Istrail Lab
Sorin Istrail

Sorin Istrail

James A. and Julie N. Brown Professor of Computational and Mathematical Sciences

Professor of Computer Science

Department of Computer Science

Brown University

115 Waterman Street Box 1910

Providence, RI 02912

Phone: (401)-863-6196

sorin_istrail@brown.edu

Engaging the world, one inspiring course, one innovative student, one influential research leader at a time.

Sorin Istrail

Vision For Brown University

Sorin Istrail is the James A. and Julie N. Brown Professor of Computational and Mathematical Sciences and Professor of Computer Science, and former Director of the Center for Computational Molecular Biology at Brown University. He is Professor Honoris Causa of the "Alexandru Ioan Cuza" University, Iasi, Romania.

Professor Istrail's current research focuses on SNPs and haplotypes and genome-wide association studies (GWAS), the regulatory genome and gene regulatory networks, and protein folding theory and algorithms; algorithms and computational complexity; and theoretical computer sciene and statistical physics.

Celera Genomics
Before joining Brown, he was the Senior Director and 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 Sequence of the Human Genome" (Science, 2001) which, with over 20,000+ citations to date, is one of the most cited scientific paper.

His group at Celera Genomics also built a powerful suite of genome-assembly-to-genome-assembly alignment algorithms that was used for the comparison of all human genome assemblies to date in the paper:
Sorin Istrail, Granger Sutton, Liliana Florea, ... , Andrew Clark, Michael Waterman, Evan Eichler, Mark Adams, Michael Hunkapiller, Eugene Myers, and Craig Venter "Whole-genome shotgun assembly and comparison of human genome assemblies" Proceeding of the National Academy of Sciences, Vol 101, No. 7, 1916–1921 (2004) "Whole Genome Shotgun Assembly and Comparison of Human Genome Assemblies" (PNAS 2004).

In 2004 they publish the paper:
Sorin Istrail, Liliana Florea, Bjarni V Halldorsson, Oliver Kohlbacher, Russell Schwartz, Von Bing Yap, Jonathan Yewdell, Stephen Hoffman, "Comparative Immuno-Peptidomics of Humans and their Pathogens" In Proceedings of the National Academy of Sciences, (2004) vol. 101, no. 36, pg. 13268-13272


In 2002, his Celera group in collaboration with the company ClearForrest won the ACM KDD Cup - the top international data mining/machine learning competition. The challenge then was the automatic annotation of a section 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).



Sandia national Laboratories
At Sandia National Labs, 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 (STOC 2000). 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 of DOE in Advanced Scientific Computing.





He is the former Co-Editor-In-Chief of the Journal of Computational Biology (2000 - 2020) and together with Pavel Pevnzer and Mike Waterman, he is the co-founded the RECOMB Conference Series (Annual International Conference on Computational Molecular Biology) in 1997. He is the co-editor of the MIT Press Computational Molecular Biology series, and co-editor of the Springer-Verlag Lecture Notes in Bioinfromatics series.

He has Erdos number 2 and postcard-Erdos number 1. In the PhD advisor genealogy he has 9 links to Euler and 11 links to Leibniz.

Director, Center of Computational Biology

Brown University

2006 — 2011

Senior Director and Head of Informatics

Celera Genomics

2000 — 2005

Principal Member of Technical Staff and Project Leader

Sandia National Laboratories

1992 — 2000

Co-Founder and Steering Committee Member

International Conference on Research in Computational Biology

1997 — Present

Co-Editor-In-Chief

Journal of Computational Biology

2000 — 2020

John von Neumann Lecture Series

Brown University

2010 & 2015

Featured Essays

Read more

Ode to Computational Biology: A letter in support of awarding the National Medal of Science to Professor Michael Waterman

2012

Sorin Istrail

Professor Solomon Marcus' Axioms

2011

Sorin Istrail

In Meetings with Marcus: 85th Birthday Celebration of Professor Solomon Marcus Editurea Academiei Romane

Storytelling about Lighthouses: When Professor Dijkstra Slapped Me in the Quest for Beautiful Code

2010

Sorin Istrail

In Conduit, vol. 19.1

Storytelling about Lighthouses: Criticizing Professor Dijkstra Considered Harmless

2008

Sorin Istrail

In Conduit, vol. 17.2

Sorin's Honor Roll Students

Pinar Demetci

  • PhD student co-advised with Ritambhara Singh

Derek Aguiar

  • "The ARIADNE Browser for Genome-Wide Association Studies"
  • "Genome-wide Algorithms for Haplotype Assembly, Haplotype Phasing, and Identical-by-Descent Inference" PhD thesis defended in May 2014

Assistant Professor at University of Connecticut

Ryan Tarpine

  • "The CYRENE cisGRN Browser for the Regulatory Genome" Master's Thesis
  • "A Database of Causality-Inferred Structure-Function Information for Genomic cis-Regulatory Architecture," PhD thesis defended in May 2012

Software Engineer at Google

Dejan Zivkovic

  • "Bounded-Width Polynomial Size Boolean Formuals Compute Exactly Those Functions from AC^0" PhD thesis defended in May 1994

Professor of Computer Science in Serbia

Fumei Lam

  • Postdoctoral Student

UC Davis/UC Berkeley

Austin Huang

  • Postdoctoral Student
  • Researcher at Pfizer Research Center
  • Vice President of Artifical Intelligence and Machine Learning at Fidelity Investments

Google DeepMind

Alper Uzun

    Associate Professor, Department of Pediatrics, Brown Medical School

    Ning Hou

    • "Two Problems Related to cis-Regulatory Architecture of Transcription Factor Encoding Genes Homologous Translation and Evolutionary Conservation-Based cis-Module Inference" Master's Thesis (2014)

    Amazon

    Lan Nguyen

    • "Survey on Protein Folding Algorithms of HP Model and Proposal of a Hybrid Heuristic Algorithm" Master's Thesis (2019)

    Startup Software Company in Massachusetts

    Lian Garton

    • "Population Substructure and MCMC" (S.C. Lamport Honor Thesis Award, 2008)

    Amazon

    Kyle Schutter

    • "The cis-Regulatory Genomics Quintessential Graph Problem" (2010)

    Founded Startup in Africa

    Allan Stewart

    • "Face-Centered Cubic Lattice Models for Protein Folding: Energy Function Inference and Biplane Packing (2010)"

    Facebook

    Tim Johnstone

    • "Gene Networks: An Algorithm to Discover Causal Relationships Through Systematic Experimentation" (Senior Prize for Biology, 2012)

    PhD Student at Yale University

    Jake Franco

    • "MCMC Algorithms for Haplotype Phasing" (2012)

    Stony Brook Medical School

    James Weiss

    • "Computational Genomics and Bioenergy: Modeling and Clustering of RNA-seq Data" (2012)

    PhD Student at MIT

    Jeffrey Herman

    • "A Markov Random Field Model for Inferring Population Structure" (2012)

    Google

    Andy Ly

    • "Towards Unifying Tagging SNP Selection Algorithms" (2016)

    Software Engineer at Google Brain

    Sudheesha Perera

    • "A Haplotype-Based Predictive Model for Genotype/Expression Datasets" (2017)

    Brown Medical School

    Nick Goelz

    • "Exact Backtracking Algorithms for Optimal Bipole Packing in HP Model of Protein Folding" (2015)

    Full Stack Engineer

    Alex Gillmore

    • "Linear Models for SNPs selection" (2012)

    Yelp

    Douglas McErlean

    • "One Constraint to Rule Them All: How to Simplify Optimizations Under Constant Variable Sum, with Applications for Maximum Likelihood" (Top Honors Thesis, CS Department, 2014)

    Google

    Kshitij Lauria

    • "Bipole Self-Assembly and the Biplane Conjecture" (2015)

    D. E. Shaw Research

    Ning Hou

    • "Two Problems Releated to cis-Regulatory Architecture of Transcription Factor Encoding Genes: Homologous Translation and Evolutionary Conservation-Based cis-Module Inference" (2017)

    Amazon

    Daniel Seidman

    • "LumberTracts: A Method for TIme Efficient Determination of Identical by Descent Tracts Between Unphased Genotypes" (2016)

    PhD Student at Cornell University

    Sam Crisanto

    • "HapROSEA Software Package for Long Range Haplotype Phasing" (2016)

    Microsoft Research, Cambridge, MA

    Youn Kim

    • "Algebraic Connectivity of Graphs with Applications to Protein Folding" (2016)

    PhD Student at MIT with Presidential Fellowship

    Marko Fejzo

    • "Spectral Graph Theory and Markov Chains" (2019)

    TwoSigma

    Shivam Nadimpalli

    • "Discrete Isoperimetry and Protein Folding" (2019)

    PhD Student at Columbia University

    Sam Hinthorn

    • "cis-Lexicon Ontology Search Engine for Gene Regulatory Networks" (2019)

    Biology PhD Student at Brown University

    Bethany Dubois

    • Metropolois-Coupled Monte Carlo in Application to Protein Structure Prediction (2018)
    • D. E. Shaw Research

    Mount Sinai Medical School

    Adrian Turcu

    • "Protein Folding Prediction and Visualization Techniques Based on Hydrophobic Side Chain Interactions" (2019)

    Brown Medical School

    Min Jean Cho

    • "Genomic Privacy Algorithms Based on Information Theory" (2020)

    Intel

    Arun Das

    • "Approaches to Genomic Privacy (2018)"

    Johns Hopkins Medical School

    Daniel Ben-Isvy

    • "Multilocus Informativeness: A Novel Method for Fine-Mapping Disease-Causing Variants in Genome-Wide Association Studies" (2020)

    Harvard Medical School