K. Vandepoele

Molecular fingerprints of cell size sensing and mating type differentiation in pennate diatoms

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.

MINI-EX version 2: cell-type-specific gene regulatory network inference using an integrative single-cell transcriptomics approach

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.

Diatom adhesive trail proteins acquired by horizontal gene transfer from bacteria serve as primers for marine biofilm formation

The paper identifies diatom-specific adhesive proteins acquired via horizontal gene transfer from bacteria, which function as primers for marine biofilm formation.

Regulatory annotation identifies KAN1, MYB44 and PIF4 as regulators of Arabidopsis lincRNAs expressed in root

The paper constructs a gene regulatory network in Arabidopsis to identify TFs regulating root-specific lincRNAs, revealing key regulators and their associated lincRNAs linked to root development.

Identification of new growth regulators using cross-species network analysis in plants

Cross-species network analysis identifies and validates new growth regulators in Arabidopsis by integrating transcriptional networks and functional orthologs.

Multi-omics network-based functional annotation of unknown Arabidopsis genes

This paper develops an automated function prediction algorithm for Arabidopsis genes using multi-omics data, annotating 42.6% of unknown genes with validated functions.

Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators

The paper integrates multiple regulatory data types in Arabidopsis to build an iGRN that predicts gene regulatory interactions and identifies novel ROS signaling regulators.

Chromatin accessibility landscapes activated by cell surface and intracellular immune receptors

The paper uses RNA-seq and ATAC-seq to show that both SRMI and IRMI increase chromatin accessibility at defense genes, revealing overlapping transcriptional regulatory mechanisms.

Subfunctionalization of paralog transcription factors contributes to regulation of alkaloid pathway branch choice in Catharanthus roseus

The paper identifies subfunctionalization of ORCA transcription factors in Catharanthus roseus, revealing their role in regulating specific branches of the alkaloid pathway and their interaction with MYC2.

Traceback of Core Transcription Factors for Soybean Root Growth Maintenance under Water Deficit

The paper identifies core transcription factors regulating root growth in soybean under water deficit by integrating phylogenetic analysis and transcriptome data.

Systematic and functional analysis of horizontal gene transfer events in diatoms.

This study systematically analyzes horizontal gene transfer in diatoms, finding that 3-5% of their proteome has horizontal origin and HGT contributes to metabolic expansion and ecological success.

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

This study uses phylogenomic analysis to determine the origin and diversification of green seaweeds, finding they originated in the late Tonian/Cryogenian and diversified during the Ordovician.

Evolution of vascular plants through redeployment of ancient developmental regulators

This study traces the evolutionary origin and functional adaptation of the TMO5/LHW transcription factor complex in vascular plant development.

Virus-host coexistence in phytoplankton through the genomic lens

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.

Genome-Wide Characterization Of Differential Transcript Usage In Arabidopsis thaliana

The paper characterizes differential transcript usage in Arabidopsis thaliana using RNA-Seq data, identifying 138,722 isoform switches across 8,162 genes and showing 23% of these alter protein sequences.