List of works - Karsten Borgwardt

3DString

A Kernel Method for the Two-Sample-Problem ⬇️

scientific article published in January 2007

A Lasso multi-marker mixed model for association mapping with population structure correction.

scientific article published on 22 November 2012

A dependence maximization view of clustering

A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series

scientific article published on March 2010

Aberrant working memory processing in major depression: evidence from multivoxel pattern classification

scholarly article by Matti Gärtner et al published August 2018 in Neuropsychopharmacology

Accurate and adaptive imputation of summary statistics in mixed-ethnicity cohorts

scholarly article by Matteo Togninalli published in September 2018

Accurate detection of differential RNA processing

scientific article

Accurate indel prediction using paired-end short reads

scientific article published on 27 February 2013

AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana

scientific article published on 01 January 2020

AraPheno: a public database for Arabidopsis thaliana phenotypes

scientific article published on 24 October 2016

Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis

scientific article published on 28 September 2012

Association mapping in biomedical time series via statistically significant shapelet mining.

scientific article published in July 2018

CASMAP: detection of statistically significant combinations of SNPs in association mapping

scientific article published on 01 August 2019

Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage

scientific article

Class prediction from time series gene expression profiles using dynamical systems kernels.

scientific article published in January 2006

Colored Maximum Variance Unfolding ⬇️

scientific article published in January 2008

Correcting Sample Selection Bias by Unlabeled Data ⬇️

scientific article published in January 2007

Covariate Shift by Kernel Mean Matching

Detecting regulatory gene-environment interactions with unmeasured environmental factors

scientific article published on 4 April 2013

Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area

scientific article published on 17 March 2022

Discriminative frequent subgraph mining with optimality guarantees

article

EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units

scientific article

Early prediction of circulatory failure in the intensive care unit using machine learning

scientific article published on 09 March 2020

Efficient branch-and-bound techniques for two-locus association mapping.

scientific article

Efficient inference in matrix-variate Gaussian models with \\iid observation noise ⬇️

scientific article published in January 2011

Efficient network-guided multi-locus association mapping with graph cuts

scientific article published on July 2013

Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs ⬇️

scientific article

Fast Computation of Graph Kernels ⬇️

scientific article published in January 2007

Fast and Memory-Efficient Significant Pattern Mining via Permutation Testing

Fast subtree kernels on graphs ⬇️

scientific article published in January 2009

Finding significant combinations of features in the presence of categorical covariates ⬇️

scientific article published in January 2016

Future trends in data mining

scholarly article by Hans-Peter Kriegel et al published 23 March 2007 in Data Mining and Knowledge Discovery

GLIDE: GPU-based linear regression for detection of epistasis

scientific article published on 4 September 2012

Gene function prediction from synthetic lethality networks via ranking on demand

scientific article published on 12 February 2010

Gene selection via the BAHSIC family of algorithms

scientific article published in July 2007

Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids.

scientific article

Genome-wide detection of intervals of genetic heterogeneity associated with complex traits.

scientific article

Genome-wide genetic heterogeneity discovery with categorical covariates

scientific article published on 14 February 2017

Genomic Profiles of Diversification and Genotype-Phenotype Association in Island Nematode Lineages.

scientific article

Geometric tree kernels: classification of COPD from airway tree geometry.

scientific article published in January 2013

Graph kernels for disease outcome prediction from protein-protein interaction networks

scientific article published on 01 January 2007

Guest editorial to the special issue on inductive logic programming, mining and learning in graphs and statistical relational learning

Halting in Random Walk Kernels ⬇️

In silico phenotyping via co-training for improved phenotype prediction from genotype

scientific article

Integrating structured biological data by Kernel Maximum Mean Discrepancy

scientific article

It is all in the noise: Efficient multi-task Gaussian process inference with structured residuals ⬇️

Kernel Conditional Clustering

Kernel Methods in Bioinformatics

Kernel extrapolation

Kernelized rank learning for personalized drug recommendation.

scientific article published on 8 March 2018

Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping

scientific article published on 15 July 2020

Methods and Tools in Genome-wide Association Studies

scientific article published on 01 January 2018

Metropolis Algorithms for Representative Subgraph Sampling

scholarly article published December 2008

Multi-Task Feature Selection on Multiple Networks via Maximum Flows

Multi-target drug repositioning by bipartite block-wise sparse multi-task learning.

scientific article published on 24 April 2018

Multi-view Spectral Clustering on Conflicting Views

Near-optimal supervised feature selection among frequent subgraphs

article

Pattern Mining in Frequent Dynamic Subgraphs

article

Persistent complement dysregulation with signs of thromboinflammation in active Long Covid

scientific article published on 18 January 2024

Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model

scientific article published on August 2008

Pretransplant Kinetics of Anti-HLA Antibodies in Patients on the Waiting List for Kidney Transplantation

scientific article published on 25 October 2019

Protein function prediction via graph kernels

scientific article published in June 2005

Rapid Distance-Based Outlier Detection via Sampling ⬇️

Scalable kernels for graphs with continuous attributes ⬇️

scientific article published in January 2013

ShapePheno: unsupervised extraction of shape phenotypes from biological image collections.

scientific article published on 13 February 2012

Significant Subgraph Mining with Multiple Testing Correction

Spatio-Spectral Remote Sensing Image Classification With Graph Kernels

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

scientific article published on 20 September 2011

Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts

Supervised feature selection via dependence estimation

The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog

scientific article published on 20 October 2017

The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity

scientific article

The genome of the simian and human malaria parasite Plasmodium knowlesi

scientific article

The graphlet spectrum

The skew spectrum of graphs

Two-locus association mapping in subquadratic time

Wasserstein Weisfeiler-Lehman Graph Kernels ⬇️

scientific article published in January 2019

Whole-genome sequencing of multiple Arabidopsis thaliana populations

scientific article published on 28 August 2011

ccSVM: correcting Support Vector Machines for confounding factors in biological data classification ⬇️

scientific article

easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies.

scientific article published on 16 December 2016

graphkernels: R and Python packages for graph comparison

scientific article

List of works by Karsten Borgwardt

3DString

A Kernel Method for the Two-Sample-Problem ⬇️

A Lasso multi-marker mixed model for association mapping with population structure correction.

A dependence maximization view of clustering

A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series

Aberrant working memory processing in major depression: evidence from multivoxel pattern classification

Accurate and adaptive imputation of summary statistics in mixed-ethnicity cohorts

Accurate detection of differential RNA processing

Accurate indel prediction using paired-end short reads

AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana

AraPheno: a public database for Arabidopsis thaliana phenotypes

Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis

Association mapping in biomedical time series via statistically significant shapelet mining.

CASMAP: detection of statistically significant combinations of SNPs in association mapping

Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage

Class prediction from time series gene expression profiles using dynamical systems kernels.

Colored Maximum Variance Unfolding ⬇️

Correcting Sample Selection Bias by Unlabeled Data ⬇️

Covariate Shift by Kernel Mean Matching

Detecting regulatory gene-environment interactions with unmeasured environmental factors

Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area

Discriminative frequent subgraph mining with optimality guarantees

EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units

Early prediction of circulatory failure in the intensive care unit using machine learning

Efficient branch-and-bound techniques for two-locus association mapping.

Efficient inference in matrix-variate Gaussian models with \\iid observation noise ⬇️

Efficient network-guided multi-locus association mapping with graph cuts

Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs ⬇️

Fast Computation of Graph Kernels ⬇️

Fast and Memory-Efficient Significant Pattern Mining via Permutation Testing

Fast subtree kernels on graphs ⬇️

Finding significant combinations of features in the presence of categorical covariates ⬇️

Future trends in data mining

GLIDE: GPU-based linear regression for detection of epistasis

Gene function prediction from synthetic lethality networks via ranking on demand

Gene selection via the BAHSIC family of algorithms

Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids.

Genome-wide detection of intervals of genetic heterogeneity associated with complex traits.

Genome-wide genetic heterogeneity discovery with categorical covariates

Genomic Profiles of Diversification and Genotype-Phenotype Association in Island Nematode Lineages.

Geometric tree kernels: classification of COPD from airway tree geometry.

Graph kernels for disease outcome prediction from protein-protein interaction networks

Guest editorial to the special issue on inductive logic programming, mining and learning in graphs and statistical relational learning

Halting in Random Walk Kernels ⬇️

In silico phenotyping via co-training for improved phenotype prediction from genotype

Integrating structured biological data by Kernel Maximum Mean Discrepancy

It is all in the noise: Efficient multi-task Gaussian process inference with structured residuals ⬇️

Kernel Conditional Clustering

Kernel Methods in Bioinformatics

Kernel extrapolation

Kernelized rank learning for personalized drug recommendation.

Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping

Methods and Tools in Genome-wide Association Studies

Metropolis Algorithms for Representative Subgraph Sampling

Multi-Task Feature Selection on Multiple Networks via Maximum Flows

Multi-target drug repositioning by bipartite block-wise sparse multi-task learning.

Multi-view Spectral Clustering on Conflicting Views

Near-optimal supervised feature selection among frequent subgraphs

Pattern Mining in Frequent Dynamic Subgraphs

Persistent complement dysregulation with signs of thromboinflammation in active Long Covid

Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model

Pretransplant Kinetics of Anti-HLA Antibodies in Patients on the Waiting List for Kidney Transplantation

Protein function prediction via graph kernels

Rapid Distance-Based Outlier Detection via Sampling ⬇️

Scalable kernels for graphs with continuous attributes ⬇️

ShapePheno: unsupervised extraction of shape phenotypes from biological image collections.

Significant Subgraph Mining with Multiple Testing Correction

Spatio-Spectral Remote Sensing Image Classification With Graph Kernels

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts

Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts

Supervised feature selection via dependence estimation

The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog

The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity

The genome of the simian and human malaria parasite Plasmodium knowlesi

The graphlet spectrum

The skew spectrum of graphs

Two-locus association mapping in subquadratic time

Wasserstein Weisfeiler-Lehman Graph Kernels ⬇️