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Items: 24

1.

An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome.

Ferlaino M, Rogers MF, Shihab HA, Mort M, Cooper DN, Gaunt TR, Campbell C.

BMC Bioinformatics. 2017 Oct 6;18(1):442. doi: 10.1186/s12859-017-1862-y.

2.

FATHMM-XF: accurate prediction of pathogenic point mutations via extended features.

Rogers MF, Shihab HA, Mort M, Cooper DN, Gaunt TR, Campbell C.

Bioinformatics. 2018 Feb 1;34(3):511-513. doi: 10.1093/bioinformatics/btx536.

3.

CScape: a tool for predicting oncogenic single-point mutations in the cancer genome.

Rogers MF, Shihab HA, Gaunt TR, Campbell C.

Sci Rep. 2017 Sep 14;7(1):11597. doi: 10.1038/s41598-017-11746-4.

4.

Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.

Tachmazidou I, Süveges D, Min JL, Ritchie GRS, Steinberg J, Walter K, Iotchkova V, Schwartzentruber J, Huang J, Memari Y, McCarthy S, Crawford AA, Bombieri C, Cocca M, Farmaki AE, Gaunt TR, Jousilahti P, Kooijman MN, Lehne B, Malerba G, Männistö S, Matchan A, Medina-Gomez C, Metrustry SJ, Nag A, Ntalla I, Paternoster L, Rayner NW, Sala C, Scott WR, Shihab HA, Southam L, St Pourcain B, Traglia M, Trajanoska K, Zaza G, Zhang W, Artigas MS, Bansal N, Benn M, Chen Z, Danecek P, Lin WY, Locke A, Luan J, Manning AK, Mulas A, Sidore C, Tybjaerg-Hansen A, Varbo A, Zoledziewska M, Finan C, Hatzikotoulas K, Hendricks AE, Kemp JP, Moayyeri A, Panoutsopoulou K, Szpak M, Wilson SG, Boehnke M, Cucca F, Di Angelantonio E, Langenberg C, Lindgren C, McCarthy MI, Morris AP, Nordestgaard BG, Scott RA, Tobin MD, Wareham NJ; SpiroMeta Consortium; GoT2D Consortium, Burton P, Chambers JC, Smith GD, Dedoussis G, Felix JF, Franco OH, Gambaro G, Gasparini P, Hammond CJ, Hofman A, Jaddoe VWV, Kleber M, Kooner JS, Perola M, Relton C, Ring SM, Rivadeneira F, Salomaa V, Spector TD, Stegle O, Toniolo D, Uitterlinden AG; arcOGEN Consortium; Understanding Society Scientific Group; UK10K Consortium, Barroso I, Greenwood CMT, Perry JRB, Walker BR, Butterworth AS, Xue Y, Durbin R, Small KS, Soranzo N, Timpson NJ, Zeggini E.

Am J Hum Genet. 2017 Jun 1;100(6):865-884. doi: 10.1016/j.ajhg.2017.04.014. Epub 2017 May 25.

5.

Predicting the Pathogenic Impact of Sequence Variation in the Human Genome.

Rogers MF, Shihab HA, Ferlaino M, Gaunt TR, Campbell C.

Stud Health Technol Inform. 2017;235:91-95.

PMID:
28423762
6.

Role of DNA Methylation in Type 2 Diabetes Etiology: Using Genotype as a Causal Anchor.

Elliott HR, Shihab HA, Lockett GA, Holloway JW, McRae AF, Smith GD, Ring SM, Gaunt TR, Relton CL.

Diabetes. 2017 Jun;66(6):1713-1722. doi: 10.2337/db16-0874. Epub 2017 Feb 28.

7.

HIPred: an integrative approach to predicting haploinsufficient genes.

Shihab HA, Rogers MF, Campbell C, Gaunt TR.

Bioinformatics. 2017 Jun 15;33(12):1751-1757. doi: 10.1093/bioinformatics/btx028.

8.

GTB - an online genome tolerance browser.

Shihab HA, Rogers MF, Ferlaino M, Campbell C, Gaunt TR.

BMC Bioinformatics. 2017 Jan 6;18(1):20. doi: 10.1186/s12859-016-1436-4.

9.

Collapsed methylation quantitative trait loci analysis for low frequency and rare variants.

Richardson TG, Shihab HA, Hemani G, Zheng J, Hannon E, Mill J, Carnero-Montoro E, Bell JT, Lyttleton O, McArdle WL, Ring SM, Rodriguez S, Campbell C, Smith GD, Relton CL, Timpson NJ, Gaunt TR.

Hum Mol Genet. 2016 Oct 1;25(19):4339-4349. doi: 10.1093/hmg/ddw283. Epub 2016 Aug 24.

10.

Frequency of KLK3 gene deletions in the general population.

Rodriguez S, Al-Ghamdi OA, Guthrie PA, Shihab HA, McArdle W, Gaunt T, Alharbi KK, Day IN.

Ann Clin Biochem. 2017 Jul;54(4):472-480. doi: 10.1177/0004563216666999. Epub 2016 Aug 23.

PMID:
27555663
11.

A Protein Domain and Family Based Approach to Rare Variant Association Analysis.

Richardson TG, Shihab HA, Rivas MA, McCarthy MI, Campbell C, Timpson NJ, Gaunt TR.

PLoS One. 2016 Apr 29;11(4):e0153803. doi: 10.1371/journal.pone.0153803. eCollection 2016.

12.

Systematic identification of genetic influences on methylation across the human life course.

Gaunt TR, Shihab HA, Hemani G, Min JL, Woodward G, Lyttleton O, Zheng J, Duggirala A, McArdle WL, Ho K, Ring SM, Evans DM, Davey Smith G, Relton CL.

Genome Biol. 2016 Mar 31;17:61. doi: 10.1186/s13059-016-0926-z.

13.

Importance of Genetic Studies in Consanguineous Populations for the Characterization of Novel Human Gene Functions.

Erzurumluoglu AM, Shihab HA, Rodriguez S, Gaunt TR, Day IN.

Ann Hum Genet. 2016 May;80(3):187-96. doi: 10.1111/ahg.12150. Epub 2016 Mar 22. Review.

14.

Identifying Highly Penetrant Disease Causal Mutations Using Next Generation Sequencing: Guide to Whole Process.

Erzurumluoglu AM, Rodriguez S, Shihab HA, Baird D, Richardson TG, Day IN, Gaunt TR.

Biomed Res Int. 2015;2015:923491. doi: 10.1155/2015/923491. Epub 2015 Apr 6. Review.

15.

Copy number variations and cognitive phenotypes in unselected populations.

Männik K, Mägi R, Macé A, Cole B, Guyatt AL, Shihab HA, Maillard AM, Alavere H, Kolk A, Reigo A, Mihailov E, Leitsalu L, Ferreira AM, Nõukas M, Teumer A, Salvi E, Cusi D, McGue M, Iacono WG, Gaunt TR, Beckmann JS, Jacquemont S, Kutalik Z, Pankratz N, Timpson N, Metspalu A, Reymond A.

JAMA. 2015 May 26;313(20):2044-54. doi: 10.1001/jama.2015.4845.

16.

Erratum: Whole-genome sequence-based analysis of thyroid function.

Taylor PN, Porcu E, Chew S, Campbell PJ, Traglia M, Brown SJ, Mullin BH, Shihab HA, Min J, Walter K, Memari Y, Huang J, Barnes MR, Beilby JP, Charoen P, Danecek P, Dudbridge F, Forgetta V, Greenwood C, Grundberg E, Johnson AD, Hui J, Lim EM, McCarthy S, Muddyman D, Panicker V, Perry JR, Bell JT, Yuan W, Relton C, Gaunt T, Schlessinger D, Abecasis G, Cucca F, Surdulescu GL, Woltersdorf W, Zeggini E, Zheng HF, Toniolo D, Dayan CM, Naitza S, Walsh JP, Spector T, Smith GD, Durbin R, Richards JB, Sanna S, Soranzo N, Timpson NJ, Wilson SG; UK10K Consortium.

Nat Commun. 2015 May 20;6:7172. doi: 10.1038/ncomms8172. No abstract available.

17.

Maternal pre-pregnancy BMI and gestational weight gain, offspring DNA methylation and later offspring adiposity: findings from the Avon Longitudinal Study of Parents and Children.

Sharp GC, Lawlor DA, Richmond RC, Fraser A, Simpkin A, Suderman M, Shihab HA, Lyttleton O, McArdle W, Ring SM, Gaunt TR, Davey Smith G, Relton CL.

Int J Epidemiol. 2015 Aug;44(4):1288-304. doi: 10.1093/ije/dyv042. Epub 2015 Apr 8.

18.

Whole-genome sequence-based analysis of thyroid function.

Taylor PN, Porcu E, Chew S, Campbell PJ, Traglia M, Brown SJ, Mullin BH, Shihab HA, Min J, Walter K, Memari Y, Huang J, Barnes MR, Beilby JP, Charoen P, Danecek P, Dudbridge F, Forgetta V, Greenwood C, Grundberg E, Johnson AD, Hui J, Lim EM, McCarthy S, Muddyman D, Panicker V, Perry JR, Bell JT, Yuan W, Relton C, Gaunt T, Schlessinger D, Abecasis G, Cucca F, Surdulescu GL, Woltersdorf W, Zeggini E, Zheng HF, Toniolo D, Dayan CM, Naitza S, Walsh JP, Spector T, Davey Smith G, Durbin R, Richards JB, Sanna S, Soranzo N, Timpson NJ, Wilson SG; UK0K Consortium.

Nat Commun. 2015 Mar 6;6:5681. doi: 10.1038/ncomms6681. Erratum in: Nat Commun. 2015;6:7172. Lotchkova, Valentina [corrected to Iotchkova, Valentina]; Quai, Michael A [corrected to Quail, Michael].

19.

Mosaic structural variation in children with developmental disorders.

King DA, Jones WD, Crow YJ, Dominiczak AF, Foster NA, Gaunt TR, Harris J, Hellens SW, Homfray T, Innes J, Jones EA, Joss S, Kulkarni A, Mansour S, Morris AD, Parker MJ, Porteous DJ, Shihab HA, Smith BH, Tatton-Brown K, Tolmie JL, Trzaskowski M, Vasudevan PC, Wakeling E, Wright M, Plomin R, Timpson NJ, Hurles ME; Deciphering Developmental Disorders Study.

Hum Mol Genet. 2015 May 15;24(10):2733-45. doi: 10.1093/hmg/ddv033. Epub 2015 Jan 29.

20.

An integrative approach to predicting the functional effects of non-coding and coding sequence variation.

Shihab HA, Rogers MF, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR, Campbell C.

Bioinformatics. 2015 May 15;31(10):1536-43. doi: 10.1093/bioinformatics/btv009. Epub 2015 Jan 11.

21.

EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization.

Rackham OJ, Shihab HA, Johnson MR, Petretto E.

Nucleic Acids Res. 2015 Mar 11;43(5):e33. doi: 10.1093/nar/gku1322. Epub 2014 Dec 29.

22.

Ranking non-synonymous single nucleotide polymorphisms based on disease concepts.

Shihab HA, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR.

Hum Genomics. 2014 Jun 30;8:11. doi: 10.1186/1479-7364-8-11.

23.

Predicting the functional consequences of cancer-associated amino acid substitutions.

Shihab HA, Gough J, Cooper DN, Day IN, Gaunt TR.

Bioinformatics. 2013 Jun 15;29(12):1504-10. doi: 10.1093/bioinformatics/btt182. Epub 2013 Apr 25.

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.

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