Publications

Publications

2018

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease.
Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RWF, Huttenhower C, Dijkstra G, Xavier RJ, Festen EAM, Wijmenga C, Zhernakova A, Weersma RK.
Gut Volume 67 (2018) p.108-119

2017

Open Targets: a platform for therapeutic target identification and validation.
Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I.
Nucleic acids research Volume 45 (2017) p.D985-D994

Genetic variants regulating expression levels and isoform diversity during embryogenesis.
Cannavò E, Koelling N, Harnett D, Garfield D, Casale FP, Ciglar L, Gustafson HE, Viales RR, Marco-Ferreres R, Degner JF, Zhao B, Stegle O, Birney E, Furlong EE.
Nature Volume 541 (2017) p.402-406

Identifying genes for neurobehavioural traits in rodents: progress and pitfalls.
Baud A, Flint J.
Disease models & mechanisms Volume 10 (2017) p.373-383

easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies.
Grimm DG, Roqueiro D, Salomé PA, Kleeberger S, Greshake B, Zhu W, Liu C, Lippert C, Stegle O, Schölkopf B, Weigel D, Borgwardt KM.
The Plant cell Volume 29 (2017) p.5-19

Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.
Cabezas-Wallscheid N, Buettner F, Sommerkamp P, Klimmeck D, Ladel L, Thalheimer FB, Pastor-Flores D, Roma LP, Renders S, Zeisberger P, Przybylla A, Schönberger K, Scognamiglio R, Altamura S, Florian CM, Fawaz M, Vonficht D, Tesio M, Collier P, Pavlinic D, Geiger H, Schroeder T, Benes V, Dick TP, Rieger MA, Stegle O, Trumpp A.
Cell Volume 169 (2017) p.807-823.e19

Common genetic variation drives molecular heterogeneity in human iPSCs.
Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ.
Nature Volume 546 (2017) p.370-375

11,670 whole-genome sequences representative of the Han Chinese population from the CONVERGE project.
Cai N, Bigdeli TB, Kretzschmar WW, Li Y, Liang J, Hu J, Peterson RE, Bacanu S, Webb BT, Riley B, Li Q, Marchini J, Mott R, Kendler KS, Flint J.
Scientific data Volume 4 (2017) p.170011

Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity.
Wahl S, Drong A, Lehne B, Loh M, Scott WR, Kunze S, Tsai PC, Ried JS, Zhang W, Yang Y, Tan S, Fiorito G, Franke L, Guarrera S, Kasela S, Kriebel J, Richmond RC, Adamo M, Afzal U, Ala-Korpela M, Albetti B, Ammerpohl O, Apperley JF, Beekman M, Bertazzi PA, Black SL, Blancher C, Bonder MJ, Brosch M, Carstensen-Kirberg M, de Craen AJ, de Lusignan S, Dehghan A, Elkalaawy M, Fischer K, Franco OH, Gaunt TR, Hampe J, Hashemi M, Isaacs A, Jenkinson A, Jha S, Kato N, Krogh V, Laffan M, Meisinger C, Meitinger T, Mok ZY, Motta V, Ng HK, Nikolakopoulou Z, Nteliopoulos G, Panico S, Pervjakova N, Prokisch H, Rathmann W, Roden M, Rota F, Rozario MA, Sandling JK, Schafmayer C, Schramm K, Siebert R, Slagboom PE, Soininen P, Stolk L, Strauch K, Tai ES, Tarantini L, Thorand B, Tigchelaar EF, Tumino R, Uitterlinden AG, van Duijn C, van Meurs JB, Vineis P, Wickremasinghe AR, Wijmenga C, Yang TP, Yuan W, Zhernakova A, Batterham RL, Smith GD, Deloukas P, Heijmans BT, Herder C, Hofman A, Lindgren CM, Milani L, van der Harst P, Peters A, Illig T, Relton CL, Waldenberger M, Järvelin MR, Bollati V, Soong R, Spector TD, Scott J, McCarthy MI, Elliott P, Bell JT, Matullo G, Gieger C, Kooner JS, Grallert H, Chambers JC.
Nature Volume 541 (2017) p.81-86

Multi-tissue DNA methylation age predictor in mouse.
Stubbs TM, Bonder MJ, Stark AK, Krueger F, BI Ageing Clock Team, von Meyenn F, Stegle O, Reik W.
Genome biology Volume 18 (2017) p.68

Disease variants alter transcription factor levels and methylation of their binding sites.
Bonder MJ, Luijk R, Zhernakova DV, Moed M, Deelen P, Vermaat M, van Iterson M, van Dijk F, van Galen M, Bot J, Slieker RC, Jhamai PM, Verbiest M, Suchiman HE, Verkerk M, van der Breggen R, van Rooij J, Lakenberg N, Arindrarto W, Kielbasa SM, Jonkers I, van 't Hof P, Nooren I, Beekman M, Deelen J, van Heemst D, Zhernakova A, Tigchelaar EF, Swertz MA, Hofman A, Uitterlinden AG, Pool R, van Dongen J, Hottenga JJ, Stehouwer CD, van der Kallen CJ, Schalkwijk CG, van den Berg LH, van Zwet EW, Mei H, Li Y, Lemire M, Hudson TJ, BIOS Consortium, Slagboom PE, Wijmenga C, Veldink JH, van Greevenbroek MM, van Duijn CM, Boomsma DI, Isaacs A, Jansen R, van Meurs JB, 't Hoen PA, Franke L, Heijmans BT.
Nature genetics Volume 49 (2017) p.131-138

The Genetic Architecture of Major Depressive Disorder in Han Chinese Women.
Peterson RE, Cai N, Bigdeli TB, Li Y, Reimers M, Nikulova A, Webb BT, Bacanu SA, Riley BP, Flint J, Kendler KS.
JAMA psychiatry Volume 74 (2017) p.162-168

Reevaluation of SNP heritability in complex human traits.
Speed D, Cai N, UCLEB Consortium, Johnson MR, Nejentsev S, Balding DJ.
Nature genetics Volume 49 (2017) p.986-992

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS.
Cell reports Volume 20 (2017) p.2201-2214

Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.
Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MS, Fogg LG, Nair AS, Liligeto U, Stubbington MJ, Ly LH, Bagger FO, Zwiessele M, Lawrence ND, Souza-Fonseca-Guimaraes F, Bunn PT, Engwerda CR, Heath WR, Billker O, Stegle O, Haque A, Teichmann SA.
Science immunology Volume 2 (2017) p.

Promoter shape varies across populations and affects promoter evolution and expression noise.
Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE.
Nature genetics Volume 49 (2017) p.550-558

DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.
Kraiczy J, Nayak KM, Howell KJ, Ross A, Forbester J, Salvestrini C, Mustata R, Perkins S, Andersson-Rolf A, Leenen E, Liebert A, Vallier L, Rosenstiel PC, Stegle O, Dougan G, Heuschkel R, Koo BK, Zilbauer M.
Gut Volume (2017) p.

Single-cell epigenomics: Recording the past and predicting the future.
Kelsey G, Stegle O, Reik W.
Science (New York, N.Y.) Volume 358 (2017) p.69-75

Joint genetic analysis using variant sets reveals polygenic gene-context interactions.
Casale FP, Horta D, Rakitsch B, Stegle O.
PLoS Genetics Volume 13 (2017) p.e1006693

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.
Angermueller C, Lee HJ, Reik W, Stegle O, Stegle O.
Genome biology Volume 18 (2017) p.67

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.
Howell KJ, Kraiczy J, Nayak KM, Gasparetto M, Ross A, Lee C, Mak TN, Koo BK, Kumar N, Lawley T, Sinha A, Rosenstiel P, Heuschkel R, Stegle O, Zilbauer M.
Gastroenterology Volume (2017) p.

Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus.
Schulz H, Ruppert AK, Herms S, Wolf C, Mirza-Schreiber N, Stegle O, Czamara D, Forstner AJ, Sivalingam S, Schoch S, Moebus S, Pütz B, Hillmer A, Fricker N, Vatter H, Müller-Myhsok B, Nöthen MM, Becker AJ, Hoffmann P, Sander T, Cichon S.
Nature Communications Volume 8 (2017) p.1511

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.
American journal of human genetics Volume 100 (2017) p.865-884

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.
Imprialou M, Kahles A, Steffen JG, Osborne EJ, Gan X, Lempe J, Bhomra A, Belfield E, Visscher A, Greenhalgh R, Harberd NP, Goram R, Hein J, Robert-Seilaniantz A, Jones J, Stegle O, Kover P, Tsiantis M, Nordborg M, Rätsch G, Clark RM, Mott R.
Genetics Volume 205 (2017) p.1425-1441

Platelet function is modified by common sequence variation in megakaryocyte super enhancers.
Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts AS, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide ME, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M, Ouwehand WH, Astle WJ, Downes K, Kostadima M, Frontini M.
Nature Communications Volume 8 (2017) p.16058

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 biology Volume 18 (2017) p.18

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.
Buettner F, Pratanwanich N, McCarthy DJ, Marioni JC, Stegle O.
Genome biology Volume 18 (2017) p.212

The emerging landscape of dynamic DNA methylation in early childhood.
Xu CJ, Bonder MJ, Söderhäll C, Bustamante M, Baïz N, Gehring U, Jankipersadsing SA, van der Vlies P, van Diemen CC, van Rijkom B, Just J, Kull I, Kere J, Antó JM, Bousquet J, Zhernakova A, Wijmenga C, Annesi-Maesano I, Sunyer J, Melén E, Li Y, Postma DS, Koppelman GH.
BMC genomics Volume 18 (2017) p.25

BRIE: transcriptome-wide splicing quantification in single cells.
Huang Y, Sanguinetti G.
Genome biology Volume 18 (2017) p.123

A GWAS meta-analysis suggests roles for xenobiotic metabolism and ion channel activity in the biology of stool frequency.
Jankipersadsing SA, Hadizadeh F, Bonder MJ, Tigchelaar EF, Deelen P, Fu J, Andreasson A, Agreus L, Walter S, Wijmenga C, Hysi P, D'Amato M, Zhernakova A.
Gut Volume 66 (2017) p.756-758

The influence of proton pump inhibitors and other commonly used medication on the gut microbiota.
Imhann F, Vich Vila A, Bonder MJ, Lopez Manosalva AG, Koonen DPY, Fu J, Wijmenga C, Zhernakova A, Weersma RK.
Gut microbes Volume 8 (2017) p.351-358

Genetic Variation in the Social Environment Contributes to Health and Disease.
Baud A, Mulligan MK, Casale FP, Ingels JF, Bohl CJ, Callebert J, Launay JM, Krohn J, Legarra A, Williams RW, Stegle O.
PLoS genetics Volume 13 (2017) p.e1006498

ODE-Based Modeling of Complex Regulatory Circuits.
Seaton DD.
Methods in molecular biology (Clifton, N.J.) Volume 1629 (2017) p.317-330

Identification of context-dependent expression quantitative trait loci in whole blood.
Zhernakova DV, Deelen P, Vermaat M, van Iterson M, van Galen M, Arindrarto W, van 't Hof P, Mei H, van Dijk F, Westra HJ, Bonder MJ, van Rooij J, Verkerk M, Jhamai PM, Moed M, Kielbasa SM, Bot J, Nooren I, Pool R, van Dongen J, Hottenga JJ, Stehouwer CD, van der Kallen CJ, Schalkwijk CG, Zhernakova A, Li Y, Tigchelaar EF, de Klein N, Beekman M, Deelen J, van Heemst D, van den Berg LH, Hofman A, Uitterlinden AG, van Greevenbroek MM, Veldink JH, Boomsma DI, van Duijn CM, Wijmenga C, Slagboom PE, Swertz MA, Isaacs A, van Meurs JB, Jansen R, Heijmans BT, 't Hoen PA, Franke L.
Nature genetics Volume 49 (2017) p.139-145

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.
McCarthy DJ, Campbell KR, Lun AT, Wills QF.
Bioinformatics (Oxford, England) Volume 33 (2017) p.1179-1186

2016

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.
Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ.
Cell Volume 167 (2016) p.1125-1136.e8

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.
Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ.
Cell Volume 167 (2016) p.1897

A multiple-phenotype imputation method for genetic studies.
Dahl A, Iotchkova V, Baud A, Johansson Å, Gyllensten U, Soranzo N, Mott R, Kranis A, Marchini J.
Nature genetics Volume 48 (2016) p.466-472

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 JH, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N.
Cell Volume 167 (2016) p.1398-1414.e24

Classification of low quality cells from single-cell RNA-seq data.
Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ, Marioni JC, Teichmann SA.
Genome biology Volume 17 (2016) p.29

The genetic architecture of type 2 diabetes.
Fuchsberger C, Flannick J, Teslovich TM, Mahajan A, Agarwala V, Gaulton KJ, Ma C, Fontanillas P, Moutsianas L, McCarthy DJ, Rivas MA, Perry JRB, Sim X, Blackwell TW, Robertson NR, Rayner NW, Cingolani P, Locke AE, Tajes JF, Highland HM, Dupuis J, Chines PS, Lindgren CM, Hartl C, Jackson AU, Chen H, Huyghe JR, van de Bunt M, Pearson RD, Kumar A, Müller-Nurasyid M, Grarup N, Stringham HM, Gamazon ER, Lee J, Chen Y, Scott RA, Below JE, Chen P, Huang J, Go MJ, Stitzel ML, Pasko D, Parker SCJ, Varga TV, Green T, Beer NL, Day-Williams AG, Ferreira T, Fingerlin T, Horikoshi M, Hu C, Huh I, Ikram MK, Kim BJ, Kim Y, Kim YJ, Kwon MS, Lee J, Lee S, Lin KH, Maxwell TJ, Nagai Y, Wang X, Welch RP, Yoon J, Zhang W, Barzilai N, Voight BF, Han BG, Jenkinson CP, Kuulasmaa T, Kuusisto J, Manning A, Ng MCY, Palmer ND, Balkau B, Stančáková A, Abboud HE, Boeing H, Giedraitis V, Prabhakaran D, Gottesman O, Scott J, Carey J, Kwan P, Grant G, Smith JD, Neale BM, Purcell S, Butterworth AS, Howson JMM, Lee HM, Lu Y, Kwak SH, Zhao W, Danesh J, Lam VKL, Park KS, Saleheen D, So WY, Tam CHT, Afzal U, Aguilar D, Arya R, Aung T, Chan E, Navarro C, Cheng CY, Palli D, Correa A, Curran JE, Rybin D, Farook VS, Fowler SP, Freedman BI, Griswold M, Hale DE, Hicks PJ, Khor CC, Kumar S, Lehne B, Thuillier D, Lim WY, Liu J, van der Schouw YT, Loh M, Musani SK, Puppala S, Scott WR, Yengo L, Tan ST, Taylor HA, Thameem F, Wilson G, Wong TY, Njølstad PR, Levy JC, Mangino M, Bonnycastle LL, Schwarzmayr T, Fadista J, Surdulescu GL, Herder C, Groves CJ, Wieland T, Bork-Jensen J, Brandslund I, Christensen C, Koistinen HA, Doney ASF, Kinnunen L, Esko T, Farmer AJ, Hakaste L, Hodgkiss D, Kravic J, Lyssenko V, Hollensted M, Jørgensen ME, Jørgensen T, Ladenvall C, Justesen JM, Käräjämäki A, Kriebel J, Rathmann W, Lannfelt L, Lauritzen T, Narisu N, Linneberg A, Melander O, Milani L, Neville M, Orho-Melander M, Qi L, Qi Q, Roden M, Rolandsson O, Swift A, Rosengren AH, Stirrups K, Wood AR, Mihailov E, Blancher C, Carneiro MO, Maguire J, Poplin R, Shakir K, Fennell T, DePristo M, de Angelis MH, Deloukas P, Gjesing AP, Jun G, Nilsson P, Murphy J, Onofrio R, Thorand B, Hansen T, Meisinger C, Hu FB, Isomaa B, Karpe F, Liang L, Peters A, Huth C, O'Rahilly SP, Palmer CNA, Pedersen O, Rauramaa R, Tuomilehto J, Salomaa V, Watanabe RM, Syvänen AC, Bergman RN, Bharadwaj D, Bottinger EP, Cho YS, Chandak GR, Chan JCN, Chia KS, Daly MJ, Ebrahim SB, Langenberg C, Elliott P, Jablonski KA, Lehman DM, Jia W, Ma RCW, Pollin TI, Sandhu M, Tandon N, Froguel P, Barroso I, Teo YY, Zeggini E, Loos RJF, Small KS, Ried JS, DeFronzo RA, Grallert H, Glaser B, Metspalu A, Wareham NJ, Walker M, Banks E, Gieger C, Ingelsson E, Im HK, Illig T, Franks PW, Buck G, Trakalo J, Buck D, Prokopenko I, Mägi R, Lind L, Farjoun Y, Owen KR, Gloyn AL, Strauch K, Tuomi T, Kooner JS, Lee JY, Park T, Donnelly P, Morris AD, Hattersley AT, Bowden DW, Collins FS, Atzmon G, Chambers JC, Spector TD, Laakso M, Strom TM, Bell GI, Blangero J, Duggirala R, Tai ES, McVean G, Hanis CL, Wilson JG, Seielstad M, Frayling TM, Meigs JB, Cox NJ, Sladek R, Lander ES, Gabriel S, Burtt NP, Mohlke KL, Meitinger T, Groop L, Abecasis G, Florez JC, Scott LJ, Morris AP, Kang HM, Boehnke M, Altshuler D, McCarthy MI.
Nature Volume 536 (2016) p.41-47

Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression.
Rakitsch B, Stegle O.
Genome biology Volume 17 (2016) p.33

GWAS for executive function and processing speed suggests involvement of the CADM2 gene.
Ibrahim-Verbaas CA, Bressler J, Debette S, Schuur M, Smith AV, Bis JC, Davies G, Trompet S, Smith JA, Wolf C, Chibnik LB, Liu Y, Vitart V, Kirin M, Petrovic K, Polasek O, Zgaga L, Fawns-Ritchie C, Hoffmann P, Karjalainen J, Lahti J, Llewellyn DJ, Schmidt CO, Mather KA, Chouraki V, Sun Q, Resnick SM, Rose LM, Oldmeadow C, Stewart M, Smith BH, Gudnason V, Yang Q, Mirza SS, Jukema JW, deJager PL, Harris TB, Liewald DC, Amin N, Coker LH, Stegle O, Lopez OL, Schmidt R, Teumer A, Ford I, Karbalai N, Becker JT, Jonsdottir MK, Au R, Fehrmann R, Herms S, Nalls M, Zhao W, Turner ST, Yaffe K, Lohman K, van Swieten JC, Kardia S, Knopman DS, Meeks WM, Heiss G, Holliday EG, Schofield PW, Tanaka T, Stott DJ, Wang J, Ridker P, Gow AJ, Pattie A, Starr JM, Hocking LJ, Armstrong NJ, McLachlan S, Shulman JM, Pilling LC, Eiriksdottir G, Scott RJ, Kochan NA, Palotie A, Hsieh YC, Eriksson JG, Penman A, Gottesman RF, Oostra BA, Yu L, DeStefano AL, Beiser A, Garcia M, Rotter JI, Nöthen MM, Hofman A, Slagboom PE, Westendorp R, Buckley BM, Wolf PA, Uitterlinden AG, Psaty BM, Grabe HJ, Bandinelli S, Chasman DI, Grodstein F, Räikkönen K, Lambert JC, Porteous DJ, Generation Scotland, Price JF, Sachdev PS, Ferrucci L, Attia JR, Rudan I, Hayward C, Wright AF, Wilson JF, Cichon S, Franke L, Schmidt H, Ding J, de Craen A, Fornage M, Bennett DA, Deary IJ, Ikram MA, Launer LJ, Fitzpatrick AL, Seshadri S, van Duijn CM, Mosley TH.
Molecular psychiatry Volume 21 (2016) p.189-197

Proton pump inhibitors affect the gut microbiome.
Imhann F, Bonder MJ, Vich Vila A, Fu J, Mujagic Z, Vork L, Tigchelaar EF, Jankipersadsing SA, Cenit MC, Harmsen HJ, Dijkstra G, Franke L, Xavier RJ, Jonkers D, Wijmenga C, Weersma RK, Zhernakova A.
Gut Volume 65 (2016) p.740-748

Deep learning for computational biology.
Angermueller C, Pärnamaa T, Parts L, Stegle O.
Molecular systems biology Volume 12 (2016) p.878

Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana.
Meng D, Dubin M, Zhang P, Osborne EJ, Stegle O, Clark RM, Nordborg M.
PLoS Genetics Volume 12 (2016) p.e1006141

GeneCodeq: quality score compression and improved genotyping using a Bayesian framework.
Greenfield DL, Stegle O, Rrustemi A.
Bioinformatics (Oxford, England) Volume 32 (2016) p.3124-3132

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.
Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood S, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W.
Nature methods Volume 13 (2016) p.229-232

A high-content platform to characterise human induced pluripotent stem cell lines.
Leha A, Moens N, Meleckyte R, Culley OJ, Gervasio MK, Kerz M, Reimer A, Cain SA, Streeter I, Folarin A, Stegle O, Kielty CM, HipSci Consortium, Durbin R, Watt FM, Danovi D.
Methods (San Diego, Calif.) Volume 96 (2016) p.85-96

Genetic and environmental influences interact with age and sex in shaping the human methylome.
van Dongen J, Nivard MG, Willemsen G, Hottenga JJ, Helmer Q, Dolan CV, Ehli EA, Davies GE, van Iterson M, Breeze CE, Beck S, BIOS Consortium, Suchiman HE, Jansen R, van Meurs JB, Heijmans BT, Slagboom PE, Boomsma DI.
Nature communications Volume 7 (2016) p.11115

Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs.
Ricaño-Ponce I, Zhernakova DV, Deelen P, Luo O, Li X, Isaacs A, Karjalainen J, Di Tommaso J, Borek ZA, Zorro MM, Gutierrez-Achury J, Uitterlinden AG, Hofman A, van Meurs J, BIOS Consortium, Lifelines Cohort Study, Netea MG, Jonkers IH, Withoff S, van Duijn CM, Li Y, Ruan Y, Franke L, Wijmenga C, Kumar V.
Journal of autoimmunity Volume 68 (2016) p.62-74

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.
Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F, BLUEPRINT Consortium, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P.
Cell Volume 167 (2016) p.1369-1384.e19

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.
Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA, LifeLines cohort study, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J.
Science (New York, N.Y.) Volume 352 (2016) p.565-569

Population-level analysis of gut microbiome variation.
Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D'hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J.
Science (New York, N.Y.) Volume 352 (2016) p.560-564

Gut microbiota composition associated with stool consistency.
Tigchelaar EF, Bonder MJ, Jankipersadsing SA, Fu J, Wijmenga C, Zhernakova A.
Gut Volume 65 (2016) p.540-542

The effect of host genetics on the gut microbiome.
Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, Deelen P, Vatanen T, Schirmer M, Smeekens SP, Zhernakova DV, Jankipersadsing SA, Jaeger M, Oosting M, Cenit MC, Masclee AA, Swertz MA, Li Y, Kumar V, Joosten L, Harmsen H, Weersma RK, Franke L, Hofker MH, Xavier RJ, Jonkers D, Netea MG, Wijmenga C, Fu J, Zhernakova A.
Nature genetics Volume 48 (2016) p.1407-1412

The influence of a short-term gluten-free diet on the human gut microbiome.
Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, Zhong H, Vatanen T, Gevers D, Wijmenga C, Wang Y, Zhernakova A.
Genome medicine Volume 8 (2016) p.45

Tobacco smoking is associated with DNA methylation of diabetes susceptibility genes.
Ligthart S, Steenaard RV, Peters MJ, van Meurs JB, Sijbrands EJ, Uitterlinden AG, Bonder MJ, BIOS consortium, Hofman A, Franco OH, Dehghan A.
Diabetologia Volume 59 (2016) p.998-1006

Blood lipids influence DNA methylation in circulating cells.
Dekkers KF, van Iterson M, Slieker RC, Moed MH, Bonder MJ, van Galen M, Mei H, Zhernakova DV, van den Berg LH, Deelen J, van Dongen J, van Heemst D, Hofman A, Hottenga JJ, van der Kallen CJ, Schalkwijk CG, Stehouwer CD, Tigchelaar EF, Uitterlinden AG, Willemsen G, Zhernakova A, Franke L, 't Hoen PA, Jansen R, van Meurs J, Boomsma DI, van Duijn CM, van Greevenbroek MM, Veldink JH, Wijmenga C, BIOS Consortium, van Zwet EW, Slagboom PE, Jukema JW, Heijmans BT.
Genome biology Volume 17 (2016) p.138

Genome-wide analysis identifies 12 loci influencing human reproductive behavior.
Barban N, Jansen R, de Vlaming R, Vaez A, Mandemakers JJ, Tropf FC, Shen X, Wilson JF, Chasman DI, Nolte IM, Tragante V, van der Laan SW, Perry JR, Kong A, BIOS Consortium, Ahluwalia TS, Albrecht E, Yerges-Armstrong L, Atzmon G, Auro K, Ayers K, Bakshi A, Ben-Avraham D, Berger K, Bergman A, Bertram L, Bielak LF, Bjornsdottir G, Bonder MJ, Broer L, Bui M, Barbieri C, Cavadino A, Chavarro JE, Turman C, Concas MP, Cordell HJ, Davies G, Eibich P, Eriksson N, Esko T, Eriksson J, Falahi F, Felix JF, Fontana MA, Franke L, Gandin I, Gaskins AJ, Gieger C, Gunderson EP, Guo X, Hayward C, He C, Hofer E, Huang H, Joshi PK, Kanoni S, Karlsson R, Kiechl S, Kifley A, Kluttig A, Kraft P, Lagou V, Lecoeur C, Lahti J, Li-Gao R, Lind PA, Liu T, Makalic E, Mamasoula C, Matteson L, Mbarek H, McArdle PF, McMahon G, Meddens SF, Mihailov E, Miller M, Missmer SA, Monnereau C, van der Most PJ, Myhre R, Nalls MA, Nutile T, Kalafati IP, Porcu E, Prokopenko I, Rajan KB, Rich-Edwards J, Rietveld CA, Robino A, Rose LM, Rueedi R, Ryan KA, Saba Y, Schmidt D, Smith JA, Stolk L, Streeten E, Tönjes A, Thorleifsson G, Ulivi S, Wedenoja J, Wellmann J, Willeit P, Yao J, Yengo L, Zhao JH, Zhao W, Zhernakova DV, Amin N, Andrews H, Balkau B, Barzilai N, Bergmann S, Biino G, Bisgaard H, Bønnelykke K, Boomsma DI, Buring JE, Campbell H, Cappellani S, Ciullo M, Cox SR, Cucca F, Toniolo D, Davey-Smith G, Deary IJ, Dedoussis G, Deloukas P, van Duijn CM, de Geus EJ, Eriksson JG, Evans DA, Faul JD, Sala CF, Froguel P, Gasparini P, Girotto G, Grabe HJ, Greiser KH, Groenen PJ, de Haan HG, Haerting J, Harris TB, Heath AC, Heikkilä K, Hofman A, Homuth G, Holliday EG, Hopper J, Hyppönen E, Jacobsson B, Jaddoe VW, Johannesson M, Jugessur A, Kähönen M, Kajantie E, Kardia SL, Keavney B, Kolcic I, Koponen P, Kovacs P, Kronenberg F, Kutalik Z, La Bianca M, Lachance G, Iacono WG, Lai S, Lehtimäki T, Liewald DC, LifeLines Cohort Study, Lindgren CM, Liu Y, Luben R, Lucht M, Luoto R, Magnus P, Magnusson PK, Martin NG, McGue M, McQuillan R, Medland SE, Meisinger C, Mellström D, Metspalu A, Traglia M, Milani L, Mitchell P, Montgomery GW, Mook-Kanamori D, de Mutsert R, Nohr EA, Ohlsson C, Olsen J, Ong KK, Paternoster L, Pattie A, Penninx BW, Perola M, Peyser PA, Pirastu M, Polasek O, Power C, Kaprio J, Raffel LJ, Räikkönen K, Raitakari O, Ridker PM, Ring SM, Roll K, Rudan I, Ruggiero D, Rujescu D, Salomaa V, Schlessinger D, Schmidt H, Schmidt R, Schupf N, Smit J, Sorice R, Spector TD, Starr JM, Stöckl D, Strauch K, Stumvoll M, Swertz MA, Thorsteinsdottir U, Thurik AR, Timpson NJ, Tung JY, Uitterlinden AG, Vaccargiu S, Viikari J, Vitart V, Völzke H, Vollenweider P, Vuckovic D, Waage J, Wagner GG, Wang JJ, Wareham NJ, Weir DR, Willemsen G, Willeit J, Wright AF, Zondervan KT, Stefansson K, Krueger RF, Lee JJ, Benjamin DJ, Cesarini D, Koellinger PD, den Hoed M, Snieder H, Mills MC.
Nature genetics Volume 48 (2016) p.1462-1472

CHRONICITY OF DEPRESSION AND MOLECULAR MARKERS IN A LARGE SAMPLE OF HAN CHINESE WOMEN.
Edwards AC, Aggen SH, Cai N, Bigdeli TB, Peterson RE, Docherty AR, Webb BT, Bacanu SA, Flint J, Kendler KS.
Depression and anxiety Volume (2016) p.

Genome-wide association of multiple complex traits in outbred mice by ultra-low-coverage sequencing.
Nicod J, Davies RW, Cai N, Hassett C, Goodstadt L, Cosgrove C, Yee BK, Lionikaite V, McIntyre RE, Remme CA, Lodder EM, Gregory JS, Hough T, Joynson R, Phelps H, Nell B, Rowe C, Wood J, Walling A, Bopp N, Bhomra A, Hernandez-Pliego P, Callebert J, Aspden RM, Talbot NP, Robbins PA, Harrison M, Fray M, Launay JM, Pinto YM, Blizard DA, Bezzina CR, Adams DJ, Franken P, Weaver T, Wells S, Brown SD, Potter PK, Klenerman P, Lionikas A, Mott R, Flint J.
Nature genetics Volume 48 (2016) p.912-918

Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms.
Slieker RC, van Iterson M, Luijk R, Beekman M, Zhernakova DV, Moed MH, Mei H, van Galen M, Deelen P, Bonder MJ, Zhernakova A, Uitterlinden AG, Tigchelaar EF, Stehouwer CD, Schalkwijk CG, van der Kallen CJ, Hofman A, van Heemst D, de Geus EJ, van Dongen J, Deelen J, van den Berg LH, van Meurs J, Jansen R, 't Hoen PA, Franke L, Wijmenga C, Veldink JH, Swertz MA, van Greevenbroek MM, van Duijn CM, Boomsma DI, BIOS consortium, Slagboom PE, Heijmans BT.
Genome biology Volume 17 (2016) p.191

A Genome-Wide Association Study for Regulators of Micronucleus Formation in Mice.
McIntyre RE, Nicod J, Robles-Espinoza CD, Maciejowski J, Cai N, Hill J, Verstraten R, Iyer V, Rust AG, Balmus G, Mott R, Flint J, Adams DJ.
G3 (Bethesda, Md.) Volume 6 (2016) p.2343-2354

Evidence for mitochondrial genetic control of autosomal gene expression.
Kassam I, Qi T, Lloyd-Jones L, Holloway A, Jan Bonder M, Henders AK, Martin NG, Powell JE, Franke L, Montgomery GW, Visscher PM, McRae AF.
Human molecular genetics Volume 25 (2016) p.5332-5338

2015

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M.
eLife Volume 4 (2015) p.e05255

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.
Lehmann KV, Kahles A, Kandoth C, Lee W, Schultz N, Stegle O, Rätsch G.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Volume (2015) p.44-55

MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo.
Sheikh BN, Downer NL, Phipson B, Vanyai HK, Kueh AJ, McCarthy DJ, Smyth GK, Thomas T, Voss AK.
Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.5437-5442

Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.
Dudley JT, Listgarten J, Stegle O, Brenner SE, Parts L.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Volume (2015) p.342-346

Fine mapping of bone structure and strength QTLs in heterogeneous stock rat.
Alam I, Koller DL, Cañete T, Blázquez G, Mont-Cardona C, López-Aumatell R, Martínez-Membrives E, Díaz-Morán S, Tobeña A, Fernández-Teruel A, Stridh P, Diez M, Olsson T, Johannesson M, Baud A, Econs MJ, Foroud T.
Bone Volume 81 (2015) p.417-426

Computational and analytical challenges in single-cell transcriptomics.
Stegle O, Teichmann SA, Marioni JC.
Nature reviews. Genetics Volume 16 (2015) p.133-145

Estimation of Free-Living Energy Expenditure by Heart Rate and Movement Sensing: A Doubly-Labelled Water Study.
Brage S, Westgate K, Franks PW, Stegle O, Wright A, Ekelund U, Wareham NJ.
PLoS ONE Volume 10 (2015) p.e0137206

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, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, 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 Volume 526 (2015) p.75-81

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 Volume 526 (2015) p.68-74

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.
Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J, GTEx Consortium, Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG.
Science (New York, N.Y.) Volume 348 (2015) p.666-669

Genome-wide studies of verbal declarative memory in nondemented older people: the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium.
Debette S, Ibrahim Verbaas CA, Bressler J, Schuur M, Smith A, Bis JC, Davies G, Wolf C, Gudnason V, Chibnik LB, Yang Q, deStefano AL, de Quervain DJ, Srikanth V, Lahti J, Grabe HJ, Smith JA, Priebe L, Yu L, Karbalai N, Hayward C, Wilson JF, Campbell H, Petrovic K, Fornage M, Chauhan G, Yeo R, Boxall R, Becker J, Stegle O, Mather KA, Chouraki V, Sun Q, Rose LM, Resnick S, Oldmeadow C, Kirin M, Wright AF, Jonsdottir MK, Au R, Becker A, Amin N, Nalls MA, Turner ST, Kardia SL, Oostra B, Windham G, Coker LH, Zhao W, Knopman DS, Heiss G, Griswold ME, Gottesman RF, Vitart V, Hastie ND, Zgaga L, Rudan I, Polasek O, Holliday EG, Schofield P, Choi SH, Tanaka T, An Y, Perry RT, Kennedy RE, Sale MM, Wang J, Wadley VG, Liewald DC, Ridker PM, Gow AJ, Pattie A, Starr JM, Porteous D, Liu X, Thomson R, Armstrong NJ, Eiriksdottir G, Assareh AA, Kochan NA, Widen E, Palotie A, Hsieh YC, Eriksson JG, Vogler C, van Swieten JC, Shulman JM, Beiser A, Rotter J, Schmidt CO, Hoffmann W, Nöthen MM, Ferrucci L, Attia J, Uitterlinden AG, Amouyel P, Dartigues JF, Amieva H, Räikkönen K, Garcia M, Wolf PA, Hofman A, Longstreth WT, Psaty BM, Boerwinkle E, DeJager PL, Sachdev PS, Schmidt R, Breteler MM, Teumer A, Lopez OL, Cichon S, Chasman DI, Grodstein F, Müller-Myhsok B, Tzourio C, Papassotiropoulos A, Bennett DA, Ikram MA, Deary IJ, van Duijn CM, Launer L, Fitzpatrick AL, Seshadri S, Mosley TH, Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium.
Biological psychiatry Volume 77 (2015) p.749-763

A random forest approach to capture genetic effects in the presence of population structure.
Stephan J, Stegle O, Beyer A.
Nature communications Volume 6 (2015) p.7432

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O.
Nature biotechnology Volume 33 (2015) p.155-160

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders.
Taylor JC, Martin HC, Lise S, Broxholme J, Cazier JB, Rimmer A, Kanapin A, Lunter G, Fiddy S, Allan C, Aricescu AR, Attar M, Babbs C, Becq J, Beeson D, Bento C, Bignell P, Blair E, Buckle VJ, Bull K, Cais O, Cario H, Chapel H, Copley RR, Cornall R, Craft J, Dahan K, Davenport EE, Dendrou C, Devuyst O, Fenwick AL, Flint J, Fugger L, Gilbert RD, Goriely A, Green A, Greger IH, Grocock R, Gruszczyk AV, Hastings R, Hatton E, Higgs D, Hill A, Holmes C, Howard M, Hughes L, Humburg P, Johnson D, Karpe F, Kingsbury Z, Kini U, Knight JC, Krohn J, Lamble S, Langman C, Lonie L, Luck J, McCarthy D, McGowan SJ, McMullin MF, Miller KA, Murray L, Németh AH, Nesbit MA, Nutt D, Ormondroyd E, Oturai AB, Pagnamenta A, Patel SY, Percy M, Petousi N, Piazza P, Piret SE, Polanco-Echeverry G, Popitsch N, Powrie F, Pugh C, Quek L, Robbins PA, Robson K, Russo A, Sahgal N, van Schouwenburg PA, Schuh A, Silverman E, Simmons A, Sørensen PS, Sweeney E, Taylor J, Thakker RV, Tomlinson I, Trebes A, Twigg SR, Uhlig HH, Vyas P, Vyse T, Wall SA, Watkins H, Whyte MP, Witty L, Wright B, Yau C, Buck D, Humphray S, Ratcliffe PJ, Bell JI, Wilkie AO, Bentley D, Donnelly P, McVean G.
Nature genetics Volume 47 (2015) p.717-726

Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage.
Hagmann J, Becker C, Müller J, Stegle O, Meyer RC, Wang G, Schneeberger K, Fitz J, Altmann T, Bergelson J, Borgwardt K, Weigel D.
PLoS genetics Volume 11 (2015) p.e1004920

Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders.
van Schouwenburg PA, Davenport EE, Kienzler AK, Marwah I, Wright B, Lucas M, Malinauskas T, Martin HC, WGS500 Consortium, Lockstone HE, Cazier JB, Chapel HM, Knight JC, Patel SY.
Clinical immunology (Orlando, Fla.) Volume 160 (2015) p.301-314

Efficient set tests for the genetic analysis of correlated traits.
Casale FP, Rakitsch B, Lippert C, Stegle O.
Nature methods Volume 12 (2015) p.755-758

Computational assignment of cell-cycle stage from single-cell transcriptome data.
Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, Marioni JC, Buettner F.
Methods (San Diego, Calif.) Volume 85 (2015) p.54-61

2014

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, Andrews SR, Stegle O, Reik W, Kelsey G.
Nature methods Volume 11 (2014) p.817-820

High-resolution genome screen for bone mineral density in heterogeneous stock rat.
Alam I, Koller DL, Cañete T, Blázquez G, López-Aumatell R, Martínez-Membrives E, Díaz-Morán S, Tobeña A, Fernández-Teruel A, Stridh P, Diez M, Olsson T, Johannesson M, Baud A, Econs MJ, Foroud T.
Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research Volume 29 (2014) p.1619-1626

The architecture of parent-of-origin effects in mice.
Mott R, Yuan W, Kaisaki P, Gan X, Cleak J, Edwards A, Baud A, Flint J.
Cell Volume 156 (2014) p.332-342

Protease inhibitor 15, a candidate gene for abdominal aortic internal elastic lamina ruptures in the rat.
Falak S, Schafer S, Baud A, Hummel O, Schulz H, Gauguier D, Hubner N, Osborne-Pellegrin M.
Physiological genomics Volume 46 (2014) p.418-428

Genomes and phenomes of a population of outbred rats and its progenitors.
Baud A, Guryev V, Hummel O, Johannesson M, Rat Genome Sequencing and Mapping Consortium, Flint J.
Scientific data Volume 1 (2014) p.140011

Natural polymorphisms in Tap2 influence negative selection and CD4∶CD8 lineage commitment in the rat.
Tuncel J, Haag S, Yau AC, Norin U, Baud A, Lönnblom E, Maratou K, Ytterberg AJ, Ekman D, Thordardottir S, Johannesson M, Gillett A, EURATRANS Consortium, Stridh P, Jagodic M, Olsson T, Fernández-Teruel A, Zubarev RA, Mott R, Aitman TJ, Flint J, Holmdahl R.
PLoS genetics Volume 10 (2014) p.e1004151

Warped linear mixed models for the genetic analysis of transformed phenotypes.
Fusi N, Lippert C, Lawrence ND, Stegle O.
Nature Communications Volume 5 (2014) p.4890

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
SEQC/MAQC-III Consortium.
Nature biotechnology Volume 32 (2014) p.903-914

Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis.
Cubillos FA, Stegle O, Grondin C, Canut M, Tisné S, Gy I, Loudet O.
The Plant cell Volume 26 (2014) p.4298-4310

2013

The future of genome-based medicine.
Morris Q, Brenner SE, Listgarten J, Stegle O.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Volume (2013) p.456-458

Detecting regulatory gene-environment interactions with unmeasured environmental factors.
Fusi N, Lippert C, Borgwardt K, Lawrence ND, Stegle O.
Bioinformatics (Oxford, England) Volume 29 (2013) p.1382-1389

Accurate detection of differential RNA processing.
Drewe P, Stegle O, Hartmann L, Kahles A, Bohnert R, Wachter A, Borgwardt K, Rätsch G.
Nucleic acids research Volume 41 (2013) p.5189-5198

A Lasso multi-marker mixed model for association mapping with population structure correction.
Rakitsch B, Lippert C, Stegle O, Borgwardt K.
Bioinformatics (Oxford, England) Volume 29 (2013) p.206-214

[Genome sequencing and genetic mapping to dissect the genetic basis of complex traits].
Baud A, Calderari S, Mott R, Flint J, Gauguier D, Rat Genome Sequencing and Mapping Consortium.
Medecine sciences : M/S Volume 29 (2013) p.671-674

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.
Rat Genome Sequencing and Mapping Consortium, Baud A, Hermsen R, Guryev V, Stridh P, Graham D, McBride MW, Foroud T, Calderari S, Diez M, Ockinger J, Beyeen AD, Gillett A, Abdelmagid N, Guerreiro-Cacais AO, Jagodic M, Tuncel J, Norin U, Beattie E, Huynh N, Miller WH, Koller DL, Alam I, Falak S, Osborne-Pellegrin M, Martinez-Membrives E, Canete T, Blazquez G, Vicens-Costa E, Mont-Cardona C, Diaz-Moran S, Tobena A, Hummel O, Zelenika D, Saar K, Patone G, Bauerfeind A, Bihoreau MT, Heinig M, Lee YA, Rintisch C, Schulz H, Wheeler DA, Worley KC, Muzny DM, Gibbs RA, Lathrop M, Lansu N, Toonen P, Ruzius FP, de Bruijn E, Hauser H, Adams DJ, Keane T, Atanur SS, Aitman TJ, Flicek P, Malinauskas T, Jones EY, Ekman D, Lopez-Aumatell R, Dominiczak AF, Johannesson M, Holmdahl R, Olsson T, Gauguier D, Hubner N, Fernandez-Teruel A, Cuppen E, Mott R, Flint J.
Nature genetics Volume 45 (2013) p.767-775

Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype.
Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, Schuon AK, Pe'er D, Steinmetz LM.
PLoS genetics Volume 9 (2013) p.e1003803

Transcriptome and genome sequencing uncovers functional variation in humans.
Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM, Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET.
Nature Volume 501 (2013) p.506-511

A Palaeolithic-type diet causes strong tissue-specific effects on ectopic fat deposition in obese postmenopausal women.
Ryberg M, Sandberg S, Mellberg C, Stegle O, Lindahl B, Larsson C, Hauksson J, Olsson T.
Journal of internal medicine Volume 274 (2013) p.67-76

2012

Patterns of cis regulatory variation in diverse human populations.
Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET.
PLoS Genetics Volume 8 (2012) p.e1002639

ShapePheno: unsupervised extraction of shape phenotypes from biological image collections.
Karaletsos T, Stegle O, Dreyer C, Winn J, Borgwardt KM.
Bioinformatics (Oxford, England) Volume 28 (2012) p.1001-1008

Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies.
Fusi N, Stegle O, Lawrence ND.
PLoS Computational Biology Volume 8 (2012) p.e1002330

Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis.
Windram O, Madhou P, McHattie S, Hill C, Hickman R, Cooke E, Jenkins DJ, Penfold CA, Baxter L, Breeze E, Kiddle SJ, Rhodes J, Atwell S, Kliebenstein DJ, Kim YS, Stegle O, Borgwardt K, Zhang C, Tabrett A, Legaie R, Moore J, Finkenstadt B, Wild DL, Mead A, Rand D, Beynon J, Ott S, Buchanan-Wollaston V, Denby KJ.
The Plant cell Volume 24 (2012) p.3530-3557

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses.
Stegle O, Parts L, Piipari M, Winn J, Durbin R.
Nature protocols Volume 7 (2012) p.500-507

Unknown year

LIMIX: genetic analysis of multiple traits
Lippert C, Casale F, Rakitsch B, Stegle O.
Volume (0) p.

The Human Cell Atlas
Regev A, Teichmann S, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Gottgens B, Hacohen N, Haniffa M, Hemberg M, Kim SK, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundeberg J, Majumder P, Marioni J, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Philipakis A, Ponting CP, Quake SR, Reik W, Rozenblatt-Rosen O, Sanes JR, Satija R, Shumacher T, Shalek AK, Shapiro E, Sharma P, Shin J, Stegle O, Stratton M, Stubbington MJT, van Oudenaarden A, Wagner A, Watt FM, Weissman JS, Wold B, Xavier RJ, Yosef N, Human Cell Atlas Meeting Participants.
Volume (0) p.

Pan-cancer study of heterogeneous RNA aberrations
Fonseca NA, Kahles A, Lehmann K, Calabrese C, Chateigner A, Davidson NR, Demircioglu D, He Y, Lamaze FC, Li S, Liu D, Liu F, Perry MD, Su H, Xiang L, Zhang J, Amin SB, Bailey P, Craft B, Frenkel-Morgenstern M, Goldman M, Greger L, Hoadley KA, Hou Y, Khurana E, Korbel JO, Li C, Li X, Li X, Liu X, Lu Y, Marin MG, Meyerson M, Nandi T, Nielsen MM, Ojesina AI, Ouellette B, Pan-Hammarstroem Q, Pedamallu CS, Pedersen JS, Shiraishi Y, Siebert R, Soulette CM, Stark SG, Tan P, Tean Teh B, Valencia A, Wang J, Xing R, Xiong H, Yakneen S, Ye C, Yung C, Zhang F, Zhang X, Zheng L, Zhu J, Zhu S, Awadalla P, Creighton CJ, Goeke J, Schwarz RA, Stegle O, Wu K, Yang H, Zhang Z, Brazma A, Raetsch G, Brooks AN, PCAWG Network.
Volume (0) p.

SpatialDE - Identification Of Spatially Variable Genes
Svensson V, Teichmann SA, Stegle O.
Volume (0) p.

Joint Profiling Of Chromatin Accessibility, DNA Methylation And Transcription In Single Cells
Clark SJ, Argelaguet R, Kapourani C, Stubbs TM, Lee HJ, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W.
Volume (0) p.

Warped Matrix Factorisation for Multi-view Data Integration
Pratanwanich N, Lió P, Stegle O.
Volume (0) p.789-804

A pan cancer analysis of promoter activity highlights the regulatory role of alternative transcription start sites and their association with noncoding mutations
Demircioglu D, Kindermans M, Nandi T, Cukuroglu E, Calabrese C, Fonseca NA, Kahles A, Lehmann K, Stegle O, PCAWG-3, PCAWG-Network, Brazma A, Brooks A, Raetsch G, Tan P, Goeke J.
Volume (0) p.