Research Group Leader

Dr. Karsten Borgwardt
Phone: +49 7071 601-1784
karsten.borgwardt[at]tuebingen.mpg.de
 

More about the Research Group

 

Publication List Research Group Borgwardt

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2012

Articles (5):

Song L, Smola A, Gretton A, Bedo J and Borgwardt K (May-2012) Feature Selection via Dependence Maximization Journal of Machine Learning Research 13 1393-1434.
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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.
Gretton A, Borgwardt K, Rasch M, Schölkopf B and Smola A (March-2012) A Kernel Two-Sample Test Journal of Machine Learning Research 13 723−773.
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.

Conference papers (1):

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), Curran, Red Hook, NY, USA, 630-638.
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Talks (1):

Stegle O (September-2012) Invited Lecture: 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 52.

2011

Articles (6):

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.
Lippert C, Listgarten J, Liu Y, Kadie CM, Davidson RI and Heckerman D (October-2011) FaST linear mixed models for genome-wide association studies Nature Methods 8(10) 833–835.
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.
Shervashidze N, Schweitzer P, van Leeuwen EJ, Mehlhorn K and Borgwardt M (September-2011) Weisfeiler-Lehman Graph Kernels Journal of Machine Learning Research 12 2539−2561.
Kam-Thong T, Czamara D, Tsuda K, Borgwardt K, Lewis CM, Erhardt-Lehmann A, Hemmer B, Rieckmann P, Daake M, Weber F, Wolf C, Ziegler A, Pütz B, Holsboer F, Schölkopf B and Müller-Myhsok B (April-2011) EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units European Journal of Human Genetics 19(4) 465-471.
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Conference papers (4):

Achlioptas P, Schölkopf B and Borgwardt K (August-2011) Two-locus association mapping in subquadratic time, 17th ACM SIGKKD Conference on Knowledge Discovery and Data Mining (KDD 2011), ACM Press, New York, NY, USA, 726-734.
Li L, Rakitsch B and Borgwardt K (July-2011) ccSVM: correcting Support Vector Machines for confounding factors in biological data classification, 19th International Conference on Intelligent Systems for Molecular Biology (ISMB 2011), Bioinformatics, 27(13), i342-i348.
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.
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Kam-Thong T, Pütz B, Karbalai N, Müller−Myhsok B and Borgwardt K (July-2011) Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs, 19th International Conference on Intelligent Systems for Molecular Biology (ISMB 2011), Bioinformatics, 27(13), i214-i221.

Contributions to books (1):

Borgwardt KM: Kernel Methods in Bioinformatics, 317-334. In: Handbook of Statistical Bioinformatics, (Ed) H.H.-S. Lu, Springer, Berlin, Germany, (2011).

Talks (1):

Borgwardt K (October-18-2011) Invited Lecture: Two-locus association mapping in subquadratic time, Seminar Series: European Molecular Biology Laboratory, Heidelberg, Germany.

2010

Articles (6):

Thoma M, Cheng H, Gretton A, Han J, Kriegel H-P, Smola AJ, Song L, Yu PS, Yan X and Borgwardt KM (October-2010) Discriminative frequent subgraph mining with optimality guarantees Statistical Analysis and Data Mining 3(5) 302–318.
Camps-Valls G, Shervashidze N and Borgwardt K (October-2010) Spatio-Spectral Remote Sensing Image Classification With Graph Kernels IEEE Geoscience and Remote Sensing Letters 7(4) 741-745.
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.
Lippert C, Ghahramani Z and Borgwardt KM (April-2010) Gene function prediction from synthetic lethality networks via ranking on demand Bioinformatics 26(7) 912-918.
Vishwanathan SVN, Schraudolph NN, Kondor R and Borgwardt KM (April-2010) Graph Kernels Journal of Machine Learning Research 11 1201−1242.
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Conference papers (1):

Shervashidze N and Borgwardt KM (April-2010) Fast subtree kernels on graphs In: Advances in Neural Information Processing Systems 22, , 23rd Annual Conference on Neural Information Processing Systems (NIPS 2009), Curran, Red Hook, NY, USA, 1660-1668.
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Posters (3):

Drewe P, Stegle O, Bohnert R, Borgwardt KM and Rätsch G (July-2010): Detecting differential RNA-transcript expression, 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, MA, USA, F1000Posters, 2010(1) 269.
Lippert C, Stegle O, Nickisch H, Borgwardt K and Weigel D (July-2010): Experimental design for genome-wide association studies, 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, MA, USA, F1000Posters, 2010(1) 324.
Stegle O, Drewe P, Bohnert R, Borgwardt K and Rätsch G (June-2010): Detecting Differential Transcript Expression from RNA-SEQ Experiments, 3rd Berlin Summer Meeting: Computational & Experimental Molecular Biology Meet, Berlin, Germany.

2009

Conference papers (6):

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 (GCB 2009), Gesellschaft für Informatik, Bonn, Germany, 133-142.
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Kondor R, Shervashidze N and Borgwardt KM (June-2009) The graphlet spectrum, 26th International Conference on Machine Learning (ICML 2009), ACM Press, New York, NY, USA, 529-536.
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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, Series: Lecture Notes in Computer Science ; 5541.
Thoma M, Cheng H, Gretton A, Han J, Kriegel H-P, Smola AJ, Song L, Yu PS, Yan X and Borgwardt KM (May-2009) Near-optimal supervised feature selection among frequent subgraphs, Ninth SIAM International Conference on Data Mining (SDM 2009), Society for Industrial and Applied Mathematics, Philadelphia, PA, USA, 1076-1087.
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Lippert C, Stegle O, Ghahramani Z and Borgwardt KM (April-2009) A kernel method for unsupervised structured network inference, Twelfth International Conference on Artificial Intelligence and Statistics (AISTATS 2009), International Machine Learning Society, Madison, WI, USA, 368-375, Series: JMLR Workshop and Conference Proceedings ; 5.
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Shervashidze N, Vishwanathan SVN, Petri TH, Mehlhorn K and Borgwardt KM (April-2009) Efficient Graphlet Kernels for Large Graph Comparison, Twelfth International Conference on Artificial Intelligence and Statistics (AISTATS 2009), International Machine Learning Society, Madison, WI, USA, 488-495, Series: JMLR Workshop and Conference Proceedings ; 5.
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Contributions to books (1):

Gretton A, Smola AJ, Huang J, Schmittfull M, Borgwardt KM and Schölkopf B: Covariate Shift by Kernel Mean Matching, 131-160. In: Dataset Shift in Machine Learning, (Ed) J. Quiñonero Candela, MIT Press, Cambridge, MA, USA, (February-2009).
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Posters (2):

Klotzbücher K, Kobayashi Y, Shervashidze N, Borgwardt KM and Weigel D (September-2009): A flowering-time gene network model for association analysis in Arabidopsis thaliana, German Conference on Bioinformatics (GCB 2009), Halle, Germany.
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Lippert C, Stegle O, Jegelka S, Altun Y and Borgwardt KM (September-2009): Predicting related traits from SNP markers by multi-task learning, German Conference on Bioinformatics (GCB 2009), Halle, Germany.

2005

Talks (1):

Borgwardt KM, Vishwanathan SVM, Schraudolph N and Kriegel H-P (December-10-2005) Invited Lecture: Protein function prediction via faster graph kernels, NIPS Workshop on Computational Biology and the Analysis of Heterogeneous Data (MLCB 2005), Whistler, BC, Canada.

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Last updated: Tuesday, 27.03.2012