Oliver Kohlbacher
A5053621010- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Mass Spectrometry Techniques and Applications
- vaccines and immunoinformatics approaches
- Bioinformatics and Genomic Networks
- Scientific Computing and Data Management
- Immunotherapy and Immune Responses
- Genomics and Phylogenetic Studies
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Monoclonal and Polyclonal Antibodies Research
- Machine Learning in Bioinformatics
- Computational Drug Discovery Methods
- Genetics, Bioinformatics, and Biomedical Research
- Microbial Metabolic Engineering and Bioproduction
- Distributed and Parallel Computing Systems
- Gene expression and cancer classification
- Analytical Chemistry and Chromatography
- Cancer Genomics and Diagnostics
- Cancer Immunotherapy and Biomarkers
- Research Data Management Practices
- T-cell and B-cell Immunology
- Glycosylation and Glycoproteins Research
- Biomedical Text Mining and Ontologies
- Peptidase Inhibition and Analysis
University of Tübingen
2016-2025
Universitätsklinikum Tübingen
2013-2024
Quantitative Biology Center
2012-2023
Max Planck Institute for Developmental Biology
2014-2023
German Cancer Research Center
2016-2023
University Children's Hospital Tübingen
2019-2023
University Hospital Leipzig
2022
Heinrich Heine University Düsseldorf
2021
Deutschen Konsortium für Translationale Krebsforschung
2021
Bernstein Center for Computational Neuroscience Tübingen
2007-2020
Our comprehensive analysis of alternative splicing across 32 The Cancer Genome Atlas cancer types from 8,705 patients detects events and tumor variants by reanalyzing RNA whole-exome sequencing data. Tumors have up to 30% more than normal samples. Association somatic with confirmed known trans associations in SF3B1 U2AF1 identified additional trans-acting (e.g., TADA1, PPP2R1A). Many tumors thousands not detectable samples; on average, we ≈930 exon-exon junctions ("neojunctions") typically...
Abstract Motivation: The human leukocyte antigen (HLA) gene cluster plays a crucial role in adaptive immunity and is thus relevant many biomedical applications. While next-generation sequencing data are often available for patient, deducing the HLA genotype difficult because of substantial sequence similarity within exceptionally high variability loci. Established approaches, therefore, rely on specific enrichment techniques, coming at an additional cost extra turnaround time. Result: We...
Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers experimental protocols a very active field research. This leads to more complex setups yielding ever increasing amounts data. Consequently, the data currently often bottleneck studies. Although software tools many tasks are available today, they hard combine with each other or not flexible enough allow rapid...
The products of many bacterial non-ribosomal peptide synthetases (NRPS) are highly important secondary metabolites, including vancomycin and other antibiotics. ability to predict substrate specificity newly detected NRPS Adenylation (A-) domains by genome sequencing efforts is great importance identify annotate new gene clusters that produce metabolites. Prediction A-domain based on the sequence alone can be achieved through signatures or, more accurately, machine learning methods. We...
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source information about is the evolutionary sequence record. Building on earlier work, we show that analysis correlated changes across proteins identifies residues close in space with sufficient accuracy determine three-dimensional structure We...
Personalized, precision, P4, or stratified medicine is understood as a medical approach in which patients are based on their disease subtype, risk, prognosis, treatment response using specialized diagnostic tests. The key idea to base decisions individual patient characteristics, including molecular and behavioral biomarkers, rather than population averages. Personalized deeply connected dependent data science, specifically machine learning (often named Artificial Intelligence the mainstream...
Abstract Motivation: Functional annotation of unknown proteins is a major goal in proteomics. A key the prediction protein's subcellular localization. Numerous techniques have been developed, typically focusing on single underlying biological aspect or predicting subset all possible localizations. An important step taken towards emulating protein sorting process by capturing and bringing together biologically relevant information, addressing clear need to improve accuracy localization...
Predicting subcellular localization has become a valuable alternative to time-consuming experimental methods. Major drawbacks of many these predictors is their lack interpretability and the fact that they do not provide an estimate confidence individual prediction. We present YLoc, interpretable web server for predicting localization. YLoc uses natural language explain why prediction was made which biological property protein mainly responsible it. In addition, estimates reliability its own...
Knowledge of subcellular localization proteins is crucial to proteomics, drug target discovery and systems biology since biological function are highly correlated. In recent years, numerous computational prediction methods have been developed. Nevertheless, there still a need for that show more robustness higher accuracy. We extended our previous MultiLoc predictor by incorporating phylogenetic profiles Gene Ontology terms. Two different datasets were used training the system, resulting in...
Background The human leucocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Understanding benign HLA ligand repertoire is a prerequisite define safe T-cell-based immunotherapies against cancer. Due poor availability tissues, if available, normal tissue adjacent tumor has been used as surrogate when defining tumor-associated antigens. However, this comparison proven be insufficient even...
Abstract Increasing numbers of protein interactions have been identified in high-throughput experiments, but only a small proportion solved structures. Recently, sequence coevolution-based approaches led to breakthrough predicting monomer structures and interaction interfaces. Here, we address the challenges large-scale prediction at residue resolution with fast alignment concatenation method probabilistic score for residues. Importantly, this (EVcomplex2) is able assess likelihood...