O. Kohlbacher

Russell Schwartz, Daniel H. Huson, Shibu Yooseph, 2001, Proceedings IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics (Cat. No.01EX520).

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

Konrad U. Förstner, Philipp H. Schiffer, D. Pe’er, 2020, Immunity.

The role of phosphorylatable serine residues in the DNA-binding domain of Arabidopsis bZIP transcription factors.

O. Kohlbacher, K. Harter, M. Teige, 2010, European journal of cell biology.

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

F. Glöckner, O. Kohlbacher, J. Blom, 2019, F1000Research.

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

F. Glöckner, O. Kohlbacher, J. Blom, 2019, F1000Research.

Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry.

Karl Mechtler, Andrew R Jones, Christoph H Borchers, 2020, Structure.

Comparison of different sample preparation techniques for NIR screening and their influence on the geographical origin determination of almonds (Prunus dulcis MILL.)

O. Kohlbacher, Marc Rurik, M. Fischer, 2020 .

Identification of HCMV-derived T cell epitopes in seropositive individuals through viral deletion models

H. Rammensee, S. Stevanović, O. Kohlbacher, 2019, The Journal of experimental medicine.

BALL – A Framework for Rapid Application Development in Molecular Modeling

O. Kohlbacher, 2001 .

The HLA ligandome landscape of chronic myeloid leukemia delineates novel T-cell epitopes for immunotherapy.

Chih-Chiang Tsou, H. Rammensee, S. Stevanović, 2018, Blood.

Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry

Andrew R. Jones, J. Cox, A. Sali, 2020, 2007.00383.

Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases

Keith A. Boroevich, Mathew R Divine, Benjamin J. Hescott, 2019 .

The HLA Ligand Atlas. A resource of natural HLA ligands presented on benign tissues

H. Rammensee, S. Stevanović, M. Weller, 2019, bioRxiv.

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

O. Kohlbacher, T. Skopal, D. Hoksza, 2013, Journal of integrative bioinformatics.

Population Genetics and Signatures of Selection in Early Neolithic European Farmers

O. Kohlbacher, J. Krause, H. Meller, 2022, Molecular biology and evolution.

A proteomics sample metadata representation for multiomics integration and big data analysis

A. Brazma, Mathias Wilhelm, E. Deutsch, 2021, Nature Communications.

Computational modeling of the sugar-lectin interaction.

Claus-Michael Lehr, Hans-Peter Lenhof, Oliver Kohlbacher, 2004, Advanced drug delivery reviews.

Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways.

Lennart Martens, Oliver Kohlbacher, Marc Vaudel, 2014, Blood.

Structural Glycomics – Molecular Details of Protein-Carbohydrate Interactions and their Prediction

O. Kohlbacher, D. Neumann, 2010 .

Multiple Layers of Phospho-Regulation Coordinate Metabolism and the Cell Cycle in Budding Yeast

O. Kohlbacher, J. Skotheim, Lichao Zhang, 2019, Frontiers in cell and developmental biology.

Dithiothreitol (DTT) Acts as a Specific, UV-inducible Cross-linker in Elucidation of Protein–RNA Interactions*

O. Kohlbacher, C. Lenz, H. Urlaub, 2015, Molecular & Cellular Proteomics.

Genome sequencing and transcriptome profiling in twins discordant for Mayer-Rokitansky-Kuester-Hauser syndrome

O. Kohlbacher, M. Sturm, O. Riess, 2022, medRxiv.

Clinical and non-targeted metabolomic profiling of homozygous carriers of Transcription Factor 7-like 2 variant rs7903146

O. Kohlbacher, Guowang Xu, E. Kenar, 2014, Scientific Reports.

Global Analysis of the Mammalian MHC class I Immunopeptidome at the Organism-Wide Scale

Kevin A. Kovalchik, David J. Hamelin, H. Rammensee, 2020, SSRN Electronic Journal.

Food fingerprinting: Mass spectrometric determination of the cocoa shell content (Theobroma cacao L.) in cocoa products by HPLC-QTOF-MS.

O. Kohlbacher, M. Fischer, Oliver Alka, 2019, Food chemistry.

The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience*

Jun Fan, Christoph Steinbeck, Johannes Griss, 2014, Molecular & Cellular Proteomics.

A proteomics sample metadata representation for multiomics integration and big data analysis

A. Brazma, Mathias Wilhelm, E. Deutsch, 2021, Nature Communications.

Proteome-scale discovery of protein interactions with residue-level resolution using sequence coevolution

Anna G. Green, D. Marks, O. Kohlbacher, 2019, bioRxiv.

Rebuilding KEGG Maps - An integrative approach for visual analytics of metabolic networks

Michael Kaufmann, Oliver Kohlbacher, Andreas Gerasch, 2014, PacificVis 2014.

Structural and Functional Characterization of the Bacterial Type III Secretion Export Apparatus

Matthias J. Brunner, Charlotta P. I. Schärfe, B. Maček, 2016, PLoS pathogens.

Challenges in Large-Scale Computational Mass Spectrometry and Multiomics.

Oliver Kohlbacher, Olga Vitek, Susan T Weintraub, 2016, Journal of Proteome Research.

Food Authentication: Small-Molecule Profiling as a Tool for the Geographic Discrimination of German White Asparagus.

O. Kohlbacher, Marc Rurik, M. Fischer, 2018, Journal of agricultural and food chemistry.

Displacement chromatography as first separating step in online two-dimensional liquid chromatography coupled to mass spectrometry analysis of a complex protein sample--the proteome of neutrophils.

O. Kohlbacher, M. Kwiatkowski, H. Schlüter, 2012, Journal of chromatography. A.

German Conference on Bioinformatics GCB 2006, 19.09. 2006 - 22.09. 2006 in Tübingen, Germany

Andreas Zell, Daniel H. Huson, Kay Nieselt, 2006, German Conference on Bioinformatics.

In melanoma, Hippo signaling is affected by copy number alterations and YAP1 overexpression impairs patient survival

Nora C. Toussaint, O. Kohlbacher, C. Ottmann, 2014, Pigment Cell & Melanoma Research.

Genetic variation in human drug-related genes you.

D. Marks, O. Kohlbacher, M. Schwab, 2017 .

Data Integration for Future Medicine (DIFUTURE) An Architectural and Methodological Overview

O. Kohlbacher, K. Kuhn, U. Mansmann, 2018 .

Novel Visual Metaphors for Multivariate Networks

Jonathan C. Roberts, Matthew O. Ward, Jing Yang, 2013, Multivariate Network Visualization.

The Global Architecture Shaping the Heterogeneity and Tissue-Dependency of the MHC Class I Immunopeptidome is Evolutionarily Conserved

Kevin A. Kovalchik, David J. Hamelin, H. Rammensee, 2020, bioRxiv.

Erratum to “Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient”

H. Rammensee, S. Stevanović, O. Kohlbacher, 2016, Journal of hepatology.

FLASHIda enables intelligent data acquisition for top–down proteomics to boost proteoform identification counts

O. Kohlbacher, Kyowon Jeong, V. Gorshkov, 2022, Nature Communications.

Supporting Advances in Proteome Informatics*□S

Andrew R. Jones, E. Deutsch, O. Kohlbacher, 2020 .

German Conference on Bioinformatics

A. Zell, O. Kohlbacher, D. Huson, 2006 .

Comparison of displacement versus gradient mode for separation of a complex protein mixture by anion-exchange chromatography.

O. Kohlbacher, M. Kwiatkowski, H. Schlüter, 2012, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo

O. Kohlbacher, M. Eisenacher, V. Gieselmann, 2022, Nature Communications.

Metabolites from Liquid Chromatography-Mass Spectrometry Data

A. Zell, O. Kohlbacher, E. Kenar, 2014 .

Genome Sequencing and Transcriptome Profiling in Twins Discordant for Mayer-Rokitansky-Küster-Hauser Syndrome

O. Kohlbacher, M. Sturm, R. Buchert, 2022, Journal of clinical medicine.

Sequence co-evolution gives 3D contacts and structures of protein complexes

Debora S. Marks, Chris Sander, Thomas A. Hopf, 2014, bioRxiv.

Modeling Protein‐Protein and Protein‐DNA Docking

O. Kohlbacher, A. Hildebrandt, Hans-Peter Lenhof, 2008 .

Visualization Challenges for a New Cyberpharmaceutical Computing

Russell Schwartz, Daniel H. Huson, Shibu Yooseph, 2001 .

Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics

Kathryn S. Lilley, Oliver Kohlbacher, Sean B. Holden, 2015, bioRxiv.

Going from where to why—interpretable prediction of protein subcellular localization

Oliver Kohlbacher, Jörg Rahnenführer, Sebastian Briesemeister, 2010, Bioinform..

From hype to reality: data science enabling personalized medicine

Holger Fröhlich, Thomas Lengauer, Blaz Zupan, 2018, BMC Medicine.

Charting a dynamic DNA methylation landscape of the human genome

A. Gnirke, D. Bennett, B. Bernstein, 2013, Nature.

Mass-Spectrometry-Based Proteomics Reveals Organ-Specific Expression Patterns To Be Used as Forensic Evidence.

Oliver Kohlbacher, Sven Nahnsen, Marius Ueffing, 2016, Journal of proteome research.

NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity

Kai Blin, Tilmann Weber, Oliver Kohlbacher, 2011, Nucleic Acids Res..

Resource Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

David R. Kelley, A. Gnirke, E. Lander, 2013 .

Implications for selectivity of 3,4-diarylquinolinones as p38alphaMAP kinase inhibitors.

Mohammed M. Abadleh, O. Kohlbacher, C. Peifer, 2008, Bioorganic & medicinal chemistry letters.

Feature-Based Molecular Networking in the GNPS Analysis Environment

Simon Rogers, Nuno Bandeira, Mingxun Wang, 2019, Nature Methods.

Lectin-sugar interaction. Calculated versus experimental binding energies.

O. Kohlbacher, Hans-Peter Lenhof, C. Lehr, 2002, European journal of biochemistry.

Calculated versus experimental binding energies

O. Kohlbacher, Hans-Peter Lenhof, C. Lehr, 2002 .

Interplay of pH and binding of multivalent metal ions: charge inversion and reentrant condensation in protein solutions.

O. Kohlbacher, F. Roosen‐Runge, Fajun Zhang, 2013, The journal of physical chemistry. B.

Interactive Visualization for Large-Scale Multi-factorial Research Designs

Andreas Friedrich, Oliver Kohlbacher, Sven Nahnsen, 2018, DILS.

Competing salt effects on phase behavior of protein solutions: tailoring of protein interaction by the binding of multivalent ions and charge screening.

O. Kohlbacher, A. Hildebrandt, S. Leibfarth, 2014, The journal of physical chemistry. B.

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

Gunnar Rätsch, Oliver Kohlbacher, Wolfgang Busch, 2009, Bioinformatics.

MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction

Oliver Kohlbacher, Torsten Blum, Sebastian Briesemeister, 2009, BMC Bioinformatics.

Favorable immune signature in CLL patients, defined by antigen-specific T-cell responses, might prevent second skin cancers

H. Rammensee, S. Stevanović, O. Kohlbacher, 2018, Leukemia & lymphoma.

The Endometrial Transcription Landscape of MRKH Syndrome

O. Kohlbacher, N. Casadei, O. Riess, 2020, bioRxiv.

Rescoring of docking poses using force field-based methods

Oliver Kohlbacher, Nina M. Fischer, Wolfgang M. Schneider, 2010, J. Cheminformatics.

A Fully Computational Model for Predicting Percutaneous Drug Absorption

Dirk Neumann, Thomas Lengauer, Oliver Kohlbacher, 2006, J. Chem. Inf. Model..

The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

Martin Eisenacher, Johannes Griss, Juan Antonio Vizcaíno, 2012, Molecular & Cellular Proteomics.

OpenMS – An open-source software framework for mass spectrometry

Knut Reinert, Oliver Kohlbacher, Ole Schulz-Trieglaff, 2008, BMC Bioinformatics.

OptiType: precision HLA typing from next-generation sequencing data

Benjamin Schubert, Oliver Kohlbacher, Magdalena Feldhahn, 2014, Bioinform..

Application of displacement chromatography for the analysis of a lipid raft proteome.

O. Kohlbacher, H. Schlüter, A. Bertsch, 2010, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

FRED—a framework for T-cell epitope detection

Oliver Kohlbacher, Magdalena Feldhahn, Philipp Thiel, 2009, Bioinform..

Genetic authentication: Differentiation of hazelnut cultivars using polymorphic sites of the chloroplast genome

O. Kohlbacher, M. Fischer, C. Lang, 2021 .

A Universal Language for Finding Mass Spectrometry Data Patterns

Paul D. Boudreau, Allegra T. Aron, Scott A. Jarmusch, 2022, bioRxiv.

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.

Martin Eisenacher, Yasset Perez-Riverol, Katrin Marcus, 2015, Journal of proteome research.

Reentrant condensation of proteins in solution induced by multivalent counterions.

O. Kohlbacher, A. Hildebrandt, Fan Zhang, 2008, Physical review letters.

A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis

Christina Backes, Eckart Meese, Andreas Keller, 2009, Bioinform..

De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet

O. Kohlbacher, A. Nordheim, Sebastian Winkler, 2021, bioRxiv.

Genetic variation in human drug-related genes

Charlotta P. I. Schärfe, D. Marks, O. Kohlbacher, 2017, bioRxiv.

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

Oliver Kohlbacher, Pierre Dönnes, Torsten Blum, 2006, Bioinform..

YLoc—an interpretable web server for predicting subcellular localization

Oliver Kohlbacher, Jörg Rahnenführer, Sebastian Briesemeister, 2010, Nucleic Acids Res..

Genetic variation in human drug-related genes

Charlotta P. I. Schärfe, D. Marks, O. Kohlbacher, 2017, Genome Medicine.

Immunoinformatics and epitope prediction in the age of genomic medicine

O. Kohlbacher, L. Backert, Linus Backert, 2015, Genome Medicine.

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

Hagit Shatkay, Oliver Kohlbacher, Scott Brady, 2007, Bioinformatics.

Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data

Hagit Shatkay, Oliver Kohlbacher, Scott Brady, 2005, Pacific Symposium on Biocomputing.

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

P. Dönnes, O. Kohlbacher, Annette Höglund, 2006 .

Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localizations

Oliver Kohlbacher, Pierre Dönnes, Torsten Blum, 2005, German Conference on Bioinformatics.

Integrative analysis of cancer‐related data using CAP

Christina Backes, Eckart Meese, Hans-Peter Lenhof, 2004, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization

Oliver Kohlbacher, Torsten Blum, O. Kohlbacher, 2008, Bioinform..

BioMiner - modeling, analyzing, and visualizing biochemical pathways and networks

Erich Bornberg-Bauer, Hans-Peter Lenhof, Markus Eiglsperger, 2002, ECCB.

OpenMS - A platform for reproducible analysis of mass spectrometry data.

Knut Reinert, Oliver Kohlbacher, Timo Sachsenberg, 2017, Journal of biotechnology.

HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy

H. Rammensee, S. Stevanović, M. Weller, 2021, Journal for ImmunoTherapy of Cancer.

ImmunoNodes – graphical development of complex immunoinformatics workflows

Benjamin Schubert, Oliver Kohlbacher, Mathias Walzer, 2017, BMC Bioinformatics.

Designing string-of-beads vaccines with optimal spacers

O. Kohlbacher, B. Schubert, 2016, Genome Medicine.

Induction of neoantigen-reactive T cells from healthy donors

O. Kohlbacher, T. Schumacher, B. Schubert, 2019, Nature Protocols.

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

H. Rammensee, S. Stevanović, B. Maček, 2019, Genome medicine.

Visualization of omics data for systems

Hiroaki Kitano, Alexander Goesmann, Dan Tenenbaum, 2010 .

Where Natural Protein Sequences Stand out From Randomness

T. Dijkstra, O. Kohlbacher, A. Lupas, 2019, bioRxiv.

Minor deviations from randomness have huge repercussions on the functional structuring of sequence space

T. Dijkstra, O. Kohlbacher, A. Lupas, 2021 .

Analysis of Genomic DNA from Medieval Plague Victims Suggests Long-Term Effect of Yersinia pestis on Human Immunity Genes

O. Kohlbacher, J. Krause, Ben Krause-Kyora, 2021, Molecular biology and evolution.

Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry

O. Kohlbacher, J. Krause, A. Franke, 2021, Communications biology.

Neolithic genomes reveal a distinct ancient HLA allele pool and population transformation in Europe

I. Mathieson, O. Kohlbacher, J. Krause, 2019, bioRxiv.

Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19

Konrad U. Förstner, Philipp H. Schiffer, Joseph M. Johnson, 2021, Immunity.

Identifying disease-causing mutations with privacy protection

Oliver Kohlbacher, Nico Pfeifer, Bekir Ergüner, 2020, Bioinform..

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients

Konrad U. Förstner, Philipp H. Schiffer, P. Bork, 2020, Genome Medicine.

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins

Oliver Kohlbacher, Timo Sachsenberg, Henning Urlaub, 2014, Nature Methods.

DrugTargetInspector: An assistance tool for patient treatment stratification

Eckart Meese, Andreas Keller, Hans-Peter Lenhof, 2016, International journal of cancer.

Enabling ad-hoc reuse of private data repositories through schema extraction

Lukas Zimmermann, Oliver Kohlbacher, Stefan Decker, 2020, Journal of Biomedical Semantics.

Identification of Pparγ-modulated miRNA hubs that target the fibrotic tumor microenvironment

C. Plass, R. Geffers, O. Kohlbacher, 2019, Proceedings of the National Academy of Sciences.

Cross-linking of the Endolysosomal System Reveals Flotillin Structures and Putative Cargo

O. Kohlbacher, M. Eisenacher, V. Gieselmann, 2022, bioRxiv.

Intuitive Web-Based Experimental Design for High-Throughput Biomedical Data

Andreas Friedrich, Erhan Kenar, Oliver Kohlbacher, 2015, BioMed research international.

Understanding the constitutive presentation of MHC class I immunopeptidomes in primary tissues

Kevin A. Kovalchik, David J. Hamelin, O. Kohlbacher, 2022, iScience.

MHCquant: Automated and reproducible data analysis for immunopeptidomics.

Timo Sachsenberg, Oliver Kohlbacher, Alexander Peltzer, 2019, Journal of proteome research.

Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient

Oliver Kohlbacher, Sven Nahnsen, Mathias Walzer, 2016, Journal of hepatology.

SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition

H. Rammensee, S. Stevanović, O. Kohlbacher, 2020, Nature immunology.

A community proposal to integrate proteomics activities in ELIXIR

Lennart Martens, Martin Eisenacher, Wout Bittremieux, 2017, F1000Research.

Tools for Label-free Peptide Quantification

Knut Reinert, Sven Nahnsen, Oliver Kohlbacher, 2012, Molecular & Cellular Proteomics.

Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays

Oliver Kohlbacher, Klaus Harter, Dierk Wanke, 2013, Nucleic acids research.

Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach.

Oliver Kohlbacher, Christian G Huber, Nico Pfeifer, 2009, Journal of proteome research.

Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics

Oliver Kohlbacher, Nico Pfeifer, Christian G. Huber, 2007, BMC Bioinformatics.

Exploring protein-protein interactions at the proteome level.

O. Kohlbacher, A. Lupas, F. Merino, 2022, Structure.

SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins.

Hagit Shatkay, Yin Lam, Oliver Kohlbacher, 2009, Journal of proteome research.

SVMHC: a server for prediction of MHC-binding peptides

Oliver Kohlbacher, Pierre Dönnes, P. Dönnes, 2006, Nucleic Acids Res..

Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences

Anna G. Green, D. Marks, O. Kohlbacher, 2021, Nature Communications.

WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome

P. Dönnes, O. Kohlbacher, T. Proikas-Cezanne, 2015, Journal of Cell Science.

Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection Clusters Based on Integrated Genomic Surveillance, Outbreak Analysis and Contact Tracing in an Urban Setting

Konrad U. Förstner, Philipp H. Schiffer, Jonathan L. Schmid-Burgk, 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics

Tim W. Nattkemper, Oliver Kohlbacher, Sebastian Böcker, 2008, BMC Bioinformatics.

Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry

Andy M. Lau, O. Kohlbacher, H. Urlaub, 2020, Nature Communications.

Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry.

A. Marchfelder, O. Kohlbacher, H. Urlaub, 2015, Methods.

SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria

Oliver Kohlbacher, Marnix H. Medema, Fabian Aicheler, 2017, Bioinform..

High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques

Knut Reinert, Oliver Kohlbacher, Andreas Hildebrandt, 2005, Pacific Symposium on Biocomputing.

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

O. Kohlbacher, Lukas Zimmermann, Florian König, 2022, ArXiv.

SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing.

Markus J. Herrgård, O. Kohlbacher, L. Nielsen, 2020, Analytical Chemistry.

Application of displacement chromatography for the proteome analysis of a human plasma protein fraction.

O. Kohlbacher, H. Schlüter, A. Bertsch, 2010, Journal of chromatography. A.

SmartPeak automates targeted and quantitative metabolomics data processing

Timo Sachsenberg, Oliver Kohlbacher, Svetlana Kutuzova, 2020, bioRxiv.

LFQProfiler and RNP(xl): Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer.

Oliver Kohlbacher, Timo Sachsenberg, Henning Urlaub, 2016, Journal of proteome research.

An innovative approach for HLA typing, molecular tumor testing and the validation of tumor exclusive antigens

H. Rammensee, S. Stevanović, O. Kohlbacher, 2020, bioRxiv.

Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry

O. Kohlbacher, J. Krause, D. Ellinghaus, 2021, Communications Biology.

Epitope prediction algorithms for peptide-based vaccine design

Russell Schwartz, Sorin Istrail, Bjarni V. Halldórsson, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

Distributed Analytics on Sensitive Medical Data: The Personal Health Train

Luiz Olavo Bonino da Silva Santos, Lukas Zimmermann, Michel Dumontier, 2020, Data Intelligence.

Data Integration for Future Medicine (DIFUTURE)

Fabian Prasser, Klaus A. Kuhn, Ulrich Mansmann, 2018, Methods of Information in Medicine.

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016): part one

Charles J. Vaske, Rohan N. Borkar, Brian D. Kelly, 2016, Journal of Immunotherapy for Cancer.

An automated pipeline for high-throughput label-free quantitative proteomics.

Andreas Quandt, Lars Malmström, Ruedi Aebersold, 2013, Journal of proteome research.

Trailblazing Precision Medicine in Europe: a joint view by Genomic Medicine Sweden and the Centers for Personalized Medicine, ZPM, in Germany.

S. Fröhling, L. Levin, D. Gisselsson, 2021, Seminars in cancer biology.

MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics.

Martin Taubert, Jana Seifert, Oliver Kohlbacher, 2015, Journal of proteome research.

Machine learning competition in immunology - Prediction of HLA class I binding peptides.

Harris Papadopoulos, Tomer Hertz, Vladimir Brusic, 2011, Journal of immunological methods.

qPortal: A platform for data-driven biomedical research

Andreas Friedrich, Erhan Kenar, Oliver Kohlbacher, 2018, PloS one.

EPIFANY – A method for efficient high-confidence protein inference

Oliver Serang, Knut Reinert, Timo Sachsenberg, 2019, bioRxiv.

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

Martin Eisenacher, Yasset Perez-Riverol, Knut Reinert, 2017, Journal of proteomics.

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

Johannes Griss, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2016, Nature Methods.

Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks

Oliver Kohlbacher, Torsten Blum, O. Kohlbacher, 2008, J. Comput. Biol..

FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics.

Oliver Kohlbacher, Jihyung Kim, Manasi Gaikwad, 2020, Cell systems.

Activation of lymphoma-associated MyD88 mutations via allostery-induced TIR-domain oligomerization.

Charlotta P. I. Schärfe, O. Kohlbacher, R. Jerala, 2014, Blood.

EpiToolKit—a web server for computational immunomics

Oliver Kohlbacher, Stefan Stevanovic, Magdalena Feldhahn, 2008, Nucleic Acids Res..

Differenzielle Proteomanalyse – Experimentelle Methoden, algorithmische Herausforderungen (Differential Analysis in Proteomics: Experimental Methods, Algorithmic Challenges)

Knut Reinert, Oliver Kohlbacher, K. Reinert, 2004, it Inf. Technol..

Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces

Oliver Kohlbacher, Philipp Thiel, Christian Ottmann, 2014, J. Chem. Inf. Model..

POPISK: T-cell reactivity prediction using support vector machines and string kernels

Shinn-Ying Ho, Chun-Wei Tung, Oliver Kohlbacher, 2011, BMC Bioinformatics.

Multiple Instance Learning Allows MHC Class II Epitope Predictions Across Alleles

Oliver Kohlbacher, Nico Pfeifer, O. Kohlbacher, 2008, WABI.

The HLA ligandome of oropharyngeal squamous cell carcinomas reveals shared tumour-exclusive peptides for semi-personalised vaccination

H. Kestler, O. Kohlbacher, J. Kraus, 2023, British Journal of Cancer.

Distinct transcriptional changes in non-small cell lung cancer patients associated with multi-antigenic RNActive® CV9201 immunotherapy

O. Kohlbacher, J. Billingsley, S. Koch, 2016, Oncoimmunology.

A Mathematical Framework for the Selection of an Optimal Set of Peptides for Epitope-Based Vaccines

Oliver Kohlbacher, Pierre Dönnes, Nora C. Toussaint, 2008, PLoS Comput. Biol..

HLA ligandome analysis of primary chronic lymphocytic leukemia (CLL) cells under lenalidomide treatment confirms the suitability of lenalidomide for combination with T-cell-based immunotherapy

Oliver Kohlbacher, Hans-Georg Rammensee, Annika Nelde, 2017, Oncoimmunology.

Carfilzomib alters the HLA-presented peptidome of myeloma cells and impairs presentation of peptides with aromatic C-termini

H. Rammensee, S. Stevanović, O. Kohlbacher, 2016, Blood Cancer Journal.

Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation.

H. Rammensee, S. Stevanović, P. Adam, 2018, Cancer research.

Population-specific design of de-immunized protein biotherapeutics

Debora S. Marks, Benjamin Schubert, Oliver Kohlbacher, 2017, PLoS Comput. Biol..

SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition

S. Stevanović, O. Kohlbacher, J. Karbach, 2020, Nature Immunology.

T-cell epitope prediction based on self-tolerance

Oliver Kohlbacher, Stefan Stevanovic, Magdalena Feldhahn, 2011, BCB '11.

SNEP: SNP-derived Epitope Prediction program for minor H antigens

Oliver Kohlbacher, Hans-Georg Rammensee, Pierre Dönnes, 2005, Immunogenetics.

The HLA Ligand Atlas: A novel immuno-oncology resource for T-cell antigen discovery.

H. Rammensee, S. Stevanović, M. Weller, 2020 .

Abstract B124: Personalized peptide vaccination based on patient-individual tumor-specific variants induces T-cell responses in pediatric patients

H. Rammensee, S. Stevanović, O. Kohlbacher, 2019, Novel Vaccine Platforms and Combinations.

OptiTope—a web server for the selection of an optimal set of peptides for epitope-based vaccines

Oliver Kohlbacher, Nora C. Toussaint, O. Kohlbacher, 2009, Nucleic Acids Res..

Novel Machine Learning Methods for MHC Class I Binding Prediction

Gunnar Rätsch, Yasemin Altun, Oliver Kohlbacher, 2010, PRIB.

FRED 2: an immunoinformatics framework for Python

Benjamin Schubert, Oliver Kohlbacher, Mathias Walzer, 2016, Bioinform..

Electrostatic potentials of proteins in water: a structured continuum approach

Hans-Peter Lenhof, Sergej Rjasanow, Oliver Kohlbacher, 2007, Bioinform..

EpiToolKit—a web-based workbench for vaccine design

Benjamin Schubert, Oliver Kohlbacher, Hans-Philipp Brachvogel, 2015, Bioinform..

Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families

Oliver Kohlbacher, Marc Röttig, Christian Rausch, 2010, PLoS Comput. Biol..

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry

Oliver Kohlbacher, Benjamin A. Garcia, Timo Sachsenberg, 2018, Nature Communications.

Food authentication: Determination of the geographical origin of almonds (Prunus dulcis Mill.) via near-infrared spectroscopy

Oliver Kohlbacher, Markus Fischer, Marc Rurik, 2021, Microchemical Journal.

Neonatal apnea and hypopnea prediction in infants with Robin sequence with neural additive models for time series

J. Macke, T. Dijkstra, O. Kohlbacher, 2023, medRxiv.

Determination of the Geographical Origin of Asparagus officinalis L. by 1H NMR Spectroscopy.

Julia L. Klare, O. Kohlbacher, T. Hackl, 2020, Journal of agricultural and food chemistry.

Poster abstracts of the 25th German Conference on Bioinformatics

Kay Nieselt, Oliver Kohlbacher, Andrei N. Lupas, 2017 .

Proteins and Molecular Pathways Relevant for the Malignant Properties of Tumor-Initiating Pancreatic Cancer Cells

O. Kohlbacher, Marc Rurik, C. Huber, 2020, Cells.

Scaling home automation to public buildings: A distributed multiuser setup for OpenHAB 2

Michael Menth, Oliver Kohlbacher, Florian Heimgaertner, 2017, 2017 Global Internet of Things Summit (GIoTS).

No Longer Confidential: Estimating the Confidence of Individual Regression Predictions

Oliver Kohlbacher, Sebastian Briesemeister, Jörg Rahnenführer, 2012, PloS one.

User-Driven Development of a Novel Molecular Tumor Board Support Tool

Peter Gerjets, Holger Stenzhorn, Oliver Kohlbacher, 2018, DILS.

Testing and Validation of Computational Methods for Mass Spectrometry.

Henning Hermjakob, Oliver Kohlbacher, Laurent Gatto, 2016, Journal of proteome research.

Bioinformatics for qualitative and quantitative proteomics.

Knut Reinert, Oliver Kohlbacher, Clemens Gröpl, 2011, Methods in molecular biology.

OpenMS and TOPP: Open Source Software for LC-MS Data Analysis

Knut Reinert, Oliver Kohlbacher, K. Reinert, 2010, Proteome Bioinformatics.

LC-MSsim – a simulation software for liquid chromatography mass spectrometry data

Knut Reinert, Oliver Kohlbacher, Ole Schulz-Trieglaff, 2008, BMC Bioinformatics.

TOPP - the OpenMS proteomics pipeline

Knut Reinert, Oliver Kohlbacher, Ole Schulz-Trieglaff, 2007, Bioinform..

The mzQuantML Data Standard for Mass Spectrometry–based Quantitative Studies in Proteomics

Martin Eisenacher, Jun Fan, Juan Antonio Vizcaíno, 2013, Molecular & Cellular Proteomics.

Comparative immunopeptidomics of humans and their pathogens.

Sorin Istrail, Oliver Kohlbacher, Liliana Florea, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Untargeted Metabolomics Reveals Molecular Effects of Ketogenic Diet on Healthy and Tumor Xenograft Mouse Models

O. Kohlbacher, R. Reischl, C. Huber, 2019, International journal of molecular sciences.

DIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics

O. Kohlbacher, H. Röst, M. Witting, 2022, Nature Communications.

DIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics

O. Kohlbacher, H. Röst, M. Witting, 2022, Nature communications.

Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future

E. Deutsch, O. Kohlbacher, J. Vizcaíno, 2021, Molecular & cellular proteomics : MCP.

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics*

Harald Barsnes, Martin Eisenacher, Yasset Perez-Riverol, 2017, Molecular & Cellular Proteomics.

qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments*

Lennart Martens, Wout Bittremieux, Juan Antonio Vizcaíno, 2014, Molecular & Cellular Proteomics.

Improved particle-packed HPLC/MS microchips for proteomic analysis.

O. Kohlbacher, H. Schlüter, A. Bertsch, 2010, Journal of separation science.

Induction of neoantigen-reactive T cells from healthy donors

O. Kohlbacher, T. Schumacher, B. Schubert, 2019, Nature Protocols.

A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics

Thomas Steinke, Bernd Schuller, Richard Grunzke, 2012, Journal of Grid Computing.

DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics.

Philip A. Ewels, O. Kohlbacher, L. Kuchenbecker, 2021, Journal of proteome research.

Development of a fluorescence-based assay for screening of modulators of human organic anion transporter 1B3 (OATP1B3).

O. Kohlbacher, Hans-Peter Lenhof, C. Lehr, 2006, European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V.

Nephron Toxicity Profiling via Untargeted Metabolome Analysis Employing a High Performance Liquid Chromatography-Mass Spectrometry-based Experimental and Computational Pipeline*

Oliver Kohlbacher, Christian G Huber, Paul Jennings, 2015, The Journal of Biological Chemistry.

Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities.

O. Kohlbacher, E. Allen-Vercoe, Timo Sachsenberg, 2020, Journal of proteomics.

A distributed analytics platform to execute FHIR based phenotyping algorithms

Stefan Decker, Lukas Zimmermann, Holger Stenzhorn, 2018, SWAT4LS.

Generic User Management for Science Gateways via Virtual Organizations

Richard Grunzke, Sandra Gesing, Jens Krüger, 2012 .

Clinical outcome of biomarker-guided therapies in adult patients with tumors of the nervous system

C. Lengerke, O. Kohlbacher, S. Nahnsen, 2023, Neuro-oncology advances.

Analysis of MHC-Peptide Binding Using Amino Acid Property-Based Decision Rules

Oliver Kohlbacher, Pierre Dönnes, Jochen Supper, 2005, ICAPR.

Exploiting physico-chemical properties in string kernels

Gunnar Rätsch, Oliver Kohlbacher, Christian Widmer, 2010, BMC Bioinformatics.

Fluorescence-based imaging of autophagy progression by human WIPI protein detection.

P. Dönnes, O. Kohlbacher, T. Proikas-Cezanne, 2015, Methods.

The future of metabolomics in ELIXIR.

Alejandra N. González-Beltrán, Ralf J. M. Weber, Rachel A. Spicer, 2017, F1000Research.

UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis

O. Kohlbacher, T. Weber, Timo Sachsenberg, 2023, Journal of Cheminformatics.

Modeling metabolic networks in C . glutamicum : a comparison of rate laws in combination with various parameter optimization strategies

Andreas Zell, Marco Oldiges, Andreas Dräger, 2009 .

TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data.

Knut Reinert, Oliver Kohlbacher, Marc Sturm, 2012, Journal of proteome research.

The MoSGrid - e-science gateway: molecular simulations in a distributed computing environment

Thomas Steinke, Richard Grunzke, Sandra Gesing, 2013, Journal of Cheminformatics.

Food monitoring: Screening of the geographical origin of white asparagus using FT-NIR and machine learning

Oliver Kohlbacher, Markus Fischer, Marc Rurik, 2019, Food Control.

Annotation and initial evaluation of a large annotated German oncological corpus

U. Leser, O. Kohlbacher, D. Rieke, 2021, JAMIA open.

Machine learning identifies ICU outcome predictors in a multicenter COVID-19 cohort

O. Kohlbacher, C. Putensen, P. Meybohm, 2021, Critical Care.

OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS

Oliver Kohlbacher, Timo Sachsenberg, Mathias Walzer, 2020, Molecular & Cellular Proteomics.

BALLDock/SLICK: A New Method for Protein-Carbohydrate Docking

Dirk Neumann, Jan Fuhrmann, Oliver Kohlbacher, 2008, J. Chem. Inf. Model..

SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions

Dirk Neumann, Oliver Kohlbacher, Andreas Kerzmann, 2006, J. Chem. Inf. Model..

The future of metabolomics in ELIXIR

Alejandra N. González-Beltrán, Ralf J. M. Weber, Rachel A. Spicer, 2017, F1000Research.

Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry

Knut Reinert, Erhan Kenar, Timo Sachsenberg, 2015, Proteomics.

miHA-match: computational detection of tissue-specific minor histocompatibility antigens

Benjamin Schubert, Oliver Kohlbacher, Magdalena Feldhahn, 2012, BCB.

The future of metabolomics in ELIXIR [version 1; peer review: 2 approved, 1 approved with reservations]

Alejandra N. González-Beltrán, Ralf J. M. Weber, Rachel A. Spicer, 2021 .

TOPPView: an open-source viewer for mass spectrometry data.

Oliver Kohlbacher, Marc Sturm, O. Kohlbacher, 2009, Journal of proteome research.

A combinatorial approach to protein docking with flexible side-chains

Ernst Althaus, Hans-Peter Lenhof, Oliver Kohlbacher, 2000, RECOMB '00.

Computational life sciences II

Ingrid Fischer, Robert C. Glen, Oliver Kohlbacher, 2005 .

FLASHIda: Intelligent data acquisition for top-down proteomics that doubles proteoform level identification count

O. Kohlbacher, O. Jensen, Kyowon Jeong, 2021, bioRxiv.

GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments

Hans-Peter Lenhof, Oliver Kohlbacher, Andreas Keller, 2008, BMC Bioinformatics.

Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells

O. Kohlbacher, Marc Rurik, C. Huber, 2020, Cell Communication and Signaling.

Copper oxide nanoparticle toxicity profiling using untargeted metabolomics

O. Kohlbacher, R. Reischl, Marc Rurik, 2015, Particle and Fibre Toxicology.

BiNA: A Visual Analytics Tool for Biological Network Data

Hans-Peter Lenhof, Oliver Kohlbacher, Michael Kaufmann, 2014, PloS one.

BN++ – A Biological Information System

Christina Backes, Hans-Peter Lenhof, Oliver Kohlbacher, 2008, J. Integr. Bioinform..

Novel formulation of nonlocal electrostatics.

O. Kohlbacher, A. Hildebrandt, Hans-Peter Lenhof, 2004, Physical review letters.

11th German Conference on Chemoinformatics (GCC 2015)

Timothy Clark, Jonathan W. Essex, Peter Kolb, 2016, Journal of Cheminformatics.

PREDICT-juvenile-stroke: PRospective evaluation of a prediction score determining individual clinical outcome three months after ischemic stroke in young adults – a study protocol

H. Kestler, O. Kohlbacher, M. Dieterich, 2023, BMC Neurology.

BALL-SNPgp - from genetic variants toward computational diagnostics

Sabine C. Mueller, Christina Backes, Eckart Meese, 2016, Bioinform..

BALL - biochemical algorithms library 1.3

Sabine C. Mueller, Hans-Peter Lenhof, Oliver Kohlbacher, 2010, BMC Bioinformatics.

BALLView: a tool for research and education in molecular modeling

Hans-Peter Lenhof, Oliver Kohlbacher, Andreas Hildebrandt, 2006, Bioinform..

Protein (multi-)location prediction: utilizing interdependencies via a generative model

Hagit Shatkay, Oliver Kohlbacher, Ramanuja Simha, 2015, Bioinform..

Studies on COVID-19 lethality: Causes and dynamics at German University Hospitals

O. Kohlbacher, J. Schüttler, H. Prokosch, 2021 .

DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats

O. Kohlbacher, Jens Krüger, T. Lahaye, 2015, Nucleic acids research.

Virtual screening and experimental validation reveal novel small-molecule inhibitors of 14-3-3 protein-protein interactions.

O. Kohlbacher, C. Ottmann, Philipp Thiel, 2013, Chemical communications.

FLASHDeconv: Ultrafast, high-quality feature deconvolution for top-down proteomics

Jihyung Kim, Oliver Kohlbacher, Kyowon Jeong, 2019, bioRxiv.

BIOINF 4371 Drug Design 1

O. Kohlbacher, 2011 .

Efficient Mass Spectra Prediction through Container Orchestration with a Scientific Workflow

Jens Krüger, Oliver Kohlbacher, Maximilian Hanussek, 2017, IWSG.

The personalized cancer network explorer (PeCaX) as a visual analytics tool to support molecular tumor boards

O. Kohlbacher, Thorsten Tiede, Mirjam Figaschewski, 2021, bioRxiv.

Graphlet Data Mining of Energetical Interaction Patterns in Protein 3D Structures

Andreas Zell, Oliver Kohlbacher, Carsten Henneges, 2018, IJCCI.

Multivariate Networks in the Life Sciences

Matthew O. Ward, Falk Schreiber, Oliver Kohlbacher, 2013, Multivariate Network Visualization.

Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics

William Stafford Noble, S. Degroeve, Mathias Wilhelm, 2022, Journal of proteome research.

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

Gunnar Rätsch, Oliver Kohlbacher, Wolfgang Busch, 2009, BMC Bioinformatics.

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

H. Shatkay, P. Dönnes, O. Kohlbacher, 2007, Bioinform..

Rebuilding KEGG Maps: Algorithms and Benefits

Michael Kaufmann, Oliver Kohlbacher, Andreas Gerasch, 2014, 2014 IEEE Pacific Visualization Symposium.

DIAproteomics: A multi-functional data analysis pipeline for data-independent-acquisition proteomics and peptidomics

Timo Sachsenberg, Oliver Kohlbacher, George Rosenberger, 2020, bioRxiv.

Untargeted metabolomics reveals molecular effects of 2 ketogenic diet on healthy and tumor xenograft mouse 3 models 4

O. Kohlbacher, R. Reischl, B. Kofler, 2019 .

6th European Congress of Immunology, 1-4 September 2021, Virtual meeting.

Konrad U. Förstner, Philipp H. Schiffer, M. Nöthen, 2021, European journal of immunology.

Machine Learning Competition in Immunology – Prediction of HLA class I molecules

Christos, M. Polycarpou, O. Lund, 2011 .

The future of metabolomics in ELIXIR

Alejandra N. González-Beltrán, Ralf J. M. Weber, Rachel A. Spicer, 2017 .

The future of metabolomics in ELIXIR

Alejandra N. González-Beltrán, Ralf J. M. Weber, Rachel A. Spicer, 2017, F1000Research.

Performance Studies on Distributed Virtual Screening

Richard Grunzke, Sandra Gesing, Jens Krüger, 2014, BioMed research international.

ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification

Christina Backes, Eckart Meese, Andreas Keller, 2019, Bioinform..

Binding Pocket Optimization by Computational Protein Design

Oliver Kohlbacher, Marcel Schumann, Birte Höcker, 2012, PloS one.

A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data

O. Kohlbacher, M. Sturm, C. Huber, 2007, Nucleic acids research.

Automated scaffold selection for enzyme design

Birte Höcker, Oliver Kohlbacher, Christoph Malisi, 2009, Proteins.

SARS-CoV-2 T-cell epitopes define heterologous and COVID-19-induced T-cell recognition

H. Rammensee, S. Stevanović, O. Kohlbacher, 2020 .

Covalent attachment of pyridoxal-phosphate derivatives to 14-3-3 proteins

O. Kohlbacher, C. Ottmann, Philipp Thiel, 2012, Proceedings of the National Academy of Sciences.

Deterministic clustering of the available chemical space

Oliver Kohlbacher, Philipp Thiel, Christian Ottmann, 2013, Journal of Cheminformatics.

A NMR-spectra-based scoring function for protein docking

Hans-Peter Lenhof, Oliver Kohlbacher, Andreas Hildebrandt, 2001, RECOMB.

On Open Problems in Biological Network Visualization

Mario Albrecht, Karsten Klein, Petra Mutzel, 2009, GD.

A Graph-drawing Perspective to Some Open Problems in Molecular Biology

Petra Mutzel, Oliver Kohlbacher, Wolfgang Paul, 2008 .

BNDB – The Biochemical Network Database

Christina Backes, Michael Kaufmann, Hans-Peter Lenhof, 2007, BMC Bioinformatics.

The COVID-19 Data Exchange Platform of the German University Medicine

T. Bahls, O. Kohlbacher, M. Marschollek, 2022, MIE.

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

David R. Kelley, A. Gnirke, E. Lander, 2013, Cell.

Application of displacement chromatography for the proteome analysis of a human plasma protein fraction.

O. Kohlbacher, H. Schlüter, A. Bertsch, 2010, Journal of chromatography. A.

From sequence to structure and back again: approaches for predicting protein-DNA binding

O. Kohlbacher, Annette Höglund, 2004, Proteome Science.

Prediction of dual protein targeting to plant organelles.

O. Kohlbacher, S. Rensing, R. Reski, 2009, The New phytologist.

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

K. Reinert, R. Aebersold, O. Kohlbacher, 2016, Nature Methods.

A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics

Anna Szikszay Fabri, P. Kacsuk, A. Brinkmann, 2012, Journal of Grid Computing.

The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations.

Thomas Steinke, Richard Grunzke, Sandra Gesing, 2014, Journal of chemical theory and computation.

Ballaxy: Web Services for Structural Bioinformatics

Hans-Peter Lenhof, Jens Krüger, Oliver Kohlbacher, 2015, Bioinform..

From the Desktop to the Grid: conversion of KNIME Workflows to gUSE

Jens Krüger, Knut Reinert, Oliver Kohlbacher, 2013, IWSG.

A Science Gateway for Molecular Simulations

Thomas Steinke, Richard Grunzke, Sandra Gesing, 2011 .

Workflow Interoperability in a Grid Portal for Molecular Simulations

Bernd Schuller, Richard Grunzke, Sandra Gesing, 2010 .

BALL-rapid software prototyping in computational molecular biology

Hans-Peter Lenhof, Oliver Kohlbacher, O. Kohlbacher, 2000, Bioinform..

A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis

O. Kohlbacher, A. Keller, C. Backes, 2009, Bioinform..

Integer Linear Programming in Computational Biology

Ernst Althaus, Hans-Peter Lenhof, Knut Reinert, 2009, Efficient Algorithms.

Finding Relevant Biotransformation Routes in Weighted Metabolic Networks

Oliver Kohlbacher, Torsten Blum, O. Kohlbacher, 2007, German Conference on Bioinformatics.

OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS.

T. Dijkstra, O. Kohlbacher, H. Urlaub, 2020, Molecular & cellular proteomics : MCP.

Managing expectations when publishing tools and methods for computational proteomics.

Lennart Martens, Oliver Kohlbacher, Susan T Weintraub, 2015, Journal of proteome research.

Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies

A. Zell, O. Kohlbacher, M. Oldiges, 2009, BMC Systems Biology.

A Science Gateway Getting Ready for Serving the International Molecular Simulation Community

André Brinkmann, Miklos Kozlovszky, Thomas Steinke, 2012 .