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Prof. Dr. Karsten Borgwardt

Address:	Spemannstr. 41 72076 Tübingen
Room number:	1.B.02
Phone:	+49 7071 601 1784
Fax:	+49 7071 601 552
E-Mail:	karsten.borgwardt

Picture of Borgwardt, Karsten, Prof. Dr.

Karsten Borgwardt

Position: Research Group Leader Unit: Schölkopf Borgwardt

Overview
Publications

I am Professor of Data Mining in the Life Sciences at the Eberhard Karls Universität Tübingen and a permanent W2 research group leader at the Max Planck Institutes in Tübingen. For full information, including all publications, visit my official homepage here.

Articles (21):
•	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.
•	Song L , Smola A , Gretton A , Bedo J and Borgwardt K (March-2012) Feature Selection via Dependence Maximization Journal of Machine Learning Research . accepted
•	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.
•	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.
•	Li L , Rakitsch B and Borgwardt K (July-2011) ccSVM: correcting Support Vector Machines for confounding factors in biological data classification Bioinformatics 27(13: ISMB/ECCB 2011) i342-i348.
•	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 Bioinformatics 27(13: ISMB/ECCB 2011) i214-i221.
•	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.
•	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.
•	Pain A , Böhme U , Berry AE , Mungall K , Finn RD , Jackson AP , Mourier T , Mistry J , Pasini EM , Aslett MA , Balasubrammaniam S , Borgwardt K , Brooks K , Carret C , Carver TJ , Cherevach I , Chillingworth T , Clarke T , Galinski MR , Hall N , Harper D , Harris D , Hauser H , Ivens A , Janssen CS , Keane T , Larke N , Lapp S , Marti M , Moule S , Meyer IM , Ormond D , Peters N , Sanders M , Sanders T , Sergeant TJ , Simmonds M , Smith F , Squares R , Thurston S , Tivey AR , Walker D , White B , Zuiderwijk E , Churcher C , Quail MA , Cowman AF , Turner CMR , Rajandream MA , Kocken CHM , Thomas AW , Newbold C , Barrell BG and Berriman M (October-2008) The genome of the simian and human malaria parasite Plasmodium knowlesi Nature 455(7214) 799-803.
•	Borgwardt K (August-2008) Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model BioEssays 30(8) 707–710.
•	Song L , Bedo J , Borgwardt KM , Gretton A and Smola A (July-2007) Gene selection via the BAHSIC family of algorithms Bioinformatics 23(13: ISMB/ECCB 2007 Conference Proceedings) i490-i498.
•	Borgwardt KM , Gretton A , Rasch M , Kriegel H-P , Schölkopf B and Smola A (August-2006) Integrating Structured Biological data by Kernel Maximum Mean Discrepancy Bioinformatics 22(4: ISMB 2006 Conference Proceedings) e49-e57.
•	Vishwanathan SVN , Borgwardt KM , Guttman O and Smola AJ (March-2006) Kernel extrapolation Neurocomputing 69(7-9) 721-729.
•	Borgwardt KM , Ong CS , Schönauer S , Vishwanathan , Smola AJ and Kriegel H-P (June-2005) Protein function prediction via graph kernels Bioinformatics 21(Suppl. 1: ISMB 2005 Proceedings) i47-i56.
Conference papers (24):
•	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.
•	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.
•	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.
•	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.
•	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.
•	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.
•	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 9th SIAM Conference on Data Mining (SDM 2009), Philadelphia, PA, USA, Society for Industrial and Applied Mathematics, 1076-1087.
•	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.
•	Shervashidze N , Vishwanathan SVN , Petri TH , Mehlhorn K and Borgwardt KM (April-2009) Efficient Graphlet Kernels for Large Graph Comparison In: JMLR Workshop and Conference Proceedings Volume 5: AISTATS 2009, Twelfth International Conference on Artificial Intelligence and Statistics, MIT Press, Cambridge, MA, USA, 488-495.
•	Hübler C , Kriegel H-P , Borgwardt K and Ghahramani Z (December-2008) Metropolis Algorithms for Representative Subgraph Sampling Eighth IEEE International Conference on Data Mining (ICDM '08), IEEE, Piscataway, NJ, USA, 283-292.
•	Song L , Smola AJ , Borgwardt K and Gretton A (September-2008) Colored Maximum Variance Unfolding In: Advances in neural information processing systems 20, Twenty-First Annual Conference on Neural Information Processing Systems (NIPS 2007), Curran, Red Hook, NY, USA, 1385-1392.
•	Kondor R and Borgwardt K (July-2008) The skew spectrum of graphs Twenty-Fifth International Conference on Machine Learning (ICML 2008), ACM Press, New York, NY, USA, 496-503.
•	Gretton A , Borgwardt KM , Rasch M , Schölkopf B and Smola A (September-2007) A Kernel Method for the Two-Sample-Problem In: Advances in Neural Information Processing Systems 19, Twentieth Annual Conference on Neural Information Processing Systems (NIPS 2006), MIT Press, Cambridge, MA, USA, 513-520.
•	Huang J , Smola A , Gretton A , Borgwardt KM and Schölkopf B (September-2007) Correcting Sample Selection Bias by Unlabeled Data In: Advances in Neural Information Processing Systems 19, Twentieth Annual Conference on Neural Information Processing Systems (NIPS 2006), MIT Press, Cambridge, MA, USA, 601-608.
•	Vishwanathan SVN , Borgwardt KM and Schraudolph N (September-2007) Fast Computation of Graph Kernels In: Advances in Neural Information Processing Systems 19, Twentieth Annual Conference on Neural Information Processing Systems (NIPS 2006), MIT Press, Cambridge, MA, USA, 1449-1456.
•	Gretton A , Borgwardt KM , Rasch M , Schölkopf B and Smola AJ (July-2007) A Kernel Approach to Comparing Distributions Twenty-Second AAAI Conference on Artificial Intelligence (IAAI-07), AAAI Press, Menlo Park, CA, USA, 1637-1641.
•	Song L , Smola AJ , Gretton A and Borgwardt KM (June-2007) A Dependence Maximization View of Clustering Twenty-Fourth Annual International Conference on Machine Learning (ICML 2007), ACM Press, New York, NY, USA, 815-822.
•	Song L , Smola AJ , Gretton A , Borgwardt KM and Bedo J (June-2007) Supervised Feature Selection via Dependence Estimation Twenty-Fourth Annual International Conference on Machine Learning (ICML 2007), ACM Press, New York, NY, USA, 823-830.
•	Borgwardt KM , Vishwanathan SVN , Schraudolph N and Kriegel H-P (January-2007) Graph kernels for disease outcome prediction from protein-protein interaction networks Pacific Symposium on Biocomputing (PSB 2007), World Scientific, Hackensack, NJ, USA, 4-15.
•	Borgwardt KM , Kriegel H-P and Wackersreuther P (December-2006) Pattern Mining in Frequent Dynamic Subgraphs Sixth International Conference on Data Mining (ICDM 2006), IEEE Computer Society, Los Alamitos, CA, USA, 818-822.
•	Assfalg J , Borgwardt KM and Kriegel H-P (November-2006) 3DString: a feature string kernel for 3D object classification on voxelized data 15th ACM International Conference on Information and Knowledge Management (CIKM 2006), ACM Press, New York, NY, USA, 198-207.
•	Borgwardt KM , Vishwanathan SVN and Kriegel H-P (January-2006) Class prediction from time series gene expression profiles using dynamical systems kernels Pacific Symposium on Biocomputing (PSB 2006), World Scientific, Singapore, 547-558.
•	Borgwardt KM and Kriegel H-P (November-2005) Shortest-path kernels on graphs Fifth International Conference on Data Mining (ICDM 2005), IEEE Computer Society, Los Alamitos, CA, USA, 74-81.
•	Borgwardt KM , Guttman O , Vishwanathan SVN and Smola AJ (April-2005) Joint Regularization 13th European Symposium on Artificial Neural Networks (ESANN 2005), d-side, Evere, Belgium, 455-460.
Contributions to books (2):
•	Borgwardt KM : Kernel Methods in Bioinformatics, 317-334. In: Handbook of Statistical Bioinformatics, (Ed) H.H.-S. Lu, Springer, Berlin, Germany, (2011).
•	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).
Technical reports (1):
•	Gretton A , Borgwardt K , Rasch M , Schölkopf B and Smola A : A Kernel Method for the Two-sample Problem, 157, Max-Planck-Institute for Biological Cybernetics Tübingen, (April-2008).
Posters (1):
•	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 '09), Halle, Germany.