Systems and Population Genetics Group

Department of Computational Biology

University of Lausanne

Activities

Systems genetics

We are interested by the regulatory machinery controlling gene expression. We investigate it by analysing population scale multi-omics datasets (e.g. genomics, transcriptomics, epigenomics, proteomics) in which we use genetic variations as natural perturbations of the systems in order to unravel the interactions between molecular features (e.g. genes, regulatory elements, proteins).

Population genetics

We are also interested by characterizing how individuals are genetically related in a population. We look at this by identifying shared chromosome stretches (i.e. haplotypes) between individuals in a given population. To do so, we apply sophisticated statistical models in large scale genomics datasets containing up to millions of genetic variations typed and thousands of individuals.

Method Development

One leitmotiv in our research is the development of innovative computational methods to efficiently process and analyse large scale genomic datasets. We maintain multiple software that have been developed in previous work and that have been used in collaborative projects such as the 1000 Genomes project, UK biobank and GTEx.

Software

QTLtools

LINK

QTLtools is a tool set for molecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps.

FastQTL

LINK

FastQTL is a fast QTL mapper for molecular phenotypes such as gene expression measured via RNA-seq. Used to map cis-eQTL in GTEx.

SHAPEIT

LINK

SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. Used to infer haplotypes in 1000 Genomes, UK biobank and HRC.

XSI

LINK

XSI is a VCF/BCF Genotype data compressor based on sparse representation for rare variants and positional Burrows-Wheeler transform (PBWT) followed by 16-bit Word Aligned Hybrid (WAH) encoding for common variants.

GLIMPSE

LINK

GLIMPSE is a fast and accurate method for imputing haplotypes and genotypes from low-coverage sequencing data.

Group Members

Olivier Delaneau
Olivier
Delaneau

SNSF professor

Diogo Ribeiro
Diogo
Ribeiro

Postdoc

Simone Rubinacci
Simone
Rubinacci

Postdoc

Robin Hofmeister
Robin
Hofmeister

PhD student

Robin Hofmeister
Diana
Avalos

PhD student

Barbara Mota
Barbara
Mota

PhD student

Barbara Mota
Rick
Wertenbroek

PhD student

Publications (copy/paste from PUBMED)

Google Scholar

Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy.

Parikh VN, Ioannidis AG, Jimenez-Morales D, Gorzynski JE, De Jong HN, Liu X, Roque J, Cepeda-Espinoza VP, Osoegawa K, Hughes C, Sutton SC, Youlton N, Joshi R, Amar D, Tanigawa Y, Russo D, Wong J, Lauzon JT, Edelson J, Mas Montserrat D, Kwon Y, Rubinacci S, Delaneau O, Cappello L, Kim J, Shoura MJ, Raja AN, Watson N, Hammond N, Spiteri E, Mallempati KC, Montero-Martín G, Christle J, Kim J, Kirillova A, Seo K, Huang Y, Zhao C, Moreno-Grau S, Hershman SG, Dalton KP, Zhen J, Kamm J, Bhatt KD, Isakova A, Morri M, Ranganath T, Blish CA, Rogers AJ, Nadeau K, Yang S, Blomkalns A, O'Hara R, Neff NF, DeBoever C, Szalma S, Wheeler MT, Gates CM, Farh K, Schroth GP, Febbo P, deSouza F, Cornejo OE, Fernandez-Vina M, Kistler A, Palacios JA, Pinsky BA, Bustamante CD, Rivas MA, Ashley EA.

Nat Commun. 2022 Aug 30;13(1):5107. doi: 10.1038/s41467-022-32397-8.

PMID: 36042219

Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis.

M Ribeiro D, Ziyani C, Delaneau O.

Commun Biol. 2022 Aug 26;5(1):876. doi: 10.1038/s42003-022-03831-w.

PMID: 36028576

XSI - A genotype compression tool for compressive genomics in large biobanks.

Wertenbroek R, Rubinacci S, Xenarios I, Thoma Y, Delaneau O.

Bioinformatics. 2022 Jun 24;38(15):3778-84. doi: 10.1093/bioinformatics/btac413. Online ahead of print.

PMID: 35748697

GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing.

Valls-Margarit J, Galván-Femenía I, Matías-Sánchez D, Blay N, Puiggròs M, Carreras A, Salvoro C, Cortés B, Amela R, Farre X, Lerga-Jaso J, Puig M, Sánchez-Herrero JF, Moreno V, Perucho M, Sumoy L, Armengol L, Delaneau O, Cáceres M, de Cid R, Torrents D.

Nucleic Acids Res. 2022 Mar 21;50(5):2464-2479. doi: 10.1093/nar/gkac076.

PMID: 35176773

Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome.

Porcu E, Sadler MC, Lepik K, Auwerx C, Wood AR, Weihs A, Sleiman MSB, Ribeiro DM, Bandinelli S, Tanaka T, Nauck M, Völker U, Delaneau O, Metspalu A, Teumer A, Frayling T, Santoni FA, Reymond A, Kutalik Z.

Nat Commun. 2021 Sep 24;12(1):5647. doi: 10.1038/s41467-021-25805-y.

PMID: 34561431

The molecular basis, genetic control and pleiotropic effects of local gene co-expression.

Ribeiro DM, Rubinacci S, Ramisch A, Hofmeister RJ, Dermitzakis ET, Delaneau O.

Nat Commun. 2021 Aug 10;12(1):4842. doi: 10.1038/s41467-021-25129-x.

PMID: 34376650

Mapping the human genetic architecture of COVID-19.

COVID-19 Host Genetics Initiative.

Nature. 2021 Dec;600(7889):472-477. doi: 10.1038/s41586-021-03767-x. Epub 2021 Jul 8.

PMID: 34237774

The genomic history of the Aegean palatial civilizations.

Clemente F, Unterländer M, Dolgova O, Amorim CEG, Coroado-Santos F, Neuenschwander S, Ganiatsou E, Cruz Dávalos DI, Anchieri L, Michaud F, Winkelbach L, Blöcher J, Arizmendi Cárdenas YO, Sousa da Mota B, Kalliga E, Souleles A, Kontopoulos I, Karamitrou-Mentessidi G, Philaniotou O, Sampson A, Theodorou D, Tsipopoulou M, Akamatis I, Halstead P, Kotsakis K, Urem-Kotsou D, Panagiotopoulos D, Ziota C, Triantaphyllou S, Delaneau O, Jensen JD, Moreno-Mayar JV, Burger J, Sousa VC, Lao O, Malaspinas AS, Papageorgopoulou C.

Cell. 2021 May 13;184(10):2565-2586.e21. doi: 10.1016/j.cell.2021.03.039. Epub 2021 Apr 29.

PMID: 33930288

Gene regulation contributes to explain the impact of early life socioeconomic disadvantage on adult inflammatory levels in two cohort studies.

Carmeli C, Kutalik Z, Mishra PP, Porcu E, Delpierre C, Delaneau O, Kelly-Irving M, Bochud M, Dhayat NA, Ponte B, Pruijm M, Ehret G, Kähönen M, Lehtimäki T, Raitakari OT, Vineis P, Kivimäki M, Chadeau-Hyam M, Dermitzakis E, Vuilleumier N, Stringhini S.

Sci Rep. 2021 Feb 4;11(1):3100. doi: 10.1038/s41598-021-82714-2.

PMID: 33542415 Free PMC article.

Efficient phasing and imputation of low-coverage sequencing data using large reference panels.

Rubinacci S, Ribeiro DM, Hofmeister RJ, Delaneau O.

Nat Genet. 2021 Jan;53(1):120-126. doi: 10.1038/s41588-020-00756-0. Epub 2021 Jan 7.

PMID: 33414550

Genotype imputation using the Positional Burrows Wheeler Transform.

Rubinacci S, Delaneau O, Marchini J.

PLoS Genet. 2020 Nov 16;16(11):e1009049. doi: 10.1371/journal.pgen.1009049. eCollection 2020 Nov.

PMID: 33196638 Free PMC article.

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S; MC3 Working Group; PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L; PCAWG Consortium.

Nat Commun. 2020 Sep 21;11(1):4748. doi: 10.1038/s41467-020-18151-y.

PMID: 32958763 Free PMC article.

Sex differences in oncogenic mutational processes.

Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N; PCAWG Tumour Subtypes and Clinical Translation, Boutros PC; PCAWG Consortium.

Nat Commun. 2020 Aug 28;11(1):4330. doi: 10.1038/s41467-020-17359-2.

PMID: 32859912 Free PMC article.

High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs.

Gorzynski JE, De Jong HN, Amar D, Hughes CR, Ioannidis A, Bierman R, Liu D, Tanigawa Y, Kistler A, Kamm J, Kim J, Cappello L, Neff NF, Rubinacci S, Delaneau O, Shoura MJ, Seo K, Kirillova A, Raja A, Sutton S, Huang C, Sahoo MK, Mallempati KC, Montero-Martin G, Osoegawa K, Jimenez-Morales D, Watson N, Hammond N, Joshi R, Fernandez-Vina M, Christle JW, Wheeler MT, Febbo P, Farh K, Schroth G, Desouza F, Palacios J, Salzman J, Pinsky BA, Rivas MA, Bustamante CD, Ashley EA, Parikh VN.

medRxiv. 2020 Jul 29:2020.07.27.20163147. doi: 10.1101/2020.07.27.20163147. Preprint.

PMID: 32766602 Free PMC article.

Pan-cancer analysis of whole genomes.

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.

Nature. 2020 Feb;578(7793):82-93. doi: 10.1038/s41586-020-1969-6. Epub 2020 Feb 5.

PMID: 32025007 Free PMC article.

Accurate, scalable and integrative haplotype estimation.

Delaneau O, Zagury JF, Robinson MR, Marchini JL, Dermitzakis ET.

Nat Commun. 2019 Nov 28;10(1):5436. doi: 10.1038/s41467-019-13225-y.

PMID: 31780650 Free PMC article.

Chromatin three-dimensional interactions mediate genetic effects on gene expression.

Delaneau O, Zazhytska M, Borel C, Giannuzzi G, Rey G, Howald C, Kumar S, Ongen H, Popadin K, Marbach D, Ambrosini G, Bielser D, Hacker D, Romano L, Ribaux P, Wiederkehr M, Falconnet E, Bucher P, Bergmann S, Antonarakis SE, Reymond A, Dermitzakis ET.

Science. 2019 May 3;364(6439):eaat8266. doi: 10.1126/science.aat8266.

PMID: 31048460

Expression estimation and eQTL mapping for HLA genes with a personalized pipeline.

Aguiar VRC, César J, Delaneau O, Dermitzakis ET, Meyer D.

PLoS Genet. 2019 Apr 22;15(4):e1008091. doi: 10.1371/journal.pgen.1008091. eCollection 2019 Apr.

PMID: 31009447 Free PMC article.

A genome-wide association study of shared risk across psychiatric disorders implicates gene regulation during fetal neurodevelopment.

Schork AJ, Won H, Appadurai V, Nudel R, Gandal M, Delaneau O, Revsbech Christiansen M, Hougaard DM, Bækved-Hansen M, Bybjerg-Grauholm J, Giørtz Pedersen M, Agerbo E, Bøcker Pedersen C, Neale BM, Daly MJ, Wray NR, Nordentoft M, Mors O, Børglum AD, Bo Mortensen P, Buil A, Thompson WK, Geschwind DH, Werge T.

Nat Neurosci. 2019 Mar;22(3):353-361. doi: 10.1038/s41593-018-0320-0. Epub 2019 Jan 28.

PMID: 30692689 Free PMC article.

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 Free PMC article.

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.

PMID: 29116076 Free PMC article.

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

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

Genetic effects on gene expression across human tissues.

GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz; Lead analysts:; Laboratory, Data Analysis &Coordinating Center (LDACC):; NIH program management:; Biospecimen collection:; Pathology:; eQTL manuscript working group:, Battle A, Brown CD, Engelhardt BE, Montgomery SB.

Nature. 2017 Oct 11;550(7675):204-213. doi: 10.1038/nature24277.

PMID: 29022597 Free PMC article.

The impact of rare variation on gene expression across tissues.

Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Bassik MC, Merker JD; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Hall IM, Battle A, Montgomery SB.

Nature. 2017 Oct 11;550(7675):239-243. doi: 10.1038/nature24267.

PMID: 29022581 Free PMC article.

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.

PMID: 28516912 Free PMC article.

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.

PMID: 28186259 Free PMC article.

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.

Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP, Sidiropoulos N, Rapin N, Merkel A; BLUEPRINT Consortium, Stunnenberg HG, Stegle O, Frontini M, Downes K, Pastinen T, Kuijpers TW, Rico D, Valencia A, Beck S, Soranzo N, Paul DS.

Genome Biol. 2017 Jan 26;18(1):18. doi: 10.1186/s13059-017-1156-8.

PMID: 28126036 Free PMC article.

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.

PMID: 27863252 Free PMC article.

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.

PMID: 27863251 Free PMC article.

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.

PMID: 27548312 Free PMC article.

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.

PMID: 27270105 Free PMC article.

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.

PMID: 27153703 Free PMC article.

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.

PMID: 26708335 Free PMC article.

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

SIB Swiss Institute of Bioinformatics Members.

Nucleic Acids Res. 2016 Jan 4;44(D1):D27-37. doi: 10.1093/nar/gkv1310. Epub 2015 Nov 28.

PMID: 26615188 Free PMC article.

A global reference for human genetic variation.

1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR.

Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393.

PMID: 26432245 Free PMC article.

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.

PMID: 26423011 Free PMC article.

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.

PMID: 26367535 Free PMC article.

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.

PMID: 26300124

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.

PMID: 25653097 Free PMC article.

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.

PMID: 25557783 Free PMC article.

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C; 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.

Genome Biol. 2014 Jun 30;15(6):R88. doi: 10.1186/gb-2014-15-6-r88.

PMID: 24980144 Free PMC article.

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

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.

PMID: 24743097 Free PMC article.

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.

PMID: 24094745 Free PMC article.

Integrative annotation of variants from 1092 humans: application to cancer genomics.

Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M.

Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587.

PMID: 24092746 Free PMC article.

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.

PMID: 23935489 Free PMC article.

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.

PMID: 23269371 No abstract available.

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.

PMID: 23223146

An integrated map of genetic variation from 1,092 human genomes.

1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.

Nature. 2012 Nov 1;491(7422):56-65. doi: 10.1038/nature11632.

PMID: 23128226 Free PMC article.

Haplotype inference.

Delaneau O, Zagury JF.

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

PMID: 22665282

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.

PMID: 22362864 Free PMC article.

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

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.

PMID: 21811574 Free PMC article.

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.

PMID: 21750674 Free PMC article.

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.

PMID: 21502085 Free PMC article.

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.

PMID: 21107268 Free PMC article.

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.

PMID: 20704485 Free PMC article.

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

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

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.

PMID: 19087329 Free PMC article.

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. doi: 10.1186/1471-2105-8-205.

PMID: 17573965 Free PMC article.

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. doi: 10.1186/1471-2156-7-50.

PMID: 17067372 Free PMC article.

Find Us

University of Lausanne

Department of Computational Biology

Genopode building, Bureau GEN-2015

Quarter UNIL-Sorge, 1015 Lausanne

Switzerland

Call Us

Direct line: +41 (0)21 692 40 55

Secretary: +41 (0)21 692 53 97

Email Us

olivier.delaneau@unil.ch