Martin Kuiper

According to our database, Martin Kuiper authored at least 51 papers between 2005 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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, Laurent-Philippe Albou, Dustin Ebert, Michael J. Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra A. LaBonte, Deborah A. Siegele, Giulia Antonazzo, Helen Attrill, Nick H. Brown, Phani V. Garapati, Steven J. Marygold, Vitor Trovisco, Gilberto dos Santos, Kathleen Falls, Christopher J. Tabone, Pinglei Zhou, Joshua L. Goodman, Victor B. Strelets, Jim Thurmond, Penelope Garmiri, Rizwan Ishtiaq, Milagros Rodríguez-López, Marcio Luis Acencio, Martin Kuiper, Astrid Lægreid, Colin Logie, Ruth C. Lovering, Barbara Kramarz, Shirin C. C. Saverimuttu, Sandra M. Pinheiro, Heather Gunn, Renzhi Su, Katherine E. Thurlow, Marcus C. Chibucos, Michelle G. Giglio, Suvarna Nadendla, James B. Munro, Rebecca C. Jackson, Margaret J. Duesbury, Noemi del-Toro, Birgit H. M. Meldal, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras, Sandra E. Orchard, Anjali Shrivastava, Hsin-Yu Chang, Robert D. Finn, Alex L. Mitchell, Neil D. Rawlings, Lorna J. Richardson, Amaia Sangrador-Vegas, Judith A. Blake, Karen R. Christie, Mary E. Dolan, Harold J. Drabkin, David P. Hill, Li Ni, Dmitry M. Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford, Valerie Wood, Jaqueline Hayles, Jürg Bähler, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek, Stanley J. F. Laulederkind, Cody Plasterer, Marek Tutaj, Mahima Vedi, Shur-Jen Wang, Peter D'Eustachio, Lisa Matthews, James P. Balhoff, Suzi A. Aleksander, Michael J. Alexander, J. Michael Cherry, Stacia R. Engel, Felix Gondwe, Kalpana Karra, Stuart R. Miyasato, Robert S. Nash, Matt Simison, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Marc Feuermann, Pascale Gaudet, Anne Morgat, Erica Bakker, Tanya Z. Berardini, Leonore Reiser, Shabari Subramaniam, Eva Huala, Cecilia N. Arighi, Andrea H. Auchincloss, Kristian B. Axelsen, Ghislaine Argoud-Puy, Alex Bateman, Marie-Claude Blatter, Emmanuel Boutet, Emily Bowler, Lionel Breuza, Alan J. Bridge, Ramona Britto, Hema Bye-A-Jee, Cristina Casals-Casas, Elisabeth Coudert, Paul Denny, Anne Estreicher, Maria Livia Famiglietti, George E. Georghiou, Arnaud Gos, Nadine Gruaz-Gumowski, Emma Hatton-Ellis, Chantal Hulo, Alexandr Ignatchenko, Florence Jungo, Kati Laiho, Philippe Le Mercier, Damien Lieberherr, Antonia Lock, Yvonne Lussi, Alistair MacDougall, Michele Magrane, Maria Jesus Martin, Patrick Masson, Darren A. Natale, Nevila Hyka-Nouspikel, Ivo Pedruzzi, Lucille Pourcel, Sylvain Poux, Sangya Pundir, Catherine Rivoire, Elena Speretta, Shyamala Sundaram, Nidhi Tyagi, Kate Warner, Rossana Zaru, Cathy H. Wu, Alexander D. Diehl, Juancarlos Chan, Christian A. Grove, Raymond Y. N. Lee, Hans-Michael Müller, Daniela Raciti, Kimberly Van Auken, Paul W. Sternberg, Matthew Berriman, Michael Paulini, Kevin L. Howe, Sibyl Gao, Adam Wright, Lincoln Stein, Douglas G. Howe, Sabrina Toro, Monte Westerfield, Pankaj Jaiswal, Laurel Cooper, Justin Elser

Nucleic Acids Res., 2021

UniBioDicts: Unified access to Biological Dictionaries.

John Zobolas, Vasundra Touré, Martin Kuiper, Steven Vercruysse

Bioinform., 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, Charles Tapley Hoyt, Luana Licata, Astrid Lægreid, Christopher J. Mungall, Anne Niknejad, Simona Panni, Livia Perfetto, Pablo Porras, Dexter Pratt, Julio Saez-Rodriguez, Denis Thieffry, Paul D. Thomas, Dénes Türei, Martin Kuiper

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 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

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, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone

Briefings Bioinform., 2021

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

A foundation for reference models for drug combinations with an application to Loewe's reference model.

Wim De Mulder, Martin Kuiper

BMC Bioinform., 2020

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

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, Sandra E. Orchard, Pablo Porras, Paul D. Thomas, Vasundra Touré, John Zobolas, Luana Licata

Bioinform., 2019

Network Building with Cytoscape App Queries to the BioGateway 3.0 Triple Store.

Stian Holmås, Vladimir Mironov, Martin Kuiper

Proceedings of the 12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2019

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

Proceedings of the Joint Ontology Workshops 2019 Episode V: The Styrian Autumn of Ontology, 2019

2016

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

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

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

2014

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

Ward Blondé, Erick Antezana, Vladimir Mironov, Stefan Schulz, Martin Kuiper, Bernard De Baets

Semantic Web, 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

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

Ole Kristian Ekseth, Martin Kuiper, Vladimir Mironov

Bioinform., 2014

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

Vinay Kumar Gautam, Eugen Czeizler, Pauline C. Haddow, Martin Kuiper

Proceedings of the Theory and Practice of Natural Computing, 2014

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

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

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

Vinay Kumar Gautam, Pauline C. Haddow, Martin Kuiper

Proceedings of the Theory and Practice of Natural Computing, 2013

2012

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

Steven Vercruysse, Aravind Venkatesan, Martin Kuiper

BMC Bioinform., 2012

Gauging triple stores with actual biological data.

Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Andrea Splendiani, Martin Kuiper

BMC Bioinform., 2012

Profiling of Semantically Annotated Proteins.

Jens Hollunder, Vladimir Mironov, Erick Antezana, Robert Hoehndorf, Martin Kuiper

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.

Aravind Venkatesan, Vladimir Mironov, Martin Kuiper

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.

Ward Blondé, Vladimir Mironov, Aravind Venkatesan, Erick Antezana, Bernard De Baets, Martin Kuiper

Bioinform., 2011

Flexibility and utility of the cell cycle ontology.

Vladimir Mironov, Erick Antezana, Mikel Egaña, Ward Blondé, Bernard De Baets, Martin Kuiper, Robert Stevens

Appl. Ontology, 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

Proceedings of the International Conference on Web Intelligence, Mining and Semantics, 2011

Semantic systems biology: enabling integrative biology via semantic web technologies.

Erick Antezana, Ward Blondé, Aravind Venkatesan, Bernard De Baets, Vladimir Mironov, Martin Kuiper

Proceedings of the International Conference on Web Intelligence, Mining and Semantics, 2011

WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary.

Steven Vercruysse, Martin Kuiper

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.

Wim De Mulder, Martin Kuiper, René K. Boel

J. Integr. 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

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy.

Erick Antezana, Aravind Venkatesan, Chris Mungall, Vladimir Mironov, Martin Kuiper

BMC Bioinform., 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

Bioinform., 2010

Benchmarking Triple Stores with Biological Data.

Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Bjorn Lindi, Martin Kuiper

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.

Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper

BMC 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

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

Erick Antezana, Martin Kuiper, Vladimir Mironov

Briefings Bioinform., 2009

2008

Extracting expression modules from perturbational gene expression compendia.

Steven Maere, Patrick Van Dijck, Martin Kuiper

BMC Syst. Biol., 2008

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

Mikel Egaña Aranguren, Erick Antezana, Martin Kuiper, Robert Stevens

BMC Bioinform., 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

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

Erick Antezana, Mikel Egaña, Ward Blondé, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper

Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences ( SWAT4LS ) Edinburgh, 2008

BioGateway: Integrated RDF for Life Science Queries.

Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper

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.

Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper

Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences ( SWAT4LS ) Edinburgh, 2008

Initialization Dependence of Clustering Algorithms.

Wim De Mulder, Stefan Schliebs, René K. Boel, Martin Kuiper

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.

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

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

2006

A Cell-Cycle Knowledge Integration Framework.

Erick Antezana, Elena Tsiporkova, Vladimir Mironov, Martin Kuiper

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.

Steven Vercruysse, Martin Kuiper

Bioinform., 2005

<i>BiNGO</i>: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks.

Steven Maere, Karel Heymans, Martin Kuiper

Bioinform., 2005