Cédric Notredame

FAMSA2 provides high-accuracy multiple sequence alignments for large-scale protein datasets with significantly improved speed.

This paper discusses the adoption of Nextflow and nf-core frameworks to standardize bioinformatics pipelines, improving collaboration and interoperability across research communities.

The paper presents an nf-core framework for comparing multiple sequence aligners, aiming to streamline deployment and evaluation of MSA tools in HPC environments.

The paper identifies RNA-initiating sites at STRs and links them to gene expression, revealing regulatory roles and interactions with Alu repeats.

The paper introduces EuPRI, a resource of RNA motifs for 34,736 RBPs across 690 eukaryotes, expanding motif knowledge and enabling functional and evolutionary insights.

This study uses multi-omics analysis to show that aneuploidy in Leishmania causes proportional changes in transcript and protein abundance, with post-transcriptional regulation compensating for some effects.

This study shows that AlphaFold2 improves sequence alignments even when structural models are not highly accurate, outperforming sequence-based alignments.

This paper provides a guide for applying compositional data analysis to NGS count data, emphasizing log-ratio transformations and addressing limitations of conventional normalization methods.

The paper introduces a regressive alignment algorithm that starts with the most dissimilar sequences, producing more accurate alignments for large datasets.

This paper introduces a normalization-free method for detecting differential gene expression by analyzing changes in gene ratio proportionality between sample groups.

This paper describes OpenEBench, a continuous automated benchmarking system for bioinformatics methods, tools, and web services to improve reproducibility and interoperability.