Klaas Vandepoele

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.

The paper creates a single-cell transcriptome atlas of barley root apical meristem, identifying 24 cell populations and showing HvWOX5's role in meristem organization and metaxylem patterning.

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.

MINI-EX version 2 infers cell-type-specific gene regulatory networks in plants using single-cell transcriptomics and TF motif integration, improving accuracy and enabling analysis of non-model species.

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

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

This study shows that modulating SlSAMBA, an APC/C regulator in tomato, affects fruit growth, sugar content, and antioxidant levels.

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 paper integrates maize cis-regulatory element profiling methods to improve the identification of functional CREs and applies them to study drought-specific gene regulatory networks.

This study identifies genes and pathways involved in size-dependent sexual maturation and mating type differentiation in pennate diatoms using transcriptomic analysis of microsurgically manipulated cells.

DiatOmicBase integrates public diatom omics data to connect genes to functional processes, enabling exploratory analysis and experiment design.

The paper presents an improved chromosome-scale genome assembly for Populus tremula and integrates population genetics and genomics data to study leaf physiognomy traits through GWAS and functional analysis.

The paper identifies transit amplifying cells in maize meristems using spatial transcriptomics and shows their growth and differentiation are independently controlled.

MINI-AC infers plant gene regulatory networks using bulk or single-cell accessible chromatin data, outperforming existing methods in identifying TF binding sites and revealing cell-type specific regulators.

The paper shows E2FA and E2FB transcription factors in Arabidopsis differently contribute to the plant response to DNA replication defects, working cooperatively with SOG1.

MINI-EX infers cell-type specific gene regulatory networks in plants using single-cell transcriptomic data and TF motif information, identifying key regulators in root, leaf, and ear development.

TRAPID 2.0 processes de novo transcriptomes to provide taxonomic and functional annotations, enabling gene space analysis and evolutionary studies.

This study profiles the diurnal transcriptome of the benthic diatom Seminavis robusta, revealing rhythmic gene expression patterns and adaptations to its environment.

The paper shows that mitotic interhomolog recombination generates genomic diversity in diatom clonal populations, with recombination rates exceeding 4% per cell division and increasing under stress.

The paper identifies genes responding to sex-inducing pheromones in the diatom Seminavis robusta and links them to sexual reproduction processes.

The paper reports the genome of Seminavis robusta, a benthic diatom, revealing gene family expansions and adaptations related to light and oxygen sensing, and provides insights into genetic diversity and gene function in benthic diatoms.

The paper evaluates motif mapping tools for Arabidopsis, showing that an ensemble approach improves gene regulatory network reconstruction from chromatin data.

This study shows that virus-host coexistence in phytoplankton is maintained through bet hedging, where susceptible and resistant phenotypes switch, allowing continuous growth of both microalga and virus.

TF2Network predicts transcription factor regulators and gene regulatory networks in Arabidopsis using binding site data and co-expressed genes, achieving 75-92% accuracy in validation.

The paper presents an ensemble gene function prediction method for Arabidopsis thaliana and identifies genes involved in mitochondrial complex I formation.

This study identifies that the chloroplast genome of Cladophorales green algae is fragmented into hairpin plasmids, a unique structure not previously observed in eukaryotes.

PhyD3 extends the PhyloXML standard for functional genomics data visualization and provides an open-source web tool for advanced phylogenetic tree display.