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Items: 1 to 50 of 60

1.

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.

2.

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.

3.

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
4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

PMID:
26246501
10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

A probabilistic model to predict clinical phenotypic traits from genome sequencing.

Chen YC, Douville C, Wang C, Niknafs N, Yeo G, Beleva-Guthrie V, Carter H, Stenson PD, Cooper DN, Li B, Mooney S, Karchin R.

PLoS Comput Biol. 2014 Sep 4;10(9):e1003825. doi: 10.1371/journal.pcbi.1003825. eCollection 2014 Sep.

16.

Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks.

Das J, Lee HR, Sagar A, Fragoza R, Liang J, Wei X, Wang X, Mort M, Stenson PD, Cooper DN, Yu H.

Hum Mutat. 2014 May;35(5):585-93. doi: 10.1002/humu.22534. Epub 2014 Apr 7.

17.

Using exome data to identify malignant hyperthermia susceptibility mutations.

Gonsalves SG, Ng D, Johnston JJ, Teer JK, Stenson PD, Cooper DN, Mullikin JC, Biesecker LG; NISC Comparative Sequencing Program.

Anesthesiology. 2013 Nov;119(5):1043-53. doi: 10.1097/ALN.0b013e3182a8a8e7.

18.
19.

Interpreting secondary cardiac disease variants in an exome cohort.

Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, Lewis KL, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG; NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program.

Circ Cardiovasc Genet. 2013 Aug;6(4):337-46. doi: 10.1161/CIRCGENETICS.113.000039. Epub 2013 Jul 16.

20.

Identifying Mendelian disease genes with the variant effect scoring tool.

Carter H, Douville C, Stenson PD, Cooper DN, Karchin R.

BMC Genomics. 2013;14 Suppl 3:S3. doi: 10.1186/1471-2164-14-S3-S3. Epub 2013 May 28.

21.

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures.

Niknafs N, Kim D, Kim R, Diekhans M, Ryan M, Stenson PD, Cooper DN, Karchin R.

Hum Genet. 2013 Nov;132(11):1235-43. doi: 10.1007/s00439-013-1325-0. Epub 2013 Jun 23.

22.

CRAVAT: cancer-related analysis of variants toolkit.

Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R.

Bioinformatics. 2013 Mar 1;29(5):647-8. doi: 10.1093/bioinformatics/btt017. Epub 2013 Jan 16.

23.

Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing.

Xue Y, Chen Y, Ayub Q, Huang N, Ball EV, Mort M, Phillips AD, Shaw K, Stenson PD, Cooper DN, Tyler-Smith C; 1000 Genomes Project Consortium.

Am J Hum Genet. 2012 Dec 7;91(6):1022-32. doi: 10.1016/j.ajhg.2012.10.015.

24.

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models.

Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, Day IN, Gaunt TR.

Hum Mutat. 2013 Jan;34(1):57-65. doi: 10.1002/humu.22225. Epub 2012 Nov 2.

25.

The Human Gene Mutation Database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution.

Stenson PD, Ball EV, Mort M, Phillips AD, Shaw K, Cooper DN.

Curr Protoc Bioinformatics. 2012 Sep;Chapter 1:Unit1.13. doi: 10.1002/0471250953.bi0113s39.

PMID:
22948725
26.

Insights into hominid evolution from the gorilla genome sequence.

Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R.

Nature. 2012 Mar 7;483(7388):169-75. doi: 10.1038/nature10842.

27.

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques.

Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li Q, Li Y, van Gool AJ, Du H, Chen J, Chen R, Zhang P, Huang Z, Thompson JR, Meng Y, Bai Y, Wang J, Zhuo M, Wang T, Huang Y, Wei L, Li J, Wang Z, Hu H, Yang P, Le L, Stenson PD, Li B, Liu X, Ball EV, An N, Huang Q, Zhang Y, Fan W, Zhang X, Li Y, Wang W, Katze MG, Su B, Nielsen R, Yang H, Wang J, Wang X, Wang J.

Nat Biotechnol. 2011 Oct 16;29(11):1019-23. doi: 10.1038/nbt.1992.

PMID:
22002653
28.

Single base-pair substitutions at the translation initiation sites of human genes as a cause of inherited disease.

Wolf A, Caliebe A, Thomas NS, Ball EV, Mort M, Stenson PD, Krawczak M, Cooper DN.

Hum Mutat. 2011 Oct;32(10):1137-43. doi: 10.1002/humu.21547. Epub 2011 Sep 8.

PMID:
21681852
29.

Delineating the Hemostaseome as an aid to individualize the analysis of the hereditary basis of thrombotic and bleeding disorders.

Fechtel K, Osterbur ML, Kehrer-Sawatzki H, Stenson PD, Cooper DN.

Hum Genet. 2011 Jul;130(1):149-66. doi: 10.1007/s00439-011-0984-y. Epub 2011 May 3. Review.

30.

Comparative analysis of germline and somatic microlesion mutational spectra in 17 human tumor suppressor genes.

Ivanov D, Hamby SE, Stenson PD, Phillips AD, Kehrer-Sawatzki H, Cooper DN, Chuzhanova N.

Hum Mutat. 2011 Jun;32(6):620-32. doi: 10.1002/humu.21483. Epub 2011 Mar 22.

PMID:
21432943
31.

Meiotic recombination favors the spreading of deleterious mutations in human populations.

Necşulea A, Popa A, Cooper DN, Stenson PD, Mouchiroud D, Gautier C, Duret L.

Hum Mutat. 2011 Feb;32(2):198-206. doi: 10.1002/humu.21407. Epub 2011 Jan 25.

32.

Prospects for the automated extraction of mutation data from the scientific literature.

Stenson PD, Cooper DN.

Hum Genomics. 2010 Oct;5(1):1-4. No abstract available.

34.

Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics.

Cooper DN, Chen JM, Ball EV, Howells K, Mort M, Phillips AD, Chuzhanova N, Krawczak M, Kehrer-Sawatzki H, Stenson PD.

Hum Mutat. 2010 Jun;31(6):631-55. doi: 10.1002/humu.21260. Review.

PMID:
20506564
35.

Complete ascertainment of intragenic copy number mutations (CNMs) in the CFTR gene and its implications for CNM formation at other autosomal loci.

Quemener S, Chen JM, Chuzhanova N, Bénech C, Casals T, Macek M Jr, Bienvenu T, McDevitt T, Farrell PM, Loumi O, Messaoud T, Cuppens H, Cutting GR, Stenson PD, Giteau K, Audrézet MP, Cooper DN, Férec C.

Hum Mutat. 2010 Apr;31(4):421-8. doi: 10.1002/humu.21196.

36.

The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalized genomics.

Stenson PD, Ball EV, Howells K, Phillips AD, Mort M, Cooper DN.

Hum Genomics. 2009 Dec;4(2):69-72. No abstract available.

37.

The Human Gene Mutation Database: 2008 update.

Stenson PD, Mort M, Ball EV, Howells K, Phillips AD, Thomas NS, Cooper DN.

Genome Med. 2009 Jan 22;1(1):13. doi: 10.1186/gm13.

38.

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties.

Bacolla A, Larson JE, Collins JR, Li J, Milosavljevic A, Stenson PD, Cooper DN, Wells RD.

Genome Res. 2008 Oct;18(10):1545-53. doi: 10.1101/gr.078303.108. Epub 2008 Aug 7.

39.

The Human Gene Mutation Database (HGMD) and its exploitation in the study of mutational mechanisms.

Cooper DN, Stenson PD, Chuzhanova NA.

Curr Protoc Bioinformatics. 2006 Jan;Chapter 1:Unit 1.13. doi: 10.1002/0471250953.bi0113s12.

PMID:
18428754
40.

Human Gene Mutation Database: towards a comprehensive central mutation database.

Stenson PD, Ball E, Howells K, Phillips A, Mort M, Cooper DN.

J Med Genet. 2008 Feb;45(2):124-6. doi: 10.1136/jmg.2007.055210. No abstract available.

PMID:
18245393
41.

Molecular and electronic structures of one-electron oxidized Ni(II)-(dithiosalicylidenediamine) complexes: Ni(III)-thiolate versus Ni(II)-thiyl radical states.

Stenson PA, Board A, Marin-Becerra A, Blake AJ, Davies ES, Wilson C, McMaster J, Schröder M.

Chemistry. 2008;14(8):2564-76. doi: 10.1002/chem.200701108.

PMID:
18213560
42.

A mechanistic study of the dynamic quenching of the excited state of europium(III) and terbium(III) macrocyclic complexes by charge- or electron transfer.

Kielar F, Montgomery CP, New EJ, Parker D, Poole RA, Richardson SL, Stenson PA.

Org Biomol Chem. 2007 Sep 21;5(18):2975-82. Epub 2007 Aug 7.

PMID:
17728864
43.

Evolutionary and biomedical insights from the rhesus macaque genome.

Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS.

Science. 2007 Apr 13;316(5822):222-34.

44.

On the role of the counter-ion in defining water structure and dynamics: order, structure and dynamics in hydrophilic and hydrophobic gadolinium salt complexes.

Thompson AL, Parker D, Fulton DA, Howard JA, Pandya SU, Puschmann H, Senanayake K, Stenson PA, Badari A, Botta M, Avedano S, Aime S.

Dalton Trans. 2006 Dec 21;(47):5605-16. Epub 2006 Aug 25.

PMID:
17225897
45.

A ratiometric and non-enzymatic luminescence assay for uric acid: differential quenching of lanthanide excited states by anti-oxidants.

Poole RA, Kielar F, Richardson SL, Stenson PA, Parker D.

Chem Commun (Camb). 2006 Oct 21;(39):4084-6. Epub 2006 Sep 18. Erratum in: Chem Commun (Camb). 2006 Dec 14;(46):4862.

PMID:
17024256
46.
47.

Azaxanthones and azathioxanthones are effective sensitisers for europium and terbium luminescence.

Atkinson P, Findlay KS, Kielar F, Pal R, Parker D, Poole RA, Puschmann H, Richardson SL, Stenson PA, Thompson AL, Yu J.

Org Biomol Chem. 2006 May 7;4(9):1707-22. Epub 2006 Mar 23. Erratum in: Org Biomol Chem. 2006 Oct 7;4(19):3708.

PMID:
16633563
48.

Formation of [(L)Ni(mu2-S)x{Fe(CO)3}x] adducts (x = 1 or 2): analogues of the active site of [NiFe] hydrogenase.

Stenson PA, Marin-Becerra A, Wilson C, Blake AJ, McMaster J, Schröder M.

Chem Commun (Camb). 2006 Jan 21;(3):317-9. Epub 2005 Nov 24.

PMID:
16391746
49.

Intrachromosomal serial replication slippage in trans gives rise to diverse genomic rearrangements involving inversions.

Chen JM, Chuzhanova N, Stenson PD, Férec C, Cooper DN.

Hum Mutat. 2005 Oct;26(4):362-73.

PMID:
16110485
50.

Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity.

Ball EV, Stenson PD, Abeysinghe SS, Krawczak M, Cooper DN, Chuzhanova NA.

Hum Mutat. 2005 Sep;26(3):205-13.

PMID:
16086312

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