Menden MP, Casale FP, Stephan J, Bignell GR, Iorio F, McDermott U, Garnett MJ, Saez-Rodriguez J, Stegle O. (2018)

The germline genetic component of drug sensitivity in cancer cell lines.

Nat Commun 9(1) doi: 10.1038/s41467-018-05811-3
Europe PMC | doi

Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C, Sander C, Rätsch G. (2018)

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.

Cancer Cell 34(2) doi: 10.1016/j.ccell.2018.07.001
Europe PMC | doi

Rulands S, Lee HJ, Clark SJ, Angermueller C, Smallwood SA, Krueger F, Mohammed H, Dean W, Nichols J, Rugg-Gunn P, Kelsey G, Stegle O, Simons BD, Reik W. (2018)

Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency.

Cell Syst 7(1):63-76.e12. doi: 10.1016/j.cels.2018.06.012
Europe PMC | doi

Argelaguet R, Velten B, Arnol D, Dietrich S, Zenz T, Marioni JC, Buettner F, Huber W, Stegle O. (2018)

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

Mol. Syst. Biol. 14(6) doi: 10.15252/msb.20178124
Europe PMC | doi

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. (2018)

Interactions between genetic variation and cellular environment in skeletal muscle gene expression.

PLoS One 13(4) doi: 10.1371/journal.pone.0195788
Europe PMC | doi

Svensson V, Teichmann SA, Stegle O. (2018)

SpatialDE: identification of spatially variable genes.

Nat. Methods 15(5) doi: 10.1038/nmeth.4636
Europe PMC | doi

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. (2018)

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.

Nat Commun 9(1) doi: 10.1038/s41467-018-03149-4
Europe PMC | doi

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. (2018)

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.

Gastroenterology 154(3) doi: 10.1053/j.gastro.2017.10.007
Europe PMC | doi

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. (2018)

Expression Atlas: gene and protein expression across multiple studies and organisms.

Nucleic Acids Res. 46(D1) doi: 10.1093/nar/gkx1158
Europe PMC | doi

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell PJ, 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 SK, 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 SR, Reik W, Rozenblatt-Rosen O, Sanes JR, Satija R, Schumacher TN, Shalek AK, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton MR, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt FM, Weissman JS, Wold BJ, Xavier RJ, Yosef N, Yosef N. (2017)

Science Forum: The Human Cell Atlas.

Elife 6 doi: 10.7554/eLife.27041
Europe PMC | doi

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. (2017)

DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.

Gut doi: 10.1136/gutjnl-2017-314817
Europe PMC | doi

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. (2017)

Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus.

Nat Commun 8(1) doi: 10.1038/s41467-017-01818-4
Europe PMC | doi

Buettner F, Pratanwanich N, McCarthy DJ, Marioni JC, Stegle O. (2017)

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.

Genome Biol 18(1):212. doi: 10.1186/s13059-017-1334-8
Europe PMC | doi

Kelsey G, Stegle O, Reik W. (2017)

Single-cell epigenomics: Recording the past and predicting the future.

Science 358(6359):69-75. doi: 10.1126/science.aan6826
Europe PMC | doi

Roumeliotis TI, Williams SP, Goncalves E, Alsinet C, Velasco-Herrera MD, 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. (2017)

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells

Cell Rep 20(9):2201-2214. doi: 10.1016/j.celrep.2017.08.010
Europe PMC | doi

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. (2017)

Platelet function is modified by common sequence variation in megakaryocyte super enhancers.

Nat Commun 8 doi: 10.1038/ncomms16058
Europe PMC | doi

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. (2017)

Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs.

Nature 546(7660):686. doi: 10.1038/nature23012
Europe PMC | doi

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. (2017)

Common genetic variation drives molecular heterogeneity in human iPSCs.

Nature 546(7658) doi: 10.1038/nature22403
Europe PMC | doi

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, Wareham NJ, Wareham NJ, 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, Uitterlinden AG, Uitterlinden AG, Uitterlinden AG, Barroso I, Greenwood CMT, Perry JRB, Walker BR, Butterworth AS, Xue Y, Durbin R, Small KS, Soranzo N, Timpson NJ, Zeggini E. (2017)

Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.

Am. J. Hum. Genet. 100(6):865-884. doi: 10.1016/j.ajhg.2017.04.014
Europe PMC | doi

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. (2017)

Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.

Cell 169(5):807-823. doi: 10.1016/j.cell.2017.04.018
Europe PMC | doi

Angermueller C, Lee HJ, Reik W, Stegle O. (2017)

Erratum to: DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.

Genome Biol. 18(1) doi: 10.1186/s13059-017-1233-z
Europe PMC | doi

Casale FP, Horta D, Rakitsch B, Stegle O. (2017)

Joint genetic analysis using variant sets reveals polygenic gene-context interactions.

PLoS Genet. 13(4):1-27. doi: 10.1371/journal.pgen.1006693
Europe PMC | doi

Angermueller C, Lee HJ, Reik W, Stegle O. (2017)

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.

Genome Biol. 18(1):1-13. doi: 10.1186/s13059-017-1189-z
Europe PMC | doi

Stubbs TM, Bonder MJ, Stark AK, Krueger F, von Meyenn F, Stegle O, Reik W. (2017)

Multi-tissue DNA methylation age predictor in mouse

Genome Biol. 18(1):1-14. doi: 10.1186/s13059-017-1203-5
Europe PMC | doi

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. (2017)

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.

Genetics 205(4):1425-1441. doi: 10.1534/genetics.116.192823
Europe PMC | doi

Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE. (2017)

Promoter shape varies across populations and affects promoter evolution and expression noise.

Nat. Genet. 49(4):550-558. doi: 10.1038/ng.3791
Europe PMC | doi

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. (2017)

Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.

Sci Immunol 2(9):eaal2192. doi: 10.1126/sciimmunol.aal2192
Europe PMC | doi

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. (2017)

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

Genome Biol. 18(1):18. doi: 10.1186/s13059-017-1156-8
Europe PMC | doi

Baud A, Mulligan MK, Casale FP, Ingels JF, Bohl CJ, Callebert J, Launay JM, Krohn J, Legarra A, Williams RW, Stegle O. (2017)

Genetic Variation in the Social Environment Contributes to Health and Disease.

PLoS Genet. 13(1):e1006498. doi: 10.1371/journal.pgen.1006498
Europe PMC | doi

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. (2017)

Genetic variants regulating expression levels and isoform diversity during embryogenesis.

Nature 541(7637):402-406. doi: 10.1038/nature20802
Europe PMC | doi

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. (2017)

Open Targets: a platform for therapeutic target identification and validation.

Nucleic Acids Res. 45(D1):D985-D994. doi: 10.1093/nar/gkw1055
Europe PMC | doi

Grimm DG, Roqueiro D, Salome P, Kleeberger S, Greshake B, Zhu W, Liu C, Lippert C, Stegle O, Schölkopf B, Weigel D, Borgwardt K. (2016)

easyGWAS: A Cloud-based Platform for Comparing the Results of Genome-wide Association Studies.

Plant Cell 29(1) doi: 10.1105/tpc.16.00551
Europe PMC | doi

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. (2016)

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

Cell 167(5):1398-1414.e24. doi: 10.1016/j.cell.2016.10.026
Europe PMC | doi

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. (2016)

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.

Cell 167(5):1369-1384.e19. doi: 10.1016/j.cell.2016.09.037
Europe PMC | doi

Angermueller C, Parnamaa T, Parts L, Stegle O. (2016)

Deep learning for computational biology.

Mol. Syst. Biol. 12(7) doi: 10.15252/msb.20156651
Europe PMC | doi

Meng D, Dubin M, Zhang P, Osborne EJ, Stegle O, Clark RM, Nordborg M. (2016)

Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana.

PLoS Genet. 12(7):e1006141. doi: 10.1371/journal.pgen.1006141
Europe PMC | doi

Greenfield D, Stegle O, Rrustemi A. (2016)

GeneCodeq: quality score compression and improved genotyping using a Bayesian framework.

Bioinformatics 32(20) doi: 10.1093/bioinformatics/btw385
Europe PMC | doi

Leha A, Moens N, Meleckyte R, Culley OJ, Gervasio MK, Kerz M, Reimer A, Cain SA, Streeter I, Folarin A, Stegle O, Kielty CM, Kielty CM, Durbin R, Watt FM, Danovi D. (2016)

A high-content platform to characterise human induced pluripotent stem cell lines.

Methods 96:85-96. doi: 10.1016/j.ymeth.2015.11.012
Europe PMC | doi

Rakitsch B, Stegle O. (2016)

Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression.

Genome Biol. 17(1) doi: 10.1186/s13059-016-0895-2
Europe PMC | doi

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 RSN, Herms S, Nalls M, Zhao W, Turner ST, Yaffe K, Lohman K, van Swieten JC, Kardia SLR, 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, Nothen MM, Hofman A, Slagboom PE, Westendorp RGJ, Buckley BM, Wolf PA, Uitterlinden AG, Psaty BM, Grabe HJ, Bandinelli S, Chasman DI, Grodstein F, Roikkonen K, Lambert JC, Porteous DJ, 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 AJM, Fornage M, Bennett DA, Deary IJ, Ikram MA, Launer LJ, Fitzpatrick AL, Seshadri S, van Duijn CM, Mosley TH. (2016)

GWAS for executive function and processing speed suggests involvement of the CADM2 gene

Mol Psychiatry 21(2):189-197. doi: 10.1038/mp.2015.37
Europe PMC | doi

Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood SA, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W. (2016)

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.

Nat. Methods 13(3) doi: 10.1038/nmeth.3728
Europe PMC | doi

Dudley JT, Listgarten J, Stegle O, Brenner SE, Parts L. (2015)

Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.

Paper presented at the Pacific Symposium on Biocomputing 2015, Kohala Coast, Hawaii, USA, 4–8 January 2015.In: Altman RB, Dunker AK, Hunter L, Murray TA, Klein TE, Ritchie MD (eds.), Pacific Symposium on Biocomputing 2015. pp 342-6.Pac Symp Biocomput 342-6. doi: 10.1142/9789814644730_0033
Europe PMC | doi

1000 Genomes Project Consortium. (2015)

A global reference for human genetic variation.

Nature 526(7571):68-74. doi: 10.1038/nature15393
Europe PMC | doi

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. (2015)

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

Nature 526(7571):75-81. doi: 10.1038/nature15394
Europe PMC | doi

Brage S, Westgate K, Franks PW, Stegle O, Wright A, Ekelund U, Wareham NJ. (2015)

Estimation of Free-Living Energy Expenditure by Heart Rate and Movement Sensing: A Doubly-Labelled Water Study

PLoS One 10(9) doi: 10.1371/journal.pone.0137206
Europe PMC | doi

Casale FP, Rakitsch B, Lippert C, Stegle O. (2015)

Efficient set tests for the genetic analysis of correlated traits

Nat. Methods 12(8):755-U93. doi: 10.1038/NMETH.3439
Europe PMC | doi

Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, Marioni JC, Buettner F. (2015)

Computational assignment of cell-cycle stage from single-cell transcriptome data.

Methods 85 doi: 10.1016/j.ymeth.2015.06.021
Europe PMC | doi

Stephan J, Stegle O, Beyer A. (2015)

A random forest approach to capture genetic effects in the presence of population structure.

Nat Commun 6 doi: 10.1038/ncomms8432
Europe PMC | doi

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. (2015)

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.

Elife 4 doi: 10.7554/elife.05255
Europe PMC | doi

Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O. (2015)

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.

Nat. Biotechnol. 33(2) doi: 10.1038/nbt.3102
Europe PMC | doi

Lehmann KV, Kahles A, Kandoth C, Lee W, Schultz N, Stegle O, Rätsch G. (2015)

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.

Paper presented at the Pacific Symposium, Kohala Coast, Hawaii, USA, 4–8 January 2015.In: Altman RB, Dunker AK, Hunter L, Ritchie MD, Murray TA, Klein TE (eds.), Proceedings of the Pacific Symposium. pp 44-55.Pac Symp Biocomput 44-55. doi: 10.1142/9789814644730_0006
Europe PMC | doi

Stegle O, Teichmann SA, Marioni JC. (2015)

Computational and analytical challenges in single-cell transcriptomics.

Nat. Rev. Genet. 16(3) doi: 10.1038/nrg3833
Europe PMC | doi

Hagmann J, Becker C, Müller J, Stegle O, Meyer RC, Wang G, Schneeberger K, Fitz J, Altmann T, Bergelson J, Borgwardt K, Weigel D. (2015)

Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage.

PLoS Genet. 11(1) doi: 10.1371/journal.pgen.1004920
Europe PMC | doi

Listgarten J, Stegle O, Morris Q, Brenner SE, Parts L. (2014)

Personalized medicine: from genotypes and molecular phenotypes towards therapy- session introduction.

Paper presented at the Pacific Symposium on Biocomputing 2014, Kohala Coast, Hawaii, USA, 3–7 January 2014.In: Altman RB, Dunker AK, Hunter L, Murray TA, Klein TE, Ritchie MD (eds.), Pacific Symposium on Biocomputing 2014, vol 19. pp 224-8.Pac Symp Biocomput 19:224-8. doi: 10.1142/9789814583220_0022
Europe PMC | doi

Cubillos FA, Stegle O, Grondin C, Canut M, Tisné S, Gy I, Loudet O. (2014)

Extensive cis-Regulatory Variation Robust to Environmental Perturbation in Arabidopsis.

Plant Cell 26(11):4298-4310. doi: 10.1105/tpc.114.130310
Europe PMC | doi

Fusi N, Lippert C, Lawrence ND, Stegle O. (2014)

Warped linear mixed models for the genetic analysis of transformed phenotypes

Nat Commun 5:Article No:4890. doi: 10.1038/ncomms5890
Europe PMC | doi

SEQC/MAQC-III Consortium. (2014)

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.

Nat. Biotechnol. 32(9):903-914. doi: 10.1038/nbt.2957
Europe PMC | doi

Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, Andrews SR, Stegle O, Reik W, Kelsey G. (2014)

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

Nat. Methods 11(8):817-820. doi: 10.1038/nmeth.3035
Europe PMC | doi

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, Geuvadis Consortium. (2013)

Transcriptome and genome sequencing uncovers functional variation in humans

Nature 501(7468):506-511. doi: 10.1038/nature12531
Europe PMC | doi

Ryberg M, Sandberg S, Mellberg C, Stegle O, Lindahl B, Larsson C, Hauksson J, Olsson T. (2013)

A Palaeolithic-type diet causes strong tissue-specific effects on ectopic fat deposition in obese postmenopausal women

J. Intern. Med. 274(1):67-76. doi: 10.1111/joim.12048
Europe PMC | doi

Fusi N, Lippert C, Borgwardt K, Lawrence ND, Stegle O. (2013)

Detecting regulatory gene-environment interactions with unmeasured environmental factors

Bioinformatics 29(11):1382-1389. doi: 10.1093/bioinformatics/btt148
Europe PMC | doi

Drewe P, Stegle O, Hartmann L, Kahles A, Bohnert R, Wachter A, Borgwardt K, Rätsch G. (2013)

Accurate detection of differential RNA processing

Nucleic Acids Res. 41(10):5189-5198. doi: 10.1093/nar/gkt211
Europe PMC | doi

Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, Schuon AK, Pe'er D, Steinmetz LM. (2013)

Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype

PLoS Genet. 9(9):e1003803. doi: 10.1371/journal.pgen.1003803
Europe PMC | doi

Morris Q, Brenner SE, Listgarten J, Stegle O. (2013)

The future of genome-based medicine

Pac Symp Biocomput 456-458.
Europe PMC

Rakitsch B, Lippert C, Stegle O, Borgwardt K. (2013)

A Lasso multi-marker mixed model for association mapping with population structure correction

Bioinformatics 29(2):206-214. doi: 10.1093/bioinformatics/bts669
Europe PMC | doi

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. (2012)

Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis

Plant Cell 24(9):3530-3557. doi: 10.1105/tpc.112.102046
Europe PMC | doi

Karaletsos T, Stegle O, Dreyer C, Winn J, Borgwardt KM. (2012)

ShapePheno: unsupervised extraction of shape phenotypes from biological image collections

Bioinformatics 28(7):1001-1008. doi: 10.1093/bioinformatics/bts081
Europe PMC | doi

Stegle O, Parts L, Piipari M, Winn J, Durbin R. (2012)

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

Nat Protoc 7(3):500-507. doi: 10.1038/nprot.2011.457
Europe PMC | doi

Fusi N, Stegle O, Lawrence ND. (2012)

Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies

PLoS Comput. Biol. 8(1):e1002330. doi: 10.1371/journal.pcbi.1002330
Europe PMC | doi

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. (2012)

Patterns of cis regulatory variation in diverse human populations

PLoS Genet. 8(4):e1002639. doi: 10.1371/journal.pgen.1002639
Europe PMC | doi

Becker C, Hagmann J, Müller J, Koenig D, Stegle O, Borgwardt K, Weigel D. (2011)

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

Nature 480(7376):245-249. doi: 10.1038/nature10555
Europe PMC | doi

Klotzbucher K, Kobayashi Y, Shervashidze N, Stegle O, Muller-Myhsok B, Weigel D, Borgwardt K. (2011)

Efficient branch-and-bound techniques for two-locus association mapping

Paper presented at the Seventh International Society for Computational Biology (ISCB) Student Council Symposium 2011, Vienna, Austria, 15 July 2011.BMC BIOINFORMATICS 12 doi: 10.1186/1471-2105-12-S11-A3
doi

Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Müller J, Alonso-Blanco C, Borgwardt K, Schmid KJ, Weigel D. (2011)

Whole-genome sequencing of multiple Arabidopsis thaliana populations

Nat. Genet. 43(10):956-963. doi: 10.1038/ng.911
Europe PMC | doi

Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Rätsch G, Mott R. (2011)

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

Nature 477(7365):419-423. doi: 10.1038/nature10414
Europe PMC | doi

Parts L, Stegle O, Winn J, Durbin R. (2011)

Joint genetic analysis of gene expression data with inferred cellular phenotypes

PLoS Genet. 7(1):e1001276. doi: 10.1371/journal.pgen.1001276
Europe PMC | doi

Stegle O, Parts L, Durbin R, Winn J. (2010)

A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies

PLoS Comput. Biol. 6(5):e1000770. doi: 10.1371/journal.pcbi.1000770
Europe PMC | doi

Stegle O, Denby KJ, Cooke EJ, Wild DL, Ghahramani Z, Borgwardt KM. (2010)

A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series

J. Comput. Biol. 17(3):355-367. doi: 10.1089/cmb.2009.0175
Europe PMC | doi

Wong HM, Stegle O, Rodgers S, Huppert JL. (2010)

A toolbox for predicting g-quadruplex formation and stability

J Nucleic Acids 2010:930-933. doi: 10.4061/2010/564946
Europe PMC | doi

Stegle O, Payet L, Mergny JL, MacKay DJ, Leon JH. (2009)

Predicting and understanding the stability of G-quadruplexes

Paper presented at the Joint Conference of Intelligent Systems for Molecular Biology and the European Conference on Computational Biology, Stockholm, SWEDEN, JUN 27-JUL 02, 2009.Bioinformatics 25(12):i374-82. doi: 10.1093/bioinformatics/btp210
Europe PMC | doi

Stegle O, Fallert SV, MacKay DJ, Brage S. (2008)

Gaussian process robust regression for noisy heart rate data

IEEE Trans Biomed Eng 55(9):2143-2151. doi: 10.1109/tbme.2008.923118
Europe PMC | doi

Stegle O, Kannan A, Durbin R, Winn J. (2008)

Accounting for non-genetic factors improves the power of eQTL studies

Paper presented at the RECOMB 2008: Annual International Conference on Research in Computational Molecular Biology, Singapore, Singapore, 30 March - 2 April.In: Vingron M, Wong L (eds.), Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955. pp 411-+.LECT N BIOINFORMAT 4955:411. doi: 10.1007/978-3-540-78839-3_35
doi