Henning Hermjakob
Orcid: 0000-0001-8479-0262
According to our database1,
Henning Hermjakob
authored at least 120 papers
between 1997 and 2024.
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Bibliography
2024
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.
Database J. Biol. Databases Curation, January, 2024
Building an Ethical and Trustworthy Biomedical AI Ecosystem for the Translational and Clinical Integration of Foundational Models.
CoRR, 2024
2023
Umbrella Data Management Plans to Integrate FAIR Data: Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness.
Data Sci. J., January, 2023
The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study.
Database J. Biol. Databases Curation, 2023
2022
Nucleic Acids Res., 2022
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Nucleic Acids Res., 2022
Nucleic Acids Res., 2022
KNIME workflow for retrieving causal drug and protein interactions, building networks, and performing topological enrichment analysis demonstrated by a DILI case study.
J. Cheminformatics, 2022
Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology</i>.
Briefings Bioinform., 2022
2021
Bioinform., 2021
IntAct App: a Cytoscape application for molecular interaction network visualization and analysis.
Bioinform., 2021
Bioinform., 2021
2020
Nucleic Acids Res., 2020
Nucleic Acids Res., 2020
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.
Nucleic Acids Res., 2020
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).
J. Integr. Bioinform., 2020
BioModels Parameters: a treasure trove of parameter values from published systems biology models.
Bioinform., 2020
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions.
Database J. Biol. Databases Curation, 2020
2019
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes.
Nucleic Acids Res., 2019
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.
Bioinform., 2019
Database J. Biol. Databases Curation, 2019
2018
PLoS Comput. Biol., 2018
Nucleic Acids Res., 2018
Int. J. Data Min. Bioinform., 2018
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.
BMC Bioinform., 2018
Bioinform., 2018
2017
Nucleic Acids Res., 2017
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.
Nucleic Acids Res., 2017
BMC Bioinform., 2017
2016
Organizational principles of the Reactome human BioPAX model using graph theory methods.
J. Complex Networks, 2016
Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences.
Bioinform., 2016
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.
Database J. Biol. Databases Curation, 2016
2015
Nucleic Acids Res., 2015
Development of data representation standards by the human proteome organization proteomics standards initiative.
J. Am. Medical Informatics Assoc., 2015
ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.
Bioinform., 2015
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.
Database J. Biol. Databases Curation, 2015
Database J. Biol. Databases Curation, 2015
2014
Proceedings of the Encyclopedia of Computational Neuroscience, 2014
The MIntAct project - IntAct as a common curation platform for 11 molecular interaction databases.
Nucleic Acids Res., 2014
F1000Research, 2014
2013
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013.
Nucleic Acids Res., 2013
Path2Models: large-scale generation of computational models from biochemical pathway maps.
BMC Syst. Biol., 2013
Bioinform., 2013
Database J. Biol. Databases Curation, 2013
Database J. Biol. Databases Curation, 2013
Database J. Biol. Databases Curation, 2013
The Apoptosis Gene Ontology project and the IntAct-Apoptosis dataset: updating the conceptual representation of apoptosis.
Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2013
2012
Nucleic Acids Res., 2012
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.
BMC Bioinform., 2012
Database J. Biol. Databases Curation, 2012
Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012
2011
Nucleic Acids Res., 2011
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations.
Database J. Biol. Databases Curation, 2011
2010
<i>R</i> spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases.
Nucleic Acids Res., 2010
Database J. Biol. Databases Curation, 2010
2009
Nucleic Acids Res., 2009
2008
Nucleic Acids Res., 2008
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.
Nucleic Acids Res., 2008
OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology.
BMC Bioinform., 2008
InteroPORC: an automated tool to predict highly conserved protein interaction networks.
BMC Bioinform., 2008
BMC Bioinform., 2008
The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Bioinform., 2008
Bioinform., 2008
Rintact: enabling computational analysis of molecular interaction data from the IntAct repository.
Bioinform., 2008
The HUPO proteomics standards initiative - easing communication and minimizing data loss in a changing world.
Briefings Bioinform., 2008
Proceedings of the Data Integration in the Life Sciences, 5th International Workshop, 2008
Proceedings of the Data Integration in the Life Sciences, 5th International Workshop, 2008
2007
Nucleic Acids Res., 2007
BMC Syst. Biol., 2007
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
BMC Bioinform., 2007
Analysing latent topics in large-scale proteomics.
Proceedings of the LWA 2007: Lernen - Wissen, 2007
An Application of Latent Topic Document Analysis to Large-Scale Proteomics Databases.
Proceedings of the German Conference on Bioinformatics, 2007
2006
PRIDE: a public repository of protein and peptide identifications for the proteomics community.
Nucleic Acids Res., 2006
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.
BMC Bioinform., 2006
Proceedings of the Winter Simulation Conference WSC 2006, 2006
2005
Bioinform., 2005
The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic Experiments.
Proceedings of the Biocomputing 2005, 2005
2004
2002
InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites
Briefings Bioinform., 2002
2001
The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
Nucleic Acids Res., 2001
Towards a New Curation Environment for the TrEMBL Database.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001
2000
A comparison of signal sequence prediction methods using a test set of signal peptides.
Bioinform., 2000
VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL.
Bioinform., 2000
InterPro-an integrated documentation resource for protein families, domains and functional sites.
Bioinform., 2000
1999
Feature Propagation - Semi Automatic transfer of position dependent SWISS-PROT annotation.
Proceedings of the German Conference on Bioinformatics, 1999
1998
Nucleic Acids Res., 1998
SPTR: A comprehensive, non redundant and up-to-date view of the protein sequence world.
Proceedings of the German Conference on Bioinformatics, 1998
1997
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997