Martin Kuiper

发表

orthAgogue: an agile tool for the rapid prediction of orthology relations

Ole Kristian Ekseth, Martin Kuiper, Vladimir Mironov, 2014, Bioinform..

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Nigel W. Hardy, Chris F. Taylor, John M. Hancock, 2008, Nature Biotechnology.

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy

Martin Kuiper, Vladimir Mironov, Chris Mungall, 2010, BMC Bioinformatics.

A Cell-Cycle Knowledge Integration Framework

Elena Tsiporkova, Martin Kuiper, Vladimir Mironov, 2006, DILS.

VSM-box: the general-purpose curation interface as an open-source web-component

Martin Kuiper, Vasundra Touré, Steven Vercruysse, 2019 .

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

Yves Moreau, Martin Kuiper, Philippe Reymond, 2007, BMC Bioinformatics.

BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

Martin Kuiper, Steven Maere, Karel Heymans, 2005, Bioinform..

Semantic systems biology: enabling integrative biology via semantic web technologies

Bernard De Baets, Martin Kuiper, Vladimir Mironov, 2011, WIMS '11.

Gauging triple stores with actual biological data

Andrea Splendiani, Martin Kuiper, Vladimir Mironov, 2012, BMC Bioinformatics.

A Middle-Out Modeling Strategy to Extend a Colon Cancer Logical Model Improves Drug Synergy Predictions in Epithelial-Derived Cancer Cell Lines

Martin Kuiper, Vasundra Touré, Eirini Tsirvouli, 2020, Frontiers in Molecular Biosciences.

Structuring the Life Science Resourceome for Semantic Systems Biology: Lessons from the BioGateway Project

Bernard De Baets, Robert Stevens, Martin Kuiper, 2008, SWAT4LS.

Extracting expression modules from perturbational gene expression compendia

Martin Kuiper, Steven Maere, Patrick Van Dijck, 2008, BMC Systems Biology.

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

Rachael P. Huntley, Henning Hermjakob, Judith A. Blake, 2016, Database J. Biol. Databases Curation.

A Cell-Cycle Knowledge Integration Framework Research Paper

Elena Tsiporkova, Martin Kuiper, Vladimir Mironov, 2006 .

BioGateway: Integrated RDF for Life Science Queries

Bernard De Baets, Robert Stevens, Martin Kuiper, 2008, SWAT4LS.

Networks for Knowledge

Martin Kuiper, 2014, BIBM 2014.

Biological knowledge management: the emerging role of the Semantic Web technologies

Martin Kuiper, Vladimir Mironov, Erick Antezana, 2009, Briefings Bioinform..

WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary

Martin Kuiper, Steven Vercruysse, 2011, IHCI.

Initialization Dependence of Clustering Algorithms

Stefan Schliebs, Martin Kuiper, Wim De Mulder, 2008, ICONIP.

Profiling of Semantically Annotated Proteins

Martin Kuiper, Vladimir Mironov, Robert Hoehndorf, 2012, SWAT4LS.

Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology

Robert Stevens, Martin Kuiper, Mikel Egaña Aranguren, 2008, BMC Bioinformatics.

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

Rachael P. Huntley, Judith A. Blake, Martin Kuiper, 2013, Database J. Biol. Databases Curation.

Simulating genetic networks made easy: network construction with simple building blocks

Martin Kuiper, Steven Vercruysse, M. Kuiper, 2005, Bioinform..

Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling

Denis Thieffry, Martin Kuiper, Anaïs Baudot, 2015, PLoS Comput. Biol..

Reasoning with bio-ontologies: using relational closure rules to enable practical querying

Bernard De Baets, Martin Kuiper, Vladimir Mironov, 2011, Bioinform..

emba: R package for analysis and visualization of biomarkers in boolean model ensembles

Martin Kuiper, John Zobolas, Åsmund Flobak, 2020, J. Open Source Softw..

BioGateway: a semantic systems biology tool for the life sciences

Bernard De Baets, Robert Stevens, Martin Kuiper, 2009, BMC Bioinformatics.

CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination

Henning Hermjakob, Martin Kuiper, Marcio Luis Acencio, 2018, bioRxiv.

The Cell Cycle Ontology: an application ontology supporting the study of cell cycle control

Bernard De Baets, Martin Kuiper, Vladimir Mironov, 2009 .

The Cell Cycle Ontology: An Application Ontology Supporting the Life Sciences

Bernard De Baets, Robert Stevens, Martin Kuiper, 2008, SWAT4LS.

Genes2GO: A web application for querying gene sets for specific GO terms

Martin Kuiper, Konika Chawla, 2016, Bioinformation.

Experimental Verification of the Quality of Clusterings Produced by Hard Clustering Algorithms after the Removal of Unstable Data Elements

Martin Kuiper, Wim De Mulder, Zahra Zavareh, 2014, BIOINFORMATICS 2014.

Validating clusterings of gene expression data

Martin Kuiper, Rene Boel, Wim De Mulder, 2010, 2010 The 2nd International Conference on Computer and Automation Engineering (ICCAE).

DrugLogics: An ensemble model analysis related to drug prediction performance

Martin Kuiper, Miguel Vazquez, John Zobolas, 2019 .

Jointly creating digital abstracts: dealing with synonymy and polysemy

Martin Kuiper, Steven Vercruysse, Steven Vercruysse, 2012, BMC Research Notes.

The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms

Martin Kuiper, Anaïs Baudot, Astrid Lægreid, 2015, BMC Systems Biology.

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL

Koenraad Van Leemput, Thanh Hai Dang, Martin Kuiper, 2009, BMC Bioinformatics.

Finding gene regulatory network candidates using the gene expression knowledge base

Martin Kuiper, Vladimir Mironov, Aravind Venkatesan, 2014, BMC Bioinformatics.

Toward a new paradigm for user interaction on the semantic web to support life sciences investigation

Andrea Splendiani, Martin Kuiper, Chris J Rawlings, 2009 .

Benchmarking Triple Stores with Biological Data pdf

Martin Kuiper, Vladimir Mironov, Erick Antezana, 2010, SWAT4LS.

TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors

Martin Kuiper, Astrid Lægreid, Liv Thommesen, 2013, Bioinform..

The RDF foundry: call for an initiative to build enhanced RDF resources for biological data integration

Bernard De Baets, Martin Kuiper, Vladimir Mironov, 2011, WIMS '11.

Silencing trust: confidence and familiarity in re-engineering knowledge infrastructures

Rune Nydal, Martin Kuiper, Astrid Lægreid, 2020, Medicine, Health Care and Philosophy.

Contributions of the EMERALD project to assessing and improving microarray data quality.

Audrey Kauffmann, Martin Kuiper, James Malone, 2011, BioTechniques.

Gene expression trends and protein features effectively complement each other in gene function prediction

Gerrit T. S. Beemster, Martin Kuiper, Jan Komorowski, 2009, Bioinform..

OLSVis: an animated, interactive visual browser for bio-ontologies

Martin Kuiper, Aravind Venkatesan, Steven Vercruysse, 2011, BMC Bioinformatics.

Towards an integrated knowledge system for capturing gene expression events

Martin Kuiper, Vladimir Mironov, Aravind Venkatesan, 2012, ICBO.

The Cytoscape BioGateway App: explorative network building from an RDF store

Martin Kuiper, Marcio Luis Acencio, Stian Holmås, 2019, Bioinform..

Reliable Self-assembly by Self-triggered Activation of Enveloped DNA Tiles

Pauline C. Haddow, Martin Kuiper, Vinay Kumar Gautam, 2013, TPNC.

Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction

Miguel Vazquez, Martin Kuiper, Vasundra Touré, 2020, Frontiers in Physiology.

Clustering of gene expression profiles: creating initialization-independent clusterings by eliminating unstable genes

Martin Kuiper, Wim De Mulder, René K. Boel, 2010, J. Integr. Bioinform..

Using the relation ontology Metarel for modelling Linked Data as multi-digraphs

Bernard De Baets, Stefan Schulz, Martin Kuiper, 2014, Semantic Web.

Validating module network learning algorithms using simulated data

Kathleen Marchal, Yvan Saeys, Koenraad Van Leemput, 2007, BMC Bioinformatics.

ONTO-PERL: An API for supporting the development and analysis of bio-ontologies

Bernard De Baets, Martin Kuiper, Vladimir Mironov, 2008, Bioinform..

Design of a Minimal System for Self-replication of Rectangular Patterns of DNA Tiles

Pauline C. Haddow, Martin Kuiper, Eugen Czeizler, 2014, TPNC.

The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling

Anna Niarakis, Martin Kuiper, Vasundra Touré, 2020, Briefings Bioinform..

Gene Ontology representation for transcription factor functions.

Martin Kuiper, Paul D Thomas, Pascale Gaudet, 2021, Biochimica et Biophysica Acta. Gene Regulatory Mechanisms.

Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2020, Briefings Bioinform..

The Gene Ontology resource: enriching a GOld mine

Anushya Muruganujan, Cathy H. Wu, Alex Bateman, 2020, Nucleic Acids Res..

Genetic Analysis of Variation in Gene Expression in Arabidopsis thaliana

Martin Kuiper, Fred van Eeuwijk, Marc Zabeau, 2005, Genetics.

Specific Impact of Tobamovirus Infection on the Arabidopsis Small RNA Profile

Martin Kuiper, Jens Hollunder, Franck Vazquez, 2011, PloS one.

The emergence of Semantic Systems Biology.

Martin Kuiper, Erick Antezana, Vladimir Mironov, 2013, New biotechnology.

Metarel : an Ontology to support the inferencing of Semantic Web relations within Biomedical Ontologies

Bernard De Baets, Martin Kuiper, Erick Antezana, 2009 .

The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process

Robert Stevens, Martin Kuiper, Bernard De Baets, 2009, Genome Biology.

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

Martin Kuiper, Dirk Inzé, Pierre Hilson, 2010, Molecular systems biology.