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Journal Article (11)

Journal Article
Karaletsos, T.; Stegle, O.; Dreyer, C.; Winn, J.; Borgwardt, K.: ShapePheno: Unsupervised extraction of shape phenotypes from biological image collections. Bioinformatics 28 (7), pp. 1001 - 1008 (2012)
Journal Article
Stegle, O.; Parts, L.; Piipari, M.; Winn, J.; Durbin, R.: Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nature Protocols 7 (3), pp. 500 - 507 (2012)
Journal Article
Fusi, N.; Stegle, O.; Lawrence, N.: Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies. PLoS Computational Biology 8 (1), pp. 1 - 9 (2012)
Journal Article
Becker, C.; Hagmann, J.; Müller, J.; Koenig, D.; Stegle, O.; Borgwardt, K.; Weigel, D.: Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480 (7376), pp. 245 - 249 (2011)
Journal Article
Cao, J.; Schneeberger, K.; Ossowski , S.; Günther, T.; Bender , S.; Fitz, J.; Koenig, D.; Lanz, C.; Stegle, O.; Lippert, C. et al.; Wang, X.; Ott, F.; Müller, J.; Alonso-Blanco, C.; Borgwardt, K.; Schmid, K.; Weigel, D.: Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nature Genetics 43 (10), pp. 956 - 963 (2011)
Journal Article
Gan, X.; Stegle, O.; Behr, J.; Steffen, J.; Drewe, P.; Hildebrand, K.; Lyngsoe , R.; Schultheiss, S.; Osborne, E.; Sreedharan, V. et al.; Kahles, A.; Bohnert, R.; Jean, G.; Derwent, P.; Kersey, P.; Belfield, E.; Harberd, N.; Kemen, F.; Toomajian, C.; Kover , P.; Clark, R.; Rätsch, G.; Mott, R.: Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477 (7365), pp. 419 - 423 (2011)
Journal Article
Parts, L.; Stegle, O.; Winn, J.; Durbin, R.: Joint Genetic Analysis of Gene Expression Data with Inferred Cellular Phenotypes. PLoS Genetics 7 (1), pp. 1 - 10 (2011)
Journal Article
Stegle, O.; Denby, K.; Cooke, E.; Wild, D.; Ghahramani, Z.; Borgwardt, K.: A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series. Journal of Computational Biology 17 (3), pp. 355 - 367 (2010)
Journal Article
Stegle, O.; Drewe, P.; Bohnert, R.; Borgwardt, K.; Rätsch, G.: Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts. Nature Precedings 2010, pp. 1 - 11 (2010)
Journal Article
Stegle, O.; Parts, L.; Durbin, R.; Winn, J.: 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), pp. 1 - 11 (2010)
Journal Article
Wong, H.; Stegle, O.; Rodgers, S.; Huppert, J.: A toolbox for predicting G-quadruplex formation and stability. Journal of Nucleic Acids 2010, 564946, pp. 1 - 6 (2010)

Conference Paper (8)

Conference Paper
Stegle, O.; Lippert, C.; Mooij, J.; Lawrence, N.; Borgwardt, K.: Efficient inference in matrix-variate Gaussian models with iid observation noise. In: Advances in Neural Information Processing Systems 24, pp. 630 - 638 (Eds. Shawe-Taylor, J.; Zemel, R.; Bartlett, P.; Pereira, F.; Weinberger, K.). Twenty-Fifth Annual Conference on Neural Information Processing Systems (NIPS 2011), Granada, Spain. Curran, Red Hook, NY, USA (2012)
Conference Paper
Stegle, O.; Roth, F.; Morris, Q.; Listgarten, J.: Personalized medicine: from genotypes and molecular phenotypes towards computed therapy. In: Biocomputing 2012: Proceedings of the Pacific Symposium, pp. 323 - 326 (Eds. Altman, R.; Dunker, A.; Hunter, L.; Murray, T.; Klein, T.). Pacific Symposium on Biocomputing (PSB 2012), Kohala Coast, HI, USA, January 03, 2012 - January 07, 2012. World Scientific Publishing, Singapore (2012)
Conference Paper
Janzing, D.; Sgouritsa, E.; Stegle, O.; Peters, J.; Schölkopf, B.: Detecting low-complexity unobserved causes. In: 27th Conference on Uncertainty in Artificial Intelligence (UAI 2011), pp. 383 - 391 (Eds. Cozman, F.; Pfeffer, A.). 27th Conference on Uncertainty in Artificial Intelligence (UAI 2011), Barcelona, Spain. AUAI Press, Corvallis, OR, USA (2011)
Conference Paper
Mooij, J.; Stegle, O.; Janzing, D.; Zhang, K.; Schölkopf, B.: Probabilistic latent variable models for distinguishing between cause and effect. Twenty-Fourth Annual Conference on Neural Information Processing Systems (NIPS 2010), Vancouver, BC, Canada, December 06, 2010 - December 11, 2010. Advances in Neural Information Processing Systems 23: 24th Annual Conference on Neural Information Processing Systems 2010, pp. 1687 - 1695 (2011)
Conference Paper
Rattray, M.; Stegle, O.; Sharp, K.; Winn, J.: Inference algorithms and learning theory for Bayesian sparse factor analysis. International Workshop on Statistical-Mechanical Informatics 2009 (IW-SMI 2009), Kyoto, Japan, September 13, 2009 - September 16, 2009. Journal of Physics: Conference Series 197 (1), 012002, pp. 1 - 10 (2009)
Conference Paper
Stegle, O.; Denby, K.; Wild, D.; McHattie, S.; Mead, A.; Ghahramani, Z.; Borgwardt, K.: Discovering Temporal Patterns of Differential Gene Expression in Microarray Time Series. In: German Conference on Bioinformatics 2009 (GCB 2009), pp. 133 - 142 (Eds. Grosse, I.; Neumann, S.; Posch, S.; Schreiber, F.; Stadler, P.). German Conference on Bioinformatics 2009 (GCB 2009), Halle, Germany, September 28, 2009 - September 30, 2009. Gesellschaft für Informatik, Bonn, Germany (2009)
Conference Paper
Stegle, O.; Denby , K.; Wild, D.; Ghahramani, Z.; Borgwardt, K.: 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, RECOMB 2009, Tucson, AZ, USA, May 18-21, 2009, pp. 201 - 216 (Ed. Batzoglou, S.). 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009), Tucson, AZ, USA, May 18, 2009 - May 21, 2009. Springer, Berlin, Germany (2009)
Conference Paper
Lippert, C.; Stegle, O.; Ghahramani, Z.; Borgwardt, K.: A kernel method for unsupervised structured network inference. In: Twelfth International Conference on Artificial Intelligence and Statistics (AIStats 2009), pp. 368 - 375 (Eds. Van Dyk, D.; Welling, M.). Twelfth International Conference on Artificial Intelligence and Statistics (AIStats 2009), Clearwater Beach, FL, USA, April 16, 2009 - April 18, 2009. MIT Press, Cambridge, MA, USA (2009)

Talk (9)

Talk
Stegle, O.: Exploiting NGS technologies for efficient and accurate genotype to phenotype mapping in plant systems. XVth Meeting of the EUCARPIA Section: Biometrics in Plant Breeding, Stuttgart-Hohenheim, Germany (2012)
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