Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli . - Rafael S. Costa; Daniel Machado; Isabel Rocha; Eugénio C. Ferreira (IWANN (2), 2009)

A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. - Daniel Machado; Rafael S. Costa; Miguel Rocha 001; Isabel Rocha; Bruce Tidor; Eugénio C. Ferreira (IWANN (2), 2009)

Model Transformation of Metabolic Networks using a Petri Net Based Framework. - Daniel Machado; Rafael S. Costa; Miguel Rocha 001; Isabel Rocha; Bruce Tidor; Eugénio C. Ferreira (ACSD/Petri Nets Workshops, 2010)

Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations. - Rafael S. Costa; Daniel Machado; Isabel Rocha; Eugénio C. Ferreira (Biosyst., 2010)

Multi-level Dynamic Modeling in Biological Systems - Application of Hybrid Petri Nets to Network Simulation. - Rafael S. Costa; Daniel Machado; Ana Rute Neves; Susana Vinga (BIOINFORMATICS, 2012)

Exploring the Cellular Objective in Flux Balance Constraint-Based Models. - Rafael S. Costa; Son Nguyen; András Hartmann; Susana Vinga (CMSB, 2014)

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. - Rafael S. Costa; André Veríssimo; Susana Vinga (BMC Syst. Biol., 2014)

Identifying IIR filter coefficients using particle swarm optimization with application to reconstruction of missing cardiovascular signals. - András Hartmann; João Miranda Lemos; Rafael S. Costa; Susana Vinga (Eng. Appl. Artif. Intell., 2014)

Toward Community Standards and Software for Whole-Cell Modeling. - Dagmar Waltemath; Jonathan R. Karr; Frank T. Bergmann; Vijayalakshmi Chelliah; Michael Hucka; Marcus Krantz; Wolfram Liebermeister; Pedro Mendes 001; Chris J. Myers; Pinar Pir; Begum Alaybeyoglu; Naveen K. Aranganathan; et al. (IEEE Trans. Biomed. Eng., 2016)

KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling. - Hugo Mochão; Pedro Barahona; Rafael S. Costa (Database J. Biol. Databases Curation, 2020)

DI2: prior-free and multi-item discretization of biological data and its applications. - Leonardo Alexandre; Rafael S. Costa; Rui Henriques (BMC Bioinform., 2021)

DI2: prior-free and multi-item discretization ofbiomedical data and its applications. - Leonardo Alexandre; Rafael S. Costa; Rui Henriques (CoRR, 2021)

On the predictability of postoperative complications for cancer patients: a Portuguese cohort study. - Daniel Gonçalves; Rui Henriques; Lucio Lara-Santos; Rafael S. Costa (BMC Medical Informatics Decis. Mak., 2021)

Mining Pre-Surgical Patterns Able to Discriminate Post-Surgical Outcomes in the Oncological Domain. - Leonardo Alexandre; Rafael S. Costa; Lucio Lara-Santos; Rui Henriques (IEEE J. Biomed. Health Informatics, 2021)

Context-situated visualization of biclusters to aid decisions: going beyond subspaces with parallel coordinates. - Daniel Gonçalves; Rafael S. Costa; Rui Henriques (AVI, 2022)

Enrichment analysis on regulatory subspaces: A novel direction for the superior description of cellular responses to SARS-CoV-2. - Pedro Rodrigues; Rafael S. Costa; Rui Henriques (Comput. Biol. Medicine, 2022)

A general deep hybrid model for bioreactor systems: Combining first principles with deep neural networks. - José Pinto 007; Mykaella Mestre; J. Ramos; Rafael S. Costa; Gerald Striedner; Rui Oliveira 002 (Comput. Chem. Eng., 2022)

IPOscore: An interactive web-based platform for postoperative surgical complications analysis and prediction in the oncology domain. - Hugo Mochão; Daniel Gonçalves; Leonardo Alexandre; Carolina Castro; Duarte Valério; Pedro Barahona; Daniel Moreira-Gonçalves; Paulo Matos da Costa; Rui Henriques; Lucio Lara-Santos; Rafael S. Costa (Comput. Methods Programs Biomed., 2022)

Scaling pattern mining through non-overlapping variable partitioning. - Leonardo Alexandre; Rafael S. Costa; Rui Henriques (CoRR, 2022)

TriSig: Assessing the statistical significance of triclusters. - Leonardo Alexandre; Rafael S. Costa; Rui Henriques (CoRR, 2023)

SBML2HYB: a Python interface for SBML compatible hybrid modeling. - José Pinto 007; Rafael S. Costa; Leonardo Alexandre; João Ramos; Rui Oliveira 002 (Bioinform., 2023)

TriSig: Evaluating the statistical significance of triclusters. - Leonardo Alexandre; Rafael S. Costa; Rui Henriques (Pattern Recognit., 2024)

Integrating statistical significance and discriminative power in pattern discovery. - Leonardo Alexandre; Rafael S. Costa; Rui Henriques (Knowl. Based Syst., 2025)