Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology. - Jacek Puchalka; Matthew A. Oberhardt; Miguel Godinho; Agata Bielecka; Daniela Regenhardt; Kenneth N. Timmis; Jason A. Papin; Vítor A. P. Martins dos Santos (PLoS Comput. Biol., 2008)

Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction. - Kechi Fang; Hansheng Zhao; Changyue Sun; Carolyn M. C. Lam; Suhua Chang; Kunlin Zhang; Gurudutta Panda; Miguel Godinho; Vítor A. P. Martins dos Santos; Jing Wang 003 (BMC Syst. Biol., 2011)

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis. - Matthew A. Oberhardt; Jacek Puchalka; Vítor A. P. Martins dos Santos; Jason A. Papin (PLoS Comput. Biol., 2011)

Modeling and analysis of flux distributions in the two branches of the phosphotransferase system in Pseudomonas putida. - Andreas Kremling; Katharina Pflüger-Grau; Max Chavarría; Jacek Puchalka; Vítor A. P. Martins dos Santos; Victor de Lorenzo (BMC Syst. Biol., 2012)

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)

Efficient Reconstruction of Predictive Consensus Metabolic Network Models. - Ruben G. A. van Heck; Mathias Ganter; Vítor A. P. Martins dos Santos; Jörg Stelling (PLoS Comput. Biol., 2016)

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)

SyNDI: synchronous network data integration framework. - Erno Lindfors; Jesse C. J. van Dam; Carolyn M. C. Lam; Niels A. Zondervan; Vítor A. P. Martins dos Santos; María Suárez-Diez (BMC Bioinform., 2018)

DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems. - Robert W. Smith 003; Rik P. van Rosmalen; Vítor A. P. Martins dos Santos; Christian Fleck 001 (BMC Syst. Biol., 2018)

SciBERT-based Semantification of Bioassays in the Open Research Knowledge Graph. - Marco Anteghini; Jennifer D'Souza 001; Vítor A. P. Martins dos Santos; Sören Auer (EKAW (Posters & Demos), 2020)

Representing Semantified Biological Assays in the Open Research Knowledge Graph. - Marco Anteghini; Jennifer D'Souza 001; Vítor A. P. Martins dos Santos; Sören Auer (ICADL, 2020)

Easy Semantification of Bioassays. - Marco Anteghini; Jennifer D'Souza 001; Vítor A. P. Martins dos Santos; Sören Auer (AI*IA, 2021)

Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism. - Neeraj Sinha; Evert M. van Schothorst; Guido J. E. K. Hooiveld; Jaap Keijer; Vítor A. P. Martins dos Santos; María Suárez-Diez (BMC Bioinform., 2021)

The Digitalization of Bioassays in the Open Research Knowledge Graph. - Jennifer D'Souza 001; Anita Monteverdi; Muhammad Haris 001; Marco Anteghini; Kheir Eddine Farfar; Markus Stocker; Vítor A. P. Martins dos Santos; Sören Auer (DEXA (1), 2022)

Decision support system and outcome prediction in a cohort of patients with necrotizing soft-tissue infections. - Sonja Katz; Jaco Suijker; Christopher Hardt; Martin Bruun Madsen; Annebeth Meij-de Vries; Anouk Pijpe; Steinar Skrede; Ole Hyldegaard; Erik Solligård; Anna Norrby-Teglund; Edoardo Saccenti; Vítor A. P. Martins dos Santos (Int. J. Medical Informatics, 2022)

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)

Exploring the Impact of Tensions in Stakeholder Norms on Designing for Value Change: The Case of Biosafety in Industrial Biotechnology. - Enrique Asin-Garcia; Zoë Robaey; Linde F. C. Kampers; Vítor A. P. Martins dos Santos (Sci. Eng. Ethics, 2023)

Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping. - Zuqi Li; Sonja Katz; Edoardo Saccenti; David W. Fardo; Peter Claes; Vítor A. P. Martins dos Santos; Kristel Van Steen; Gennady V. Roshchupkin (Briefings Bioinform., 2024)

Making PBPK models more reproducible in practice. - Elena Domínguez Romero; Stanislav Mazurenko; Martin Scheringer; Vítor A. P. Martins dos Santos; Chris T. A. Evelo; Mihail Anton; John M. Hancock; Anze Zupanic; María Suárez-Diez (Briefings Bioinform., 2024)

Response to Letter to Editor by A. Derbalah et al.: the role of automation in enhancing reproducibility and interoperability of PBPK models. - Elena Domínguez Romero; Stanislav Mazurenko; Martin Scheringer; Vítor A. P. Martins dos Santos; Chris T. A. Evelo; Mihail Anton; John M. Hancock; Anze Zupanic; María Suárez-Diez (Briefings Bioinform., 2024)