Jonas Koeppel

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.

The paper shows that human centromeres and neocentromeres evolve epigenetically, with instability linked to loss of heterochromatin boundaries and CENP-A overexpression.

This paper introduces Shred-seq, a method to scan large-scale deletions in the human genome, revealing essential regions including noncoding sequences and establishing a lower bound for viability.

This paper develops a pooled paired prime editing screen to generate large-scale deletions across the genome, identifying non-coding regions with fitness effects and demonstrating the feasibility of genome-wide deletion perturbation.

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.

This paper develops a CRISPR-based method to generate large-scale structural genomic rearrangements in human cells, revealing selection pressures and gene expression impacts of these changes.

The paper uses enhancer scrambling to study a super-enhancer of the OTX2 gene, finding that a single DNase I hypersensitive site predominantly controls its expression.

The paper identifies misexpression of inactive genes in whole blood and links it to nearby rare structural variants using RNA and genome sequencing data.

This paper identifies position-specific sequence determinants of base editing efficiency and develops a machine learning model to predict editing outcomes for adenine and cytosine editors.

The paper predicts insertion efficiency of short sequences into the genome using prime editing by analyzing sequence features and developing a machine learning model.