Martin Kuiper

According to our database1, Martin Kuiper authored at least 40 papers between 2005 and 2016.

Collaborative distances :
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

Legend:

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PhD thesis 
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Bibliography

2016
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.
Database, 2016

2015
Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling.
PLoS Computational Biology, 2015

The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms.
BMC Systems Biology, 2015

2014
Using the relation ontology Metarel for modelling Linked Data as multi-digraphs.
Semantic Web, 2014

Finding gene regulatory network candidates using the gene expression knowledge base.
BMC Bioinformatics, 2014

orthAgogue: an agile tool for the rapid prediction of orthology relations.
Bioinformatics, 2014

Design of a Minimal System for Self-replication of Rectangular Patterns of DNA Tiles.
Proceedings of the Theory and Practice of Natural Computing, 2014

2013
TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors.
Bioinformatics, 2013

Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort.
Database, 2013

Reliable Self-assembly by Self-triggered Activation of Enveloped DNA Tiles.
Proceedings of the Theory and Practice of Natural Computing, 2013

2012
OLSVis: an animated, interactive visual browser for bio-ontologies.
BMC Bioinformatics, 2012

Gauging triple stores with actual biological data.
BMC Bioinformatics, 2012

Profiling of Semantically Annotated Proteins.
Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012

Towards an integrated knowledge system for capturing gene expression events.
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

2011
Reasoning with bio-ontologies: using relational closure rules to enable practical querying.
Bioinformatics, 2011

Flexibility and utility of the cell cycle ontology.
Applied Ontology, 2011

The RDF foundry: call for an initiative to build enhanced RDF resources for biological data integration.
Proceedings of the International Conference on Web Intelligence, Mining and Semantics, 2011

Semantic systems biology: enabling integrative biology via semantic web technologies.
Proceedings of the International Conference on Web Intelligence, Mining and Semantics, 2011

WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary.
Proceedings of the Third International Conference on Intelligent Human Computer Interaction (IHCI 2011), 2011

2010
Clustering of gene expression profiles: creating initialization-independent clusterings by eliminating unstable genes.
J. Integrative Bioinformatics, 2010

Benchmarking triple stores with biological data
CoRR, 2010

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.
BMC Bioinformatics, 2010

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy.
BMC Bioinformatics, 2010

DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data.
Bioinformatics, 2010

Benchmarking Triple Stores with Biological Data.
Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences, 2010

2009
BioGateway: a semantic systems biology tool for the life sciences.
BMC Bioinformatics, 2009

Gene expression trends and protein features effectively complement each other in gene function prediction.
Bioinformatics, 2009

Biological knowledge management: the emerging role of the Semantic Web technologies.
Briefings in Bioinformatics, 2009

2008
Extracting expression modules from perturbational gene expression compendia.
BMC Systems Biology, 2008

Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology.
BMC Bioinformatics, 2008

ONTO-PERL: An API for supporting the development and analysis of bio-ontologies.
Bioinformatics, 2008

The Cell Cycle Ontology: An Application Ontology Supporting the Life Sciences.
Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences ( SWAT4LS ) Edinburgh, 2008

BioGateway: Integrated RDF for Life Science Queries.
Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences ( SWAT4LS ) Edinburgh, 2008

Structuring the Life Science Resourceome for Semantic Systems Biology: Lessons from the BioGateway Project.
Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences ( SWAT4LS ) Edinburgh, 2008

Initialization Dependence of Clustering Algorithms.
Proceedings of the Advances in Neuro-Information Processing, 15th International Conference, 2008

2007
CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes.
BMC Bioinformatics, 2007

Validating module network learning algorithms using simulated data.
BMC Bioinformatics, 2007

2006
A Cell-Cycle Knowledge Integration Framework.
Proceedings of the Data Integration in the Life Sciences, Third International Workshop, 2006

2005
Simulating genetic networks made easy: network construction with simple building blocks.
Bioinformatics, 2005

BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks.
Bioinformatics, 2005


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