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Emanuel J. V. Gonçalves
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2020 – today
- 2021
- [j9]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:
Project Score database: a resource for investigating cancer cell dependencies and prioritizing therapeutic targets. Nucleic Acids Res. 49(Database-Issue): D1365-D1372 (2021)
2010 – 2019
- 2017
- [j8]Claudia Hernandez-Armenta, David Ochoa, Emanuel J. V. Gonçalves, Julio Saez-Rodriguez, Pedro Beltrão:
Benchmarking substrate-based kinase activity inference using phosphoproteomic data. Bioinform. 33(12): 1845-1851 (2017) - [j7]Emanuel J. V. Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrão, Julio Saez-Rodriguez:
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. PLoS Comput. Biol. 13(1) (2017) - 2014
- [j6]Anke Ryll, Joachim Bucher, Anne Bonin, Sophia Bongard, Emanuel J. V. Gonçalves, Julio Saez-Rodriguez, Jens Niklas, Steffen Klamt:
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. Biosyst. 124: 26-38 (2014) - 2013
- [j5]Clare Pacini, Francesco Iorio, Emanuel J. V. Gonçalves, Murat Iskar, Thomas Klabunde, Peer Bork, Julio Saez-Rodriguez:
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. Bioinform. 29(1): 132-134 (2013) - [j4]Emanuel J. V. Gonçalves, Martijn P. van Iersel, Julio Saez-Rodriguez:
CySBGN: A Cytoscape plug-in to integrate SBGN maps. BMC Bioinform. 14: 17 (2013) - [j3]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:
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7: 135 (2013) - [i1]Emanuel J. V. Gonçalves, Julio Saez-Rodriguez:
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages. F1000Research 2: 192 (2013) - 2012
- [j2]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:
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Syst. Biol. 6: 133 (2012) - [j1]Emanuel J. V. Gonçalves, Rui Pereira, Isabel Rocha, Miguel Rocha:
Optimization Approaches for the In Silico Discovery of Optimal Targets for Gene Over/Underexpression. J. Comput. Biol. 19(2): 102-114 (2012) - [c2]Emanuel J. V. Gonçalves, Isabel Rocha, Miguel Rocha:
Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression. PACBB 2012: 251-258 - 2011
- [c1]Pedro Evangelista, Jorge Henrique Martins de Pinho, Emanuel J. V. Gonçalves, Paulo Maia, João Luís Ferreira Sobral, Miguel Francisco de Almeida Pereira da Rocha:
A Software Platform for Evolutionary Computation with Pluggable Parallelism and Quality Assurance. EANN/AIAI (2) 2011: 45-50
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