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Принадлежит к подразделению: Отдел математических методов в биологии
Руководитель: кандидат физ.-мат. наук, в.н.с., Алексеевский Андрей Владимирович

 

История. Со времени организации межфакультетской лаборатории математических методов в биологии Израиль Моисеевич Гельфанд пригласил в нее ряд сильных математиков, работавших в Москве.   Среди них были С.Г.Гиндикин, Д.Б.Фукс, И.Чередник и другие. Многие математики, работавшие с Израилем Моисеевичем (а круг мкатематиков - соавторов И.М.Гельфанда невереятно широк!), часто приходили к нему в "корпус А", в котором находится нынешний НИИ ФХБ имени А.Н.Белозерского.  Поэтому сейчас мне трудно вспомнить всех постоянно бывавших здесь математиков и, тем более, выделить из них штатных сотрудников межфакультетской лаборатории. 

В лабораторию были также приглашены специалисты в области, скажем так, обработки данных в прикладных задачах. Среди них Ш.А.Губерман (хотя, наверное, он никогда не числился в штате лаборатории), М.Л.Извекова, Б.Розенфельд (работал ли он в штате?), М.А.Шифрин (в штате не числился), И.Лукашевич, М.А.Алексеевская,  С.Ю.Лукашенко и это далеко не все. Задачами из этой области в сфере Израиля Моисеевича были медицинские, вернее, клинические задачи - задачи, встающие перед лечащим врачем в его повседневной практике и требующие систематизации результатов их решения врачем для получения обоснованных фактическими данными выводов. Далее, задачи прогнозирования землетрясений, нефтеносных пластов, схода лавин и ряд других.     

Немного другими задачами занимались Шапиро-Пятецкий и его группа: А.М.Леонтович, Н.Васильев, О.Ставская и другие.

Семен Григорьевич Гиндикин был организатором семинара по тем задачам, которые сейчас относятся к биоинформатике и вычислительной биологии. На рубеже 70-х и 80-х я ходил иногда на эти семинары. Среди участников были Е.Кунин,  К.Чумаков, А.Леонтович, Н.Васильев ( это те, кого помню).  

Перечисленные частично пересекающиеся кружки исследователей и составляли "математическую группу" в лаборатории, объединенную личностью Израиля Моисеевича. Со временем, надеюсь, удастся полнее восстановить славную историю нанешней математической группы.

Многие сотрудники группы разъехались по разным странам. 

В настоящее время группа представлена

- математика: Д.А.Поповым, С.М.Натанзоном и, в какой-то мере, А.В.Алексеевским

- биоинформатика: А.В.Алексеевским, А.М.Леонтовичем, С.А.Спириным, Е.А.Аксяновым, О.Н.Занегиной, А.С.Карягиной, А.С.Ершовой, коллегами из др. подразделений, аспирантами и студентами

-  медицинская информатика: С.Ю.Лукашенко, в какой-то мере А.В.Алексеевским и Л.К.Смирениной 

А.Алексеевский

PS. Представленный ниже список литературы составлен автоматической программой и требует существенной переделки, которая планируется. 

Приношу извинения за эту недоработку. А.Ал.

 

 

 

 

Обновлено 04.06.2012 14:28
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  1. Rusinov I., Ershova A., Karyagina A., Spirin S., Alexeevski A. (2015) Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes. BMC Genomics, 16: . >>

  2. Popov Y.V., Galitsyna A.A., Alexeevski A.V., Karyagina A.S., Spirin S.A. (2015) StructAlign, a program for alignment of structures of DNA-protein complexes. Biochem.-Moscow, 80 (11): 1465-1468. >>

  3. Goryunov D.V., Nagaev B.E., Nikolaev M.Y., Alexeevski A.V., Troitsky A.V. (2015) Moss phylogeny reconstruction using nucleotide pangenome of complete Mitogenome sequences. Biochem.-Moscow, 80 (11): 1522-1527. >>

  4. Ershova A.S., Rusinov I.S., Spirin S.A., Karyagina A.S., Alexeevski A.V. (2015) Role of restriction-modification systems in prokaryotic evolution and ecology. Biochem.-Moscow, 80 (10): 1373-1386. >>

  5. Brett K., Kordyukova L.V., Serebryakova M.V., Mintaev R.R., Alexeevski A.V., Veit M. (2014) Site-specific S-Acylation of Influenza Virus Hemagglutinin THE LOCATION OF THE ACYLATION SITE RELATIVE TO THE MEMBRANE BORDER IS THE DECISIVE FACTOR FOR ATTACHMENT OF STEARATE. J. Biol. Chem., 289 (50): 34978-34989. >>

  6. Konarev P.V., Kachalova G.S., Ryazanova A.Y., Kubareva E.A., Karyagina A.S., Bartunik H.D., Svergun D.I. (2014) Flexibility of the Linker between the Domains of DNA Methyltransferase SsoII Revealed by Small-Angle X-Ray Scattering: Implications for Transcription Regulation in SsoII Restriction-Modification System. PLoS One, 9 (4): . >>

  7. Krivozubov M., Goebels F., Spirin S. (2014) Estimation of relative effectiveness of phylogenetic programs by machine learning. J. Bioinform. Comput. Biol., 12 (2): . >>

  8. Mintaev R.R., Alexeevski A.V., Kordyukova L.V. (2014) Co-evolution analysis to predict protein-protein interactions within influenza virus envelope. J. Bioinform. Comput. Biol., 12 (2): . >>

  9. Medvedeva S.A., Panchin A.Y., Alexeevski A.V., Spirin S.A., Panchin Y.V. (2013) Comparative Analysis of Context-Dependent Mutagenesis Using Human and Mouse Models. Biomed Res. Int., 2013: . >>

  10. Medvedeva S.A., Panchin A.Y., Alexeevski A.V., Spirin S.A., Panchin Y.V. (2013) Comparative Analysis of Context-Dependent Mutagenesis in Humans and Fruit Flies. Int. J. Genomics, 2013: . >>

  11. Kirsanov D.D., Zanegina O.N., Aksianov E.A., Spirin S.A., Karyagina A.S., Alexeevski A.V. (2013) NPIDB: nucleic acid-protein interaction database. Nucleic Acids Res., 41: 0-0. >>

  12. Ershova A.S., Karyagina A.S., Vasiliev M.O., Lyashchuk A.M., Lunin V.G., Spirin S.A., Alexeevski A.V. (2012) Solitary restriction endonucleases in prokaryotic genomes. Nucleic Acids Res., 40 (20): 10107-10115. >>

  13. Sekerina S.A., Grishin A.V., Ryazanova A.Y., Artyukh R.I., Rogulin E.A., Yunusova A.K., Oretskaya T.S., Zheleznaya L.A., Kubareva E.A. (2012) Oligomerization of site-specific nicking endonuclease BspD6I at high protein concentrations. Russ. J. Bioorg. Chem., 38 (4): 376-382. >>

  14. Kordyukova L.V., Serebryakova M.V., Polyansky A.A., Kropotkina E.A., Alexeevski A.V., Veit M., Efremov R.G., Filippova I.Y., Baratova L.A. (2011) Linker and/or transmembrane regions of influenza A/Group-1, A/Group-2, and type B virus hemagglutinins are packed differently within trimers. Biochimica et Biophysica Acta-Biomembranes, 1808 (7): 1843-1854.

  15. Panchin A.Y., Mitrofanov S.I., Alexeevski A.V., Spirin S.A., Panchin Y.V. (2011) New words in human mutagenesis. BMC Bioinformatics, 12: -.

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  18. Velikodvorskaya G.A., Tikhonova T.V., Gurvits I.D., Karyagina A.S., Lavrova N.V., Sergienko O.V., Tashlitskii V.N., Lunina N.A., Lunin V.G. (2010) Chimeric Lactase Capable of Spontaneous and Strong Immobilization on Cellulose and Development of a Continuous-Flow System for Lactose Hydrolysis at High Temperatures. Applied and Environmental Microbiology, 76 (24): 8071-8075.

  19. Ryazanova A.Y., Molochkov N.V., Abrosimova L.A., Alexeevsky A.V., Karyagina A.S., Protsenko A.S., Friedhoff P., Oretskaya T.S., Kubareva E.A. (2010) Secondary structure of SsoII-like (Cytosine-5)-DNA methyltransferases N-terminal region determined by Circular dichroism spectroscopy. Molecular Biology, 44 (5): 807-816.

  20. Natanzon S.M. (2010) Cyclic foam topological field theories. Journal of Geometry and Physics, 60 (6): 874-883.

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  23. Nurtdinov R.N., Vasiliev M.O., Ershova A.S., Lossev I.S., Karyagina A.S. (2010) PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays. Nucleic Acids Research, 38: D726-D730.

  24. Karyagina A.S., Alexeevsky A.V., Spirin S.A., Zigangirova N.A., Gintsburg A.L. (2009) Effector proteins of chlamydiae. Molecular Biology, 43 (6): 897-916.

  25. Costa A.F., Natanzon S.M. (2009) Poincare's theorem for the modular group of real Riemann surfaces. Differential Geometry and Its Applications, 27 (5): 680-690.

  26. Grishin A.V., Alexeevsky A.V., Spirin S.A., Karyagina A.S. (2009) Conserved structural features of ETS domain-DNA complexes. Molecular Biology, 43 (4): 612-619.

  27. Fedotova E.A., Protsenko A.S., Zakharova M.V., Lavrova N.V., Alekseevsky A.V., Oretskaya T.S., Karyagina A.S., Solonin A.S., Kubareva E.A. (2009) SsoII-like DNA-methyltransferase Ecl18kI: Interaction between regulatory and methylating functions. Biochemistry-Moscow, 74 (1): 85-91.

  28. Spirin S., Titov M., Karyagina A., Alexeevski A. (2007) NPIDB: A database of Nucleic Acids-Protein Interactions. Bioinformatics, 23 (23): 3247-3248.

  29. Petrova N.V., Yakilitenko I.I., Alexeevski A.V., Verbovoy V.A., Razin S.V., Iarovaia O.V. (2007) Changes in chromosome positioning may contribute to the development of diseases related to X-chromosome aneuploidy. Journal of Cellular Physiology, 213 (1): 278-283.

  30. Dmitrieva T.M., Alexeevski A.V., Shatskaya G.S., Tolskaya E.A., Gmyl A.P., Khitrina E.V., Agol V.I. (2007) Significance of the C-terminal amino acid residue in mengovirus RNA-dependent RNA polymerase. Virology, 365 (1): 79-91.

  31. Alexeevski A., Natanzon S. (2006) Noncommutative two-dimensional topological field theories and Hurwitz numbers for real algebraic curves. Selecta Mathematica-New Series, 12 (3): 307-377.

  32. Romanenkov A.S., Kisil O.V., Zatsepin T.S., Yamskova O.V., Karyagina A.S., Metelev V.G., Oretskaya T.S., Kubareva E.A. (2006) DNA-methyltransferase SsoII as a bifunctional protein: Features of the interaction with the promoter region of SsoII restriction-modification genes. Biochemistry-Moscow, 71 (12): 1341-1349.

  33. Vasiliev J.M., Gelfand I.M. (2006) Cellular search migrations in normal development and carcinogenesis. Biochemistry-Moscow, 71 (8): 821-826.

  34. Pletjushkina O.Y., Fetisova E.K., Lyamzaev K.G., Ivanova O.Y., Domnina L.V., Vyssokikh M.Y., Pustovidko A.V., Alexeevski A.V., Alexeeski D.A., Vasiliev J.M., Murphy M.P., Chernyak B.V., Skulachev V.P. (2006) Hydrogen peroxide produced inside mitochondria takes part in cell-to-cell transmission of apoptotic signal. Biochemistry-Moscow, 71 (1): 60-67.

  35. Kachalova G.S., Artyukh R.I., Lavrova N.V., Ryazanova E.M., Karyagina A.S., Kubareva E.A., Bartunik H.D. (2005) Crystallization and preliminary crystallographic analysis of the (cytosine-5)-DNA methyltransferase NlaX from Neisseria lactamica. Acta Crystallographica Section F-Structural Biology and Crystallization Communications, 61: 852-854.

  36. Omelchenko T.A., Vasiliev J.M., Gelfand I.M., Feder H.H., Bonder E.M. (2004) Overexpression of Rho leads to mitosis-associated detachment of cells from epithelial sheets. Molecular Biology of the Cell, 15: 23A-23A.

  37. Vasiliev J.M., Omelchenko T., Gelfand I.M., Feder H.H., Bonder E.M. (2004) Rho overexpression leads to mitosis-associated detachment of cells from epithelial sheets: A link to the mechanism of cancer dissemination. Proceedings of the National Academy of Sciences of the United States of America, 101 (34): 12526-12530.

  38. Omelchenko T., Vasiliev J.M., Gelfand I.M., Feder H.H., Bonder E.M. (2003) Rho-dependent formation of epithelial "leader" cells during wound healing. Proceedings of the National Academy of Sciences of the United States of America, 100 (19): 10788-10793.

  39. Potapova T.V., Boytzova L.J., Alekseevskii A.V., Smolianinov V.V., Belozerskaya T.A. (2003) Tip growth of Neurospora crassa mutant strains: Effects of electrical isolation and nitrogen depletion. Biologicheskie Membrany, 20 (5): 395-400.

  40. Vorob'eva O.V., Romanenkov A.S., Metelev V.G., Karyagina A.S., Lavrova N.V., Oretskaya T.S., Kubareva E.A. (2003) Crosslinking of Cys142 of methyltransferase SsoII with DNA duplexes containing a single internucleotide phosphoryldisulfide link. Molecular Biology, 37 (5): 772-779.

  41. Vorob'eva O.V., Karyagina A.S., Volkov E.M., Viryasov M.B., Oretskaya T.S., Kubareva E.A. (2002) An analysis of methyltransferase SsoII-DNA contacts in the enzyme-substrate complex. Russian Journal of Bioorganic Chemistry, 28 (5): 363-370.

  42. Omelchenko T., Vasiliev J.M., Gelfand I.M., Feder H.H., Bonder E.M. (2002) Mechanisms of polarization of the shape of fibroblasts and epitheliocytes: Separation of the roles of microtubules and Rho-dependent actin-myosin contractility. Proceedings of the National Academy of Sciences of the United States of America, 99 (16): 10452-10457.

  43. Shishkov A.V., Ksenofontov A.L., Bogacheva E.N., Kordyukova L.V., Badun G.A., Alekseevsky A.V., Tsetlin V.I., Baratova L.A. (2002) Studying the spatial organization of membrane proteins by means of tritium stratigraphy: bacteriorhodopsin in purple membrane. Bioelectrochemistry, 56 (1): 147-149.

  44. Vasil'ev S.A., Alexeevski A.V., Spirin S.A., Tashlitski V.N., Karyagina-zhulina A.S., Kalaidzidis Y. (2002) DNA-Protein Interaction DataBaseProject: Bioinformatic DataBase of third genertion. European Journal of Human Genetics, 10: 199-200.

  45. Kubareva E.A., Walter J., Vorob'eva O.V., Razumikhin M.V., Karyagina A.S., Lau P.C.K., Trautner T. (2001) Determination of a non-methylated deoxycytidine residue in the recognition site of DNA-methyltransferases. Biochemistry-Moscow, 66 (12): 1356-1360.

  46. Omelchenko T.A., Fetisova E.K., Ivanova O.Y., Feder H.H., Vasiliev J.M., Gelfand I.M., Bonder E.M. (2001) Analysis of heterocellular contact interactions between epitheliocytes and fibroblasts. Molecular Biology of the Cell, 12: 475A-475A.

  47. Potapova T.V., Boytzova L.J., Alexeevski A., Smoljaninov V.V. (2001) The functional role of intercellular interactions at the Neurospora crassa hyphae: Influence of distant mycelium part on the tip growth. Biologicheskie Membrany, 18 (5): 389-394.

  48. Vorob'eva O.V., Vasil'ev S.A., Karyagina A.S., Oretskaya T.S., Kubareva E.A. (2000) Analysis of DNA-protein contacts in a complex between methyltransferase SsoII and a promoter region of the SsoII restriction-modification genes. Molecular Biology, 34 (6): 921-926.

  49. Kubareva E.A., Thole H., Karyagina A.S., Oretskaya T.S., Pingoud A., Pingoud V. (2000) Identification of a base-specific contact between the restriction endonuclease SsoII and its recognition sequence by photocross-linking. Nucleic Acids Research, 28 (5): 1085-1091.

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  51. Krendel M., Gloushankova N.A., Bonder E.M., Feder H.H., Vasiliev J.M., Gelfand I.M. (1999) Myosin-dependent contractile activity of the actin cytoskeleton modulates the spatial organization of cell-cell contacts in cultured epitheliocytes. Proceedings of the National Academy of Sciences of the United States of America, 96 (17): 9666-9670.

  52. Gloushankova N.A., Krendel M.F., Alieva N.O., Bonder E.M., Feder H.H., Vasiliev J.M., Gelfand I.M. (1998) Dynamics of contacts between lamellae of fibroblasts: Essential role of the actin cytoskeleton. Proceedings of the National Academy of Sciences of the United States of America, 95 (8): 4362-4367.

  53. Kubareva E.A., Kuznetsova S.A., Kanevsky I.A., Karyagina A.S., Nikolskaya I.I., Shabarova Z.A. (1997) DNA dumbbells as substrates for studying of restriction-modification and repair enzymes. FASEB Journal, 11 (9): A1309-A1309.

  54. Spirin S.A. (1997) A class of infinite-dimensional weight sl(3)-modules. Functional Analysis and Its Applications, 31 (2): 142-144.

  55. Gloushankova N.A., Alieva N.A., Krendel M.F., Bonder E.M., Feder H.H., Vasiliev J.M., Gelfand I.M. (1997) Cell-cell contact changes the dynamics of lamellar activity in nontransformed epitheliocytes but net in their ras-transformed descendants. Proceedings of the National Academy of Sciences of the United States of America, 94 (3): 879-883.

  56. Sheflyan G.Y., Kubareva E.A., Kuznetsova S.A., Karyagina A.S., Nikolskaya I.I., Gromova E.S., Shabarova Z.A. (1996) Cross-linking of SsoII restriction endonuclease to cognate and non-cognate DNAs. FEBS Letters, 390 (3): 307-310.

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  58. Petrauskene O.V., Schmidt S., Karyagina A.S., Nikolskaya I.I., Gromova E.S., Cech D. (1995) The Interaction of DNA Duplexes Containing 2-Aminopurine with Restriction Endonucleases Ecorii and Ssoii. Nucleic Acids Research, 23 (12): 2192-2197.

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  60. Brevnov M.G., Kubareva E.A., Romanova E.A., Volkov E.M., Karyagina A.S., Nikolskaya I.I., Gromova E.S. (1995) Interaction of the Mvai and Ssoii Methyltransferases with DNAs Altered at the Central Base-Pair of the Recognition Sequence. Gene, 157 (1): 149-152.

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  63. Spirin S.A. (1993) Algebras with Polynomial Relations Associated with A Class of Representations of Kac-Moody Algebras. Functional Analysis and Its Applications, 27 (1): 75-77.

  64. Kubareva E.A., Petrauskene O.V., Karyagina A.S., Tashlitsky V.N., Nikolskaya I.I., Gromova E.S. (1992) Cleavage of Synthetic Substrates Containing Nonnucleotide Inserts by Restriction Endonucleases - Change in the Cleavage Specificity of Endonuclease Ssoii. Nucleic Acids Research, 20 (17): 4533-4538.

  65. Tint I.S., Bonder E.M., Feder H.H., Reboulleau C.P., Vasiliev J.M., Gelfand I.M. (1992) Reversible Structural Alterations of Undifferentiated and Differentiated Human Neuroblastoma-Cells Induced by Phorbol Ester. Proceedings of the National Academy of Sciences of the United States of America, 89 (17): 8160-8164.

  66. Gelfand I.M., Kapranov M.M., Zelevinsky A.V. (1990) Generalized Euler Integrals and A-Hypergeometric Functions. Advances in Mathematics, 84 (2): 255-271.

  67. Gelfand I.M., Kapranov M.M., Zelevinsky A.V. (1990) Newton Polytopes of the Classical Resultant and Discriminant. Advances in Mathematics, 84 (2): 237-254.

  68. Gelfand I.M., Kapranov M.M., Zelevinsky A.V. (1990) Generalized Euler Integrals and A-Hypergeometric Functions. Advances in Mathematics, 84 (2): 255-271.

  69. Gelfand I.M., Kapranov M.M., Zelevinsky A.V. (1990) Newton Polytopes of the Classical Resultant and Discriminant. Advances in Mathematics, 84 (2): 237-254.

  70. Arshavsky Y.I., Deliagina T.G., Gelfand I.M., Orlovsky G.N., Panchin Y.V., Pavlova G.A., Popova L.B. (1990) Neural Control of Heart Beat in the Pteropod Mollusk Clione-Limacina - Coordination of Circulatory and Locomotor Systems. Journal of Experimental Biology, 148: 461-475.

  71. Arshavsky Y.I., Deliagina T.G., Gelfand I.M., Orlovsky G.N., Panchin Y.V., Pavlova G.A., Popova L.B. (1990) Neural Control of Heart Beat in the Pteropod Mollusk Clione-Limacina - Coordination of Circulatory and Locomotor Systems. Journal of Experimental Biology, 148: 461-475.

  72. Ivanova O.Y., Domnina L.V., Vasiliev J.M., Gelfand I.M. (1987) Migration of Nuclei and Perikaryal Cytoplasm Along the Cytoplasmic Processes of Differentiated Neurolastoma Cells. Cell Biology International Reports, 11 (10): 699-705.

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