Tools

Transcriptional regulation - Networks

Curse: Building expression atlases and co-expression networks from public RNA-Seq data. Vaneechoutte and Vandepoele, 2019
MINI-EX: Motif-Informed Network Inference based on single-cell EXpression data. Ferrari et al.,
TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. Kulkarni et al., 2018
vHRR: co-expression based gene function prediction. Depuydt and Vandepoele, 2021

Comparative - Functional Genomics

PLAZA, a resource for plant comparative genomics. Proost et al., 2009 - Van Bel et al., 2012, 2018, 2022
PLAZA Diatoms, a resource for diatom comparative genomics. Vandepoele et al., 2013
pico-PLAZA, a resource for algal comparative genomics. Osuna-Cruz et al., 2020
TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. Van Bel et al., 2013; Bucchini et al., 2021

Supplementary data

Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators. De Clercq, Van de Velde et al., 2021. Nature Plants - Supplementary iGRN website
Enhanced Maps of Transcription Factor Binding Sites Improve Regulatory Networks Learned from Accessible Chromatin Data. Kulkarni S, Jones M & Vandepoele K. Plant Physiology 2019 - Supplementary website
A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. Heyndrickx KS, Van de Velde J, Wang C, Weigel D & Vandepoele K. Plant Cell 2014 - Supplementary website
Inference of transcriptional networks in Arabidopsis thaliana through conserved non-coding sequence analysis. Van de Velde J, Heyndrickx KS & Vandepoele K. Plant Cell 2014 - Supplementary website.
Systematic identification of functional plant modules through the integration of complementary data sources. Heyndrickx KS & Vandepoele K. Plant Physiology 2012 - Supplementary website
For Tools & Supplementary data from papers before 2005, please check here.