Email: ilyin@mozart.bio.neu.edu

Phone: 617.373.7032
Fax: 617.373.3724

Location: 110 Mugar Life Sciences
Mail: NU/Biology
         134 Mugar Life Sciences
         360 Huntington Avenue
         Boston, MA 02115 USA

Ilyin Lab

Research Description

Valentin Ilyin's lab on Theoretical Molecular Biology and Bioinformatics.
To understand cellular processes at several levels we employ approaches from biology, physics, chemistry, mathematics, and computer science to work on:

1) methods of theoretical and computational analysis of biological macromolecules, including study of atomic interaction in protein and DNA structure, processes of protein folding and protein functionality, interaction a protein with ligands, another proteins, and DNA or RNA molecules;

2) methods of sequence alignment of protein and genes, clustering and statistical analysis of the families of macromolecules, gene annotation, exon-intron structure of genes and alternative splicing;

3) analysis of microarray expression data corresponding to a specific affect on set of genes or at different steps of organism (mouse embryos) grows;

4) development of computer front-end bioinformatics application for visualization and analysis of multiple protein structures, proteins and gene sequences, sequence alignments, to study sequence-structure-function relationship in biological macromolecules, to create user-friendly programming environment for inter-field research in bioinformatics, for effective use of bioinformatics methods by non-programmer scientists, and for effective teaching of computational methods of analysis of genomes and proteomes;

5) large-scale computational effort for data-mining, protein modeling, gene annotation and development and support of biomedical databases.

Selected Publications

Abyzov A, Uzun A, Strauss PR, Ilyin VA. An AP endonuclease 1 - DNA polymerase &beta complex: Theoretical prediction of interacting surfaces.
PLoS Computational Biology, 2008, In Press.

Godoy VG, Jarosz DF, Simon SM, Abyzov A, Ilyin VA, Walker GC.
UmuD and RecA Directly Modulate the Mutagenic Potential of the Y-family DNA Polymerase DinB. Molecular Cell. 2007 2007 Dec 28;28(6):1058-70

Abyzov A, Ilyin VA. A comprehensive analysis of non-sequential alignments between all protein structures. BMC Structural Biology 2007, 7:78.

Uzun A, Leslin CM, Abyzov A, Ilyin V. Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. Nucleic Acids Res. 2007 Jul 1;35:W384-92.

Leslin CM, Abyzov A, Ilyin VA. TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. Nucleic Acids Res. 2007 Jan;35:D317-21.

Abyzov A, Errami M, Leslin CM, Ilyin VA. Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics. 2005 Sep 15;21(18):3677-8.

Ilyin VA, Abyzov A, Leslin CM. Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. Protein Sci. 2004 Jul;13(7):1865-74.

Leslin CM, Abyzov A, Ilyin VA. Structural exon database, SEDB, mapping exon boundaries on multiple protein structures. Bioinformatics. 2004 Jul 22;20(11):1801-3.

more publications at the Ilyin lab web site: http://mozart.bio.neu.edu/main/refs.html

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