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Martin Kuiper
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2020 – today
- 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)
2010 – 2019
- 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) - [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 - 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) - [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
- [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) - [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
- [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) - [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
- [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) - [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
- [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) - [c6]Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Bjorn Lindi, Martin Kuiper:
Benchmarking Triple Stores with Biological Data. SWAT4LS 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)
2000 – 2009
- 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) - [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 - 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) - 2006
- [c1]Erick Antezana
, Elena Tsiporkova, Vladimir Mironov, Martin Kuiper
:
A Cell-Cycle Knowledge Integration Framework. DILS 2006: 19-34 - 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)
Coauthor Index
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