Research

Current large-scale projects the group is involved with:

  • FANTOM6: Functional annotation of lncRNAs using CAGE and perturbation experiments.
  • ZENCODE: Marie-Curie HO20 initial training program to understand genome regulation in Zebrafish.
  • DANIOCODE: An international collaboration that aims to annotate the functional elements of the zebrafish genome.

Resources developed by the group:

  • ANCORA: Genome-wide visualisation of highly conserved noncoding element densities.
  • Synorth: Web resource for exploring genomic regulatory blocks.
  • JASPAR: Open database of high quality transcription factor binding profiles.
  • TFBS: Perl modules for transcription factor binding site detection and analysis.
  • Lenhard group Genome Browser (access restricted to collaborators)

R/bioconductor packages developed by the group:

  • r3Cseq: 3C-seq analysis in R.
  • CAGEr: Analysis of cap analysis of gene expression data.
  • TFBStools: Analysis and manipulation of TFBS and TF profile matrices.
  • CNEr: Detection and analysis of Conserved Noncoding Elements.
  • TFMPvalue: Efficient and accurate P-value computation for Position Weight Matrices
  • GenomicInteractions: Bioconductor package for exploring chromatin interaction data.