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Sorin Istrail - Publications

Affiliations: 
Computer Science Brown University, Providence, RI 
Area:
Algorithms and Theory, Computational Biology
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48 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
2022 Pevzner P, Vingron M, Reidys C, Sun F, Istrail S. Michael Waterman's Contributions to Computational Biology and Bioinformatics. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 35727100 DOI: 10.1089/cmb.2022.29066.pp  0.311
2020 Armanious D, Schuster J, Tollefson GA, Agudelo A, DeWan AT, Istrail S, Padbury J, Uzun A. Proteinarium: Multi-sample protein-protein interaction analysis and visualization tool. Genomics. PMID 32702417 DOI: 10.1016/J.Ygeno.2020.07.028  0.31
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  0.693
2019 Istrail S. Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic -Regulatory Code. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 26: 653-684. PMID 31356126 DOI: 10.1089/Cmb.2019.0144  0.39
2019 Istrail S, Peter IS. How Does the Regulatory Genome Work Journal of Computational Biology. 26: 685-695. PMID 31166788 DOI: 10.1089/Cmb.2019.0097  0.403
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  0.725
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  0.769
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  0.778
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  0.406
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  0.343
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  0.791
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  0.747
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  0.418
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  0.326
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  0.795
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  0.793
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  0.398
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  0.374
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  0.78
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  0.78
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  0.762
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  0.334
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  0.4
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  0.773
2009 Istrail S, Lam F. Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results Communications in Information and Systems. 9: 303-346. DOI: 10.4310/Cis.2009.V9.N4.A2  0.324
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  0.393
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  0.437
2006 Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, ... ... Istrail S, et al. The genome of the sea urchin Strongylocentrotus purpuratus. Science (New York, N.Y.). 314: 941-52. PMID 17095691 DOI: 10.1126/Science.1133609  0.45
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  0.337
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  0.469
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  0.322
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  0.455
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  0.394
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  0.432
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  0.434
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  0.309
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  0.445
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.  0.311
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.  0.311
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  0.337
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  0.451
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.  0.337
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  0.526
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.  0.336
2001 Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, ... ... Istrail S, et al. The sequence of the human genome. Science (New York, N.Y.). 291: 1304-51. PMID 11181995 DOI: 10.1126/Science.1058040  0.486
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  0.398
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  0.402
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  0.302
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