Data-driven discovery
Research at EMBL-EBIResearch at EMBL-EBI
Nick Goldman
www.ebi.ac.uk/research
Key facts about research at EMBL-EBI
• A unique environment for
bioinformatics research
• 9 dedicated research
groups
• 6 services teams also carry
out R&D
• Research and services are
mutually supportive
Research Group Leaders
Paul
BertoneSarah
TeichmannJulio Saez-
Rodriguez
Systems biology
Genes
Ewan
BirneyNick
Goldman
Paul
Flicek
John
MarioniOliver
Stegle
Anton
Enright
Expression
Alvis
Brazma
Pedro
Beltrao
Proteins & structures
Janet
Thornton
Gerard
Kleywegt
Alex
Bateman
Chemical biology
John
Overington
Christoph
Steinbeck
KeyKeyKeyKey
Biology
Physics
Maths
Chemistry
Research themes
GenesGenesGenesGenes•Nick Goldman•Ewan Birney
•Paul Flicek
ExpressionExpressionExpressionExpression•Anton Enright•John Marioni•Oliver Stegle
•Alvis Brazma
Proteins & structuresProteins & structuresProteins & structuresProteins & structures•Janet Thornton•Pedro Beltrao
•Alex Bateman•Gerard Kleywegt
Systems biologySystems biologySystems biologySystems biology•Paul Bertone•Julio Saez-Rodriguez
•Sarah Teichmann
Chemical biologyChemical biologyChemical biologyChemical biology•Christoph Steinbeck•John Overington
Genes & expression
• Birney: Birney: Birney: Birney: Sequence algorithms and intra-species variation
• BrazmaBrazmaBrazmaBrazma: : : : Functional genomics research
• EnrightEnrightEnrightEnright: : : : Functional genomics and analysis of small RNA function
• FlicekFlicekFlicekFlicek: : : : Evolution of transcriptional regulation
• Goldman: Goldman: Goldman: Goldman: Evolutionary tools for genomic analysis
• MarioniMarioniMarioniMarioni: : : : Computational and evolutionary genomics
• StegleStegleStegleStegle:::: Statistical genomics and systems genetics
Proteins, structures & chemical biology
• Bateman: Bateman: Bateman: Bateman: Analysis of protein and RNA sequence
• BeltraoBeltraoBeltraoBeltrao: : : : Evolution of cellular networks
• OveringtonOveringtonOveringtonOverington: : : : Drug discovery informatics
• Steinbeck: Steinbeck: Steinbeck: Steinbeck: Small molecule metabolism in biological systems
• Thornton: Thornton: Thornton: Thornton: Proteins: structure, function and evolution
Systems biology
• BertoneBertoneBertoneBertone:::: Pluripotency, reprogramming and differentiation
• SaezSaezSaezSaez----Rodriguez:Rodriguez:Rodriguez:Rodriguez: Systems biomedicine
• TeichmannTeichmannTeichmannTeichmann: : : : Gene expression regulation and protein complex
assembly
High-profile research
• 1000 Genomes Project delivers data
• ENCODE analysis
• Using DNA to store digital data
• Sequencing and analysis of genomes
Research Group case study: GoldmanResearch Group case study: Goldman
Nick GoldmanNick GoldmanNick GoldmanNick Goldman
FocusFocusFocusFocus: 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.
Evolutionary tools for sequence analysis
…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
‘traditional’ aligners make phylogenetically unrealistic gaps,
create deletion ‘hotspots’, and
make insertions rare, implying sequences shrink over time
PAGAN: a phylogeny-aware
sequence graph aligner
Löytynoja, Vilella & Goldman,
Bioinformatics 28, 1684–1691 (2012)
http://code.google.com/p/pagan-msa/wiki/PAGAN
PAGAN
genome structure
differential splicing
sequence-graph
alignment
Isoform detection; short transcript alignment
Repetitive sequences
PAGAN
454 sequencing
PacBio sequencing
PAGAN
Comparison of methods
for reference alignment
extension
PAGAN
Comparison of methods
for reference alignment
extension
PAGAN PAGAN
DNA-storage
Goldman et al., Nature 494, 77–80 (2013)
DNA-storage
DNA-storage
What is it like to be a 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 Research Scientist at EMBL-EBI