Key facts about research at EMBL-EBI Research at EMBL-EBI • A unique environment for bioinformatics research Data-driven discovery • 9 dedicated research groups • 6 services teams also carry out R&D • Research and services are mutually supportive Nick Goldman www.ebi.ac.uk/research Research Group Leaders Research themes Genes Key Genes Ewan Paul Nick Birney Flicek Goldman Biology •Nick Goldman •Ewan Birney Physics •Paul Flicek Chemical biology Maths Expression •Christoph Steinbeck Chemistry •John Overington Alvis Anton John Oliver Expression Brazma Enright Marioni Expression Stegle •Anton Enright •John Marioni Proteins & structures •Oliver Stegle •Alvis Brazma Systems biology Alex Pedro Gerard Janet Systems biology Bateman Beltrao Kleywegt Thornton •Paul Bertone Proteins & structures •Julio Saez-Rodriguez •Sarah Teichmann Systems biology Chemical biology •Janet Thornton •Pedro Beltrao Paul Julio Saez- Sarah John Christoph Bertone Rodriguez Teichmann Overington Steinbeck •Alex Bateman •Gerard Kleywegt Genes & expression Proteins, structures & chemical biology • Birney: Sequence algorithms and intra-species variation • Bateman: Analysis of protein and RNA sequence • BrazmaBrazma:: Functional genomics research • BeltraoBeltrao:: Evolution of cellular networks • EnrightEnright:: Functional genomics and analysis of small RNA function • OveringtonOverington:: Drug discovery informatics • FlicekFlicek:: Evolution of transcriptional regulation • Steinbeck: Small molecule metabolism in biological systems • Goldman: Evolutionary tools for genomic analysis • Thornton: Proteins: structure, function and evolution • MarioniMarioni:: Computational and evolutionary genomics • StegleStegle:::: Statistical genomics and systems genetics Systems biology High-profile research • BertoneBertone:::: Pluripotency, reprogramming and differentiation • 1000 Genomes Project delivers data • SaezSaez----Rodriguez:Rodriguez: Systems biomedicine • ENCODE analysis • TeichmannTeichmann:: Gene expression regulation and protein complex • Using DNA to store digital data assembly • Sequencing and analysis of genomes Evolutionary tools for sequence analysis Research Group case study: Goldman Nick Goldman FocusFocus: The mathematics and statistics of data analyses that use evolutionary information, to increase our understanding of evolution and to provide new tools to elucidate the function of biological molecules as they evolve over time. …what the new alignments look like …what the new alignments look like bis PRANK, a phylogeny-aware multiple sequence aligner …what the new alignments look like PAGAN: a phylogeny-aware sequence graph aligner Löytynoja, Vilella & Goldman, Bioinformatics 28, 1684–1691 (2012) http://code.google.com/p/pagan-msa/wiki/PAGAN ‘traditional’ aligners make phylogenetically unrealistic gaps, create deletion ‘hotspots’, and make insertions rare, implying sequences shrink over time Repetitive sequences Isoform detection; short transcript alignment genome structure differential splicing sequence-graph alignment PAGAN PAGAN 454 sequencing Comparison of methods for reference alignment extension PacBio sequencing PAGAN PAGAN Comparison of methods for reference alignment extension PAGAN PAGAN DNA-storage Goldman et al., Nature 494, 77–80 (2013) DNA-storage DNA-storage Research Scientist at EMBL-EBI What is it like to be a research scientist at EMBL-EBI? Research Scientist at EMBL-EBI Research Scientist at EMBL-EBI.