Publications of O Stegle

Kahles, A.; Lehmann, K.-V.; Toussaint, N.; Hüser, M.; Sachsenberg, T.; Stegle, O.; Kohlbacher, O.; Sander, C.; Cancer Genome Atlas Research Network; Rätsch, G.: Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer Cell 34 (2), pp. 211 - 224 (2018)

Ibrahim-Verbaas, C.; Bressler, J.; Debette, S.; Schuur, M.; Smith, A.; Bis, J.; Davies, G.; Trompet, S.; Smith, J.; Wolf, C. et al.; Chibnik, L.; Liu, Y.; Vitart, V.; Kirin, M.; Petrovic, K.; Polasek, O.; Zgaga, L.; Fawns-Ritchie, C.; Hoffmann, P.; Karjalainen, J.; Lahti, J.; Llewellyn, D.; Schmidt, C.; Mather, K.; Chouraki, V.; Sun, Q.; Resnick, S.; Rose, L.; Oldmeadow, C.; Stewart, M.; Smith, B.; Gudnason, V.; Yang, Q.; Mirza, S.; Jukema, J.; Dejager, P.; Harris, T.; Liewald, D.; Amin, N.; Coker, L.; Stegle, O.; Lopez, O.; Schmidt, R.; Teumer, A.; Ford, I.; Karbalai, N.; Becker, J.; Jonsdottir, M.; Au, R.; Fehrmann, R.; Herms, S.; Nalls, M.; Zhao, W.; Turner, S.; Yaffe, K.; Lohman, K.; van Swieten, J.; Kardia, S.; Knopman, D.; Meeks, W.; Heiss, G.; Holliday, E.; Schofield, P.; Tanaka, T.; Stott, D.; Wang, J.; Ridker, P.; Gow, A.; Pattie, A.; Starr, J.; Hocking, L.; Armstrong, N.; McLachlan, S.; Shulman, J.; Pilling, L.; Eiriksdottir, G.; Scott, R.; Kochan, N.; Palotie, A.; Hsieh, Y.-C.; Eriksson, J.; Penman, A.; Gottesman, R.; Oostra, B.; Yu, L.; DeStefano, A.; Beiser, A.; Garcia, M.; Rotter, J.; Noethen, M.; Hofman, A.; Slagboom, P.; Westendorp, R.; Buckley, B.; Wolf, P.; Uitterlinden, A.; Psaty, B.; Grabe, H.; Bandinelli, S.; Chasman, D.; Grodstein, F.; Roikkonen, K.; Lambert, J.-C.; Porteous, D.; Price, J.; Sachdev, P.; Ferrucci, L.; Attia, J.; Rudan, I.; Hayward, C.; Wright, A.; Wilson, J.; Cichon, S.; Franke, L.; Schmidt, H.; Ding, J.; de Craen, A.; Fornage, M.; Bennett, D.; Deary, I.; Ikram, M.; Launer, L.; Fitzpatrick, A.; Seshadri, S.; van Duijn, C.; Mosley, T.: GWAS for executive function and processing speed suggests involvement of the CADM2 gene. Molecular Psychiatry 21 (2), pp. 189 - 197 (2016)

Debette, S.; Verbaas, C.; Bressler, J.; Schuur, M.; Smith, A.; Bis, J.; Davies, G.; Wolf, C.; Gudnason, V.; Chibnik, L. et al.; Yang, Q.; deStefano, A.; de Quervain, D.; Srikanth, V.; Lahti, J.; Grabe, H.; Smith, J.; Priebe, L.; Yu, L.; Karbalai, N.; Hayward, C.; Wilson, J.; Campbell, H.; Petrovic, K.; Fornage, M.; Chauhan, G.; Yeo, R.; Boxall, R.; Becker, J.; Stegle, O.; Mather, K.; Chouraki, V.; Sun, Q.; Rose, L.; Resnick, S.; Oldmeadow, C.; Kirin, M.; Wright, A.; Jonsdottir, M.; Au, R.; Becker, A.; Amin, N.; Nalls, M.; Turner, S.; Kardia, S.; Oostra, B.; Windham, G.; Coker, L.; Zhao, W.; Knopman, D.; Heiss, G.; Griswold, M.; Gottesman, R.; Vitart, V.; Hastie, N.; Zgaga, L.; Rudan, I.; Polasek, O.; Holliday, E.; Schofield, P.; Choi, S.; Tanaka, T.; An, Y.; Perry, R.; Kennedy, R.; Sale, M.; Wang, J.; Wadley, V.; Liewald, D.; Ridker, P.; Gow, A.; Pattie, A.; Starr, J.; Porteous, D.; Liu, X.; Thomson, R.; Armstrong, N.; Eiriksdottir, G.; Assareh, A.; Kochan, N.; Widen, E.; Palotie, A.; Hsieh, Y.-C.; Eriksson, J.; Vogler, C.; van Swieten, J.; Shulman, J.; Beiser, A.; Rotter, J.; Schmidt, C.; Hoffmann, W.; Noethen, M.; Ferrucci, L.; Attia, J.; Uitterlinden, A.; Amouyel, P.; Dartigues, J.-F.; Amieva, H.; Raeikkoenen, K.; Garcia, M.; Wolf, P.; Hofman, A.; Longstreth Jr., W.; Psaty, B.; Boerwinkle, E.; DeJager, P.; Sachdev, P.; Schmidt, R.; Breteler, M.; Teumer, A.; Lopez, A.; Cichon, S.; Chasman, D.; Grodstein, F.; Müller-Myhsok, B.; Tzourio, C.; Papassotiropoulos, A.; Bennett, D.; Ikram, M.; Deary, I.; van Duijn, C.; Launer, L.; Fitzpatrick, A.; Seshadri, S.; Mosley Jr., T.: Genome-wide Studies of Verbal Declarative Memory in Nondemented Older People: The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium. Biological Psychiatry 77 (8), pp. 749 - 763 (2015)

Hagmann, J.; Becker, C.; Müller, J.; Stegle, O.; Meyer, R.; Wang, G.; Schneeberger, K.; Fitz, J.; Altmann, T.; Bergelson, J. et al.; Borgwardt, K.; Weigel, D.: Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage. PLoS Genetics 11 (1), e1004920 (2015)

Cubillos, F.; Stegle, O.; Grondin, C.; Canut, M.; Tisné, G.; Loudet, O.: Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis. Plant Cell 26 (11), pp. 4298 - 4310 (2014)

Rakitsch, B.; Lippert, C.; Stegle, O.; Borgwardt, K.: LMM-Lasso: A Lasso Multi-Marker Mixed Model for Association Mapping with Population Structure Correction. Bioinformatics 29 (2), pp. 206 - 214 (2013)

Windram, O.; Madhou, P.; McHattie, S.; Hill, C.; Hickman, V.; Cooke, E.; Jenkins, D.; Penfold, C.; Baxter, L.; Breeze, E. et al.; Kiddle, S.; Rhodes, J.; Atwell, S.; Kliebenstein, D.; Kim, Y.-S.; Stegle, O.; Borgwardt, K.; Zhang, C.; Tabrett, A.; Legaie, R.; Moore, J.; Finkenstadt, B.; Wild, D.; Mead, A.; Rand, D.; Beynon, J.; Ott, S.; Buchanan-Wollaston, V.; Denby, K.: Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. The Plant Cell 24 (9), pp. 3530 - 3557 (2012)

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)

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)

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), e1002330 (2012)

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)

Cao, J.; Schneeberger, K.; Ossowski, S.; Günther, T.; Bender, S.; Fitz, J.; König, 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)

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)

Parts, L.; Stegle, O.; Winn, J.; Durbin, R.: Joint Genetic Analysis of Gene Expression Data with Inferred Cellular Phenotypes. PLoS Genetics 7 (1), e1001276 (2011)

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)

Stegle, O.; Drewe, P.; Bohnert, R.; Borgwardt, K.; Rätsch, G.: Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts. Nature Precedings 2010 (2010)

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), e1000770 (2010)

Wong, H.; Stegle, O.; Rodgers, S.; Huppert, J.: A toolbox for predicting G-quadruplex formation and stability. Journal of Nucleic Acids 2010, 564946 (2010)

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, December 12, 2011 - December 17, 2011. Curran, Red Hook, NY, USA (2012)

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)