Publications
Combinatorial and Statistical Predictions of Gene Expression from Haplotype Sequence
2020Bert Alpay, Pinar Demetci, Sorin Istrail, Derek Aguiar
Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic cis-Regulatory Code
2019Sorin Istrail
How Does the Regulatory Genome Work?
2019Sorin Istrail, Isabelle S. Peter
Transcriptome of American oysters, Crassostrea virginica, in response to bacterial challenge: Insights into potential mechanisms of disease resistance
2014Ian C. McDowell, Chamilani Nikapitiya, Derek Aguiar, Christopher E. Lane, Sorin Istrail, Marta Gomez-Chiarri
Tumor haplotype assembly algorithms for cancer genomics
2014Derek Aguiar, Wendy SW Wong, Sorin Istrail
Tractatus: an exact and subquadratic algorithm for inferring identity-by-descent multi-shared haplotype tracts
2014Derek Aguiar, Eric Morrow, Sorin Istrail
Intellectual Disability Is Associated with Increased Runs of Homozygosity in Simplex Autism
2013Ece D Gamsiz, Emma W Viscidi, Abbie M Frederick, Shailender Nagpal, Stephan J Sanders, Michael T Murtha, Michael Schmidt, Elizabeth W Triche, Daniel H Geschwind, Matthew W State, others
Pathway-based genetic analysis of preterm birth
2013Alper Uzun, Andrew T. Dewan, Sorin Istrail, James F. Padbury
A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems
2013Sarah Tulin, Derek Aguiar, Sorin Istrail, Joel Smith
Haplotype assembly in polyploid genomes and identical by descent shared tracts
2013Derek Aguiar, Sorin Istrail
HAPCOMPASS: A fast cycle basis algorithm for accurate haplotype assembly of sequence data
2012Derek Aguiar, Sorin Istrail
dbPTB: a database for preterm birth
2012Alper Uzun, Alyse Laliberte, Jeremy Parker, Caroline Andrew, Emily Winterrowd, Surendra Sharma, Sorin Istrail, James F. Padbury
OCR-based Image Features for Biomedical Image and Article Classification: Identifying Documents Relevant to Cis-Regulatory Elements
2012Hagit Shatkay, Ramya Narayanaswamy, Santosh Nagaral, Na Harrington, Dorothea Blostein, Ryan Tarpine, Kyle Schutter, Rohith Mv, Gowri Somanath, Sorin Istrail, Chandra Kambahmettu
Computer Science Through Urn Games: An Unified Framework for a Hierarchy of Solvable and Unsolvable Problems
2012Sorin Istrail
Turing and von Neumann's Brains and their Computers
2012Sorin Istrail, Solomon Marcus
Global analysis of sequence diversity within HIV-1 subtypes across geographic regions
2012Austin Huang, Joseph W Hogan, Sorin Istrail, Allison DeLong, David A Katzenstein, Rami Kantor
Mental Experience and the Turing Test: This Double Face is the Face of Mathematics
2012Leon N Cooper, Sorin Istrail
DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism
2012Derek Aguiar, Bjarni V. Halldorsson, Eric M. Morrow, Sorin Istrail
Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-loci and Algorithms for Optimal tagsging SNP Selection
2011Ryan Tarpine, Fumei Lam, Sorin Istrail
QColors: An algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads
2011Austin Huang, Rami Kantor, Allison DeLong, Leeann Schreier, Sorin Istrail
The Clark Phaseable Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS
2011Bjarni Halldorsson, Derek Aguiar, Ryan Tarpine, Sorin Istrail
Haplotype phasing by multi-assembly of shared haplotypes: phase-dependent interactions between rare variants
2011Bjarni Halldorsson, Derek Aguiar, Sorin Istrail
Functional cis-regulatory genomics for systems biology
2010Jongmin Nam, Ping Dong, Ryan Tarpine, Sorin Istrail, Eric H. Davidson
The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy
2010Fumei Lam, Ryan Tarpine, Sorin Istrail
Practical Computational Methods for Regulatory Genomics: A cisGRN-Lexicon and cisGRN-Browser for Gene Regulatory Networks
2010Sorin Istrail, Ryan Tarpine, Kyle Schutter, Derek Aguiar
The Clark Phase-able Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS
2010Bjarni Halldorsson, Derek Aguiar, Ryan Tarpine, Sorin Istrail
The regulatory genome and the computer
2007Sorin Istrail, Smadar Ben-Tabou De-Leon, Eric H. Davidson
The Transcriptome of the Sea Urchin Embryo
2006Manoj P. Samanta, Waraporn Tongprasit, Sorin Istrail, R. Andrew Cameron, Qiang Tu, Eric H. Davidson, Viktor Stolc
Islands of Tractability for Parsimony Haplotyping
2006Bjarni V Halldorsson, Roded Sharan, Sorin Istrail
The Genome of the Sea Urchin Strongylocentrotus purpuratus
2006Sea Urchin Genome Sequencing Consortium, Erica Sodergren, George M. Weinstock, Eric H Davidson, R. Andrew Cameron, Richard A. Gibbs, Robert C. Angerer, Lynne M. Angerer, Maria Ina Arnone, David R. Burgess, Robert D. Burke, James A. Coffman, Michael Dean, Maurice R. Elphick, Charles A. Ettensohn, Kathy R. Foltz, Amro Hamdoun, Richard O. Hynes, William H. Klein, William Marzluff, David R. McClay, Robert L. Morris, Arcady Mushegian, Jonathan P. Rast, L. Courtney Smith, Michael C. Thorndyke, Victor D. Vacquier, Gary M. Wessel, Greg Wray, Lan Zhang, Christine G. Elsik, Olga Ermolaeva, Wratko Hlavina, Gretchen Hofmann, Paul Kitts, Melissa J. Landrum, Aaron J. Mackey, Donna Maglott, Georgia Panopoulou, Albert J. Poustka, Kim Pruitt, Victor Sapojnikov, Xingzhi Song, Alexandre Souvorov, Victor Solovyev, Zheng Wei, Charles A. Whittaker, Kim Worley, K. James Durbin, Yufeng Shen, Olivier Fedrigo, David Garfield, Ralph Haygood, Alexander Primus, Rahul Satija, Tonya Severson, Manuel L. Gonzalez-Garay, Andrew R. Jackson, Aleksandar Milosavljevic, Mark Tong, Christopher E. Killian, Brian T. Livingston, Fred H. Wilt, Nikki Adams, Robert Bell, Seth Carbonneau, Rocky Cheung, Patrick Cormier, Bertrand Cosson, Jenifer Croce, Antonio Fernandez-Guerra, Anne-Marie Genevire, Manisha Goel, Hemant Kelkar, Julia Morales, Odile Mulner-Lorillon, Anthony J. Robertson, Jared V. Goldstone, Bryan Cole, David Epel, Bert Gold, Mark E. Hahn, Meredith Howard-Ashby, Mark Scally, John J. Stegeman, Erin L. Allgood, Jonah Cool, Kyle M. Judkins, Shawn S. McCafferty, Ashlan M. Musante, Robert A. Obar, Amanda P. Rawson, Blair J. Rossetti, Ian R. Gibbons, Matthew P. Hoffman, Andrew Leone, Sorin Istrail, Stefan C. Materna, Manoj P. Samanta, Viktor et al. Stolc
Logic functions of the genomic cis-regulatory code
2005Sorin Istrail, Eric Davidson
Gene and alternative splicing annotation with AIR
2005Liliana Florea, Valentina Di Francesco, Jason Miller, Russell Turner, Alison Yao, Michael Harris, Brian Walenz, Clark Mobarry, Gennady V. Merkulov, Rosane Charlab, Ian Dew, Zuoming Deng, Sorin Istrail, Peter Li, Granger Sutton
The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern
2005Francisco M. De La Vega, Hadar Isaac, Andrew Collins, Charles R. Scafe, Bjarni V. Halldorsson, Xiaoping Su, Ross A. Lippert, Yu Wang, Marion Laig-Webster, Ryan T. Koehler, Janet S. Ziegle, Lewis T. Wogan, Junko F. Stevens, Kyle M. Leinen, Sheri J. Olson, Karl J. Guegler, Xiaoqing You, Lily H. Xu, Heinz G. Hemken, Francis Kalush, Mitsuo Itakura, Yi Zheng, Guy de Thò, Stephen J. O'Brien, Andrew G. Clark, Sorin Istrail, Michael W. Hunkapiller, Eugene G. Spier, Dennis A. Gilbert
Finding anchors for genomic sequence comparison
2004Ross Lippert, Xiaoyue Zhao, Liliana Florea, Clark Mobarry, Sorin Istrail
Whole Genome Shotgun Assembly and Comparison of Human Genome Assemblies
2004Sorin Istrail, Granger G. Sutton, Liliana Florea, Aaron L. Halpern, Clark M. Mobarry, Ross Lippert, Brian Walenz, Hagit Shatkay, Ian Dew, Jason R. Miller, Michael J. Flanigan, Nathan J. Edwards, Randall Bolanos, Daniel Fasulo, Bjarni V. Halldorsson, Sridhar Hannenhalli, Russell Turner, Shibu Yooseph, Fu Lu, Deborah R. Nusskern, Bixiong Chris Shue, Xiangqun Holly Zheng, Fei Zhong, Arthur L. Delcher, Daniel H. Huson, Saul A. Kravitz, Laurent Mouchard, Knut Reinert, Karin A. Remington, Andrew G. Clark, Michael S. Waterman, Evan E. Eichler, Mark D. Adams, Michael W. Hunkapiller, Eugene W. Myers, J. Craig Venter
Comparative Immuno-Peptidomics of Humans and their Pathogens
2004Sorin Istrail, Liliana Florea, Bjarni V Halldorsson, Oliver Kohlbacher, Russell Schwartz, Von Bing Yap, Jonathan Yewdell, Stephen Hoffman
Optimal haplotype block free selection of tagsging SNPs for genome-wide association studies
2004Bjarni V Halldorsson, Vineet Bafna, Ross Lippert, Russell Schwartz, Francisco M. De La Vega, Andrew G. Clark, Sorin Istrail
1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap
2004Alberto Caprara, Robert Carr, Sorin Istrail, Giuseppe Lancia, Brian Walenz
Robustness of Inference of Haplotype Block Structure
2003Russell Schwartz, Bjarni V Halldorsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail
Inferring Piecewise Ancestral History from Haploid Sequences
2003Russell Schwartz, Andrew G. Clark, Sorin Istrail
A survey of computational methods for determining haplotypes
2003Bjarni V Halldorsson, Vineet Bafna, Nathan J. Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail
Combinatorial problems arising in SNP and haplotype analysis
2003Bjarni V Halldorsson, Vineet Bafna, Nathan J. Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail
Epitope prediction algorithms for peptide-based vaccine design
2003Liliana Florea, Bjarni V Halldorsson, Oliver Kohlbacher, Russell Schwartz, Stephen Hoffman, Sorin Istrail
A Computational Pipeline for High-Throughput T-Cell Epitope Prediction
2003Liliana Florea, Bjarni V Halldorsson, Oliver Kohlbacher, Russell Schwartz, Stephen Hoffman, Sorin Istrail
Celera Genomics
Haplotypes and Informative SNP Selection Algorithms: Don't Block Out Information
2003Vineet Bafna, Bjarni V Halldorsson, Russell Schwartz, Andrew G. Clark, Sorin Istrail
Methods for inferring block-wise ancestral history from haploid sequences: The haplotype coloring problem
2002Russell Schwartz, Andrew G. Clark, Sorin Istrail
Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem
2002Romeo Rizzi, Vineet Bafna, Sorin Istrail, Giuseppe Lancia
Algorithmic Strategies for the SNP Haplotype Assembly Problem
2002Ross Lippert, Russell Schwartz, Giuseppe Lancia, Sorin Istrail
The Haplotype Phasing Problem
2002Sorin Istrail
Celera Genomics
The Sequence of the Human Genome
2001J. Craig Venter, Mark D. Adams, Eugene W. Myers, Peter W. Li, Richard J. Mural, Granger G. Sutton, Hamilton O. Smith, Mark Yandell, Cheryl A. Evans, Robert A. Holt, Jeannine D. Gocayne, Peter Amanatides, Richard M. Ballew, Daniel H. Huson, Jennifer Russo Wortman, Qing Zhang, Chinnappa D. Kodira, Xiangqun H. Zheng, Lin Chen, Marian Skupski, Gangadharan Subramanian, Paul D. Thomas, Jinghui Zhang, George L. Gabor Miklos, Catherine Nelson, Samuel Broder, Andrew G. Clark, Joe Nadeau, Victor A. McKusick, Norton Zinder, Arnold J. Levine, Richard J. Roberts, Mel Simon, Carolyn Slayman, Michael Hunkapiller, Randall Bolanos, Arthur Delcher, Ian Dew, Daniel Fasulo, Michael Flanigan, Liliana Florea, Aaron Halpern, Sridhar Hannenhalli, Saul Kravitz, Samuel Levy, Clark Mobarry, Knut Reinert, Karin Remington, Jane Abu-Threideh, Ellen Beasley, Kendra Biddick, Vivien Bonazzi, Rhonda Brandon, Michele Cargill, Ishwar Chandramouliswaran, Rosane Charlab, Kabir Chaturvedi, Zuoming Deng, Valentina Di Francesco, Patrick Dunn, Karen Eilbeck, Carlos Evangelista, Andrei E. Gabrielian, Weiniu Gan, Wangmao Ge, Fangcheng Gong, Zhiping Gu, Ping Guan, Thomas J. Heiman, Maureen E. Higgins, Rui-Ru Ji, Zhaoxi Ke, Karen A. Ketchum, Zhongwu Lai, Yiding Lei, Zhenya Li, Jiayin Li, Yong Liang, Xiaoying Lin, Fu Lu, Gennady V. Merkulov, Natalia Milshina, Helen M. Moore, Ashwinikumar K Naik, Vaibhav A. Narayan, Beena Neelam, Deborah Nusskern, Douglas B. Rusch, Steven Salzberg, Wei Shao, Bixiong Shue, Jingtao Sun, Zhen Yuan Wang, Aihui Wang, Xin Wang, Jian Wang, Ming-Hui Wei, Ron Wides, Chunlin Xiao, Chunhua et al. Yan
Visualization challenges for a new cyberpharmaceutical computing paradigm
2001Russell J. Turner, Kabir Chaturvedi, Nathan J. Edwards, Daniel Fasulo, Aaron L. Halpern, Daniel H. Huson, Oliver Kohlbacher, Jason R. Miller, Knut Reinert, Karin A. Remington, Russell Schwartz, Brian Walenz, Shibu Yooseph, Sorin Istrail
Frequencies of amino-acid strings in globular proteins sequences indicate suppression of blocks of consecutive hydrophobic residues
2001Russell Schwartz, Sorin Istrail, Jonathan King
Haplotype Reconstruction from SNP Alignment
2001M. Li, Ross Lippert, Russell Schwartz, Michael Waterman, Sorin Istrail
Celera Genomics
101 Optimal PDB Structure Alignments: A Branch-and-Cut Algorithm for the Maximum Contact Map Overlap Problem
2001Giuseppe Lancia, Robert Carr, Brian Walenz, Sorin Istrail
SNPs Problems: Complexity and Algorithms
2001Giuseppe Lancia, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz
Prediction of Self-Assembly of Energetic Tiles and Dominos: Experiments, Mathematics and Software
2000Sorin Istrail, Alan Hurd, Ross A. Lippert, Brian Walenz, Serafim Batzoglou, John H. Conway, Fredrick W. Peyerl
Statistical Mechanics, Three-Dimensionality and NP-Completeness: I. Universality of Intractability of the Partition Functions of the Ising Model Across Non-Planar Lattices
2000Sorin Istrail
Algorithmic Strategies in Combinatorial Chemistry
2000Debbie Goldman, Sorin Istrail, Giuseppe Lancia, Antonio Piccolboni, Brian Walenz
Insights Into the Association of Partially Folded Chains Derived From Lattice Simulation Models
1999Russell Schwartz, Sorin Istrail, Jonathan King
Sandia Labs
Prediction of Energetic Tiles Self-Assembly
1999Ross A. Lippert, Sorin Istrail, Alan Hurd
Sandia Labs
Lattice Simulations of Aggregation Funnels of Protein Folding
1999Sorin Istrail, Russell Schwartz, Jonathan King
Algorithmic Aspects of Protein Structure Similarity
1999Deborah Goldman, Sorin Istrail, Christos H. Papadimitriou
Mathematics of Self-Assembly
1999John H. Conway, Sorin Istrail
Sandia Labs
Branch-and-Bound LP-algorithms for Protein Structure Alignment Based on Contact Map Overlap
1999Robert Carr, Giuseppe Lancia, Sorin Istrail
Sandia Labs
Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem
1999Serafim Batzoglou, Sorin Istrail
What is a Good Objective for Multiple Sequence Alignment?
1998Sorin Istrail, R. Ravi
In Sandia Labs
Multiple Sequence Alignment and Voting Paradoxes
1998Sorin Istrail
In Sandia Labs
Robust Proofs of NP-Hardness for Protein Folding: General Lattices and Energy Potentials
1997William E. Hart, Sorin Istrail
Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better than 86% of Optimal
1997William E. Hart, Sorin Istrail
Approximations Algorithms on Matroids Based on Cycle-Bases and Applications
1996Sorin Istrail
In Sandia Labs
Fast Protein Folding in the Hydrophobic-Hydrophilic Model Within Three-eighths of Optimal
1996William E. Hart, Sorin Istrail
Invariant Patterns in Crystal Lattices: Implications for Protein Folding Algorithms
1996William E. Hart, Sorin Istrail
Fast Protein Folding in the Hydrophobic-Hydrophilic Model Within Three-eighths of Optimal
1995William E. Hart, Sorin Istrail
Crystallographical universal approximation: A complexity theory of protein folding algorithms for crystal lattices
1995William E. Hart, Sorin Istrail
In Sandia Labs
Physical Mapping by STS Hybridization: Algorithmic Strategies and the Challenge of Software Evaluation
1995David Greenberg, Sorin Istrail
Bisimulation can't be traced
1995Bard Bloom, Sorin Istrail, Albert R. Meyer
Bounded-width polynomial size Boolean formulas compute exactly those functions from AC^0
1994Dejan Zivkovic, Sorin Istrail
The Chimeric Mapping Problem: Algorithmic Strategies and Performance Evaluation on Synthetic Genomic Data
1994David Greenberg, Sorin Istrail
A non-probabilistic switching lemma for the Sipser function
1993Sorin Istrail, Dejan Zivkovic
The Chimeric Clones Problem
1993Sorin Istrail
Sandia Labs
On the impossibility of the crossover method for proving NP-completeness of the planar chromatic index problem
1991J Zipoli, Sorin Istrail
Wesleyan University
Constructing generalized universal traversing sequences of polynomial size for graphs of small diameter
1990Sorin Istrail
On the complexity of unpredictability
1990Sorin Istrail
Wesleyan University
An arithmetical hierarchy in propositional dynamic logic
1989Sorin Istrail
An algorithm for embedding planar graphs in six pages
1988Sorin Istrail
Polynomial universal traversing sequences for cycles are constructible
1988Sorin Istrail
The pagenumber of genus g graphs is O(g)
1987Lenwood S. Heath, Sorin Istrail
Nivat's processing systems: decision problems related to protection and synchronization
1983Cristian Masalagiu, Sorin Istrail
On protection in Nivat processing systems
1983Cristian Masalagiu, Sorin Istrail
Springer
In Colloquium of Automata and Programming (CAAP83), vol. 159, pg. 255-268
N-contextual schemes
1982Nguyen Xuan My, Sorin Istrail
In Bulletin Mathematique, vol. Tome 26 (74), no. 3, pg. 241-249
Some remarks on non-algebraic adherences
1982Sorin Istrail
Generalizations of Ginsburg-Rice-Schutzenberger fixed-point theorem for context-sensitive and recursive-enumerable sets
1982Sorin Istrail
In Theoretical Computer Science, vol. 18, pg. 333-341
Decision problems for languages associated with protection of systems
1981Cristian Masalagiu, Sorin Istrail
Polytechnic Institute of Bucharest
In Automatic Systems and Informatics, pg. 306-312
On a linear theory of recursive-enumerable sets
1981Sorin Istrail
In Series in Mathematics, vol. Inst. de Mat., vol. 38 Increst, pg. 20
Chomsky-Schutzenberger representations for families of languages and grammatical types
1981Sorin Istrail
An efficient data-structure for computer-graphics
1980L Olaru, Sorin Istrail
In Artificial Intelligence and Information Control Systems of Robots, pg. 83-85
A fixed-point approach to contextual languages
1980Sorin Istrail
In Revue Roumaine de Mathematiques Pures et Appliquees, vol. 25, no. 6, pg. 861-869
On complements of some bounded context-sensitive languages
1979Sorin Istrail
In Information and Control, vol. 42, no. 3, pg. 283-289
On the complexity of program divergence
1979Sorin Istrail
In Foundations of Control Engineering, vol. 4, no. 1, pg. 19-26
A fixed-point theorem for recursive-enumerable languages and some considerations about semantics of monadic programs
1979Sorin Istrail
Computing grammars and context-sensitive languages
1978Sorin Istrail, Dan Simovici
In Revue Francais D'Automatique, Informatique et Recherche Operationelle, vol. 12, no. 1, pg. 33-48
Contextual grammars with regular choice
1978Sorin Istrail
In Studii si Cercetari Matematice, vol. 30, no. 3, pg. 287-294
A problem about contextual grammars with choice
1978Sorin Istrail
In Studii si Cercetari Matematice, vol. 30, no. 4, pg. 401-408
Elementary bounded languages
1978Sorin Istrail
In Information and Control, vol. 39, no. 2, pg. 177-191
On irreducible languages and nonrational numbers
1977Sorin Istrail
In Bulletin Mathematique, vol. 21, no. 3-4, pg. 301-308
On formal constructions of algebraic numbers of degree two
1977Sorin Istrail
In Revue Roumaine de Mathematiques Pures et Appliquees, vol. 22, no. 9, pg. 1235-1239
On the weak equivalence problem of OL-systems with some generative devices
1977Sorin Istrail
In Studii si Cercetari Matematice, vol. 23, no. 2, pg. 419-422
On some symmetric operators on free semigroups
1976Sorin Istrail
In Studii si Cercetari Matematice, vol. 28, no. 1, pg. 111-121