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Items: 36

1.

The UK Biobank resource with deep phenotyping and genomic data.

Bycroft C, Freeman C, Petkova D, Band G, Elliott LT, Sharp K, Motyer A, Vukcevic D, Delaneau O, O'Connell J, Cortes A, Welsh S, Young A, Effingham M, McVean G, Leslie S, Allen N, Donnelly P, Marchini J.

Nature. 2018 Oct;562(7726):203-209. doi: 10.1038/s41586-018-0579-z. Epub 2018 Oct 10.

PMID:
30305743
2.

The effect of genetic variation on promoter usage and enhancer activity.

Garieri M, Delaneau O, Santoni F, Fish RJ, Mull D, Carninci P, Dermitzakis ET, Antonarakis SE, Fort A.

Nat Commun. 2017 Nov 7;8(1):1358. doi: 10.1038/s41467-017-01467-7.

3.

Estimating the causal tissues for complex traits and diseases.

Ongen H, Brown AA, Delaneau O, Panousis NI, Nica AC; GTEx Consortium, Dermitzakis ET.

Nat Genet. 2017 Dec;49(12):1676-1683. doi: 10.1038/ng.3981. Epub 2017 Oct 23.

PMID:
29058715
4.

Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues.

Brown AA, Viñuela A, Delaneau O, Spector TD, Small KS, Dermitzakis ET.

Nat Genet. 2017 Dec;49(12):1747-1751. doi: 10.1038/ng.3979. Epub 2017 Oct 23.

PMID:
29058714
5.

A complete tool set for molecular QTL discovery and analysis.

Delaneau O, Ongen H, Brown AA, Fort A, Panousis NI, Dermitzakis ET.

Nat Commun. 2017 May 18;8:15452. doi: 10.1038/ncomms15452.

6.

MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets.

Fort A, Panousis NI, Garieri M, Antonarakis SE, Lappalainen T, Dermitzakis ET, Delaneau O.

Bioinformatics. 2017 Jun 15;33(12):1895-1897. doi: 10.1093/bioinformatics/btx074.

7.

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.

Astle WJ, Elding H, Jiang T, Allen D, Ruklisa D, Mann AL, Mead D, Bouman H, Riveros-Mckay F, Kostadima MA, Lambourne JJ, Sivapalaratnam S, Downes K, Kundu K, Bomba L, Berentsen K, Bradley JR, Daugherty LC, Delaneau O, Freson K, Garner SF, Grassi L, Guerrero J, Haimel M, Janssen-Megens EM, Kaan A, Kamat M, Kim B, Mandoli A, Marchini J, Martens JHA, Meacham S, Megy K, O'Connell J, Petersen R, Sharifi N, Sheard SM, Staley JR, Tuna S, van der Ent M, Walter K, Wang SY, Wheeler E, Wilder SP, Iotchkova V, Moore C, Sambrook J, Stunnenberg HG, Di Angelantonio E, Kaptoge S, Kuijpers TW, Carrillo-de-Santa-Pau E, Juan D, Rico D, Valencia A, Chen L, Ge B, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yang Y, Guigo R, Beck S, Paul DS, Pastinen T, Bujold D, Bourque G, Frontini M, Danesh J, Roberts DJ, Ouwehand WH, Butterworth AS, Soranzo N.

Cell. 2016 Nov 17;167(5):1415-1429.e19. doi: 10.1016/j.cell.2016.10.042.

8.

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.

Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N.

Cell. 2016 Nov 17;167(5):1398-1414.e24. doi: 10.1016/j.cell.2016.10.026.

9.

A reference panel of 64,976 haplotypes for genotype imputation.

McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A, Kang HM, Fuchsberger C, Danecek P, Sharp K, Luo Y, Sidore C, Kwong A, Timpson N, Koskinen S, Vrieze S, Scott LJ, Zhang H, Mahajan A, Veldink J, Peters U, Pato C, van Duijn CM, Gillies CE, Gandin I, Mezzavilla M, Gilly A, Cocca M, Traglia M, Angius A, Barrett JC, Boomsma D, Branham K, Breen G, Brummett CM, Busonero F, Campbell H, Chan A, Chen S, Chew E, Collins FS, Corbin LJ, Smith GD, Dedoussis G, Dorr M, Farmaki AE, Ferrucci L, Forer L, Fraser RM, Gabriel S, Levy S, Groop L, Harrison T, Hattersley A, Holmen OL, Hveem K, Kretzler M, Lee JC, McGue M, Meitinger T, Melzer D, Min JL, Mohlke KL, Vincent JB, Nauck M, Nickerson D, Palotie A, Pato M, Pirastu N, McInnis M, Richards JB, Sala C, Salomaa V, Schlessinger D, Schoenherr S, Slagboom PE, Small K, Spector T, Stambolian D, Tuke M, Tuomilehto J, Van den Berg LH, Van Rheenen W, Volker U, Wijmenga C, Toniolo D, Zeggini E, Gasparini P, Sampson MG, Wilson JF, Frayling T, de Bakker PI, Swertz MA, McCarroll S, Kooperberg C, Dekker A, Altshuler D, Willer C, Iacono W, Ripatti S, Soranzo N, Walter K, Swaroop A, Cucca F, Anderson CA, Myers RM, Boehnke M, McCarthy MI, Durbin R; Haplotype Reference Consortium.

Nat Genet. 2016 Oct;48(10):1279-83. doi: 10.1038/ng.3643. Epub 2016 Aug 22.

10.

Haplotype estimation for biobank-scale data sets.

O'Connell J, Sharp K, Shrine N, Wain L, Hall I, Tobin M, Zagury JF, Delaneau O, Marchini J.

Nat Genet. 2016 Jul;48(7):817-20. doi: 10.1038/ng.3583. Epub 2016 Jun 6.

11.

Phasing for medical sequencing using rare variants and large haplotype reference panels.

Sharp K, Kretzschmar W, Delaneau O, Marchini J.

Bioinformatics. 2016 Jul 1;32(13):1974-80. doi: 10.1093/bioinformatics/btw065. Epub 2016 Feb 27.

12.

Fast and efficient QTL mapper for thousands of molecular phenotypes.

Ongen H, Buil A, Brown AA, Dermitzakis ET, Delaneau O.

Bioinformatics. 2016 May 15;32(10):1479-85. doi: 10.1093/bioinformatics/btv722. Epub 2015 Dec 26.

13.

Novel insights into the genetics of smoking behaviour, lung function, and chronic obstructive pulmonary disease (UK BiLEVE): a genetic association study in UK Biobank.

Wain LV, Shrine N, Miller S, Jackson VE, Ntalla I, Soler Artigas M, Billington CK, Kheirallah AK, Allen R, Cook JP, Probert K, Obeidat M, Bossé Y, Hao K, Postma DS, Paré PD, Ramasamy A; UK Brain Expression Consortium (UKBEC), Mägi R, Mihailov E, Reinmaa E, Melén E, O'Connell J, Frangou E, Delaneau O; OxGSK Consortium, Freeman C, Petkova D, McCarthy M, Sayers I, Deloukas P, Hubbard R, Pavord I, Hansell AL, Thomson NC, Zeggini E, Morris AP, Marchini J, Strachan DP, Tobin MD, Hall IP.

Lancet Respir Med. 2015 Oct;3(10):769-81. doi: 10.1016/S2213-2600(15)00283-0. Epub 2015 Sep 27. Erratum in: Lancet Respir Med. 2016 Jan;4(1):e4.

14.

Identification of Genes Whose Expression Profile Is Associated with Non-Progression towards AIDS Using eQTLs.

Spadoni JL, Rucart P, Le Clerc S, van Manen D, Coulonges C, Ulveling D, Laville V, Labib T, Taing L, Delaneau O, Montes M, Schuitemaker H, Noirel J, Zagury JF.

PLoS One. 2015 Sep 14;10(9):e0136989. doi: 10.1371/journal.pone.0136989. eCollection 2015.

15.

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans.

Waszak SM, Delaneau O, Gschwind AR, Kilpinen H, Raghav SK, Witwicki RM, Orioli A, Wiederkehr M, Panousis NI, Yurovsky A, Romano-Palumbo L, Planchon A, Bielser D, Padioleau I, Udin G, Thurnheer S, Hacker D, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET.

Cell. 2015 Aug 27;162(5):1039-50. doi: 10.1016/j.cell.2015.08.001. Epub 2015 Aug 20.

16.

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.

17.

Biased allelic expression in human primary fibroblast single cells.

Borel C, Ferreira PG, Santoni F, Delaneau O, Fort A, Popadin KY, Garieri M, Falconnet E, Ribaux P, Guipponi M, Padioleau I, Carninci P, Dermitzakis ET, Antonarakis SE.

Am J Hum Genet. 2015 Jan 8;96(1):70-80. doi: 10.1016/j.ajhg.2014.12.001. Epub 2014 Dec 31.

18.

Evidence after imputation for a role of MICA variants in nonprogression and elite control of HIV type 1 infection.

Le Clerc S, Delaneau O, Coulonges C, Spadoni JL, Labib T, Laville V, Ulveling D, Noirel J, Montes M, Schächter F, Caillat-Zucman S, Zagury JF.

J Infect Dis. 2014 Dec 15;210(12):1946-50. doi: 10.1093/infdis/jiu342. Epub 2014 Jun 16.

PMID:
24939907
19.

A general approach for haplotype phasing across the full spectrum of relatedness.

O'Connell J, Gurdasani D, Delaneau O, Pirastu N, Ulivi S, Cocca M, Traglia M, Huang J, Huffman JE, Rudan I, McQuillan R, Fraser RM, Campbell H, Polasek O, Asiki G, Ekoru K, Hayward C, Wright AF, Vitart V, Navarro P, Zagury JF, Wilson JF, Toniolo D, Gasparini P, Soranzo N, Sandhu MS, Marchini J.

PLoS Genet. 2014 Apr 17;10(4):e1004234. doi: 10.1371/journal.pgen.1004234. eCollection 2014 Apr.

20.

Haplotype estimation using sequencing reads.

Delaneau O, Howie B, Cox AJ, Zagury JF, Marchini J.

Am J Hum Genet. 2013 Oct 3;93(4):687-96. doi: 10.1016/j.ajhg.2013.09.002.

21.

Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls.

McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, Carrington M, Cossarizza A, Dalmau J, Deeks SG, Delaneau O, De Luca A, Goedert JJ, Haas D, Herbeck JT, Kathiresan S, Kirk GD, Lambotte O, Luo M, Mallal S, van Manen D, Martinez-Picado J, Meyer L, Miro JM, Mullins JI, Obel N, O'Brien SJ, Pereyra F, Plummer FA, Poli G, Qi Y, Rucart P, Sandhu MS, Shea PR, Schuitemaker H, Theodorou I, Vannberg F, Veldink J, Walker BD, Weintrob A, Winkler CA, Wolinsky S, Telenti A, Goldstein DB, de Bakker PI, Zagury JF, Fellay J.

PLoS Pathog. 2013;9(7):e1003515. doi: 10.1371/journal.ppat.1003515. Epub 2013 Jul 25.

22.

Improved whole-chromosome phasing for disease and population genetic studies.

Delaneau O, Zagury JF, Marchini J.

Nat Methods. 2013 Jan;10(1):5-6. doi: 10.1038/nmeth.2307. No abstract available.

PMID:
23269371
23.

A genome-wide association study in Caucasian women points out a putative role of the STXBP5L gene in facial photoaging.

Le Clerc S, Taing L, Ezzedine K, Latreille J, Delaneau O, Labib T, Coulonges C, Bernard A, Melak S, Carpentier W, Malvy D, Jdid R, Galan P, Hercberg S, Morizot F, Guinot C, Tschachler E, Zagury JF.

J Invest Dermatol. 2013 Apr;133(4):929-35. doi: 10.1038/jid.2012.458. Epub 2012 Dec 6.

24.

Haplotype inference.

Delaneau O, Zagury JF.

Methods Mol Biol. 2012;888:177-96. doi: 10.1007/978-1-61779-870-2_11.

PMID:
22665282
25.

Multicohort genomewide association study reveals a new signal of protection against HIV-1 acquisition.

Limou S, Delaneau O, van Manen D, An P, Sezgin E, Le Clerc S, Coulonges C, Troyer JL, Veldink JH, van den Berg LH, Spadoni JL, Taing L, Labib T, Montes M, Delfraissy JF, Schachter F, O'Brien SJ, Buchbinder S, van Natta ML, Jabs DA, Froguel P, Schuitemaker H, Winkler CA, Zagury JF.

J Infect Dis. 2012 Apr 1;205(7):1155-62. doi: 10.1093/infdis/jis028. Epub 2012 Feb 23.

26.

A linear complexity phasing method for thousands of genomes.

Delaneau O, Marchini J, Zagury JF.

Nat Methods. 2011 Dec 4;9(2):179-81. doi: 10.1038/nmeth.1785.

PMID:
22138821
27.

Genome-wide association scan in HIV-1-infected individuals identifying variants influencing disease course.

van Manen D, Delaneau O, Kootstra NA, Boeser-Nunnink BD, Limou S, Bol SM, Burger JA, Zwinderman AH, Moerland PD, van 't Slot R, Zagury JF, van 't Wout AB, Schuitemaker H.

PLoS One. 2011;6(7):e22208. doi: 10.1371/journal.pone.0022208. Epub 2011 Jul 21.

28.

CD39/adenosine pathway is involved in AIDS progression.

Nikolova M, Carriere M, Jenabian MA, Limou S, Younas M, Kök A, Huë S, Seddiki N, Hulin A, Delaneau O, Schuitemaker H, Herbeck JT, Mullins JI, Muhtarova M, Bensussan A, Zagury JF, Lelievre JD, Lévy Y.

PLoS Pathog. 2011 Jul;7(7):e1002110. doi: 10.1371/journal.ppat.1002110. Epub 2011 Jul 7.

29.

Genome-wide association study implicates PARD3B-based AIDS restriction.

Troyer JL, Nelson GW, Lautenberger JA, Chinn L, McIntosh C, Johnson RC, Sezgin E, Kessing B, Malasky M, Hendrickson SL, Li G, Pontius J, Tang M, An P, Winkler CA, Limou S, Le Clerc S, Delaneau O, Zagury JF, Schuitemaker H, van Manen D, Bream JH, Gomperts ED, Buchbinder S, Goedert JJ, Kirk GD, O'Brien SJ.

J Infect Dis. 2011 May 15;203(10):1491-502. doi: 10.1093/infdis/jir046.

30.

Screening low-frequency SNPS from genome-wide association study reveals a new risk allele for progression to AIDS.

Le Clerc S, Coulonges C, Delaneau O, Van Manen D, Herbeck JT, Limou S, An P, Martinson JJ, Spadoni JL, Therwath A, Veldink JH, van den Berg LH, Taing L, Labib T, Mellak S, Montes M, Delfraissy JF, Schächter F, Winkler C, Froguel P, Mullins JI, Schuitemaker H, Zagury JF.

J Acquir Immune Defic Syndr. 2011 Mar 1;56(3):279-84. doi: 10.1097/QAI.0b013e318204982b.

31.

Multiple-cohort genetic association study reveals CXCR6 as a new chemokine receptor involved in long-term nonprogression to AIDS.

Limou S, Coulonges C, Herbeck JT, van Manen D, An P, Le Clerc S, Delaneau O, Diop G, Taing L, Montes M, van't Wout AB, Gottlieb GS, Therwath A, Rouzioux C, Delfraissy JF, Lelièvre JD, Lévy Y, Hercberg S, Dina C, Phair J, Donfield S, Goedert JJ, Buchbinder S, Estaquier J, Schächter F, Gut I, Froguel P, Mullins JI, Schuitemaker H, Winkler C, Zagury JF.

J Infect Dis. 2010 Sep 15;202(6):908-15. doi: 10.1086/655782.

32.

Genomewide association study of a rapid progression cohort identifies new susceptibility alleles for AIDS (ANRS Genomewide Association Study 03).

Le Clerc S, Limou S, Coulonges C, Carpentier W, Dina C, Taing L, Delaneau O, Labib T, Sladek R; ANRS Genomic Group, Deveau C, Guillemain H, Ratsimandresy R, Montes M, Spadoni JL, Therwath A, Schächter F, Matsuda F, Gut I, Lelièvre JD, Lévy Y, Froguel P, Delfraissy JF, Hercberg S, Zagury JF.

J Infect Dis. 2009 Oct 15;200(8):1194-201. doi: 10.1086/605892.

PMID:
19754311
33.

Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02).

Limou S, Le Clerc S, Coulonges C, Carpentier W, Dina C, Delaneau O, Labib T, Taing L, Sladek R, Deveau C, Ratsimandresy R, Montes M, Spadoni JL, Lelièvre JD, Lévy Y, Therwath A, Schächter F, Matsuda F, Gut I, Froguel P, Delfraissy JF, Hercberg S, Zagury JF; ANRS Genomic Group.

J Infect Dis. 2009 Feb 1;199(3):419-26. doi: 10.1086/596067.

PMID:
19115949
34.

Shape-IT: new rapid and accurate algorithm for haplotype inference.

Delaneau O, Coulonges C, Zagury JF.

BMC Bioinformatics. 2008 Dec 16;9:540. doi: 10.1186/1471-2105-9-540.

35.

ISHAPE: new rapid and accurate software for haplotyping.

Delaneau O, Coulonges C, Boelle PY, Nelson G, Spadoni JL, Zagury JF.

BMC Bioinformatics. 2007 Jun 15;8:205.

36.

Computation of haplotypes on SNPs subsets: advantage of the "global method".

Coulonges C, Delaneau O, Girard M, Do H, Adkins R, Spadoni JL, Zagury JF.

BMC Genet. 2006 Oct 26;7:50.

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