Laboratory 6

"Mathematic methods and models in bioinformatics"
Institute for Information Transmission Problems,
Russian Academy of Sciences

Head of the Laboratory - Professor, Doctor of Sciences (Math) Vassily Lyubetsky

E-mail: lyubetsk@iitp.ru, tel. +7(495)299-8354, +7(495)413-4643

In 1998, the sector of "Computer logic in information processes" was established as a research branch of Laboratory 1. Research directions it was developing were conceived in the D.Sc. habilitation thesis of its head, Vassily Lyubetsky, and related to effective description of mathematical structures within the framework of model theory, intuitionistic and descriptive set theory, stochastic games theory, etc., as well as to developing models of information interaction, in the field of bioinformatics inclusive (jointly with the group of M. Gelfand at Integrated Genomics and, later, at the Institute's Center for Bioinformatics). The latter projects focused mainly on signal detection and modeling metabolic regulation (gene expression) in bacteria (at the RNA secondary structure level in processes of transcription, translation and protein-DNA interaction), reconstruction of evolutionary events at molecular level and inferring species trees. In 2004 the sector has been transformed into the dedicated "Laboratory for mathematic methods and models in bioinformatics", Laboratory 6.

Scientific outcome in field of mathematics produced at the sector and the successor laboratory over past years is published in a number of established journals like "Progress in mathematic sciences" [Uspekhi matematicheskikh nauk], "Proceedings of Steklov Mathematic Institute of the RAS" [Trudy matematicheskogo instituta RAN im. Steklova], "Information Transmission Problems of the RAS" [Problemy peredachi informatsii] and others, as well as contributed toward selected chapters in books "Topics in classical and intuitionistic model theory" and "Nonstandard Analysis: Axiomatically". Biological results are published in FEMS Microbiological letters, In Silico Biology, Bioinformatics, Biophysics, Molecular Biology [Molekulyarnaya Biologiya]. Currently in preparation is the book "Modern set theory".

Laboratory staff is involved in research and teaching activities at universities in Russia and abroad. The textbook "Fundamentals of elementary mathematics" has now been published in second edition. Two D.Sc. and six Ph.D. dissertation theses are defended under the supervision of Vassily Lyubetsky, two other Ph.D.'s are currently submitted.

Leading research staff of the laboratory includes A.V. Chagrov, P.V. Golubtsov, K.Y. Gorbunov, V.G. Kanovey, L.Y. Rusin, A.V. Seliverstov, A.G. Vitreschak.
Close professional contacts are maintained with V.V. Aleshin, A.V. Chernavsky, M.S. Gelfand, E.V. Lyubetskaya, A.A. Mironov, S.A. Pirogov, L.I. Rubanov, N.K. Vereschagin, V.V. V'yugin.

Principal publications since 1999:

1999 2000 2001 2002 2003 2004 2005 2006

1999

  1. В.А. Любецкий. Логика устной речи в сравнении с логикой письменной речи. Труды второго философского конгресса, Екатеринбург, часть 1, 1999, с. 222.
  2. В.А. Любецкий. О преобразовании классических выводов в интуиционистские. Труды второй международной конференции «Смирновские чтения», Москва, 1999, с. 38-41.
  3. В.А. Любецкий. Об основах интеллектуальных процессов. Труды второго философского конгресса, Екатеринбург, часть 1, 1999, с. 223-224.
  4. Lyubetsky V.A. Logic models of informational interaction processes. Proceedings of I international conference of the RAS «Issues in control and modeling in complex systems», Samara, 1999, p. 133-145. [in Russian]
  5. Kuznetsov N.A., Lyubetsky V.A. Computer logics in information processes. Information transmission problems, RAS, V. 35, issue 2, 1999, p. 107-111. [in Russian]
  6. Голубцов П.В. Аксиоматическое описание категорий преобразователей информации. Пробл. передачи информ., Т.35, №3, 1999, с. 80-99.
  7. Gelfand M.S., Mironov A.A., Jomantas J., Kozlov Yu.I. and Perumov D.A. A conserved RNA structure element involved in the regulation of bacterial riboflavin biosynthesis genes. Trends Genet., 15, 1999, p.p. 439-442.
  8. Chagrov A.V. A first-order effect and modal propositional formulas. Andrea Cantini, etc. (Eds.) Logic and Foundation of Mathematics. Kluwer Academic Publishers, 1999. p. 209-217.
  9. R. Diestel, T.R. Jensen K. Gorbunov and C. Thomassen. Highly connected sets and the excluded grid theorem. Journal of Combinatorial Theory, Series B vol. 75, 1999, p. 61-73.

    2000

    1999 2000 2001 2002 2003 2004 2005 2006

  10. V.A. Lyubetsky, M.J.A. Larijani. Topics in Classical and Intuitionistic Model Theory. Gardariki, Moscow, 2000, 390 pages.
  11. Kuznetsov N.A., Lyubetsky V.A., Chernavsky A.V. 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, 2000, RAS Press, p. 8-20. [in Russian]
  12. V’yugin V.V., Gorbunov K.Y., Lyubetsky V.A. 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, 2000, RAS Press, p. 130-137. [in Russian]
  13. Gorbunov K.Y., Lyubetsky V.A. On an algorithm of detecting regulatory signal in sequence data. Logic research. Issue 7, Moscow, Nauka, 2000, p. 159-163. [in Russian]
  14. Vereschagin N.K., Lyubetsky V.A. An algorithm of inferring RNA secondary structure. Proceedings of scientific workshop of the Logic Center of RAS, Issue 14, Moscow, RAS Press, 2000, p. 99-109. [in Russian]
  15. Gorbunov K.Yu. On an estimate of matrix complexity of a set. Proceedings of II international conference of the RAS «Issues in control and modeling in complex systems», Samara, 2000, RAS Press, p. 138-140. [in Russian]
  16. Новичков П.С., Гельфанд М.С., Миронов А.А. Предсказание экзон-интронной структуры сравнением геномных последовательностей. Молекулярная биология, т. 34, № 2, 2000, с. 230-236.
  17. Панина Е.М., Миронов А.А., Гельфанд М.С. Статистический анализ полных бактериальных геномов: палиндромы и системы рестрикции-модификации. Молекулярная биология, т. 34, № 2, 2000, с. 246-252.
  18. Миронов А.А., Винокурова Н.П., Гельфанд М.С. Программное обеспечение анализа бактериальных геномов. Молекулярная биология, т. 34, № 2, 2000, с. 253-262.
  19. Gelfand M.S., Koonin E.V., Mironov A.A. Prediction of transcription regulatory sites in Archaea by a comparative-genomic approach. Nucleic Acids Res., vol. 28, no. 3, 2000, p. 695-705.
  20. Vitreschak A.G., Gelfand M.S. Comparative approach to analysis of regulation in complete genomes: Attenuators of aromatic amino acid operons of gamma-proteobacteria. II Международная конференции "Проблемы управления и моделирования в сложных системах", Самара, Издательство РАН, 2000, p. 141-142.
  21. Ramensky V.E., Makeev V.Ju., Gelfand M.S., Roytberg M.A., Tumanyan V.G. Bayesian approach to DNA segmentation into regions with different average nucleotide composition. JOBIM’2000 “Journees Ouvertes Biologie Informatique Mathematiques”, Montpellier, France, Mai 2000, p. 241-248.
  22. Vereschagin N.K., Shen' A. Mathematical logic and the theory of algorithms. Computable functions. Publishing of Moscow Center of continuous mathematical education. Moscow, 1999, 174 pages.
  23. Vereschagin N.K., Shen' A. Mathematical logic and the theory of algorithms. Languages and computations. Publishing of Moscow Center of continuous mathematical education. Moscow, 2000, 274 pages.
  24. Vereshchagin N., Vyugin M. Independent minimum length programs to translate between given strings. Proc. of 15th Annual IEEE Conference on Computational Complexity, Florence, July 2000, р. 138-144.
  25. Romashchenko A., Shen A., Vereshchagin N. Combinatorial interpretation of Kolmogorov complexity. Proc. of 15th Annual IEEE Conference on Computational Complexity, Florence, July 2000, р. 131-137.
  26. Голубцов П.В., Старикова О.В. Проблема калибровки для инвариантных измерительно-вычислительных систем. Проблемы управления и моделирования в сложных системах, II международная конференция, Самара, 19-24 июня 2000, с. 143-148.
  27. Голубцов П.В., Сизарёв Д.В. Синтез оптимальных систем формирования изображений с непрерывным полем зрения. Проблемы управления и моделирования в сложных системах, II международная конференция, Самара, 19-24 июня 2000, с. 149-154.
  28. Чагров А.В. Об интерполяционном свойстве полных по Э.Посту модальных логик. Труды VI Общероссийской научной конференции «Современная логика: проблемы теории, истории и применения в науке», 22-24 июня 2000, Санкт-Петербург, Издательство ЛГУ, 2000, с. 258-259.
  29. Чагров А.В. Два замечания о строго импликативных формулах в модальной логике S3. Логические исследования, выпуск 7, Москва, Наука, 2000, с. 84-89.
  30. Чагров А.В. Об эффективных теоремах дедукции в нормальных модальных логиках. Логические исследования, выпуск 7, Москва, Наука, 2000, с. 209-216.
  31. Чагров А.В. Логика, не являющаяся ни конечнозначной, ни бесконечнозначной. Труды научно-исследовательского семинара логического центра ИФ РАН, выпуск 14, Москва, Издательство РАН, 2000, с. 59-67.
  32. Рыбаков М.Н., Чагров А.В. Стандарные переводы неклассических формул и относительная разрешимость логик. Труды научно-исследовательского семинара логического центра ИФ РАН, выпуск 14, Москва, Издательство РАН, 2000, с. 81-98.
  33. А.В. Зарелуа, В.А. Любецкий. Предисловие редакторов к первому тому книги А. Маллиос «Геометрия векторных пучков», Мир, 2000 (460 страниц в книге).

    2001

    1999 2000 2001 2002 2003 2004 2005 2006

  34. А.В. Зарелуа, В.А. Любецкий. Предисловие редакторов ко второму тому книги А. Маллиос «Геометрия векторных пучков», Мир, 2001 (442 страницы в книге).
  35. Danilova L.V., Gorbunov K.Y., Gelfand M.S., Lyubetsky V.A. An algorithm to detect regulatory signals in DNA sequence data (1). Information processes, V. 1, No 1, 2001, p. 56-63. [in Russian]
  36. Gelfand M.S., V’yugin V.V., Lyubetsky V.A. An approach to infer evolutionary species tree from multiple gene data. Information processes, V. 1, No 1, 2001, p. 64-77. [in Russian]
  37. Danilova L.V., Gorbunov K.Y., Gelfand M.S., Lyubetsky V.A. An algorithm to detect regulatory signals in DNA sequence data (2). Molecular Biology, V. 35, No 6, 2001, p. 987-995. [in Russian]
  38. V’yugin V.V., Lyubetsky V.A. An algorithm to detect horizontal gene transfer events with multiple gene trees. Information processes, V. 1, No 2, 2001, p. 167-177. [in Russian]
  39. Gorbunov K.Y., Lyubetskaya E.V., Lyubetsky V.A. On two algorithms of searching for alternative RNA structures. Information processes, V. 1, No 2, 2001, p. 178-187. [in Russian]
  40. Lyubetsky V.A., Seliverstov A.V. 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]
  41. Danilova L.V., Lyubetsky V.A. 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, RAS, 2001, p. 632-634. [in Russian]
  42. Kuznetsov N.A., Lyubetsky V.A., Chernavsky A.V. 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, RAS, 2001, p. 25-42. [in Russian]
  43. Lyubetsky V.A. First projective sets, AE-prefix and quantifiers elimination. Abstracts of International conference Mathematical Logic, Algebra and Set theory dedicated to the 100-th anniversary of P.S. Novikov, August 27-31 2001, Steklov Mathematical Institute RAS, Moscow, 2001, p. 27.
  44. Mironov A.A, Novichkov P.S., Gelfand M.S. Pro-frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. Bioinformatics, vol. 17, No 1, 2001, p. 13-15.
  45. Rodionov D.A., Gelfand M.S., Mironov A.A., Rakhmaninova A.B. Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria. Journal of molecular microbiology and biotechnology, vol. 3, No 2, 2001, p. 319-324.
  46. Makarova K.S., Mironov A.A., Gelfand M.S. Conservation of the arginine repressor DNA binding signal in all bacterial lineages. Genome biology, vol. 2, No 4, 2001, pp. research0013.1-0013.8.
  47. Panina E.M., Vitreschak A.G., Mironov A.A., Gelfand M.S. Regulation of aromatic amino acid biosynthesis in gamma-proteobacteria. Journal of molecular microbiology and biotechnology, vol. 3, No 4, 2001, p. 529-543.
  48. Brudno M., Gelfand M.S., Spengler S., Zorn M., Dubchak I., Conboy J.G. Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-MRNA splicing. Nucleic acids research, vol. 29, No 11, 2001, p. 2338-2348.
  49. Боринская С.А., Гельфанд М.С., Миронов А.А. Компьютерная геномика: в поисках генов. Химия и жизнь, No 2, 2001, с. 36-40.
  50. Гельфанд М.С. Биология in silico. Компьютерра, No 36(413), 2001, с. 20-22.
  51. Гельфанд М.С. Аннотация геномов – от последовательности к функции. Компьютерра, No 36(413), 2001, с. 22-25.
  52. Витрещак А.Г., Гельфанд М.С. Предсказание вторичной структуры РНК. Программа rnapattern – поиск вторичной структуры по паттерну. Труды 3-й международной конференции «Проблемы управления и моделирования в сложных системах», Самара, РАН, 2001, с. 623–625.
  53. Vitreschak A.G. 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. In the abstracts of international school "Artifical intelligence and heuristic methods for bioinformatics", Italy, San-miniato, October 1-11, 2001, p. 63.
  54. Gelfand M.S., Laikova O., Mironov A.A., Novichkov P.S., Panina E.M., Rodionov D.A., Vitreschak A.G. Comparative analysis of bacterial patterns. In the abstracts of meeting of HHMI international research scholars, Vancouver, Canada, June 20-23, 2001, p. 75.
  55. Gorbunov K.Yu. On some model of informational dependence in algebraic geometry. Information processes (http://www.jip.ru/), vol. 1, No 2, 2001, p. 147-149.[in Russian]
  56. Голубцов П.В., Старикова О.В. Инвариантность и калибровка измерительно-вычислительных систем в непрерывно-дискретном случае. Труды 3-й международной конференции «Проблемы управления и моделирования в сложных системах», Самара, РАН, 2001, с. 635–641.
  57. Голубцов П.В., Старикова О.В. Оптимальная калибровка инвариантных измерительно-вычислительных систем в случае параметрической информации о схеме измерения. VII конференция «Обратные и некорректно поставленные задачи», Москва, 2001, с. 19.
  58. Голубцов П.В., Старикова О.В. Калибровка инвариантных преобразователей информации. Информационные процессы, том 1, No 1, 2001, с. 78-88.
  59. Golubtsov P.V, Starikova O.V. Invariance considerations in problems of synthesis and optimal calibration of measurement computer system. First SIAM-EMS conference applied mathematics in our changing world, Berlin 2001, Collection of Abstracts, p. 66.
  60. Голубцов П.В., Старикова О.В. Редукция параметрически заданных инвариантных измерительно-вычислительных систем. Вестник Московского университета, сер. 3 "физика и астрономия", No 6, 2001, с. 3-6.
  61. V'yugin V.V. On non-stability of the individual ergodic theorem. Problemy peredachi informatcii, vol. 37, issue 2, 2001, p. 27-39. [in Russian]
  62. V'yugin V.V. Most sequences are stochastic. Information and computation, vol. 169, 2001, p. 252-263.
  63. V'yugin V.V. Non-robustness property of the individual ergodic theorem. Problems of information transmission, v.37, No 2, 2001, p. 23-33.
  64. Чагров А.В. Логика, не являющаяся ни конечно-значной, ни бесконечно значной. Труды научно-исследовательского семинара логического центра института философии РАН, вып. XIV, Москва 2000, с. 59-67.
  65. Рыбаков М.Н., Чагров А.В. Стандартные переводы неклассических формул и относительная разрешимость логик. Труды научно-исследовательского семинара логического центра института философии РАН, вып. XIV, Москва, 2000, c. 81-98.
  66. Chagrov A.V. All tabular generally post-complete extensions of k4 have interpolation property. Information processes, vol. 1, No 1, 2001, p. 50-55.
  67. Чагров А.В. Алгоритмическая проблематика в неклассических пропозициональных логиках. Смирновские чтения, третья международная конференция, Москва: ИФ РАН, 2001, с. 69-71.
  68. Чагров А.В., Чагрова Л.А. Первопорядковая определимость интуиционистских формул на конечных шкалах крипке: алгоритмический аспект. Смирновские чтения, третья международная конференция, Москва: ИФ РАН, 2001, с. 71-75.
  69. Чагров А.В. К логическим проблемам семантических аспектов информационного взаимодействия. Труды 3-ей международной конференции «Проблемы управления и моделирования в сложных системах», Самара, РАН, 2001, с. 611-616.
  70. Zakharyaschev M., Wolter F. and Chagrov A. Advanced modal logic. In Gabbay D.M., Guenthner F. (eds.). Handbook of philosophical logic, 2nd edition, vol. 3, Kluver academic publishers, 2001, p. 83-266.
  71. Muchnik An., Vereshchagin N. Logical operations and kolmogorov complexity. Proc. of 16th annual IEEE Conference on Computational Complexity, Chicago, June 2001, p. 256-265.

    2002

    1999 2000 2001 2002 2003 2004 2005 2006

  72. Gorbunov K.Y., Lyubetsky V.A. An algorithm to search for conservative RNA secondary structures in a database of RNA fragments. Information processes, 2002, V. 2, No 1, p. 55-58. [in Russian]
  73. Istomina S.N., Rubanov L.I. Parallel algorithm for searching regulatory signal in bacterial genome. Information processes, 2002, vol. 2, No 1, p. 85-90. [in Russian]
  74. Leontyev L.A., Lyubetskaya E.V., Lyubetsky V.A. Description and performance of a modified algorithm to search for alternative RNA secondary structures. Information processes, 2002, V. 2, No 1, p. 100-105. [in Russian]
  75. V’yugin V.V., Lyubetsky V.A. Some approaches to detect HGTs with phylogenetic data. Information processes, 2002, V. 2, No 1, p. 120-140. [in Russian]
  76. Kuznetsov N.A., Lyubetsky V.A., Chernavsky A.V. 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, RAS, 2002, p. 7-17. [in Russian]
  77. Lyubetsky V.A., V’yugin V.V. Method of horizontal gene transfer determination using phylogenetic data. Proceedings of the third international conference of bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 2, p. 60-62.
  78. Lyubetsky E.V., Lyubetsky V.A. Algorithm for searching alternative secondary RNA structures. Proceedings of the third international conference of bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 3, p. 15-17.
  79. Gorbunov K.Yu., Lyubetsky V.A. An algorithm for searching common secondary structures in a set of RNA sequences. Proceedings of the third international conference of bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 3, p. 25-23.
  80. Lyubetsky V.A., Rubanov L.I. Parallel algorithm for searching regulatory signal in bacterial genome. Proceedings of the third international conference of bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 1, p. 23-25.
  81. V’yugin V.V., Gelfand M.S., Lyubetsky V.A. Trees reconciliation: inferring species tree with multiple gene trees. Molecular biology, 2002, V. 36, No 5, p. 807-816. [in Russian]
  82. Vitreschak A.G., Rodionov D.A., Mironov A.A., Gelfand M.S. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Research. 2002. V. 30. No 14. P. 3141-3151.
  83. Rodionov D.A., Vitreschak A.G., Mironov A.A., Gelfand M.S. Comparative Genomics of Thiamin Biosynthesis in Procaryotes. New Genes and Regulatory Mechanisms. J. Biol. Chem. 2002 Dec 13. V. 277. No 50. P. 48949-48959.
  84. Panina E.M, Vitreschak A.G., Mironov A.A., Gelfand M.S. 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, v. 2, p. 32-34.
  85. Vitreschak A.G., Rodionov D.A., Mironov A.A., Gelfand M.S. 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. v. 2,. p. 44-46.
  86. Sze S.-H., Gelfand M.S. and Pevzner P.A. Finding weak motifs in DNA sequences. Pacific symposium on biocomputing, 2002, p. 235-246.
  87. Ponomarenko J.V., Orlova G.V., Frolov A.S., Gelfand M.S, Ponomarenko M.P. Selex_DB, a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPS and site-directed mutagenesis data. Nucleic acids res. 2002. V. 30. No 1. P. 195-199.
  88. Mirny L.A., Gelfand M.S. Structural analysis of conserved base-pairs in protein-DNA complexes. Nucleic acids res. 2002. V. 30. No. 7. P. 1704-1711.
  89. Котельникова Е.А., Гельфанд М.С. Выработка бактериоцинов грам-положительными бактериями и механизмы транскрипционной регуляции. Генетика. 2002. Т. 38. № 6. c. 758-772.
  90. Mirny L.A., Gelfand M.S. Using orthologous and paralogous proteins to identify specificity determining residues bacterial transcription factors. J. Mol. Biol. 2002. V. 321. No. 1. P. 7-20.
  91. Permina E.A., Mironov A.A, Gelfand M.S. Damage-repair error-prone polymerase of bacteria: association with mobile genome elements. Gene. 2002. V. 293. No 1-2. P. 133-140.
  92. Baytalulk M.V., Gelfand M.S., Mironov A.A. Exact mapping of prokaryotic gene starts. Briefings in bioinformatics. 2002. V. 3. No 2. P. 181-194.
  93. Байталюк М.В., Гельфанд М.С., Миронов А.А. Сравнительный подход к уточнению начал генов в полных бактериальных геномах. Биофизика. 2002, Т. 47, № 2, c. 197-203.
  94. Равчеев Д.А., Гельфанд М.С, Миронов А.А., Рахманинова А.Б. Пуриновый регулон гамма-протеобактерий. Детальное описание. Генетика. 2002. Т. 38. № 9, c. 1203-1214.
  95. Котельникова Е.А., Гельфанд М.С. Регуляция транскрипции в системе выработки бактериоцинов streptococcus equi. Генетика. 2002. Т. 38. № 7, c. 911-915.
  96. Rodionov D.A., Mironov A.A., Gelfand M.S. Conservation of the biotin regulon and the BIRA regulatory signal in eubacteria and archaea. Genome research. 2002. V. 12. No 10. P. 1507 - 1516.
  97. Полуэктова Е.У., Хольсаппель С., Гагарина Е.Ю., Гельфанд М.С., Брон С., Прозоров А.А. Наличие генетического мобильного элемента isbsu2 из криптической плазмиды в хромосоме ряда штаммов bacillus subtilis. Доклады РАН. 2002. Т. 386. № 4. c. 552-554.
  98. Нуртдинов Р.Н., Миронов А.А., Гельфанд М.С. Консервативен ли альтернативный сплайсинг генов млекопитающих? Биофизика. 2002. Т. 47. № 4. c. 197-203.
  99. Gelfand M.S., Laikova O.N. Prolegomena to the evolution of transcriptional regulation in bacterial genomes. Functional Genomics Series, Caister AcademicPress, V. 3: Frontiers in Computational Genomics, Galperin M.Y and Koonin E.V., eds. 2003. p. 195-216.
  100. Permina E.A., Gelfand M.S. Regulation of the heat-shock response of β-, γ-, ε-proteobacteria. Proc. Recomb 2002, Washington DC, USA, April 2002. p. 150-151.
  101. Vitreschak A.G., Panina E.M., Rodionov D.A., Mironov A.A., Gelfand M.S. Comparative analysis of RNA regulation in bacterial genomes. 2002. Proc. Meeting of howard hughes medical institute international research scholars, palm cove, Australia, June 2002. p. 89.
  102. Vitreschak A.G. 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. Proc. Int. Summer school “from genome to life”. Structural, functional and evolutionary approaches, Cargese, Corsica, France, July 2002. p. 57-58.
  103. Nurtdinov R.N., Artamonova I.I., Mironov A.A., Gelfand M.S. Are patterns of alternative splicing of mammalian genes conserved? Proceedings of the third International Conference on Bioinformatics of Genome Regulation and Structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 3, p. 36-39.
  104. Sutormin R.A., Rakhmaninova A.B., Gelfand M.S. Batmas30 – the amino acid substitution matrix for alignment of bacterial transporters. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 3, p. 90-92.
  105. Kalinina O.V., Makeev V. Ju., Sutormin R.A., Gelfand M.S., Rakhmaninova A.B. Rare residues form the chanel in transmembrane transporter proteins. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 3, p. 100-103.
  106. Sadovskaya N.S., Sutormin R.A., Rakhmaninova A.B., Gelfand M.S. Benchmarking of programs for recognition of transmembrane segments in transporter proteins // Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 3, p. 115-116.
  107. Novichkov P.S., Gelfand M.S., Mironov A.A. Mutation rate of ribosomal proteins and the 3d structure of the small ribosomal subunit. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 3, p. 174-176.
  108. Novichkov P.S., Gelfand M.S., Mironov A.A. Relative mutation rate of bacterial proteins and prediction of the distance between orthologous genes. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 3, p. 177-180.
  109. Gerasimova A.V., Rodionov D.A., Mironov A.A., Gelfand M.S. fnr/dnr/anr-regulon in gamma-proteobacteria. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 2, p. 19-20.
  110. Kotelnikova E.A., Gelfand M.S. Transcriptional regulation of a novel bacteriocin-producing system in streptococcus equi. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 2, p. 23-25.
  111. Panina E.M., Vassieva O., Gelfand M.S., Overbeek R. Prediction of new enzyme involved in peptidoglican recycling. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 2, p. 29-31.
  112. Permina E.A., Gelfand M.S. Regulation of the heat shock response of β-, γ- and ε-proteobacteria. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 2, p. 35-37.
  113. Ravcheev D.A., Gelfand M.S., Mironov A.A., Rakhmaninova A.B. The purine regulon of gamma-proteobacteria. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 2, p. 38-39.
  114. Rodionov D.A., Mironov A.A., Gelfand M.S. Computational analysis of the biotin regulon in bacterial genomes. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia July 14-20, 2002, v. 2, p. 40-43.
  115. Kazakov A.E., Vassieva O., Gelfand M.S., Osterman A., Overbeek R. Bioinformatics analysis of PHOH function and regulation in actinobacteria. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 1, p. 20-22.
  116. Favorov A., Gelfand M.S., Mironov A.A., Makeev V. Yu. Yet another digging for DNA motifs GIBBS sampler. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 1, p. 31-33.
  117. Baytaluk M.V., Gelfand M.S., Mironov A.A. Exact mapping of prokaryotic gene starts. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 1, p. 113-115.
  118. Neverov A.D., Gelfand M.S., Mironov A.A. Gene prediction in genomic DNA of aspergillus. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 1, p. 116-118.
  119. Paskhin A.I., Ramensky V.E., Gelfand M.S., Makeev V.J. Identification of coding regions in genomes of lower eukaryotes by compositional segmentation of complete genomes. Proceedings of the third international conference on bioinformatics of genome regulation and structure, BGRS’2002, Novosibirsk, Russia, July 14-20, 2002, v. 1, p. 119-121.
  120. Витрещак А.Г. Компьютерное предсказание регуляторных сайтов мРНК. Анализ регуляции экспрессии генов биосинтеза аминокислот и генов, кодирующих тРНК-синтетазы в грамм-положительных бактериях. Информационные процессы, 2002, Т. 2, No 1, c. 91-95.
  121. Данилова Л.В., Гельфанд М.С. Поиск регуляторных сайтов в группах ортологичных генов гамма-протеобактрий. Информационные процессы, 2002, Т. 2, No 1, c. 59-61.
  122. Danilova L.V, Gelfand M.S. 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, v. 2, p. 21-22.
  123. Vyugin M.V., V'yugin V.V. Predictive complexity and information. Proceedings Fifteen International Conference on Computational Learning Theory -- COLT'02, Lecture Notes on Artificial Intelligence. 2002. v. 2375, p. 90-104.
  124. V'yugin V.V. Does snooping help? Theoretical Computer Science. 2002, v. 276, p. 407-415.
  125. V'yugin V.V. Suboptimal measures of predictive complexity for absolute loss function. Information and Computation. 2002, v. 175, p. 146-157.
  126. Vyugin M.V., V'yugin V.V. On complexity of easy predictable sequences. Information and Computation. 2002, v. 178, p. 241-252.
  127. Чагров А.В. К вопросу об обратной математике модальной логики. Логические исследования,  выпуск 8. М.: Наука, 2001. c. 224-243.
  128. Чагров А.В. Доказательство одной теоремы Крипке. Труды научно-исследовательского семинара Логического центра Института философии РАН. Вып. XV. М.: 2001, c. 113-119.
  129. Чагров А.В., Чагрова Л.А. Алгоритмическая проблема первопорядковой определимости интуиционистских формул на конечных шкалах Крипке. Российской математике – триста лет: Материалы юбилейной науч. конф. Тверь: Твер. гос. ун-т, 2002. c. 115-120.
  130. Чагров А.В. Суперинтуиционистские логики, консервативные относительно безымпликативных фрагментов  интуиционистской логики. Российской математике – триста лет: Материалы юбилейной науч. конф. Тверь: Твер. гос. ун-т, 2002. c. 121-126.
  131. Chagrov A.V., Chagrova A.A. Normal modal logics with (in)finite sets of nonequivalent modalities. Российской математике – триста лет: Материалы юбилейной науч. конф. Тверь: Твер. гос. ун-т, 2002. c. 127-139.
  132. Рыбаков М.Н., Чагров А.В. Модальные формулы без переменных и PSPACE-полнота. Современная логика: Проблемы теории, истории и применения в науке. Материалы VII Общероссийской научной конференции. Спб, 2002. c. 498-500.
  133. Kanovei V.G., Reeken M. New Radon-Nikodym ideals. Mathematika. 2002, v. 47, p. 219-227.
  134. Kanovei V.G., Reeken M. Borel and countably determined reducibility in nonstandard domain. Front for the Mathematics Arxiv, Preprint math.LO 0202290, 34 pp. http://front.math.ucdavis.edu/math.LO/0202290
  135. Kanovei V.G. Some new results in Borel irreducibility of equivalence relations. Nonstandard methods and applications in mathematics. Pisa, Italia, 2002, p. 1.
  136. Kanovei V.G., Reeken M. Borel and countably determined reducibility in nonstandard domain. Logic Colloquium 2002, ASL European Summer meeting. Munster, Germany, 2002, p. 38-39.
  137. Kanovei V.G. Reducibility of equivalence relations in "hyperfinite" descriptive set theory. Abstract. Workshop on Descriptive Set Theory, Analysis, and Dynamical Systems. Fields Institute, Toronto, Canada, 2002. http://www.fields.utoronto.ca/programs/scientific/0203/settheory/workshop1/abstracts.html#kanovei
  138. Vereshchagin N. and Vitanyi P. Kolmogorov's Structure Functions with an Application to the Foundations of Model Selection. Proc. 47th IEEE Symposium on Foundations of Computer Science (FOCS’02), 2002, p. 751-760.
  139. Chernov A.V., Skvortsov D.P., Skvortsova E.Z., Vereshchagin N.K. Variants of Realizability for Propositional Formulas and the Logic of the Weak Law of Excluded Middle. Proc. of the Annual Symposium on Computer Science Logic, Edinburgh, Scotland, UK, September 22-25, 2002, p. 74-88.
  140. Shen A., Vereshchagin N. Logical operations and Kolmogorov complexity. Theoretical Computer Science. 2002, v. 271, p. 125-129.
  141. Vereshchagin N. Kolmogorov Complexity Conditional to Large Integers. Theoretical Computer Science. 2002, v. 271, p. 59-67.
  142. Vereshchagin N., Vyugin M. Independent minimum length programs to translate between given strings. Theoretical Computer Science. 2002, v. 271, p. 131-143.
  143. Romashchenko A., Shen A., Vereshchagin N. Combinatorial interpretation of Kolmogorov complexity. Theoretical Computer Science. 2002, v. 271. p. 111-123.
  144. Голубцов П.В., Старикова О.В. Учет инвариантности в задаче калибровки инвариантных измерительно-вычислительных систем. Математическое моделирование. 2002. Т. 14, № 4, c. 45-56.
  145. Golubtsov P.V., Moskaliuk S.S. Method of Additional Structures on the Objects of a Monoidal Kleisli Category as a Background for Information Transformers. Hadronic Journal. 2002. V. 25. No. 2. p. 179-238.
  146. Golubtsov P.V. Monoidal Kleisli Categry as a Background for Information Transformers Theory. Information processes, 2002, v. 2, No 1, p. 62-84.

    2003

    1999 2000 2001 2002 2003 2004 2005 2006

  147. Lyubetsky V.A., Seliverstov A.V. Some algorithms related to finite groups, Information processes, V 3, No 1, 2003, p. 39-46. [in Russian]
  148. Golubtsov P.V., Lyubetsky V.A. Stochastic dynamic games with information of various type. Information transmission problems, 2003, V 39, issue 3, p. 40-71. [in Russian]
  149. Lyubetsky V.A., V’yugin V.V. Methods of horizontal gene transfer determination using phylogenetic data (2). In Silico Biology (An International Journal on Computational Molecular Biology), V. 3, No 1,2, 2003, p. 17-31 (the computer version http://www.bioinfo.de/isb/2003/03/0003).
  150. 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, V. 3, No 1,2, 2003, p. 33-47 (the computer version: http://www.bioinfo.de/isb/2003/03/0004).
  151. V’yugin V.V., Gelfand M.S., Lyubetsky V.A. Identifying HTG events with phylogenetic data. Molecular biology, V. 37, No 4, 2003, p. 673-687. [in Russian]
  152. Lyubetskaya E.V., Leontyev L.A., Gelfand M.S., Lyubetsky V.A. Searching for alternative RNA secondary structures – gene expression regulators in bacteria. Molecular biology, V. 37, No 5, 2003, p. 834-842. [in Russian]
  153. Danilova L.V., Gelfand M.S., Lyubetsky V.A., Laikova O.N. Computer analysis of glycerol-3-phosphate metabolism regulation in proteobacterial genomes. Molecular Biology, No 5, 2003, с. 843-849.
  154. Lyubetskaya E.V., Leontyev L.A., Lyubetsky V.A. Searching for alternative RNA secondary structures in gamma-proteobacteria. Information processes, V. 3, No 1, 2003, p. 23-38. [in Russian]
  155. Lyubetsky V.A., Gorbunov K.Y. Searching for alternative RNA secondary structures. Information processes, V. 3, No 1, 2003, p. 47-60. [in Russian]
  156. Kuznetsov N.A., Lyubetsky V.A., Chernavsky A.V. On the concept of informational interaction, 1: pre-psychic level. Information processes, V. 3, No 1, 2003, p. 1-22. [in Russian]
  157. Gorbunov K.Y., Mironov A.A., Lyubetsky V.A. Searching for conservative RNA secondary structures, Molecular biology, V. 37, No 5, 2003, p. 850-860. [in Russian]
  158. Golubtsov P.V., Lyubetsky V.A. The result of an information process depends on the nature and content of information available to its participants. International conference of RAS, Samara, 2003, p. 445-453. [in Russian]
  159. Kanovey V.G.., Lyubetsky V.A. Classic problems of descriptive set theory, Proceedings of IV international Smirnov conference, RAS, Moscow, 2003, p. 32-34. [in Russian]
  160. V.G. Kanovei, V.A. Lyubetsky. On the existence of regular non-definable sets of reals. Proceedings of conference “Kolmogorov and current mathematics (Kolmogorov’s centennial)”, Moscow, p. 690, 2003. [in Russian]
  161. Gelfand M.S., Lyubetsky V.A. 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]
  162. Danilova L.V., Lyubetsky V.A., Laikova O.N. Computer detecting of glycerol-3-phosphate metabolism regulation in proteobacterial genomes. MCCMB’03, 2003, p. 52-53.
  163. Gorbunov K.Yu., Lyubetsky V.A. Detecting common secondary structures in a set of RNA sequences and its testing. MCCMB’03, 2003, p. 83-85.
  164. Lyubetsky V.A., V’uygin V.V. Complex phylogenetic analysis of evolutionary history for prokaryotes families. MCCMB’03, 2003, p. 146-147.
  165. Lyubetskaya E.V., Leontiev L.A., Lyubetsky V.A. Algorithm for detecting alternative secondary RNA structures and mass analysis attenuator regulation in proteobacteria. MCCMB’03, 2003, p. 144-145.
  166. Kanovey V.G., Lyubetsky V.A. On some classic problems in descriptive set theory. Russian mathematical surveys (Uspekhi matematicheskih nauk), V. 55, No 5, 2003, p. 3-88. [in Russian]
  167. Kuznetsov N.A., Lyubetsky V.A., Chernavsky A.V. On the concept of informational interaction, 2: pre-psychic level. Information processes, V. 3, No 2, 2003, p. 1-22. [in Russian]
  168. Golubtsov P.V., Lyubetsky V.A. Informational structure of dynamic games and the information content available to players, Logic research, RAS, 2003, p. 36-47. [in Russian]
  169. Vitreschak A.G., Rodionov D.A., Mironov A.A., Gelfand M.S. Regulation of the vitamin B(12) metabolism and transport in bacteria by a conserved RNA structural element. RNA. 2003 Sep. V. 9, No. 9, p. 1084-1097.
  170. Rodionov D.A., Vitreschak A.G., Mironov A.A., Gelfand M.S. Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Research. 2003. V. 31. No. 23. P. 1-10.
  171. Rodionov D.A., Vitreschak A.G., Mironov A.A., Gelfand M.S. Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J. Biol. Chem. 2003 Oct 17. V. 278. No. 42. P. 41148-41159.
  172. Panina E.M., Vitreschak A.G., Mironov A.A., Gelfand M.S. Regulation of biosynthesis and transport of aromatic amino acids in low-GC Gram-positive bacteria. FEMS Microbiol Lett. 2003 May 28. V. 222. No. 2. P. 211-220.
  173. Zhang Z., Feige J.N., Chang A.B., Anderson I.J., Brodianski V.M., Vitreschak A.G., Gelfand M.S., Saier M.H.Jr. A transporter of Escherichia coli specific for l- and d-methionine is the prototype for a new family within the ABC superfamily. Arch. Microbiol. 2003 Aug. V. 180. No. 2. P. 88-100.
  174. Vitreschak A.G. 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, MCCMB’03, Moscow, Russia, July 22-25, 2003. P. 233.
  175. Vitreschak A.G., Rodionov D.A., Mironov A.A., Gelfand M.S. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Research. 2002. V. 30. No 14. P. 3141-3151.
  176. Rodionov D.A., Vitreschak A.G., Mironov A.A., Gelfand M.S. Comparative Genomics of Thiamin Biosynthesis in Procaryotes. New Genes and Regulatory Mechanisms. J. Biol. Chem. 2002 Dec 13. V. 277. No 50. P. 48949 - 48959.
  177. Gelfand M.S., Laikova O.N. Prolegomena to the evolution of transcriptional regulation in bacterial genomes. Functional Genomics Series, Caister AcademicPress, V. 3: Frontiers in Computational Genomics, Galperin M.Y and Koonin E.V., eds. 2003. P. 195-216.
  178. Kalinina O.V., Makeev V.Yu., Sutormin R.A., Gelfand M.S. Rare residues form the channel in transmembrane transporters. In Silico Biology. 2003. V. 3. No 1-2. P. 197-204.
  179. Kazakov A.E., Laikova O.N., Rodionov D.A., Gelfand M.S. Carbohydrate metabolism in streptococci. Proceedings of the International Moscow Conference on Computational Molecular Biology, MCCMB’03, Moscow, Russia, July 22-25, 2003. P. 101-102.
  180. Kazakov A.E., Vassieva O., Gelfand M.S., Osterman A., Overbeek R. Bioinformatics classification and analysis of PhoH homologs. In Silico Biology. 2003. V. 3. No 1-2. P. 3-15.
  181. Хольсаппель С., Гагарина Е.Ю., Полуэктова Е.У., Незаметдинова В.З., Гельфанд М.С., Прозоров А.А., Брон С. Структура мобильного генетического элемента ISBsu2 из криптической плазмиды p1516 почвенного штамма Bacillus subtilis и наличие гомологов этого элемента в хромосоме различных штаммов этой бактерии. Микробиология. 2003. Т. 72, № 1, c. 70-75.
  182. Sutormin R.A., Rakhmaninova A.B., Gelfand M.S. BATMAS30 – amino acid substitution matrix for alignment of bacterial transporters. Proteins. 2003. V.51. No 1. P. 85-95.
  183. Eskin E., Keich U., Gelfand M.S., Pevzner P.A. Genome-wide analysis of bacterial promoter regions. Pacific Symposium on Biocomputing. 2003. P. 29-40.
  184. Kriventseva E.V., Koch I., Apweiler R., Vingron M., Bork P., Gelfand M.S., Sunyaev S. Increase of functional diversity by alternative splicing. Trends in Genetics. 2003. V.19. No 3. P. 124-128.
  185. Gelfand M.S. Computational identification of regulatory sites in DNA sequences. Artificial Intelligence and Heuristic Methods in Bioinformatics, IOS Press, Frasconi P. and Shamir R., eds. 2003. P. 148-172.
  186. Nurtdinov R.N., Artamonova I.I., Mironov A.A., Gelfand M.S. Low conservation of alternative splicing patterns in the human and mouse genomes. Hum. Mol. Genet. 2003. V. 12. No 11. P. 1313-1320.
  187. Panina E.M., Mironov A.A., Gelfand M.S. Comparative genomics of bacterial zinc regulons: Enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins. PNAS. 2003. V. 100. No 17. P. 9912-9917.
  188. Gerdes S.Y., Scholle M.D., Campbell J.W., Balazsi G., Ravasz E., Daugherty M.D., Somera A.L., Kyrpides N.C., Anderson I., Gelfand M.S., Bhattacharya A., Kapatral V., D'Souza M., Baev M.V., Grechkin Y., Mseeh F., Fonstein M.Y., Overbeek R., Barabasi A.L., Oltvai Z.N., Osterman A.L. Experimental determination and system-level analysis of essential genes in E. coli MG1655. J. Bacteriol. 2003. V. 185. No 19. P. 5673-5684.
  189. Gelfand M.S., Nurtdinov R.N., Kriventseva E.V., Artamonova I.I., Ramensky V.E., Mironov A.A., Sunyaev S.R. Evolutionary and functional role of alternative splicing. 1st Int. Con. «Functional Genomics and Disease», Prague, May 2003, poster PT4/181.
  190. Gelfand M.S. Comparative genomics of regulatory interactions in prokaryotes. Proceedings of the International Moscow Conference on Computational Molecular Biology, MCCMB’03, Moscow, Russia, July 22-25, 2003. P. 75-77.
  191. Gelfand M.S. Riboswitches: possibly the oldest regulatory system. 4th Int. Georgia Tech. Conf. on Bioinformatics, November 2003, Atlanta, USA, P. 19.
  192. Spirin V., Gelfand M.S., Mirny L.A. Computational analysis of metaboliс modules and pathways in the E. coli metabolic network. 4th Int. Georgia Tech. Conf. on Bioinformatics, November 2003, Atlanta, USA, p. 109.
  193. Голубцов П.В., Сизарев Д.В., Старикова О.В. Синтез оптимальных инвариантных систем формирования изображений на плоскости. Вестник Московского Университета, Сер. 3 "Физика и астрономия". 2003. № 2. c. 3-6.
  194. Golubtsov P.V. Monoidal Kleisli Category Structure of Classes of Information Transformers. Ukr. J. Phys. 2003. V. 48. No. 4. 9 pages.
  195. Golubtsov P.V. Information Transformers: Category-Theoretical Structure, Informativeness, Decision-Making Problems. Hadronic Journal, V. 26, 2003, 36 pages.
  196. Chagrov A.V., Rybakov M.N. Least number of variables for PSPACE-hardness of provability problem in systems of modal logic. Advances in Modal Logic: 30 Septembre -- 2 Octobre 2002. Institut de recherche en informatique de Toulouse, Universit\'e Paul Sabatier, Toulouse, France, 2002, p. 178-188.
  197. Чагров А.В., Чагрова Л.А. О семантике Крипке со взрывающимися мирами для базисной логики. Смирновские чтения. 4 международная конференция. М.: ИФ РАН, 2003. c. 53-54.
  198. Чагров А.В. О расширениях «суперинтуиционистской» логики доказуемости формулами от одной переменной. Смирновские чтения. 4 международная конференция. М.: ИФ РАН, 2003. c. 51-53.
  199. Рыбаков М.Н., Чагров А.В. О сложности модальных логик, имеющих доказуемостную интерпретацию, с ограничениями на число переменных. Тезисы докладов Международной конференции «Колмогоров и современная математика», Москва, 16-21 июня 2003. М., МГУ, 2003. С. 707-708.
  200. Chagrov A.V., Rybakov M.N. How Many Variables Does One Need to Prove PSPACE-hardness of Modal Logics. Advances in Modal Logic, V. 4. London, King's College Publications, 2003. P. 71-82.
  201. Kanovei V.G., Reeken M. Borel and countably determined reducibility in nonstandard domain. Monatshefte fuer Mathematik. 2003. V. 140. No. 3. P. 197-231; Mathematika. 2002. V. 47. P. 219-227.
  202. Кановей В.Г., Реекен М. Некоторые новые результаты о борелевской несводимости отношений эквивалентности. Известия РАН, сер. матем. 2003. Т. 67. № 1. С. 59-82.
  203. Kanovei V.G., Reeken M. A theorem on ROD-hypersmooth equivalence relations in the Solovay model. Math. Logic Quarterly. 2003. V. 49. No 3. P. 299-304.
  204. Kanovei V.G., Duran B., Uspensky V.A., Vereschagin N.K. Do stronger definitions of randomness exist? Theoretical Computer Science. 2003. V. 290. No 3. P. 1987-1996.
  205. Kanovei V.G. On ROD-hyperfinite equivalence relations. Logic Colloquium 2003, Helsinki, Finland, August 14-20, 2003. Abstracts.
  206. V'yugin V.V. Variation tasks for additive loss functions and Kolmogorov complexity. Doklady Akademii Nauk. 2003. vol. 390. no 5. p. 595-598.
  207. V'yugin V.V. Problems of stability for universal schemes of information compression. Problemy peredachi informatcii. 2003. vol. 39. no 1. p. 36-52. [in Russian]
  208. V'yugin V.V., Maslov V.P. On extremal relations for Kolmogorov complexity and additive loss functions. Problemy peredachi informatcii. 2003. vol. 39. no 4. p. 71-87.
  209. Nuretdinov I., V'yugin V.V., Gammerman A. Transductive Confidence Machine is Universal. Lecture Notes in Computer Science, Algorithmic Learning Theory, 2842, Springer, Heidelberg, 2003. P. 283-297.
  210. Vereshchagin N.K., Skvortsov D.P., Skvortsova E.Z., Chernov A.V. Variants of Realizability for Propositional Formulas and the Logic of the Weak Law of Excluded Middle. In: Mathematical Logic and Algebra. Proc. of MIAN. 2003. V. 242. P. 77-97.
  211. Mitina O., Vereshchagin N. How to use several noisy channels with unknown error probabilities. Information and Computation. 2003. V. 182. P. 229-241.
  212. Makarychev K., Makarychev Yu., Romashchenko A., Vereshchagin N. A New class of non Shannon type inequalities for entropies. Communications in Information and Systems. December 2002. V. 2. No 2. P. 147-166.
  213. Gorbunov K.Yu. A Generalization of the Hilbert Basis Theorem. Mathematical Notes (Transl. from Mat. Zametki). 2003. V. 74. No 4. P. 483-490.

    2004

    1999 2000 2001 2002 2003 2004 2005 2006

  214. Kuznetsov N.A., Lyubetsky V.A., Chernavsky A.V. On the concept of informational interaction, 3: speech intellect. Information processes, V. 4, No 2, 2004, p. 127 - 132. [in Russian]
  215. Vitreschak A.G., Lyubetskaya E.V., Shirshin M.A., Gelfand M.S., Lyubetsky V.A. Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis. FEMS Microbiol Lett. 2004 May 15; 234(2), p. 357-370.
  216. Leontiev L.A., Shirsin M.A., Lyubetsky V.A. Detection of classical attenuation in bacterial genomes. Proceedings of the fourth international conference on bioinformatics of genome regulation and structure, volume 1, BGRS’2004, Novosibirsk, July 25-30, 2004, p. 116-118.
  217. Lyubetsky V.A., Seliverstov A.V. Amino acid biosynthesis attenuation in bacteria. Proceedings of the fourth international conference on bioinformatics of genome regulation and structure, volume 1, BGRS’2004, Novosibirsk, July 25-30, 2004, p. 307-310.
  218. Gorbunov K.Yu., Lyubetsky V.A. A model of tryptophan biosynthesis regulation. Proceedings of the fourth international conference on bioinformatics of genome regulation and structure, volume 2, BGRS’2004, Novosibirsk, July 25-30, 2004, p. 53-55.
  219. Lyubetsky V.A., V’yugin V.V. 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, volume 2, BGRS’2004, Novosibirsk, July 25-30, 2004, p. 281-284.
  220. Gorbunov K.Y., Lyubetsky V.A. 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]
  221. Lyubetsky V.A., Seliverstov A.V. 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]
  222. Lyubetskaya E.V., Leontyev L.A., Shirshin M.A., Lyubetsky V.A. 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]
  223. Kuznetsov N.A., Gelfand M.S., Lyubetsky V.A. 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]
  224. Lyubetsky V.A. Fundamentals of elementary mathematics. Recommended as student textbook for universities and teacher's training colleges, Iris-press, 625 pages. [in Russian]
  225. Lyubetsky V.A., Seliverstov A.V. Multifraction graphs with two vertices per fraction. Information processes, 2004, V. 4, No 2, p. 127-132. [in Russian]
  226. Kanovey V.G.., Lyubetsky V.A. On the set of all constructive Godel reals. Proceedings of Steklov Mathematic Institute of the RAS, V 247, 2004, p. 95 - 128. [in Russian]
  227. Lyubetsky V.A., Seliverstov A.V. Note on Cliques and Alignments. Information processes, 2004, V. 4, No 3, p. 241-246. [in Russian]
  228. Seliverstov A.V., Lyubetsky V.A. Properties of cysteine synthesis in Corynebacterium, Mycobacterium and Propionibacterium. Information processes, 2004, V. 4, No 3, p. 247-250. [in Russian]
  229. Kanovey V.G.., Lyubetsky V.A. On perfect subsets of invariant CA-sets, Proceedings (Matematicheskie zametki) of RAN, 2005, 77, 3, p. 334 – 338. [in Russian]
  230. V.A. Lyubetsky, A.V. Seliverstov. Note on Cliques and Alignments. Information processes, 2004, vol. 4, No 3, p. 241-246.
  231. Кановей В.Г., Любецкий В.А. О совершенных подмножествах инвариантных СА-множеств. Математические заметки РАН, 2005, 77, 3, с. 334-338.
  232. Gorbunov K.Yu., Lyubetsky V.A. New approach for detecting common secondary structures in a set of RNA sequences. Biophysics (Moscow), vol. 48, Suppl. 1 (2003), 2004, p. 56-67.
  233. Lyubetsky V.A., Vyugin V.V. Complex phylogenetic analysis of the evolutionary history for some prokaryotes family. Biophysics (Moscow), vol. 48, Suppl. 1 (2003), 2004, p. 97–106.
  234. Lyubetsky V.A., Gorbunov K.Yu., V’yugin V.V. Inferring evolutionary events, quality of COGs, measuring the dissimilarity between gene and species trees. Presentation abstracts of the EMBO World Phylogenetic Course 2004. November 1-7, 2004, Rio de Janeiro, Brazil (oral presentation).
  235. Чагров А.В. Финитарное семантическое следование для базисной и формальной логик А.Виссера: алгоритмический аспект. Современная логика: Проблемы теории, истории и применения в науке. Материалы VIII Общероссийской научной конференции. Спб, 2004. С. 542-543.
  236. Чагров А.В. Алгоритмическая проблема финитарного семантического следования для базисной и формальной логик А. Виссера. Логические исследования. Вып. 11. М., Наука, 2004. С. 282-289.
  237. Чагров А.В., Чагрова Л.А. Алгоритмическая проблема модальной определимости формул первого порядка с ограничениями на число переменных в модальных пропозициональных формулах. Современная логика: Проблемы теории, истории и применения в науке. Материалы VIII Общероссийской научной конференции. Спб, 2004. С. 544-546.
  238. Чагров А.В., Чагрова Л.А. Об алгоритмической проблеме пропозициональной определимости формул первого порядка в семантике формальной логики А.Виссера. Труды научно-исследовательского семинара Логического центра Института философии РАН. Вып. XVII. – М., 2004. С. 94-102.
  239. Golubtsov P.V. Information Transformers: Category-Theoretical Structure, Informativeness, Decision-Making Problems. In “Proceedings of the XIVth International Hutsulian Workshop on Mathematical Theories and their Applications in Physics & Technology” S. Moskaliuk Ed., TIMPANI. 2004. P. 9-58.
  240. Grishicheva J.V., Seliverstov A.V. A Note on Cliques in Multipartite Graphs. ArXiV e-print, math.CO/0404125. http://ru.arxiv.org/pdf/math.CO/0404125.
  241. Kanovei V.G., Reeken M. Nonstandard Analysis: Axiomatically. Springer Monographs in Mathematics, 2004, XVI+408 p.
  242. Kanovei V.G., Reeken M. Borel irreducibility between two large families of Borel equivalence relations. Logic Colloquium 99 (Lecture Notes in Logic, 17), ASL. 2004. P. 100-110.
  243. Kanovei V.G., Shelah S. A definable nonstandard model of the reals. J. Symbolic Logic. 2004. V. 69. No. 1. P. 159-164.
  244. McKelvey R., Miller K. and Golubtsov P. Fish Wars Revisited: A Stochastic Incomplete-Information Harvesting Game. In: Risk and Uncertainty in Environmental and Natural Resource Economics. Edited by Justus Wesseler, Hans-Peter Weikard, and Robert D. Weaver. Edward Elgar, Cheltenham, UK. 2004. P. 93-112.
  245. Rodionov D.A., Vitreschak A.G., Mironov A.A., Gelfand M.S. Comparative genomics of the regulation of methionine metabolism in Gram-positive bacteria. Nucleic Acids Res. 2004. V. 32. No. 11. P. 3340-3353.
  246. Kanovei V.G., Reeken M., Shelah S. Fully saturated extensions of standard universe. Logic, Algebra and Geometry, June 1--7, 2004, Abstracts, RAS EIMI, SPb, 2004, P. 16-17.
  247. Kanovei V.G., Reeken M., Shelah S. Fully saturated extensions of standard universe. Models of Arithmetic and Analysis, International Congress, Pisa, June 25-26, 2004, Program and abstracts, Pisa, Italy, 2004. P. 1.
  248. Kanovei V.G., Reeken M., Shelah S. Fully saturated extensions of standard universe. Timetable and abstracts, Logic Colloquium 2004. Torino, Italy, 2004. P. 117.
  249. Kanovei V.G. On problems on the structure of final relations and gaps in earlier Hausdorff's papers. Eighth Luminy Set Theory Workshop, Luminy, France, September 20-24, 2004.
  250. McKelvey R., Golubtsov P. and Cripe G. The Incomplete-Information Stochastic Split-Stream Model:  An Overview. In "Conference on Fisheries Economics and Management in Honour of Professor Gordon R Munro. Univ. of British Columbia, August 5-6. 2004.
  251. McKelvey R., Golubtsov P.V., Miller K., and Cripe G. Bi-National Management of a Transboundary Marine Fishery: Modeling the Destabilizing Impacts of Erratic Climatic Shifts. The SPACC Workshop, University of Portsmouth, UK, 13-15 September. 2004.
  252. Rusin L. Circumventing limitations of parsimony heuristic search: screening the equal tree space under minimum homoplasy requirement. Proceedings of The Annual New Zealand Phylogenetics Meeting 2004, February 15-20, 2004, Mt Ruapehu, New Zealand. P. 9.
  253. Rusin L. Inferring large animal phylogeny: a multiple gene phylogenetic analysis of minor phyla. Presentation abstracts of the EMBO World Phylogenetic Course 2004. November 1-7, 2004, Rio de Janeiro, Brazil.
  254. Vitreschak, A., Noe L., Kucherov G. Computer analysis of multiple repeats in bacteria. Proceedings of the fourth International Conference on Bionnformatics of Genome Regulation and Structure, BGRS’2004, Novosibirsk, Russia, July 25-30, 2004, V. 2. P. 297-299.

    2005

    1999 2000 2001 2002 2003 2004 2005 2006

  255. V. Kanovei, V. Lyubetsky. A cofinal family of equivalence relations generated by Borel ideals, Conference of Association for Symbolic Logic, Greece, Logic Colloquium 2005, ASL European Summer Meeting, July 28 - August 2, Athens, Greece, University of Athens, Greece, p. 83.
  256. Gorbunov K.Y., Lyubetsky V.A. Searching for ancestral genes introducing incongruence between gene and species trees. Molecular biology, 2005, 39, No 5, p. 847-858. [in Russian]
  257. V. Lyubetsky, K. Gorbunov, L. Rusin, V. V'yugin, Algorithms to reconstruct evolutionary events at molecular level and infer species phylogeny. An article in the book: Bioinformatics of Genome Regulation and Structure II. (Eds. N. Kolchanov and R. Hofestaedt) Springer Science & Business Media, Inc. 2005, p. 189-204.
  258. 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 2005, 5:54 (http://www.biomedcentral.com/1471-2180/5/54).
  259. Lyubetsky V.A., Seliverstov A.V. Gene expression regulation in amino acid and aminoacyl-tRNA synthetase biosynthesis in Actinobacteria. Molecular biology, 2005, 39, No 6, p. 1072-1075. [in Russian]
  260. Leontyev L.A., Lyubetsky V.A., Seliverstov A.V. An algorithms of bulk search for T-box-mediated transcription regulation in bacteria. Molecular biology, 2005, 39, No 6, p. 1076-1078. [in Russian]
  261. Lyubetsky V.A., Gorbunov K.Y., Pirogov S.A., Rubanov L.I., Seliverstov A.V. An algorithm and search results for a model of gene expression regulation with RNA secondary structures in bacteria, Information processes, 2005, V. 5, No 5, p. 337-366. [in Russian]
  262. Lyubetsky V.A., Gorbunov K.Y., V’yugin V.V., Rusin L.Y. Removing noise in protein multiple alignment, Information processes, 2005, V.5, No 5, p. 380-391. [in Russian]
  263. Lyubetsky V.A., Seliverstov A.V. Searching for conservative motifs in leader regions of genes on a fixed species tree, Information processes, 2005, V. 5, No 4, p. 265-270. [in Russian]
  264. Seliverstov A.V., Lyubetsky V.A. Translation regulation in chloroplasts, Information processes, 2005, V. 5, No 5, p. 400-404. [in Russian]
  265. V.A. Lyubetsky, S.A. Pirogov. A model for bacterial gene expression regulation with secondary RNA structures, МССМВ05, 2005, p. 214-216.
  266. A.V. Seliverstov, V.A. Lyubetsky. RNA regulatory structures in Actinobacteria and Cyanobacteri, МССМВ05, 2005, p. 351-353.
  267. K.Yu. Gorbunov, V.A. Lyubetsky. Algorithms to reconstruct ancestral gene evolution events, МССМВ05, 2005, p. 128-129.
  268. L.Yu. Rusin, V.V. V'yugin, V.A. Lyubetsky. Enhancing phylogenetic inference: concentration of the signal in sequence data, МССМВ05, 2005, p. 342-346.
  269. V.A. Lyubetsky, V.V. V'yugin A model for evolutionary event reconstruction, МССМВ05, 2005, p. 217-219.
  270. L.A. Leontiev, A.V. Seliverstov, V.A. Lyubetsky. An algorithm for mass searching of T-box structures in bacteria, МССМВ05, 2005, p. 202-206.
  271. Lyubetsky V.A., Pirogov S.А. A model of attenuator regulation in bacteria. Proceedings of the RAS conference «Issues of control and modeling in complex systems, VII International conference», 27 June - 1 July 2005, Samara, p. 205-209.
  272. Pirogov S.А., Gorbunov K.Y., Lyubetsky V.A. 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», 27 June - 1 July 2005, Samara, p. 210-215.
  273. Lyubetsky V.A., Seliverstov A.V. 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», 27 June - 1 July 2005, Samara, p. 216-221.
  274. Leontiev L.А., Seliverstov A.V., Lyubetsky V.A. Transcription regulation with T-boxes. Proceedings of the RAS conference «Issues of control and modeling in complex systems, VII International conference», 27 June - 1 July 2005, Samara, p. 222-224.
  275. Lyubetsky V.A. Mathematic models of evolution and gene expression regulation. Proceedings of the RAS conference «Mathematic models of pattern recognition», 20-26 November 2005, Moscow, p. 366-368.

    2006

    1999 2000 2001 2002 2003 2004 2005 2006

  276. A.V. Seliverstov, V.A. Lyubetsky, Translation regulation of intron containing genes in chloroplasts, Journal of Bioinformatics and Computational Biology, 2006 (in print).
  277. Leontiev L.А., Lyubetsky V.A. Mass detection of conserved T-box containing regulatory structures: search results. Information processes, 2006 (in print).
  278. Leontiev L.А., Lyubetsky V.A. An algorithm of searching for proteins coherent with a given phylogenetic profile. Information processes, 2006 (in print).
  279. Seliverstov А.V., Lyubetsky V.A. An algorithm for detecting conserved motifs in nucleotide sequences. Information processes, 2006 (in print).
  280. Lyubetsky V.A., Rubanov L.I., Seliverstov А.V., Pirogov S.А. A model of gene expression regulation in bacteria based on the formation of RNA secondary structures. Molecular biology, 2006, № 3 (in print).
  281. Kanovey V.G.., Lyubetsky V.A. A cofinal family of equivalence relations generated by Borel ideals. Proceedings of Steklov mathematical institute of RAS, 2006, V. 252 (in print).
  282. Kanovey V.G.., Lyubetsky V.A. Problems of set theoretic nonstandard analysis. Russian mathematical surveys (Uspekhi matematicheskih nauk), 2006 (in print).
  283. Kanovey V.G.., Lyubetsky V.A., Reeken M. On reducibility of monadic equivalence relations, Proceedings (Matematicheskie zametki) of RAS, 2006 (in print).
  284. Kanovey V.G.., Lyubetsky V.A. Contemporary set theory: descriptive dynamics. Nauka, 2006 (in print).
  285. Lyubetsky V.A., Pirogov S.A. Nonstandard representations of locally compact groups. Proceedings (Matematicheskie zametki) of RAS, 2006 (in print).
  286. Golubtsov P.V., Lyubetsky V.A. Modeling results of stochastic games in relation to various types and content of information available to players. Information transmission problems, 2006 (in print).

1999 2000 2001 2002 2003 2004 2005 2006