Carlos Pulido-Quetglas

TRACEY updates SNARE protein domain annotation with improved HMMs and expanded sequence coverage, improving domain detection across species.

The paper analyzes SNARE transmembrane domains to show how their composition adapts to different membrane environments, with early pathway SNAREs having more Phe and late pathway SNAREs having more Ile.

The paper identifies TPL1 as a novel long noncoding RNA that drives triple-negative breast cancer hallmarks through multiple molecular mechanisms.

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

The paper identifies 60 high-confidence oncogenic lncRNAs in NSCLC using CRISPR deletion screens and ASO validation, revealing therapeutic vulnerabilities.

The paper introduces a paired-guide RNA CRISPR-Cas9 system to identify protein-coding and lncRNA genes involved in human B-cell to macrophage transdifferentiation, identifying 26 potential novel genes.

This paper shows that temporarily inhibiting DNA-PK increases CRISPR-Cas9 deletion efficiency by delaying NHEJ, improving experimental outcomes across multiple cell lines and guide RNAs.

CRISPETa is a scalable bioinformatic pipeline for designing paired CRISPR guide RNAs for genomic deletion, achieving ≥50% deletion efficiency in tested cases.