José Tomás Matus

SlMYB21 and SlMYB24 cooperatively regulate petal coloration and movement in Solanum lycopersicum

This study identifies SlMYB21 and SlMYB24 as cooperative regulators of petal coloration and movement in tomato by modulating carotenoid biosynthesis, ABA levels, and water transport.

SlEIL3-1 associates with a conserved EIL3/SLIM1 sulfate deficiency response core in tomato

The paper identifies SlEIL3-1 as a key regulator of sulfate deficiency response in tomato, showing its conserved function across species and its role in regulating S-related genes.

Hydroxylated monoterpenes mimic bacterial attack to trigger jasmonate-dependent self-amplifying immunity in tomato

This study shows hydroxylated monoterpenes (HMTPs) mimic bacterial attack, triggering jasmonate-dependent immunity in tomato through self-amplifying signaling loops.

MYB28 and MYB29 transcription factors regulate iron homeostasis and iron-mobilizing coumarin biosynthesis in Arabidopsis thaliana

This study identifies MYB28 and MYB29 as regulators of iron homeostasis and coumarin biosynthesis in Arabidopsis under iron deficiency.

AEGIS: an annotation extraction and genomic integration resource

AEGIS standardizes and validates genome annotation files, enabling reliable downstream analysis through error correction and comparative genomics tools.

Biosynthesis of oxyresveratrol in mulberry (Morus alba L.) is mediated by a group of p-coumaroyl-CoA 2'-hydroxylases acting upstream of stilbene synthases

The paper identifies and validates p-coumaroyl-CoA 2'-hydroxylases as key enzymes in oxyresveratrol biosynthesis in mulberry, using genomic, transcriptomic, and functional approaches.

Consistent drought regulation in grapevine is driven by directional transcription factor activity

This study identifies a core set of drought-responsive genes and their regulatory network in grapevine, revealing key transcription factors involved in drought tolerance.

Organ-level Gene Regulatory Network models enable the identification of central transcription factors in Solanum lycopersicum

The paper constructs organ-level gene regulatory networks in tomato using RNA-seq data and validates them with DAP-seq, identifying key and novel transcription factors involved in fruit ripening and ABA response.

Developing the Grapevine Hydric Stress Atlas: A Meta-Analysis Resource for Exploring transcriptome Responses to Drought

The paper constructs a grapevine drought stress transcriptome atlas using meta-analysis of 1107 datasets, enabling exploration of gene expression and co-expression networks related to drought tolerance.

A Grapevine MYC2-MYB24 Regulatory Module Activates Terpenoid Biosynthesis Upon Methyl Jasmonate Elicitation

The paper identifies a MYC2-MYB24 regulatory module that activates terpenoid biosynthesis in grapevines in response to methyl jasmonate.

The Plantae Visualization Platform: a comprehensive web-based tool for the integration, visualization, and analysis of omic data across plant and related species

The paper introduces PlantaeViz, a web-based platform for integrating, visualizing, and analyzing multi-omics data across plant species, with a focus on transcriptomics and functional annotations.

First large-scale peach gene coexpression network: A new tool for predicting gene function

The paper constructs the first large-scale gene coexpression network for peach and validates its ability to predict gene function related to fruit softening.

NAC61 regulates late- and post-ripening associated processes in grapes involving a NAC60-dependent regulatory network

The paper identifies NAC61 as a key regulator of late- and post-ripening processes in grapevines, showing its role in stress responses and interacting with NAC60 in a regulatory network.

An improved reference of the grapevine genome supports reasserting the origin of the PN40024 highly-homozygous genotype

The paper improves the grapevine genome reference PN40024.v4 using long-read sequencing, enhancing continuity, haplotype resolution, and gene annotation.