K. Vandepoele

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

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.

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

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

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

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.

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.

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

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.

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.

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

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.