Bert De Rybel

Navigating the rapidly evolving landscape of sequencing-based spatial transcriptomics technologies: a comprehensive multi-platform benchmark

This study benchmarks multiple sequencing-based spatial transcriptomics platforms across tissue types and preservation methods to evaluate their performance and establish standardized metrics for future research.

Decoding stage-specific symbiotic programs in the Rhizophagus irregularis-tomato interaction using single-nucleus transcriptomics

This study uses single-nucleus transcriptomics to identify stage-specific transcriptional programs in tomato roots colonized by Rhizophagus irregularis, revealing key regulatory factors and cellular responses during arbuscular mycorrhizal symbiosis.

Cytosolic GLUCOSE-6-PHOSPHATE DEHYDROGENASE 5 is a key player in redox homeostasis during oxidative stress and in oxidative stress-triggered activation of the salicylic acid pathway

This study identifies cytosolic G6PD5 as essential for redox homeostasis and oxidative stress-triggered salicylic acid signaling in Arabidopsis.

A Myb-dominated gene regulatory network universally controls sexual cell fate transitions in diatoms

The paper identifies a Myb-dominated gene regulatory network that controls sexual cell fate transitions in diatoms, revealing its role in size expansion and ploidy transitions.

An AINTEGUMENTA phospho-switch controls bilateral stem cell activity during secondary growth

This paper identifies a phosphorylation mechanism controlled by the ERECTA receptor and auxin signaling that regulates stem cell activity and vascular cell differentiation in plants.

Conserved transcriptional reprogramming in nematode infected root cells

The paper identifies conserved transcriptional reprogramming in nematode-infected root cells across Arabidopsis and rice, revealing a key regulator involved in nematode resistance.

Secretory carrier membrane proteins regulate aquaporin trafficking in Arabidopsis.

This study identifies SCAMP proteins as regulators of aquaporin abundance in Arabidopsis root cells, showing reduced PIP levels in mutants lead to improved drought response.

Gene regulatory network analysis of somatic embryogenesis identifies morphogenic genes that increase maize transformation frequency

The paper identifies morphogenic genes that enhance maize transformation frequency by analyzing gene regulatory networks in induced somatic embryos.

Unraveling the cis-regulatory code controlling abscisic acid-dependent gene expression in Arabidopsis using deep learning

The paper uses deep learning to predict ABA-responsive gene regulation in Arabidopsis by analyzing promoter sequences and identifies motifs beyond canonical ABF binding sites.

The dynamic and diverse nature of parenchyma cells in the Arabidopsis root during secondary growth

The study identifies 20 cell types in Arabidopsis root secondary growth using single-cell RNA sequencing and lineage tracing, revealing dynamic parenchyma cell diversity and functional roles.

Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics

The paper uses single-cell RNA sequencing to reveal dual drought response mechanisms in Arabidopsis leaf mesophyll cells.

Scywalker: scalable end-to-end data analysis workflow for nanopore single-cell transcriptome sequencing

Scywalker provides a scalable analysis pipeline for nanopore single-cell transcriptome data, showing good correlation with short-read analyses and enabling isoform-level cell-type-specific expression identification.

bHLH heterodimer complex variations shape meristems in Arabidopsis thaliana by affecting target gene specificity

The paper shows that variations in bHLH heterodimer complexes regulate cell proliferation in different plant meristems by affecting target gene specificity.

RCD1 Coordinates Chloroplastic and Mitochondrial Electron Transfer through Interaction with ANAC Transcription Factors

The paper shows RCD1 interacts with ANAC transcription factors to regulate chloroplastic and mitochondrial retrograde signaling via ROS-dependent mechanisms.

IQD proteins integrate auxin and calcium signaling to regulate microtubule dynamics during Arabidopsis development

This study shows IQD proteins integrate auxin and calcium signaling to control microtubule dynamics and cell shape in Arabidopsis.

OsIQD14 regulates rice grain shape through modulating the microtubule cytoskeleton

This study identifies OsIQD14 as a regulator of rice grain shape by modulating microtubule cytoskeleton organization through interactions with SPIRAL2 and calmodulin proteins.