A. Tsherniak

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.

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.

Pan-cancer single cell RNA-seq uncovers recurring programs of cellular heterogeneity

The paper uses single-cell RNA-seq to analyze cancer cell lines and identifies recurring expression programs of heterogeneity that mirror those in tumors, suggesting intrinsic plasticity contributes to intra-tumoral diversity.

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.

Extracting Biological Insights from the Project Achilles Genome-Scale CRISPR Screens in Cancer Cell Lines

The paper describes updates to the Project Achilles processing pipeline for CRISPR screens in cancer cell lines, including quality control improvements and dependency score calculations.

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.

Inhibition of mitochondrial ferredoxin 1 (FDX1) prevents adaptation to proteotoxic stress

This study identifies FDX1 inhibition as a strategy to prevent proteasome inhibitor resistance in cancer by targeting mitochondrial Fe-S cluster biosynthesis.