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Istrail Laboratory Publications

2014
[109]	Derek Aguiar, Wendy SW Wong, Sorin Istrail, "Tumor haplotype assembly algorithms for cancer genomics.", In Pacific Symposium on Biocomputing, vol. 19, pp. 3-14, 2014. [bib] [pdf]
[108]	Derek Aguiar, Eric Morrow, Sorin Istrail, "Tractatus: an exact and subquadratic algorithm for inferring identity-by-descent multi-shared haplotype tracts", In RECOMB, vol. , no. , pp. 158-173, 2014. [bib] [pdf]
2013
[107]	Ece 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, "Intellectual Disability Is Associated with Increased Runs of Homozygosity in Simplex Autism", In The American Journal of Human Genetics, Elsevier, vol. 93, no. 1, pp. 103-109, 2013. [bib]
[106]	Alper Uzun, Andrew T. Dewan, Sorin Istrail, James F. Padbury, "Pathway-based genetic analysis of preterm birth", In Genomics, vol. 101, no. 3, pp. 163 - 170, 2013. [bib] [pdf] [doi]
[105]	Sarah Tulin, Derek Aguiar, Sorin Istrail, Joel Smith, "A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems", In EvoDevo, vol. 4, no. 16, 2013. [bib] [pdf]
[104]	Derek Aguiar, Sorin Istrail, "Haplotype assembly in polyploid genomes and identical by descent shared tracts", In Bioinformatics, vol. 29, no. 13, pp. i352-i360, 2013. [bib] [pdf] [doi]
2012
[103]	Derek Aguiar, Sorin Istrail, "HAPCOMPASS: A fast cycle basis algorithm for accurate haplotype assembly of sequence data", In Journal of Computational Biology, vol. 19, no. 6, pp. 577-590, 2012. [bib] [pdf] [doi]
[102]	Alper Uzun, Alyse Laliberte, Jeremy Parker, Caroline Andrew, Emily Winterrowd, Surendra Sharma, Sorin Istrail, James F. Padbury, "dbPTB: a database for preterm birth", In Database (Oxford), vol. 2012, pp. bar069, 2012. [bib] [pdf] [doi]
[101]	Hagit Shatkay, Ramya Narayanaswamy, Santosh Nagaral, Na Harrington, Dorothea Blostein, Ryan Tarpine, Kyle Schutter, Rohith Mv, Gowri Somanath, Sorin Istrail, Chandra Kambahmettu, "OCR-based Image Features for Biomedical Image and Article Classification: Identifying Documents Relevant to Cis-Regulatory Elements", In ACM BCB, 2012. [bib] [pdf]
[100]	Sorin Istrail, "Computer Science Through Urn Games: An Unified Framework for a Hierarchy of Solvable and Unsolvable Problems", In Proceedings of the Turing Centenary Conference, 2012. [bib] [pdf]
[99]	Sorin Istrail, Solomon Marcus, "Turing and von Neumann's Brains and their Computers", In Proceedings of the Turing Centenary Conference, 2012. [bib] [pdf]
[98]	Austin Huang, Joseph W Hogan, Sorin Istrail, Allison DeLong, David A Katzenstein, Rami Kantor, "Global analysis of sequence diversity within HIV-1 subtypes across geographic regions", In Future Virology, vol. 7, no. 5, pp. 505-517, 2012. [bib] [pdf]
[97]	Leon N Cooper, Sorin Istrail, "Mental Experience and the Turing Test: This Double Face is the Face of Mathematics", In Proceedings of the Turing Centenary Conference, 2012. [bib] [pdf]
[96]	Derek Aguiar, Bjarni V. Halldorsson, Eric M. Morrow, Sorin Istrail, "DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism", In Bioinformatics, vol. 28, no. 12, pp. i154-i162, 2012. [bib] [pdf] [doi]
2011
[95]	Ryan Tarpine, Fumei Lam, Sorin Istrail, "Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-loci and Algorithms for Optimal Tagging SNP Selection", Chapter in Research in Computational Molecular Biology, Springer Berlin / Heidelberg, vol. 6577, pp. 468-482, 2011. [bib] [pdf]
[94]	Austin Huang, Rami Kantor, Allison DeLong, Leeann Schreier, Sorin Istrail, "QColors: An algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads", In BIBM Workshops, IEEE, pp. 130-136, 2011. [bib] [pdf]
[93]	Bjarni Halldorsson, Derek Aguiar, Ryan Tarpine, Sorin Istrail, "The Clark Phaseable Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS", In Journal of Computational Biology, vol. 18, no. 3, pp. 323-333, 2011. [bib] [pdf] [doi]
[92]	Bjarni Halldorsson, Derek Aguiar, Sorin Istrail, "Haplotype phasing by multi-assembly of shared haplotypes: phase-dependent interactions between rare variants", In Pac Symp Biocomput., pp. 88-99, 2011. [bib] [pdf] [doi]
2010
[91]	Jongmin Nam, Ping Dong, Ryan Tarpine, Sorin Istrail, Eric H. Davidson, "Functional cis-regulatory genomics for systems biology", In Proceedings of the National Academy of Sciences, vol. 107, no. 8, pp. 3930-3935, 2010. [bib] [pdf] [doi]
[90]	Fumei Lam, Ryan Tarpine, Sorin Istrail, "The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy", In Journal of Computational Biology, vol. 17, no. 6, pp. 767-781, 2010. [bib] [pdf]
[89]	Sorin Istrail, Ryan Tarpine, Kyle Schutter, Derek Aguiar, "Practical Computational Methods for Regulatory Genomics: A cisGRN-Lexicon and cisGRN-Browser for Gene Regulatory Networks", Chapter in Computational Biology of Transcription Factor Binding, Humana Press, vol. 674, pp. 369-399, 2010. [bib] [pdf] [doi]
[88]	Bjarni Halldorsson, Derek Aguiar, Ryan Tarpine, Sorin Istrail, "The Clark Phase-able Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS", In RECOMB, vol. 6044, pp. 158-173, 2010. [bib] [pdf] [doi]
2009
[87]	Ryan Tarpine, Sorin Istrail, "On the Concept of Cis-Regulatory Information: From Sequence Motifs to Logic Functions", Chapter in Algorithmic Bioprocesses, Springer-Verlag, pp. 731-742, 2009. [bib] [pdf]
[86]	Sorin Istrail, Fumei Lam, "Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results", In Communications in Information and Systems, vol. 9, no. 4, pp. 303-346, 2009. [bib] [pdf]
[85]	"Special Issue Dedicated to Michael Waterman on the Occasion of his 67th Birthday: Parts III-IV", In Communications in Information and Systems, vol. 9, China, 2009. [bib] [pdf]