2020

• Puig, Rafael Riudavets; Holmås, Stian; Mironov, Vladimir; Kuiper, Martin. (2020) Network Building with the Cytoscape BioGateway App Explained in Five Use Cases. Current Protocols in Bioinformatics. volum 72 (1).
  Academic article

2019

• Holmås, Stian; Riudavets Puig, Rafael; Acencio, Marcio Luis; Mironov, Vladimir; Kuiper, Martin. (2019) The Cytoscape BioGateway App: explorative network building from an RDF store. Bioinformatics.
  Academic article

2017

• Nordgård, Anna Synnøve Røstad; Bergland, Wenche Hennie; Vadstein, Olav; Mironov, Vladimir; Bakke, Rune; Østgaard, Kjetill; Bakke, Ingrid. (2017) Anaerobic digestion of pig manure supernatant at high ammonia concentrations characterized by high abundances of Methanosaeta and non-euryarchaeotal archaea. Scientific Reports. volum 7:15077.
  Academic article

2014

• Blondé, Ward; Antezana, Erick; Mironov, Vladimir; Schulz, Stefan; Kuiper, Martin; De baets, Bernard. (2014) Using the relation ontology Metarel for modelling Linked Data as multi-digraphs. Semantic Web Journal. volum 5 (2).
  Academic article
• Mironov, Vladimir; Kuiper, Martin; Ekseth, Ole Kristian. (2014) OrthAgogue: An agile tool for the rapid prediction of orthology relations. Bioinformatics. volum 30 (5).
  Academic article
• Venkatesan, Aravind; Tripathi, Sushil; Sanz de Galdeano, Alejandro; Blondé, Ward; Lægreid, Astrid; Mironov, Vladimir; Kuiper, Martin. (2014) Finding gene regulatory network candidates using the gene expression knowledge base. BMC Bioinformatics. volum 15 (1).
  Academic article

2013

• Antezana, Erick; Mironov, Vladimir; Kuiper, Martin. (2013) The emergence of Semantic Systems Biology. New Biotechnology. volum 30 (3).
  Academic article
• Kuiper, Martin; Antezana, Erick; Mironov, Vladimir. (2013) Cell Cycle Ontology (CCO).
  Website (informational material)

2012

• Kuiper, Martin; Venkatesan, Aravind; Antezana, Erick; Vercruysse, Steven; Mironov, Vladimir; Blondé, Ward. (2012) Putting Semantics in Systems Biology. META. volum 2012 (3).
  Article
• Mironov, Vladimir; Seethappan, Nirmala; Blondé, Ward; Antezana, Erick; Splendiani, Andrea; Kuiper, Martin. (2012) Gauging triple stores with actual biological data. BMC Bioinformatics. volum 13.
  Academic article

2011

• Blondé, Ward; Mironov, Vladimir; Venkatesan, Aravind; Antezana, Erick; De baets, Bernard; Kuiper, Martin. (2011) Reasoning with bio-ontologies: using relational closure rules to enable practical querying. Bioinformatics. volum 27 (11).
  Academic article
• Mironov, Vladimir; Antezana, Erick; Egaña, Mikel; Blondé, Ward; De baets, Bernard; Kuiper, Martin; Stevens, Robert. (2011) Flexibility and utility of the cell cycle ontology. Applied Ontology. volum 6 (3).
  Academic article

2010

• Antezana, Erick; Venkatesan, Aravind; Mungall, Chris; Mironov, Vladimir; Kuiper, Martin. (2010) ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. BMC Bioinformatics. volum 11.
  Academic article

2009

• Antezana, E; Kuiper, Martin; Mironov, Vladimir. (2009) Biological knowledge management: the emerging role of the Semantic Web technologies. Briefings in Bioinformatics. volum 10 (4).
  Academic literature review
• Antezana, Erick; Blondé, Ward; Egaña, Mikel; Rutherford, Alistair; Stevens, Robert; De baets, Bernard; Mironov, Vladimir; Kuiper, Martin. (2009) BioGateway: A Semantic Systems Biology Tool for the Life Sciences. BMC Bioinformatics. volum 10 (S11).
  Academic article