Stegle O - Search Results

1

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.

McCarthy DJ, Rostom R, Huang Y, Kunz DJ, Danecek P, Bonder MJ, Hagai T, Lyu R; HipSci Consortium; Wang W, Gaffney DJ, Simons BD, Stegle O, Teichmann SA. McCarthy DJ, et al. Among authors: stegle o. Nat Methods. 2020 Apr;17(4):414-421. doi: 10.1038/s41592-020-0766-3. Epub 2020 Mar 16. Nat Methods. 2020. PMID: 32203388

2

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.

3

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.

4

Multiple reference genomes and transcriptomes for Arabidopsis thaliana.

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. Gan X, et al. Among authors: stegle o. Nature. 2011 Aug 28;477(7365):419-23. doi: 10.1038/nature10414. Nature. 2011. PMID: 21874022 Free PMC article.

5

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.

6

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. Lappalainen T, et al. Among authors: stegle o. Nature. 2013 Sep 26;501(7468):506-11. doi: 10.1038/nature12531. Epub 2013 Sep 15. Nature. 2013. PMID: 24037378 Free PMC article.

7

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. Smallwood SA, et al. Among authors: stegle o. Nat Methods. 2014 Aug;11(8):817-820. doi: 10.1038/nmeth.3035. Epub 2014 Jul 20. Nat Methods. 2014. PMID: 25042786 Free PMC article.

8

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. Buettner F, et al. Among authors: stegle o. Nat Biotechnol. 2015 Feb;33(2):155-60. doi: 10.1038/nbt.3102. Epub 2015 Jan 19. Nat Biotechnol. 2015. PMID: 25599176

9

Computational and analytical challenges in single-cell transcriptomics.

Stegle O, Teichmann SA, Marioni JC. Stegle O, et al. Nat Rev Genet. 2015 Mar;16(3):133-45. doi: 10.1038/nrg3833. Epub 2015 Jan 28. Nat Rev Genet. 2015. PMID: 25628217 Review.

10

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

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