F. Vazquez

Generation of a biliary tract cancer cell line atlas reveals molecular subtypes and therapeutic targets

This study creates a biliary tract cancer cell line atlas using multi-omics data to identify molecular subtypes and therapeutic targets.

CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution

CTAT-LR-fusion detects fusion transcripts from long and short read RNA-seq data, improving accuracy in bulk and single cell transcriptomes.

RPL22 is a tumor suppressor in MSI-high cancers and a key splicing regulator of MDM4

This study identifies RPL22 as a tumor suppressor in MSI-H cancers that regulates MDM4 splicing and reveals its role in oncogenic pathways.

Human aneuploid cells depend on the RAF/MEK/ERK pathway for overcoming increased DNA damage

This study identifies the RAF/MEK/ERK pathway as a critical dependency for aneuploid cells, showing increased pathway activity and sensitivity to its inhibition in aneuploid cancer cells.

Increased RNA and protein degradation is required for counteracting transcriptional burden and proteotoxic stress in human aneuploid cells

This study identifies increased RNA and protein degradation as mechanisms by which aneuploid cells counteract transcriptional burden and proteotoxic stress, revealing potential therapeutic targets.

Mapping the landscape of genetic dependencies in chordoma

This study identifies essential genes in chordoma using CRISPR screens, revealing new therapeutic targets like PTPN11 and confirming known dependencies such as TBXT.

Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal

This study compares CRISPR-Cas9 and RNAi screens to identify cancer vulnerabilities, finding that RNAi better detects pan-dependencies while CRISPR identifies more dependencies overall.

A Mesenchymal Tumor Cell State Confers Increased Dependency on the BCL-XL Anti-apoptotic Protein in Kidney Cancer

The paper identifies a mesenchymal tumor cell state that increases dependency on BCL-XL in kidney cancer, showing anti-tumor efficacy of a BCL-XL inhibitor.

Spatial effects in parasite induced marine diseases of immobile hosts

This study develops a spatially-explicit model to analyze how parasite mobility affects disease transmission in sessile marine hosts, showing that higher mobility leads to more severe epidemics and faster extinction.

Species exclusion and coexistence in a noisy voter model with a competition-colonization tradeoff

This study uses a noisy voter model to examine species competition, showing outcomes like exclusion, mono-stable, and bi-stable coexistence depending on immigration and competition-dispersal tradeoffs.

Phosphate dysregulation via the XPR1:KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer

The paper identifies XPR1 and KIDINS220 as therapeutic targets in ovarian cancer by showing their role in phosphate dysregulation leading to cell death.

Epigenetic transgenerational effects on RNAi in Arabidopsis

This study shows that RNA silencing states in Arabidopsis can be transgenerationally inherited but are progressively lost over generations.

Global computational alignment of tumor and cell line transcriptional profiles

The paper develops an unsupervised alignment method to compare tumor and cell line transcriptional profiles, revealing differences in similarity across cancer types and identifying cell lines with distinct transcriptional states.

Gene expression has more power for predicting in vitro cancer cell vulnerabilities than genomics

This study compares DNA- and expression-based models for predicting cancer cell viability and finds expression models are more accurate and interpretable.

Multiplexed single-cell profiling of post-perturbation transcriptional responses to define cancer vulnerabilities and therapeutic mechanism of action

The paper introduces MIX-Seq, a method for multiplexed single-cell transcriptional profiling of cancer cell responses to perturbations, revealing drug mechanisms and predicting cell viability.

Non-oncology drugs are a source of previously unappreciated anti-cancer activity

The paper identifies non-oncology drugs with anti-cancer activity across 578 cancer cell lines using PRISM, finding that many drugs selectively inhibit cancer cells based on molecular features.

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency datasets

This study compares two large pan-cancer CRISPR-Cas9 screens, finding high concordance in gene dependencies despite differences in protocols and reagents.

WRN Helicase is a Synthetic Lethal Target in Microsatellite Unstable Cancers

The paper identifies WRN helicase as a synthetic lethal target in microsatellite unstable cancers through CRISPR/Cas9 and RNAi screens, showing its essentiality in MSI cell lines.