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Items: 1 to 20 of 223

1.

Epigenome-wide Association Studies and the Interpretation of Disease -Omics.

Birney E, Smith GD, Greally JM.

PLoS Genet. 2016 Jun 23;12(6):e1006105. doi: 10.1371/journal.pgen.1006105. eCollection 2016 Jun. Review.

2.

The topography of mutational processes in breast cancer genomes.

Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H, Staaf J, Sieuwerts AM, Brinkman AB, Martin S, Ramakrishna M, Butler A, Kim HY, Borg Å, Sotiriou C, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Sale J, Rada C, Stratton MR, Birney E, Nik-Zainal S.

Nat Commun. 2016 May 2;7:11383. doi: 10.1038/ncomms11383.

PMID:
27136393
3.

Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GK, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van't Veer L, Tutt A, Knappskog S, Tan BK, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR.

Nature. 2016 May 2;534(7605):47-54. doi: 10.1038/nature17676.

PMID:
27135926
4.

The EMBL-EBI channel.

McEntyre J, Birney E.

F1000Res. 2016 Jan 12;5:52. doi: 10.12688/f1000research.7764.1. eCollection 2016.

5.

Ensembl regulation resources.

Zerbino DR, Johnson N, Juetteman T, Sheppard D, Wilder SP, Lavidas I, Nuhn M, Perry E, Raffaillac-Desfosses Q, Sobral D, Keefe D, Gräf S, Ahmed I, Kinsella R, Pritchard B, Brent S, Amode R, Parker A, Trevanion S, Birney E, Dunham I, Flicek P.

Database (Oxford). 2016 Feb 17;2016. pii: bav119. doi: 10.1093/database/bav119. Print 2016.

6.

MinION Analysis and Reference Consortium: Phase 1 data release and analysis.

Ip CL, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, Simpson JT, Snutch TP, Birney E, Buck D, Goodwin S, Jansen HJ, O'Grady J, Olsen HE; MinION Analysis and Reference Consortium.

F1000Res. 2015 Oct 15;4:1075. doi: 10.12688/f1000research.7201.1. eCollection 2015.

7.

Progress in Medicine: Experts Take Stock.

PLOS Medicine Editors, Beck A, Birney E, Graeber M, Tumwine J, Hay P, Ahn HS, Patel A, du Cros P, von Seidlein L, Wareham N, Low N.

PLoS Med. 2015 Dec 29;12(12):e1001933. doi: 10.1371/journal.pmed.1001933. eCollection 2015 Dec.

8.

Ensembl 2016.

Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, Flicek P.

Nucleic Acids Res. 2016 Jan 4;44(D1):D710-6. doi: 10.1093/nar/gkv1157. Epub 2015 Dec 19.

9.

The European Bioinformatics Institute in 2016: Data growth and integration.

Cook CE, Bergman MT, Finn RD, Cochrane G, Birney E, Apweiler R.

Nucleic Acids Res. 2016 Jan 4;44(D1):D20-6. doi: 10.1093/nar/gkv1352. Epub 2015 Dec 15.

10.

Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.

Gaulton KJ, Ferreira T, Lee Y, Raimondo A, Mägi R, Reschen ME, Mahajan A, Locke A, Rayner NW, Robertson N, Scott RA, Prokopenko I, Scott LJ, Green T, Sparso T, Thuillier D, Yengo L, Grallert H, Wahl S, Frånberg M, Strawbridge RJ, Kestler H, Chheda H, Eisele L, Gustafsson S, Steinthorsdottir V, Thorleifsson G, Qi L, Karssen LC, van Leeuwen EM, Willems SM, Li M, Chen H, Fuchsberger C, Kwan P, Ma C, Linderman M, Lu Y, Thomsen SK, Rundle JK, Beer NL, van de Bunt M, Chalisey A, Kang HM, Voight BF, Abecasis GR, Almgren P, Baldassarre D, Balkau B, Benediktsson R, Blüher M, Boeing H, Bonnycastle LL, Bottinger EP, Burtt NP, Carey J, Charpentier G, Chines PS, Cornelis MC, Couper DJ, Crenshaw AT, van Dam RM, Doney AS, Dorkhan M, Edkins S, Eriksson JG, Esko T, Eury E, Fadista J, Flannick J, Fontanillas P, Fox C, Franks PW, Gertow K, Gieger C, Gigante B, Gottesman O, Grant GB, Grarup N, Groves CJ, Hassinen M, Have CT, Herder C, Holmen OL, Hreidarsson AB, Humphries SE, Hunter DJ, Jackson AU, Jonsson A, Jørgensen ME, Jørgensen T, Kao WH, Kerrison ND, Kinnunen L, Klopp N, Kong A, Kovacs P, Kraft P, Kravic J, Langford C, Leander K, Liang L, Lichtner P, Lindgren CM, Lindholm E, Linneberg A, Liu CT, Lobbens S, Luan J, Lyssenko V, Männistö S, McLeod O, Meyer J, Mihailov E, Mirza G, Mühleisen TW, Müller-Nurasyid M, Navarro C, Nöthen MM, Oskolkov NN, Owen KR, Palli D, Pechlivanis S, Peltonen L, Perry JR, Platou CG, Roden M, Ruderfer D, Rybin D, van der Schouw YT, Sennblad B, Sigurðsson G, Stančáková A, Steinbach G, Storm P, Strauch K, Stringham HM, Sun Q, Thorand B, Tikkanen E, Tonjes A, Trakalo J, Tremoli E, Tuomi T, Wennauer R, Wiltshire S, Wood AR, Zeggini E, Dunham I, Birney E, Pasquali L, Ferrer J, Loos RJ, Dupuis J, Florez JC, Boerwinkle E, Pankow JS, van Duijn C, Sijbrands E, Meigs JB, Hu FB, Thorsteinsdottir U, Stefansson K, Lakka TA, Rauramaa R, Stumvoll M, Pedersen NL, Lind L, Keinanen-Kiukaanniemi SM, Korpi-Hyövälti E, Saaristo TE, Saltevo J, Kuusisto J, Laakso M, Metspalu A, Erbel R, Jöcke KH, Moebus S, Ripatti S, Salomaa V, Ingelsson E, Boehm BO, Bergman RN, Collins FS, Mohlke KL, Koistinen H, Tuomilehto J, Hveem K, Njølstad I, Deloukas P, Donnelly PJ, Frayling TM, Hattersley AT, de Faire U, Hamsten A, Illig T, Peters A, Cauchi S, Sladek R, Froguel P, Hansen T, Pedersen O, Morris AD, Palmer CN, Kathiresan S, Melander O, Nilsson PM, Groop LC, Barroso I, Langenberg C, Wareham NJ, O'Callaghan CA, Gloyn AL, Altshuler D, Boehnke M, Teslovich TM, McCarthy MI, Morris AP; DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium.

Nat Genet. 2015 Dec;47(12):1415-25. doi: 10.1038/ng.3437. Epub 2015 Nov 9.

11.

Human genomics: The end of the start for population sequencing.

Birney E, Soranzo N.

Nature. 2015 Oct 1;526(7571):52-3. doi: 10.1038/526052a. No abstract available.

PMID:
26432243
12.

Using human genetics to make new medicines.

Barrett JC, Dunham I, Birney E.

Nat Rev Genet. 2015 Oct;16(10):561-2. doi: 10.1038/nrg3998. Epub 2015 Sep 15. Review.

PMID:
26370900
13.

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.

Huang J, Howie B, McCarthy S, Memari Y, Walter K, Min JL, Danecek P, Malerba G, Trabetti E, Zheng HF; UK10K Consortium, Gambaro G, Richards JB, Durbin R, Timpson NJ, Marchini J, Soranzo N.

Nat Commun. 2015 Sep 14;6:8111. doi: 10.1038/ncomms9111.

14.

The UK10K project identifies rare variants in health and disease.

UK10K Consortium, Walter K, Min JL, Huang J, Crooks L, Memari Y, McCarthy S, Perry JR, Xu C, Futema M, Lawson D, Iotchkova V, Schiffels S, Hendricks AE, Danecek P, Li R, Floyd J, Wain LV, Barroso I, Humphries SE, Hurles ME, Zeggini E, Barrett JC, Plagnol V, Richards JB, Greenwood CM, Timpson NJ, Durbin R, Soranzo N.

Nature. 2015 Oct 1;526(7571):82-90. doi: 10.1038/nature14962. Epub 2015 Sep 14.

15.

Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E.

PLoS Genet. 2015 Apr 28;11(4):e1005177. doi: 10.1371/journal.pgen.1005177. eCollection 2015 Apr.

16.

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].

17.

Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E.

PLoS Genet. 2014 Nov 20;10(11):e1004798. doi: 10.1371/journal.pgen.1004798. eCollection 2014 Nov. Erratum in: PLoS Genet. 2015 Apr;11(4):e1005177.

18.

Ensembl 2015.

Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SM, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P.

Nucleic Acids Res. 2015 Jan;43(Database issue):D662-9. doi: 10.1093/nar/gku1010. Epub 2014 Oct 28.

19.

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3366. No abstract available.

20.

A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans.

Timpson NJ, Walter K, Min JL, Tachmazidou I, Malerba G, Shin SY, Chen L, Futema M, Southam L, Iotchkova V, Cocca M, Huang J, Memari Y, McCarthy S, Danecek P, Muddyman D, Mangino M, Menni C, Perry JR, Ring SM, Gaye A, Dedoussis G, Farmaki AE, Burton P, Talmud PJ, Gambaro G, Spector TD, Smith GD, Durbin R, Richards JB, Humphries SE, Zeggini E, Soranzo N; UK1OK Consortium Members; UK1OK Consortium Members.

Nat Commun. 2014 Sep 16;5:4871. doi: 10.1038/ncomms5871. Erratum in: Nat Commun. 2015;6:7171.

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