Emanuel Gonšalves
Emanuel Gonšalves
Ophiomics
Verified email at ophiomics.com - Homepage
Title
Cited by
Cited by
Year
A landscape of pharmacogenomic interactions in cancer
F Iorio, TA Knijnenburg, DJ Vis, GR Bignell, MP Menden, M Schubert, ...
Cell 166 (3), 740-754, 2016
8742016
Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens
FM Behan, F Iorio, G Picco, E Gonšalves, CM Beaver, G Migliardi, ...
Nature 568 (7753), 511-516, 2019
3182019
Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition
M Sciacovelli, E Gonšalves, TI Johnson, VR Zecchini, ASH Da Costa, ...
Nature 537 (7621), 544-547, 2016
2862016
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms
CDA Terfve, T Cokelaer, D Henriques, A MacNamara, E Gonšalves, ...
BMC Systems Biology 6 (1), 133, 2012
1832012
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
C Chaouiya, D BÚrenguier, SM Keating, A Naldi, MP Van Iersel, ...
BMC systems biology 7 (1), 1-15, 2013
1272013
Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models
E Gonšalves, J Bucher, A Ryll, J Niklas, K Mauch, S Klamt, M Rocha, ...
Molecular BioSystems 9 (7), 1576-1583, 2013
962013
Genomic determinants of protein abundance variation in colorectal cancer cells
TI Roumeliotis, SP Williams, E Goncalves, FZ Ghavidel, N Aben, ...
Cell Reports 20 (9), 2201–2214, 2017
642017
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
C Pacini, F Iorio, E Gonšalves, M Iskar, T Klabunde, P Bork, ...
Bioinformatics 29 (1), 132-134, 2013
592013
Widespread post-transcriptional attenuation of genomic copy-number variation in cancer
E Gonšalves, A Fragoulis, L Garcia-Alonso, T Cramer, J Saez-Rodriguez, ...
Cell systems 5 (4), 386-398. e4, 2017
492017
Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets
JM Dempster, C Pacini, S Pantel, FM Behan, T Green, J Krill-Burger, ...
Nature communications 10 (1), 1-14, 2019
482019
Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting
F Iorio, FM Behan, E Gonšalves, SG Bhosle, E Chen, R Shepherd, ...
BMC genomics 19 (1), 1-16, 2018
382018
Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening
G Picco, ED Chen, LG Alonso, FM Behan, E Gonšalves, G Bignell, ...
Nature communications 10 (1), 1-12, 2019
322019
Benchmarking substrate-based kinase activity inference using phosphoproteomic data
C Hernandez-Armenta, D Ochoa, E Gonšalves, J Saez-Rodriguez, ...
Bioinformatics 33 (12), 1845-1851, 2017
302017
Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast
E Gonšalves, Z Raguz Nakic, M Zampieri, O Wagih, D Ochoa, U Sauer, ...
PLoS computational biology 13 (1), e1005297, 2017
282017
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M K÷nig, F Zhang, A Drńger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
202020
Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression
E Gonšalves, R Pereira, I Rocha, M Rocha
Journal of Computational Biology 19 (2), 102-114, 2012
192012
Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects
E Gonšalves, FM Behan, S Louzada, D Arnol, EA Stronach, F Yang, ...
Genome biology 20 (1), 1-10, 2019
182019
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models
A Ryll, J Bucher, A Bonin, S Bongard, E Gonšalves, J Saez-Rodriguez, ...
Biosystems 124, 26-38, 2014
182014
CySBGN: a cytoscape plug-in to integrate SBGN maps
E Gonšalves, M van Iersel, J Saez-Rodriguez
BMC bioinformatics 14 (1), 1-7, 2013
172013
A community challenge for inferring genetic predictors of gene essentialities through analysis of a functional screen of cancer cell lines
M G÷nen, BA Weir, GS Cowley, F Vazquez, Y Guan, A Jaiswal, ...
Cell systems 5 (5), 485-497. e3, 2017
142017
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Articles 1–20