Emanuel J. V. Gonçalves

12 papers Misc 2Journal 10
YearRankTypeTitle / Venue / Authors
2025 J jnl
A technical review of multi-omics data integration methods: from classical statistical to deep generative approaches.
Briefings Bioinform.
Ana Rita Baião, Zhaoxiang Cai, Rebecca C. Poulos, Phillip J. Robinson, Roger R. Reddel, Qing Zhong, Susana Vinga, Emanuel J. V. Gonçalves
2021 J jnl
Project Score database: a resource for investigating cancer cell dependencies and prioritizing therapeutic targets.
Nucleic Acids Res.
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
2017 J jnl
Benchmarking substrate-based kinase activity inference using phosphoproteomic data.
Bioinform.
Claudia Hernandez-Armenta, David Ochoa, Emanuel J. V. Gonçalves, Julio Saez-Rodriguez, Pedro Beltrão
2017 J jnl
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.
PLoS Comput. Biol.
Emanuel J. V. Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrão, Julio Saez-Rodriguez
2014 J jnl
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.
Biosyst.
Anke Ryll, Joachim Bucher, Anne Bonin, Sophia Bongard, Emanuel J. V. Gonçalves, Julio Saez-Rodriguez, Jens Niklas, Steffen Klamt
2013 J jnl
CySBGN: A Cytoscape plug-in to integrate SBGN maps.
BMC Bioinform.
Emanuel J. V. Gonçalves, Martijn P. van Iersel, Julio Saez-Rodriguez
2013 J jnl
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Bioinform.
Clare Pacini, Francesco Iorio, Emanuel J. V. Gonçalves, Murat Iskar, Thomas Klabunde, Peer Bork, Julio Saez-Rodriguez
2013 J jnl
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst. Biol.
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
2012 J jnl
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.
BMC Syst. Biol.
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
2012 Misc conf
Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression.
PACBB
Emanuel J. V. Gonçalves, Isabel Rocha, Miguel Rocha
2012 J jnl
Optimization Approaches for the
J. Comput. Biol.
Emanuel J. V. Gonçalves, Rui Pereira, Isabel Rocha, Miguel Rocha
2011 Misc conf
A Software Platform for Evolutionary Computation with Pluggable Parallelism and Quality Assurance.
AIAI
Pedro Evangelista, Jorge Henrique Martins de Pinho, Emanuel J. V. Gonçalves, Paulo Maia, João Luís Ferreira Sobral, Miguel Francisco de Almeida Pereira da Rocha