PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium. (2020)

Genomic basis for RNA alterations in cancer.

Nature 578(7793):129-136. doi: 10.1038/s41586-020-1970-0
Europe PMC | doi

Holland CH, Tanevski J, Perales-Patón J, Gleixner J, Kumar MP, Mereu E, Joughin BA, Stegle O, Lauffenburger DA, Heyn H, Szalai B, Saez-Rodriguez J. (2020)

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.

Genome Biol. 21(1) doi: 10.1186/s13059-020-1949-z
Europe PMC | doi

Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, HipSci Consortium, Vallier L, Marioni JC, Stegle O, Chhatriwala M. (2020)

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.

Nat Commun 11(1) doi: 10.1038/s41467-020-14457-z
Europe PMC | doi

Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Balvert M, Baaijens J, Cappuccio A, Barbanson B, Dutilh BE, Corleone G, Guryev V, Florescu M, Jahn K, Holmer R, Keizer EM, Lobo TJ, Kielbasa SM, Khatri I, Kozlov AM, Korbel JO, Mandoiu II, Marioni JC, Kuo TH, Lelieveldt BPF, Niknejad A, Raczkowski L, Marschall T, Mölder F, Saliba AE, Somarakis A, Reinders M, Ridder J, Yang H, Zelikovsky A, Stegle O, Theis FJ, Schönhuth A, Shah SP, Raphael BJ, McHardy AC. (2020)

Eleven grand challenges in single-cell data science.

Genome Biol. 21(1) doi: 10.1186/s13059-020-1926-6
Europe PMC | doi

Huang Y, McCarthy DJ, Stegle O. (2020)

Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.

Genome Biol. 20(1) doi: 10.1186/s13059-019-1865-2
Europe PMC | doi

Cook CE, Stroe O, Cochrane G, Birney E, Apweiler R. (2020)

The European bioinformatics institute in 2020: building a global infrastructure of interconnected data resources for the life sciences.

Nucleic Acids Res. doi: 10.1093/nar/gkz1033
Europe PMC | doi

Argelaguet R, Clark SJ, Mohammed H, Stapel LC, Krueger C, Kapourani CA, Imaz-Rosshandler I, Lohoff T, Xiang Y, Hanna CW, Smallwood S, Ibarra-Soria X, Buettner F, Sanguinetti G, Xie W, Göttgens B, Krueger F, Kelsey G, Rugg-Gunn PJ, Nichols J, Dean W, Marioni JC, Stegle O, Reik W. (2019)

Multi-omics profiling of mouse gastrulation at single-cell resolution.

Nature 576(7787):487-491. doi: 10.1038/s41586-019-1825-8
Europe PMC | doi

Madissoon E, Wilbrey-Clark A, Miragaia RJ, Saeb-Parsy K, Mahbubani KT, Georgakopoulos N, Harding P, Polanski K, Huang N, Nowicki-Osuch K, Fitzgerald RC, Loudon KW, Ferdinand JR, Clatworthy MR, Tsingene A, Dabrowska M, van Dongen S, Stubbington MJT, Patel M, Stegle O, Teichmann SA, Meyer KB. (2019)

scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation.

Genome Biol. 21(1) doi: 10.1186/s13059-019-1906-x
Europe PMC | doi

D'Antonio M, Reyna J, Jakubosky D, Donovan MK, Bonder MJ, Matsui H, Stegle O, Nariai N, D'Antonio-Chronowska A, Frazer KA. (2019)

Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease.

Elife 8 doi: 10.7554/eLife.48476
Europe PMC | doi

Arnol D, Schapiro D, Bodenmiller B, Saez-Rodriguez J, Stegle O. (2019)

Modeling cell-cell interactions from spatial molecular data with spatial variance component analysis.

Cell Rep 29(1):202-211.e6. doi: 10.1016/j.celrep.2019.08.077
Europe PMC | doi

Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J. (2019)

A pan-cancer transcriptome analysis reveals pervasive regulation through alternative promoters.

Cell 178(6):1465-1477.e17. doi: 10.1016/j.cell.2019.08.018
Europe PMC | doi

Martin-Herranz DE, Aref-Eshghi E, Bonder MJ, Stubbs TM, Choufani S, Weksberg R, Stegle O, Sadikovic B, Reik W, Thornton JM. (2019)

Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1.

Genome Biol. 20(1) doi: 10.1186/s13059-019-1753-9
Europe PMC | doi

Avsec Ž, Kreuzhuber R, Israeli J, Xu N, Cheng J, Shrikumar A, Banerjee A, Kim DS, Beier T, Urban L, Kundaje A, Stegle O, Gagneur J. (2019)

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.

Nat Biotechnol 37(6):592-600. doi: 10.1038/s41587-019-0140-0
Europe PMC | doi

Sousa A, Gonçalves E, Mirauta B, Ochoa D, Stegle O, Beltrao P. (2019)

Multi-omics characterization of interaction-mediated control of human protein abundance levels.

Mol. Cell Proteomics 18 doi: 10.1074/mcp.RA118.001280
Europe PMC | doi

Perron U, Kozlov AM, Stamatakis A, Goldman N, Moal IH. (2019)

Modeling structural constraints on protein evolution via side-chain conformational states.

Mol Biol Evol 36(9) doi: 10.1093/molbev/msz122
Europe PMC | doi

Gonçalves E, Behan FM, Louzada S, Arnol D, Stronach EA, Yang F, Yusa K, Stegle O, Iorio F, Garnett MJ. (2019)

Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects.

Genome Biol. 20(1) doi: 10.1186/s13059-019-1637-z
Europe PMC | doi

Vigilante A, Laddach A, Moens N, Meleckyte R, Leha A, Ghahramani A, Culley OJ, Kathuria A, Hurling C, Vickers A, Wiseman E, Tewary M, Zandstra PW, HipSci Consortium, Durbin R, Fraternali F, Stegle O, Birney E, Luscombe NM, Danovi D, Watt FM. (2019)

Identifying extrinsic versus intrinsic drivers of variation in cell behavior in human iPSC lines from healthy donors.

Cell Rep 26(8):2078-2087.e3. doi: 10.1016/j.celrep.2019.01.094
Europe PMC | doi

Linker SM, Urban L, Clark SJ, Chhatriwala M, Amatya S, McCarthy DJ, Ebersberger I, Vallier L, Reik W, Stegle O, Bonder MJ. (2019)

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity.

Genome Biol. 20(1) doi: 10.1186/s13059-019-1644-0
Europe PMC | doi

Moore R, Casale FP, Jan Bonder M, Horta D, Franke L, Barroso I, Stegle O. (2019)

A linear mixed-model approach to study multivariate gene-environment interactions.

Nat Genet 51(1) doi: 10.1038/s41588-018-0271-0
Europe PMC | doi

Cook CE, Lopez R, Stroe O, Cochrane G, Brooksbank C, Birney E, Apweiler R. (2019)

The European Bioinformatics Institute in 2018: tools, infrastructure and training.

Nucleic Acids Res. 47(D1) doi: 10.1093/nar/gky1124
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. (2019)

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

Gut 68(1) doi: 10.1136/gutjnl-2017-314817
Europe PMC | doi

Vamathevan J, Apweiler R, Birney E. (2019)

Biomolecular Data Resources: Bioinformatics Infrastructure for Biomedical Data Science

Annu Rev Biomed Data Sci 2:199-222. doi: 10.1146/annurev-biodatasci-072018-021321
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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

Vialle RA, Tamuri AU, Goldman N. (2018)

Alignment modulates ancestral sequence reconstruction accuracy.

Mol Biol Evol 35(7) doi: 10.1093/molbev/msy055
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

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

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

Apweiler R, Beissbarth T, Berthold MR, Blüthgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Höfer T, Jansen PL, Kaderali L, Klingmüller U, Koch I, Kohlbacher O, Kuepfer L, Lammert F, Maier D, Pfeifer N, Radde N, Rehm M, Roeder I, Saez-Rodriguez J, Sax U, Schmeck B, Schuppert A, Seilheimer B, Theis FJ, Vera J, Wolkenhauer O. (2018)

Whither systems medicine?

Exp Mol Med 50(3) doi: 10.1038/emm.2017.290
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

Hesketh EE, Sayir J, Goldman N. (2018)

Improving communication for interdisciplinary teams working on storage of digital information in DNA.

F1000Res 7 doi: 10.12688/f1000research.13482.1
Europe PMC | doi

Cook CE, Bergman MT, Cochrane G, Apweiler R, Birney E. (2018)

The European bioinformatics institute in 2017: data coordination and integration.

Nucleic Acids Res. 46(D1):D21-D29. doi: 10.1093/nar/gkx1154
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):D246-D251. 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

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

Klopfstein S, Massingham T, Goldman N. (2017)

More on the Best Evolutionary Rate for Phylogenetic Analysis.

Syst Biol 66(5):769-785. doi: 10.1093/sysbio/syx051
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

Löytynoja A, Goldman N. (2017)

Short template switch events explain mutation clusters in the human genome.

Genome Res. 27(6):1039-1049. doi: 10.1101/gr.214973.116
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

Anderson WP; Global Life Science Data Resources Working Group.. (2017)

Data management: A global coalition to sustain core data.

Nature 543(7644):179. doi: 10.1038/543179a
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

Durinx C, McEntyre J, Appel R, Apweiler R, Barlow M, Blomberg N, Cook C, Gasteiger E, Kim JH, Lopez R, Redaschi N, Stockinger H, Teixeira D, Valencia A. (2016)

Identifying ELIXIR Core Data Resources.

F1000Res 5:1-15. doi: 10.12688/f1000research.9656.1
Europe PMC | doi

Andrews BJ, Walhout AJM, Iyengar R. (2016)

Quantitative human cell encyclopedia

Sci Signal 9(443) doi: 10.1126/scisignal.aah4406
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

Gori K, Suchan T, Alvarez N, Goldman N, Dessimoz C. (2016)

Clustering Genes of Common Evolutionary History.

Mol. Biol. Evol. 33(6):1590-1605. doi: 10.1093/molbev/msw038
Europe PMC | doi

Schwarz RF, Tamuri AU, Kultys M, King J, Godwin J, Florescu AM, Schultz J, Goldman N. (2016)

ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.

Nucleic Acids Res. 44(8):e77. doi: 10.1093/nar/gkw022
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

Truszkowski J, Goldman N. (2016)

Maximum likelihood phylogenetic inference is consistent on multiple sequence alignments, with or without gaps.

Syst. Biol. 65(2):328-333. doi: 10.1093/sysbio/syv089
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

Cook CE, Bergman MT, Finn RD, Cochrane G, Birney E, Apweiler R. (2016)

The European Bioinformatics Institute in 2016: Data growth and integration.

Nucleic Acids Res. 44(D1):D20-6. doi: 10.1093/nar/gkv1352
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

Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C. (2015)

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.

Syst. Biol. 64(5):778-791. doi: 10.1093/sysbio/syv033
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

Lowe R, Slodkowicz G, Goldman N, Rakyan VK. (2015)

The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues

Epigenetics 10(4):274-281. doi: 10.1080/15592294.2014.1003744
Europe PMC | doi

Suzek BE, Wang YQ, Huang HZ, McGarvey PB, Wu CH. (2015)

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

Bioinformatics 31(6):926-932. doi: 10.1093/bioinformatics/btu739
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

The UniProt Consortium. (2015)

UniProt: a hub for protein information

Nucleic Acids Res. 43(D1):D204-D212. doi: 10.1093/nar/gku989
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

Tan G, Gil M, Löytynoja AP, Goldman N, Dessimoz C. (2015)

Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.

Proc. Natl. Acad. Sci. U.S.A. 112(2) doi: 10.1073/pnas.1417526112
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

Chen L, Kostadima M, Martens JH, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SB, Astle WJ, Attwood A, Bariana T, de Bono B, Breschi A, Chambers JC, BRIDGE Consortium, Choudry FA, Clarke L, Coupland P, van der Ent M, Erber WN, Jansen JH, Favier R, Fenech ME, Foad N, Freson K, van Geet C, Gomez K, Guigo R, Hampshire D, Kelly AM, Kerstens HH, Kooner JS, Laffan M, Lentaigne C, Labalette C, Martin T, Meacham S, Mumford A, Nürnberg S, Palumbo E, van der Reijden BA, Richardson D, Sammut SJ, Slodkowicz G, Tamuri AU, Vasquez L, Voss K, Watt S, Westbury S, Flicek P, Loos R, Goldman N, Bertone P, Read RJ, Richardson S, Cvejic A, Soranzo N, Ouwehand WH, Stunnenberg HG, Frontini M, Rendon A. (2014)

Transcriptional diversity during lineage commitment of human blood progenitors

Science 345(6204) doi: 10.1126/science.1251033
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

Behjati S, Huch M, van Boxtel R, Karthaus W, Wedge DC, Tamuri AU, Martincorena I, Petljak M, Alexandrov LB, Gundem G, Tarpey PS, Roerink S, Blokker J, Maddison M, Mudie L, Robinson B, Nik-Zainal S, Campbell P, Goldman N, van de Wetering M, Cuppen E, Clevers H, Stratton MR. (2014)

Genome sequencing of normal cells reveals developmental lineages and mutational processes

Nature 513(7518):422-425. doi: 10.1038/nature13448
Europe PMC | doi

Parks SL, Goldman N. (2014)

Maximum Likelihood Inference of Small Trees in the Presence of Long Branches

Syst. Biol. 63(5):798-811. doi: 10.1093/sysbio/syu044
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

Kultys M, Nicholas L, Schwarz R, Goldman N, King J. (2014)

Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs

BMC Proceedings 8(Suppl 2):S8. doi: 10.1186/1753-6561-8-S2-S8
Europe PMC | doi