Emanuel J. V. Gonçalves

According to our database, Emanuel J. V. Gonçalves authored at least 12 papers between 2011 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2021

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

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

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

2014

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

2013

<i>Cyrface</i>: An interface from <i>Cytoscape</i> to <i>R </i>that provides a user interface to <i>R</i> packages.

Emanuel J. V. Gonçalves, Julio Saez-Rodriguez

F1000Research, 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, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar

BMC Syst. Biol., 2013

CySBGN: A Cytoscape plug-in to integrate SBGN maps.

Emanuel J. V. Gonçalves, Martijn P. van Iersel, Julio Saez-Rodriguez

BMC Bioinform., 2013

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

2012

Optimization Approaches for the <i>In Silico</i> Discovery of Optimal Targets for Gene Over/Underexpression.

Emanuel J. V. Gonçalves, Rui Pereira, Isabel Rocha, Miguel Rocha

J. Comput. Biol., 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

Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression.

Emanuel J. V. Gonçalves, Isabel Rocha, Miguel Rocha

Proceedings of the 6th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2012

2011

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

Proceedings of the Artificial Intelligence Applications and Innovations, 2011