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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. Fusi N, et al. Among authors: stegle o. PLoS Comput Biol. 2012 Jan;8(1):e1002330. doi: 10.1371/journal.pcbi.1002330. Epub 2012 Jan 5. PLoS Comput Biol. 2012. PMID: 22241974 Free PMC article.
A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.
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. Demircioğlu D, et al. Among authors: stegle o. Cell. 2019 Sep 5;178(6):1465-1477.e17. doi: 10.1016/j.cell.2019.08.018. Cell. 2019. PMID: 31491388
A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies.
Stegle O, Parts L, Durbin R, Winn J. Stegle O, et al. PLoS Comput Biol. 2010 May 6;6(5):e1000770. doi: 10.1371/journal.pcbi.1000770. PLoS Comput Biol. 2010. PMID: 20463871 Free PMC article.
Joint genetic analysis of gene expression data with inferred cellular phenotypes.
Parts L, Stegle O, Winn J, Durbin R. Parts L, et al. Among authors: stegle o. PLoS Genet. 2011 Jan 20;7(1):e1001276. doi: 10.1371/journal.pgen.1001276. PLoS Genet. 2011. PMID: 21283789 Free PMC article.
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses.
Stegle O, Parts L, Piipari M, Winn J, Durbin R. Stegle O, et al. Nat Protoc. 2012 Feb 16;7(3):500-7. doi: 10.1038/nprot.2011.457. Nat Protoc. 2012. PMID: 22343431 Free PMC article.
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. Stranger BE, et al. Among authors: stegle o. PLoS Genet. 2012;8(4):e1002639. doi: 10.1371/journal.pgen.1002639. Epub 2012 Apr 19. PLoS Genet. 2012. PMID: 22532805 Free PMC article.
Detecting regulatory gene-environment interactions with unmeasured environmental factors.
Fusi N, Lippert C, Borgwardt K, Lawrence ND, Stegle O. Fusi N, et al. Among authors: stegle o. Bioinformatics. 2013 Jun 1;29(11):1382-9. doi: 10.1093/bioinformatics/btt148. Epub 2013 Apr 4. Bioinformatics. 2013. PMID: 23559640
Efficient set tests for the genetic analysis of correlated traits.
Casale FP, Rakitsch B, Lippert C, Stegle O. Casale FP, et al. Among authors: stegle o. Nat Methods. 2015 Aug;12(8):755-8. doi: 10.1038/nmeth.3439. Epub 2015 Jun 15. Nat Methods. 2015. PMID: 26076425
A random forest approach to capture genetic effects in the presence of population structure.
Stephan J, Stegle O, Beyer A. Stephan J, et al. Among authors: stegle o. Nat Commun. 2015 Jun 25;6:7432. doi: 10.1038/ncomms8432. Nat Commun. 2015. PMID: 26109276
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. Sudmant PH, et al. Among authors: stegle o. Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394. Nature. 2015. PMID: 26432246 Free PMC article.
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