Cédric Chauve

The paper introduces PlasBin-HMF, a method for plasmid binning from short-read assemblies, which outperforms existing methods by preserving explainability.

HyPlAs improves plasmid assembly from hybrid sequencing data by classifying short-read contigs as chromosomal or plasmidic, outperforming Plassembler on bacterial samples.

Pangebin improves plasmid binning in bacterial isolates by using pangenome-assembly graphs to enhance accuracy across different assemblers.

PlasEval evaluates plasmid binning tools by comparing their results to ground truth or other methods using a dissimilarity measure.

TKSM simulates transcriptomic long-read sequencing data by modularly combining steps, enabling customizable and scalable benchmarking of sequencing tools.

Freddie detects and discovers transcriptomic alternative splicing isoforms without relying on existing annotations, outperforming other tools in recall and identifying a novel Androgen Receptor isoform in prostate cancer.

scTagger matches cellular barcodes from long- and short-reads in single-cell RNA-seq experiments, showing improved accuracy and speed over existing methods.

plASgraph uses graph neural networks to detect plasmid contigs in genome assemblies, outperforming existing methods by leveraging assembly graph information.

The paper introduces a method to identify driver cell populations in flow cytometry data using a new score called SpecEnr and provides an R package for implementation.

This study uses machine learning on whole-genome sequencing data from multiple geographic regions to predict drug resistance in Mycobacterium tuberculosis, finding that performance varies across datasets due to geographical heterogeneity.

HASLR is a hybrid assembler that combines second and third generation sequencing reads to generate fast and accurate genome assemblies, outperforming other assemblers in speed and misassembly count.

The paper improves Anopheles genome assemblies using comparative genomics methods and experimental data, resulting in more contiguous and chromosomally anchored assemblies.

This paper demonstrates that the number of designable RNA secondary structures decreases exponentially with size, due to undesignable motifs.

A decentralized open-source web platform lets public health labs run outbreak sequencing pipelines on local compute, keeping data under their own governance while still exchanging results between instances.

MentaLiST is a fast and accurate MLST caller designed for large MLST schemes, outperforming existing tools in speed while maintaining or improving accuracy.

The paper improves the assembly of two ancient Yersinia pestis genomes using an optimization-based gap-filling method, resulting in highly supported assemblies with 95% ancient read coverage.