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.