Martin Kuiper

Publication Activity (10 Years)

Years Active: 2005-2021
Publications (10 Years): 15

Top Topics

Biological Data

Saccharomyces Cerevisiae

Transcription Factors

Reference Model

Top Venues

Database J. Biol. Databases Curation

Briefings Bioinform.

Publications

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
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). Bioinform. 36 (24) (2021)
Vasundra Touré, John Zobolas, Martin Kuiper, Steven Vercruysse
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator. Database J. Biol. Databases Curation 2021 (2021)
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
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. Briefings Bioinform. 22 (2) (2021)
Vasundra Touré, Åsmund Flobak, Anna Niarakis, Steven Vercruysse, Martin Kuiper
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. Briefings Bioinform. 22 (4) (2021)
John Zobolas, Vasundra Touré, Martin Kuiper, Steven Vercruysse
UniBioDicts: Unified access to Biological Dictionaries. Bioinform. 37 (1) (2021)
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 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
The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 49 (Database-Issue) (2021)
John Zobolas, Martin Kuiper, Åsmund Flobak
emba: R package for analysis and visualization of biomarkers in boolean model ensembles. J. Open Source Softw. 5 (53) (2020)
Wim De Mulder, Martin Kuiper
A foundation for reference models for drug combinations with an application to Loewe's reference model. BMC Bioinform. 21 (1) (2020)
Stian Holmås, Rafel Riudavets Puig, Marcio Luis Acencio, Vladimir Mironov, Martin Kuiper
The Cytoscape BioGateway App: explorative network building from an RDF store. Bioinform. 36 (6) (2020)
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
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. Bioinform. 35 (19) (2019)
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
An Example of Multimodal Biological Knowledge Representation. JOWO (2019)
Stian Holmås, Vladimir Mironov, Martin Kuiper
Network Building with Cytoscape App Queries to the BioGateway 3.0 Triple Store. SWAT4HCLS (2019)
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
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. Database J. Biol. Databases Curation 2016 (2016)
Åsmund Flobak, Anaïs Baudot, Elisabeth Remy, Liv Thommesen, Denis Thieffry, Martin Kuiper, Astrid Lægreid
Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLoS Comput. Biol. 11 (8) (2015)
Sushil Tripathi, Åsmund Flobak, Konika Chawla, Anaïs Baudot, Torunn Bruland, Liv Thommesen, Martin Kuiper, Astrid Lægreid
The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms. BMC Syst. Biol. 9 (2015)
Ole Kristian Ekseth, Martin Kuiper, Vladimir Mironov
orthAgogue: an agile tool for the rapid prediction of orthology relations. Bioinform. 30 (5) (2014)
Ward Blondé, Erick Antezana, Vladimir Mironov, Stefan Schulz, Martin Kuiper, Bernard De Baets
Using the relation ontology Metarel for modelling Linked Data as multi-digraphs. Semantic Web 5 (2) (2014)
Vinay Kumar Gautam, Eugen Czeizler, Pauline C. Haddow, Martin Kuiper
Design of a Minimal System for Self-replication of Rectangular Patterns of DNA Tiles. TPNC (2014)
Aravind Venkatesan, Sushil Tripathi, Alejandro Sanz de Galdeano, Ward Blondé, Astrid Lægreid, Vladimir Mironov, Martin Kuiper
Finding gene regulatory network candidates using the gene expression knowledge base. BMC Bioinform. 15 (2014)
Sushil Tripathi, Karen R. Christie, Rama Balakrishnan, Rachael P. Huntley, David P. Hill, Liv Thommesen, Judith A. Blake, Martin Kuiper, Astrid Lægreid
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. Database J. Biol. Databases Curation 2013 (2013)
Konika Chawla, Sushil Tripathi, Liv Thommesen, Astrid Lægreid, Martin Kuiper
TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors. Bioinform. 29 (19) (2013)
Vinay Kumar Gautam, Pauline C. Haddow, Martin Kuiper
Reliable Self-assembly by Self-triggered Activation of Enveloped DNA Tiles. TPNC (2013)
Steven Vercruysse, Aravind Venkatesan, Martin Kuiper
OLSVis: an animated, interactive visual browser for bio-ontologies. BMC Bioinform. 13 (2012)
Jens Hollunder, Vladimir Mironov, Erick Antezana, Robert Hoehndorf, Martin Kuiper
Profiling of Semantically Annotated Proteins. SWAT4LS (2012)
Aravind Venkatesan, Vladimir Mironov, Martin Kuiper
Towards an integrated knowledge system for capturing gene expression events. ICBO (2012)
Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Andrea Splendiani, Martin Kuiper
Gauging triple stores with actual biological data. BMC Bioinform. 13 (S-1) (2012)
Aravind Venkatesan, Ward Blondé, Erick Antezana, Mats Skillingstad, M. Scott Marshall, Bernard De Baets, Vladimir Mironov, Martin Kuiper
The RDF foundry: call for an initiative to build enhanced RDF resources for biological data integration. WIMS (2011)
Erick Antezana, Ward Blondé, Aravind Venkatesan, Bernard De Baets, Vladimir Mironov, Martin Kuiper
Semantic systems biology: enabling integrative biology via semantic web technologies. WIMS (2011)
Vladimir Mironov, Erick Antezana, Mikel Egaña, Ward Blondé, Bernard De Baets, Martin Kuiper, Robert Stevens
Flexibility and utility of the cell cycle ontology. Appl. Ontology 6 (3) (2011)
Ward Blondé, Vladimir Mironov, Aravind Venkatesan, Erick Antezana, Bernard De Baets, Martin Kuiper
Reasoning with bio-ontologies: using relational closure rules to enable practical querying. Bioinform. 27 (11) (2011)
Steven Vercruysse, Martin Kuiper
WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary. IHCI (2011)
Jens Hollunder, Maik Friedel, Martin Kuiper, Thomas Wilhelm
DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data. Bioinform. 26 (7) (2010)
Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Bjorn Lindi, Martin Kuiper
Benchmarking triple stores with biological data CoRR (2010)
Wim De Mulder, Martin Kuiper, René K. Boel
Clustering of gene expression profiles: creating initialization-independent clusterings by eliminating unstable genes. J. Integr. Bioinform. 7 (3) (2010)
Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Bjorn Lindi, Martin Kuiper
Benchmarking Triple Stores with Biological Data. SWAT4LS (2010)
Erick Antezana, Aravind Venkatesan, Chris Mungall, Vladimir Mironov, Martin Kuiper
ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. BMC Bioinform. 11 (S-12) (2010)
Kris Laukens, Jens Hollunder, Thanh Hai Dang, Geert De Jaeger, Martin Kuiper, Erwin Witters, Alain Verschoren, Koenraad Van Leemput
Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. BMC Bioinform. 11 (2010)
Erick Antezana, Martin Kuiper, Vladimir Mironov
Biological knowledge management: the emerging role of the Semantic Web technologies. Briefings Bioinform. 10 (4) (2009)
Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper
BioGateway: a semantic systems biology tool for the life sciences. BMC Bioinform. 10 (S-10) (2009)
Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper
Structuring the Life Science Resourceome for Semantic Systems Biology: Lessons from the BioGateway Project. SWAT4LS (2008)
Erick Antezana, Mikel Egaña, Bernard De Baets, Martin Kuiper, Vladimir Mironov
ONTO-PERL: An API for supporting the development and analysis of bio-ontologies. Bioinform. 24 (6) (2008)
Steven Maere, Patrick Van Dijck, Martin Kuiper
Extracting expression modules from perturbational gene expression compendia. BMC Syst. Biol. 2 (2008)
Erick Antezana, Mikel Egaña, Ward Blondé, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper
The Cell Cycle Ontology: An Application Ontology Supporting the Life Sciences. SWAT4LS (2008)
Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper
BioGateway: Integrated RDF for Life Science Queries. SWAT4LS (2008)
Mikel Egaña Aranguren, Erick Antezana, Martin Kuiper, Robert Stevens
Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. BMC Bioinform. 9 (S-5) (2008)
Wim De Mulder, Stefan Schliebs, René K. Boel, Martin Kuiper
Initialization Dependence of Clustering Algorithms. ICONIP (2) (2008)
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
Validating module network learning algorithms using simulated data. BMC Bioinform. 8 (S-2) (2007)
Erick Antezana, Elena Tsiporkova, Vladimir Mironov, Martin Kuiper
A Cell-Cycle Knowledge Integration Framework. DILS (2006)
Steven Maere, Karel Heymans, Martin Kuiper
: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinform. 21 (16) (2005)
Steven Vercruysse, Martin Kuiper
Simulating genetic networks made easy: network construction with simple building blocks. Bioinform. 21 (2) (2005)