Publications

Publications

2018

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.
Argelaguet R, Velten B, Arnol D, Dietrich S, Zenz T, Marioni JC, Buettner F, Huber W, Stegle O. Molecular systems biology Volume 14 (2018) p.e8124 DOI: 10.15252/msb.20178124
Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.
Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TMF, Bacanu SA, Bækvad-Hansen M, Beekman AFT, Bigdeli TB, Binder EB, Blackwood DRH, Bryois J, Buttenschøn HN, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen JH, Clarke TK, Coleman JIR, Colodro-Conde L, Couvy-Duchesne B, Craddock N, Crawford GE, Crowley CA, Dashti HS, Davies G, Deary IJ, Degenhardt F, Derks EM, Direk N, Dolan CV, Dunn EC, Eley TC, Eriksson N, Escott-Price V, Kiadeh FHF, Finucane HK, Forstner AJ, Frank J, Gaspar HA, Gill M, Giusti-Rodríguez P, Goes FS, Gordon SD, Grove J, Hall LS, Hannon E, Hansen CS, Hansen TF, Herms S, Hickie IB, Hoffmann P, Homuth G, Horn C, Hottenga JJ, Hougaard DM, Hu M, Hyde CL, Ising M, Jansen R, Jin F, Jorgenson E, Knowles JA, Kohane IS, Kraft J, Kretzschmar WW, Krogh J, Kutalik Z, Lane JM, Li Y, Li Y, Lind PA, Liu X, Lu L, MacIntyre DJ, MacKinnon DF, Maier RM, Maier W, Marchini J, Mbarek H, McGrath P, McGuffin P, Medland SE, Mehta D, Middeldorp CM, Mihailov E, Milaneschi Y, Milani L, Mill J, Mondimore FM, Montgomery GW, Mostafavi S, Mullins N, Nauck M, Ng B, Nivard MG, Nyholt DR, O'Reilly PF, Oskarsson H, Owen MJ, Painter JN, Pedersen CB, Pedersen MG, Peterson RE, Pettersson E, Peyrot WJ, Pistis G, Posthuma D, Purcell SM, Quiroz JA, Qvist P, Rice JP, Riley BP, Rivera M, Saeed Mirza S, Saxena R, Schoevers R, Schulte EC, Shen L, Shi J, Shyn SI, Sigurdsson E, Sinnamon GBC, Smit JH, Smith DJ, Stefansson H, Steinberg S, Stockmeier CA, Streit F, Strohmaier J, Tansey KE, Teismann H, Teumer A, Thompson W, Thomson PA, Thorgeirsson TE, Tian C, Traylor M, Treutlein J, Trubetskoy V, Uitterlinden AG, Umbricht D, Van der Auwera S, van Hemert AM, Viktorin A, Visscher PM, Wang Y, Webb BT, Weinsheimer SM, Wellmann J, Willemsen G, Witt SH, Wu Y, Xi HS, Yang J, Zhang F, eQTLGen, 23andMe, Arolt V, Baune BT, Berger K, Boomsma DI, Cichon S, Dannlowski U, de Geus ECJ, DePaulo JR, Domenici E, Domschke K, Esko T, Grabe HJ, Hamilton SP, Hayward C, Heath AC, Hinds DA, Kendler KS, Kloiber S, Lewis G, Li QS, Lucae S, Madden PFA, Magnusson PK, Martin NG, McIntosh AM, Metspalu A, Mors O, Mortensen PB, Müller-Myhsok B, Nordentoft M, Nöthen MM, O'Donovan MC, Paciga SA, Pedersen NL, Penninx BWJH, Perlis RH, Porteous DJ, Potash JB, Preisig M, Rietschel M, Schaefer C, Schulze TG, Smoller JW, Stefansson K, Tiemeier H, Uher R, Völzke H, Weissman MM, Werge T, Winslow AR, Lewis CM, Levinson DF, Breen G, Børglum AD, Sullivan PF, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium. Nature genetics Volume 50 (2018) p.668-681 DOI: 10.1038/s41588-018-0090-3
Interactions between genetic variation and cellular environment in skeletal muscle gene expression.
Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Casale FP, Wolford BN, Guan L, Varshney A, Albanus RD, Parker SCJ, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS. PloS one Volume 13 (2018) p.e0195788 DOI: 10.1371/journal.pone.0195788
SpatialDE: identification of spatially variable genes.
Svensson V, Teichmann SA, Stegle O. Nature methods Volume 15 (2018) p.343-346 DOI: 10.1038/nmeth.4636
Molecular Genetic Analysis Subdivided by Adversity Exposure Suggests Etiologic Heterogeneity in Major Depression.
Peterson RE, Cai N, Dahl AW, Bigdeli TB, Edwards AC, Webb BT, Bacanu SA, Zaitlen N, Flint J, Kendler KS. The American journal of psychiatry Volume 175 (2018) p.545-554 DOI: 10.1176/appi.ajp.2017.17060621
scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.
Clark SJ, Argelaguet R, Kapourani CA, Stubbs TM, Lee HJ, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W. Nature communications Volume 9 (2018) p.781 DOI: 10.1038/s41467-018-03149-4
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A SNP panel for identification of DNA and RNA specimens.
Yousefi S, Abbassi-Daloii T, Kraaijenbrink T, Vermaat M, Mei H, van 't Hof P, van Iterson M, Zhernakova DV, Claringbould A, Franke L, 't Hart LM, Slieker RC, van der Heijden A, de Knijff P, BIOS consortium, 't Hoen PAC. BMC genomics Volume 19 (2018) p.90 DOI: 10.1186/s12864-018-4482-7
Expression Atlas: gene and protein expression across multiple studies and organisms.
Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AM, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R. Nucleic acids research Volume 46 (2018) p.D246-D251 DOI: 10.1093/nar/gkx1158

2017

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Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.
Flannick J, Fuchsberger C, Mahajan A, Teslovich TM, Agarwala V, Gaulton KJ, Caulkins L, Koesterer R, Ma C, 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, 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 JC, 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, Mohlke KL, Meitinger T, Groop L, Abecasis G, Scott LJ, Morris AP, Kang HM, Altshuler D, Burtt NP, Florez JC, Boehnke M, McCarthy MI. Scientific data Volume 4 (2017) p.170179 DOI: 10.1038/sdata.2017.179
The Human Cell Atlas.
Regev A, Teichmann SA, 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, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N, Human Cell Atlas Meeting Participants. eLife Volume 6 (2017) DOI: 10.7554/elife.27041
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DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation.
Richard MA, Huan T, Ligthart S, Gondalia R, Jhun MA, Brody JA, Irvin MR, Marioni R, Shen J, Tsai PC, Montasser ME, Jia Y, Syme C, Salfati EL, Boerwinkle E, Guan W, Mosley TH, Bressler J, Morrison AC, Liu C, Mendelson MM, Uitterlinden AG, van Meurs JB, BIOS Consortium, Franco OH, Zhang G, Li Y, Stewart JD, Bis JC, Psaty BM, Chen YI, Kardia SLR, Zhao W, Turner ST, Absher D, Aslibekyan S, Starr JM, McRae AF, Hou L, Just AC, Schwartz JD, Vokonas PS, Menni C, Spector TD, Shuldiner A, Damcott CM, Rotter JI, Palmas W, Liu Y, Paus T, Horvath S, O'Connell JR, Guo X, Pausova Z, Assimes TL, Sotoodehnia N, Smith JA, Arnett DK, Deary IJ, Baccarelli AA, Bell JT, Whitsel E, Dehghan A, Levy D, Fornage M. American journal of human genetics Volume 101 (2017) p.888-902 DOI: 10.1016/j.ajhg.2017.09.028
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 DOI: 10.1038/s41467-017-01818-4
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 (2017) DOI: 10.1136/gutjnl-2017-314817
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 DOI: 10.1186/s13059-017-1334-8
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NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease.
Schwerd T, Bryant RV, Pandey S, Capitani M, Meran L, Cazier JB, Jung J, Mondal K, Parkes M, Mathew CG, Fiedler K, McCarthy DJ, WGS500 Consortium, Oxford IBD cohort study investigators, COLORS in IBD group investigators, UK IBD Genetics Consortium, Sullivan PB, Rodrigues A, Travis SPL, Moore C, Sambrook J, Ouwehand WH, Roberts DJ, Danesh J, INTERVAL Study, Russell RK, Wilson DC, Kelsen JR, Cornall R, Denson LA, Kugathasan S, Knaus UG, Serra EG, Anderson CA, Duerr RH, McGovern DP, Cho J, Powrie F, Li VS, Muise AM, Uhlig HH. Mucosal immunology Volume 11 (2018) p.562-574 DOI: 10.1038/mi.2017.74
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 154 (2018) p.585-598 DOI: 10.1053/j.gastro.2017.10.007
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 DOI: 10.1126/science.aan6826
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C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis.
Lepik K, Annilo T, Kukuškina V, eQTLGen Consortium, Kisand K, Kutalik Z, Peterson P, Peterson H. PLoS computational biology Volume 13 (2017) p.e1005766 DOI: 10.1371/journal.pcbi.1005766
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Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Fonseca NA, He Y, Kahles A, Lehmann K, Liu F, Shiraishi Y, Soulette CM, Urban L, Demircioğlu D, Greger L, Li S, Liu D, Perry MD, Xiang L, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Sekhar Pedamallu C, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Francis Ouellette B, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, PCAWG Transcriptome Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/183889
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Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
Seaton D, Graf A, Baerenfaller K, Stitt M, Millar A, Gruissem W. Preprint DOI: 10.1101/182071
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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. Preprint DOI: 10.1101/176487
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 DOI: 10.1016/j.celrep.2017.08.010
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 DOI: 10.1038/ncomms16058
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Corrigendum: 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.686 DOI: 10.1038/nature23012
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SpatialDE - Identification Of Spatially Variable Genes
Svensson V, Teichmann SA, Stegle O. Preprint DOI: 10.1101/143321
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 DOI: 10.1016/j.ajhg.2017.04.014
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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. Preprint DOI: 10.1101/138685
Erratum to: DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.
Angermueller C, Lee HJ, Reik W, Stegle O. Genome biology Volume 18 (2017) p.90 DOI: 10.1186/s13059-017-1233-z
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 DOI: 10.1038/nature22403
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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. Preprint DOI: 10.1101/121202
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 DOI: 10.1016/j.cell.2017.04.018
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 DOI: 10.1371/journal.pgen.1006693
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 DOI: 10.1186/s13059-017-1189-z
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 DOI: 10.1186/s13059-017-1203-5
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 DOI: 10.1093/bioinformatics/btw777
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) DOI: 10.1126/sciimmunol.aal2192
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 DOI: 10.1038/ng.3791
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 DOI: 10.1534/genetics.116.192823
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Interactions between genetic variation and cellular environment in skeletal muscle gene expression
Taylor D, Knowles DA, Scott LJ, Ramirez AH, Paolo Casale F, Wolford BN, Guan L, Varshney A, D'Oliveira Albanus R, Parker SCJ, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS. Preprint DOI: 10.1101/105429
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 DOI: 10.1001/jamapsychiatry.2016.3578
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 DOI: 10.1186/s13059-017-1156-8
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 DOI: 10.1371/journal.pgen.1006498
ODE-Based Modeling of Complex Regulatory Circuits.
Seaton DD. Methods in molecular biology (Clifton, N.J.) Volume 1629 (2017) p.317-330 DOI: 10.1007/978-1-4939-7125-1_20

2016

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 DOI: 10.1038/nature20802
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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 DOI: 10.1016/j.cell.2016.11.046
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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 DOI: 10.1093/hmg/ddw347
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 DOI: 10.1093/nar/gkw1055
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 Volume 167 (2016) p.1398-1414.e24 DOI: 10.1016/j.cell.2016.10.026
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 DOI: 10.1016/j.cell.2016.09.037
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Warped Matrix Factorisation for Multi-view Data Integration
Pratanwanich N, Lió P, Stegle O. Machine Learning and Knowledge Discovery in Databases. ECML PKDD 2016. Springer , Cham (Lecture Notes in Computer Science, vol 9852) DOI: 10.1007/978-3-319-46227-1_49
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.
Lun AT, McCarthy DJ, Marioni JC. F1000Research Volume 5 (2016) p.2122 DOI: 10.12688/f1000research.9501.1
Deep learning for computational biology.
Angermueller C, Pärnamaa T, Parts L, Stegle O. Molecular systems biology Volume 12 (2016) p.878 DOI: 10.15252/msb.20156651
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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 DOI: 10.1038/nature18642
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 DOI: 10.1371/journal.pgen.1006141
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 DOI: 10.1093/bioinformatics/btw385
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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 DOI: 10.1038/ncomms11115
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 DOI: 10.1186/s13059-016-0895-2
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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 DOI: 10.1016/j.jaut.2016.01.002
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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 DOI: 10.1007/s00125-016-3872-0
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 DOI: 10.1038/nmeth.3728

2015

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 DOI: 10.1016/j.ymeth.2015.11.012
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 DOI: 10.1038/nature15394
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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 DOI: 10.1038/nature15393
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 DOI: 10.1371/journal.pone.0137206
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Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability.
Twigg SR, Forecki J, Goos JA, Richardson IC, Hoogeboom AJ, van den Ouweland AM, Swagemakers SM, Lequin MH, Van Antwerp D, McGowan SJ, Westbury I, Miller KA, Wall SA, WGS500 Consortium, van der Spek PJ, Mathijssen IM, Pauws E, Merzdorf CS, Wilkie AO. American journal of human genetics Volume 97 (2015) p.378-388 DOI: 10.1016/j.ajhg.2015.07.007
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 DOI: 10.1016/j.ymeth.2015.06.021
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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 DOI: 10.1016/j.clim.2015.05.020
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 DOI: 10.1038/ncomms8432
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 DOI: 10.1038/nmeth.3439
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 DOI: 10.7554/elife.05255
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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 DOI: 10.1126/science.1261877
Computational and analytical challenges in single-cell transcriptomics.
Stegle O, Teichmann SA, Marioni JC. Nature reviews. Genetics Volume 16 (2015) p.133-145 DOI: 10.1038/nrg3833
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 DOI: 10.1038/nbt.3102
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 DOI: 10.1371/journal.pgen.1004920
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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 (2015) p.44-55
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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 (2015) p.342-346

2014

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 DOI: 10.1105/tpc.114.130310
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 DOI: 10.1038/ncomms5890
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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 DOI: 10.1038/nbt.2957
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 DOI: 10.1038/nmeth.3035
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LIMIX: genetic analysis of multiple traits
Lippert C, Casale F, Rakitsch B, Stegle O. Preprint DOI: 10.1101/003905

2013

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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 DOI: 10.1371/journal.pgen.1003803
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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 DOI: 10.1038/nature12531
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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 DOI: 10.1093/nar/gkt211
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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 DOI: 10.1093/bioinformatics/btt148
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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 DOI: 10.1111/joim.12048
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The future of genome-based medicine.
Morris Q, Brenner SE, Listgarten J, Stegle O. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2013) p.456-458

2012

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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 DOI: 10.1093/bioinformatics/bts669
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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 DOI: 10.1105/tpc.112.102046
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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 DOI: 10.1371/journal.pgen.1002639
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ShapePheno: unsupervised extraction of shape phenotypes from biological image collections.
Karaletsos T, Stegle O, Dreyer C, Winn J, Borgwardt KM. Bioinformatics Volume 28 (2012) p.1001-1008 DOI: 10.1093/bioinformatics/bts081
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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 DOI: 10.1371/journal.pcbi.1002330