Shepelev Valery Anatolievich | Institute of Molecular Genetics
Academic degree:
Doctor of Philosophy (Physics and Mathematics)

Academic title:
without academic rank


Division of IMG:
Laboratory of bioinformatics

Position:
Researcher


Telephone:
+7-499-196-02-00

Е-mail:
spl@img.ras.ru



Main research interests

  • algorithms of sequence analysis
  • molecular principles of  DNA-protein interaction
  • search of the regulatory protein binding sites
  • statistical properties of DNA sequences
  • principles of genome organization
  • molecular evolution of primates.

 

1977-1980. Main achievements in the field of bioorganic compounds

   
      Studied the reaction kinetics and equilibrium between nucleotides and  hydroxymethyl derivatives of beta-alanine as a perspective reagent for probing DNA structure. Proposed the reaction scheme, product structure, measured equilibrium and kinetic constants.
 
1980-1983. Main achievements in the field of molecular biophysics
 Studied of the interaction of the non-histone protein HMG1 with DNA of different origin and synthetic DNA matrices of different nucleotide sequence. Developed a micro method of measurement of protein binding constants to DNA by the gel-filtration. Measured binding constants and nucleotide specificity of binding. Described the HMG1-DNA complexes by the thermal melting, thermal profiles of CD spectra, analytical ultracentrifugation, and modified kinetic formaldehyde method.

1984-2015. Main achievements in the field of bioinformatics.
 
 1) Developed a package of programs for digitizing, storing, picturing and computer treatment of UV adsorption spectra, titration and kinetic curves, elution profiles, thermal melting curves etc.
 
2) Developed a package of program for the routine analysis of DNA and protein sequences
     (for ISKRA-226).
 
3) Took part in the development of the All-Union database GENEXPESS of primary
      structures of biopolymers (closest analog is EMBL database)
4) Developed a package of program for the study of some statistical properties of
      DNA sequences mainly the statistics of oligonucleotides, context-dependent
      codon bias, prediction of the protein coding regions, back translation of proteins
      (for ISKRA-226).  In collaboration with M. Borodovsky showed that context-  
      dependence mainly reduce code degeneracy in E. coli.
 
5)  Developed a package of program for the study of DNA sequences (for IBM PC).

6) Proposed and implemented an accelerated algorithm of dot-matrix calculation, as well as an algorithm of multidimensional dot-matrices.

7)  Developed a method of fast sequence comparison.

8) Developed a Bayesian method of alphoid sequences classification. In collaboration with I. Alexandrov and coworkers, classified alphoid sequences and studied its chromosomal topography, interspersed repeats inhabitation, and proposed a scenario of alphoid sequences origin and evolution. It is shown that subtypes of old alpha-satellite are arranged in concentric manner around living centromere originated during molecular evolution of centromere. 

9) Implemented an advanced version of Exon-Intron Database. Based on this DB is a number of workson the structure and identification of some classes of genes, RNA, introns etc. 


Publications

  1. Shepelev V.A., Kosaganov Yu.N., Lazurkin Yu.S., Interaction of oxymethyl derivatives of beta-alanine with nucleotides. Bioorganic Chemistry, 1982, 8(5),  686-694 (in Russian).
  2. Volodin A.A., Shepelev V.A., Kosaganov Yu.N. Stoichiometry and kinetics of complex formation by the RecA protein and double-stranded DNA.FEBS Lett., 1982, v.145, N 1, p.53-56.
  3. Shepelev V.A., Kosaganov Yu.N., Lazurkin Yu.S., Lindigkeit R., Grade K. Interaction of the HMG1 protein with DNA. Stud.biophys.,1982, v.182, N 2/3, p.163-164.
  4. Shepelev V.A., Kosaganov Yu.N., Lazurkin Yu.S. Interaction of the HMG1 protein with nucleic acids. FEBS Lett., 1984, v.172, N2, p.172-176.
  5. Shepelev V.A. Interaction of HMG1 protein with nucleic acids. Ph.D. Thesis autoreferat, Moscow State University, 1985 (in Russian).
  6. Borodovskii M.Iu., Shepelev V.A., Aleksandrov A.A. Characteristics of the context shift in the frequency of synonymic codons in Escherichia coli. Mol. Biol. (Mosk). 1988, 22(3), 767-779 (in Russian).
  7. A.A.Alexandrov, N.A.Akimova, O.V.Nitsai, G.G.Palmbakh, A.E.Sedov, L.A.Vitzon, G.T.Zhangeldina, E.I.Golovanov, Yu.A.Sprizhitsky, V.A.Shepelev. "GENEXPRESS, database of primary biopolymer structures". Studia Biophysica, 1989, v.129, p.117-122.
  8. Shepelev V.A. Database storage of information in the field of molecular genetics. Application program packages for analysis of the nucleotide sequences. In:  Alexandrov A.A. Alexandrov N.N., Borodovsky M.Yu. et al. Computer analysis of the genetic texts. Moscow, Nauka Publ., 1990, 221-241 (in Russian).
  9. Shepelev V.A. Algorithm of accelerated calculation of dot-matrices. Biopolymers and Cell. 1991, 7(1), 22-24 (in Russian).
  10. Shepelev V.A., Yanishevsky N.V. Multidimensional dot-Matrices. Comput. Applic. Biosci. 1994. V.10, N6, 605-611.
  11. Aleksandrov A.A., Snitsar' R.V., Drozdov-Tikhomirov L.N., Skurida G.I., Shepelev V.A., Charikova E.V., Volkova L.I., Fedoseeva V.B., Kazachenko K.Iu., Krupenko M.A. Computer encyclopedia on human molecular and general biology. Mol Biol (Mosk). 1999, 33(1), 80-85 (in Russian).
  12. Alexandrov I, Kazakov A, Tumeneva I, Shepelev V, Yurov Y. Alpha-satellite DNA of primates: old and new families. Chromosoma. 2001 Aug;110(4):253-266.
  13. Kazakov A.E., Shepelev V.A., Tumeneva I.G., Alexandrov A.A., Yurov Y.B., Alexandrov I.A.  Interspersed repeats are found predominantly in the "old" alpha satellite families. Genomics. 2003, 82(6), 619-627.
  14. Aleksandrov A.A, Drozdov-Tikhomirov L.N., Shepelev V.A. Bioinformatics, in: Problems and perspectives of molecular genetics. V.2 Ed. Sverdlov E.D. Moskow, Nauka Publ . 2003-2004, p.302-329 (in Russian).
  15. Aleksandrov A.A., Drozdov-Tikhomirov L.N., Shepelev V.A., Fedoseeva V.B., Buchatskii A.G., Kazachenko K. Yu., Krupenko M.A., Kovalev P.V., Charikova E.V., Revkova N.V.The “HUMBIO” Information Base on Human Biology: Two Years in Internet. Uspekhi sovremennoi biologii. 2004, 124(4), p. 397-403 (in Russian).
  16. Krupnik O.V., Fadeeva N.V., Kvitko N.P., Shepelev V.A., Nielsen P.E., Lazurkin Y.S.  Stability and transformations of bis-PNA/DNA triplex structural isomers.  J. Biomol. Struct. Dyn. 2004, 21(4), 503-512.
  17. Fedorov A., Stombaugh J., Harr M.W., Yu S., Nasalean L., Shepelev V. Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database. Nucleic Acids Res. 2005, 33(14), 4578-4583.
  18. Shepelev V. and Fedorov A.  Advances in the Exon-Intron Database (EID). Briefings in Bioinformatics, 2006, 7(2), 178-185.
  19. Shao X., Shepelev V., Fedorov A. Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans. Bioinformatics. 2006, 22(6), 692-698.
  20. Bazeley P.S., Shepelev V., Talebizadeh Z., Butler M.G., Fedorova L., Filatov V., Fedorov A. snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions. Gene. 2008, 408(1-2), 172-179.
  21. Shepelev V.A., Alexandrov A.A., Yurov Y.B., Alexandrov I.A. The evolutionary origin of man can be traced in the layers of defunct ancestral alpha satellites flanking the active centromeres of human chromosomes. PLoS Genet. 2009 Sep;5(9):e1000641.
  22. Shepelev VA, Uralsky LI, Alexandrov AA, Yurov YB, Rogaev EI, Alexandrov IA. Annotation of suprachromosomal families reveals uncommon types of alpha satellite organization in pericentromeric regions of hg38 human genome assembly. Genom Data. 2015 Sep 1;5:139-146.