List of works - Gunnar Rätsch

A General and Efficient Multiple Kernel Learning Algorithm ⬇️

scientific article published in January 2006

A Mathematical Programming Approach to the Kernel Fisher Algorithm ⬇️

A New Discriminative Kernel From Probabilistic Models ⬇️

A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters

scientific article published on 01 September 2019

A new discriminative kernel from probabilistic models

scientific article published in October 2002

A spatial and temporal map of C. elegans gene expression

scientific article published on 22 December 2010

ARTS: accurate recognition of transcription starts in human

scientific article published in July 2006

Abstract 389: Integrating diverse transcriptomic alterations to identify cancer-relevant genes

article

Abstract 892: Functional characterization of EIF1AX mutations in thyroid cancer predicts for gain of function by increasing translational rate with concomitant derepression of upstream inputs from mTOR

Abstract A45: Targeting eIF4A dependent translation as therapeutics in pancreatic cancer

Abstracts from the 5th International Society for Computational Biology Student Council Symposium at the 17th Annual International Conference on Intelligent Systems for Molecular Biology and the 8th European Conference on Computational Biology. June 2

scholarly article by Sebastian J Schultheiss published in January 2009

Accurate detection of differential RNA processing

scientific article

Accurate splice site prediction using support vector machines

scientific article

Active Learning in the Drug Discovery Process ⬇️

Active Learning with Support Vector Machines in the Drug Discovery Process

Active learning with support vector machines in the drug discovery process.

scientific article

Adapting Codes and Embeddings for Polychotomies ⬇️

scientific article published in January 2003

Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis.

scientific article published in November 2016

An Empirical Analysis of Domain Adaptation Algorithms for Genomic Sequence Analysis ⬇️

An Empirical Analysis of Topic Modeling for Mining Cancer Clinical Notes

An Introduction to Boosting and Leveraging

An introduction to kernel-based learning algorithms

scientific article published in January 2001

At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana

scientific article published on 9 July 2008

BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2

scientific article published on 26 December 2018

Building an International Consortium for Tracking Coronavirus Health Status

scientific article published on 06 April 2020

Building an international consortium for tracking coronavirus health status

scientific article published on 02 June 2020

CANCER PANOMICS: COMPUTATIONAL METHODS AND INFRASTRUCTURE FOR INTEGRATIVE ANALYSIS OF CANCER HIGH-THROUGHPUT “OMICS” DATA

Classifying 'drug-likeness' with kernel-based learning methods.

scientific article

Cohesin rings devoid of Scc3 and Pds5 maintain their stable association with the DNA

scientific article

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana

scientific article

Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins.

scientific article published on 7 June 2019

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

article

Constructing boosting algorithms from SVMs: an application to one-class classification

scholarly article by Gunnar Rätsch et al published September 2002 in IEEE Transactions on Pattern Analysis and Machine Intelligence

Constructing descriptive and discriminative nonlinear features: rayleigh coefficients in kernel feature spaces

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.

scientific article published on 5 May 2015

Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays

scientific article published on 6 March 2008

Determination and inference of eukaryotic transcription factor sequence specificity

scientific article

Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana

scientific article (publication date: 24 June 2008)

Dynamic compression schemes for graph coloring

scientific article published on 01 February 2019

EIF1AX and RAS mutations cooperate to drive thyroid tumorigenesis through ATF4 and c-MYC

article

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

scientific article published on 09 March 2020

Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota

scientific article

Efficient Privacy-Preserving String Search and an Application in Genomics

Efficient Training of Graph-Regularized Multitask SVMs

Efficient privacy-preserving string search and an application in genomics

scientific article

Engineering support vector machine kernels that recognize translation initiation sites

scientific article published in September 2000

Experimental analysis of support vector machines with different kernels based on non-intrusive monitoring data

Exploiting physico-chemical properties in string kernels

scientific article published on 26 October 2010

Fisher discriminant analysis with kernels

article

Genome-wide analysis of alternative splicing in Volvox carteri

scientific article

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

scholarly article

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits

scientific article published on 07 February 2017

Genomic basis for RNA alterations in cancer

scientific article published on 05 February 2020

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance

scientific article published on 06 August 2019

Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome

scientific article

Graph Based Semi-supervised Learning with Sharper Edges

article published in 2006

Graph-regularized 3D shape reconstruction from highly anisotropic and noisy images

scientific article

HBEGF macrophages in rheumatoid arthritis induce fibroblast invasiveness

scientific article published on 01 May 2019

Hierarchical Multitask Structured Output Learning for Large-scale Sequence Segmentation ⬇️

scientific article published in January 2011

HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing

scientific article

INTEGRATIVE GENOME-WIDE ANALYSIS OF THE DETERMINANTS OF RNA SPLICING IN KIDNEY RENAL CLEAR CELL CARCINOMA

Identification of HIF-dependent alternative splicing in gastrointestinal cancers and characterization of a long, coding isoform of SLC35A3

scientific article published on 05 January 2021

Image Reconstruction by Linear Programming ⬇️

scientific article published in January 2004

Image reconstruction by linear programming

scientific article published in June 2005

Improving the Caenorhabditis elegans Genome Annotation using Machine Learning

scientific article published in 2005

Improving the Caenorhabditis elegans genome annotation using machine learning

scientific article

Inferring latent task structure for Multitask Learning by Multiple Kernel Learning

scientific article published on 26 October 2010

Input space versus feature space in kernel-based methods

scientific article published on January 1999

Integrative Analysis of Transcriptome Variation in Uterine Carcinosarcoma and Comparison to Sarcoma and Endometrial Carcinoma

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

scientific article

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma

scientific article published on January 2015

Interferon-γ regulates cellular metabolism and mRNA translation to potentiate macrophage activation

scientific article published on 29 June 2015

Invariant Feature Extraction and Classification in Kernel Spaces ⬇️

KIRMES: kernel-based identification of regulatory modules in euchromatic sequences

scientific article

Kernel PCA Pattern Reconstruction via Approximate Pre-Images

Kernel PCA and De-Noising in Feature Spaces ⬇️

scientific article published in January 1999

Large scale genomic sequence SVM classifiers

article published in 2005

Learning interpretable SVMs for biological sequence classification

scientific article published on 20 March 2006

Learning to Predict the Leave-One-Out Error of Kernel Based Classifiers

Leveraging Sequence Classification by Taxonomy-Based Multitask Learning

MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples

scientific article

MMR: A Tool for Read Multi-Mapper Resolution

MMR: a tool for read multi-mapper resolution

scientific article published on 30 October 2015

Marcus Leonardo Boyd

scientific article published on 26 May 2021

Matrix Exponential Gradient Updates for On-line Learning and Bregman Projection ⬇️

Maximizing the Margin with Boosting

Metannot: A succinct data structure for compression of colors in dynamic de Bruijn graphs

article published in 2017

Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes

scientific article

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

scientific article published on 28 August 2011

Mutational signature learning with supervised negative binomial non-negative matrix factorization

scientific article published on 01 July 2020

NIPS workshop on New Problems and Methods in Computational Biology

scientific article

New Methods for Splice Site Recognition

article

Next generation genome annotation with mGene.ngs

article

Nonsense-mediated decay of alternative precursor mRNA splicing variants is a major determinant of the Arabidopsis steady state transcriptome

scientific article published on 25 October 2013

Novel Machine Learning Methods for MHC Class I Binding Prediction

scholarly article by Christian Widmer et al published 2010 in Lecture Notes in Computer Science

On the Convergence of Leveraging ⬇️

Opening the Black Box: Revealing Interpretable Sequence Motifs in Kernel-Based Learning Algorithms

Optimal spliced alignments of short sequence reads

scientific article

Optimal spliced alignments of short sequence reads

Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data ⬇️

scientific article published on 21 November 2011

Oqtans: a multifunctional workbench for RNA-seq data analysis

scholarly article by Vipin T Sreedharan et al published 2014 in BMC Bioinformatics

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis

scientific article published on 11 January 2014

PALMA: mRNA to genome alignments using large margin algorithms

scientific article

POIMs: positional oligomer importance matrices--understanding support vector machine-based signal detectors

scientific article published on July 2008

Persistence and availability of Web services in computational biology

scientific article (publication date: 2011)

Polypyrimidine tract binding protein homologs from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes

scientific article published on 27 November 2012

Prediction of potent shRNAs with a sequential classification algorithm

scientific article

Probabilistic clustering of time-evolving distance data

Protein translational control and its contribution to oncogenesis revealed by computational methods.

scientific article published on 28 January 2015

Prototype classification: insights from machine learning

scientific article

Publisher Correction: Building an international consortium for tracking coronavirus health status

scientific article published on 26 June 2020

Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes.

scientific article

RASE: recognition of alternatively spliced exons in C.elegans.

scientific article

RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer

scientific article

RNA-Seq Read Alignments with PALMapper

scholarly article published December 2010

RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation

scientific article

Receptor-type guanylate cyclase is required for carbon dioxide sensation by Caenorhabditis elegans

scientific article

Registered access: authorizing data access

scientific article published on 2 August 2018

Regularizing AdaBoost ⬇️

Revealing sequence variation patterns in rice with machine learning methods

scholarly article by Regina Bohnert et al published 2008 in BMC Bioinformatics

RiboDiff: Detecting Changes of Translation Efficiency from Ribosome Footprints

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints

scientific article

Robust Ensemble Learning for Data Mining

SCIM: universal single-cell matching with unpaired feature sets

scientific article published on 01 December 2020

SPHN/PHRT: Forming a Swiss-Wide Infrastructure for Data-Driven Sepsis Research

scientific article published on 01 June 2020

SVM2Motif--Reconstructing Overlapping DNA Sequence Motifs by Mimicking an SVM Predictor

scientific article published on 21 December 2015

Soft Margins for AdaBoost

Solving Semi-infinite Linear Programs Using Boosting-Like Methods

Sparse Binary Relation Representations for Genome Graph Annotation

scientific article published on 20 December 2019

Species-wide genetic incompatibility analysis identifies immune genes as hot spots of deleterious epistasis

scientific article

SplAdder: Identification, quantification and testing of alternative splicing events from RNA-Seq data

scholarly article published 26 March 2015

SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data

scientific article

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

Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays

scientific article published on 13 February 2009

Support vector machines and kernels for computational biology

scientific article

Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays

scientific article

Systematic evaluation of spliced alignment programs for RNA-seq data

scientific article

TRANSCRIPT NORMALIZATION AND SEGMENTATION OF TILING ARRAY DATA

The Feature Importance Ranking Measure

article

The Solution of Semi-Infinite Linear Programs Using Boosting-Like Methods

Totally corrective boosting algorithms that maximize the margin

scholarly article published 2006

Transcript normalization and segmentation of tiling array data.

scientific article

Transcript quantification with RNA-Seq data.

scientific article

Tumor Necrosis Factor dynamically regulates the mRNA stabilome in rheumatoid arthritis fibroblast-like synoviocytes

scientific article published on 14 July 2017

c-MYC regulates mRNA translation efficiency and start-site selection in lymphoma

scientific article published on 29 May 2019

mGene.web: a web service for accurate computational gene finding

scientific article

mGene: accurate SVM-based gene finding with an application to nematode genomes

scientific article published on 29 June 2009

rQuant.web: a tool for RNA-Seq-based transcript quantitation

scientific article

List of works by Gunnar Rätsch

A General and Efficient Multiple Kernel Learning Algorithm ⬇️

A Mathematical Programming Approach to the Kernel Fisher Algorithm ⬇️

A New Discriminative Kernel From Probabilistic Models ⬇️

A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters

A new discriminative kernel from probabilistic models

A spatial and temporal map of C. elegans gene expression

ARTS: accurate recognition of transcription starts in human

Abstract 389: Integrating diverse transcriptomic alterations to identify cancer-relevant genes

Abstract 892: Functional characterization of EIF1AX mutations in thyroid cancer predicts for gain of function by increasing translational rate with concomitant derepression of upstream inputs from mTOR

Abstract A45: Targeting eIF4A dependent translation as therapeutics in pancreatic cancer

Abstracts from the 5th International Society for Computational Biology Student Council Symposium at the 17th Annual International Conference on Intelligent Systems for Molecular Biology and the 8th European Conference on Computational Biology. June 2

Accurate detection of differential RNA processing

Accurate splice site prediction using support vector machines

Active Learning in the Drug Discovery Process ⬇️

Active Learning with Support Vector Machines in the Drug Discovery Process

Active learning with support vector machines in the drug discovery process.

Adapting Codes and Embeddings for Polychotomies ⬇️

Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis.

An Empirical Analysis of Domain Adaptation Algorithms for Genomic Sequence Analysis ⬇️

An Empirical Analysis of Topic Modeling for Mining Cancer Clinical Notes

An Empirical Analysis of Topic Modeling for Mining Cancer Clinical Notes

An Introduction to Boosting and Leveraging

An introduction to kernel-based learning algorithms

At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana

BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2

Building an International Consortium for Tracking Coronavirus Health Status

Building an international consortium for tracking coronavirus health status

CANCER PANOMICS: COMPUTATIONAL METHODS AND INFRASTRUCTURE FOR INTEGRATIVE ANALYSIS OF CANCER HIGH-THROUGHPUT “OMICS” DATA

Classifying 'drug-likeness' with kernel-based learning methods.

Cohesin rings devoid of Scc3 and Pds5 maintain their stable association with the DNA

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana

Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins.

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

Constructing boosting algorithms from SVMs: an application to one-class classification

Constructing descriptive and discriminative nonlinear features: rayleigh coefficients in kernel feature spaces

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.

Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays

Determination and inference of eukaryotic transcription factor sequence specificity

Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana

Dynamic compression schemes for graph coloring

Dynamic compression schemes for graph coloring

EIF1AX and RAS mutations cooperate to drive thyroid tumorigenesis through ATF4 and c-MYC

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

Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota

Efficient Privacy-Preserving String Search and an Application in Genomics

Efficient Training of Graph-Regularized Multitask SVMs

Efficient privacy-preserving string search and an application in genomics

Engineering support vector machine kernels that recognize translation initiation sites

Experimental analysis of support vector machines with different kernels based on non-intrusive monitoring data

Exploiting physico-chemical properties in string kernels

Fisher discriminant analysis with kernels

Genome-wide analysis of alternative splicing in Volvox carteri

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits

Genomic basis for RNA alterations in cancer

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance

Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome

Graph Based Semi-supervised Learning with Sharper Edges

Graph-regularized 3D shape reconstruction from highly anisotropic and noisy images

HBEGF macrophages in rheumatoid arthritis induce fibroblast invasiveness

Hierarchical Multitask Structured Output Learning for Large-scale Sequence Segmentation ⬇️

HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing

INTEGRATIVE GENOME-WIDE ANALYSIS OF THE DETERMINANTS OF RNA SPLICING IN KIDNEY RENAL CLEAR CELL CARCINOMA

Identification of HIF-dependent alternative splicing in gastrointestinal cancers and characterization of a long, coding isoform of SLC35A3

Image Reconstruction by Linear Programming ⬇️

Image reconstruction by linear programming

Improving the Caenorhabditis elegans Genome Annotation using Machine Learning

Improving the Caenorhabditis elegans genome annotation using machine learning

Inferring latent task structure for Multitask Learning by Multiple Kernel Learning

Input space versus feature space in kernel-based methods

Integrative Analysis of Transcriptome Variation in Uterine Carcinosarcoma and Comparison to Sarcoma and Endometrial Carcinoma

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma

Interferon-γ regulates cellular metabolism and mRNA translation to potentiate macrophage activation

Invariant Feature Extraction and Classification in Kernel Spaces ⬇️

KIRMES: kernel-based identification of regulatory modules in euchromatic sequences

Kernel PCA Pattern Reconstruction via Approximate Pre-Images