Sorin Istrail - Publications

Affiliations: 
Computer Science Brown University, Providence, RI 
Area:
Algorithms and Theory, Computational Biology

76 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Alpay BA, Demetci P, Istrail S, Aguiar D. Combinatorial and statistical prediction of gene expression from haplotype sequence. Bioinformatics (Oxford, England). 36: i194-i202. PMID 32657373 DOI: 10.1093/Bioinformatics/Btaa318  0.88
2016 Istrail S. Eric Davidson: Master of the universe Developmental Biology. 412: S47-S54. DOI: 10.1016/J.Ydbio.2016.01.029  1
2015 Ma K, Jeong H, Rohith MV, Somanath G, Tarpine R, Schutter K, Blostein D, Istrail S, Kambhamettu C, Shatkay H. Utilizing image-based features in biomedical document classification Proceedings - International Conference On Image Processing, Icip. 2015: 4451-4455. DOI: 10.1109/ICIP.2015.7351648  0.36
2015 Istrail S. On humans, plants and disease: Algorithmic strategies for haplotype assembly problems Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9133: XI-XII.  1
2014 McDowell IC, Nikapitiya C, Aguiar D, Lane CE, Istrail S, Gomez-Chiarri M. Transcriptome of American oysters, Crassostrea virginica, in response to bacterial challenge: insights into potential mechanisms of disease resistance. Plos One. 9: e105097. PMID 25122115 DOI: 10.1371/Journal.Pone.0105097  1
2014 Aguiar D, Wong WS, Istrail S. Tumor haplotype assembly algorithms for cancer genomics. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 3-14. PMID 24297529  1
2014 Aguiar D, Morrow E, Istrail S. Tractatus: An exact and subquadratic algorithm for inferring identical-by-descent multi-shared haplotype tracts Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8394: 1-17. DOI: 10.1007/978-3-319-05269-4_1  1
2013 Atias N, Istrail S, Sharan R. Pathway-based analysis of genomic variation data. Current Opinion in Genetics & Development. 23: 622-6. PMID 24209906 DOI: 10.1016/J.Gde.2013.09.002  1
2013 Gamsiz ED, Viscidi EW, Frederick AM, Nagpal S, Sanders SJ, Murtha MT, Schmidt M, Triche EW, Geschwind DH, State MW, Istrail S, Cook EH, Devlin B, Morrow EM. Intellectual disability is associated with increased runs of homozygosity in simplex autism. American Journal of Human Genetics. 93: 103-9. PMID 23830515 DOI: 10.1016/J.Ajhg.2013.06.004  0.36
2013 Aguiar D, Istrail S. Haplotype assembly in polyploid genomes and identical by descent shared tracts. Bioinformatics (Oxford, England). 29: i352-60. PMID 23813004 DOI: 10.1093/Bioinformatics/Btt213  1
2013 Tulin S, Aguiar D, Istrail S, Smith J. A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems. Evodevo. 4: 16. PMID 23731568 DOI: 10.1186/2041-9139-4-16  1
2013 Uzun A, Dewan AT, Istrail S, Padbury JF. Pathway-based genetic analysis of preterm birth. Genomics. 101: 163-70. PMID 23298525 DOI: 10.1016/J.Ygeno.2012.12.005  1
2012 Huang A, Hogan JW, Istrail S, Delong A, Katzenstein DA, Kantor R. Global analysis of sequence diversity within HIV-1 subtypes across geographic regions. Future Virology. 7: 505-517. PMID 22822410 DOI: 10.2217/Fvl.12.37  1
2012 Aguiar D, Istrail S. HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 577-90. PMID 22697235 DOI: 10.1089/Cmb.2012.0084  1
2012 Aguiar D, Halldórsson BV, Morrow EM, Istrail S. DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism. Bioinformatics (Oxford, England). 28: i154-62. PMID 22689755 DOI: 10.1093/Bioinformatics/Bts234  1
2012 Uzun A, Laliberte A, Parker J, Andrew C, Winterrowd E, Sharma S, Istrail S, Padbury JF. dbPTB: a database for preterm birth. Database : the Journal of Biological Databases and Curation. 2012: bar069. PMID 22323062 DOI: 10.1093/Database/Bar069  1
2012 Shatkay H, Narayanaswamy R, Nagaral SS, Harrington N, Rohith MV, Somanath G, Tarpine R, Schutter K, Johnstone T, Blostein D, Istrail S, Kambhamettu C. OCR-based image features for biomedical image and article classification: Identifying documents relevant to cis-regulatory elements 2012 Acm Conference On Bioinformatics, Computational Biology and Biomedicine, Bcb 2012. 98-104. DOI: 10.1145/2382936.2382949  1
2012 Istrail S, Marcus S. Alan Turing and John von Neumann - Their brains and their computers Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7762: 26-35. DOI: 10.1007/978-3-642-36751-9_2  1
2012 Shatkay H, Narayanaswamy R, Nagaral SS, Harrington N, Mv R, Somanath G, Tarpine R, Schutter K, Johnstone T, Blostein D, Istrail S, Kambhamettu C. OCR-based image features for biomedical image and article classification: Identifying documents relevant to genomic cis-regulatory elements Aaai Fall Symposium - Technical Report. 51-58.  1
2011 Huang A, Kantor R, DeLong A, Schreier L, Istrail S. QColors: an algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads. In Silico Biology. 11: 193-201. PMID 23202421 DOI: 10.3233/Isb-2012-0454  1
2011 Halldórsson BV, Aguiar D, Tarpine R, Istrail S. The Clark phaseable sample size problem: long-range phasing and loss of heterozygosity in GWAS. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 323-33. PMID 21385037 DOI: 10.1089/Cmb.2010.0288  0.36
2011 Halldórsson BV, Aguiar D, Istrail S. Haplotype phasing by multi-assembly of shared haplotypes: phase-dependent interactions between rare variants. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 88-99. PMID 21121036  1
2011 Tarpine R, Lam F, Istrail S. Conservative extensions of linkage disequilibrium measures from pairwise to multi-loci and algorithms for optimal tagging SNP selection Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6577: 468-482. DOI: 10.1007/978-3-642-20036-6_42  1
2010 Istrail S, Tarpine R, Schutter K, Aguiar D. Practical computational methods for regulatory genomics: a cisGRN-Lexicon and cisGRN-browser for gene regulatory networks. Methods in Molecular Biology (Clifton, N.J.). 674: 369-99. PMID 20827603 DOI: 10.1007/978-1-60761-854-6_22  0.36
2010 Lam F, Tarpine R, Istrail S. The imperfect ancestral recombination graph reconstruction problem: upper bounds for recombination and homoplasy. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 767-81. PMID 20583925 DOI: 10.1089/Cmb.2009.0249  0.36
2010 Nam J, Dong P, Tarpine R, Istrail S, Davidson EH. Functional cis-regulatory genomics for systems biology. Proceedings of the National Academy of Sciences of the United States of America. 107: 3930-5. PMID 20142491 DOI: 10.1073/Pnas.1000147107  0.36
2010 Halldórsson BV, Aguiar D, Tarpine R, Istrail S. The clark phase-able sample size problem: Long-range phasing and loss of heterozygosity in GWAS Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6044: 158-173. DOI: 10.1007/978-3-642-12683-3_11  1
2009 Istrail S, Pevzner P, Waterman M, Rajasekaran S. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5462: v-vi.  0.36
2007 Istrail S, De-Leon SB, Davidson EH. The regulatory genome and the computer. Developmental Biology. 310: 187-95. PMID 17822690 DOI: 10.1016/J.Ydbio.2007.08.009  0.36
2007 Istrail S, Pevzner P, Shamir R. Preface Discrete Applied Mathematics. 155: 673-674. DOI: 10.1016/j.dam.2006.09.001  0.36
2006 Samanta MP, Tongprasit W, Istrail S, Cameron RA, Tu Q, Davidson EH, Stolc V. The transcriptome of the sea urchin embryo. Science (New York, N.Y.). 314: 960-2. PMID 17095694 DOI: 10.1126/Science.1131898  1
2006 Sharan R, Halldórsson BV, Istrail S. Islands of tractability for parsimony haplotyping. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 3: 303-11. PMID 17048467 DOI: 10.1109/Tcbb.2006.40  1
2005 Sharan R, Halldósson BV, Istrail S. Islands of tractability for parsimony haplotyping. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 65-72. PMID 16447963 DOI: 10.1109/CSB.2005.37  1
2005 Lippert RA, Zhao X, Florea L, Mobarry C, Istrail S. Finding anchors for genomic sequence comparison. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 762-76. PMID 16108715 DOI: 10.1089/Cmb.2005.12.762  0.36
2005 Istrail S, Davidson EH. Logic functions of the genomic cis-regulatory code. Proceedings of the National Academy of Sciences of the United States of America. 102: 4954-9. PMID 15788531 DOI: 10.1073/Pnas.0409624102  0.36
2005 De La Vega FM, Isaac H, Collins A, Scafe CR, Halldórsson BV, Su X, Lippert RA, Wang Y, Laig-Webster M, Koehler RT, Ziegle JS, Wogan LT, Stevens JF, Leinen KM, Olson SJ, ... ... Istrail S, et al. The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Research. 15: 454-62. PMID 15781572 DOI: 10.1101/Gr.3241705  0.36
2005 Florea L, Di Francesco V, Miller J, Turner R, Yao A, Harris M, Walenz B, Mobarry C, Merkulov GV, Charlab R, Dew I, Deng Z, Istrail S, Li P, Sutton G. Gene and alternative splicing annotation with AIR. Genome Research. 15: 54-66. PMID 15632090 DOI: 10.1101/Gr.2889405  0.36
2005 Bafna V, Istrail S, Lancia G, Rizzi R. Polynomial and APX-hard cases of the individual haplotyping problem Theoretical Computer Science. 335: 109-125. DOI: 10.1016/J.Tcs.2004.12.017  0.36
2004 Halldórsson BV, Istrail S, De La Vega FM. Optimal selection of SNP markers for disease association studies. Human Heredity. 58: 190-202. PMID 15812176 DOI: 10.1159/000083546  0.36
2004 Istrail S, Florea L, Halldórsson BV, Kohlbacher O, Schwartz RS, Yap VB, Yewdell JW, Hoffman SL. Comparative immunopeptidomics of humans and their pathogens. Proceedings of the National Academy of Sciences of the United States of America. 101: 13268-72. PMID 15326311 DOI: 10.1073/Pnas.0404740101  0.36
2004 Halldórsson BV, Bafna V, Lippert R, Schwartz R, De La Vega FM, Clark AG, Istrail S. Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies. Genome Research. 14: 1633-40. PMID 15289481 DOI: 10.1101/Gr.2570004  0.36
2004 Caprara A, Carr R, Istrail S, Lancia G, Walenz B. 1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 27-52. PMID 15072687 DOI: 10.1089/106652704773416876  0.36
2004 Istrail S, Sutton GG, Florea L, Halpern AL, Mobarry CM, Lippert R, Walenz B, Shatkay H, Dew I, Miller JR, Flanigan MJ, Edwards NJ, Bolanos R, Fasulo D, Halldorsson BV, et al. Whole-genome shotgun assembly and comparison of human genome assemblies. Proceedings of the National Academy of Sciences of the United States of America. 101: 1916-21. PMID 14769938 DOI: 10.1073/Pnas.0307971100  0.36
2004 Nöthen MM, Hao K, Schulze TG, Ott J, Granath RO, Rietschel M, Lindholm E, Shmulewitz D, Zhang J, Greenberg DA, Hodge SE, Halldórsson BV, Istrail S, Vega FMDL, McMahon FJ, et al. Contents Vol. 58, 2004 Human Heredity. 58: 207-208. DOI: 10.1159/000085013  0.44
2004 Nöthen MM, Hao K, Schulze TG, Ott J, Granath RO, Rietschel M, Lindholm E, Shmulewitz D, Zhang J, Greenberg DA, Hodge SE, Halldórsson BV, Istrail S, Vega FMDL, McMahon FJ, et al. Subject Index Vol. 58, 2004 Human Heredity. 58: 206. DOI: 10.1159/000085012  0.44
2004 Halldórsson BV, Bafna V, Edwards N, Lippert R, Yooseph S, Istrail S. A Survey of Computational Methods for Determining Haplotypes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2983: 26-47.  0.36
2004 Schwartz R, Clark AG, Istrail S. Inferring piecewise ancestral history from haploid sequences Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2983: 62-73.  0.36
2003 Florea L, Halldórsson B, Kohlbacher O, Schwartz R, Hoffman S, Istrail S. Epitope prediction algorithms for peptide-based vaccine design. Proceedings / Ieee Computer Society Bioinformatics Conference. Ieee Computer Society Bioinformatics Conference. 2: 17-26. PMID 16826643 DOI: 10.1109/CSB.2003.1227293  0.36
2003 Schwartz R, Halldórsson BV, Bafna V, Clark AG, Istrail S. Robustness of inference of haplotype block structure. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 13-9. PMID 12676048 DOI: 10.1089/106652703763255642  0.36
2003 Halldórsson BV, Bafna V, Edwards N, Lippert R, Yooseph S, Istrail S. Combinatorial problems arising in SNP and haplotype analysis Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2731: 26-47. DOI: 10.1007/3-540-45066-1_3  0.36
2003 Lancia G, Istrail S. Protein structure comparison: Algorithms and applications Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2666: 1-33.  0.36
2003 Bafna V, Halldórsson BV, Schwartz R, Clark AG, Istrail S. Haplotypes and informative SNP selection algorithms: Don't block out information Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 19-27.  0.36
2002 Lippert R, Schwartz R, Lancia G, Istrail S. Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem. Briefings in Bioinformatics. 3: 23-31. PMID 12002221 DOI: 10.1093/Bib/3.1.23  0.36
2002 Rizzi R, Bafna V, Istrail S, Lancia G. Practical algorithms and fixed-parameter tractability for the single individual SNP haplotyping problem Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2452: 29-43.  0.36
2001 Schwartz R, Istrail S, King J. Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues Protein Science. 10: 1023-1031. PMID 11316883 DOI: 10.1110/Ps.33201  0.36
2001 Turner RJ, Chaturvedi K, Edwards NJ, Fasulo D, Halpern AL, Huson DH, Kohlbacher O, Miller JR, Reinert K, Remington KA, Schwartz R, Walenz B, Yooseph S, Istrail S. Visualization challenges for a new cyber-pharmaceutical computing paradigm Proceedings - Ieee 2001 Symposium On Parallel and Large-Data Visualization and Graphics. 7-18. DOI: 10.1109/PVGS.2001.964398  0.36
2001 Lancia G, Carr R, Walenz B, Istrail S. 101 Optimal PDB structure alignments: A branch-and-cut algorithm for the maximum contact map overlap problem Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 193-202.  0.36
2001 Lancia G, Bafna V, Istrail S, Lippert R, Schwartz R. SNPs problems, complexity, and algorithms Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2161: 182-193.  0.36
2000 Hart WE, Istrail S. Invariant patterns in crystal lattices: Implications for protein folding algorithms Journal of Universal Computer Science. 6: 560-579. DOI: 10.1007/3-540-61258-0_21  0.36
1999 Istrail S, Schwartz R, King J. Lattice simulations of aggregation funnels for protein folding Journal of Computational Biology. 6: 143-162. PMID 10421520 DOI: 10.1089/Cmb.1999.6.143  0.36
1999 Istrail S. Special RECOMB'99 issue Journal of Computational Biology. 6: 279. DOI: 10.1089/106652799318265  0.36
1999 Batzoglou S, Istrail S. Physical mapping with repeated probes: The hypergraph superstring problem Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1645: 66-77. DOI: 10.1007/3-540-48452-3_5  0.36
1997 Hart WE, Istrail S. Robust proofs of NP-Hardness for protein folding: General lattices and energy potentials Journal of Computational Biology. 4: 1-22. PMID 9109034 DOI: 10.1089/Cmb.1997.4.1  0.36
1996 Istrail SC. Fast protein folding in the hydrophobic-hydrophilic model within three-eighths of optimal Journal of Computational Biology. 3: 53-96. PMID 8697239  0.36
1995 Greenberg DS, Istrail S. Physical mapping by STS hybridization: algorithmic strategies and the challenge of software evaluation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 2: 219-73. PMID 7497128 DOI: 10.1089/Cmb.1995.2.219  0.36
1994 Greenberg D, Istrail S. The chimeric mapping problem: Algorithmic strategies and performance evaluation on synthetic genomic data Computers and Chemistry. 18: 207-220. PMID 7952891 DOI: 10.1016/0097-8485(94)85015-1  0.36
1994 Istrail S, Zivkovic D. Bounded-width polynomial-size Boolean formulas compute exactly those functions in AC0 Information Processing Letters. 50: 211-216. DOI: 10.1016/0020-0190(94)00036-0  0.36
1992 Heath LS, Istrail S. The Pagenumber of Genus g Graphs is O(g) Journal of the Acm (Jacm). 39: 479-501. DOI: 10.1145/146637.146643  0.36
1989 Istrail S. An arithmetical hierarchy in propositional dynamic logic Information and Computation. 81: 280-289. DOI: 10.1016/0890-5401(89)90033-3  0.36
1988 Istrail S. Polynomial universal traversing sequences for cycles are constructible Proceedings of the Annual Acm Symposium On Theory of Computing. 491-503. DOI: 10.1145/62212.62260  0.36
1983 Istrail S, Masalagiu C. Nivat's processing systems: decision problems related to protection and synchronization Theoretical Computer Science. 26: 83-103. DOI: 10.1016/0304-3975(83)90080-4  0.36
1982 Istrail S. Some remarks on non-algebraic adherences Theoretical Computer Science. 21: 341-349. DOI: 10.1016/0304-3975(82)90080-9  0.36
1982 Istrail S. Generalization of the Ginsburg-Rice Schützenberger fixed-point theorem for context-sensitive and recursive-enumerable languages Theoretical Computer Science. 18: 333-341. DOI: 10.1016/0304-3975(82)90073-1  0.36
1979 Istrail S. On complements of some bounded context-sensitive languages Information and Control. 42: 283-289. DOI: 10.1016/S0019-9958(79)90272-9  0.36
1978 Istrail S. Elementary bounded languages Information and Control. 39: 177-191. DOI: 10.1016/S0019-9958(78)90839-2  0.36
1978 Istrail S. Tag systems generating thue irreductible sequences Information Processing Letters. 7: 129-131. DOI: 10.1016/0020-0190(78)90074-1  0.36
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