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Journal Articles
- 2021
[j36]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): 1848-1859 (2021)- [j35]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) - [j34]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) - [j33]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): 5712-5718 (2021) - [j32]John Zobolas, Vasundra Touré, Martin Kuiper, Steven Vercruysse:
UniBioDicts: Unified access to Biological Dictionaries. Bioinform. 37(1): 143-144 (2021) - [j31]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:
The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 49(Database-Issue): D325-D334 (2021) - 2020
- [j30]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): 1966-1967 (2020) - [j29]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): 460 (2020) - [j28]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): 2583 (2020) - 2019
- [j27]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): 3779-3785 (2019) - 2016
- [j26]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) - 2015
- [j25]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: 40 (2015) - [j24]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) - 2014
- [j23]Ole Kristian Ekseth, Martin Kuiper, Vladimir Mironov:
orthAgogue: an agile tool for the rapid prediction of orthology relations. Bioinform. 30(5): 734-736 (2014) - [j22]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: 386 (2014) - [j21]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): 115-126 (2014) - 2013
- [j20]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) - [j19]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): 2519-2520 (2013) - 2012
- [j18]Steven Vercruysse, Aravind Venkatesan, Martin Kuiper:
OLSVis: an animated, interactive visual browser for bio-ontologies. BMC Bioinform. 13: 116 (2012) - [j17]Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Andrea Splendiani, Martin Kuiper:
Gauging triple stores with actual biological data. BMC Bioinform. 13(S-1): S3 (2012) - 2011
- [j16]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): 247-261 (2011) - [j15]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): 1562-1568 (2011) - 2010
- [j14]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): 987-989 (2010) - [j13]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: 360 (2010) - [j12]Erick Antezana, Aravind Venkatesan, Chris Mungall, Vladimir Mironov, Martin Kuiper:
ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. BMC Bioinform. 11(S-12): S8 (2010) - [j11]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) - 2009
- [j10]Erick Antezana, Martin Kuiper, Vladimir Mironov:
Biological knowledge management: the emerging role of the Semantic Web technologies. Briefings Bioinform. 10(4): 392-407 (2009) - [j9]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:
Gene expression trends and protein features effectively complement each other in gene function prediction. Bioinform. 25(3): 322-330 (2009) - [j8]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): 11 (2009) - 2008
- [j7]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): 885-887 (2008) - [j6]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) - [j5]Steven Maere, Patrick Van Dijck, Martin Kuiper:
Extracting expression modules from perturbational gene expression compendia. BMC Syst. Biol. 2: 33 (2008) - 2007
- [j4]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) - [j3]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:
CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes. BMC Bioinform. 8 (2007) - 2005
- [j2]Steven Vercruysse, Martin Kuiper:
Simulating genetic networks made easy: network construction with simple building blocks. Bioinform. 21(2): 269-271 (2005) - [j1]Steven Maere, Karel Heymans, Martin Kuiper:
BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinform. 21(16): 3448-3449 (2005)
Conference and Workshop Papers
- 2019
- [c15]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 - [c14]Stian Holmås, Vladimir Mironov, Martin Kuiper:
Network Building with Cytoscape App Queries to the BioGateway 3.0 Triple Store. SWAT4HCLS 2019: 169-170 - 2014
- [c13]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: 119-133 - 2013
- [c12]Vinay Kumar Gautam, Pauline C. Haddow, Martin Kuiper:
Reliable Self-assembly by Self-triggered Activation of Enveloped DNA Tiles. TPNC 2013: 68-79 - 2012
- [c11]Aravind Venkatesan, Vladimir Mironov, Martin Kuiper:
Towards an integrated knowledge system for capturing gene expression events. ICBO 2012 - [c10]Jens Hollunder, Vladimir Mironov, Erick Antezana, Robert Hoehndorf, Martin Kuiper:
Profiling of Semantically Annotated Proteins. SWAT4LS 2012 - 2011
- [c9]Steven Vercruysse, Martin Kuiper:
WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary. IHCI 2011: 137-145 - [c8]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: 58 - [c7]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: 59 - 2010
- [c6]Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Bjorn Lindi, Martin Kuiper:
Benchmarking Triple Stores with Biological Data. SWAT4LS 2010 - 2008
- [c5]Wim De Mulder, Stefan Schliebs, René K. Boel, Martin Kuiper:
Initialization Dependence of Clustering Algorithms. ICONIP (2) 2008: 615-622 - [c4]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 - [c3]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 - [c2]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 - 2006
- [c1]Erick Antezana, Elena Tsiporkova, Vladimir Mironov, Martin Kuiper:
A Cell-Cycle Knowledge Integration Framework. DILS 2006: 19-34
Informal and Other Publications
- 2010
- [i1]Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Bjorn Lindi, Martin Kuiper:
Benchmarking triple stores with biological data. CoRR abs/1012.1632 (2010)
Coauthor Index
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