Ph.D., A.V. Shubnikov Institute of Crystallography, Moscow
Tel: (617) 552-1342
E-mail: valentin.ilyin@bc.edu
Dr. Ilyin's Lab Web site
Computational biology, bioinformatics, biostatistics, computational structural biology. Protein structure analysis, comparison, functionality, evolution. Protein-DNA/RNA interactions, specificity, functionality. Protein-ligand interactions, drug design, docking. Macromolecular dynamics. Bioinformatics databases, web servers, software development and hosting. Focus on applying everything of the above to real biomedical problems in collaboration with wet labs.
Academic Profile
We develop mathematical, statistical models, using physical and chemical lows, implement them in computer algorithms, programs, databases toward solving problems in biology and medicine, specifically biomedical/biotech problems involving large scale (genome wide) analysis, rational bases of functionality for proteins, small molecules and DNA/RNA and their interactions and complexes.
Representative Publications
Bioinformatics methods, databases and 'in silico' analysis:
Abyzov, A., and Ilyin, V.A. 2007. A comprehensive analysis of non-sequential alignments between all protein structures. BMC Structural Biology 7: 78.
Leslin, C. M., Abyzov, A., and Ilyin, V.A. 2007. TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. Nucleic Acids Research 35: D317–D321.
Uzun, A., Leslin, C.M., Abyzov, A., Ilyin, V. 2007. Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. Nucleic Acids Research 35.
Ilyin, V.A., Abyzov, A., and Leslin, C. M. 2004. Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. Protein Science 13: 1865–1874.
Leslin, C. M., Abyzov, A., and Ilyin, V.A. 2004. Structural exon database, SEDB, mapping exon boundaries on multiple protein structures. Bioinformatics 20(11): 1801–1803.
Eswar, N., John, B., Mirkovic, N., Fiser, A., Ilyin, V.A., Pieper, U., Stuart, A.C., Marti-Renom, M., Madhusudhan, M., Yerkovich, B., and Sali, A. 2003. Tools for comparative protein structure modeling and analysis. Nucleic Acids Research 31(13):3375-3380.
Pieper, U., Eswar, N., Stuart, A.C., Ilyin, V.A., and Sali, A. 2002. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Research 30: 255-259.
Stuart, A.C., Ilyin, V.A., and Sali, A. 2002. LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics 18(1): 200.
Marti-Renom, M.A., Ilyin, V.A., and Sali, A. 2001. DBAli: A database of protein structure alignments. Bioinformatics 17(8): 746.
In collaboration with experiment:
Onnis-Hayden, A., Weng, H., He, M., Hansen, S., Ilyin, V., Lewis, K., Gu, A. 2009. Prokaryotic real time gene expression profiling for toxicity. Environmental Science & Technology 43(12): 4574–81.
Uzun, A., Rodriguez-Osorio, N., Wang, H., Ilyin, V., and Memili, E. 2009. Comparative functional genomics of chromatin remodeling proteins HMGN3a and SMARCAL1 during early mammalian embryogenesis. BMC Genomics 10(1): 183.
Marziale, F., Pucciarelli, S., Ballarini, P., Melki, R., Uzun, A., Ilyin, V., Detrich, H. W. III, Miceli, C. 2008. Different roles of two g-tubulin isotypes in the cytoskeleton of the Antarctic ciliate Euplotes focardii. The Federation of European Biochemical Societies Journal 275(21): 5367–82.
Stoeck, T., Kasper, J., Bunge, J., Leslin, C., Ilyin, V., Epstein, S. 2007. Protistan diversity in the Arctic: A case of paleoclimate shaping modern biodiversity? PLoS ONE 2(1): e728.
Godoy, V.G., Jarosz, D.F., Simon, S.M., Abyzov, A., Ilyin, V.A., Walker, G.C. 2007. UmuD and RecA directly modulate the mutagenic potential of the Y-family DNA polymerase DinB. Molecular Cell 28(6): 1058–70.
Bonanno, J.B, Edo, C., Eswar, N., Pieper, U., Ilyin, V., Romanowski, M.J., Gerhaman S.E., Kycia H., Sudier F.W., Sali A., and Burley S. 2001. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Proceedings of the National Academy of Sciences of the USA 98(23): 12896–901.
Experiment:
Retailleau, P., Huang, X., Yin, Y, Hu, M., Vachette, P., Vonrhein, C., Bricogne, G., Roversi, P., Ilyin, V., and Carter, C.W.Jr. 2003. 2.2Å crystal structure of tryptophanyl-tRNA synthetase complexed with ATP in a closed, pre-transition-state conformation. Journal of Molecular Biology 325(1): 39–63.
Ilyin V.A., Temple, B., Li, G., Yin, Y., Vachette, P., Carter, C.W. Jr. 2000.
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