Oliver Kohlbacher

Orcid: 0000-0003-1739-4598

Affiliations:
  • University of Tübingen, Germany


According to our database1, Oliver Kohlbacher authored at least 132 papers between 1999 and 2023.

Collaborative distances:

Timeline

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Bibliography

2023
UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis.
J. Cheminformatics, December, 2023

The personalized cancer network explorer (PeCaX) as a visual analytics tool to support molecular tumor boards.
BMC Bioinform., December, 2023

Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities.
Proceedings of the 1st Conference on Research Data Infrastructure - Connecting Communities, 2023

2022
De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet.
BMC Bioinform., December, 2022

Bringing the Algorithms to the Data - Secure Distributed Medical Analytics using the Personal Health Train (PHT-meDIC).
CoRR, 2022

Efficient privacy-preserving whole-genome variant queries.
Bioinform., 2022


2021
Identifying disease-causing mutations with privacy protection.
Bioinform., 2021

2020
Distributed Analytics on Sensitive Medical Data: The Personal Health Train.
Data Intell., 2020

Enabling ad-hoc reuse of private data repositories through schema extraction.
J. Biomed. Semant., 2020

ClinVAP: a reporting strategy from variants to therapeutic options.
Bioinform., 2020

2019
The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR.
F1000Research, 2019

ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification.
Bioinform., 2019

BOOTABLE: Bioinformatics Benchmark Tool Suite.
Proceedings of the 19th IEEE/ACM International Symposium on Cluster, 2019

Reproducible Scientific Workflows for High Performance and Cloud Computing.
Proceedings of the 19th IEEE/ACM International Symposium on Cluster, 2019

Biological Network Knowledge in Molecular Tumor Boards.
Proceedings of the AMIA 2019, 2019

2018
Population-specific design of de-immunized protein biotherapeutics.
PLoS Comput. Biol., 2018

A distributed analytics platform to execute FHIR based phenotyping algorithms.
Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018

User-Driven Development of a Novel Molecular Tumor Board Support Tool.
Proceedings of the Data Integration in the Life Sciences - 13th International Conference, 2018

Interactive Visualization for Large-Scale Multi-factorial Research Designs.
Proceedings of the Data Integration in the Life Sciences - 13th International Conference, 2018

2017
qPortal - A science gateway for biomedical applications.
PeerJ Prepr., 2017

From the desktop to the grid and cloud: conversion of KNIME workflows to WS-PGRADE.
PeerJ Prepr., 2017

The future of metabolomics in ELIXIR.
F1000Research, 2017

ImmunoNodes - graphical development of complex immunoinformatics workflows.
BMC Bioinform., 2017

SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria.
Bioinform., 2017

Efficient Mass Spectra Prediction through Container Orchestration with a Scientific Workflow.
Proceedings of the 9th International Workshop on Science Gateways, 2017

Scaling home automation to public buildings: A distributed multiuser setup for OpenHAB 2.
Proceedings of the Global Internet of Things Summit, 2017

2016
Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics.
PLoS Comput. Biol., 2016

Containerization and wrapping of a mass spectra prediction workflow.
PeerJ Prepr., 2016

From the desktop to the grid: scalable bioinformatics via workflow conversion.
BMC Bioinform., 2016

FRED 2: an immunoinformatics framework for Python.
Bioinform., 2016

BALL-SNPgp - from genetic variants toward computational diagnostics.
Bioinform., 2016

2015
Network-based interactive navigation and analysis of large biological datasets.
it Inf. Technol., 2015

Computational Mass Spectrometry (Dagstuhl Seminar 15351).
Dagstuhl Reports, 2015

Protein (multi-)location prediction: utilizing interdependencies via a generative model.
Bioinform., 2015

EpiToolKit - a web-based workbench for vaccine design.
Bioinform., 2015

ballaxy: web services for structural bioinformatics.
Bioinform., 2015

2014
Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces.
J. Chem. Inf. Model., 2014

OptiType: precision HLA typing from next-generation sequencing data.
Bioinform., 2014

Rebuilding KEGG Maps: Algorithms and Benefits.
Proceedings of the IEEE Pacific Visualization Symposium, 2014

2013
On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications.
J. Integr. Bioinform., 2013

Deterministic clustering of the available chemical space.
J. Cheminformatics, 2013

Development of a pharmacorphore model for pharmacological chaperones targeting mutant trafficking-deficient CNG channels.
J. Cheminformatics, 2013

The MoSGrid - e-science gateway: molecular simulations in a distributed computing environment.
J. Cheminformatics, 2013

Computational Mass Spectrometry (Dagstuhl Seminar 13491).
Dagstuhl Reports, 2013

A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools.
Proceedings of the 7th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2013

From the Desktop to the Grid: conversion of KNIME Workflows to gUSE.
Proceedings of the 5th International Workshop on Science Gateways, 2013

Novel Visual Metaphors for Multivariate Networks.
Proceedings of the Multivariate Network Visualization, 2013

Multivariate Networks in the Life Sciences.
Proceedings of the Multivariate Network Visualization, 2013

2012
CADDSuite - a workflow-enabled suite of open-source tools for drug discovery.
J. Cheminformatics, 2012

MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment.
J. Cheminformatics, 2012

A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics.
J. Grid Comput., 2012

In silico design of targeted SRM-based experiments.
BMC Bioinform., 2012

Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway.
Proceedings of the HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences, 2012

miHA-match: computational detection of tissue-specific minor histocompatibility antigens.
Proceedings of the ACM International Conference on Bioinformatics, 2012

2011
NRPSpredictor2 - a web server for predicting NRPS adenylation domain specificity.
Nucleic Acids Res., 2011

A framework and workflow system for virtual screening and molecular docking.
J. Cheminformatics, 2011

MoSGrid - a molecular simulation grid as a new tool in computational chemistry, biology and material science.
J. Cheminformatics, 2011

Molecular simulation grid.
J. Cheminformatics, 2011

Special Issue: Portals for life sciences - Providing intuitive access to bioinformatic tools.
Concurr. Comput. Pract. Exp., 2011

POPISK: T-cell reactivity prediction using support vector machines and string kernels.
BMC Bioinform., 2011


T-cell epitope prediction based on self-tolerance.
Proceedings of the ACM International Conference on Bioinformatics, 2011

2010
Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families.
PLoS Comput. Biol., 2010

YLoc - an interpretable web server for predicting subcellular localization.
Nucleic Acids Res., 2010

Rescoring of docking poses using force field-based methods.
J. Cheminformatics, 2010

Exploiting physico-chemical properties in string kernels.
BMC Bioinform., 2010

BALL - biochemical algorithms library 1.3.
BMC Bioinform., 2010

Going from where to why - interpretable prediction of protein subcellular localization.
Bioinform., 2010

Grid-Workflows in Molecular Science.
Proceedings of the Software Engineering 2010, 2010

Novel Machine Learning Methods for MHC Class I Binding Prediction.
Proceedings of the Pattern Recognition in Bioinformatics, 2010

Graphlet Data Mining of Energetical Interaction Patterns in Protein 3D Structures.
Proceedings of the ICFC-ICNC 2010, 2010

TOPP goes Rapid The OpenMS Proteomics Pipeline in a Grid-Enabled Web Portal.
Proceedings of the 10th IEEE/ACM International Conference on Cluster, 2010

OpenMS and TOPP: Open Source Software for LC-MS Data Analysis.
Proceedings of the Proteome Bioinformatics, 2010

2009
OptiTope - a web server for the selection of an optimal set of peptides for epitope-based vaccines.
Nucleic Acids Res., 2009

Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies.
BMC Syst. Biol., 2009

KIRMES: kernel-based identification of regulatory modules in euchromatic sequences.
BMC Bioinform., 2009

MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction.
BMC Bioinform., 2009

A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis.
Bioinform., 2009

FRED - a framework for T-cell epitope detection.
Bioinform., 2009

Portals for Life Sciences - a Brief Introduction.
Proceedings of the International Workshop on Portals for Life Sciences, 2009

On Open Problems in Biological Network Visualization.
Proceedings of the Graph Drawing, 17th International Symposium, 2009

Integer Linear Programming in Computational Biology.
Proceedings of the Efficient Algorithms, 2009

2008
A Mathematical Framework for the Selection of an Optimal Set of Peptides for Epitope-Based Vaccines.
PLoS Comput. Biol., 2008

EpiToolKit - a web server for computational immunomics.
Nucleic Acids Res., 2008

BALLDock/SLICK: A New Method for Protein-Carbohydrate Docking.
J. Chem. Inf. Model., 2008

Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks.
J. Comput. Biol., 2008

Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics.
BMC Bioinform., 2008

OpenMS - An open-source software framework for mass spectrometry.
BMC Bioinform., 2008

LC-MSsim - a simulation software for liquid chromatography mass spectrometry data.
BMC Bioinform., 2008

GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments.
BMC Bioinform., 2008

MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization.
Bioinform., 2008

Multiple Instance Learning Allows MHC Class II Epitope Predictions Across Alleles.
Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

08101 Abstracts Collection - Computational Proteomics.
Proceedings of the Computational Proteomics, 02.03. - 07.03.2008, 2008

08191 Executive Summary - Graph Drawing with Applications to Bioinformatics and Social Sciences.
Proceedings of the Graph Drawing with Applications to Bioinformatics and Social Sciences, 04.05., 2008

08191 Abstracts Collection - Graph Drawing with Applications to Bioinformatics and Social Sciences.
Proceedings of the Graph Drawing with Applications to Bioinformatics and Social Sciences, 04.05., 2008

08191 Working Group Summary - Visually Comparing a Set of Graphs.
Proceedings of the Graph Drawing with Applications to Bioinformatics and Social Sciences, 04.05., 2008

2007
Abstract analysis of pathways using the BN++ software framework.
BMC Syst. Biol., 2007

Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.
BMC Bioinform., 2007

BNDB - The Biochemical Network Database.
BMC Bioinform., 2007

SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data.
Bioinform., 2007

TOPP - the OpenMS proteomics pipeline.
Bioinform., 2007

Electrostatic potentials of proteins in water: a structured continuum approach.
Bioinform., 2007

Finding Relevant Biotransformation Routes in Weighted Metabolic Networks.
Proceedings of the German Conference on Bioinformatics, 2007

2006
SVMHC: a server for prediction of MHC-binding peptides.
Nucleic Acids Res., 2006

BN++ - A Biological Information System.
J. Integr. Bioinform., 2006

A Fully Computational Model for Predicting Percutaneous Drug Absorption.
J. Chem. Inf. Model., 2006

SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions.
J. Chem. Inf. Model., 2006

BALLView: a tool for research and education in molecular modeling.
Bioinform., 2006

MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition.
Bioinform., 2006

High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques.
Proceedings of the Biocomputing 2006, 2006

Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data .
Proceedings of the Biocomputing 2006, 2006

2005
BALLView: An object-oriented molecular visualization and modeling framework.
J. Comput. Aided Mol. Des., 2005

Analysis of MHC-Peptide Binding Using Amino Acid Property-Based Decision Rules.
Proceedings of the Pattern Recognition and Data Mining, 2005

Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localizations.
Proceedings of the German Conference on Bioinformatics (GCB 2005), Hamburg, 2005

A machine learning approach for prediction of DNA and peptide retention times.
Proceedings of the Computational Proteomics, 20.-25. November 2005, 2005

High-accuracy peak picking of proteomics data.
Proceedings of the Computational Proteomics, 20.-25. November 2005, 2005

05471 Abstract Collection - Computational Proteomics.
Proceedings of the Computational Proteomics, 20.-25. November 2005, 2005

05471 Executive Summary - Computational Proteomics.
Proceedings of the Computational Proteomics, 20.-25. November 2005, 2005

Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins.
Proceedings of the Computational Proteomics, 20.-25. November 2005, 2005

Algorithms for the Automated Absolute Quantification of Diagnostic Markers in Complex Proteomics Samples.
Proceedings of the Computational Life Sciences, First International Symposium, 2005

2004
Differenzielle Proteomanalyse - Experimentelle Methoden, algorithmische Herausforderungen (Differential Analysis in Proteomics: Experimental Methods, Algorithmic Challenges).
it Inf. Technol., 2004

2003
Epitope Prediction Algorithms for Peptide based Vaccine Design.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002
A Combinatorial Approach to Protein Docking with Flexible Side Chains.
J. Comput. Biol., 2002

BioMiner - modeling, analyzing, and visualizing biochemical pathways and networks.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002

2001
New approaches to protein docking.
PhD thesis, 2001

A NMR-spectra-based scoring function for protein docking.
Proceedings of the Fifth Annual International Conference on Computational Biology, 2001

Visualization challenges for a new cyberpharmaceutical computing paradigm.
Proceedings of the IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics, 2001

2000
Rapid Software Prototyping in Molecular Modeling Using the Biochemical Algorithms Library (BALL).
ACM J. Exp. Algorithmics, 2000

BALL-rapid software prototyping in computational molecular biology.
Bioinform., 2000

1999
BALL: Biochemical Algorithms Library.
Proceedings of the Algorithm Engineering, 1999

Rapid Software Prototyping in Computational Molecular Biology.
Proceedings of the German Conference on Bioinformatics, 1999


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