Tools and Data

Tools

  • Curse: Building expression atlases and co-expression networks from public RNA-Seq data. Vaneechoutte and Vandepoele, 2019
  • PLAZA, a resource for plant comparative genomics. Proost et al., 2009 - Van Bel et al., 2012 - Proost et al., 2015
  • pico-PLAZA, a resource for algal comparative genomics. Vandepoele et al., 2013
  
  • TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. Kulkarni et al.,
  • TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. Van Bel et al., 2013
  • ATCOECIS, a toolbox to study transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Vandepoele et al., 2009
  • SPPG, Sequence Platform for the phylogenetic analysis of Plant Genes. Vandepoele et al., 2005
  

Supplemental data

  • 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. Access the recommendation on F1000Prime
  • 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.