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Items: 1 to 20 of 68

1.

SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data.

Zhang P, Boisson B, Stenson PD, Cooper DN, Casanova JL, Abel L, Itan Y.

Nucleic Acids Res. 2019 May 2. pii: gkz326. doi: 10.1093/nar/gkz326. [Epub ahead of print]

PMID:
31045209
2.

S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing.

Jagadeesh KA, Paggi JM, Ye JS, Stenson PD, Cooper DN, Bernstein JA, Bejerano G.

Nat Genet. 2019 Apr;51(4):755-763. doi: 10.1038/s41588-019-0348-4. Epub 2019 Feb 25.

PMID:
30804562
3.

Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis.

Maffucci P, Bigio B, Rapaport F, Cobat A, Borghesi A, Lopez M, Patin E, Bolze A, Shang L, Bendavid M, Scott EM, Stenson PD, Cunningham-Rundles C, Cooper DN, Gleeson JG, Fellay J, Quintana-Murci L, Casanova JL, Abel L, Boisson B, Itan Y.

Proc Natl Acad Sci U S A. 2019 Jan 15;116(3):950-959. doi: 10.1073/pnas.1808403116. Epub 2018 Dec 27.

PMID:
30591557
4.

CDG: An Online Server for Detecting Biologically Closest Disease-Causing Genes and its Application to Primary Immunodeficiency.

Requena D, Maffucci P, Bigio B, Shang L, Abhyankar A, Boisson B, Stenson PD, Cooper DN, Cunningham-Rundles C, Casanova JL, Abel L, Itan Y.

Front Immunol. 2018 Jun 27;9:1340. doi: 10.3389/fimmu.2018.01340. eCollection 2018.

5.

The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies.

Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN.

Hum Genet. 2017 Jun;136(6):665-677. doi: 10.1007/s00439-017-1779-6. Epub 2017 Mar 27. Review.

6.

iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations.

Liang S, Tippens ND, Zhou Y, Mort M, Stenson PD, Cooper DN, Yu H.

Genome Biol. 2017 Jan 18;18(1):10. doi: 10.1186/s13059-016-1138-2.

7.

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity.

Jagadeesh KA, Wenger AM, Berger MJ, Guturu H, Stenson PD, Cooper DN, Bernstein JA, Bejerano G.

Nat Genet. 2016 Dec;48(12):1581-1586. doi: 10.1038/ng.3703. Epub 2016 Oct 24.

PMID:
27776117
8.

Analysis of protein-coding genetic variation in 60,706 humans.

Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, Tukiainen T, Birnbaum DP, Kosmicki JA, Duncan LE, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J, Cooper DN, Deflaux N, DePristo M, Do R, Flannick J, Fromer M, Gauthier L, Goldstein J, Gupta N, Howrigan D, Kiezun A, Kurki MI, Moonshine AL, Natarajan P, Orozco L, Peloso GM, Poplin R, Rivas MA, Ruano-Rubio V, Rose SA, Ruderfer DM, Shakir K, Stenson PD, Stevens C, Thomas BP, Tiao G, Tusie-Luna MT, Weisburd B, Won HH, Yu D, Altshuler DM, Ardissino D, Boehnke M, Danesh J, Donnelly S, Elosua R, Florez JC, Gabriel SB, Getz G, Glatt SJ, Hultman CM, Kathiresan S, Laakso M, McCarroll S, McCarthy MI, McGovern D, McPherson R, Neale BM, Palotie A, Purcell SM, Saleheen D, Scharf JM, Sklar P, Sullivan PF, Tuomilehto J, Tsuang MT, Watkins HC, Wilson JG, Daly MJ, MacArthur DG; Exome Aggregation Consortium.

Nature. 2016 Aug 18;536(7616):285-91. doi: 10.1038/nature19057.

9.

mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome.

Meyer MJ, Lapcevic R, Romero AE, Yoon M, Das J, Beltrán JF, Mort M, Stenson PD, Cooper DN, Paccanaro A, Yu H.

Hum Mutat. 2016 May;37(5):447-56. doi: 10.1002/humu.22963. Epub 2016 Feb 18.

10.

The mutation significance cutoff: gene-level thresholds for variant predictions.

Itan Y, Shang L, Boisson B, Ciancanelli MJ, Markle JG, Martinez-Barricarte R, Scott E, Shah I, Stenson PD, Gleeson J, Cooper DN, Quintana-Murci L, Zhang SY, Abel L, Casanova JL.

Nat Methods. 2016 Feb;13(2):109-10. doi: 10.1038/nmeth.3739. No abstract available.

11.

The human gene damage index as a gene-level approach to prioritizing exome variants.

Itan Y, Shang L, Boisson B, Patin E, Bolze A, Moncada-Vélez M, Scott E, Ciancanelli MJ, Lafaille FG, Markle JG, Martinez-Barricarte R, de Jong SJ, Kong XF, Nitschke P, Belkadi A, Bustamante J, Puel A, Boisson-Dupuis S, Stenson PD, Gleeson JG, Cooper DN, Quintana-Murci L, Claverie JM, Zhang SY, Abel L, Casanova JL.

Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13615-20. doi: 10.1073/pnas.1518646112. Epub 2015 Oct 19.

12.

Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel).

Douville C, Masica DL, Stenson PD, Cooper DN, Gygax DM, Kim R, Ryan M, Karchin R.

Hum Mutat. 2016 Jan;37(1):28-35. doi: 10.1002/humu.22911. Epub 2015 Oct 26.

13.

A global reference for human genetic variation.

1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR.

Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393.

14.

Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns.

Turner TN, Douville C, Kim D, Stenson PD, Cooper DN, Chakravarti A, Karchin R.

Hum Mol Genet. 2015 Nov 1;24(21):5995-6002. doi: 10.1093/hmg/ddv309. Epub 2015 Aug 5.

15.

Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach.

Karageorgos I, Mizzi C, Giannopoulou E, Pavlidis C, Peters BA, Zagoriti Z, Stenson PD, Mitropoulos K, Borg J, Kalofonos HP, Drmanac R, Stubbs A, van der Spek P, Cooper DN, Katsila T, Patrinos GP.

Hum Genomics. 2015 Jun 20;9:12. doi: 10.1186/s40246-015-0034-2.

16.

Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations.

Johnston JJ, Lewis KL, Ng D, Singh LN, Wynter J, Brewer C, Brooks BP, Brownell I, Candotti F, Gonsalves SG, Hart SP, Kong HH, Rother KI, Sokolic R, Solomon BD, Zein WM, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG.

Am J Hum Genet. 2015 Jun 4;96(6):913-25. doi: 10.1016/j.ajhg.2015.04.013.

17.

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.

Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J; GTEx Consortium; Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG.

Science. 2015 May 8;348(6235):666-9. doi: 10.1126/science.1261877.

18.

The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity.

Grimm DG, Azencott CA, Aicheler F, Gieraths U, MacArthur DG, Samocha KE, Cooper DN, Stenson PD, Daly MJ, Smoller JW, Duncan LE, Borgwardt KM.

Hum Mutat. 2015 May;36(5):513-23. doi: 10.1002/humu.22768. Epub 2015 Mar 26.

19.

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.

Delaneau O, Marchini J; 1000 Genomes Project Consortium; 1000 Genomes Project Consortium.

Nat Commun. 2014 Jun 13;5:3934. doi: 10.1038/ncomms4934.

20.

A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations.

Wei X, Das J, Fragoza R, Liang J, Bastos de Oliveira FM, Lee HR, Wang X, Mort M, Stenson PD, Cooper DN, Lipkin SM, Smolka MB, Yu H.

PLoS Genet. 2014 Dec 11;10(12):e1004819. doi: 10.1371/journal.pgen.1004819. eCollection 2014 Dec.

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