Marie‐France Sagot

BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data.

BrumiR is a toolkit for de novo discovery of microRNAs from sRNA-seq data, achieving high recall and efficiency without a reference genome.

The transposable element-rich genome of the cereal pest Sitophilus oryzae

The paper presents the genome of Sitophilus oryzae, revealing high transposable element content and host-symbiont metabolic interactions.

MOMO - Multi-Objective Metabolic mixed integer Optimization: application to yeast strain engineering

The paper introduces a multi-objective optimization framework for metabolic engineering to identify genetic manipulations that improve bioproductivity in yeast.

Wengan: Efficient and high quality hybrid de novo assembly of human genomes

The paper introduces WO_SCPCAPENGANC_SCPCAP, a hybrid de novo assembler for human genomes that improves contiguity and quality using long and short reads, achieving results better than the current reference genome.

Sparse network-based regularization for the analysis of patientomics high-dimensional survival data

This paper introduces sparse network-based regularization for survival analysis, improving predictive performance and interpretability in breast cancer transcriptomic data.

FAST-SG: An alignment-free algorithm for hybrid assembly

FAST-SG is an alignment-free algorithm for hybrid genome assembly that outperforms short read aligners and enables accurate genome reconstruction with low coverage and resources.

MassBlast: A workflow to accelerate RNA-seq and DNA database analysis

MassBlast accelerates RNA-seq and DNA database analysis by combining BLAST+ with an automated workflow to improve annotation of sequencing databases.