Traver Hart

Functional modules predict genetic interactions, revealing evolutionary conservation and rewiring

The paper identifies human gene modules enriched for genetic interactions using a combinatorial knockout platform and validates their conservation and rewiring across cancer cell lines.

Combinatorial CRISPR/Cas12a excises targeted loci in the mammalian genome at very low efficiency

This study evaluates combinatorial CRISPR/Cas12a for locus excision in mammalian cells and finds low efficiency despite targeting intronic regions.

Mapping the genetic landscape of the DNA damage response with Cas12a-based combinatorial knockout screens

This study uses Cas12a-based knockout screens to identify genetic interactions in the DNA damage response, revealing synthetic lethal and buffering interactions with therapeutic implications.

Double-CRISPR Knockout Simulation (DKOsim): A Monte-Carlo Randomization System to Model Cell Growth Behavior and Infer the Optimal Library Design for Growth-Based Double Knockout Screens

DKOsim generates synthetic double knockout CRISPR data to simulate genetic interactions and optimize library design for growth-based screens.

Analysis of Combinatorial Knockout CRISPR screens with GRAPE: Genetic interaction Regression Analysis of Pairwise Effects

GRAPE identifies genetic interactions from combinatorial CRISPR screens with higher precision and recall than existing methods, revealing additional high-confidence interactions in published datasets.

Integrated Metabolic Complex Genetic Interaction Network of Chromosome 4p Loss in Basal Breast Cancer

This study maps the metabolic complex genetic interaction network of chromosome 4p loss in basal breast cancer to identify targetable vulnerabilities.

Therapeutic modulation of ROCK overcomes metabolic adaptation of cancer cells to OXPHOS inhibition and drives synergistic anti-tumor activity

This study identifies ROCK inhibition as a strategy to overcome metabolic adaptation in cancer cells to OXPHOS inhibition, showing synergistic anti-tumor effects.

Optimal methods for analyzing targeted pairwise knockout screens

The paper compares methods for identifying synthetic lethal interactions from CRISPR screens and finds ZdLFC provides more consistent results across cell lines.

Recovering false negatives in CRISPR fitness screens with JLOE

The paper shows CRISPR screens have a 20% false negative rate and introduces JLOE to recover false negatives without increasing false discoveries.

Efficient gene knockout and genetic interactions: the IN4MER CRISPR/Cas12a multiplex knockout platform

The paper introduces the in4mer CRISPR/Cas12a platform for efficient multiplex gene knockout, demonstrating improved sensitivity and reduced clone numbers compared to CRISPR/Cas9.

Optimal construction of a functional interaction network from pooled library CRISPR fitness screens

This study identifies optimal methods for constructing functional interaction networks from CRISPR knockout screens by evaluating scoring schemes and normalization techniques.

PICKLES v3: the updated database of pooled in vitro CRISPR knockout library essentiality screens

PICKLES v3 provides an updated database of CRISPR knockout screens in human cell lines, enabling exploration of gene fitness across multiple libraries and cell lines.

Dynamic rewiring of biological activity across genotype and lineage revealed by context-dependent functional interactions

The paper identifies context-dependent functional interactions from CRISPR screens, revealing how genotype and lineage influence gene coessentiality and pathway rewiring.

Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier

The paper introduces BAGEL2, an improved CRISPR fitness screen analysis tool that reduces off-target effects and enhances detection of tumor suppressor genes.

Multiplex enCas12a screens show functional buffering by paralogs is systematically absent from genome-wide CRISPR/Cas9 knockout screens

The paper shows that paralog buffering limits detection of synthetic lethal interactions in CRISPR screens, revealing many under-detected genetic dependencies.

Discovery of novel putative tumor suppressors from CRISPR screens reveals rewired lipid metabolism in AML cells

The paper identifies novel tumor suppressors from CRISPR screens and reveals rewired lipid metabolism in AML cells through functional analysis of gene modules.

Biases and Blind-Spots in Genome-Wide CRISPR Knockout Screens

This study identifies significant false negatives and blind spots in CRISPR knockout screens, showing that many genes are functionally buffered and never detected as essential.

A consensus set of genetic vulnerabilities to ATR inhibition

The paper identifies a consensus set of 117 genes that promote survival when ATR kinase activity is suppressed, validated through CRISPR/Cas9 screens and including previously unknown modulators of ATR inhibitor response.

Multiplexed pooled library screening with Cpf1

The paper develops a multiplexed CRISPR/Cas9-based screening strategy using AsCpf1 to create a smaller, more efficient genome-wide knockout library.

Hierarchical organization of the human cell from a cancer coessentiality network

The paper constructs a coessentiality network from CRISPR knockout screens to infer gene function and reveal hierarchical cell organization.

Identifying chemogenetic interactions from CRISPR knockout screens with drugZ

drugZ identifies chemogenetic interactions from CRISPR screens, finding more homologous recombination repair pathway genes and confirming KEAP1 loss as a resistance factor for ERK inhibitors.

The functional genomic circuitry of human glioblastoma stem cells

This study uses CRISPR-Cas9 screens in patient-derived glioblastoma stem cells to identify essential genes and pathways for stemness and drug resistance, revealing new therapeutic targets.

Coessentiality And Cofunctionality: A Network Approach To Learning Genetic Vulnerabilities From Cancer Cell Line Fitness Screens

The paper develops a network approach to identify genetic vulnerabilities in cancer cell lines by analyzing shRNA screens and clustering coessential genes to discover context-specific essential genes and biomarkers.

Evaluation and Design of Genome-wide CRISPR/Cas9 Knockout Screens

The paper evaluates CRISPR/Cas9 knockout screens in human cell lines and designs an optimized gRNA library to improve gene knockout efficiency and accuracy.

BAGEL: A computational framework for identifying essential genes from pooled library screens.

BAGEL identifies essential genes from pooled CRISPR screens with high sensitivity and specificity, improving upon existing methods by 10-fold in runtime and accuracy.

A CRISPR screen reveals a WNT7B-FZD5 signaling circuit as a therapeutic opportunity in pancreatic cancer.

The paper identifies a WNT7B-FZD5 signaling circuit as a therapeutic target in pancreatic cancer using CRISPR screening and validates it with antibodies.

Systematic discovery and classification of human cell line essential genes

This study identifies and classifies human cell line essential genes using an optimized CRISPR-Cas9 screen, finding twice to thrice as many essential genes as previous RNAi studies.

Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

This paper develops a Bayesian classifier to improve gene essentiality analysis in genomic perturbation screens and shows CRISPR is more sensitive than RNAi with manageable false discovery rates.