Jaime Huerta‐Cepas

This study shows that cholinergic and monoaminergic signaling originated before Bilateria, using a combination of metabolomics, phylogenetics, and single-cell analysis.

KEDROS is a web platform that performs phylogenetic profiling across proteomes to identify lineage-specific genes and functional divergence, offering a user-defined workflow for comparative genomics.

The paper surveys global prokaryotic carbon fixation pathways, revealing an oxygen-tolerant rTCA cycle in surface ocean Campylobacterota lineages.

This paper presents a coupled strategy for enzyme discovery, evolution, and yeast chassis adaptation to improve microbial biopolymer valorisation, demonstrating it with laccases for lignin depolymerisation.

This study shows Penicillium melinii promotes root growth and plant biomass across species and environments, enhancing yield in tomato field trials through auxin signaling and subtle molecular interactions.

The paper catalogs diazotroph genomes and analyzes their distribution across environments, identifying freshwater and sedimentary ecosystems as key nitrogen-fixation reservoirs.

This study investigates diazotrophy in the diatom Epithemia adnata by analyzing diazoplast genome and proteomic data under different nitrogen conditions, revealing host-symbiont metabolic integration and regulatory mechanisms.

deluxpore is a Nextflow pipeline that demultiplexes Illumina dual-indexed Nanopore libraries using BLAST and Levenshtein distance, achieving high accuracy in hybrid capture-long-read sequencing.

TreeProfiler profiles biological traits along gene and species trees, enabling analysis of functional diversification and species abundance across biomes.

The paper develops a target capture sequencing method to detect low-abundance chemoreceptor genes in diverse environments, revealing novel microbial chemosensory biodiversity.

This study compares gene clustering criteria in prokaryotic pangenomes, showing that clustering methods significantly affect functional characterization and core genome inference, with methodological inconsistencies often exceeding ecological and phylogenetic effects.

The paper analyzes RNA degradation in microbiome samples to study ribosome dynamics and species-specific responses to stress and drugs.

The paper identifies 18 cell types in sponges, including neuroid cells with synaptic gene expression, suggesting early neuro-immune system evolution.

Rebuilt on eggNOG v5, eggNOG-mapper v2 raises average annotation rate by 608% over v1 and adds Prodigal gene calling, pairwise ortholog reports, and PFAM/SMART domain prediction.

The paper analyzes pan-genomes of 155 prokaryotic species to assess how environmental and phylogenetic factors influence strain diversity and pan-genome features.

NG-meta-profiler is a fast metagenome profiler using NGLess, offering reproducibility and customization over existing tools.