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Items: 1 to 20 of 137

1.

Making sense of big data in health research: Towards an EU action plan.

Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G.

Genome Med. 2016 Jun 23;8(1):71. doi: 10.1186/s13073-016-0323-y.

PMID:
27338147
2.

The Ensembl gene annotation system.

Aken BL, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S, Fernandez Banet J, Billis K, García Girón C, Hourlier T, Howe K, Kähäri A, Kokocinski F, Martin FJ, Murphy DN, Nag R, Ruffier M, Schuster M, Tang YA, Vogel JH, White S, Zadissa A, Flicek P, Searle SM.

Database (Oxford). 2016 Jun 23;2016. pii: baw093. doi: 10.1093/database/baw093. Print 2016.

PMID:
27337980
3.

The Ensembl Variant Effect Predictor.

McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F.

Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4.

4.

Ensembl comparative genomics resources.

Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P.

Database (Oxford). 2016 May 2;2016. pii: baw053. doi: 10.1093/database/baw053. Print 2016. No abstract available.

5.

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.

Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GR, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich Y, Handsaker RE; 1000 Genomes Project Consortium, Bustamante CD, Tyler-Smith C.

Nat Genet. 2016 Jun;48(6):593-9. doi: 10.1038/ng.3559. Epub 2016 Apr 25.

PMID:
27111036
6.

ncRNA orthologies in the vertebrate lineage.

Pignatelli M, Vilella AJ, Muffato M, Gordon L, White S, Flicek P, Herrero J.

Database (Oxford). 2016 Mar 15;2016. pii: bav127. doi: 10.1093/database/bav127. Print 2016.

7.

Divergence in gene expression within and between two closely related flycatcher species.

Uebbing S, Künstner A, Mäkinen H, Backström N, Bolivar P, Burri R, Dutoit L, Mugal CF, Nater A, Aken B, Flicek P, Martin FJ, Searle SM, Ellegren H.

Mol Ecol. 2016 May;25(9):2015-28. doi: 10.1111/mec.13596. Epub 2016 Apr 2.

8.

LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order.

Fontanesi L, Di Palma F, Flicek P, Smith AT, Thulin CG, Alves PC; Lagomorph Genomics Consortium.

J Hered. 2016 Jul;107(4):295-308. doi: 10.1093/jhered/esw010. Epub 2016 Feb 26.

9.

Ensembl comparative genomics resources.

Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P.

Database (Oxford). 2016 Feb 20;2016. pii: bav096. doi: 10.1093/database/bav096. Print 2016. Erratum in: Database (Oxford). 2016;2016. pii: baw053. doi: 10.1093/database/baw053.

10.

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.

11.

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.

12.

Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.

Zepeda-Mendoza CJ, Mukhopadhyay S, Wong ES, Harder N, Splinter E, de Wit E, Eckersley-Maslin MA, Ried T, Eils R, Rohr K, Mills A, de Laat W, Flicek P, Sengupta AM, Spector DL.

BMC Genomics. 2015 Nov 21;16:982. doi: 10.1186/s12864-015-2137-5.

13.

DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control.

Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, Kolarova J, Lu Q, Otto C, Wagener R, Arnolds J, Burkhardt B, Claviez A, Drexler HG, Eberth S, Eils R, Flicek P, Haas S, Hummel M, Karsch D, Kerstens HH, Klapper W, Kreuz M, Lawerenz C, Lenze D, Loeffler M, López C, MacLeod RA, Martens JH, Kulis M, Martín-Subero JI, Möller P, Nagel I, Picelli S, Vater I, Rohde M, Rosenstiel P, Rosolowski M, Russell RB, Schilhabel M, Schlesner M, Stadler PF, Szczepanowski M, Trümper L, Stunnenberg HG; ICGC MMML-Seq project; BLUEPRINT project, Küppers R, Ammerpohl O, Lichter P, Siebert R, Hoffmann S, Radlwimmer B.

Nat Genet. 2015 Nov;47(11):1316-25. doi: 10.1038/ng.3413. Epub 2015 Oct 5.

PMID:
26437030
14.

An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.

Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.

15.

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.

Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC, Odom DT.

PLoS One. 2015 Sep 4;10(9):e0137367. doi: 10.1371/journal.pone.0137367. eCollection 2015.

16.

Third Report on Chicken Genes and Chromosomes 2015.

Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RP, Damas J, Davis RV, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MA, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JM, Wragg D, Zhou H.

Cytogenet Genome Res. 2015;145(2):78-179. doi: 10.1159/000430927. Epub 2015 Jul 14. No abstract available.

PMID:
26282327
17.

Epigenome data release: a participant-centered approach to privacy protection.

Dyke SO, Cheung WA, Joly Y, Ammerpohl O, Lutsik P, Rothstein MA, Caron M, Busche S, Bourque G, Rönnblom L, Flicek P, Beck S, Hirst M, Stunnenberg H, Siebert R, Walter J, Pastinen T.

Genome Biol. 2015 Jul 17;16:142. doi: 10.1186/s13059-015-0723-0.

18.

The European Genome-phenome Archive of human data consented for biomedical research.

Lappalainen I, Almeida-King J, Kumanduri V, Senf A, Spalding JD, Ur-Rehman S, Saunders G, Kandasamy J, Caccamo M, Leinonen R, Vaughan B, Laurent T, Rowland F, Marin-Garcia P, Barker J, Jokinen P, Torres AC, de Argila JR, Llobet OM, Medina I, Puy MS, Alberich M, de la Torre S, Navarro A, Paschall J, Flicek P.

Nat Genet. 2015 Jul;47(7):692-5. doi: 10.1038/ng.3312. No abstract available.

PMID:
26111507
19.

Whole-genome fingerprint of the DNA methylome during human B cell differentiation.

Kulis M, Merkel A, Heath S, Queirós AC, Schuyler RP, Castellano G, Beekman R, Raineri E, Esteve A, Clot G, Verdaguer-Dot N, Duran-Ferrer M, Russiñol N, Vilarrasa-Blasi R, Ecker S, Pancaldi V, Rico D, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, Pascual M, Agirre X, Prosper F, Alignani D, Paiva B, Caron G, Fest T, Muench MO, Fomin ME, Lee ST, Wiemels JL, Valencia A, Gut M, Flicek P, Stunnenberg HG, Siebert R, Küppers R, Gut IG, Campo E, Martín-Subero JI.

Nat Genet. 2015 Jul;47(7):746-56. doi: 10.1038/ng.3291. Epub 2015 Jun 8.

PMID:
26053498
20.

Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.

Benjelloun B, Alberto FJ, Streeter I, Boyer F, Coissac E, Stucki S, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Leempoel K, Alberti A, Engelen S, Chikhi A, Clarke L, Flicek P, Joost S, Taberlet P, Pompanon F; NextGen Consortium.

Front Genet. 2015 Apr 7;6:107. doi: 10.3389/fgene.2015.00107. eCollection 2015.

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