lyubetsky, O.A. Zverkov, L.I. Rubanov, A.V. Seliverstov “Interaction between nucleome and plastome: heat shock response regulation in plastids of plants”, Proceedings of the Seventh International Conference on Bioinformatics of Genome Regulation and StructureSystems Biology (BGRSSB"2010), Novosibirsk, Russia, June 20–27 2010, P. 161
• V.A. Lyubetsky, A.V. Seliverstov “Fast and slow evolution of bacterial type promoters in plastids of Streptophyta”, Molecular Phylogenetics: Contributions to the 2nd Moscow International Conference “Molecular Phylogenetics” (MolPhy-2), Moscow, Russia, May 18–21 2010, Torus Press, P. 54
• K.V. Lopatovskaya, K.Yu. Gorbunov, A.V. Seliverstov, V.A. Lyubetsky “The Evolution of Proline Synthesis Transcriptional Regulation in Gamma Proteobacteria”, Molecular Phylogenetics: Contributions to the 2nd Moscow International Conference “Molecular Phylogenetics” (MolPhy-2), Moscow, Russia, May 18–21 2010, Torus Press, P. 132–133
• K.V. Lopatovskaya, A.V. Seliverstov, V.A. Lyubetsky “The Evolution of NtcA- and NtcB-regulons in Cyanobacteria and Rhodophyte Chloroplasts”, Molecular Phylogenetics: Contributions to the 2nd Moscow International Conference “Molecular Phylogenetics” (MolPhy-2), Moscow, Russia, May 18–21 2010, Torus Press, P. 134–135
• К.В. Лопатовская, А.В. Селиверстов, В.А. Любецкий «Регулоны факторов NtcA и NtcB у цианобактерий и багрянок», Труды 33-й конференции «Информационные технологии и системы» (ИТиС’10), г. Геленджик, 20–24 сентября 2010, стр. 339–342, URL: http://www.itas-proceedings.iitp.ru/search.html
• М.И. Щелкунов, В.А. Любецкий «Электростатическое поле и длина межгенных областей связаны с диффузией белковых факторов», Труды 33-й конференции «Информационные технологии и системы» (ИТиС’10), г. Геленджик, 20–24 сентября 2010, стр. 382–384, URL: http://www.itas-proceedings.iitp.ru/search.html
• А.В. Селиверстов, В.А. Любецкий «О функции Гильберта множества вершин куба», Труды 53-й научной конференции МФТИ, часть 1, том 1, М.: МФТИ, 2010, стр. 123–124
• V.G. Kanovei, V.A. Lyubetsky “Julius Koenig sets as higher infinity”, Abstracts of the International Workshop “Infinite and Infinitesimal in Mathematics, Computing and Natural Sciences”, Grand Hotel San Michele, Cetraro, Italy, May 17–21 2010, University of Calabria, Italy, P. 27, URL: http://www.theinfinitycomputer.com/Infinity2010/
• K.Yu. Gorbunov, V.A. Lyubetsky “A fast algorithm of building species supertrees with a set of gene trees”, Proceedings of the Seventh International Conference on Bioinformatics of Genome Regulation and StructureSystems Biology (BGRSSB"2010), Novosibirsk, Russia, June 20–27 2010, P. 92
• A.V. Seliverstov, L.I. Rubanov, V.A. Lyubetsky “Lack of conservation of bacterial type promoters in plastids of Streptophyta”, Proceedings of the Seventh International Conference on Bioinformatics of Genome Regulation and StructureSystems Biology (BGRSSB"2010), Novosibirsk, Russia, June 20–27 2010, P. 170
• О.А. Зверков, А.В. Селиверстов, В.А. Любецкий «Позиционная связь генов пластомов растений и водорослей», Труды 33-й конференции «Информационные технологии и системы» (ИТиС’10), г. Геленджик, 20–24 сентября 2010, стр. 326–330, URL: http://www.itas-proceedings.iitp.ru/search.html
• О.А. Зверков, А.В. Селиверстов, В.А. Любецкий «Об одном алгоритме кластеризации белков», Труды 53-й научной конференции МФТИ, часть 1, том 1, М.: МФТИ, 2010, стр. 118–119

2011

Articles

• K.V. Lopatovskaya, A.V. Seliverstov, V. A. Lyubetsky “NtcA and NtcB regulons in cyanobacteria and rhodophyta chloroplasts”, Molecular Biology (Moscow), Vol. 45, No. 3, 2011, P. 522–526, URL: http://www.springerlink.com/content/83173k2162213k56/, DOI: 10.1134/S0026893311030083
• V.M. Azriel, E.V. Kolesnikova, L.Yu. Rusin, M.B. Sevryuk “Dynamical mechanisms of direct three-body recombination”, The journal of physical chemistry. A, Vol. 115, No. 25, Jun 30 2011, P. 7055–7064, PMID: 21557593
• V.N. Lazarev, S.A. Levitskii, Y.I. Basovskii, M.M. Chukin, T.A. Akopian, V.V. Vereshchagin, E.S. Kostrjukova, G.Y. Kovaleva, M.D. Kazanov, D.B. Malko, A.G. Vitreschak, N.V. Sernova, M.S. Gelfand, I.A. Demina, M.V. Serebryakova, M.A. Galyamina, N.N. Vtyurin, S.I. Rogov, D.G. Alexeev, V.G. Ladygina, V.M. Govorun “Complete Genome and Proteome of Acholeplasma laidlawii”, Journal of bacteriology, Vol. 193, No. 18, Sep 2011, P. 4943–4953, PMID: 21784942
• V.G.Kanovei, V.A. Lyubetsky “Effective minimal coding of nonenumerable sets”, Siberian mathematical journal, 2011, (in press)
• V.G. Kanovei, V.A. Lyubetsky “On effective compactness and sigma compactness”, Mathematical notes, 2011, (in press)
• V.A. Lyubetsky, O.A. Zverkov, L.I. Rubanov, A.V. Seliverstov “Modeling RNA polymerase competition: the effect of σ-subunit knockout and heat shock on gene transcription level”, Biology Direct, Vol. 6, No. 1, 3, 2011, URL: http://www.biology-direct.com/content/6/1/3, DOI: 10.1186/1745-6150-6-3, PMID: 21255416
• K.Yu. Gorbunov, V.A. Lyubetsky “The tree nearest in average to a given set of trees”, Information transmission problems, Vol. 47, Iss. 3, 2011

Preprints

• А.В. Селиверстов, В.А. Любецкий «О функции Гильберта на множестве вершин куба», Информационные процессы, том 11, № 1, 2011, (в печати)

Abstracts

• K.V. Lopativskaya, A.V. Seliverstov, V.A. Lyubetsky “NtcA and NtcB regulons in cyanobacteria and chloroplasts”, Proceedings of the VI Moscow International Congress “Biotechnology: State of the Art and Prospects of Development”, Moscow, Russia, March 21–25 2011, P. 395–396
• K.V. Lopatovskaya, A.V. Seliverstov, V.A. Lyubetsky “Bacterial type RNA polymerase sigma subunits and their specific promoters in plastids”, Proceedings of the International Moscow Conference on Computational Molecular Biology: MCCMB’11, Moscow, Russia, July 21–24 2011, P. 209–210, URL: http://mccmb.belozersky.msu.ru/2011/
• К.В. Лопатовская, А.В. Селиверстов, В.А. Любецкий «Транскрипция в пластидах кокцидий», Труды 34-й конференции «Информационные технологии и системы» (ИТиС’11), г. Геленджик, 2–7 октября 2011
• А.В. Селиверстов, В.А. Любецкий «Эволюция РНК-полимераз и их промоторов в пластидах», Записки юбилейной биологической конференции ИППИ РАН, сентябрь 2011
• В.А. Любецкий, Л.И. Рубанов, А.В. Селиверстов «Тканеспецифичная транскрипция в митохондриях хордовых в развитии организма», Записки юбилейной биологической конференции ИППИ РАН, сентябрь 2011
• V.G. Kanovei, V.A. Lyubetsky “On the Hausdorff pantachy existance problem”, Proceedings of the International Mathematical Conference “50 Years Of IITP”, Moscow, Russia, July 25–29 2011
• K.Yu. Gorbunov, L.I. Rubanov, L.Yu. Rusin, V.A. Lyubetsky “An accurate algorithm of cubic complexity to build supertrees”, Proceedings of Conference “Deep Metazoan Phylogeny 2011”, Germany, October 2011
• V.A. Lyubetsky, A.V. Seliverstov “Mathematical problems in biological evolution and molecular regulation”, Proceedings of the International Mathematical Conference “50 Years Of IITP”, Moscow, Russia, July 25–29 2011
• В.A. Любецкий, А. Миссарова «Суперкомпьютерное моделирование конкуренции РНК-полимераз», Записки юбилейной конференции ИППИ РАН, декабрь 2011

2012

Articles

• О.А. Зверков, Л.Ю. Русин, А.В. Селиверстов, В.А. Любецкий «Вставки прямых повторов в микроэволюции пластид и митохондрий семенных растений», Вестник МГУ (биология), 2012, (в печати)
• K.Yu. Gorbunov, V.A. Lyubetsky “A fast algorithm to build a species supertree with a set of gene trees”, Molecular Biology (Moscow), 2011, (in print)

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