Annual Scientific Report 2015

Research Summaries
Beltrao group
• Studied the conservation and structural properties of
phosphosites in proteins from the African clawed frog
(X. laevis);
• Developed a method to predict the specificity of protein
kinases using protein phosphorylation data and functional
interaction information;
• Measured 250 000 conditional gene–gene interactions in
yeast to study condition-dependent genetic interactions.
Birney group
• Published an overview of Oxford Nanopore Reference data as
part of the MARC consortium;
• Published the first transcription factor QTL study, the CTCF
transcription factor in human LCL lines;
• Published an analysis of the Kiyosu population of Medaka,
and showed that this population has good properties for
establishing an isogenic panel appropriate for quantitative
trait mapping.
Enright group
• Worked on two important papers illustrating the
CaptureSeq methodology for deep characterisation of
transcript isoforms;
• Published a major new computational system for the
assessment of microRNA uridylation and modifcations;
• Developed new computational techniques for the prediction
and characterisation of long non-coding RNAs in mouse and
D. melanogaster.
Flicek group
• In collaboration the Odom group at the University of
Cambridge, mapped and analysed evolution of genomic
promoter and enhancer elements across 20 mammalian
species to produce the most comprehensive view of shared
and lineage-specific promoter and enhancer elements in the
mammalian lineage;
• In collaboration with the Merkenschlager group at Imperial
College London, gained new insights into the role of cohesin
in genome regulation;
• In collaboration with the Spector group at Cold Spring
Harbor, investigated chromatin changes in response to a
large genomic deletion.
Goldman group
• With support from the BBSRC, continued our work
to re-purpose DNA as a medium for archiving digital
information, developing computational and laboratory
DNA-handling technologies needed to bring DNA-storage
closer to market.
• Investigated how the presence of gaps in a multiple
sequence alignment (MSA) affects the accuracy of
inferred phylogenies, and derived a new proof of statistical
consistency of maximum likelihood phylogenetic
reconstruction for un-gapped alignments;
• To improve ‘cell lineage trees’, extending existing
phylogenetic methods to cope with error-prone data,,
developed a scalable algorithm that gives more accurate trees
than those produced using standard methods;
• Investigated the impact of popular MSA programs on
reconstruction of ancestral sequences, and discovered that
different aligners introduce biases;
• Published the results of a long-running comparative study of
MSA filtering methods, and showed that alignment filtering
generally worsens the resulting trees;
• Developed treeCl, a clustering method that groups loci that
share a common evolutionary history and distinguishes sets
that do not, offering insights into the underlying causes of
incongruence.
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2015 EMBL-EBI Annual Scientific Report