A Software Platform for Evolutionary Computation with Pluggable Parallelism and Quality Assurance. - Pedro Evangelista; Jorge Henrique Martins de Pinho; Emanuel J. V. Gonçalves; Paulo Maia; João Luís Ferreira Sobral; Miguel Francisco de Almeida Pereira da Rocha (AIAI, 2011)

Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression. - Emanuel J. V. Gonçalves; Isabel Rocha; Miguel Rocha 001 (PACBB, 2012)

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. - Camille Terfve; Thomas Cokelaer; David Henriques; Aidan MacNamara; Emanuel J. V. Gonçalves; Melody K. Morris; Martijn P. van Iersel; Douglas A. Lauffenburger; Julio Saez-Rodriguez (BMC Syst. Biol., 2012)

Optimization Approaches for the In Silico Discovery of Optimal Targets for Gene Over/Underexpression. - Emanuel J. V. Gonçalves; Rui Pereira; Isabel Rocha; Miguel Rocha 001 (J. Comput. Biol., 2012)

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. - Clare Pacini; Francesco Iorio; Emanuel J. V. Gonçalves; Murat Iskar; Thomas Klabunde; Peer Bork; Julio Saez-Rodriguez (Bioinform., 2013)

CySBGN: A Cytoscape plug-in to integrate SBGN maps. - Emanuel J. V. Gonçalves; Martijn P. van Iersel; Julio Saez-Rodriguez (BMC Bioinform., 2013)

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. - Claudine Chaouiya; Duncan Bérenguier; Sarah M. Keating; Aurélien Naldi; Martijn P. van Iersel; Nicolas Rodriguez 001; Andreas Dräger; Finja Büchel; Thomas Cokelaer; Bryan M. Kowal; Benjamin Wicks; Emanuel J. V. Gonçalves; et al. (BMC Syst. Biol., 2013)

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages. - Emanuel J. V. Gonçalves; Julio Saez-Rodriguez (F1000Research, 2013)

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. - Anke Ryll; Joachim Bucher; Anne Bonin; Sophia Bongard; Emanuel J. V. Gonçalves; Julio Saez-Rodriguez; Jens Niklas; Steffen Klamt (Biosyst., 2014)

Benchmarking substrate-based kinase activity inference using phosphoproteomic data. - Claudia Hernandez-Armenta; David Ochoa; Emanuel J. V. Gonçalves; Julio Saez-Rodriguez; Pedro Beltrão (Bioinform., 2017)

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. - Emanuel J. V. Gonçalves; Zrinka Raguz Nakic; Mattia Zampieri; Omar Wagih; David Ochoa; Uwe Sauer; Pedro Beltrão; Julio Saez-Rodriguez (PLoS Comput. Biol., 2017)

Project Score database: a resource for investigating cancer cell dependencies and prioritizing therapeutic targets. - Lisa Dwane; Fiona M. Behan; Emanuel J. V. Gonçalves; Howard Lightfoot; Wanjuan Yang; Dieudonne van der Meer; Rebecca Shepherd; Miguel Pignatelli; Francesco Iorio; Mathew Garnett (Nucleic Acids Res., 2021)