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Dr. Oliver Stegle

Address:	Spemannstr. 41 72076 Tübingen
Room number:	1.B.01
Phone:	+49 7071 601 582
Fax:	+49 7071 601 552
E-Mail:	oliver.stegle

Oliver Stegle

Position: Research Scientist Unit: Borgwardt

Overview
Publications

My main research interest is probabilistic modelling applied to key problems in computational biolgoy.

For information about projects, papers and code plese visit my private web page here .

Articles (12):
•	Karaletsos T , Stegle O , Dreyer C , Winn J and Borgwardt KM (April-2012) ShapePheno: Unsupervised extraction of shape phenotypes from biological image collections Bioinformatics 28(7) 1001-1008.
•	Stegle O , Parts L , Piipari M , Winn J and Durbin R (February-2012) Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses Nature Protocols 7(3) 500–507.
•	Fusi N , Stegle O and Lawrence ND (January-2012) Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies PLoS Computational Biology 8(1) 1-9.
•	Becker C , Hagmann J , Müller J , Koenig D , Stegle O , Borgwardt K and Weigel D (December-2011) Spontaneous epigenetic variation in the Arabidopsis thaliana methylome Nature 480(7376) 245-249.
•	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 and Weigel D (October-2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations Nature Genetics 43(10) 956–963.
•	Gan XC , 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 and Mott R (September-2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana Nature 477(7365) 419–423.
•	Parts L , Stegle O , Winn J and Durbin R (January-2011) Joint Genetic Analysis of Gene Expression Data with Inferred Cellular Phenotypes PLoS Genetics 7(1) 1-10.
•	Stegle O , Parts L , Durbin R and Winn JM (May-2010) A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies PLoS Computational Biology 6(5) 1-11.
•	Stegle O , Denby KJ , Cooke EJ , Wild DL , Ghahramani Z and Borgwardt KM (May-2010) A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series Journal of Computational Biology 17(3) 355-367.
•	Stegle O , Drewe P , Bohnert R , Borgwardt K and Rätsch G (May-2010) Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts Nature Precedings 2010 1-11.
•	Wong HM , Stegle O , Rodgers S and Huppert J (March-2010) A toolbox for predicting G-quadruplex formation and stability Journal of Nucleic Acids 2010(564946) 1-6.
•	Rattray M , Stegle O , Sharp K and Winn J (September-2009) Inference algorithms and learning theory for Bayesian sparse factor analysis Journal of Physics: Conference Series 197(1: International Workshop on Statistical-Mechanical Informatics 2009) 1-10.
Conference papers (7):
•	Stegle O , Lippert C , Mooij J , Lawrence N and Borgwardt K (January-2012) Efficient inference in matrix-variate Gaussian models with iid observation noise In: Advances in Neural Information Processing Systems 24, Twenty-Fifth Annual Conference on Neural Information Processing Systems (NIPS 2011), 630-638.
•	Stegle O , Roth FP , Morris Q and Listgarten J (January-2012) Personalized medicine: from genotypes and molecular phenotypes towards computed therapy Pacific Symposium on Biocomputing (PSB 2012), World Scientific Publishing, Singapore, 323-326.
•	Janzing D , Sgouritsa E , Stegle O , Peters J and Schölkopf B (July-2011) Detecting low-complexity unobserved causes 27th Conference on Uncertainty in Artificial Intelligence (UAI 2011), AUAI Press, Corvallis, OR, USA, 383-391.
•	Mooij JM , Stegle O , Janzing D , Zhang K and Schölkopf B (June-2011) Probabilistic latent variable models for distinguishing between cause and effect In: Advances in Neural Information Processing Systems 23, Twenty-Fourth Annual Conference on Neural Information Processing Systems (NIPS 2010), Curran, Red Hook, NY, USA, 1687-1695.
•	Stegle O , Denby KJ , Wild DL , McHattie S , Mead A , Ghahramani Z and Borgwardt KM (September-2009) Discovering Temporal Patterns of Differential Gene Expression in Microarray Time Series German Conference on Bioinformatics 2009 (GCB '09), Gesellschaft für Informatik, Bonn, Germany, 133-142.
•	Stegle O , Denby K , Wild DL , Ghahramani Z and Borgwardt KM (May-2009) A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series In: Research in Computational Molecular Biology, 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009), Springer, Berlin, Germany, 201-216.
•	Lippert C , Stegle O , Ghahramani Z and Borgwardt KM (April-2009) A kernel method for unsupervised structured network inference In: JMLR Workshop and Conference Proceedings Volume 5: AISTATS 2009, Twelfth International Conference on Artificial Intelligence and Statistics, MIT Press, Cambridge, MA, USA, 368-375.