Emanuel J. V. Gonçalves

Publication Activity (10 Years)

Years Active: 2011-2021
Publications (10 Years): 3

Top Topics

Qualitative Models

Yeast Cell Cycle

Gene Expression

Regulatory Networks

Top Venues

BMC Syst. Biol.

Publications

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) (2021)
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)
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) (2017)
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 (2014)
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 (2013)
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) (2013)
Emanuel J. V. Gonçalves, Martijn P. van Iersel, Julio Saez-Rodriguez
CySBGN: A Cytoscape plug-in to integrate SBGN maps. BMC Bioinform. 14 (2013)
Emanuel J. V. Gonçalves, Julio Saez-Rodriguez
packages. F1000Research 2 (2013)
Emanuel J. V. Gonçalves, Isabel Rocha, Miguel Rocha
Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression. PACBB (2012)
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 (2012)
Emanuel J. V. Gonçalves, Rui Pereira, Isabel Rocha, Miguel Rocha
Discovery of Optimal Targets for Gene Over/Underexpression. J. Comput. Biol. 19 (2) (2012)
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)