BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. - Steven Maere; Karel Heymans; Martin Kuiper (Bioinform., 2005)

Simulating genetic networks made easy: network construction with simple building blocks. - Steven Vercruysse; Martin Kuiper (Bioinform., 2005)

A Cell-Cycle Knowledge Integration Framework. - Erick Antezana; Elena Tsiporkova; Vladimir Mironov; Martin Kuiper (DILS, 2006)

Validating module network learning algorithms using simulated data. - Tom Michoel; Steven Maere; Eric Bonnet; Anagha Joshi; Yvan Saeys; Tim Van den Bulcke; Koenraad Van Leemput; Piet van Remortel; Martin Kuiper; Kathleen Marchal; Yves Van de Peer (BMC Bioinform., 2007)

CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes. - Gert Sclep; Joke Allemeersch; Robin Liechti; Björn De Meyer; Jim Beynon; Rishikesh Bhalerao; Yves Moreau; Wilfried Nietfeld; Jean-Pierre Renou; Philippe Reymond; Martin T. R. Kuiper; Pierre Hilson (BMC Bioinform., 2007)

Initialization Dependence of Clustering Algorithms. - Wim De Mulder; Stefan Schliebs; René K. Boel; Martin Kuiper (ICONIP (2), 2008)

Structuring the Life Science Resourceome for Semantic Systems Biology: Lessons from the BioGateway Project. - Erick Antezana; Ward Blondé; Mikel Egaña; Alistair Rutherford; Robert Stevens 001; Bernard De Baets; Vladimir Mironov; Martin Kuiper (SWAT4LS, 2008)

BioGateway: Integrated RDF for Life Science Queries. - Erick Antezana; Ward Blondé; Mikel Egaña; Alistair Rutherford; Robert Stevens 001; Bernard De Baets; Vladimir Mironov; Martin Kuiper (SWAT4LS, 2008)

The Cell Cycle Ontology: An Application Ontology Supporting the Life Sciences. - Erick Antezana; Mikel Egaña; Ward Blondé; Robert Stevens 001; Bernard De Baets; Vladimir Mironov; Martin Kuiper (SWAT4LS, 2008)

ONTO-PERL: An API for supporting the development and analysis of bio-ontologies. - Erick Antezana; Mikel Egaña; Bernard De Baets; Martin Kuiper; Vladimir Mironov (Bioinform., 2008)

Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. - Mikel Egaña Aranguren; Erick Antezana; Martin Kuiper; Robert Stevens 001 (BMC Bioinform., 2008)

Extracting expression modules from perturbational gene expression compendia. - Steven Maere; Patrick Van Dijck; Martin Kuiper (BMC Syst. Biol., 2008)

Biological knowledge management: the emerging role of the Semantic Web technologies. - Erick Antezana; Martin Kuiper; Vladimir Mironov (Briefings Bioinform., 2009)

Gene expression trends and protein features effectively complement each other in gene function prediction. - Krzysztof Wabnik; Torgeir R. Hvidsten; Anna M. Kedzierska; Jelle Van Leene; Geert De Jaeger; Gerrit T. S. Beemster; Henryk Jan Komorowski; Martin T. R. Kuiper (Bioinform., 2009)

BioGateway: a semantic systems biology tool for the life sciences. - Erick Antezana; Ward Blondé; Mikel Egaña; Alistair Rutherford; Robert Stevens 001; Bernard De Baets; Vladimir Mironov; Martin Kuiper (BMC Bioinform., 2009)

Benchmarking Triple Stores with Biological Data. - Vladimir Mironov; Nirmala Seethappan; Ward Blondé; Erick Antezana; Bjorn Lindi; Martin Kuiper (SWAT4LS, 2010)

DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data. - Jens Hollunder; Maik Friedel; Martin Kuiper; Thomas Wilhelm 003 (Bioinform., 2010)

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. - Erick Antezana; Aravind Venkatesan; Chris Mungall; Vladimir Mironov; Martin Kuiper (BMC Bioinform., 2010)

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. - Kris Laukens; Jens Hollunder; Thanh Hai Dang; Geert De Jaeger; Martin Kuiper; Erwin Witters; Alain Verschoren; Koenraad Van Leemput (BMC Bioinform., 2010)

Clustering of gene expression profiles: creating initialization-independent clusterings by eliminating unstable genes. - Wim De Mulder; Martin Kuiper; René K. Boel (J. Integr. Bioinform., 2010)

WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary. - Steven Vercruysse; Martin Kuiper (IHCI, 2011)

Semantic systems biology: enabling integrative biology via semantic web technologies. - Erick Antezana; Ward Blondé; Aravind Venkatesan; Bernard De Baets; Vladimir Mironov; Martin Kuiper (WIMS, 2011)

The RDF foundry: call for an initiative to build enhanced RDF resources for biological data integration. - Aravind Venkatesan; Ward Blondé; Erick Antezana; Mats Skillingstad; M. Scott Marshall; Bernard De Baets; Vladimir Mironov; Martin Kuiper (WIMS, 2011)

Flexibility and utility of the cell cycle ontology. - Vladimir Mironov; Erick Antezana; Mikel Egaña; Ward Blondé; Bernard De Baets; Martin Kuiper; Robert Stevens 001 (Appl. Ontology, 2011)

Reasoning with bio-ontologies: using relational closure rules to enable practical querying. - Ward Blondé; Vladimir Mironov; Aravind Venkatesan; Erick Antezana; Bernard De Baets; Martin Kuiper (Bioinform., 2011)

Towards an integrated knowledge system for capturing gene expression events. - Aravind Venkatesan; Vladimir Mironov; Martin Kuiper (ICBO, 2012)

Profiling of Semantically Annotated Proteins. - Jens Hollunder; Vladimir Mironov; Erick Antezana; Robert Hoehndorf; Martin Kuiper (SWAT4LS, 2012)

Gauging triple stores with actual biological data. - Vladimir Mironov; Nirmala Seethappan; Ward Blondé; Erick Antezana; Andrea Splendiani; Martin Kuiper (BMC Bioinform., 2012)

OLSVis: an animated, interactive visual browser for bio-ontologies. - Steven Vercruysse; Aravind Venkatesan; Martin Kuiper (BMC Bioinform., 2012)

Reliable Self-assembly by Self-triggered Activation of Enveloped DNA Tiles. - Vinay Kumar Gautam; Pauline C. Haddow; Martin Kuiper (TPNC, 2013)

Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. - Sushil Tripathi; Karen R. Christie; Rama Balakrishnan; Rachael P. Huntley; David P. Hill; Liv Thommesen; Judith A. Blake; Martin Kuiper; Astrid Lægreid (Database J. Biol. Databases Curation, 2013)

TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors. - Konika Chawla; Sushil Tripathi; Liv Thommesen; Astrid Lægreid; Martin Kuiper (Bioinform., 2013)

Design of a Minimal System for Self-replication of Rectangular Patterns of DNA Tiles. - Vinay Kumar Gautam; Eugen Czeizler; Pauline C. Haddow; Martin Kuiper (TPNC, 2014)

orthAgogue: an agile tool for the rapid prediction of orthology relations. - Ole Kristian Ekseth; Martin Kuiper; Vladimir Mironov (Bioinform., 2014)

Finding gene regulatory network candidates using the gene expression knowledge base. - Aravind Venkatesan; Sushil Tripathi; Alejandro Sanz de Galdeano; Ward Blondé; Astrid Lægreid; Vladimir Mironov; Martin Kuiper (BMC Bioinform., 2014)

Using the relation ontology Metarel for modelling Linked Data as multi-digraphs. - Ward Blondé; Erick Antezana; Vladimir Mironov; Stefan Schulz 001; Martin Kuiper; Bernard De Baets (Semantic Web, 2014)

The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms. - Sushil Tripathi; Åsmund Flobak; Konika Chawla; Anaïs Baudot; Torunn Bruland; Liv Thommesen; Martin Kuiper; Astrid Lægreid (BMC Syst. Biol., 2015)

Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. - Åsmund Flobak; Anaïs Baudot; Elisabeth Remy; Liv Thommesen; Denis Thieffry; Martin Kuiper; Astrid Lægreid (PLoS Comput. Biol., 2015)

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. - Sushil Tripathi; Steven Vercruysse; Konika Chawla; Karen R. Christie; Judith A. Blake; Rachael P. Huntley; Sandra E. Orchard; Henning Hermjakob; Liv Thommesen; Astrid Lægreid; Martin Kuiper (Database J. Biol. Databases Curation, 2016)

An Example of Multimodal Biological Knowledge Representation. - José Antonio Vera-Ramos; Belén Juanes-Cortés; Jesualdo Tomás Fernández-Breis; Pascale Gaudet; Martin Kuiper; Astrid Lægreid; Colin Logie; María del Mar Roldán García; Stefan Schulz 001 (JOWO, 2019)

Network Building with Cytoscape App Queries to the BioGateway 3.0 Triple Store. - Stian Holmås; Vladimir Mironov; Martin Kuiper (SWAT4HCLS, 2019)

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. - Livia Perfetto; Marcio Luis Acencio; Glyn Bradley; Gianni Cesareni; Noemi del-Toro; Dávid Fazekas; Henning Hermjakob; Tamás Korcsmáros; Martin Kuiper; Astrid Lægreid; Prisca Lo Surdo; Ruth C. Lovering; et al. (Bioinform., 2019)

The Cytoscape BioGateway App: explorative network building from an RDF store. - Stian Holmås; Rafel Riudavets Puig; Marcio Luis Acencio; Vladimir Mironov; Martin Kuiper (Bioinform., 2020)

A foundation for reference models for drug combinations with an application to Loewe's reference model. - Wim De Mulder; Martin Kuiper (BMC Bioinform., 2020)

emba: R package for analysis and visualization of biomarkers in boolean model ensembles. - John Zobolas; Martin Kuiper; Åsmund Flobak (J. Open Source Softw., 2020)

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. - Anna Niarakis; Martin Kuiper; Marek Ostaszewski; Rahuman S. Malik-Sheriff; Cristina Casals-Casas; Denis Thieffry; Tom C. Freeman; Paul D. Thomas; Vasundra Touré; Vincent Noël; Gautier Stoll; Julio Saez-Rodriguez; et al. (Briefings Bioinform., 2021)

The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. - Vasundra Touré; Åsmund Flobak; Anna Niarakis; Steven Vercruysse; Martin Kuiper (Briefings Bioinform., 2021)

CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator. - Vasundra Touré; John Zobolas; Martin Kuiper; Steven Vercruysse (Database J. Biol. Databases Curation, 2021)

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). - Vasundra Touré; Steven Vercruysse; Marcio Luis Acencio; Ruth C. Lovering; Sandra E. Orchard; Glyn Bradley; Cristina Casals-Casas; Claudine Chaouiya; Noemi del-Toro; Åsmund Flobak; Pascale Gaudet; Henning Hermjakob; et al. (Bioinform., 2021)

UniBioDicts: Unified access to Biological Dictionaries. - John Zobolas; Vasundra Touré; Martin Kuiper; Steven Vercruysse (Bioinform., 2021)

The Gene Ontology resource: enriching a GOld mine. - Seth Carbon; Eric Douglass; Benjamin M. Good; Deepak R. Unni; Nomi L. Harris; Christopher J. Mungall; Siddartha Basu; Rex L. Chisholm; Robert J. Dodson; Eric Hartline; Petra Fey; Paul D. Thomas; et al. (Nucleic Acids Res., 2021)