Valentina Boeva's Research Projects

• Word analysis in DNA sequences

  AhoPro project: seach for overrepresentation of given motifs in DNA sequences, p-value calculation.
  
  Collaboration with
  Mireille Régnier, INRIA, France; Personal homepage
  Vsevolod Makeev, GosNIIgenetika, Moscow, Russia; Laboratory homepage
  Julien Clément, Marne-la-Valee-CNRS, France; Personal homepage
  Andrey Mironov, Moscow State University, Russia. Laboratory homepage
  
  Published:
  • Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. V. Boeva, J. Clement , M. Regnier, M.A. Roytberg, V.J. Makeev. Algorithms for Molecular Biology, 2007, 2:13. Article.
  • Assessing the Significance of Sets of Words. V. Boeva, J. Clement, M. Regnier, and M. Vandenbogaert. Proceedings of Combinatorial Pattern Matching (CPM) 2005, Jeju Island, Korea. Published online in Lecture Notes in Computer Science, Springer Verlag, 2005. V. 3537, pp. 358-370. Article(ps), presentation(pdf).
  • Probability of tandem repeats in nucleotide sequences. V. Boeva, V.J. Makeev, M. Regnier. Proceedings of International conference MCCMB’03, 2003, Moscow, Russia, pp. 46-47. Article(ps).
  
  
  

• Development of the tool TandemSWAN for tandem repeat searching
  in DNA sequences with evaluation of the repeat statistical significance

  Collaboration with
  Vsevolod Makeev, GosNIIgenetika, Moscow, Russia; Laboratory homepage
  Dmitry Papatsenko, Berkeley University, USA; Webpage
  Mireille Régnier, INRIA, France; Personal homepage
  
  Published:
  • Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. Boeva V., Regnier M., Papatsenko D., Makeev V. Bioinformatics, 2006, 22(6), pp.676-684. PMID: 16403795. Abstract.
  • SWAN: searching for highly divergent tandem repeats in DNA sequences with the evaluation of their statistical significance. V.A. Boeva, M. Regnier, V.J. Makeev. Proceedings of JOBIM 2004, Montreal, Canada, pp. 40. Article(ps).
  • Search for degenerate tandem repeats in nucleotide sequences. Their possible role in regulation of gene expression. V. Boeva, V.J. Makeev, M. Regnier. Proceedings of International conference MCCMB’05, 2005, Moscow, Russia, pp. 54-56. Article(ps).
  • Algorithm for searching for highly divergent tandem repeats in DNA sequences, statistical tests, and biological application in Drosophila melanogaster genome. V.A. Boeva, M. Regnier, V.J. Makeev. Proceedings of The Fourth International Conference on Bioinformatics of Genome Regulation and Structure, 2004, Novosibirsk, Russia, part 1, pp. 34-37. Article(ps).
  
  

• Analysis of minisatellites distributions in eukaryotic genomes.

  Collaboration with
  Vsevolod Makeev, GosNIIgenetika, Moscow, Russia; Laboratory homepage
  Marina Fridman, GosNIIgenetika, Moscow, Russia;
  
  Published:
  • Relationship between micro- and minisatellites in the human genome. V.A. Boeva, M.V. Fridman, V.J. Makeev. Biofizika , 2006, 51(4), pp.650-655. [Article in Russian] Abstract.
  • Identification and analysis of tandem repeats and close structured signals in DNA. V.A. Boeva. PhD thesis, Moscow State University, Institute of Theoretical and Experimental Biophysics RAS, 2007, [rus].

• Cancer related metabolic networks.

  Collaboration with
  Jean-Marc Steyaert, Ecole polytechnique, France; Jean-Marc Steyaert's homepage
  Mahsa Behzadi, Ecole polytechnique, France.