Anna-Sophie Fiston-Lavier

GBZ-base and GAF-base: Indexed pangenome file formats

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

Pangenome discovery of missing autism variants

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

A scalable architecture for tuning multistate differentiation ratios in synthetic microbial consortia

This paper introduces a synthetic biology framework that enables tunable differentiation ratios in microbial consortia, validated in a mouse tumor model.

Role of aridity in shaping adaptive genomic divergence and population connectivity in a Southern African rodent

This study uses genomic data from a Southern African rodent to show how aridity influences genetic divergence and population connectivity, with genes related to water conservation and neurotransmission identified.

Manual versus automatic annotation of transposable elements: case studies in Drosophila melanogaster and Aedes albopictus, balancing accuracy and biological relevance

This study compares manual and automated methods for transposable element annotation in Drosophila melanogaster and Aedes albopictus, finding that automated methods identify more TEs but manual curation provides more detailed classifications.

Structural variation turnovers and defective genomes: key drivers for the in vitro evolution of the large double-stranded DNA koi herpesvirus (KHV)

This study investigates structural variation (SV) diversity and dynamics in CyHV-3 genome during serial passages, finding SV turnovers and defective genomes drive in vitro evolution.

TrEMOLO: Accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches

TrEMOLO estimates transposable element allele frequencies using long-read sequencing data by combining assembly and mapping approaches, outperforming existing tools in benchmark tests.

RF4Del: A Random Forest approach for accurate deletion detection

RF4Del is a random forest method for accurate deletion detection that outperforms existing tools and is robust to sequencing coverage and deletion size variations.

BREC: An R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes

BREC identifies heterochromatin boundaries and estimates local recombination rates using statistical methods, validated on Drosophila melanogaster data.

PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets

PlasForest detects plasmids in unassembled bacterial genomes with high accuracy and outperforms existing tools.

Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia

The paper introduces a machine learning method to detect somatic L1 insertions in human brain tissue, revealing their widespread distribution in neurons and glia and potential role in neuropsychiatric diseases.

T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data