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)

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)

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)

The Digitalization of Bioassays in the Open Research Knowledge Graph - Jennifer D'Souza; Anita Monteverdi; Muhammad Haris; Marco Anteghini; Kheir Eddine Farfar; Markus Stocker; Vítor A. P. Martins dos Santos; Sören Auer (Database and Expert Systems Applications - 33rd International Conference, DEXA 2022, Vienna, Austria, August 22-24, 2022, Proceedings, Part I, 2022)

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

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)

Easy Semantification of Bioassays - Marco Anteghini; Jennifer D'Souza; Vítor A. P. Martins dos Santos; Sören Auer (AIxIA 2021 - Advances in Artificial Intelligence - 20th International Conference of the Italian Association for Artificial Intelligence, Virtual Event, December 1-3, 2021, Revised Selected Papers, 2021)

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

SciBERT-based Semantification of Bioassays in the Open Research Knowledge Graph - Marco Anteghini; Jennifer D'Souza; Vítor A. P. Martins dos Santos; Sören Auer (Proceedings of the EKAW 2020 Posters and Demonstrations Session co-located with 22nd International Conference on Knowledge Engineering and Knowledge Management (EKAW 2020), Globally online & Bozen-Bolzano, Italy, September 17, 2020, 2020)

Representing Semantified Biological Assays in the Open Research Knowledge Graph - Marco Anteghini; Jennifer D'Souza; Vítor A. P. Martins dos Santos; Sören Auer (Digital Libraries at Times of Massive Societal Transition - 22nd International Conference on Asia-Pacific Digital Libraries, ICADL 2020, Kyoto, Japan, November 30 - December 1, 2020, Proceedings, 2020)

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

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

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; Rik P. van Rosmalen; Vítor A. P. Martins dos Santos; Christian Fleck (BMC Syst. Biol., 2018)

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)

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)

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)

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)

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 (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)

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)