Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis. - Jesse C. J. van Dam; Peter J. Schaap; Vítor A. P. Martins dos Santos; María Suárez-Diez (BMC Syst. Biol., 2014)

RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource. - Jesse C. J. van Dam; Jasper J. Koehorst; Peter J. Schaap; Vítor A. P. Martins dos Santos; María Suárez-Diez (J. Biomed. Semant., 2015)

SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles. - Jasper J. Koehorst; Jesse C. J. van Dam; Edoardo Saccenti; Vítor A. P. Martins dos Santos; María Suárez-Diez; Peter J. Schaap (Bioinform., 2018)

The Empusa code generator: bridging the gap between the intended and the actual content of RDF resources. - Jesse C. J. van Dam; Jasper J. Koehorst; Peter J. Schaap; María Suárez-Diez (CoRR, 2018)

SALARECON connects the Atlantic salmon genome to growth and feed efficiency. - Maksim V. Zakhartsev; Filip Rotnes; Marie Gulla; Ove Øyås; Jesse C. J. van Dam; María Suárez-Diez; Fabian Grammes; Róbert Anton Hafþórsson; Wout van Helvoirt; Jasper J. Koehorst; Peter J. Schaap; Yang Jin; et al. (PLoS Comput. Biol., 2022)

A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia. - William T. Scott Jr.; Sara Benito-Vaquerizo; Johannes Zimmermann; Djordje Bajic; Almut Heinken; María Suárez-Diez; Peter J. Schaap (PLoS Comput. Biol., 2023)