- Curse: Building expression atlases and co-expression networks from public RNA-Seq data. Vaneechoutte and Vandepoele, 2019
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- PLAZA, a resource for plant comparative genomics. Proost et al., 2009 - Van Bel et al., 2012 - Proost et al., 2015
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- pico-PLAZA, a resource for algal comparative genomics. Vandepoele et al., 2013
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- TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. Kulkarni et al.,
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- TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. Van Bel et al., 2013
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- ATCOECIS, a toolbox to study transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Vandepoele et al., 2009
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- SPPG, Sequence Platform for the phylogenetic analysis of Plant Genes. Vandepoele et al., 2005
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- 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
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- 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
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- 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
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- 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.
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- Systematic identification of functional plant modules through the integration of complementary data sources. Heyndrickx KS & Vandepoele K. Plant Physiology 2012 - Supplementary website
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| For Tools & Supplementary data from papers before 2005, please check here.
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