getALife - An Artificial Life Environment for the Evaluation of Agent-Based Systems and Evolutionary Algorithms for Reinforcement Learning. - Daniel Machado; Miguel Rocha 001 (New Challenges in Applied Intelligence Technologies, 2008)

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)

Random sampling of elementary flux modes in large-scale metabolic networks. - Daniel Machado; Zita Soons; Kiran Raosaheb Patil; Eugénio C. Ferreira; Isabel Rocha (Bioinform., 2012)

A kinetic model for curcumin production in Escherichia coli. - Daniel Machado; Lígia R. Rodrigues; Isabel Rocha (Biosyst., 2014)

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism. - Daniel Machado; Markus J. Herrgård (PLoS Comput. Biol., 2014)

Care Partnerships: Toward Technology to Support Teens' Participation in Their Health Care. - Matthew K. Hong; Lauren Wilcox; Daniel Machado; Thomas A. Olson; Stephen F. Simoneaux (CHI, 2016)

Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction. - Daniel Machado; Markus J. Herrgård; Isabel Rocha (PLoS Comput. Biol., 2016)