Emanuel Gonçalves

On-target mutations confer resistance to WRN helicase inhibitors in Microsatellite Unstable Cancer Cells.

This study identifies on-target WRN mutations as resistance mechanisms in MSI cancer cells to WRN helicase inhibitors and suggests combination therapies to prevent resistance.

Genetic interaction library screening with a next-generation dual guide CRISPR system

The paper introduces a next-generation dual guide CRISPR system for efficient genetic interaction screening, achieving low undesired guide pairs and balanced expression, and demonstrates its application in colorectal cancer cells.

Synthetic augmentation of cancer cell line multi-omic datasets using unsupervised deep learning

The paper introduces a deep learning model to augment cancer cell line multi-omic data, increasing the number of profiles and uncovering drug resistance mechanisms.

Pan-cancer proteomic map of 949 human cell lines reveals principles of cancer vulnerabilities

The paper presents a pan-cancer proteomic map of 949 cell lines, revealing protein-specific biomarkers of cancer vulnerabilities and showing proteomic data's superior predictive power for drug response.

DNA methylation fingerprint for the diagnosis and monitoring of hepatocellular carcinoma from tissue and liquid biopsies

The paper develops a DNA methylation signature for HCC detection in tissue and liquid biopsies, achieving high accuracy in identifying HCC samples and distinguishing them from healthy controls and other cancers.

Integrated cross-study datasets of genetic dependencies in cancer

The paper integrates two large CRISPR-Cas9 screens to improve the detection of gene dependencies and cancer vulnerabilities by addressing biases and batch effects.

Minimal genome-wide human CRISPR-Cas9 library

The paper designs a smaller genome-wide CRISPR-Cas9 library with reduced size while maintaining sensitivity and specificity, enhancing its applicability in complex models.

A FGF2-mediated incoherent feedforward loop inducesErk inhibition and promotes naive pluripotency

This study identifies an FGF2-mediated incoherent feedforward loop that inhibits Erk and promotes naive pluripotency in ES cells and embryos.

Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens

This study integrates drug sensitivity data with CRISPR screens to identify drug mechanisms and biomarkers for cancer therapy.

Multi-omics characterization of interaction-mediated control of human protein abundance levels

The paper characterizes interaction-mediated control of protein abundance using multi-omics data from cancer samples and finds that 42% of proteins show post-transcriptional regulation.

Tandem duplications lead to loss of fitness effects in CRISPR-Cas9 data

The paper shows that targeting tandem amplified regions in CRISPR-Cas9 screens reduces cellular fitness, while chromosomal duplications have minimal effects.

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

CRISPRcleanR reduces false positives in CRISPR-Cas9 screens by correcting gene-independent responses without assuming copy number status.

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

The paper identifies phosphorylation sites in metabolic enzymes of FH-deficient cells using proteomics and computational modeling, showing PDHA1 inhibition due to increased phosphorylation.

Chromosomal rearrangements are commonly post-transcriptionally attenuated in cancer

The paper analyzes proteogenomic data to show that chromosomal rearrangements often reduce protein abundance post-transcriptionally, particularly in protein complexes, and identifies regulatory interactions linked to drug resistance.

Genomic determinants of protein abundance variation in colorectal cancer cells

The paper quantifies proteomic and genomic variation in colorectal cancer cell lines to understand how mutations affect protein levels and drug responses.

Benchmarking substrate-based kinase activity inference using phosphoproteomic data

The paper benchmarks kinase activity inference methods using phosphoproteomic data, finding the GSEA method performs best with an average AUC of 0.722.

Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast

This study integrates metabolomics, phosphoproteomics, and transcriptomics data in yeast to identify regulatory mechanisms linking signaling kinases to metabolic changes.