Jean‐Benoît Lalanne

The paper introduces OPTIMuS PRIME-Del, a CRISPR-based method for multiplexed, precise deletion of cis-regulatory elements, validated through molecular tagging and scRNA-seq analysis.

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

The paper introduces LAMPRAs to measure how cis-regulatory element composition affects gene expression using synthetic loci.

The paper develops STEAM, an evolution-augmented deep learning model, to predict mammalian enhancer landscapes across species using comparative genomics and single-cell data.

The paper presents a barcoded multiplex strategy to screen enhancer AAVs using single-cell RNA sequencing and taxonomy mapping, but finds significant technical and biological noise complicates accurate expression pattern analysis.

The paper systematically perturbs enhancer sequences to study their functional properties and robustness, revealing insights into regulatory sequence space and enhancer activity.

The paper studies the evolutionary changes of mammalian enhancers by analyzing orthologous sequences across multiple species and using deep learning to model functional changes.

The paper identifies active human neural enhancers and CRISPRa gRNAs that upregulate NDD risk genes, providing a resource for cis-regulatory therapy development.

The paper develops monoclonal gastruloids from single mouse embryonic stem cells and uses DNA Typewriter to reveal heritable lineage biases in early development.

The paper develops monoclonal embryoids with genetic barcoding to overcome clonal complexity bottlenecks in mosaic organoid screens, enabling more accurate quantification of genetic perturbation effects.

This paper introduces Genome-Shuffle-seq, a method for generating and mapping structural variants in mammalian genomes, and demonstrates its application in mouse embryonic stem cells.

The paper shows that AAV libraries packaged as pools exhibit extensive chimerism due to length and homology dependence, affecting most genomes.

The paper designs and characterizes diverse genomic parts for precise genome editing and molecular recording in mammalian cells.

The paper describes a CRISPRa screening method combining multiplex perturbations with sc-RNA-seq to identify cell-type-specific regulatory elements and their target genes.

This paper identifies epigenetic features affecting prime editing efficiency and shows how chromatin state can be manipulated to enhance or reduce editing efficiency at specific genomic loci.

This paper introduces prime-SGE, a prime editing framework for assessing drug resistance variants across multiple oncogenes in a single experiment.

The paper identifies endonucleolytic cleavage sites in Bacillus subtilis using transcriptome-wide mapping and deep mutational scanning, revealing distinct sequence determinants for different endoribonucleases.

This paper develops scQers, single-cell quantitative expression reporters, to measure enhancer activity across multicellular systems with high precision and range.