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List of works by Emanuel Gonçalves

A Software Platform for Evolutionary Computation with Pluggable Parallelism and Quality Assurance

A landscape of pharmacogenomic interactions in cancer.

scientific article published on 05 July 2016

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models

scientific article published on 23 July 2014

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets

scientific article published on 20 December 2019

Benchmarking substrate-based kinase activity inference using phosphoproteomic data

scientific article

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models

scientific article published on 25 March 2013

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

scientific article

Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression

article

CySBGN: a Cytoscape plug-in to integrate SBGN maps

scientific article

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

scientific article published on 19 September 2013

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.

scientific article

Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition

scientific article published on 31 August 2016

Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening

article

Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway

scientific article published on 29 September 2020

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

scientific article published on August 2017

Integrated cross-study datasets of genetic dependencies in cancer

scientific article published in 2021

Minimal genome-wide human CRISPR-Cas9 library

scientific article published on 21 January 2021

Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels

scientific article published on 25 June 2019

Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression

scientific article published in February 2012

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells.

scientific article published on 27 November 2017

Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens

scientific article published on 10 April 2019

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

scientific article

Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects

article

System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.

scientific article published on 12 December 2016

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast

scientific article

Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

scientific article published on 13 August 2018

Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer

scientific article published on 9 October 2017

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