Henning Hermjakob

According to our database1, Henning Hermjakob authored at least 109 papers between 1997 and 2022.

Collaborative distances:



In proceedings 
PhD thesis 


Online presence:

On csauthors.net:


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

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).
Bioinform., 2021

IntAct App: a Cytoscape application for molecular interaction network visualization and analysis.
Bioinform., 2021

Identifiers.org: Compact Identifier services in the cloud.
Bioinform., 2021

A decoupled, modular and scriptable architecture for tools to curate data platforms.
Bioinform., 2021

PhaSepDB: a database of liquid-liquid phase separation related proteins.
Nucleic Acids Res., 2020

BioModels - 15 years of sharing computational models in life science.
Nucleic Acids Res., 2020

The reactome pathway knowledgebase.
Nucleic Acids Res., 2020

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.
Nucleic Acids Res., 2020

The omics discovery REST interface.
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

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes.
Nucleic Acids Res., 2019

iProX: an integrated proteome resource.
Nucleic Acids Res., 2019

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.
Bioinform., 2019

Reactome and ORCID - fine-grained credit attribution for community curation.
Database J. Biol. Databases Curation, 2019

Reactome graph database: Efficient access to complex pathway data.
PLoS Comput. Biol., 2018

BioModels: expanding horizons to include more modelling approaches and formats.
Nucleic Acids Res., 2018

The Reactome Pathway Knowledgebase.
Nucleic Acids Res., 2018

A pipeline for identifying endogenous neuropeptides from spectral archives.
Int. J. Data Min. Bioinform., 2018

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.
BMC Bioinform., 2018

Reactome diagram viewer: data structures and strategies to boost performance.
Bioinform., 2018

AAgAtlas 1.0: a human autoantigen database.
Nucleic Acids Res., 2017

Open Targets: a platform for therapeutic target identification and validation.
Nucleic Acids Res., 2017

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.
Nucleic Acids Res., 2017

Reactome pathway analysis: a high-performance in-memory approach.
BMC Bioinform., 2017

Reactome enhanced pathway visualization.
Bioinform., 2017

ComplexViewer: visualization of curated macromolecular complexes.
Bioinform., 2017

2016 update of the PRIDE database and its related tools.
Nucleic Acids Res., 2016

The Reactome pathway Knowledgebase.
Nucleic Acids Res., 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

Introducing the PRIDE Archive RESTful web services.
Nucleic Acids Res., 2015

The complex portal - an encyclopaedia of macromolecular complexes.
Nucleic Acids Res., 2015

BioModels: ten-year anniversary.
Nucleic Acids Res., 2015

Development of data representation standards by the human proteome organization proteomics standards initiative.
J. Am. Medical Informatics Assoc., 2015

SPARQL-enabled identifier conversion with Identifiers.org.
Bioinform., 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

Shared resources, shared costs - leveraging biocuration resources.
Database J. Biol. Databases Curation, 2015

BioModels Database: a public repository for sharing models of biological processes.
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

The Reactome pathway knowledgebase.
Nucleic Acids Res., 2014

BioModels linked dataset.
BMC Syst. Biol., 2014

A new reference implementation of the PSICQUIC web service.
Nucleic Acids Res., 2013

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013.
Nucleic Acids Res., 2013

The EBI enzyme portal.
Nucleic Acids Res., 2013

Path2Models: large-scale generation of computational models from biochemical pathway maps.
BMC Syst. Biol., 2013

iAnn: an event sharing platform for the life sciences.
Bioinform., 2013

BioJS: an open source JavaScript framework for biological data visualization.
Bioinform., 2013

Capturing cooperative interactions with the PSI-MI format.
Database J. Biol. Databases Curation, 2013

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
Database J. Biol. Databases Curation, 2013

Towards the Collaborative Curation of the Registry underlying identifiers.org.
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

Improvements in the protein identifier cross-reference service.
Nucleic Acids Res., 2012

The IntAct molecular interaction database in 2012.
Nucleic Acids Res., 2012

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.
BMC Bioinform., 2012

PRIDE: Quality control in a proteomics data repository.
Database J. Biol. Databases Curation, 2012

Delivering 'Cool URIs' That Do Not Change.
Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012

Reactome: a database of reactions, pathways and biological processes.
Nucleic Acids Res., 2011

DAS Writeback: A Collaborative Annotation System.
BMC Bioinform., 2011

easyDAS: Automatic creation of DAS servers.
BMC Bioinform., 2011

Dasty3, a WEB framework for DAS.
Bioinform., 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

The Reactome BioMart.
Database J. Biol. Databases Curation, 2011

The Proteomics Identifications database: 2010 update.
Nucleic Acids Res., 2010

The Ontology Lookup Service: bigger and better.
Nucleic Acids Res., 2010

The IntAct molecular interaction database in 2010.
Nucleic Acids Res., 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

The systematic annotation of the three main GPCR families in Reactome.
Database J. Biol. Databases Curation, 2010

Reactome knowledgebase of human biological pathways and processes.
Nucleic Acids Res., 2009

ISPIDER Central: an integrated database web-server for proteomics.
Nucleic Acids Res., 2008

PRIDE: new developments and new datasets.
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

Integrating biological data - the Distributed Annotation System.
BMC Bioinform., 2008

The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Bioinform., 2008

InteroPORC: automated inference of highly conserved protein interaction networks.
Bioinform., 2008

Dasty2, an Ajax protein DAS client.
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

ENFIN - An Integrative Structure for Systems Biology.
Proceedings of the Data Integration in the Life Sciences, 5th International Workshop, 2008

EBI Proteomics Services.
Proceedings of the Data Integration in the Life Sciences, 5th International Workshop, 2008

IntAct - open source resource for molecular interaction data.
Nucleic Acids Res., 2007

Pride Wizard: generation of standards compliant quantitative proteomics data.
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

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

Development and implementation of the PSI MI standard for molecular interaction.
Proceedings of the Winter Simulation Conference WSC 2006, 2006

Dasty and UniProt DAS: a perfect pair for protein feature visualization.
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

IntAct: an open source molecular interaction database.
Nucleic Acids Res., 2004

InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites
Briefings Bioinform., 2002

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

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

Swissknife - 'lazy parsing' of SWISS-PROT entries.
Bioinform., 1999

Feature Propagation - Semi Automatic transfer of position dependent SWISS-PROT annotation.
Proceedings of the German Conference on Bioinformatics, 1999

Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL.
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

RIFLE: Rapid Identification of Microorganisms by Fragment Length Evaluation.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997