Research in Brief 2017 Research in Brief 2017 5 Careers at EMBL Directors’ Research

2017 Research in brief INTER- Contents EMBL in numbers NATIONALITY EMBL is Europe’s flagship laboratory for the life sciences. Our interdisciplinary, 2 EMBL in numbers curiosity-driven research programme fosters early independence and encourages collaboration. We offer services to the scientific community, train the next generation 4 Careers at EMBL of scientists and strive to integrate the life sciences across Europe. EMBL research 5 Directors' Research drives the development of new technology and methods in the life sciences. – Heidelberg We work to transfer this knowledge for the benefit of society.

6 Cell Biology and Biophysics – Heidelberg EXCELLENT RESEARCH EMBL is supported by over 2020 member states 9 Developmental Biology – Heidelberg Top 26 10 11 Genome Biology – Heidelberg more than 30% 13 Structural and Computational Biology EMBL ranked 26 scientists of research – Heidelberg in top 10 institutes among the top group and team worldwide for life 1% of highly cited leaders are funded science research researchers by the ERC 80 16 Core Facilities COUNTRIES – Heidelberg Over 1600 people from more than 80 countries work for EMBL

18 Bioinformatics Research INTERDISCIPLINARITY OUTSTANDING – Hinxton Scientific background of research group and team leaders: TRAINING 21 Bioinformatics Services Over Over – Hinxton

57% 250 200 25 Structural Biology – Grenoble Biologists Postdocs PhD students

27 Structural Biology Almost 6 sites – Hamburg 14% 17% Hinxton 100 • Hamburg courses and 29 Epigenetics and Neurobiology Chemists/ Physicists/ conferences per year at EMBL – Rome • Heidelberg Chemical Engineers Biophysicists sites.

31 Tissue Biology and Disease Modelling PUBLICATIONS • Grenoble – Barcelona Mathematicians/ Over 90% of PhD students publish • Barcelona • Rome a paper as first author. 12% Computer Scientists PhD students publish 2 first-author 32 Index papers on average.

2 Stand 01.2016 INTER- Contents EMBL in numbers NATIONALITY EMBL is Europe’s flagship laboratory for the life sciences. Our interdisciplinary, 2 EMBL in numbers curiosity-driven research programme fosters early independence and encourages collaboration. We offer services to the scientific community, train the next generation 4 Careers at EMBL of scientists and strive to integrate the life sciences across Europe. EMBL research 5 Directors' Research drives the development of new technology and methods in the life sciences. – Heidelberg We work to transfer this knowledge for the benefit of society.

18 Bioinformatics Research INTERDISCIPLINARITY OUTSTANDING – Hinxton Scientific background of research group and team leaders: TRAINING 21 Bioinformatics Services Over Over – Hinxton

57% 250 200 25 Structural Biology – Grenoble Biologists Postdocs PhD students

2 Stand 01.2016 Careers at EMBL Directors’ Research

Located in Heidelberg, Germany

EMBL is no ordinary place to work. We are passionate How are gene expression, metabolism and disease connected? about science and its potential to improve and enrich life. We are a vibrant, What determines cell shape? The range of themes in Directors’ Research driven and open community that welcomes new and diverse perspectives. reflects the interests of the Director of EMBL and the Director of EMBO. We are international, friendly and supportive, and our 1600 people Currently, some researchers in the unit combine biochemical and systems-level include mathematicians, physicists, chemists and computer engineers, approaches to study cell metabolism, working closely with colleagues in the as well as biologists, biochemists and bioinformaticians. Genome Biology Unit. Others investigate cell shape in Drosophila and innate immune signalling in zebrafish, often in collaboration What does it take to be an EMBL person? with the Developmental Biology Unit. We call it ‘the EMBL spirit’: passion, curiosity, openness and a drive to develop and do better.

Matthias Hentze – RNA biology, metabolism and molecular medicine EMBL Director; Senior Scientist – Joint appointment with the Genome Biology Unit

s.embl.org/phdprogr s.embl.org/postdocprogr The Hentze group combines biochemical and systems-level approaches to investigate the connections between gene expression and cell metabolism, and their roles in PhD Postdoctoral human disease. embl.org/hentze programme fellowships

First-class training, International, dedicated mentoring and interdisciplinary environment early independence and world-class in research facilities Maria Leptin – Cell shape and morphogenesis: subcellular and supracellular mechanisms EMBO Director; Group Leader

The Leptin group studies the mechanisms and forces that determine cell shape in s.embl.org/jobs s.embl.org/jobs Drosophila and uses the zebrafish to analyse innate immune signalling. embl.org/leptin Group and Other team leaders careers

Interdisciplinary, Opportunities for scientists curiosity-driven research at all career stages, as well as for programme that fosters early experts in training, communications, independence and technology development, IT and for encourages anyone who wants to push collaboration the boundaries of human knowledge

4 Research in brief 2017 Research in brief 2017 5 Careers at EMBL Directors’ Research

Located in Heidelberg, Germany

Matthias Hentze – RNA biology, metabolism and molecular medicine EMBL Director; Senior Scientist – Joint appointment with the Genome Biology Unit

4 Research in brief 2017 Research in brief 2017 5 Cell Biology and Biophysics – Heidelberg Cell Biology and

Biophysics Lars Hufnagel – Dynamics of cell growth and tissue architecture Group Leader – Joint appointment with the Developmental Biology Unit

Located in Heidelberg, Germany The Hufnagel group studies the role of mechanical constraints in processes such as cell growth, programmed cell death, orientation of division, intra-tissue rearrangements From eggs to neurons, cells take on very different shapes and sizes to fulfill their roles. and cell differentiation. embl.org/hufnagel Scientists in the Cell Biology and Biophysics Unit investigate the molecular and biophysical mechanisms that enable cells to function. In the unit, biologists, chemists and physicists probe molecular networks and machines as well as mechanical forces Martin Jechlinger – Mechanisms of oncogene dependence and and signalling. Experts in optics work with biologists to develop new tumour relapse imaging technologies to visualise life’s molecular machinery at work. Group Leader – Joint appointment with the Epigenetics and Neurobiology Unit

The Jechlinger group uses a 3D culture system of primary mouse mammary epithelial cells to study cancer-initiating oncogenes. embl.org/jechlinger Jan Ellenberg – Systems biology of cell division and nuclear organisation Head of the Cell Biology and Biophysics Unit; Senior Scientist Péter Lénárt – Cytoskeletal dynamics and function in oocytes The Ellenberg group studies cell division and nuclear organisation, focusing on Group Leader chromatin organisation and formation, segregation of mitotic and meiotic chromosomes, and nuclear pore complex structure and assembly. embl.org/ellenberg Using starfish as a model organism, the Lénárt group combines biochemistry with imaging assays to investigate how the fertilisable egg cell develops from the oocyte. embl.org/lenart

Sara Cuylen-Häring – Cellular phase separation by surfactants Group Leader François Nédélec – Cellular architecture Group Leader The Cuylen group investigates how proteins act as surfactants to regulate the spatial separation of chromosomes and other cellular organelles. embl.org/cuylen The Nédélec group combines experimental methods and physical theory to study how the interior of cells is spatially organised and how multiple cells are arranged in space. embl.org/nedelec

Alba Diz-Muñoz – Mechanics of cellular signalling Group Leader Pierre Neveu – Systems biology of stem cell differentiation Group Leader The Diz-Muñoz group studies the crosstalk between mechanical properties and signalling for cell polarity and migration of immune cells, and during zebrafish The Neveu group takes an integrated systems biology approach to investigate the development. embl.org/diz-munoz molecular changes that determine what a stem cell becomes. embl.org/neveu

Christian Häring – Chromosome structure and dynamics Rainer Pepperkok – Membrane traffic and organelle biogenesis Group Leader – Joint appointment with the Structural and Head of Core Facilities and Scientific Services; Senior Scientist Computational Biology Unit The Pepperkok team develops novel approaches to study the temporal and The Häring group aims to understand the molecular machinery that organises mitotic spatial organisation of membrane traffic and organelle biogenesis in the secretory chromosomes. embl.org/haering pathway. embl.org/pepperkok

6 Research in brief 2017 Research in brief 2017 7 Cell Biology and Biophysics – Heidelberg Cell Biology and

Biophysics Lars Hufnagel – Dynamics of cell growth and tissue architecture Group Leader – Joint appointment with the Developmental Biology Unit

6 Research in brief 2017 Research in brief 2017 7 Cell Biology and Biophysics – Heidelberg

Robert Prevedel – Advanced optical techniques for deep tissue microscopy Group Leader – Joint appointment with the Developmental Biology Unit and the Developmental Epigenetics and Neurobiology Unit

The Prevedel group develops new optical techniques for investigating dynamic cellular processes deep inside tissue in vivo. embl.org/prevedel Biology

Located in Heidelberg, Germany Jonas Ries – Cellular nanoscopy Group Leader Multicellular development is a feat of coordination. Molecular and physical cues – both intrinsic and extrinsic – are integrated at the cellular and tissue levels to The Ries group develops cutting-edge super-resolution microscopy methods to generate the morphology, pattern and physiology of living organisms, from embryo to determine structures of multi-protein assemblies in the cellular context. embl.org/ries adult. Scientists in the Developmental Biology Unit investigate these complex, dynamic interactions. They use highly interdisciplinary approaches to reveal the fundamental mechanisms that shape life during development and evolution.

Carsten Schultz – Chemical cell biology Group Leader; Senior Scientist Anne Ephrussi – RNA localisation and localised translation The Schultz group develops tools for imaging and manipulating cellular enzyme in development activities, with an emphasis on lipid signalling in diabetes and the hereditary disease Head of the Developmental Biology Unit; Senior Scientist cystic fibrosis. embl.org/schultz The Ephrussi group dissects the mechanisms underlying intracellular RNA transport and localised translation – fundamental processes mediating the functional polarisation of cells during development and in the nervous system. Yannick Schwab – Volume correlative light and electron microscopy embl.org/ephrussi Head of the Electron Microscopy Core Facility; Team Leader

The Schwab team is interested in developing tools for the 3D correlation of data generated by fluorescent imaging and electron microscopy. embl.org/schwab Detlev Arendt – Evolution of the nervous system in bilateria Group Leader; Senior Scientist

By studying and comparing simple marine organisms, the Arendt group looks to understand the origin and evolution of our central nervous system. embl.org/arendt

Alexander Aulehla – Timing of mammalian embryogenesis Group Leader

The Aulehla group studies how the precise timing and sequence of events that unfold as an embryo develops are controlled. embl.org/aulehla

Justin Crocker – Gene regulation during evolution and development Joint appointments to the Cell Biology and Biophysics Unit Group Leader Martin Beck (Structural and Computational Biology) – 14 The Crocker group aims to understand the fundamental principles driving development John Briggs (Structural and Computational Biology) – 14 to allow for programming and predictive control of cell fates. embl.org/crocker Edward Lemke (Structural and Computational Biology) – 14 Paul Heppenstall (Epigenetics and Neurobiology) – 30

8 Research in brief 2017 9 Cell Biology and Biophysics – Heidelberg

The Prevedel group develops new optical techniques for investigating dynamic cellular processes deep inside tissue in vivo. embl.org/prevedel Biology

By studying and comparing simple marine organisms, the Arendt group looks to understand the origin and evolution of our central nervous system. embl.org/arendt

Alexander Aulehla – Timing of mammalian embryogenesis Group Leader

The Aulehla group studies how the precise timing and sequence of events that unfold as an embryo develops are controlled. embl.org/aulehla

8 Research in brief 2017 9 Developmental Biology – Heidelberg

Stefano De Renzis – Cell dynamics and signalling during morphogenesis Group Leader Genome Biology The De Renzis group aims to understand how cells build tissues during organismal development using a combination of quantitative imaging and optogenetic-based Located in Heidelberg, Germany synthetic approaches. embl.org/derenzis Many of our traits stem from the information in our genome which must be expressed at the right place and time. This entails strict regulation at multiple steps, including transcriptional, post-transcriptional and post-translational. Scientists in Takashi Hiiragi – Symmetry breaking and self-organisation Group Leader the Genome Biology Unit take an integrated, multi-tiered approach to study these processes and how their alteration leads to disease. They combine wet-lab and computa- The Hiiragi group studies early mammalian development at the molecular, cellular and tional research, and work closely with colleagues in the Genomics and Proteomics systems levels to elucidate how an intricate embryo emerges from a spherical mass of Core Facilities to understand the molecular processes cells. embl.org/hiiragi leading from genotype to phenotype.

Aissam Ikmi – Plasticity of animal body design Group Leader Eileen Furlong – Genome regulation and topology The Ikmi group studies how the interplay between genetic and environmental during embryonic development factors shapes animal body plans. embl.org/ikmi Head of the Genome Biology Unit; Senior Scientist

The Furlong group dissects fundamental principles of transcriptional regulation and how that drives cell fate decisions during development, focusing on organisational and functional properties of the genome. embl.org/furlong Francesca Peri – Microglia: the guardians of the developing brain Group Leader Wolfgang Huber – Multi-omics and statistical computing The Peri group combines genetic approaches with quantitative imaging techniques to Group Leader; Senior Scientist – Joint appointment with the Structural and study how microglia shape neuronal connectivity by removing unwanted neurons and Computational Biology Unit and EMBL-EBI synapses. embl.org/peri The Huber group develops statistical and bioinformatics methods for novel assays in high-throughput biology and the integrative analysis of multi-omic data types. embl.org/huber

Jan Korbel – From genomic variation to molecular mechanism Group Leader; Senior Scientist – Joint appointment with EMBL-EBI

The Korbel group combines experimental and computational approaches, including single-cell sequencing technology, to unravel determinants and consequences of germline and somatic genetic variation. embl.org/korbel

Joint appointments to the Developmental Biology Unit Lars Hufnagel (Cell Biology and Biophysics) – 7 Arnaud Krebs – Decoding gene regulation using single molecule Robert Prevedel (Cell Biology and Biophysics) – 8 genomics John Marioni (EMBL-EBI) – 20 Group Leader Hiroki Asari (Epigenetics and Neurobiology) – 29 Cornelius Gross (Epigenetics and Neurobiology) – 29 The Krebs group develops and employs innovative genomics strategies to understand Christophe Lancrin (Epigenetics and Neurobiology) – 30 the multiple regulatory layers that control gene expression. embl.org/krebs

10 Research in brief 2017 11 Developmental Biology – Heidelberg

Jan Korbel – From genomic variation to molecular mechanism Group Leader; Senior Scientist – Joint appointment with EMBL-EBI

10 Research in brief 2017 11 Genome Biology – Heidelberg

Christoph A. Merten – Microfluidic approaches in drug discovery and personalised medicine Group Leader Structural and The Merten group develops microfluidic technology to address complex questions in biomedical sciences and developmental biology. embl.org/merten Computational Biology Kyung-Min Noh – Epigenetic mechanisms of neurodevelopment and disease Group Leader – Joint appointment with the Epigenetics and Neurobiology Unit Located in Heidelberg, Germany

The Noh group studies vital chromatin links for neurodevelopment and brain Life in the Structural and Computational Biology Unit is all about disorders. embl.org/noh interactions: from the molecular networks inside cells to the ecological relationships between species, via the collaboration between experts from different fields. Mikhail Savitski – Stability proteomics for assessing the state of the proteome Scientists in the unit cover everything from crystallography to cryo-electron microscopy Head of the Proteomics Core Facility; Team Leader – Joint appointment with the and from metabolomics to microbiomes. They support colleagues throughout EMBL Structural and Computational Biology Unit in the use of state-of-the-art structural biology instruments. The unit also serves as a hub for bioinformatics activities across EMBL in Heidelberg. The Savitski team uses and develops stability proteomics for understanding the phenomena of aggregation and disaggregation, cell phenotyping, and detection of protein interactions with drugs, metabolites, DNA and RNA. embl.org/savitski

Oliver Stegle – Statistical genomics and systems genetics Peer Bork – Deciphering function and evolution Group Leader – Joint appointment with EMBL-EBI of biological systems Head of the Structural and Computational Biology Unit; Senior Scientist The Stegle group develops computational and statistical methods to study the genotype-phenotype map on a genome-wide scale. embl.org/stegle The main focus of the Bork group is to gain insights into the functioning of biological systems and their evolution by comparative analysis and integration of complex molecular data. embl.org/bork Lars Steinmetz – Systems genetics and precision health Group Leader; Senior Scientist Christoph Müller – Molecular mechanisms of The Steinmetz group develops and applies interdisciplinary, genome-wide technologies transcriptional regulation in eukaryotes to study genome regulation, the genetic basis of complex phenotypes and the genetic Head of the Structural and Computational Biology Unit; Senior Scientist – Joint and molecular systems underpinning disease. embl.org/steinmetz appointment with the Genome Biology Unit

Nassos Typas – Dissecting bacterial lifestyle and interspecies The Müller group uses X-ray crystallography, cryo-electron microscopy and biophysical interactions with systems approaches and biochemical approaches to learn about the molecular mechanisms of transcription Group Leader – Joint appointment with the Structural and Computational Biology Unit regulation in eukaryotes, where DNA is packaged into chromatin. embl.org/mueller

The Typas group develops and utilises high-throughput methods to study the cellular networks of different bacterial species, and how these bacteria interact with the Theodore Alexandrov – Spatial metabolomics environment and with each other. embl.org/typas Head of the Metabolomics Core Facility; Team Leader

The Alexandrov team develops novel computational biology tools that aim to reveal the spatial organisation of metabolic processes. embl.org/alexandrov Joint appointments to the Genome Biology Unit Matthias Hentze (Directors’ Research) – 5 Christoph Müller (Structural and Computational Biology) – 13 Orsolya Barabas – Mechanisms, regulation and exploitation of Anne-Claude Gavin (Structural and Computational Biology) – 14 mobile DNA Judith Zaugg (Structural and Computational Biology) – 15 Group Leader Pedro Beltrão (EMBL-EBI) – 18 The Barabas group uses structural and molecular biology approaches to investigate Ewan Birney (EMBL-EBI) – 18 how DNA rearrangements are carried out and regulated, and uses this knowledge to Daniel Panne (Structural Biology, in Grenoble) – 26 develop their applications in research and medicine. embl.org/barabas Jamie Hackett (Epigenetics and Neurobiology) – 30

12 Research in brief 2017 13 Genome Biology – Heidelberg

12 Research in brief 2017 13 Structural and Computational Biology – Heidelberg Structural and Computational Biology – Heidelberg

Martin Beck – Structure and function of large molecular Julia Mahamid – In situ structural analysis of phase separation assemblies and molecular crowding Group Leader; Senior Scientist – Joint appointment with the Cell Biology and Group Leader Biophysics Unit The Mahamid group combines correlative approaches, cryo-focused ion beam milling Research in the Beck group combines biochemical approaches, proteomics and and electron tomography to study mesoscale assemblies, such as centrosomes and cryo-electron microscopy to study large macromolecular assemblies. embl.org/beck stress granules, in intact cells and model organisms at molecular resolution. embl.org/mahamid

John Briggs – Viruses and vesicles – cryo-electron Kiran Patil – Architecture and regulation of metabolic networks microscopy and tomography Group Leader Group Leader; Senior Scientist – Joint appointment with the Cell Biology and Biophysics Unit The Patil group uses a combination of modelling, bioinformatics and experimental approaches to study metabolic networks and how they are controlled. The Briggs group develops and applies cryo-electron microscopy techniques to study embl.org/patil the assembly mechanisms of enveloped viruses such as HIV and influenza, as well as coated trafficking vesicles. embl.org/briggs Carsten Sachse – Single-particle electron cryomicroscopy of the autophagy machinery Group Leader Anne-Claude Gavin – Biomolecular networks Group Leader; Senior Scientist – Joint appointment with the Genome Biology Unit The Sachse group uses electron cryomicroscopy to study the structures of autophagy complexes to elucidate the mechanisms by which cells eliminate aberrant structures The Gavin group integrates biochemical, proteomics, metabolomics and microfluidic- such as large protein aggregates. embl.org/sachse based methods to achieve a systems-level understanding of how cellular proteomes are organised. embl.org/gavin Judith Zaugg – Personalised genomics to study the genetic basis of complex diseases Group Leader – Joint appointment with the Genome Biology Unit and EMBL-EBI Toby Gibson – Biological sequence analysis Team Leader The Zaugg group investigates the variation of molecular phenotypes among individuals and their genetic variation with the aim of better understanding the molecular basis of The Gibson team investigates protein sequences, interactions and networks, undertakes complex genetic diseases and inter-individual differences in drug response. computational analyses of macromolecules, and develops tools to enhance sequence embl.org/zaugg analysis research. embl.org/gibson

Georg Zeller – Computational analysis of host-microbiota interactions in disease and drug therapy Janosch Hennig – Integrated structural biology of translation Team Leader regulation mechanisms Group Leader The Zeller team develops analysis strategies and tools to investigate how the microbiome contributes to human health, disease progression and treatment success, and how it is The Hennig group employs integrated structural biology (NMR, X-ray, and small-angle shaped by host factors such as nutrition and drug intake. embl.org/zeller scattering) to investigate the molecular mechanisms underlying translation regulation and ribonucleoprotein complex assembly. embl.org/hennig

Edward Lemke – High-resolution studies of protein plasticity Group Leader – Joint appointment with the Cell Biology and Biophysics Unit

The Lemke group uses an interdisciplinary approach to elucidate the nature of Joint appointments to the Structural and Computational Biology Unit naturally disordered proteins in biological systems and disease mechanisms at the Christian Häring (Cell Biology and Biophysics Unit) – 6 single-molecule level. embl.org/lemke Wolfgang Huber (Genome Biology) – 11 Mikhail Savitski (Genome Biology) – 12 Nassos Typas (Genome Biology) – 12

14 Research in brief 2017 15 Structural and Computational Biology – Heidelberg Structural and Computational Biology – Heidelberg

Edward Lemke – High-resolution studies of protein plasticity Group Leader – Joint appointment with the Cell Biology and Biophysics Unit

14 Research in brief 2017 15

Core Facilities – Heidelberg

Flow Cytometry Core Facility Malte Paulsen Core Facilities Facility Head The Flow Cytometry Core Facility offers access to high-end FACS analysis and state-of- Located in Heidelberg, Germany the-art cell sorting capabilities, providing scientists with adaptive setups and dedicated support. embl.org/fccf Molecular life science requires a suite of sophisticated techniques – from high-end microscopes to protein production platforms and next-generation sequencers – and the expertise to make the most of them. At EMBL’s Core Facilities, Protein Expression and Purification Core Facility experts support scientists in designing, running and refining experiments. They help Kim Remans researchers make sense of results. Core Facilities staff work closely with Facility Head technology developers, and are always aware of the latest advances in their field. They enable scientists from across EMBL and beyond to achieve ambitious The Protein Expression and Purification Core Facility produces and purifies research goals in a cost-effective way. proteins both from Escherichia coli and from insect cells. It implements a large array of chromatographic techniques and also provides support for the biophysical characterisation of the purified proteins. embl.org/pepcore

Advanced Light Microscopy Facility Rainer Pepperkok Proteomics Core Facility Head of the Core Facilities and Scientific Services; Senior Scientist Mikhail Savitski Facility Head; Team Leader The Advanced Light Microscopy Facility offers a collection of state-of-the-art light microscopy equipment and image processing tools. embl.org/almf The Proteomics Core Facility provides a full proteomics infrastructure for the identification and characterisation of proteins. embl.org/proteomics

Metabolomics Core Facility Theodore Alexandrov Electron Microscopy Core Facility Facility Head; Team Leader Yannick Schwab Facility Head; Team Leader The Metabolomics Core Facility provides a comprehensive infrastructure for analysis of metabolites and lipids. embl.org/metabolomics The Electron Microscopy Core Facility provides advanced expertise in electron microscopy, from sample preparation to image analysis, for a large variety of biological samples. embl.org/em

Genomics Core Facility Vladimír Beneš Facility Head

The Genomics Core Facility is EMBL‘s genomics service centre equipped with state-of- the-art technologies for functional genomics analyses and operated by highly qualified staff. embl.org/genecore

Chemical Biology Core Facility Joe Lewis Facility Head

The Chemical Biology Core Facility assists groups in developing primary and secondary assays for screening against the in-house compound library and guides them in developing tool compounds for their specific target. embl.org/chemcore

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Core Facilities – Heidelberg

Genomics Core Facility Vladimír Beneš Facility Head

The Genomics Core Facility is EMBL‘s genomics service centre equipped with state-of- the-art technologies for functional genomics analyses and operated by highly qualified staff. embl.org/genecore

Chemical Biology Core Facility Joe Lewis Facility Head

16 17 Bioinformatics Research – Hinxton

Anton Enright – Functional genomics and analysis of small RNA function Bioinformatics Group Leader – Joint appointment with the Epigenetics and Neurobiology Unit The Enright group studies small non-coding RNAs and develops computational tools, Research systems and algorithms to predict their functions and interactions. embl.org/enright

European Bioinformatics Institute Paul Flicek – Evolution of transcriptional regulation Team Leader; Senior Scientist EMBL-EBI, located in Hinxton, United Kingdom The Flicek team uses comparative regulatory genomics to study the evolution of Researchers at EMBL-EBI are transforming the life sciences. transcriptional regulation with the ultimate goal of understanding the mechanisms They are making sense of the vast, complex datasets produced using new and emerging and maintenance of cell-type specificity. embl.org/flicek technologies in molecular biology. Their work spans sequence analysis methods, multi-dimensional statistical analysis and data-driven biological discovery. At EMBL-EBI, researchers work closely with experimental scientists worldwide, Moritz Gerstung – Computational cancer biology increasingly tackling problems of direct significance to Group Leader medicine and the environment.. The Gerstung group develops statistical models and bioinformatics tools for understanding the cause and consequence of cancer genomes. They seek to understand the differences in therapy success and outcomes between individuals. Ewan Birney – Sequence algorithms and intra-species variation embl.org/gerstung Director of EMBL-EBI; Senior Scientist – Joint appointment with the Genome Biology Unit

The Birney group focuses on developing sequence algorithms and uses intra-species Nick Goldman – Evolutionary tools for genomic analysis variation to study basic biology. embl.org/birney Group Leader; Senior Scientist

The Goldman group’s research focuses on the processes of molecular sequence evolution, developing data analysis methods to exploit this information and glean Alex Bateman – Analysis of protein and RNA sequence powerful insights into genomic function, evolutionary processes and phylogenetic Senior Team Leader history. embl.org/goldman

The Bateman group endeavours to classify proteins and certain RNAs into functional families with a view to producing a ‘periodic table’ of these molecules. embl.org/bateman Zamin Iqbal – Computational microbial genomics Group Leader

The Iqbal group develops computational methods for analysing genetic variation Pedro Beltrão – Evolution of cellular networks and uses them to study bacteria and parasites. The group also works on translational Group Leader – Joint appointment with the Genome Biology Unit projects, especially related to antimicrobial resistance, diagnostics and surveillance. embl.org/iqbal The Beltrão group studies the molecular impacts of genetic variability on phenotypic variability to better understand the function and evolution of cellular networks. embl.org/beltrao Gerard Kleywegt – Protein structure, analysis and validation Senior Team Leader

Alvis Brazma – Functional genomics research Research in the Kleywegt team aims to transform the structural archives into a truly Senior Team Leader; Senior Scientist useful resource for biomedical and related disciplines. embl.org/kleywegt

The Brazma team’s research focuses on the analysis of gene, transcript and protein expression, cancer genomics and proteomics, and the integrative analysis of functional genomics data. embl.org/brazma

18 Research in brief 2017 Research in brief 2017 19 Bioinformatics Research – Hinxton

18 Research in brief 2017 Research in brief 2017 19

Bioinformatics Research – Hinxton

John Marioni – Computational and evolutionary genomics Group Leader – Joint appointment with the Developmental Biology Unit Bioinformatics Services The Marioni group develops statistical tools that exploit data generated using next- generation sequencing to understand the evolution and regulation of gene expression. embl.org/marioni EMBL-EBI, located in Hinxton, United Kingdom

EMBL-EBI maintains the world’s most comprehensive range of freely available molecular data resources. Developed in collaboration with Evangelia Petsalaki – Whole-cell signalling colleagues worldwide, EMBL-EBI’s databases and tools help scientists share data Group Leader efficiently, perform complex queries and analyse the results in different ways. The The Petsalaki group uses diverse ‘omics’ datasets to create data-driven models of context- service teams’ work supports millions of wet-lab and computational biologists working specific cell signalling. Their aim is to understand the principles of cell signalling and its in all areas of the life sciences, from biomedicine to rewiring in different conditions and genetic backgrounds. embl.org/petsalaki biodiversity and agri-food research.

Gene annotation and comparative genomics Oliver Stegle – Statistical genomics and systems genetics Bronwen Aken Group Leader – Joint appointment with the Genome Biology Unit Team Leader

The Stegle group develops computational and statistical methods to study the The Aken team creates gene annotation and comparative genomics data resources genotype–phenotype map on a genome-wide scale. embl.org/stegle that further our understanding of biology, evolution and the mechanisms of disease. Distributed by Ensembl, these data provide a foundation for clinical and research communities. embl.org/aken

Janet Thornton – Proteins: structure, function and evolution Data coordination and archiving Director Emeritus of EMBL-EBI; Senior Scientist Guy Cochrane Team Leader The Thornton group builds on knowledge of the 3D structures of proteins and their complexes to understand their evolution and how variants and small molecules can The Cochrane team provides data coordination services for a host of collaborative cause or modulate diseases and ageing. embl.org/thornton projects across vertebrate, microbial and marine-biodiversity domains. They maintain the European Nucleotide Archive, an open platform for sequence data. embl.org/cochrane

Enriching understanding of genomic variation Fiona Cunningham Team Leader

The Cunningham team delivers robust, reliable reference resources for consistent variant annotation in any species. The team catalogues and stores large-scale data and develops methods and tools to facilitate integration and broad access to these data. embl.org/cunningham

Bioinformatics services for RNA, protein and metagenomic sequence data Rob Finn Team Leader

Joint appointments to EMBL–EBI The Finn team is responsible for protein and RNA data resources that provide fast, Wolfgang Huber (Genome Biology) – 11 sophisticated tools for analysis, simplify access to curated data, extend annotation and provide characterisation of sequences derived from environmental samples. Jan Korbel (Genome Biology) – 11 embl.org/finn Judith Zaugg (Structural and Computational Biology) – 15

20 21

Bioinformatics Research – Hinxton

Gene annotation and comparative genomics Oliver Stegle – Statistical genomics and systems genetics Bronwen Aken Group Leader – Joint appointment with the Genome Biology Unit Team Leader

Enriching understanding of genomic variation Fiona Cunningham Team Leader

Bioinformatics services for RNA, protein and metagenomic sequence data Rob Finn Team Leader

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Bioinformatics Services – Hinxton Bioinformatics Services – Hinxton

Molecular networks, pathways, mathematical models Protein function development Henning Hermjakob Maria J. Martin Team Leader Team Leader

The Hermjakob team develops data resources for the representation, deposition, The Martin team provides the bioinformatics infrastructure for UniProt at EMBL- distribution and analysis of pathway and systems biology data, and develops EBI, maintains the Gene Ontology Annotation and Enzyme portal services, and standards for proteomics and systems biology. embl.org/hermjakob develops novel automatic methods for protein annotation and representation. embl.org/martin

Sequence and variation archive infrastructure Metabolomics Thomas Keane Claire O’Donovan Team Leader Team Leader

The Keane team is responsible for the European Genome-phenome Archive (EGA), The O’Donovan team is responsible for the MetaboLights metabolomics resource. the controlled-access database of human genomic data, and the European Variation They develop workflows to process chemical information, predict meta-bolomes Archive (EVA), an open-access resource of raw variant data. embl.org/keane based on genomic information and enable the identification of molecules with desired properties. embl.org/odonovan

Non-vertebrate genomics Paul Kersey Protein function content Team Leadere Sandra Orchard Team Leader The Kersey team develops Ensembl Genomes, which provides access to genome- scale data of bacteria, protists, fungi, plants and invertebrate metazoa. The team The Orchard team provides the manual curation for the Universal Protein is instrumental in setting relevant data standards in partnership with research Resource (UniProt) at EMBL-EBI as well as the Gene Ontology Annotation communities. embl.org/kersey and Enzyme Portal services. The team is instrumental in developing community standards for protein annotation. embl.org/orchard

Chemogenomics Andrew Leach Samples, phenotypes and ontologies Team Leader Helen Parkinson Team Leader The Leach team is responsible for EMBL-EBI’s ChEMBL database, which offers curated 2D chemical structures and abstracted quantitative bioactivity data alongside The Parkinson team is responsible for BioSamples and Semantic Data Integration, calculated molecular properties. embl.org/leach as well as Mouse Informatics. The team develops develop ontologies, tooling and data resources that provide access to samples and ontologies. embl.org/parkinson

Literature services Johanna McEntyre Imaging data services Team Leader Ardan Patwardhan Team Leader The McEntyre team runs Europe PMC and integrates its textual content with molecular databases, both at EMBL-EBI and more widely through the development of data-sharing This Patwardhan team is responsible for the EMDB and EMPIAR data resources. with collaborating organisations. embl.org/mcentyre They develop resources for search, validation and visualisation of structural and bio-imaging data, and integrate and data-mine multi-scale structural and bioimaging data to facilitate data reuse. embl.org/patwardhan

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Bioinformatics Services – Hinxton Bioinformatics Services – Hinxton

Molecular networks, pathways, mathematical models Protein function development Henning Hermjakob Maria J. Martin Team Leader Team Leader

Sequence and variation archive infrastructure Metabolomics Thomas Keane Claire O’Donovan Team Leader Team Leader

22 23 Bioinformatics Services – Hinxton

Gene expression Robert Petryszak Team Leader Structural Biology The Petryszak team is responsible for the acquisition and curation of data for Array Express and develops the Expression Atlas, a data resource for gene and protein Located in Grenoble, France expression patterns under different biological conditions. embl.org/petryszak The 3D shape of a molecule can tell you a lot about what that molecule does – and how its activity might be altered, for example to treat a disease. Scientists at EMBL in Grenoble study how proteins interact with genomes, Functional genomics development Ugis Sarkans based on their 3D structure. To do so, they work closely with instrumentation Team Leader developers and colleagues across the European Photons and Neutrons science (EPN) campus to obtain and analyse the best possible data from cryo-electron microscopy The Sarkans team develops software for ArrayExpress and the BioStudies and X-ray or neutron diffraction experiments. database. They build and maintain data management tools, user interfaces, programmatic interfaces, and annotation and data submission systems for functional genomics resources. embl.org/sarkans

Stephen Cusack – Structural biology of RNA-protein Protein Data Bank in Europe (PDBe) complexes in gene expression and host-pathogen interactions Sameer Velankar Head of the Structural Biology Unit in Grenoble; Senior Scientist Team Leader The Cusack group uses X-ray crystallography to study the structural biology of The Velankar team is responsible for PDBe, which is a founding member of the protein-RNA complexes involved in RNA virus replication, innate immunity and Worldwide Protein Data Bank. Within this international consortium, PDBe works cellular RNA metabolism. embl.org/cusack to collate, maintain and provide access to the global repository of macromolecular structure models, the Protein Data Bank (PDB). embl.org/ velankar

Proteomics resources and tools Florent Cipriani – Instrumentation team Juan Antonio Vizcaino Team Leader; Senior Scientist Team Leader The Cipriani team develops instruments and methods for structural biology The Vizcaino team is responsible for the PRIDE Archive database of mass spectrometry- research and works with industry to make them available to scientists worldwide. based proteomics data, integrates proteomics data in public data resources and embl.org/cipriani develops open-source tools. They are active in developing community standards. embl.org/ vizcaino

Technical and outreach support for Ensembl and Ensembl Genome Wojciech Galej – Structure and function of RNA-protein complexes Andy Yates Group Leader Team Leader The Galej group uses an integrated structural biology approach combined with The Yates team provides website, release, production and outreach support for the biochemistry and biophysics to investigate large RNA-protein complexes involved Ensembl and Ensembl Genomes projects. They develop the Ensembl web platform, create in gene expression. embl.org/galej distribution and deployment mechanisms, and maintain the data-mining tool BioMart. embl.org/yates

Genome-scale analysis and storage for Ensembl Eva Kowalinski – Structural biology of macromolecular Daniel Zerbino protein-RNA complexes Team Leader Group Leader

The Zerbino team stores, processes and analyses genome-wide datasets for the The Kowalinski group investigates the architecture and mechanisms of macromole- Ensembl project and maintains the services that unite its associated databases. cular complexes involved in cellular RNA editing. embl.org/kowalinski This includes the functional annotation of non-coding variants from experimental epigenomic data. embl.org/zerbino

24 Research in brief 2017 25 Bioinformatics Services – Hinxton

Genome-scale analysis and storage for Ensembl Eva Kowalinski – Structural biology of macromolecular Daniel Zerbino protein-RNA complexes Team Leader Group Leader

24 Research in brief 2017 25 Structural Biology – Grenoble

Andrew McCarthy – Synchrotron crystallography team Team Leader Structural Biology The McCarthy team works on the development and operation of MX and BioSAXS beamlines, and studies proteins involved in neuronal development and cell signalling. embl.org/mccarthy Located in Hamburg, Germany

Proteins are key components of the cell’s workforce. Alone or in sets, they can fine-tune genes, break down bacteria, or make muscles contract. At EMBL in Hamburg, scientists unveil the structure of proteins that impact Marco Marcia – Structure and function of lncRNA-protein complexes involved in transcription regulation human health. Researchers in the unit use state-of-the-art infrastructure for Group Leader integrative structural biology available on the DESY campus. They investigate how these crucial molecules act, and assess how to use that The Marcia group uses structural biology and biophysical approaches to study the information to develop new therapies. molecular interactions between long non-coding RNAs (lncRNAs) and nuclear proteins and how their complexes regulate gene expression processes. embl.org/marcia

Matthias Wilmanns – Structure and function of protein translocation machineries José A. Marquez – High-Throughput Crystallisation Laboratory Head of the Structural Biology Unit in Hamburg; Senior Scientist Head of the Crystallisation Facility; Team Leader The Wilmanns group aims to unravel the overall architecture of protein translocation The Marquez team develops methods and software supporting high-throughput and machineries across membranes by employing an integrative structural biology fully automated crystallography pipelines and uses them to study the structure of approach. embl.org/wilmanns sensing and signalling molecules. embl.org/marquez

Stefan Fiedler – Synchrotron instrumentation for structural biology Daniel Panne – Structural biology of signal transduction and beamlines at PETRA III epigenetic gene regulation Team Leader Group Leader – Joint appointment with the Genome Biology Unit The Fiedler team focuses on the selection, customisation and integration of mechanics, The Panne group looks to understand how signalling pathways control gene expression, control electronics and control software for X-ray-based structural biology research. focusing on signalling in the innate immune system, epigenetic control of gene embl.org/fiedler expression and chromatin assembly. embl.org/panne

Jan Kosinski – Integrative modelling of infection cycles Group Leader

The Kosinski group investigates infection cycles and host-pathogen interaction using computational and experimental approaches. embl.org/kosinski

Victor Lamzin – Integrative modelling for structural biology Group Leader; Senior Scientist

The Lamzin group applies and develops cutting-edge computational methods and experimental approaches for sample quality control, experimentation, data interpretation and model validation in structural biology, with a major focus on macro-molecular crystallography. embl.org/lamzin

26 Research in brief 2017 Research in brief 2017 27 Structural Biology – Grenoble

Jan Kosinski – Integrative modelling of infection cycles Group Leader

The Kosinski group investigates infection cycles and host-pathogen interaction using computational and experimental approaches. embl.org/kosinski

Victor Lamzin – Integrative modelling for structural biology Group Leader; Senior Scientist

26 Research in brief 2017 Research in brief 2017 27 Structural Biology – Hamburg

Christian Löw – Structural and dynamic insights into nutrient uptake systems Group Leader Epigenetics and Using biophysical and biochemical methods, the Löw group aims to enhance understanding of the structural basis for substrate recognition in peptide transporters. embl.org/loew Neurobiology

Located in Rome, Italy

Rob Meijers – Structural biology of cell surface receptors How do we perceive the world around us? Can our surroundings Group Leader influence our genes, and our children’s genes? At EMBL in Rome, scientists explore the connections between genome, environment and neural function. The Meijers group investigates signalling mechanisms across the cell membrane using integrated structural biology and biophysical techniques. embl.org/meijers Traditionally, neuroscientists and epigeneticists have moved in different circles. Here, they come together and draw on each other’s insights, approaches and experience.

Thomas Schneider – Tools for structure determination and analysis Group Leader; Senior Scientist Philip Avner – Dynamics of epigenetic regulation Head of the Epigenetics and Neurobiology Unit; Senior Scientist The Schneider group operates two beamlines for macromolecular crystallography at the PETRA III synchrotron and develops new methods for structure determination. The Avner group combines genetics, genomics, biochemistry and cell biology to study embl.org/schneider the nature of the X-inactivation process and the role of epistasis in genetic regulation. embl.org/avner

Dmitri Svergun – Small-angle X-ray scattering from Cornelius Gross – Neural control of instinctive behaviour macromolecular solutions Deputy Head of the Epigenetics and Neurobiology Unit; Senior Scientist – Group Leader; Senior Scientist Joint appointment with the Developmental Biology Unit

The Svergun group runs and further enhances a biological small-angle X-ray scattering The Gross group uses pharmacological, histochemical, electrophysiological and beamline at the PETRA III storage ring and develops novel approaches for the scattering behavioural genetic approaches to study the neural circuits underlying instinctive data analysis and hybrid structural modelling. embl.org/svergun behaviour in mice. embl.org/gross

Hiroki Asari – Visual systems neuroscience Group Leader – Joint appointment with the Developmental Biology Unit

The Asari group combines experimental and computational approaches to study the principles and the function of neuronal circuits, specifically in the early visual system in mice. embl.org/asari

Matthieu Boulard – Heritable gene silencing in mammals Group Leader

The Boulard group integrates genetic, molecular biology and genomic approaches to explore how cytosine methylation represses transcription. embl.org/boulard

28 Research in brief 2017 Research in brief 2017 29 Structural Biology – Hamburg

Located in Rome, Italy

Hiroki Asari – Visual systems neuroscience Group Leader – Joint appointment with the Developmental Biology Unit

The Asari group combines experimental and computational approaches to study the principles and the function of neuronal circuits, specifically in the early visual system in mice. embl.org/asari

Matthieu Boulard – Heritable gene silencing in mammals Group Leader

The Boulard group integrates genetic, molecular biology and genomic approaches to explore how cytosine methylation represses transcription. embl.org/boulard

28 Research in brief 2017 Research in brief 2017 29 Epigenetics and Neurobiology – Rome

Jamie Hackett – Epigenetic reprogramming and inheritance Group Leader – Joint appointment with the Genome Biology Unit Tissue Biology and The Hackett group aims to understand the interplay between epigenetics, genome regulation and cell identity, with emphasis on transgenerational epigenetic inheritance. embl.org/hackett Disease Modelling

Located in Barcelona, Spain Paul Heppenstall – Molecular physiology of somatosensation Group Leader – Joint appointment with the Cell Biology and Biophysics Unit An organ or a tissue is much more than just a collection of cells. It has genetic patterns, specific cell types, 3D structure and The Heppenstall group combines molecular, imaging and electrophysiological arrangement. Scientists at EMBL in Barcelona trace the connections between techniques to examine how sensory neurons turn information about touch and pain into electrical signals. embl.org/heppenstall these scales. They unveil how tissues develop, work, regenerate and heal. Thanks to the site’s imaging facilities, researchers can observe, manipulate and model how changes in genes percolate through cells, tissues and organs, in health and disease. Christophe Lancrin – Generation of a haematopoietic progenitor and stem cells during development Group Leader – Joint appointment with the Developmental Biology Unit James Sharpe – Multicellular systems biology The Lancrin group studies the haematopoietic system and looks to develop strategies to Head of the Tissue Biology and Disease Modelling Unit; Senior Scientist improve methods for generating blood cells from stem cells. embl.org/lancrin The Sharpe group brings together an interdisciplinary team of biologists, physicists and computer scientists to build a multi-scale computer simulation of a paradigm of organogenesis – mammalian limb development. embl.org/sharpe

Joint appointments to the Epigenetics and Neurobiology Unit Martin Jechlinger (Cell Biology and Biophysics) – 7 Robert Prevedel (Cell Biology and Biophysics) – 8 Kyung-Min Noh (Genome Biology) – 12 Anton Enright (EMBL-EBI) – 19

30 Research in brief 2017 31 Epigenetics and Neurobiology – Rome

30 Research in brief 2017 31 Index A H L O

Aken, Bronwen 21 Cuylen-Häring, Sara 6 Hackett, Jamie 30 Lamzin, Victor 27 O‘Donovan, Claire 23 Schwab, Yannick 17

Alexandrov, Theodore 16 Häring, Christian 6 Lancrin, Christophe 30 Orchard Sandra 23 Sharpe, James 31

Arendt, Detlev 9 D Hennig, Janosch 14 Leach, Andrew 22 Stegle, Oliver 12, 20 Asari, Hiroki 29 De Renzis, Stefano 10 Hentze, Matthias 5 Lemke, Edward 14 P Steinmetz, Lars 12

Aulehla, Alexander 9 Diz-Munoz, Alba 6 Heppenstall, Paul 30 Lénart, Peter 7 Panne, Daniel 26 Svergun, Dmitri 28

Avner, Philip 29 Hermjakob, Henning 22 Leptin, Maria 5 Parkinson, Helen 23

E Hiiragi, Takashi 10 Lewis, Joe 16 Patil, Kiran 15 T B Ellenberg, Jan 6 Huber, Wolfgang 11 Löw, Christian 28 Patwardhan, Ardan 23 Thornton, Janet 20

Barabas, Orsolya 13 Enright, Anton 19 Hufnagel, Lars 7 Paulsen, Malte 17 Typas, Nassos 12

Bateman, Alex 18 Ephrussi, Anne 9 M Pepperkok, Rainer 16 Beck, Martin 14 I McCarthy, Andrew 26 Peri, Francesca 10 V Beltrao, Pedro 18 F Ikmi, Aissam 10 McEntyre, Johanna 22 Petryszak, Robert 24 Velankar, Sameer 24

Beneš, Vladimír 16 Fiedler, Stefan 27 Iqbal, Zamin 19 Mahamid, Julia 15 Petsalaki, Evangelia 20 Vizcaino, Juan Antonio 24

Birney, Ewan 18 Finn, Rob 21 Marcia, Marco 26 Prevedel, Robert 8

Bork, Peer 13 Flicek, Paul 19 J Marioni, John 20 W Boulard, Matthieu 29 Furlong, Eileen 11 Jechlinger, Martin 7 Marquez, José A. 26 R Wilmanns, Matthias 27

Brazma, Alvis 18 Martin, Maria J. 23 Remans, Kim 17

Briggs, John 14 G K Meijers, Rob 28 Ries, Jonas 8 Y

Galej, Wojciech 25 Keane, Thomas 22 Merten, Christoph A. 12 Yates, Andy 24

C Gavin, Anne-Claude 14 Kersey, Paul 22 Müller, Christoph 13 S Cipriani, Florent 25 Gerstung, Moritz 19 Kleygwegt, Gerard 19 Sachse, Carsten 15 Z Cochrane, Guy 21 Gibson, Toby 14 Korbel, Jan 11 N Sarkans, Ugis 24 Zaugg, Judith 15

Crocker, Justin 9 Goldman, Nick 19 Kosinski, Jan 27 Nédelec, François 7 Savitski, Mikhail 17 Zeller, Georg 15

Cunningham, Fiona 21 Gross, Cornelius 29 Kowalinski, Eva 25 Neveu, Pierre 7 Schneider, Thomas 28 Zerbino, Daniel 24

Cusack, Stephen 25 Krebs, Arnaud 11 Noh, Kyung-Min 12 Schultz, Carsten 8

32 Research in brief 2017 Research in brief 2017 33 Index A H L O