Manuel D. Leonetti

The paper introduces ecCLIP for high-resolution RBP binding maps and Pythia for structure-aware RNA-protein interaction modeling, improving RNA half-life prediction and variant effect assessment.

The paper presents a multimodal perturbation atlas using CRISPR knockouts in A549 cells, combining microscopy, phase imaging, and scRNA-seq to assess phenotypic resolution.

The paper uses single-cell spatial proteomics to show that metabolic enzyme expression and localization vary between cells, revealing autonomous metabolic heterogeneity.

The paper introduces an open-source automated cell culture system that improves efficiency and precision in microplate passaging by integrating imaging-based cell counting.

The paper maps subcellular localization of human proteins and shows proteome remodeling during viral infection by combining organelle immuno-capture with mass spectrometry.

The paper introduces Mantis, a high-throughput 4D microscope, and shrimPy, software for analyzing 4D data, to study cellular dynamics and responses to perturbations like viral infection.

protoSpaceJAM automates and optimizes CRISPR/Cas9 gRNA and HDR donor design, improving knock-in efficiency through recoding mutations and customizable parameters.

The paper develops robust virtual staining methods for cellular landmarks using deep learning, showing improved performance across cell types and imaging conditions.

This study uses Perturb-seq to functionally interrogate SARS-CoV-2 host factors in human lung epithelial cells, identifying key factors that influence infection and host response.

The paper introduces split-wrmScarlet and split-sfGFP tools for faster fluorescent labeling of endogenous C. elegans proteins using CRISPR.

Long single-stranded DNA donors enable gene-sized CRISPR knock-in in human cells, though an author update notes subsequent long-read sequencing revealed high imprecise integration rates for both donor types.

Long-read sequencing with the knock-knock pipeline profiles CRISPR knock-in repair, finding perfect homology-directed repair is often a minority of integration events and mis-integration varies by context.

This paper develops a non-viral CRISPR-Cas9 system for precise genome editing in human T cells, enabling therapeutic reprogramming of cell function and specificity.