Research Articles

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2017   |   2016   |   2015   |   2014   |   2013   |   2012   |   2011

2010   |   2009   |   2008   |   2007   |   2006   |   2005

2017

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Felipe Llinares-Lopez*, Laetitia Papaxanthos*, Dean Bodenham, Damian Roqueiro, COPDGene Investigators and Karsten Borgwardt (*=equal contributions)
Genome-wide genetic heterogeneity discovery with categorical covariates
Bioinformatics 2017, 33 (12): 1820-1828. (Online)

Further information and the code can be found on the project page.

@article{Llinares-Lopes-2017-Bioinformatics,
author = {Llinares-López, Felipe and Papaxanthos, Laetitia and Bodenham, Dean and Roqueiro, Damian and {COPDGene Investigators} and Borgwardt, Karsten},
title = {Genome-wide genetic heterogeneity discovery with categorical covariates},
journal = {Bioinformatics},
volume = {33},
number = {12},
pages = {1820},
year = {2017},
doi = {10.1093/bioinformatics/btx071},
URL = {http://dx.doi.org/10.1093/bioinformatics/btx071}
}

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Ümit Seren*, Dominik G. Grimm*, Joffrey Fitz, Detlef Weigel, Magnus Nordborg, Karsten Borgwardt and Arthur Korte (*=equal contributions)
AraPheno: a public database for Arabidopsis thaliana phenotypes,
Nucleic Acids Research, 2017. 45(D1):D1054-D1059. (Online)

@article{Seren-2017-Nucleic_Acids_Res,
author = {Seren, \"{U}mit and Grimm, Dominik G. and Fitz, Joffrey and Weigel, Detlef and Nordborg, Magnus and Borgwardt, Karsten and Korte, Arthur},
title = {AraPheno: a public database for {A}rabidopsis thaliana phenotypes},
doi = {10.1093/nar/gkw986},
URL = {http://dx.doi.org/10.1093/nar/gkw986},
journal = {Nucleic Acids Research},
year = {2017},
volume= {45},
number = {D1},
pages = {D1054--D1059},
month = jan,

}

2016

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Dominik G. Grimm, Damian Roqueiro, Patrice Salome, Stefan Kleeberger, Bastian Greshake, Wangsheng Zhu, Chang Liu, Christoph Lippert, Oliver Stegle, Bernhard Schölkopf, Detlef Weigel and Karsten Borgwardt
easyGWAS: A Cloud-based Platform for Comparing the Results of Genome-wide Association Studies
The Plant Cell 2017. 29(1):5-19 (Online)

@article{Grimm-2016-Plant_Cell,
author = {Grimm, Dominik G. and Roqueiro, Damian and Salom{\'e}, Patrice A. and Kleeberger, Stefan and Greshake, Bastian and Zhu, Wangsheng and Liu, Chang and Lippert, Christoph and Stegle, Oliver and Sch{\"o}lkopf, Bernhard and Weigel, Detlef and Borgwardt, Karsten M.},
title = {easy{GWAS}: {A} {C}loud-{B}ased {P}latform for {C}omparing the {R}esults of {G}enome-{W}ide {A}ssociation {S}tudies},
volume = {29},
number = {1},
pages = {5-19},
year = {2017},
doi = {10.1105/tpc.16.00551},
URL = {http://www.plantcell.org/content/29/1/5.abstract},
journal = {The Plant Cell}
}

Further information and the code can be found on the project page and directly on easygwas.org.

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Danelle Seymour*, Eunyoung Chae*, Dominik G. Grimm*, Carmen Martín, Anette Haring-Müller, François Vasseur, Barbara Rakitsch, Karsten M. Borgwardt, Daniel Koenig and Detlef Weigel (*=equal contributions)
The Genetic Architecture of Non-additive Inheritance in Arabidopsis thaliana Hybrids,
Proceedings of the National Academy of Sciences (PNAS), 2016. 113(46):E7317-E7326. (Online)

@article{Seymour-2016-PNAS,
author = {Seymour, Danelle K. and Chae, Eunyoung and Grimm, Dominik G. and Mart{\'{i}}n Pizarro, Carmen and Habring-M{\"{u}}ller, Anette and Vasseur, Fran{\c{c}}ois and Rakitsch, Barbara and Borgwardt, Karsten M. and K{\"{o}}nig, Daniel and Weigel, Detlef},
title = {Genetic architecture of nonadditive inheritance in {A}rabidopsis thaliana hybrids},
year = {2016},
doi = {http://dx.doi.org/10.1073/pnas.1615268113},
journal = {Proceedings of the National Academy of Sciences of the United States of America: PNAS},
volume = {113},
number = {46},
pages = {E7317--E7326},
month = nov,
}

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Laetitia Papaxanthos*, Felipe Llinares-López*, Dean Bodenham and Karsten Borgwardt (*=equal contributions)
Finding significant combinations of features in the presence of categorical covariates,

Advances in Neural Information Processing Systems 29 (NIPS 2016), 2271-2279. (Online)

@incollection{Papaxanthos-2016-NIPS,
title = {Finding significant combinations of features in the presence of categorical covariates},
author = {Papaxanthos, Laetitia and Llinares-L\'{o}pez, Felipe and Bodenham, Dean and Borgwardt, Karsten},
booktitle = {Advances in Neural Information Processing Systems 29},
editor = {D. D. Lee and M. Sugiyama and U. V. Luxburg and I. Guyon and R. Garnett},
pages = {2271--2279},
year = {2016},
publisher = {Curran Associates, Inc.},
url = {http://papers.nips.cc/paper/6345-finding-significant-combinations-of-features-in-the-presence-of-categorical-covariates.pdf}
}

Further information and the code can be found on the project page.

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The 1001 Genomes Consortium*
1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana,
Cell, 2016, 166(2):481-491. (Online)
* Dominik G. Grimm and Karsten Borgwardt, as part of The 1001 Genomes Consortium

@article{The_1001_Genomes_Consortium-2016-Cell,
title = {1,135 Genomes Reveal the Global Pattern of Polymorphism in \textit{Arabidopsis thaliana}},
journal = {Cell},
volume = {166},
number = {2},
pages = {481--491},
year = {2016},
issn = {0092-8674},
doi = {http://dx.doi.org/10.1016/j.cell.2016.05.063},
url = {http://www.sciencedirect.com/science/article/pii/S0092867416306675},
author = {Carlos Alonso-Blanco and Jorge Andrade and Claude Becker and Felix Bemm and Joy Bergelson and Karsten M. Borgwardt and Jun Cao and Eunyoung Chae and Todd M. Dezwaan and Wei Ding and Joseph R. Ecker and Moises Exposito-Alonso and Ashley Farlow and Joffrey Fitz and Xiangchao Gan and Dominik G. Grimm and Angela M. Hancock and Stefan R. Henz and Svante Holm and Matthew Horton and Mike Jarsulic and Randall A. Kerstetter and Arthur Korte and Pamela Korte and Christa Lanz and Cheng-Ruei Lee and Dazhe Meng and Todd P. Michael and Richard Mott and Ni Wayan Muliyati and Thomas N\"{a}gele and Matthias Nagler and Viktoria Nizhynska and Magnus Nordborg and Polina Yu. Novikova and F. Xavier Pic\'{o} and Alexander Platzer and Fernando A. Rabanal and Alex Rodriguez and Beth A. Rowan and Patrice A. Salom\'{e} and Karl J. Schmid and Robert J. Schmitz and \"{U}mit Seren and Felice Gianluca Sperone and Mitchell Sudkamp and Hannes Svardal and Matt M. Tanzer and Donald Todd and Samuel L. Volchenboum and Congmao Wang and George Wang and Xi Wang and Wolfram Weckwerth and Detlef Weigel and Xuefeng Zhou},
}

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Angela McGaughran, Christian Rödelsperger, Dominik G. Grimm, Jan Meyer, Katy Morgan, Mark Leaver, Vahan Serobyan, Barbara Rakitsch, Karsten Borgwardt and Ralf Sommer
Genomic profiles of diversification and genotype-phenotype association in island nematode lineages,
Molecular Biology and Evolution 2016, 33(9):2257-2272. (Online)

@article{McGaughran-2016-Mol_Biology_Evol,
title = {Genomic {P}rofiles of {D}iversification and {G}enotype–{P}henotype {A}ssociation in {I}sland {N}ematode {L}ineages},
author = {McGaughran, Angela and R\"{o}delsperger, Christian and Grimm, Dominik G. and Meyer, Jan M. and Moreno, Eduardo and Morgan, Katy and Leaver, Mark and Serobyan, Vahan and Rakitsch, Barbara and Borgwardt, Karsten M. and Sommer, Ralf J.},
issn = {0737-4038, 1537-1719},
url = {http://mbe.oxfordjournals.org/lookup/doi/10.1093/molbev/msw093},
doi = "http://dx.doi.org/10.1093/molbev/msw093",
journal = {Molecular Biology and Evolution},
month = sep,
year = {2016},
volume = {33},
number = {9},
pages = {2257--2272}
}

2015

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Federica Eduati, Lara M. Mangravite, Tao Wang, Hao Tang, J. Christopher Bare, Ruili Huang, Thea Norman, Mike Kellen, Michael P. Menden, Jichen Yang, Xiaowei Zhan, Rui Zhong, Guanghua Xiao, Menghang Xia, Nour Abdo, Oksana Kosyk, The NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Stephen Friend, Allen Dearry, Anton Simeonov, Raymond R. Tice, Ivan Rusyn, Fred A. Wright, Gustavo Stolovitzky and Yang Xie
Prediction of human population responses to toxic compounds by a collaborative competition
,
Nature Biotechnology 2015 Sep;33(9):933-40. (Online)

@article{Eduati-2015-Nature_Biotechnology,
title = {Prediction of human population responses to toxic compounds by a collaborative competition},
volume = {33},
copyright = {© 2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
issn = {1087-0156},
url = {http://www.nature.com/nbt/journal/v33/n9/full/nbt.3299.html},
doi = {10.1038/nbt.3299},
number = {9},
urldate = {2016-07-08},
journal = {Nature Biotechnology},
author = {Eduati, Federica and Mangravite, Lara M. and Wang, Tao and Tang, Hao and Bare, J. Christopher and Huang, Ruili and Norman, Thea and Kellen, Mike and Menden, Michael P. and Yang, Jichen and Zhan, Xiaowei and Zhong, Rui and Xiao, Guanghua and Xia, Menghang and Abdo, Nour and Kosyk, Oksana and {The NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration} and Friend, Stephen and Dearry, Allen and Simeonov, Anton and Tice, Raymond R. and Rusyn, Ivan and Wright, Fred A. and Stolovitzky, Gustavo and Xie, Yang and Saez-Rodriguez, Julio},
month = sep,
year = {2015},
keywords = {Health occupations, High-throughput screening, Predictive medicine, Risk factors},
pages = {933--940}
}

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Mahito Sugiyama and Karsten Borgwardt
Halting in Random Walk Kernels,

Advances in Neural Information Processing Systems 28 (NIPS 2015), 1639-1647. (Online)

@incollection{Sugiyama-2015-NIPS,
title = {Halting in {R}andom {W}alk {K}ernels},
author = {Sugiyama, Mahito and Borgwardt, Karsten},
booktitle = {Advances in Neural Information Processing Systems 28},
editor = {C. Cortes and N. D. Lawrence and D. D. Lee and M. Sugiyama and R. Garnett},
pages = {1639--1647},
year = {2015},
publisher = {Curran Associates, Inc.},
url = {http://papers.nips.cc/paper/5688-halting-in-random-walk-kernels.pdf}
}

The code and further information can be found on the project page.

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Felipe Llinares-López, Mahito Sugiyama, Laetitia Papaxanthos and Karsten Borgwardt
Fast and Memory-Efficient Significant Pattern Mining via Permutation Testing
,
Proceedings of the 21st ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD2015), 2015, 725-734. (Online)

@inproceedings{Llinares-Lopez-2015-KDD,
author = {Llinares-L\'{o}pez, Felipe and Sugiyama, Mahito and Papaxanthos, Laetitia and Borgwardt, Karsten},
title = {Fast and Memory-Efficient Significant Pattern Mining via Permutation Testing},
booktitle = {Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining},
series = {KDD '15},
year = {2015},
isbn = {978-1-4503-3664-2},
location = {Sydney, NSW, Australia},
pages = {725--734},
numpages = {10},
url = {http://doi.acm.org/10.1145/2783258.2783363},
doi = "10.1145/2783258.2783363",
publisher = {ACM},
address = {New York, NY, USA},
keywords = {multiple hypothesis testing, p-value, significant pattern mining, westfall-young permutation},
}

Further information and the code can be found on the project page.

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Damian Roqueiro, Menno Witteveen, Verneri Anttila, Gisela Terwindt, Arn van den Maagdenberg and Karsten Borgwardt
In silico phenotyping via co-training for improved phenotype prediction from genotype.
ISMB 2015, Bioinformatics (2015) 31 (12): i303-i310. (Online)

The code and further information can be found on the project page.

@article{Roqueiro-2015-Bioinformatics,
author = {Roqueiro, Damian and Witteveen, Menno J. and Anttila, Verneri and Terwindt, Gisela M. and van den Maagdenberg, Arn M.J.M. and Borgwardt, Karsten},
title = {In silico phenotyping via co-training for improved phenotype prediction from genotype},
volume = {31},
number = {12},
pages = {i303-i310},
year = {2015},
doi = "10.1093/bioinformatics/btv254",
URL = {http://bioinformatics.oxfordjournals.org/content/31/12/i303.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/31/12/i303.full.pdf+html},
journal = {Bioinformatics}
}

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Felipe Llinares-López, Dominik G. Grimm, Dean A. Bodenham, Udo Gieraths, Mahito Sugiyama, Beth Rowan and Karsten Borgwardt
Genome-wide detection of intervals of genetic heterogeneity associated with complex traits,

ISMB 2015, Bioinformatics (2015) 31 (12): i240-i249. (Online)

The code and further information can be found on the project page.

@article{Llinares-Lopez-2015-Bioinformatics,
author = {Llinares-L\'{o}pez, Felipe and Grimm, Dominik G. and Bodenham, Dean A. and Gieraths, Udo and Sugiyama, Mahito and Rowan, Beth and Borgwardt, Karsten},
title = {Genome-wide detection of intervals of genetic heterogeneity associated with complex traits},
volume = {31},
number = {12},
pages = {i240-i249},
year = {2015},
doi = "10.1093/bioinformatics/btv263",
URL = {http://bioinformatics.oxfordjournals.org/content/31/12/i240.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/31/12/i240.full.pdf+html},
journal = {Bioinformatics}
}

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Dominik G. Grimm, Chloé-Agathe Azencott, Fabian Aicheler, Udo Gieraths, Daniel G. MacArthur, Kaitlin E. Samocha, David N. Cooper, Peter D. Stenson, Mark J. Daly, Jordan W. Smoller, Laramie E. Duncan and Karsten Borgwardt
The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity,
Human Mutation 2015. 36(5):513-523. (Online)

The code and further information can be found on the project page.

@article {Grimm-2015-Human_Mutation,
author = {Grimm, Dominik G. and Azencott, Chlo\'{e}-Agathe and Aicheler, Fabian and Gieraths, Udo and MacArthur, Daniel G. and Samocha, Kaitlin E. and Cooper, David N. and Stenson, Peter D. and Daly, Mark J. and Smoller, Jordan W. and Duncan, Laramie E. and Borgwardt, Karsten M.},
title = {The Evaluation of {T}ools {U}sed to {P}redict the {I}mpact of {M}issense {V}ariants {I}s {H}indered by {T}wo {T}ypes of {C}ircularity},
journal = {Human Mutation},
volume = {36},
number = {5},
issn = {1098-1004},
url = {http://dx.doi.org/10.1002/humu.22768},
doi = "10.1002/humu.22768",
pages = {513--523},
keywords = {pathogenicity prediction tools, exome sequencing},
year = {2015},
}

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Mahito Sugiyama, Felipe Llinares López, Niklas Kasenburg and Karsten Borgwardt
Significant Subgraph Mining with Multiple Testing Correction,
Proceedings of the 2015 SIAM International Conference on Data Mining. 2015, 37-45. (Online)

@inproceedings{Sugiyama-2015-SIAM_Data_Mining,
author = {Mahito Sugiyama and Felipe Llinares L{\'{o}}pez and Niklas Kasenburg and Karsten M. Borgwardt},
title = {Significant {S}ubgraph {M}ining with {M}ultiple {T}esting {C}orrection},
booktitle = {Proceedings of the 2015 SIAM International Conference on Data Mining},
year =  {2015},
publisher = {SIAM},
chapter = {5},
pages = {37-45},
doi = "10.1137/1.9781611974010.5",
URL = {http://epubs.siam.org/doi/abs/10.1137/1.9781611974010.5},
eprint = {http://epubs.siam.org/doi/pdf/10.1137/1.9781611974010.5}
}

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Jörg Hagmann, Claude Becker, Jonas Müller, Oliver Stegle, R.C. Meyer, George Wang, Korbinian Schneeberger, Joffrey Fitz, T. Altmann, Joy Bergelson, Karsten Borgwardt and Detlef Weigel
Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage
,

PLoS Genetics. 2015 Jan 8;11(1):e1004920. (Online)

@article{Hagmann-2015-PLOS,
author = {Hagmann, J\"{o}rg AND Becker, Claude AND M\"{u}ller, Jonas AND Stegle, Oliver AND Meyer, Rhonda C. AND Wang, George AND Schneeberger, Korbinian AND Fitz, Joffrey AND Altmann, Thomas AND Bergelson, Joy AND Borgwardt, Karsten AND Weigel, Detlef},
journal = {PLoS Genetics},
publisher = {Public Library of Science},
title = {Century-scale {M}ethylome {S}tability in a {R}ecently {D}iverged \textit{Arabidopsis thaliana} {L}ineage},
year = {2015},
month = jan,
volume = {11},
url = {http://dx.doi.org/10.1371%2Fjournal.pgen.1004920},
pages = {1-18},
number = {1},
doi = "10.1371/journal.pgen.1004920"
}

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Congmao Wang, Chang Liu, Damian Roqueiro, Dominik G. Grimm, Rebecca Schwab, Claude Becker, Christa Lanz and Detlef Weigel
Genome-wide analysis of local chromatin packing in Arabidopsis thaliana,
Genome Research 2015, 25(2):246-256. (Online)

@article{Wang-2015-Genome_Res,
author = {Wang, Congmao and Liu, Chang and Roqueiro, Damian and Grimm, Dominik G. and Schwab, Rebecca and Becker, Claude and Lanz, Christa and Weigel, Detlef},
title = {Genome-wide analysis of local chromatin packing in \textit{{A}rabidopsis thaliana}},
doi = "10.1101/gr.170332.113",
URL = {http://genome.cshlp.org/content/25/2/246.abstract},
eprint = {http://genome.cshlp.org/content/25/2/246.full.pdf+html},
journal = {Genome Research},
volume = {25},
number = {2},
pages = {246-256},
year = {2015},
}

2014

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Mahito Sugiyama, Chloé-Agathe Azencott, Dominik G. Grimm, Yoshinobu Kawahara and Karsten Borgwardt
Multi-Task Feature Selection on Multiple Networks via Maximum Flows,
Proceedings of the 2014 SIAM International Conference on Data Mining. 2014, 199-207. (Online)

The code and further information can be found on the project page.

The article and supplementary information can be downloaded here: (Article, Supplement (PDF, 67 KB))

@inproceedings{Sugiyama-2014-SIAM_Data_Mining,
author = {Mahito Sugiyama and Chlo\'{e}-Agathe Azencott and Dominik G. Grimm and Yoshinobu Kawahara and Karsten M. Borgwardt},
title = {Multi-{T}ask {F}eature {S}election on {M}ultiple {N}etworks via {M}aximum {F}lows},
booktitle = {Proceedings of the 2014 SIAM International Conference on Data Mining},
chapter = {23},
publisher =  {SIAM},
year = {2014},
pages = {199-207},
doi = "http://dx.doi.org/10.1137/1.9781611973440.23",
URL = {http://epubs.siam.org/doi/abs/10.1137/1.9781611973440.23},
eprint = {http://epubs.siam.org/doi/pdf/10.1137/1.9781611973440.23}
}

2013

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Chloé-Agathe Azencott, Dominik G. Grimm, Mahito Sugiyama, Yoshinobu Kawahara and Karsten Borgwardt
Efficient network-guided multi-locus association mapping with graph cuts,
Accepted at ISMB 2013 and Bioinformatics (2013) 29 (13): i171-i179. (Online)

More information and the code files for download can be found on the project page.

@article{Azencott-2013-ISMB_Bioinformatics,
author = {Azencott, Chlo\'{e}-Agathe and Grimm, Dominik G. and Sugiyama, Mahito and Kawahara, Yoshinobu and Borgwardt, Karsten M.},
title = {Efficient network-guided multi-locus association mapping with graph cuts},
volume = {29},
number = {13},
pages = {i171-i179},
year = {2013},
doi = "10.1093/bioinformatics/btt238",
URL = {http://bioinformatics.oxfordjournals.org/content/29/13/i171.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/29/13/i171.full.pdf+html},
journal = {Bioinformatics}
}

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Barbara Rakitsch, Christoph Lippert, Oliver Stegle and Karsten Borgwardt
A Lasso Multi-Marker Mixed Model for Association Mapping with Population Structure Correction,
Bioinformatics 2013 Jan 15;29(2):206-214. (Online)

The code and further information can be found on the project page.

@article{Rakitsch-2013-Bioinformatics,
author = {Rakitsch, Barbara and Lippert, Christoph and Stegle, Oliver and Borgwardt, Karsten},
title = {A {L}asso multi-marker mixed model for association mapping with population structure correction},
volume = {29},
number = {2},
pages = {206-214},
year = {2013},
doi = "10.1093/bioinformatics/bts669",
URL = {http://bioinformatics.oxfordjournals.org/content/29/2/206.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/29/2/206.full.pdf+html},
journal = {Bioinformatics}
}

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Dominik G. Grimm, Jörg Hagmann, Daniel Koenig, Detlef Weigel and Karsten Borgwardt
Accurate indel prediction using paired-end short reads,
BMC Genomics 2013, 14(1):132-141. (Online)

The code and further information can be found on the project page.

@Article{Grimm-2013-BMC_Genomics,
author="Grimm, Dominik G.
and Hagmann, J{\"o}rg
and Koenig, Daniel
and Weigel, Detlef
and Borgwardt, Karsten",
title="Accurate indel prediction using paired-end short reads",
journal="BMC Genomics",
year="2013",
volume="14",
number="1",
pages="132--141",
issn="1471-2164",
doi="10.1186/1471-2164-14-132",
url="http://dx.doi.org/10.1186/1471-2164-14-132"
}

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Philipp Drewe, Oliver Stegle, Lisa Hartmann, Andre Kahles, Regina Bohnert, Andreas Wachter, Karsten Borgwardt and Gunnar Rätsch
Accurate Detection of Differential RNA Processing,
Nucleic Acids Research 2013, 41(10):5189-5198. (Online)

@article{Drewe-2013-Nucleic_Acids_Res,
author = {Drewe, Philipp and Stegle, Oliver and Hartmann, Lisa and Kahles, Andr\'{e} and Bohnert, Regina and Wachter, Andreas and Borgwardt, Karsten and R\"{a}tsch, Gunnar},
title = {Accurate detection of differential {RNA} processing},
volume = {41},
number = {10},
pages = {5189-5198},
year = {2013},
doi = "10.1093/nar/gkt211",
URL = {http://nar.oxfordjournals.org/content/41/10/5189.abstract},
eprint = {http://nar.oxfordjournals.org/content/41/10/5189.full.pdf+html},
journal = {Nucleic Acids Research}
}

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Aasa Feragen, Jens Petersen, Dominik G. Grimm, Asger Dirksen, Jesper Holst Pedersen, Karsten Borgwardt and Marleen de Bruijne
Geometric tree kernels: Classification of COPD from airway tree geometry,
In Information Processing in Medical Imaging, Editors James C. Gee, Sarang Joshi, Kilian M. Pohl, William M. Wells, and Lilla Zllei, volume 7917 of Lecture Notes in Computer Science, pages 171–183. Springer Berlin Heidelberg, 2013. (Online)

@inproceedings{Feragen-2013-IPMI,
author="Feragen, Aasa and Petersen, Jens and Grimm, Dominik G. and Dirksen, Asger and Pedersen, Jesper Holst and Borgwardt, Karsten and de Bruijne, Marleen",
editor="Gee, James C. and Joshi, Sarang and Pohl, Kilian M. and Wells, William M. and Z{\"o}llei, Lilla",
title="Geometric {T}ree {K}ernels: {C}lassification of {COPD} from {A}irway {T}ree {G}eometry",
bookTitle="Information Processing in Medical Imaging: 23rd International Conference, IPMI 2013, Asilomar, CA, USA, June 28--July 3, 2013. Proceedings",
year="2013",
publisher="Springer",
address="Berlin, Heidelberg",
pages="171--183",
isbn="978-3-642-38868-2",
doi="10.1007/978-3-642-38868-2_15",
url="http://dx.doi.org/10.1007/978-3-642-38868-2_15"
}

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Nicolo Fusi, Christoph Lippert, Karsten Borgwardt, Neil Lawrence and Oliver Stegle
Detecting regulatory gene-environment interactions with unmeasured environmental factors,
Bioinformatics 2013 Jun 1;29(11):1382-9. (Online)

@article{Fusi-2013-Bioinformatics,
author = {Fusi, Nicol\'{o} and Lippert, Christoph and Borgwardt, Karsten and Lawrence, Neil D. and Stegle, Oliver},
title = {Detecting regulatory gene–environment interactions with unmeasured environmental factors},
volume = {29},
number = {11},
pages = {1382-1389},
year = {2013},
doi = "10.1093/bioinformatics/btt148",
URL = {http://bioinformatics.oxfordjournals.org/content/29/11/1382.abstract},
journal = {Bioinformatics}
}

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Mahito Sugiyama and Karsten Borgwardt
Rapid Distance-Based Outlier Detection via Sampling,
Advances in Neural Information Processing Systems 26 (NIPS 2013), 467-475. (Online)

Further information and the code can be found on the project page.

@incollection{Sugiyama-2013-NIPS,
title = {Rapid {D}istance-{B}ased {O}utlier {D}etection via {S}ampling},
author = {Sugiyama, Mahito and Borgwardt, Karsten},
booktitle = {Advances in Neural Information Processing Systems 26},
editor = {C. J. C. Burges and L. Bottou and M. Welling and Z. Ghahramani and K. Q. Weinberger},
pages = {467--475},
year = {2013},
publisher = {Curran Associates, Inc.},
url = {http://papers.nips.cc/paper/5127-rapid-distance-based-outlier-detection-via-sampling.pdf}
}

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Aasa Feragen, Niklas Kasenburg, Jens Petersen, Marleen de Bruijne and Karsten Borgwardt
Scalable kernels for graphs with continuous attributes,
Advances in Neural Information Processing Systems 26 (NIPS 2013), 216-224. (Online)

Further information and the code can be found on the project page.

@incollection{Feragen-2013-NIPS,
title = {Scalable kernels for graphs with continuous attributes},
author = {Feragen, Aasa and Kasenburg, Niklas and Petersen, Jens and de Bruijne, Marleen and Borgwardt, Karsten},
booktitle = {Advances in Neural Information Processing Systems 26},
editor = {C. J. C. Burges and L. Bottou and M. Welling and Z. Ghahramani and K. Q. Weinberger},
pages = {216--224},
year = {2013},
publisher = {Curran Associates, Inc.},
url = {http://papers.nips.cc/paper/5155-scalable-kernels-for-graphs-with-continuous-attributes.pdf}
}

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Barbara Rakitsch, Christoph Lippert, Karsten Borgwardt* and Oliver Stegle* (*=equal contributions)
It is all in the noise: Efficient multi-task Gaussian process inference with structured residuals,
Advances in Neural Information Processing Systems 26 (NIPS 2013), 1466-1474. (Online)

@incollection{Rakitsch-2013-NIPS,
title = {It is all in the noise: {E}fficient multi-task {G}aussian process inference with structured residuals},
author = {Rakitsch, Barbara and Lippert, Christoph and Borgwardt, Karsten and Stegle, Oliver},
booktitle = {Advances in Neural Information Processing Systems 26},
editor = {C. J. C. Burges and L. Bottou and M. Welling and Z. Ghahramani and K. Q. Weinberger},
pages = {1466--1474},
year = {2013},
publisher = {Curran Associates, Inc.},
url = {http://papers.nips.cc/paper/5089-it-is-all-in-the-noise-efficient-multi-task-gaussian-process-inference-with-structured-residuals.pdf}
}

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Mahito Sugiyama and Karsten Borgwardt
Measuring Statistical Dependence via the Mutual Information Dimension,
Proceedings of the 23rd International Joint Conference on Artificial Intelligence (IJCAI 2013), 1692-1698. (Online)

Further information and the code can be found on the project page.

@inproceedings{Sugiyama-2013-IJCAI,
title = {Measuring {S}tatistical {D}ependence via the {M}utual {I}nformation {D}imension},
author = {Sugiyama, Mahito and Borgwardt, Karsten M.},
booktitle = {Proceedings of the 23rd International Joint Conference on Artificial Intelligence (IJCAI 2013)},
pages = {1692-1698},
editors = {Francesca Rossi},
publisher = {AAAI Press},
address = {Menlo Park, California},
year = {2013}
}

2012

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Tony Kam-Thong, Chloé-Agathe Azencott, Lawrence Cayton, Benno Pütz, Andre Altmann, Philipp G. Sämann, Bernhard Schölkopf, Bertram Müller-Myhsok, Karsten M. Borgwardt
GLIDE: GPU-based linear regression for detection of epistasis,
Human Heredity, 2012;73:220-236. (Online)

The code and further information can be found on the project page.

@article{Kam-Thong-2012-Hum_Hered,
title = {{GLIDE}: {GPU}-{B}ased {L}inear {R}egression for {D}etection of {E}pistasis},
volume = {73},
issn = {0001-5652},
url = {http://www.karger.com/DOI/10.1159/000341885},
doi = "10.1159/000341885",
number = {4},
journal = {Human Heredity},
author = {Kam-Thong, T. and Azencott, C.-A. and Cayton, L. and P\"{u}tz, B. and Altmann, A. and Karbalai, N. and S\"{a}mann, P.G. and Sch\"{o}lkopf, B. and M\"{u}ller-Myhsok, B. and Borgwardt, K.M.},
year = {2012},
pages = {220--236}
}

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Oliver Windram, Priyadharshini Madhou, Stuart McHattie, Claire Hill, Richard Hickman, Emma Cooke, Dafyd J. Jenkins, Christopher A. Penfold, Laura Baxter, Emily Breeze, Steven J. Kiddle, Johanna Rhodes, Susanna Atwell, Daniel J. Kliebenstein, Youn-sung Kima, Oliver Stegle, Karsten Borgwardt, Cunjin Zhang, Alex Tabrett, Roxane Legaie, Jonathan Moore, Bärbel Finkenstadt, David L. Wild, Andrew Mead, David Rand, Jim Beynon, Sascha Ott, Vicky Buchanan-Wollaston and Katherine J. Denby
Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis,
Plant Cell 2012 Sep;24(9):3530-57. (Online)

@article{Windram-2012-Plant_Cell,
author = {Windram, Oliver and Madhou, Priyadharshini and McHattie, Stuart and Hill, Claire and Hickman, Richard and Cooke, Emma and Jenkins, Dafyd J. and Penfold, Christopher A. and Baxter, Laura and Breeze, Emily and Kiddle, Steven J. and Rhodes, Johanna and Atwell, Susanna and Kliebenstein, Daniel J. and Kim, Youn-sung and Stegle, Oliver and Borgwardt, Karsten and Zhang, Cunjin and Tabrett, Alex and Legaie, Roxane and Moore, Jonathan and Finkenstadt, Bärbel and Wild, David L. and Mead, Andrew and Rand, David and Beynon, Jim and Ott, Sascha and Buchanan-Wollaston, Vicky and Denby, Katherine J.},
title = {Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis},
volume = {24},
number = {9},
pages = {3530-3557},
year = {2012},
doi = {http://dx.doi.org/10.1105/tpc.112.102046},
URL = {http://www.plantcell.org/content/24/9/3530.abstract},
eprint = {http://www.plantcell.org/content/24/9/3530.full.pdf+html},
journal = {The Plant Cell}
}

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Le Song, Alex Smola, Arthur Gretton, Justin Bedo and Karsten Borgwardt
Feature Selection via Dependence Maximization,
Journal of Machine Learning Research (JMLR) 2012, 13(1):1393−1434. (Online)

@article{Le_Song-2012-JMLR,
author = {Song, Le and Smola, Alex and Gretton, Arthur and Bedo, Justin and Borgwardt, Karsten},
title = {Feature {S}election via {D}ependence {M}aximization},
journal = {The Journal of Machine Learning Research},
issue_date = {January 2012},
volume = {13},
number = {1},
month = may,
year = {2012},
issn = {1532-4435},
pages = {1393--1434},
numpages = {42},
url = {http://jmlr.csail.mit.edu/papers/v13/song12a.html},
publisher = {JMLR.org},
keywords = {Hilbert space embedding of distribution, Hilbert-Schmidt independence criterion, feature selection, independence measure, kernel methods},
}

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Theofanis Karaletsos, Oliver Stegle, Christine Dreyer, John Winn and Karsten Borgwardt
ShapePheno: Unsupervised extraction of shape phenotypes from biological image collections,
Bioinformatics 2012, 28 (7): 1001-1008. (Online)

@article{Karaletsos-2012-Bioinformatics,
author = {Karaletsos, Theofanis and Stegle, Oliver and Dreyer, Christine and Winn, John and Borgwardt, Karsten M.},
title = {Shape{P}heno: unsupervised extraction of shape phenotypes from biological image collections},
volume = {28},
number = {7},
pages = {1001-1008},
year = {2012},
doi = "10.1093/bioinformatics/bts081",
URL = {http://bioinformatics.oxfordjournals.org/content/28/7/1001.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/28/7/1001.full.pdf+html},
journal = {Bioinformatics}
}

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Arthur Gretton, Karsten Borgwardt, Malte Rasch, Bernhard Schölkopf and Alexander Smola
A Kernel Two-Sample Test,
Journal of Machine Learning Research (JMLR) 2012, 13:723−773, 2012. (Online)

@article{Gretton-2012-JMLR,
author = {Gretton, Arthur and Borgwardt, Karsten M. and Rasch, Malte J. and Sch\"{o}lkopf, Bernhard and Smola, Alexander},
title = {A {K}ernel {T}wo-sample {T}est},
journal = {The Journal of Machine Learning Research},
issue_date = {3/1/2012},
volume = {13},
month = mar,
year = {2012},
issn = {1532-4435},
pages = {723--773},
numpages = {51},
url = {http://www.jmlr.org/papers/v13/gretton12a.html},
publisher = {JMLR.org},
keywords = {hypothesis testing, integral probability metric, kernel methods, schema matching, two-sample test, uniform convergence bounds},
}

2011

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Claude Becker, Jörg Hagmann, Jonas Müller, Daniel Koenig, Oliver Stegle, Karsten Borgwardt and Detlef Weigel
Spontaneous epigenetic variation in the Arabidopsis thaliana methylome,
Nature 480, 245–249, 2011. (Online)

@article{Becker-2011-Nature,
title = {Spontaneous epigenetic variation in the \textit{Arabidopsis thaliana} methylome},
volume = {480},
issn = {0028-0836},
url = {http://dx.doi.org/10.1038/nature10555},
doi = "10.1038/nature10555",
number = {7376},
journal = {Nature},
author = {Becker, Claude and Hagmann, J\"{o}rg and M\"{u}ller, Jonas and Koenig, Daniel and Stegle, Oliver and Borgwardt, Karsten and Weigel, Detlef},
month = dec,
year = {2011},
pages = {245--249}
}

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Jun Cao, Korbinian Schneeberger, Stephan Ossowski, Torsten Günther, Sebastian Bender, Joffrey Fitz, Daniel Koenig, Christa Lanz, Oliver Ste- gle, Christoph Lippert, Xi Wang, Felix Ott, Jonas Müller, Carlos Alonso-Blanco, Karsten Borgwardt, Karl J Schmid and Detlef Weigel
Whole-genome sequencing of multiple Arabidopsis thaliana populations,

Nature Genetics, 43(10):956–963, 2011. (Online)

@article{Cao-2011-Nature_Genetics,
title = {Whole-genome sequencing of multiple \textit{Arabidopsis thaliana} populations},
volume = {43},
issn = {1061-4036},
url = {http://dx.doi.org/10.1038/ng.911},
doi = "10.1038/ng.911",
number = {10},
journal = {Nature Genetics},
author = {Cao, Jun and Schneeberger, Korbinian and Ossowski, Stephan and G\"{u}nther, Torsten and Bender, Sebastian and Fitz, Joffrey and Koenig, Daniel and Lanz, Christa and Stegle, Oliver and Lippert, Christoph and Wang, Xi and Ott, Felix and M\"{u}ller, Jonas and Alonso-Blanco, Carlos and Borgwardt, Karsten and Schmid, Karl J and Weigel, Detlef},
month = oct,
year = {2011},
pages = {956--963}
}

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Nino Shervashidze, Pascal Schweitzer, Erik Jan van Leeuwen, Kurt Mehlhorn and Karsten M. Borgwardt
Weisfeiler-Lehman graph kernels,
Journal of Machine Learning Research (JMLR) 12(Sep):2539−2561, 2011. (Online)

Further information and the code can be found on the project page.

@article{Shervashidze-2011-JMLR,
author = {Shervashidze, Nino and Schweitzer, Pascal and van Leeuwen, Erik Jan and Mehlhorn, Kurt and Borgwardt, Karsten M.},
title = {Weisfeiler-{L}ehman {G}raph {K}ernels},
journal = {The Journal of Machine Learning Research},
issue_date = {2/1/2011},
volume = {12},
month = nov,
year = {2011},
issn = {1532-4435},
pages = {2539--2561},
numpages = {23},
url = {http://www.jmlr.org/papers/v12/shervashidze11a.html},
publisher = {JMLR.org},
}

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Oliver Stegle, Christoph Lippert, Joris Mooij, Neil Lawrence and Karsten Borgwardt
Efficient inference in matrix-variate Gaussian models with iid observation noise,
Advances in Neural Information Processing Systems 24 (NIPS 2011), 630-638. (Online)

@incollection{Stegle-2011-NIPS,
title = {Efficient inference in matrix-variate {G}aussian models with \textbackslash iid observation noise},
author = {Stegle, Oliver and Lippert, Christoph and Joris M. Mooij and Neil D. Lawrence and Karsten M. Borgwardt},
booktitle = {Advances in Neural Information Processing Systems 24},
editor = {J. Shawe-Taylor and R. S. Zemel and P. L. Bartlett and F. Pereira and K. Q. Weinberger},
pages = {630--638},
year = {2011},
publisher = {Curran Associates, Inc.},
url = {http://papers.nips.cc/paper/4281-efficient-inference-in-matrix-variate-gaussian-models-with-iid-observation-noise.pdf}
}

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Limin Li, Barbara Rakitsch and Karsten Borgwardt
ccSVM: Correcting Support Vector Machines for confounding factors in biological data classification,
Accepted at ISMB 2011 and Bioinformatics (2011) 27 (13): i342-i348. (Online)

Further information and the code can be found on the project page.

@article{Li-2011-ISMB_Bioinformatics,
author = {Li, Limin and Rakitsch, Barbara and Borgwardt, Karsten},
title = {cc{SVM}: correcting {S}upport {V}ector {M}achines for confounding factors in biological data classification},
volume = {27},
number = {13},
pages = {i342-i348},
year = {2011},
doi = "10.1093/bioinformatics/btr204",
URL = {http://bioinformatics.oxfordjournals.org/content/27/13/i342.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/27/13/i342.full.pdf+html},
journal = {Bioinformatics}
}

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Tony Kam-Thong, Benno Pütz, Nazanin Karbalai, Bertram Müller-Myhsok and Karsten Borgwardt
Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs,
Accepted at ISMB 2011 and Bioinformatics (2011) 27 (13): i214-i221. (Online)

@article{Kam-Thong-2011-ISMB_Bioinformatics,
author = {Kam-Thong, Tony and P\"{u}tz, Benno and Karbalai, Nazanin and M\"{u}ller-Myhsok, Bertram and Borgwardt, Karsten},
title = {Epistasis detection on quantitative phenotypes by exhaustive enumeration using {GPU}s},
volume = {27},
number = {13},
pages = {i214-i221},
year = {2011},
doi = "10.1093/bioinformatics/btr218",
URL = {http://bioinformatics.oxfordjournals.org/content/27/13/i214.abstract},
journal = {Bioinformatics}
}

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Panagiotis Achlioptas, Bernhard Schölkopf and Karsten Borgwardt
Two-locus association mapping in subquadratic runtime,
Proceedings of the 17th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2011), 727-734. (Online)

The code and further information can be found on the project page.

@inproceedings{Achlioptas-2011-KDD,
author = {Achlioptas, Panagiotis and Sch\"{o}lkopf, Bernhard and Borgwardt, Karsten},
title = {Two-locus {A}ssociation {M}apping in {S}ubquadratic {T}ime},
booktitle = {Proceedings of the 17th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining},
series = {KDD '11},
year = {2011},
isbn = {978-1-4503-0813-7},
location = {San Diego, California, USA},
pages = {726--734},
numpages = {9},
url = {http://doi.acm.org/10.1145/2020408.2020521},
doi = "10.1145/2020408.2020521",
publisher = {ACM},
address = {New York, NY, USA},
keywords = {epistasis detection, lightbulb algorithm, two-locus association mapping},
}

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Tony Kam-Thong, Darina Czamara, Koji Tsuda, Karsten Borgwardt, Cathryn M. Lewis, Angelika Erhardt-Lehmann, Bernhard Hemmer, Peter Rieckmann, Markus Daake, Frank Weber, Christiane Wolf, Andreas Ziegler, Benno Pütz, Florian Holsboer, Bernhard Schölkopf and Bertram Müller-Myhsok
EPIBLASTER-Fast exhaustive two-locus epistasis detection strategy using graphical processing units,
European Journal of Human Genetics (2011) 19, 465–471. (Online)

@article{Kam-Thong-2011-EJHG,
title = {{EPIBLASTER}-fast exhaustive two-locus epistasis detection strategy using graphical processing units},
volume = {19},
issn = {1018-4813},
url = {http://dx.doi.org/10.1038/ejhg.2010.196},
doi = "http://dx.doi.org/10.1038/ejhg.2010.196",
number = {4},
journal = {European Journal of Human Genetics},
author = {Kam-Thong, Tony and Czamara, Darina and Tsuda, Koji and Borgwardt, Karsten and Lewis, Cathryn M and Erhardt-Lehmann, Angelika and Hemmer, Bernhard and Rieckmann, Peter and Daake, Markus and Weber, Frank and Wolf, Christiane and Ziegler, Andreas and P\"{u}tz, Benno and Holsboer, Florian and Sch\"{o}lkopf, Bernhard and M\"{u}ller-Myhsok, Bertram},
month = apr,
year = {2011},
pages = {465--471}
}

2010

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Gustavo Camps-Valls, Nino Shervashidze and Karsten Borgwardt
Spatio-spectral remote sensing image classification with graph kernels,
IEEE Geoscience and Remote Sensing Letters 2010, 99:741-745. (Online)

@article{Camps-Valls-2010-IEEE_Geosci_Remote_S,
author={Gustavo Camps-Valls and Nino Shervashidze and Karsten M. Borgwardt},
journal={IEEE Geoscience and Remote Sensing Letters},
title={Spatio-{S}pectral {R}emote {S}ensing {I}mage {C}lassification {W}ith {G}raph {K}ernels},
year={2010},
volume={7},
number={4},
pages={741-745},
doi="10.1109/LGRS.2010.2046618",
ISSN={1545-598X},
month=oct,}

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Marisa Thoma, Hong Cheng, Arthur Gretton, Jiawei Han, Hans-Peter Kriegel, Alexander J. Smola, Le Song, Philip S. Yu, Xifeng Yan and Karsten M. Borgwardt
Discriminative frequent subgraph mining with optimality guarantees,
Journal of Statistical Analysis and Data Mining, Volume 3, Issue 5, pages 302–318, October 2010. (Online)

@article {Thoma-2010-Stat_Anal_Data_Min,
author = {Thoma, Marisa and Cheng, Hong and Gretton, Arthur and Han, Jiawei and Kriegel, Hans-Peter and Smola, Alex and Song, Le and Yu, Philip S. and Yan, Xifeng and Borgwardt, Karsten M.},
title = {Discriminative frequent subgraph mining with optimality guarantees},
journal = {Statistical Analysis and Data Mining},
volume = {3},
number = {5},
publisher = {Wiley Subscription Services, Inc., A Wiley Company},
issn = {1932-1872},
url = {http://dx.doi.org/10.1002/sam.10084},
doi = "10.1002/sam.10084",
pages = {302--318},
keywords = {graph mining, frequent subgraphs, submodularity, feature selection, nested selection},
year = {2010},
}

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Oliver Stegle, Katherine Denby, Emma Cooke. David Wild, Zoubin Ghahramani and Karsten Borgwardt
A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series,
Journal of Computational Biology 2010, 17(3): 355-367. (Online)

@article{Stegle-2010-J_Comput_Biol,
title = {A {R}obust {B}ayesian {T}wo-{S}ample {T}est for {D}etecting {I}ntervals of {D}ifferential {G}ene {E}xpression in {M}icroarray {T}ime {S}eries},
volume = {17},
issn = {1066-5277},
url = {http://dx.doi.org/10.1089/cmb.2009.0175},
doi = "10.1089/cmb.2009.0175",
number = {3},
urldate = {2016-07-08},
journal = {Journal of Computational Biology},
author = {Stegle, Oliver and Denby, Katherine J. and Cooke, Emma J. and Wild, David L. and Ghahramani, Zoubin and Borgwardt, Karsten M.},
month = mar,
year = {2010},
pages = {355--367}
}

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Christoph Lippert, Zoubin Ghahramani and Karsten Borgwardt
Gene function prediction from synthetic lethality networks via ranking on demand,
Bioinformatics (Oxford University Press), 2010 26(7):912-918. (Online)

@article{Lippert-2010-Bioinformatics,
author = {Lippert, Christoph and Ghahramani, Zoubin and Borgwardt, Karsten M.},
title = {Gene function prediction from synthetic lethality networks via ranking on demand},
volume = {26},
number = {7},
pages = {912-918},
year = {2010},
doi = "10.1093/bioinformatics/btq053",
URL = {http://bioinformatics.oxfordjournals.org/content/26/7/912.abstract},
journal = {Bioinformatics}
}

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SVN Vishwanathan, Nic Schraudolph, Risi Kondor and Karsten M. Borgwardt
Graph Kernels,
Journal of Machine Learning Research (JMLR) 2010, 11:1201−1242. (Online)

Further information and the code can be found on the project page.

@article{Vishwanathan_Graph_2010,  
author = {Vishwanathan, S. V. N. and Schraudolph, Nicol N. and Kondor, Risi and Borgwardt, Karsten M.},  
title = {Graph Kernels},  
journal = {The Journal of Machine Learning Research},  
issue_date = {3/1/2010},  
volume = {11},  
month = aug,  
year = {2010},  
issn = {1532-4435},  
pages = {1201--1242},  
numpages = {42},  
url = {http://jmlr.csail.mit.edu/papers/v11/vishwanathan10a.html},
publisher = {JMLR.org},
}  

2009

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Nino Shervashidze and Karsten M. Borgwardt
Fast subtree kernels on graphs,
Advances in Neural Information Processing Systems 22 (NIPS 2009), 1660-1668. NIPS Outstanding Student Paper Award Winner. (Online)

@incollection{NIPS2009_3813,
title = {Fast subtree kernels on graphs},
author = {Nino Shervashidze and Karsten M. Borgwardt},
booktitle = {Advances in Neural Information Processing Systems 22},
editor = {Y. Bengio and D. Schuurmans and J. D. Lafferty and C. K. I. Williams and A. Culotta},
pages = {1660--1668},
year = {2009},
publisher = {Curran Associates, Inc.},
url = {http://papers.nips.cc/paper/3813-fast-subtree-kernels-on-graphs.pdf}
}

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Oliver Stegle, Katherine Denby, David L. Wild, Zoubin Ghahramani and Karsten Borgwardt
A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series,
Research in Computational Molecular Biology: 13th Annual International Conference, RECOMB 2009, Tucson, AZ, USA, May 18-21, 2009. Proceedings, pp. 201–216. (Online)

Also in Journal of Computational Biology 2010. (Online)

@inproceedings{Stegle_2009_Recomb,
author="Stegle, Oliver and Denby, Katherine and Wild, David L. and Ghahramani, Zoubin and Borgwardt, Karsten M.",
editor="Batzoglou, Serafim",
title="A {R}obust {B}ayesian {T}wo-{S}ample {T}est for {D}etecting {I}ntervals of {D}ifferential {G}ene {E}xpression in {M}icroarray {T}ime {S}eries",
bookTitle="Research in Computational Molecular Biology: 13th Annual International Conference, RECOMB 2009, Tucson, AZ, USA, May 18-21, 2009. Proceedings",
year="2009",
publisher="Springer",
address="Berlin, Heidelberg",
pages="201--216",
isbn="978-3-642-02008-7",
doi="10.1007/978-3-642-02008-7_14",
url="http://dx.doi.org/10.1007/978-3-642-02008-7_14"
}

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Oliver Stegle, Katherine Denby, David Wild, Stuart McHattie, Andrew Mead, Zoubin Ghahramani and Karsten Borgwardt
Discovering temporal patterns of differential gene expression in microarray time series,
Lecture Notes in Informatics "German Conference on Bioinformatics 2009", Volume 157, 133-142. (Online)

@inproceedings{Stegle_Discovering2009,
author = "Stegle, Oliver and Denby, Katherine J. and McHattie, Stuart and Mead, Andrew and Wild, David L. and Ghahramani, Zoubin and Borgwardt, Karsten M.",
editor = "Grosse, Ivo",
title = "{D}iscovering temporal patterns of differential gene expression in microarray time series",
booktitle = "German Conference on Bioinformatics 2009",
year = 2009,
volume = "157",
series = "Lecture Notes in Informatics",
pages = "133--142",
address = "Bonn",
publisher = "Gesellschaft f{\"{u}}r Informatik",
}

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Risi Kondor, Nino Shervashidze and Karsten M. Borgwardt
The graphlet spectrum,
Proceedings of the 26th Annual International Conference on Machine Learning (ICML 2009), 529-536. (Online)

@inproceedings{Kondor_The_2009,
author = {Kondor, Risi and Shervashidze, Nino and Borgwardt, Karsten M.},
title = {The {G}raphlet {S}pectrum},
booktitle = {Proceedings of the 26th Annual International Conference on Machine Learning},
series = {ICML '09},
year = {2009},
isbn = {978-1-60558-516-1},
location = {Montreal, Quebec, Canada},
pages = {529--536},
numpages = {8},
url = {http://doi.acm.org/10.1145/1553374.1553443},
doi = "10.1145/1553374.1553443",
acmid = {1553443},
publisher = {ACM},
address = {New York, NY, USA},
}

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Christoph Lippert, Oliver Stegle, Zoubin Ghahramani, Karsten Borgwardt
A kernel method for unsupervised structured network inference,
Artificial Intelligence and Statistics (AISTATS) 2009, volume 5, 368-375 (full oral presentation). (PDF)

@article{Lippert_A_2009,
author = "Lippert, Christoph and Stegle, Oliver and Ghahramani, Zoubin and Borgwardt, Karsten",
title = "{A} kernel method for unsupervised structured network inference",
journal = "Artificial Intelligence and Statistics",
year = 2009,
volume = "5",
pages = "368--375",
}

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Nino Shervashidze, SVN Vishwanathan, Tobias Petri, Kurt Mehlhorn, Karsten Borgwardt
Efficient Graphlet Kernels for Large Graph Comparison,
Artificial Intelligence and Statistics (AISTATS) 2009, volume 5, 488-495. (PDF)

@article{Shervashidze_Efficient_2009,
author = "Shervashidze, Nino and Vishwanathan, SVN and Petri, Tobias and Mehlhorn, Kurt and Borgwardt, Karsten",
title = "{E}fficient graphlet kernels for large graph comparison",
journal = "Artificial Intelligence and Statistics",
year = 2009,
volume = "5",
pages = "488--495",
}

 

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Marisa Thoma, Hong Cheng, Arthur Gretton, Jiawei Han, Hans-Peter Kriegel, Alexander J. Smola, Le Song, Philip S. Yu, Xifeng Yan, Karsten M. Borgwardt
Near-optimal supervised feature selection among frequent subgraphs,
SIAM Data Mining (SDM) 2009, 1076-1087. (Online)

You can download the paper here (PDF, 221 KB).

@inproceedings{Thoma_2009_SIAM_Data_Mining,
author = {Marisa Thoma and Hong Cheng and Arthur Gretton and Jiawei Han and Hans-Peter Kriegel and Alex Smola and Le Song and Philip S. Yu and Xifeng Yan and Karsten Borgwardt},
title = {Near-optimal supervised feature selection among frequent subgraphs},
booktitle = {Proceedings of the 2009 SIAM International Conference on Data Mining},
chapter = {91},
pages = {1076-1087},
year =  {2009},
doi = "10.1137/1.9781611972795.92",
URL = {http://epubs.siam.org/doi/abs/10.1137/1.9781611972795.92},
eprint = {http://epubs.siam.org/doi/pdf/10.1137/1.9781611972795.92}
}

2008

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A. Pain, U. Böhme, A.E. Berry, K. Mungall, R.D. Finn, A.P. Jackson, T. Mourier, J. Mistry, E.M. Pasini, M.A. Aslett, S. Balasubrammaniam, K. Borgwardt, K. Brooks, C. Carret, T.J. Carver, I. Cherevach, T. Chillingworth, T. Clarke, M.R. Galinski, N. Hall, D. Harper, D. Harris, H. Hauser, A. Ivens, C.S. Janssen, T. Keane, N. Larke, S. Lapp , M. Marti, S. Moule, I.M. Meyer, D. Ormond, N. Peters, M. Sanders, S. Sanders, T.J. Sergeant, M. Simmonds, F. Smith, R. Squares, S. Thurston, A.R. Tivey, D. Walker, B. White, E. Zuiderwijk, C. Churcher, M.A. Quail, A.F. Cowman, C.M.R. Turner, M.A. Rajandream , C.H.M. Kocken, A.W. Thomas, C. Newbold, B.G. Barrell and M. Berriman
The genome of the simian and human malaria parasite Plasmodium knowlesi,
Nature 455, 799-803 (9 October 2008). (Online)

@article{pain_genome_2008,
    title = {The genome of the simian and human malaria parasite \textit{{P}lasmodium knowlesi}},
    volume = {455},
    issn = {0028-0836},
    url = {http://dx.doi.org/10.1038/nature07306},
    doi = "10.1038/nature07306",
    number = {7214},
    journal = {Nature},
    author = {Pain, A. and Bohme, U. and Berry, A. E. and Mungall, K. and Finn, R. D. and Jackson, A. P. and Mourier, T. and Mistry, J. and Pasini, E. M. and Aslett, M. A. and Balasubrammaniam, S. and Borgwardt, K. and Brooks, K. and Carret, C. and Carver, T. J. and Cherevach, I. and Chillingworth, T. and Clark, T. G. and Galinski, M. R. and Hall, N. and Harper, D. and Harris, D. and Hauser, H. and Ivens, A. and Janssen, C. S. and Keane, T. and Larke, N. and Lapp, S. and Marti, M. and Moule, S. and Meyer, I. M. and Ormond, D. and Peters, N. and Sanders, M. and Sanders, S. and Sargeant, T. J. and Simmonds, M. and Smith, F. and Squares, R. and Thurston, S. and Tivey, A. R. and Walker, D. and White, B. and Zuiderwijk, E. and Churcher, C. and Quail, M. A. and Cowman, A. F. and Turner, C. M. R. and Rajandream, M. A. and Kocken, C. H. M. and Thomas, A. W. and Newbold, C. I. and Barrell, B. G. and Berriman, M.},
    month = oct,
    year = {2008},
    pages = {799--803},
    annote = {10.1038/nature07306}
}

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Karsten Borgwardt
Predicting phenotypic effects of gene perturbations in C.elegans using an integrated network model,
Bioessays. 2008 Jul 10;30(8):707-710. (Online)

@article {Borgwardt-2009-Bioessays,
author = {Borgwardt, Karsten},
title = {Predicting phenotypic effects of gene perturbations in {C.} elegans using an integrated network model},
journal = {BioEssays},
volume = {30},
number = {8},
publisher = {Wiley Subscription Services, Inc., A Wiley Company},
issn = {1521-1878},
url = {http://dx.doi.org/10.1002/bies.20783},
doi = "10.1002/bies.20783",
pages = {707--710},
year = {2008},
}

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Christian Hübler, Karsten Borgwardt, Hans-Peter Kriegel and Zoubin Ghahramani
Metropolis Algorithms for Representative Subgraph Sampling,
Eighth IEEE International Conference on Data Mining (ICDM) 2008, 283-292. (Online)

You can download the article here (PDF, 220 KB).

@inproceedings{Huebler_Metropolis_2008,
author={C. H\"{u}bler and H. P. Kriegel and K. Borgwardt and Z. Ghahramani},
booktitle={2008 Eighth IEEE International Conference on Data Mining},
title={Metropolis {A}lgorithms for {R}epresentative {S}ubgraph {S}ampling},
year={2008},
pages={283-292},
keywords={Internet;data analysis;data mining;graph theory;Internet;chemoinformatics;data analysis;data mining;metropolis algorithms;representative subgraph sampling;systems biology;Algorithm design and analysis;Application software;Bioinformatics;Computer science;Data analysis;Data mining;Internet;Runtime;Sampling methods;Systems biology;Markov Chain Monte Carlo;Metropolis;graph mining;representative subgraph sampling},
doi="10.1109/ICDM.2008.124",
ISSN={1550-4786},
month=dec,}

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Risi Kondor and Karsten Borgwardt
The skew spectrum of graphs,
Proceedings of the 25th International Conference on Machine Learning (ICML 2008), 496-503. (PDF)

@inproceedings{Kondor_The_2008,
author = {Kondor, Risi and Borgwardt, Karsten M.},
title = {The Skew Spectrum of Graphs},
booktitle = {Proceedings of the 25th International Conference on Machine Learning},
series = {ICML '08},
year = {2008},
isbn = {978-1-60558-205-4},
location = {Helsinki, Finland},
pages = {496--503},
numpages = {8},
url = {http://doi.acm.org/10.1145/1390156.1390219},
doi = "10.1145/1390156.1390219",
acmid = {1390219},
publisher = {ACM},
address = {New York, NY, USA},
}

2007

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Le Song, Justin Bedo, Karsten Borgwardt, Arthur Gretton and Alexander Smola
Gene Selection via the BAHSIC Family of Algorithms,
Accepted at ISMB 2007 and Bioinformatics 2007 23(13):i490-i498. (Online)

@article{Song_Gene_2007,
author = {Song, Le and Bedo, Justin and Borgwardt, Karsten M. and Gretton, Arthur and Smola, Alex},
title = {Gene selection via the {BAHSIC} family of algorithms},
volume = {23},
number = {13},
pages = {i490-i498},
year = {2007},
doi = "10.1093/bioinformatics/btm216",
URL = {http://bioinformatics.oxfordjournals.org/content/23/13/i490.abstract},
journal = {Bioinformatics}
}

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Le Song, Alexander Smola, Karsten Borgwardt and Arthur Gretton
Colored Maximum Variance Unfolding,
Advances in Neural Information Processing Systems 20 (NIPS 2007), 1385-1392. Full oral presentation. (Online)

@incollection{Song_Colored_2007,
title = {Colored {M}aximum {V}ariance {U}nfolding},
author = {Song, Le and Gretton, Arthur and Karsten M. Borgwardt and Alex J. Smola},
booktitle = {Advances in Neural Information Processing Systems 20},
editor = {J. C. Platt and D. Koller and Y. Singer and S. T. Roweis},
pages = {1385--1392},
year = {2008},
publisher = {Curran Associates, Inc.},
url = {http://papers.nips.cc/paper/3307-colored-maximum-variance-unfolding.pdf}
}

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Arthur Gretton, Karsten Borgwardt, Malte Rasch, Bernhard Schölkopf and Alexander Smola
A Kernel Approach to Comparing Distributions,
AAAI 2007, 1637-1641 (Highlights Track). (PDF)

@inproceedings{Gretton_A_2007,
author = {Gretton, Arthur and Borgwardt, Karsten M. and Rasch, Malte and Scholk\"{o}pf, Bernhard and Smola, Alexander J.},
title = {A {K}ernel {A}pproach to {C}omparing {D}istributions},
booktitle = {Proceedings of the 22nd National Conference on Artificial Intelligence - Volume 2},
series = {AAAI'07},
year = {2007},
isbn = {978-1-57735-323-2},
location = {Vancouver, British Columbia, Canada},
pages = {1637--1641},
numpages = {5},
url = {http://dl.acm.org/citation.cfm?id=1619797.1619910},
acmid = {1619910},
publisher = {AAAI Press},
}

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Le Song, Alexander Smola, Arthur Gretton and Karsten Borgwardt
A Dependence Maximization View of Clustering,
Proceedings of the 24th International Conference on Machine Learning (ICML 2007), 815-822. (Online)

The article is available for download here (PDF, 1.4 MB).

@inproceedings{Song_A_2007,
author = {Song, Le and Smola, Alex and Gretton, Arthur and Borgwardt, Karsten M.},
title = {A {D}ependence {M}aximization {V}iew of {C}lustering},
booktitle = {Proceedings of the 24th International Conference on Machine Learning},
series = {ICML '07},
year = {2007},
isbn = {978-1-59593-793-3},
location = {Corvalis, Oregon, USA},
pages = {815--822},
numpages = {8},
url = {http://doi.acm.org/10.1145/1273496.1273599},
doi = "10.1145/1273496.1273599",
acmid = {1273599},
publisher = {ACM},
address = {New York, NY, USA},
}

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Le Song, Arthur Gretton, Alexander Smola, Karsten Borgwardt and Justin Bedo
Supervised Feature Selection via Dependence Estimation,
International Conference on Machine Learning (ICML 2007), 823-830. (PDF)

@inproceedings{Song_Supervised_2007,
author = {Song, Le and Smola, Alex and Gretton, Arthur and Borgwardt, Karsten M. and Bedo, Justin},
title = {Supervised {F}eature {S}election via {D}ependence {E}stimation},
booktitle = {Proceedings of the 24th International Conference on Machine Learning},
series = {ICML '07},
year = {2007},
isbn = {978-1-59593-793-3},
location = {Corvalis, Oregon, USA},
pages = {823--830},
numpages = {8},
url = {http://www.machinelearning.org/proceedings/icml2007/papers/244.pdf},
doi = "10.1145/1273496.1273600",
acmid = {1273600},
publisher = {ACM},
address = {New York, NY, USA},
}

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Karsten Borgwardt, S.V.N. Vishwanathan, Nicol Schraudolph and Hans-Peter Kriegel
Graph kernels for disease outcome prediction from protein-protein interaction networks,
In Proc. of Pacific Symposium on Biocomputing (PSB 2007), volume 12, 4-15.

The article is available for download here (PDF, 388 KB).

@inproceedings{Borgwardt_Graph_2007,
title={Graph kernels for disease outcome prediction from protein-protein interaction networks.},
author={Borgwardt, Karsten M and Kriegel, Hans-Peter and Vishwanathan, SVN and Schraudolph, Nicol N},
booktitle={Pacific symposium on biocomputing},
volume={12},
pages={4--15},
year={2007}
}

2006

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Karsten Borgwardt, Arthur Gretton, Malte Rasch, Hans-Peter Kriegel, Bernhard Schölkopf and Alexander Smola
Integrating structured biological data by Kernel Maximum Mean Discrepancy,
Accepted at ISMB 2006 and Bioinformatics 2006 22(14):e49-5. (Online)

@article{Borgwardt_Integrating_2006,
author = {Borgwardt, Karsten M. and Gretton, Arthur and Rasch, Malte J. and Kriegel, Hans-Peter and Sch\"{o}lkopf, Bernhard and Smola, Alex J.},
title = {Integrating structured biological data by {K}ernel {M}aximum {M}ean {D}iscrepancy},
volume = {22},
number = {14},
pages = {e49-e57},
year = {2006},
doi = "10.1093/bioinformatics/btl242",
URL = {http://bioinformatics.oxfordjournals.org/content/22/14/e49.abstract},
journal = {Bioinformatics}
}

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S.V.N. Vishwanathan, Karsten Borgwardt, Omri Guttman and Alexander Smola
Kernel Extrapolation,
Neurocomputing Volume 69, Issues 7-9 , March 2006, Pages 721-729 (Online)

@article{Vishwanathan_Kernel_2006,
title = "Kernel extrapolation ",
journal = "Neurocomputing ",
volume = "69",
number = "7–9",
pages = "721 -- 729",
year = "2006",
note = "New Issues in Neurocomputing: 13th European Symposium on Artificial Neural Networks13th European Symposium on Artificial Neural Networks 2005 ",
issn = "0925-2312",
doi = "http://dx.doi.org/10.1016/j.neucom.2005.12.113",
url = "http://www.sciencedirect.com/science/article/pii/S0925231205003292",
author = "S.V.N. Vishwanathan and Karsten M. Borgwardt and Omri Guttman and Alex Smola",
keywords = "Kernel methods",
keywords = "Regularization",
keywords = "Graph kernels",
keywords = "Protein classification "
}

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Karsten Borgwardt, Hans-Peter Kriegel and Peter Wackersreuther
Pattern Mining in Frequent Dynamic Subgraphs,
In Proc. of International Conference on Data Mining (ICDM 2006), 818-822. (Online)

The paper can be downloaded here (PDF, 378 KB).

@inproceedings{Borgwardt-2006-ICDM,
author={K. M. Borgwardt and H. P. Kriegel and P. Wackersreuther},
booktitle={Sixth International Conference on Data Mining (ICDM'06)},
title={Pattern {M}ining in {F}requent {D}ynamic {S}ubgraphs},
year={2006},
pages={818--822},
keywords={data mining;graph theory;frequent dynamic subgraphs;graph-structured data;pattern mining;Application software;Bioinformatics;Computer science;Data mining;Data structures;Databases;Frequency;Graph theory;Pattern recognition;Social network services},
doi="10.1109/ICDM.2006.124",
ISSN={1550-4786},
month=dec,}

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Jiayuan Huang, Alexander Smola, Arthur Gretton, Karsten Borgwardt and Bernhard Schölkopf
Correcting Sample Selection Bias by Unlabeled Data,
Advances in Neural Information Processing Systems 20 (NIPS 2006), 601-608. (Online)

@incollection{Huang-2006-NIPS,
title = {Correcting {S}ample {S}election {B}ias by {U}nlabeled {D}ata},
author = {Jiayuan Huang and Gretton, Arthur and Karsten M. Borgwardt and Sch\"{o}lkopf, Bernhard and Alex J. Smola},
booktitle = {Advances in Neural Information Processing Systems 19},
editor = {B. Sch\"{o}lkopf and J. C. Platt and T. Hoffman},
pages = {601--608},
year = {2007},
publisher = {MIT Press},
url = {http://papers.nips.cc/paper/3075-correcting-sample-selection-bias-by-unlabeled-data.pdf}
}

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Arthur Gretton, Karsten Borgwardt, Malte Rasch, Bernhard Schölkopf and Alexander Smola
A Kernel Method for the Two-Sample-Problem,
Advances in Neural Information Processing Systems 19 (NIPS 2006), 513-520. Full oral presentation. (Online)

@incollection{Gretton_A_2006,
title = {A Kernel Method for the Two-Sample-Problem},
author = {Gretton, Arthur and Karsten M. Borgwardt and Malte Rasch and Sch\"{o}lkopf, Bernhard and Alex J. Smola},
booktitle = {Advances in Neural Information Processing Systems 19},
editor = {B. Sch\"{o}lkopf and J. C. Platt and T. Hoffman},
pages = {513--520},
year = {2007},
publisher = {MIT Press},
url = {http://papers.nips.cc/paper/3110-a-kernel-method-for-the-two-sample-problem.pdf}
}

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S.V.N. Vishwanathan, Karsten Borgwardt, Nicol Schraudolph
Fast Computation of Graph Kernels,
Advances in Neural Information Processing Systems 19 (NIPS 2006), 1449-1456. (Online)

@incollection{Borgwardt_Fast_2006,
title = {Fast {C}omputation of {G}raph {K}ernels},
author = {Karsten M. Borgwardt and Nicol N. Schraudolph and S.V.N. Vishwanathan},
booktitle = {Advances in Neural Information Processing Systems 19},
editor = {B. Sch\"{o}lkopf and J. C. Platt and T. Hoffman},
pages = {1449--1456},
year = {2007},
publisher = {MIT Press},
url = {http://papers.nips.cc/paper/2973-fast-computation-of-graph-kernels.pdf}
}

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Johannes Aßfalg, Karsten Borgwardt and Hans-Peter Kriegel
3DString: A Feature String Kernel for 3D Object Classification on Voxelized Data,
in Proc. of International Conference on Information and Knowledge Management (CIKM 2006), 198-207.

The paper is available for download here (PDF, 1.1 MB).

@inproceedings{Assfalg_3DString_2006,
author = {A{\ss}falg, Johannes and Borgwardt, Karsten M. and Kriegel, Hans-Peter},
title = {{3DS}tring: {A} {F}eature {S}tring {K}ernel for {3D} {O}bject {C}lassification on {V}oxelized {D}ata},
booktitle = {Proceedings of the 15th ACM International Conference on Information and Knowledge Management},
series = {CIKM '06},
year = {2006},
isbn = {1-59593-433-2},
location = {Arlington, Virginia, USA},
pages = {198--207},
numpages = {10},
url = {http://doi.acm.org/10.1145/1183614.1183647},
doi = "10.1145/1183614.1183647",
acmid = {1183647},
publisher = {ACM},
address = {New York, NY, USA},
keywords = {3D object classification, string kernel},
}

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Karsten Borgwardt, S.V.N. Vishwanathan and Hans-Peter Kriegel
Class prediction from time series gene expression profiles using dynamical systems kernels,
in Proc. of Pacific Symposium on Biocomputing (PSB 2006), 547-558.

The paper is available for download here (PDF, 322 KB).

@article{Borgwardt_Class_2006,
    title = {Class prediction from time series gene expression profiles using dynamical systems kernels},
    issn = {2335-6936},
    language = {eng},
    journal = {Pacific Symposium on Biocomputing},
    author = {Borgwardt, Karsten M. and Vishwanathan, S. V. N. and Kriegel, Hans-Peter},
    year = {2006},
    pmid = {17094268},
    keywords = {Artificial Intelligence, COMPUTATIONAL BIOLOGY, Databases, Genetic, Gene Expression Profiling, Humans, Linear Models, Models, Genetic, Multiple Sclerosis, Oligonucleotide Array Sequence Analysis, Pharmacogenetics, Time Factors},
    pages = {547--558}
}

2005

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Karsten Borgwardt, Cheng S. Ong, Stefan Schönauer, S.V.N. Vishwanathan, Alexander Smola and Hans-Peter Kriegel
Protein Function Prediction via Graph Kernels,
Accepted at Intelligent Systems in Molecular Biology (ISMB 2005) and Bioinformatics 2005 21(suppl_1):i47-i56. (Online)

The code and further information can be found on the project page.

@article{Borgwardt_Protein_2005,
author = {Borgwardt, Karsten M. and Ong, Cheng Soon and Sch\"{o}nauer, Stefan and Vishwanathan, S. V. N. and Smola, Alex J. and Kriegel, Hans-Peter},
title = {Protein function prediction via graph kernels},
volume = {21},
number = {suppl 1},
pages = {i47-i56},
year = {2005},
doi = "http://dx.doi.org/10.1093/bioinformatics/bti1007",
URL = {http://bioinformatics.oxfordjournals.org/content/21/suppl_1/i47.abstract},

journal = {Bioinformatics}
}

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Karsten Borgwardt and Hans-Peter Kriegel
Shortest-path kernels on graphs,
in Proc. of International Conference on Data Mining (ICDM 2005).

The paper is available for download here (PDF, 162 KB).

@inproceedings{Borgwardt_Shortest-path_2005,
author={K. M. Borgwardt and H. P. Kriegel},
booktitle={Fifth IEEE International Conference on Data Mining (ICDM'05)},
title={Shortest-path kernels on graphs},
year={2005},
pages={8 pp.-},
keywords={computational complexity;graph theory;NP-hard problem;data mining;graph data;graph kernels;polynomial time algorithm;shortest-path kernel;Computer science;Data mining;Graph theory;Kernel;Polynomials;Proteins;Statistical learning;Support vector machine classification;Support vector machines;Time measurement},
doi="10.1109/ICDM.2005.132",
ISSN={1550-4786},
month=nov,}

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Karsten Borgwardt, Omri Guttman, S.V.N. Vishwanathan and Alexander Smola
Joint Regularization,
in Proc of. European Symposium on Artificial Neural Networks (ESANN 2005), 455-460.

The paper is available for download here (PDF, 298 KB).

@inproceedings{Borgwardt_2005_ESANN,
title = {Joint Regularization},
author = {Borgwardt, KM. and Guttman, O. and Vishwanathan, SVN. and Smola, AJ.},
booktitle = {13th European Symposium on Artificial Neural Networks, ESANN 2005},
pages = {455--460},
editors = {Verleysen, M.},
publisher = {d-side},
address = {Evere, Belgium},
month = apr,
year = {2005}
}

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