Dimitri Perrin

CRISPR-DA: Adapting CRISPR gRNA design for detection assays

CRISPR-DA improves gRNA specificity assessment for CRISPR-based detection assays, outperforming BLAST in detecting cross-species off-targets and running faster.

Leveraging uncertainty quantification to optimise CRISPR guide RNA selection

The paper uses a deep ensemble approach to improve CRISPR guide RNA selection by incorporating uncertainty quantification, achieving over 91% precision in guide identification for most mouse genes.

Crackling Cloud: an event-driven, cloud-based CRISPR-Cas9 guide RNA design tool

Crackling Cloud is a cloud-based tool for designing CRISPR-Cas9 guide RNAs, offering scalability and accessibility without requiring local high-performance computing resources.

Evaluation and optimization of sequence-based gene regulatory deep learning models

The paper evaluates and optimizes sequence-based gene regulatory deep learning models using a DREAM Challenge dataset, showing improvements through architectural and training strategy refinements.

Fast and scalable off-target assessment for CRISPR guide RNAs using partial matches

This paper introduces Crackling++, a faster and scalable method for off-target assessment of CRISPR guide RNAs by using non-contiguous exact matches, outperforming existing tools.

Haplotype-phased common marmoset embryonic stem cells for genome editing using CRISPR/Cas9

This study provides haplotype-resolved genome characterization of a marmoset ESC line and demonstrates CRISPR/Cas9 targeting and neuronal differentiation capabilities.

Faster and better CRISPR guide RNA design with the Crackling method

Crackling improves CRISPR guide RNA design by combining scoring methods and using ISSL for faster off-target scoring, outperforming existing tools on 12 genomes.

A benchmark of computational CRISPR-Cas9 guide design methods

This paper benchmarks 17 CRISPR-Cas9 guide design tools, finding wide variation in performance and efficiency, with only five capable of whole-genome analysis within reasonable time and resource limits.

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

The paper provides a comprehensive whole-genome analysis of K562, identifying genomic structural features and their impact on functional genomics data.

Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

This paper provides a haplotype-resolved genome analysis of the HepG2 cell line, identifying genomic features and allele-specific regulation to support functional genomics studies.