Sorin Istrail Julie Nguyen Brown Professor of Computational and Mathematical Science

Sorin Istrail is the Julie Nguyen Brown Professor of Computational and Mathematical Sciences and former Director of the Center for Computational Molecular Biology at Brown University. Before joining Brown, he was the Senior Director and then Head of Informatics Research at Celera Genomics, where his group played a central role in the construction of the Sequence of the Human Genome; they co-authored the 2001 Science paper "The Sequence of the Human Genome," which, with over 9500 citations to date, is one of the most cited scientific paper. His group at Celera also built a powerful suite of genome-wide algorithms that was used for the comparison of all human genome assemblies to date. In 2002 his Celera group in collaboration with the company ClearForrest won the ACM KDD Cup – the top international data mining/machine learning competition – for automatic annotation of the Drosophila genome. In 2003 he joined the ranks of Applied Biosystems Science Fellows, one of just six Science Fellows in a company of 800 scientists. Before Celera, Professor Istrail founded and led the Computational Biology Project at Sandia National Laboratories (1992-2000). In 2000, he obtained the negative solution (computational intractability) of a 50 years old unresolved problem in statistical mechanics, the Three-Dimensional Ising Model Problem. This work was included in the Top 100 Most Important Discoveries of the U.S. Department of Energy's first 25 years, and as the 7th top achievement in Scientific Computing. In 1998, his work on Protein Misfolding simulations was included by Scientific American in its "Best of 1998" list.Professor Istrail's research focuses on computational molecular biology, human genetics and genome-wide associations studies, medical bioinformatics of multiple sclerosis, autism, HIV, preterm labor and viral immunology, statistical physics, algorithms and computational complexity. He is co-editor-in-chief of the Journal of Computational Biology, co-founder with of the Annual International Conference on Research on Computational Biology (RECOMB), and co-editor-in-chief of the MIT Press Computational Molecular Biology series and the Springer-Verlag Lecture Notes in Bioinformatics series. He is Professor Honoris Causa of the "Alexandru Ioan Cuza" University, Iasi, Romania.

Brown Affiliations

research overview

Professor Sorin Istrail's research focuses on computational molecular biology, medical and pharma informatics, statistical physics, combinatorial algorithms, and computational complexity. His main projects are Genomic Regulation and Gene Regulatory Networks, Computational Methods for SNPs, Haplotypes and Disease Associations, Medical Bioinformatics, Programming Languages for Genomics, Protein Folding Algorithms and Simulation, and continuing John von Neumann's Research Program on Biological Systems.

research statement

Professor Sorin Istrail's research focuses on computational molecular biology, medical informatics, statistical physics and complex systems, combinatorial algorithms, and computational complexity. The main projects in his Brown Lab are: (1) Genomic Regulatory Networks -- focusing on sea urchin developmental gene regulatory networks, building a high-resolution transcriptome map of the embryo, inferring logic functions of genomic cis-regulatory code and the principles of information processing of genomic regulation; (2) Computational Models of SNPs and Haplotypes -- dealing with HapMap-based analysis tools design for SNP selection, haplotype phasing, and genome-wide disease associations; (3) Medical Bioinformatics -- with focus on comparative immunopeptidomics of humans and their pathogens, genetic determinants of sudden cardiac death and human-rabbit comparative genomics, computational support for pathology diagnosis of cancer; (4) Building a programming language for genomics; (5) Designing protein folding algorithms; and (6) Continuing John von Neumann's research program towards developing a new computational and information theory for biological systems.

In 2000, he resolved a longstanding open problem in statistical mechanics, the Three-Dimensional Ising Model Problem; his proof showed the "impossibility" (computational intractability) of deriving closed forms explicit partition functions for every three-dimensional Ising model. Recent work of Prof. Istrail's research group at Celera Genomics was devoted to algorithmic design and software development for the following areas: genetics of SNPs and haplotypes, high-throughput EST mapping, genomic vaccine design and comparative peptidomics, compu/combichem and protein structure, BLAST-replacement tools, genomic regulatory systems, literature datamining, DNA array design and expression analysis, and theory of games and pharma economic behavior.

He is Co-Editor-in-Chief of the Journal of Computational Biology, Co-Founder of the RECOMB Conference Series, Co-Editor of the MIT Press Computational Molecular Biology Book Series, and Co-Editor of the Springer-Verlag Lecture Notes in Bioinformatics Book Series.

funded research

ONGOING RESEARCH

National Science Foundation Award (PI), $199,999 2010
EAGER: Haplotype Phasing Algorithms and Clark Consistency Graphs

National Science Foundation Award (Co-PI; PI - David Rand), $1,176,843 2010
IGERT: Reverse Ecology: Computational Integration of Genomes, Organisms, and Environments

National Science Foundation Award (PI), $25,000 2008
Sweatbox Q&A Boot Camp at Brown University: Asking Tough Scientific Questions

National Science Foundation Award (PI), $850,001 2007
The cis-GRN Browser and Database: cis-Regulatory Information Behind the Network--The goal of this project is to develop algorithms and software tools for building genomic maps of the developmental regulatory circuitry of cells.

March of Dimes (Co-PI; PI - James Padbury), one postdoc
Preterm Birth: A Novel Bioinformatics and Genomics Approach

OVPR Seed Fund Award (PI), Office of the Vice President for Research at Brown, $65,000 2007
The Cellarium Project: A Teaching and Research Environment for Computational Systems Biology--The goal of this project is to build the CELLARIUM teaching and research environment that will address the challenges of teaching computational and systems biology in the post-genome-sequence and systems biology era.

COMPLETED RESEARCH

RUI: Structured Operational Semantics of Concurrency (PI), National Science Foundation, $45,473 1988-1991
Computational Biology Project (PI), Department of Energy, $4,250,000 1992-2000
Informatics Research, Celera Genomics, $9,800,000 2000-2005