2024

• Mulero-Hernández, Juan; Mironov, Vladimir; Miñarro-Giménez, José Antonio; Kuiper, Martin; Fernández-Breis, Jesualdo Tomás. (2024) Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation. Nucleic Acids Research (NAR)
  Academic article

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
  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. (2017) Anaerobic digestion of pig manure supernatant at high ammonia concentrations characterized by high abundances of Methanosaeta and non-euryarchaeotal archaea. Scientific Reports
  Academic article

2014

• Venkatesan, Aravind; Tripathi, Sushil; Sanz de Galdeano, Alejandro; Blondé, Ward; Lægreid, Astrid; Mironov, Vladimir. (2014) Finding gene regulatory network candidates using the gene expression knowledge base. BMC Bioinformatics
  Academic article
• 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
  Academic article
• Mironov, Vladimir; Kuiper, Martin; Ekseth, Ole Kristian. (2014) OrthAgogue: An agile tool for the rapid prediction of orthology relations. Bioinformatics
  Academic article

2013

• Antezana, Erick; Mironov, Vladimir; Kuiper, Martin. (2013) The emergence of Semantic Systems Biology. New Biotechnology
  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
  Article in business/trade/industry journal
• Mironov, Vladimir; Seethappan, Nirmala; Blondé, Ward; Antezana, Erick; Splendiani, Andrea; Kuiper, Martin. (2012) Gauging triple stores with actual biological data. BMC Bioinformatics
  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
  Academic article
• Mironov, Vladimir; Antezana, Erick; Egaña, Mikel; Blondé, Ward; De baets, Bernard; Kuiper, Martin. (2011) Flexibility and utility of the cell cycle ontology. Applied Ontology
  Academic article

2010

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

2009

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