R. Fernandez

CRISPR-Cas9 editing efficiency in fission yeast is not limited by homology search and is improved by combining gap-repair with fluoride selection

Leveraging Natural Language Processing models to decode the dark proteome across the Animal Tree of Life

This paper introduces FANTASIA, a tool using protein language models to annotate functions for thousands of animal proteomes, uncovering previously unknown functions across species.

MATEdb2, a collection of high-quality metazoan proteomes across the Animal Tree of Life to speed up phylogenomic studies

MATEdb2 provides high-quality proteomes for nearly 1000 animal species to enhance phylogenomic research by reducing computational effort and standardizing data formats.

Unveiling the Hidden Viromes Across the Animal Tree of Life: Insights from a Taxonomic Classification Pipeline Applied to Invertebrates of 31 Metazoan Phyla

This study analyzes viromes across 31 invertebrate phyla using RNA-Seq data to estimate virome composition, quantify diversity, and assess host and habitat influences on virome structure.

Fundamental parameters governing the transmission of conjugative plasmids

The paper identifies two key parameters governing plasmid transmission dynamics and shows they are characteristic of the plasmid transfer machinery.

The genome sequence of the Montseny horsehair worm, Gordionus montsenyensis sp. nov., a key resource to investigate Ecdysozoa evolution

The paper presents the chromosome-level genome assembly of a newly described Nematomorpha species, providing genomic resources for studying Ecdysozoa evolution and parasitic lifestyles.

SARS-CoV-2 accessory proteins involvement in inflammatory and profibrotic processes through IL11 signaling

This study identifies SARS-CoV-2 accessory proteins ORF6, ORF8, ORF9b, and ORF9c as contributors to inflammatory and profibrotic responses via IL11 signaling in lung cells.

Highly dynamic evolution of the chemosensory gene repertoire driven by gene gain and expansion across subterranean beetles

This study investigates the evolution of chemosensory genes in subterranean beetles, finding lineage-specific duplications and losses, including IR25a and IR8a, suggesting parallel evolution in underground adaptation.

Parallel duplication and loss of aquaporin-coding genes during the 'out of the sea' transition paved the way for animal terrestrialization

The paper examines aquaporin gene evolution across terrestrial and aquatic species, finding parallel duplications and losses linked to terrestrialization.

PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time

PhenoTrack3D tracks maize organ development over time using 3D+t reconstruction from images, validated on a large dataset with high accuracy.

MATEdb, a data repository of high-quality metazoan transcriptome assemblies to accelerate phylogenomic studies

MATEdb provides a curated database of high-quality transcriptome assemblies from metazoan species to improve phylogenomic studies by standardizing analysis pipelines and reducing computational costs.

High-throughput and automatic structural and developmental root phenotyping on Arabidopsis seedlings

This paper introduces a high-throughput phenotyping method for Arabidopsis root systems, accurately measuring static and dynamic root architecture parameters.

Beyond the foliage: Using non-destructive multimodal 3D imaging and AI to phenotype and diagnose trunk diseases

This paper develops a non-invasive method using 3D imaging and AI to diagnose trunk diseases in grapevines by analyzing inner tissue health.

Acoustic array biochip combined with allele-specific PCR for multiple cancer mutation analysis in tissue and liquid biopsy

This paper presents an AS-PCR/acoustic biosensor method for detecting cancer mutations in tissue and liquid biopsy samples with high sensitivity and cost-effectiveness.

Smelling in the dark: phylogenomic insights on the chemosensory system of a subterranean beetle

This study investigates the chemosensory gene repertoire of a subterranean beetle using phylogenomic analysis, finding reduced diversity in odorant and gustatory genes and expanded odorant-binding proteins.

Local adaptation fuels cryptic speciation in terrestrial annelids

The paper identifies three cryptic species in earthworms using genomic and morphometric analyses, revealing local adaptation and regulatory divergence as key drivers of cryptic speciation.

Genome-informed integrative taxonomic description of three cryptic species in the earthworm genus Carpetania (Oligochaeta, Hormogastridae)

The paper describes three cryptic earthworm species using genomic and morphological data, identifying species-specific SNPs and genetic distances.

Hairless as a novel component of the Notch signaling pathway

The paper investigates the evolutionary origin of Hairless in the Notch pathway, showing that direct co-repressor recruitment is ancestral in protostomes and that Hairless evolved from an ancestral MTA gene through duplication.

Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies

This study uses phylogenomic data to resolve Myriapoda interrelationships, supporting the Dignatha grouping and reconciling morphological and molecular phylogenies.