Manuel D. Leonetti

A high-resolution protein-RNA binding atlas for structure-aware interaction prediction and post-transcriptional regulatory modeling

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.

A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology.

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

Dissecting autonomous enzyme variability in single cells

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

Open-source cell culture automation system with integrated cell counting for passaging microplate cultures

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

PROTOSPACEJAM: AN OPEN-SOURCE, CUSTOMIZABLE AND WEB-ACCESSIBLE DESIGN PLATFORM FOR CRISPR/CAS9 INSERTIONAL KNOCK-IN

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

Robust virtual staining of landmark organelles

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

Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq

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.

Split-wrmScarlet and split-sfGFP: Tools for faster, easier fluorescent labeling of endogenous proteins in Caenorhabditis elegans

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

Design and specificity of long ssDNA donors for CRISPR-based knock-in

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.

Deep profiling reveals substantial heterogeneity of integration outcomes in CRISPR knock-in experiments

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.

Reprogramming human T cell function and specificity with non-viral genome targeting

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.