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