| 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 | 874 | 2016 |
| Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens FM Behan, F Iorio, G Picco, E Gonçalves, CM Beaver, G Migliardi, ... Nature 568 (7753), 511-516, 2019 | 318 | 2019 |
| Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition M Sciacovelli, E Gonçalves, TI Johnson, VR Zecchini, ASH Da Costa, ... Nature 537 (7621), 544-547, 2016 | 286 | 2016 |
| CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms CDA Terfve, T Cokelaer, D Henriques, A MacNamara, E Gonçalves, ... BMC Systems Biology 6 (1), 133, 2012 | 183 | 2012 |
| SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools C Chaouiya, D Bérenguier, SM Keating, A Naldi, MP Van Iersel, ... BMC systems biology 7 (1), 1-15, 2013 | 127 | 2013 |
| Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models E Gonçalves, J Bucher, A Ryll, J Niklas, K Mauch, S Klamt, M Rocha, ... Molecular BioSystems 9 (7), 1576-1583, 2013 | 96 | 2013 |
| 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 | 64 | 2017 |
| DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data C Pacini, F Iorio, E Gonçalves, M Iskar, T Klabunde, P Bork, ... Bioinformatics 29 (1), 132-134, 2013 | 59 | 2013 |
| Widespread post-transcriptional attenuation of genomic copy-number variation in cancer E Gonçalves, A Fragoulis, L Garcia-Alonso, T Cramer, J Saez-Rodriguez, ... Cell systems 5 (4), 386-398. e4, 2017 | 49 | 2017 |
| 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 | 48 | 2019 |
| Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting F Iorio, FM Behan, E Gonçalves, SG Bhosle, E Chen, R Shepherd, ... BMC genomics 19 (1), 1-16, 2018 | 38 | 2018 |
| 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 Gonçalves, G Bignell, ... Nature communications 10 (1), 1-12, 2019 | 32 | 2019 |
| Benchmarking substrate-based kinase activity inference using phosphoproteomic data C Hernandez-Armenta, D Ochoa, E Gonçalves, J Saez-Rodriguez, ... Bioinformatics 33 (12), 1845-1851, 2017 | 30 | 2017 |
| Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast E Gonçalves, Z Raguz Nakic, M Zampieri, O Wagih, D Ochoa, U Sauer, ... PLoS computational biology 13 (1), e1005297, 2017 | 28 | 2017 |
| SBML Level 3: an extensible format for the exchange and reuse of biological models SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ... Molecular systems biology 16 (8), e9110, 2020 | 20 | 2020 |
| Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression E Gonçalves, R Pereira, I Rocha, M Rocha Journal of Computational Biology 19 (2), 102-114, 2012 | 19 | 2012 |
| Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects E Gonçalves, FM Behan, S Louzada, D Arnol, EA Stronach, F Yang, ... Genome biology 20 (1), 1-10, 2019 | 18 | 2019 |
| A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models A Ryll, J Bucher, A Bonin, S Bongard, E Gonçalves, J Saez-Rodriguez, ... Biosystems 124, 26-38, 2014 | 18 | 2014 |
| CySBGN: a cytoscape plug-in to integrate SBGN maps E Gonçalves, M van Iersel, J Saez-Rodriguez BMC bioinformatics 14 (1), 1-7, 2013 | 17 | 2013 |
| A community challenge for inferring genetic predictors of gene essentialities through analysis of a functional screen of cancer cell lines M Gönen, BA Weir, GS Cowley, F Vazquez, Y Guan, A Jaiswal, ... Cell systems 5 (5), 485-497. e3, 2017 | 14 | 2017 |
Julio Saez RodriguezHeidelberg UniversityVerified email at bioquant.uni-heidelberg.de
