Jean‐François Flot

This study shows that light availability significantly affects the morphology of Montipora capitata corals, demonstrating high phenotypic plasticity without changes in symbiont communities.

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

This study introduces a novel Core-Gene Consensus Delimitation (CGCD) method to define species in Acinetobacter baumannii, identifying 11 distinct groups supported by genomic and phylogenetic analyses.

The paper presents mitogenome sequences of Niphargus amphipods using nanopore sequencing combined with Illumina polishing, achieving high accuracy and resolving phylogenetic relationships.

This study uses DIA proteomics to analyze how Hawaiian rice coral Montipora capitata and its symbionts respond to decreased light intensity, identifying changes in protein abundance linked to metabolic and structural adaptations.

This study shows that shading corals does not reduce their thermal tolerance during heat stress under low light, but makes them less resistant to light stress and heat stress under high light.

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.

This study refines the Feulgen protocol to provide accurate and low-cost genome size measurements using ethanol-preserved samples, validated against sequencing data.

The paper identifies new enzymatic activities of GroEL/Hsp60 proteins, including thioesterase and esterase functions, and links these to palmitoylation and antibiotic resistance in M. tuberculosis.

The paper shows that clitellates experienced a burst of genomic rearrangements leading to loss of macrosynteny with marine annelids and new chromosomal interactions.

The paper introduces a rapid, inexpensive, single-tube two-step PCR protocol for DNA barcoding and metabarcoding that improves PCR product yield compared to a one-step protocol.

The paper presents the first chromosome-level genome assembly of Flaccisagitta enflata, providing a resource for comparative genomic studies in Chaetognatha and Gnathifera.

This study compares the genome of the temperate coral Astrangia poculata with the tropical coral Acropora millepora to identify gene family expansions related to winter quiescence, innate immunity, and sexual reproduction.

The paper identifies and characterizes a diverse family of allorecognition receptors in Botryllus schlosseri, revealing their genetic complexity and conserved signaling mechanisms.

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

The paper describes the European Reference Genome Atlas (ERGA) pilot project, which tests a decentralized model for producing high-quality reference genomes across 98 European species.

The paper demonstrates the use of Haxe for rewriting a bioinformatics tool, SeqPHASE, to improve security and maintainability.

The paper presents the first chromosome-level genome assembly of Botryllus schlosseri using long and short reads scaffolded by Hi-C, providing a valuable resource for studying tunicate biology.

The paper presents chromosome-level genome assemblies for two hybridogenetic lineages of Cataglyphis hispanica using long-read sequencing and 3C data, enabling studies of thermal adaptation and reproductive systems.

The paper presents a chromosome-level genome assembly for the European flat oyster, providing insights into its genetics and potential for aquaculture improvement.

The paper evaluates long-read assemblers and post-processing tools for haplotype collapsing in non-model organisms, finding methods that improve haploid assembly quality.

GraphUnzip phases assembly graphs into haplotypes using long reads and Hi-C, producing high-quality, gap-less supercontigs across simulated and real datasets.

The paper introduces Bcool, a short-read correction method using compacted de Bruijn graphs, achieving higher accuracy and scalability than existing k-mer-based approaches.

This study compares the genomes of two coral species, Stylophora pistillata and Acropora digitifera, revealing significant differences in gene expansion and function related to symbiosis and stress response.

The paper analyzes the house spider genome to identify an ancient whole-genome duplication shared by spiders and scorpions, distinct from horseshoe crab duplications.