Vincent Lacroix

Extended t-cores for the de novo identification of transposable elements and other inexact repeats from short read RNAseq data

This paper introduces a de novo method to identify transposable elements and inexact repeats from RNA-seq data without a reference genome, showing effectiveness in both model and non-model species.

Metabolic resistance of the tiger mosquito to pyrethroid insecticides in La Reunion Island likely results from local adaptation

This study identifies genetic mechanisms of pyrethroid resistance in La Reunion Island tiger mosquitoes, showing it results from local adaptation through detoxification gene over-expression and a large inverted superlocus.

Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues

This study uses long-read RNA-seq to identify and quantify transposable element transcripts at the copy level in Drosophila germline tissues, revealing differences in their transcriptional landscape between testes and ovaries.

Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

The paper compares nanopore RNA-Seq and cDNA-Seq for transcriptome profiling in mouse brain and liver, finding that nanopore RNA-Seq is more efficient but cDNA-Seq introduces bias due to read truncation.

A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between kmers and genetic events

DBGWAS is a fast, alignment-free method for bacterial GWAS that identifies interpretable genetic variants associated with phenotypes by analyzing kmer-based subgraphs.

Representing Genetic Determinants in BacterialGWAS with Compacted De Bruijn Graphs

This paper introduces an alignment-free GWAS method using compacted De Bruijn graphs to detect variable-length haplotypes associated with antimicrobial resistance in bacterial genomes.

Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data

This study compares mapping-first and assembly-first approaches for annotating and differentially analyzing alternative splicing from RNAseq data, showing complementary strengths and advocating their combined use.

De novo identification, differential analysis and functional annotation of SNPs from RNA-seq data in non-model species

The paper introduces a reference-free method to identify, quantify, and annotate SNPs from RNA-seq data in non-model species, showing comparable accuracy to reference-based methods.