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Items: 46

1.

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

Istrail S.

J Comput Biol. 2019 Jul;26(7):653-684. doi: 10.1089/cmb.2019.0144. No abstract available.

PMID:
31356126
2.

How Does the Regulatory Genome Work?

Istrail S, Peter IS.

J Comput Biol. 2019 Jun 4. doi: 10.1089/cmb.2019.0097. [Epub ahead of print]

PMID:
31166788
3.

Global Comparison of Drug Resistance Mutations After First-Line Antiretroviral Therapy Across Human Immunodeficiency Virus-1 Subtypes.

Huang A, Hogan JW, Luo X, DeLong A, Saravanan S, Wu Y, Sirivichayakul S, Kumarasamy N, Zhang F, Phanuphak P, Diero L, Buziba N, Istrail S, Katzenstein DA, Kantor R.

Open Forum Infect Dis. 2015 Nov 3;3(2):ofv158. doi: 10.1093/ofid/ofv158. eCollection 2016 Apr.

4.

Eric Davidson: Master of the universe.

Istrail S.

Dev Biol. 2016 Apr 15;412(2 Suppl):S47-54. doi: 10.1016/j.ydbio.2016.01.029. Epub 2016 Jan 26. No abstract available.

5.

Transcriptome of American oysters, Crassostrea virginica, in response to bacterial challenge: insights into potential mechanisms of disease resistance.

McDowell IC, Nikapitiya C, Aguiar D, Lane CE, Istrail S, Gomez-Chiarri M.

PLoS One. 2014 Aug 14;9(8):e105097. doi: 10.1371/journal.pone.0105097. eCollection 2014.

6.

Tumor haplotype assembly algorithms for cancer genomics.

Aguiar D, Wong WS, Istrail S.

Pac Symp Biocomput. 2014:3-14.

7.

Pathway-based analysis of genomic variation data.

Atias N, Istrail S, Sharan R.

Curr Opin Genet Dev. 2013 Dec;23(6):622-6. doi: 10.1016/j.gde.2013.09.002. Epub 2013 Oct 24. Review.

PMID:
24209906
8.

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

Gamsiz ED, Viscidi EW, Frederick AM, Nagpal S, Sanders SJ, Murtha MT, Schmidt M; Simons Simplex Collection Genetics Consortium, Triche EW, Geschwind DH, State MW, Istrail S, Cook EH Jr, Devlin B, Morrow EM.

Am J Hum Genet. 2013 Jul 11;93(1):103-9. doi: 10.1016/j.ajhg.2013.06.004. Epub 2013 Jul 3.

9.

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

Aguiar D, Istrail S.

Bioinformatics. 2013 Jul 1;29(13):i352-60. doi: 10.1093/bioinformatics/btt213.

10.

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

Tulin S, Aguiar D, Istrail S, Smith J.

Evodevo. 2013 Jun 3;4:16. doi: 10.1186/2041-9139-4-16. eCollection 2013.

11.

Pathway-based genetic analysis of preterm birth.

Uzun A, Dewan AT, Istrail S, Padbury JF.

Genomics. 2013 Mar;101(3):163-70. doi: 10.1016/j.ygeno.2012.12.005. Epub 2013 Jan 6.

12.

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

Huang A, Kantor R, DeLong A, Schreier L, Istrail S.

In Silico Biol. 2011-2012;11(5-6):193-201. doi: 10.3233/ISB-2012-0454.

13.

Global analysis of sequence diversity within HIV-1 subtypes across geographic regions.

Huang A, Hogan JW, Istrail S, Delong A, Katzenstein DA, Kantor R.

Future Virol. 2012 May;7(5):505-517.

14.

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

Aguiar D, Istrail S.

J Comput Biol. 2012 Jun;19(6):577-90. doi: 10.1089/cmb.2012.0084.

15.

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

Aguiar D, Halldórsson BV, Morrow EM, Istrail S.

Bioinformatics. 2012 Jun 15;28(12):i154-62. doi: 10.1093/bioinformatics/bts234.

16.

dbPTB: a database for preterm birth.

Uzun A, Laliberte A, Parker J, Andrew C, Winterrowd E, Sharma S, Istrail S, Padbury JF.

Database (Oxford). 2012 Feb 8;2012:bar069. doi: 10.1093/database/bar069. Print 2012.

17.

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

Halldórsson BV, Aguiar D, Tarpine R, Istrail S.

J Comput Biol. 2011 Mar;18(3):323-33. doi: 10.1089/cmb.2010.0288.

PMID:
21385037
18.
19.

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

Istrail S, Tarpine R, Schutter K, Aguiar D.

Methods Mol Biol. 2010;674:369-99. doi: 10.1007/978-1-60761-854-6_22.

PMID:
20827603
20.

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

Lam F, Tarpine R, Istrail S.

J Comput Biol. 2010 Jun;17(6):767-81. doi: 10.1089/cmb.2009.0249.

PMID:
20583925
21.

Functional cis-regulatory genomics for systems biology.

Nam J, Dong P, Tarpine R, Istrail S, Davidson EH.

Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3930-5. doi: 10.1073/pnas.1000147107. Epub 2010 Feb 8.

22.

The regulatory genome and the computer.

Istrail S, De-Leon SB, Davidson EH.

Dev Biol. 2007 Oct 15;310(2):187-95. Epub 2007 Aug 10. Review.

23.

The transcriptome of the sea urchin embryo.

Samanta MP, Tongprasit W, Istrail S, Cameron RA, Tu Q, Davidson EH, Stolc V.

Science. 2006 Nov 10;314(5801):960-2.

24.

The genome of the sea urchin Strongylocentrotus purpuratus.

Sea Urchin Genome Sequencing Consortium, 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, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevière AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R.

Science. 2006 Nov 10;314(5801):941-52. Erratum in: Science. 2007 Feb 9;315(5813):766.

25.

Islands of tractability for parsimony haplotyping.

Sharan R, Halldórsson BV, Istrail S.

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

PMID:
17048467
26.

Epitope prediction algorithms for peptide-based vaccine design.

Florea L, Halldórsson B, Kohlbacher O, Schwartz R, Hoffman S, Istrail S.

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

PMID:
16826643
27.

Islands of tractability for parsimony haplotyping.

Sharan R, Halldósson BV, Istrail S.

Proc IEEE Comput Syst Bioinform Conf. 2005:65-72.

PMID:
16447963
28.

Finding anchors for genomic sequence comparison.

Lippert RA, Zhao X, Florea L, Mobarry C, Istrail S.

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

PMID:
16108715
29.

Optimal selection of SNP markers for disease association studies.

Halldórsson BV, Istrail S, De La Vega FM.

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

PMID:
15812176
30.

Logic functions of the genomic cis-regulatory code.

Istrail S, Davidson EH.

Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):4954-9. Epub 2005 Mar 23. Review.

31.

The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern.

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, Guegler KJ, You X, Xu LH, Hemken HG, Kalush F, Itakura M, Zheng Y, de Thé G, O'Brien SJ, Clark AG, Istrail S, Hunkapiller MW, Spier EG, Gilbert DA.

Genome Res. 2005 Apr;15(4):454-62. Epub 2005 Mar 21.

32.

Gene and alternative splicing annotation with AIR.

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.

Genome Res. 2005 Jan;15(1):54-66.

33.

Comparative immunopeptidomics of humans and their pathogens.

Istrail S, Florea L, Halldórsson BV, Kohlbacher O, Schwartz RS, Yap VB, Yewdell JW, Hoffman SL.

Proc Natl Acad Sci U S A. 2004 Sep 7;101(36):13268-72. Epub 2004 Aug 23.

34.

Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies.

Halldórsson BV, Bafna V, Lippert R, Schwartz R, De La Vega FM, Clark AG, Istrail S.

Genome Res. 2004 Aug;14(8):1633-40.

35.

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

Caprara A, Carr R, Istrail S, Lancia G, Walenz B.

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

PMID:
15072687
36.

Whole-genome shotgun assembly and comparison of human genome assemblies.

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, Hannenhalli S, Turner R, Yooseph S, Lu F, Nusskern DR, Shue BC, Zheng XH, Zhong F, Delcher AL, Huson DH, Kravitz SA, Mouchard L, Reinert K, Remington KA, Clark AG, Waterman MS, Eichler EE, Adams MD, Hunkapiller MW, Myers EW, Venter JC.

Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):1916-21. Epub 2004 Feb 9.

37.

Robustness of inference of haplotype block structure.

Schwartz R, Halldórsson BV, Bafna V, Clark AG, Istrail S.

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

PMID:
12676048
38.

Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem.

Lippert R, Schwartz R, Lancia G, Istrail S.

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

PMID:
12002221
40.

The sequence of the human genome.

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, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X.

Science. 2001 Feb 16;291(5507):1304-51. Erratum in: Science 2001 Jun 5;292(5523):1838.

PMID:
11181995
41.

Lattice simulations of aggregation funnels for protein folding.

Istrail S, Schwartz R, King J.

J Comput Biol. 1999 Summer;6(2):143-62.

PMID:
10421520
42.
43.

Robust proofs of NP-hardness for protein folding: general lattices and energy potentials.

Hart WE, Istrail S.

J Comput Biol. 1997 Spring;4(1):1-22.

PMID:
9109034
44.

Fast protein folding in the hydrophobic-hydrophilic model within three-eighths of optimal.

Hart WE, Istrail SC.

J Comput Biol. 1996 Spring;3(1):53-96.

PMID:
8697239
45.
46.

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