Peter C. DeWeirdt

DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems

DefensePredictor combines ESM2 protein language model embeddings with genomic context features in a gradient boosting classifier to identify prokaryotic anti-phage defense genes, validating 45 previously unknown Escherichia coli systems.

A membrane-bound nuclease directly cleaves phage DNA during genome injection

This study identifies SNIPE as a bacterial membrane-bound nuclease that directly cleaves phage DNA during genome injection, providing a novel mechanism for distinguishing self from non-self.

Benchmarking of SpCas9 variants enables deeper base editor screens of BRCA1 and BCL2

The paper benchmarks SpCas9 variants to improve base editor screens for BRCA1 and BCL2, identifying new insights into their genetic variants.

Massively parallel assessment of human variants with base editor screens

This paper uses CRISPR-Cas9 base editors in pooled screens to assess the functional impact of human variants, identifying loss-of-function mutations and drug sensitivity/resistance mutations.

Optimization of AsCas12a for combinatorial genetic screens in human cells

This paper optimizes AsCas12a for combinatorial genetic screens in human cells by improving on-target and off-target activity and enabling higher-order multiplexing.

Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection

A genome-wide CRISPR screen with SARS-CoV-2 recovers ACE2 and Cathepsin L and nominates SWI/SNF, TGF-beta signalling and HMGB1 as pro-viral; pathway inhibitors blocked virus-induced death.

Genetic screens in isogenic mammalian cell lines without single cell cloning

The paper presents a method to generate isogenic cell pairs and screen them with CRISPR-Cas9 libraries to identify genetic interactions, demonstrating applications for BCL2L1, MCL1, and PARP1.