Sorin Istrail

Sorin Istrail

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Sorin Istrail

Sorin Istrail

Publications by authors named "Sorin Istrail"

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How Does the Regulatory Genome Work?

J Comput Biol 2019 Jul 4;26(7):685-695. Epub 2019 Jun 4.

Division of Biology and Biological Engineering, MC156-29, California Institute of Technology, Pasadena, California.

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http://dx.doi.org/10.1089/cmb.2019.0097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6661970PMC
July 2019

Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic -Regulatory Code.

Authors:
Sorin Istrail

J Comput Biol 2019 Jul;26(7):653-684

Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, Rhode Island.

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http://dx.doi.org/10.1089/cmb.2019.0144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6763962PMC
July 2019

Eric Davidson: Master of the universe.

Authors:
Sorin Istrail

Dev Biol 2016 Apr 26;412(2 Suppl):S47-54. Epub 2016 Jan 26.

Department of Computer Science and Center for Computational Molecular Biology, Brown University, USA.

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http://dx.doi.org/10.1016/j.ydbio.2016.01.029DOI Listing
April 2016

Tumor haplotype assembly algorithms for cancer genomics.

Pac Symp Biocomput 2014 :3-14

Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4051221PMC
August 2014

A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems.

Evodevo 2013 3;4:16. Epub 2013 Jun 3.

Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.

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http://dx.doi.org/10.1186/2041-9139-4-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748831PMC
May 2014

Pathway-based analysis of genomic variation data.

Curr Opin Genet Dev 2013 Dec 24;23(6):622-6. Epub 2013 Oct 24.

Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1016/j.gde.2013.09.002DOI Listing
December 2013

Haplotype phasing by multi-assembly of shared haplotypes: phase-dependent interactions between rare variants.

Pac Symp Biocomput 2011 :88-99

School of Science and Engineering, Reykjavik University, Reykjavik, Iceland.

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November 2013

Haplotype assembly in polyploid genomes and identical by descent shared tracts.

Bioinformatics 2013 Jul;29(13):i352-60

Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694639PMC
July 2013

Intellectual disability is associated with increased runs of homozygosity in simplex autism.

Am J Hum Genet 2013 Jul 3;93(1):103-9. Epub 2013 Jul 3.

Laboratory for Molecular Medicine, Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02912, USA.

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http://dx.doi.org/10.1016/j.ajhg.2013.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710760PMC
July 2013

QColors: an algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads.

In Silico Biol 2011-2012;11(5-6):193-201

Division of Infectious Disease, Computer Science Department, Brown University, Box 1910, Providence, RI 02912, USA.

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http://dx.doi.org/10.3233/ISB-2012-0454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5530257PMC
May 2013

Pathway-based genetic analysis of preterm birth.

Genomics 2013 Mar 6;101(3):163-70. Epub 2013 Jan 6.

Women and Infants Hospital of Rhode Island, Department of Pediatrics, and Brown Alpert Medical School, Providence, RI 02905, USA.

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http://dx.doi.org/10.1016/j.ygeno.2012.12.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570639PMC
March 2013

DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism.

Bioinformatics 2012 Jun;28(12):i154-62

Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bts234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371866PMC
June 2012

HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data.

J Comput Biol 2012 Jun;19(6):577-90

Department of Computer Science, Brown University, Providence RI 02912, USA.

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http://dx.doi.org/10.1089/cmb.2012.0084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375639PMC
June 2012

dbPTB: a database for preterm birth.

Database (Oxford) 2012 8;2012:bar069. Epub 2012 Feb 8.

Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI 02905, USA.

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http://dx.doi.org/10.1093/database/bar069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3275764PMC
May 2012

The Clark phaseable sample size problem: long-range phasing and loss of heterozygosity in GWAS.

J Comput Biol 2011 Mar;18(3):323-33

School of Science and Engineering, Reykjavik University, Reykjavik, Iceland.

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http://dx.doi.org/10.1089/cmb.2010.0288DOI Listing
March 2011

Practical computational methods for regulatory genomics: a cisGRN-Lexicon and cisGRN-browser for gene regulatory networks.

Methods Mol Biol 2010 ;674:369-99

Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI, USA.

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http://dx.doi.org/10.1007/978-1-60761-854-6_22DOI Listing
December 2010

The imperfect ancestral recombination graph reconstruction problem: upper bounds for recombination and homoplasy.

J Comput Biol 2010 Jun;17(6):767-81

Department of Computer Science, Brown Univerisity, Providence, Rhode Island 02912, USA.

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http://dx.doi.org/10.1089/cmb.2009.0249DOI Listing
June 2010

Functional cis-regulatory genomics for systems biology.

Proc Natl Acad Sci U S A 2010 Feb 8;107(8):3930-5. Epub 2010 Feb 8.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1073/pnas.1000147107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840491PMC
February 2010

The regulatory genome and the computer.

Dev Biol 2007 Oct 10;310(2):187-95. Epub 2007 Aug 10.

Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S001216060701254
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http://dx.doi.org/10.1016/j.ydbio.2007.08.009DOI Listing
October 2007

Islands of tractability for parsimony haplotyping.

Proc IEEE Comput Syst Bioinform Conf 2005 :65-72

School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel.

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May 2007

Islands of tractability for parsimony haplotyping.

IEEE/ACM Trans Comput Biol Bioinform 2006 Jul-Sep;3(3):303-11

School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel.

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http://ieeexplore.ieee.org/document/1668028/
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http://dx.doi.org/10.1109/TCBB.2006.40DOI Listing
November 2006

The genome of the sea urchin Strongylocentrotus purpuratus.

Authors:
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 Bellé Seth Carbonneau Rocky Cheung Patrick Cormier Bertrand Cosson Jenifer Croce Antonio Fernandez-Guerra Anne-Marie Genevière 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 Stolc Waraporn Tongprasit Qiang Tu Karl-Frederik Bergeron Bruce P Brandhorst James Whittle Kevin Berney David J Bottjer Cristina Calestani Kevin Peterson Elly Chow Qiu Autumn Yuan Eran Elhaik Dan Graur Justin T Reese Ian Bosdet Shin Heesun Marco A Marra Jacqueline Schein Michele K Anderson Virginia Brockton Katherine M Buckley Avis H Cohen Sebastian D Fugmann Taku Hibino Mariano Loza-Coll Audrey J Majeske Cynthia Messier Sham V Nair Zeev Pancer David P Terwilliger Cavit Agca Enrique Arboleda Nansheng Chen Allison M Churcher F Hallböök Glen W Humphrey Mohammed M Idris Takae Kiyama Shuguang Liang Dan Mellott Xiuqian Mu Greg Murray Robert P Olinski Florian Raible Matthew Rowe John S Taylor Kristin Tessmar-Raible D Wang Karen H Wilson Shunsuke Yaguchi Terry Gaasterland Blanca E Galindo Herath J Gunaratne Celina Juliano Masashi Kinukawa Gary W Moy Anna T Neill Mamoru Nomura Michael Raisch Anna Reade Michelle M Roux Jia L Song Yi-Hsien Su Ian K Townley Ekaterina Voronina Julian L Wong Gabriele Amore Margherita Branno Euan R Brown Vincenzo Cavalieri Véronique Duboc Louise Duloquin Constantin Flytzanis Christian Gache François Lapraz Thierry Lepage Annamaria Locascio Pedro Martinez Giorgio Matassi Valeria Matranga Ryan Range Francesca Rizzo Eric Röttinger Wendy Beane Cynthia Bradham Christine Byrum Tom Glenn Sofia Hussain Gerard Manning Esther Miranda Rebecca Thomason Katherine Walton Athula Wikramanayke Shu-Yu Wu Ronghui Xu C Titus Brown Lili Chen Rachel F Gray Pei Yun Lee Jongmin Nam Paola Oliveri Joel Smith Donna Muzny Stephanie Bell Joseph Chacko Andrew Cree Stacey Curry Clay Davis Huyen Dinh Shannon Dugan-Rocha Jerry Fowler Rachel Gill Cerrissa Hamilton Judith Hernandez Sandra Hines Jennifer Hume Laronda Jackson Angela Jolivet Christie Kovar Sandra Lee Lora Lewis George Miner Margaret Morgan Lynne V Nazareth Geoffrey Okwuonu David Parker Ling-Ling Pu Rachel Thorn Rita Wright

Science 2006 Nov;314(5801):941-52

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http://dx.doi.org/10.1126/science.1133609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423PMC
November 2006

Epitope prediction algorithms for peptide-based vaccine design.

Proc IEEE Comput Soc Bioinform Conf 2003 ;2:17-26

Celera/Applied Biosystems.

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August 2006

Finding anchors for genomic sequence comparison.

J Comput Biol 2005 Jul-Aug;12(6):762-76

Informatics Research, Celera/Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1089/cmb.2005.12.762DOI Listing
October 2005

Optimal selection of SNP markers for disease association studies.

Hum Hered 2004 ;58(3-4):190-202

Applied Biosystems, Rockville, MD, USA.

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https://www.karger.com/Article/FullText/83546
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http://dx.doi.org/10.1159/000083546DOI Listing
June 2005

Logic functions of the genomic cis-regulatory code.

Proc Natl Acad Sci U S A 2005 Apr 23;102(14):4954-9. Epub 2005 Mar 23.

Applied Biosystems/Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0409624102
Publisher Site
http://dx.doi.org/10.1073/pnas.0409624102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555989PMC
April 2005

1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap.

J Comput Biol 2004 ;11(1):27-52

D.E.I.S., Università di Bologna, Viale Risorgimento, 2 40136 Bologna, Italy.

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http://www.liebertpub.com/doi/10.1089/106652704773416876
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http://dx.doi.org/10.1089/106652704773416876DOI Listing
October 2004

Robustness of inference of haplotype block structure.

J Comput Biol 2003 ;10(1):13-9

Celera Genomics Research, Rockville, MD 20850, USA.

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http://www.liebertpub.com/doi/10.1089/106652703763255642
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http://dx.doi.org/10.1089/106652703763255642DOI Listing
September 2003

Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem.

Brief Bioinform 2002 Mar;3(1):23-31

Informatics Research department, Celera Genomics, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1093/bib/3.1.23DOI Listing
March 2002