What we do..

We are located at BJCIH (Medical School Campus) as a part of Department of Pahology&Immunology. Our lab is also a part Center Biological Systems Engineering (Danforth Campus).

Our research is focused on developing integrated experimental and computational pipeline to address important biological problems by leveraging the power of next-generation sequencing. Two major components comprise creation of such integrated pipeline: first, optimization of sequencing library preparation protocols to achieve high-throughput and cost affordability, and, second, corresponding bioinformatic processing of sequencing data and computational analysis of the high-throughput gene-expression and other kinds of sequencing data (e.g. ChipSeq, RACE etc) that allow one to gain insight into the biology in hand.

As a part of collaborative team at Broad Institute, I developed multiplexed affordable RNA-Sequencing based platform for genome-wide expression analysis by trading some of powers of traditional RNA-Seq (such as information about splicing etc) to achieve high-throughput and dramatic cost reduction making cost per sample lower than 100$. Our approach is optimized for 96-well plates, thus, allowing extreme throughput and mitigating batch-effects that plague traditional microarray based approaches.

Such a through-put makes generation of hundreds of genome wide profiles possible in reasonable cost and timeframe, dramatically changing amount of data available for analysis. This requires extension of existing and development of novel methods for analysis of gene-expression on such scale which is the subject of computational component of my research. Our current projects are focused on developing network topology analysis tools to identify most important genes and gene modules from a high-throughput expression studies.

In summary, our research is on the cross-roads between experiments and theory/computation and can be characterized most succinctly as systems immunology whereby we use high-throughput next-generation sequencing in conjunction with mathematical and statistical modeling approaches.

Latest news

  • Jul 1, 2014 Anton Alexandrov, visiting graduate student from University ITMO (Russia) starts today!
  • May 15-18, 2014 Systems biology workshop co-organized by our lab took place in St.Petersburgh, Russia
  • Feb 1, 2014 Our collaborative work with Gene Oltz's lab is published in the Journal of Immunology
  • Dec 9, 2013 Pavel Fedotov, visiting graduate student from University ITMO (Russia) starts today!
  • Nov 22, 2013 Our collaborative work with Gene Oltz's lab submitted as "Targeted Chromatin Profiling Reveals Novel Enhancers in Immunoglobulin Heavy and Light Chain Loci" is accepted to Journal of Immunology. Constratulations to Alex and Suhasni!
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