Dominique D. Lavenier

SNooPy is a statistical framework for long-read metagenomic variant calling that outperforms existing methods and is available on GitHub.

The paper introduces a de Bruijn graph partitioning method for DNA storage processing, achieving high precision and recall on synthetic and real datasets with efficient scalability.

Alice is a fast, memory-efficient long-read assembler that enables strain-resolved metagenomic analysis of large datasets with significant speed and resource improvements over existing methods.

The paper analyzes olfactory and gustatory receptor genes and transposable elements in aphid genomes to understand their evolutionary dynamics and role in host adaptation.

HairSplitter recovers more viral and bacterial strains from noisy long reads than existing tools, while being faster.

The paper describes an in vitro method to construct a 24 kb long artificial DNA sequence encoding the Universal Declaration of the Rights of Man and of the Citizen using Golden Gate assembly and long-read sequencing analysis.

The paper introduces a PIM architecture to accelerate variant calling by reducing data movement and energy consumption, achieving significant speed-up and cost savings compared to software, FPGA, and GPU solutions.

SVJedi genotypes known structural variants from long read sequencing data with high accuracy, outperforming existing methods for long reads.

The paper introduces a global optimization method for genome assembly that simultaneously solves scaffolding, gap-filling, and scaffold extension, and tests it on chloroplast genomes.

The paper benchmarks computational metagenomics software using complex datasets, showing strengths and limitations in assembly, binning, and taxonomic profiling.