Annual Scientific Report 2015

Daniel Zerbino
Ensembl Genome Analysis
MSc in Biotechnology, Ecole nationale supérieure
des Mines de Paris, 2005. PhD in Bioinformatics,
EMBL and University of Cambridge, 2009.
At EMBL-EBI since 2013.
Team leader since 2015.
2015 to improve and automate our ChIP-Seq analysis
pipelines, we will be processing most of the available
datasets, as collected by IHEC. We will also integrate
new data sources into Ensembl’s annotation. In
particular, DNA methylation datasets are very cost
effective, and many experiments have been done across
many species. Currently only available on human and
mouse, we are expecting to expand the number of species
covered by the Ensembl Regulatory Build by integrating
datasets produced by the FAANG consortium. In
addition to better detecting regulatory elements, we
wish to better understand their components, and
transcription factor binding motifs in particular. New
technologies such as SELEX or Uniprobe have produced
new collections of binding motifs that we want to use in
our detection of possible binding sites.
Our annotation of variants will be greatly expanded
by tying them empirically to nearby genes. First, we
are very excited to release GTEx eQTL data in 2016.
We have devoted a lot of efforts to develop appropriate
HDF5-based infrastructure to store these large data
matrices. Already, a prototype is running, and can
provide any selection of the GTEx data in a fraction
of a second. In parallel, we expect the first promoter
capture Hi-C datasets to be made available around the
same time. Our tissue specific annotations, as well as
phenotype and disease associations, will all be enriched
by the use of ontologies.
pass, we will be displaying the CRISPR target sites, as
computed by the WGE tool developed at the Sanger
Institute. We will also be laying the groundwork to
store external CRISPR screens in view of creating a
central archive.
In terms of tools we will continue to improve on our
current set, with a focus on the VEP and GenomeStats.
We are also currently collaborating with CTTV to
produce a GWAS functional analysis pipeline, which
will integrate all available cis-regulatory data to impute
causal genes from GWAS summary results. This new
service should be initially released in 2016, and will
eventually be made available through various entry
points, such as the Ensembl webpage, the RESTful
endpoints or as a standalone program.
Selected publications
Cunningham F, et al. (2015) Improving the Sequence
Ontology terminology for genomic variant annotation. J.
Biomed. Semantics 6:32
Nguyen N, et al. (2015) Building a pan-genome reference
for a population. J. Comput. Biol. 22:387-401
Zerbino DR, et al. (2015) The Ensembl regulatory build.
Genome Biol. 16:56.
We are also preparing for the fundamental revolution
brought about by CRISPR technologies. In a first
Experimental Promoter Capture Hi-C
loaded and displayed on the Ensembl
Genome Browser.
2015 EMBL-EBI Annual Scientific Report 86