ARISE Research Focus

Understanding life in the context of its environment

Technology development, especially with the purpose of enriching service provision in the life sciences, is currently one of EMBL’s main strategic focuses.

Research focus

EMBL runs several engineering teams, which support researchers in designing instruments and exploring new challenges in instrumentation.

EMBL provides a diverse range of practical services for life scientists worldwide by developing technologies in imaging, chemical biology, computational modelling, microfluidics, robotics, X-ray optics, high-precision mechanics, data acquisition, automation, bioinformatics and software development, and integrated structural biology. The future EMBL Imaging Centre will be one of the EMBL technology platforms and will provide access to the latest technologies in light and electron microscopy, alongside data analysis facilities and expert support. It will allow scientists and industry to use and develop new microscopy techniques to visualise the smallest building blocks of life, and thus its basic processes.

To find out more about the groups and teams that are part of the ARISE programme, see the overview of ARISE groups and partner organisations below.

Research at EMBL

Research at EMBL is conducted by more than 120 groups and teams, enabled by over 1 700 staff from more than 80 countries. As well as biologists, biochemists, and bioinformaticians, researchers include mathematicians, physicists, chemists, computer scientists, and engineers. They pursue their interests in broad thematic units spanning scales from single molecules to complex systems and organisms, combining methods and technologies from diverse disciplines.

In the past five years, EMBL researchers have published more than 3 000 articles and received 785 grants. Around one in every three EMBL scientists is an inventor — in the past 20 years, EMBL researchers have made 1 060 invention disclosures, created 20 start-up companies, and generated €100 million in income.

EMBL’s core facilities and other service platforms provide services and physical access for more than 3 200 scientists each year, and EMBL’s databases and bioinformatics tools handle more than 35 million data requests each day.

Learn more about EMBL

Participating groups and teams

The following EMBL group and team leaders are participating in the ARISE programme.

Theodore Alexandrov

Team Leader, Structural and Computational Biology Unit

EMBL Heidelberg

Technology fields:AI and machine learning, imaging, microscopy, software development, metabolomics

Life Science fields: biotechnology, cell biology, developmental biology, epigenetics, neurobiology, tissue biology, metabolism

Read more The Alexandrov team develops experimental and computational methods as well as software for spatial and single-cell metabolomics. We are seeking technology-focused method developers with experimental and/or computational skills or with expertise in software development to join us to develop next-generation services for ultrahigh-resolution spatial metabolomics.

Alex Bateman

Team Leader | Protein sequence resources

EMBL-EBi, Hinxton, UK

Technology fields: AI and machine learning, bioinformatics, data management

Life Science fields: bioinformatics research, computational biology, structural biology

Read more My group provides a wide range of world leading resources for protein and non-coding RNA sequence and families (InterPro, Pfam, RNAcentral & Rfam). We are particularly interested in applying modern ML/AI approaches to enhance our resources.

Peer Bork

Director of EMBL Heidelberg (Scientific Activities)

Group Leader | Structural and Computational Biology Unit

EMBL Heidelberg, Germany

Technology fields: bioinformatics, data science and big data, AI and machine learning

Life Science fields: bioinformatics research, computational biology, planetary biology

Read more The computational biology group has developed and is maintaining Web services and resources on (meta) genomics and function prediction with more than 400.000 different users per month. The current focus is planetary biology that includes global microbial sampling and analysis, with needs for (meta) data organisation and visualization.

Alvis Brazma

Team Leader | Functional Genomics

EMBL-EBi, Hinxton, UK

Technology fields: bioinformatics, data management, image analysis

Life Science fields: bioinformatics research, cell biology, computational biology

Read more The spatial localisation of gene and protein products in a cell or in an organism has a crucial importance in biology and are studied by a range of different technologies, including spatial transcriptomics and quantitative microscopy. These different types of data are collected in different bioinformatics resources, but are closely linked; In particular there is a growing need to link imaging data in BioImage Archive with spatial transcriptomics data in Expression Atlas, which will be the focus of the potential projects.

Guy Cochrane

Team Leader | Data Coordination and Archiving

EMBL-EBI, Hinxton, UK

Technology fields: bioinformatics, data management, data science and big data, software development, data standards

Life Science fields: bioinformatics research, computational biology, genome biology

Read more Serving a broad scientific community of data generators and consumers, Cochrane’s team builds and delivers scalable open technologies, tools and services for the management, sharing, global exchange and analysis of sequence and related data. Through our diverse collaborations, these are deployed across such areas as health (e.g. the European COVID-19 Data Platform), agriculture (e.g. the FAANG Data Centre), biodiversity (e.g. the Darwin Tree of Life) and marine science (e.g. TARA Oceans).

Alvaro Crevenna

Head of Microscopy Service

EMBL Rome, Italy

Technology fields: automation, image analysis, imaging, microscopy

Life Science fields: epigenetics, tissue biology

Read more As the head of microscopy, I am using my expertise in optics, programming and image analysis for two purposes: a, to further develop imaging technology; and b, to establish complex platforms such as spatial transcriptomics, tissue profiling and correlative X-ray imaging/super-resolution microscopy. I aim at bringing these services for the wider European research community through academic or industry collaborations.

Justin Crocker

Group Leader | Developmental Biology Unit

EMBL Heidelberg, Germany

Technology fields: automation, microfluidics, robotics

Life Science fields: biotechnology, developmental biology, planetary biology

Read more Our group builds automation and robotics pipelines for high-throughput developmental biology. We build experimental frameworks that will serve as platforms for future research by allowing a broader community of users to build, execute, and share similar technologies.

Rob Finn

Team Leader | Sequence Families

EMBL-EBI, Hinxton, UK

Technology fields: data science and big data, software development, bioinformatics

Life Science fields: computational biology, genome biology, planetary biology

Read more My group focuses on the analysis of the microbes found within the environment or associated with a host organism, such as humans or plants. DNA sequencing technologies have revolutionised modern molecular biology, facilitating large-scale sequencing of microbial genomes. However, concomitant with the data deluge, there is an urgent need to develop robust computational frameworks that enable these genomes to be rapidly and continually collated, compared, and functionally annotated. Capturing this biodiversity and presenting quality reference datasets enables biologists to gain a greater understanding of evolutionary biology and the adaptations microbes have made to enable them to survive in diverse environments.

Paul Flicek

Associate Director of EMBL-EBI Services

Head of Genes, Genomes & Variation Services

EMBL-EBI, Hinxton, UK

Technology fields: AI and machine learning, bioinformatics, data science and big data

Life Science fields: bioinformatics research, computational biology, genome biology

Read more The Ensembl/GENCODE gene annotation, the leading reference annotation in the field of human and mouse genomics, is the fruit of 20 years of collaborative research, involving a broad network of biologists, experimentalists and bioinformaticians across the world who study all facets of gene transcription, through the convergence of a wide variety of experimental datasets (ESTs, RNA-Seq, CAGE, ChIP-Seq, etc) and computational analyses (evolution, motif discovery, etc). Our work is foundational to the majority of human and mouse genomic studies, hence our utmost efforts to reach exceptional accuracy in our annotations.

Eileen Furlong

Head of Genome Biology Unit

Group Leader | Genome Biology Unit

EMBL Heidelberg, Germany

Technology fields: bioinformatics, data science and big data, image analysis, software development

Life Science fields: computational biology, genome biology, tissue biology

Read more The Genomics Technology Development (GenTechDev) Team develops a range of state-of-the-art spatial, multimodal single-cell genomics technologies (e.g. Seq-FISH+) to advance genomic research throughout EMBL, building on our rich expertise in cutting-edge single-cell genomics technology development and imaging. The GenTechDev team work closely with EMBL’s core facilities to support users throughout EMBL with their experimental design, technology development and initial data analysis, helping EMBL scientists to stay at the forefront of developments in single-cell (spatial) genomics.

Maria Garcia Alai

Head of EMBL Sample Preparation and Characterisation Facility

EMBL Hamburg, Germany

Technology fields: bioinformatics, chemistry and chemical biology, computational modelling

Life Science fields: bioinformatics research, biophysics, structural biology

Read more The SPC facility supports external and internal researchers carrying out structure determination experiments and has a strong track record in the development and implementation of new technologies and methods to precisely determine the stability, shape and size of different biomolecules and biomolecular assemblies. We develop our own software for the data analysis of biophysical interactions such as Kinetic analysis, Time resolved conformational changes, Analysis of thermal stability data beyond a simple melting temperature analysis, Ligand screening and Processing of spectral data.

Kristina Haase

Group Leader | Tissue Biology and Disease Modelling Unit

EMBL Barcelona, Spain

Technology fields: image analysis, imaging, microscopy, microfluidics

Life Science fields: biotechnology, translational research, disease modelling

Read more Our group develops human disease models using primary and iPSC-derived cells and by in-house design and fabrication of novel microfluidic chips. Development of these models and associated assays (image-based and biological) are employed for vascular tissue engineering, drug development, and stem cell therapy applications and are at the core of our research. We interface with industrial and clinical partners to develop these models for practical real-world applications.

Wolfgang Huber

Group Leader | Genome Biology Unit

EMBL Heidelberg, Germany

Technology fields: AI and machine learning, bioinformatics, software development

Life Science fields: computational biology, cancer biology, genetics

Read more This exciting opportunity in the group of Wolfgang Huber (www.huber.embl.de) includes development and maintenance of open source scientific software in statistics, data science and omics, and user experience improvement and training for a new, emerging national medical genome database. The engineer will work in the context of the Bioconductor network—the largest biological data science software project in the world and a vibrant international community (DOI 10.1038/nmeth.3252)—and will have the opportunity to drive forward one or more of the following topics: improved user experience, support tools for scientific developers, production of training and online help material, software to move forward reproducible research and open science, cloudification of research software, inter-language interfaces (R / Julia / Python / Javascript), factorization and low-dimensional embeddings of large matrices, such as from single cell multi-omics. As a contributor to the German Human Genome Archive (https://ghga.dkfz.de), a large national consortium to provide a data resource for human genomes and other omics data modalities for biomedical research and the future development of healthcare, he/she will be able to contribute to the development of its user experience and interface (in particular, programmatic access), training and online support material, in particular by developing example data analysis usage workflows.

Jan Korbel

Group Leader | Genome Biology Unit

EMBL Heidelberg, Germany

Technology fields: automation, robotics

Life Science fields: computational biology, genome biology, translational research

Read more

Dr. Korbel’s group is developing key experimental and computational methods for structural variation (SV) detection and functional dissection. In the past this has included the development of by now de facto standard methodologies used widely in human genetics and biomedicine, such as methods based on paired-end mapping, co-developed by Jan Korbel, which Science considered as one of the scientific breakthroughs of the year 2007. Recently, the group devised a method based on haplotype-resolved single cell DNA template sequencing, termed single cell tri-channel processing (scTRIP) which for the first time enables the scalable and direct detection of SVs including of structural mutational processes in single cells, and as is paves the way to obtain insights into disease pathomechanisms including cancer development. We currently see exponential growth of the use of single cell DNA template sequencing (a.k.a. Strand-seq), with 10 laboratories having used the technique this year in collaboration with us and a strong upwards trend. Application areas include single cell sequencing of genetic variation, to single cell multi-omics and haplotype-resolved genomic assemblies. An ARISE fellow joining the Korbel group could be involved in transferring this novel technique into a high-throughput service for the community by expanding its use beyond a pure research setting, and through advanced state-of-the-art instrumentation and miniaturization including via robotics and/or microfluidics, as well as big data analytical approaches. There will additionally be exciting opportunities to take part in international collaborations that will apply this technique to decipher sources of human genetic variation and their phenotypic consequences.

Anna Kreshuk

Group Leader | Cell Biology and Biophysics Unit

EMBL Heidelberg, Germany

Technology fields: AI and machine learning, image analysis, software development

Life Science fields: cell biology, developmental biology, structural biology

Read more Kreshuk Lab develops novel machine learning-based methods for microscopy image analysis, in collaboration with both internal and external scientists. To make such methods accessible to scientists without computational expertise, we also develop and maintain the ilastik software, used by thousands of biologists all over the world.

Andrew Leach

Head of Chemistry Service

EMBL-EBI, Hinxton, UK

Technology fields: AI and machine learning, software development, cheminformatics

Life Science fields: structural biology, drug design, computational biology

Read more We develop and deliver world-leading data and informatics resources, including ChEMBL, that enable important practical drug discovery questions to be addressed (e.g. “which target is best for this disease?”; “what molecule should I make next?”; “is this compound likely to be toxic?”). Our work involves leading technologies in cheminformatics, data science, software engineering, machine learning, AI and text analytics (among others) and team members develop skills that are in high demand in industry and academia.

Julia Mahamid

Group Leader | Structural and Computational Biology Unit

EMBL Heidelberg, Germany

Technology fields: imaging, microscopy, automation, software development

Life Science fields: biophysics, structural biology, computational biology

Read more Cellular cryo-electron tomography (cryo-ET) is the only method available for obtaining in situ structural information across scales - from whole cells to individual macromolecules. Fellows in the ARISE program can engage in any of the following developments of innovative technology solutions to advance in-cell cryo-ET to a higher level of robustness: engineering and 3D microprinting of tailored specimn carriers, correlative (super-resolution) light and electron microscopy, automation of cryo-focused ion beam thinning and lamella lift-out, advanced software developemnt for computational analysis. We are engaged in a large number of internal and external collaborations that lend our expertise to a wide range of biological questions, and work with industry partners for instrumentation development.

José Marquez

Head of Crystallisation Facility

EMBL Grenoble, France

Technology fields: AI and machine learning, chemistry and chemical biology, data management, data science and big data

Life Science fields: drug design, structural biology, translational research

Read more Our Team has pioneered the development of Online Crystallography; fully automated protein-to structure pipelines integrating crystallization, synchrotron data collection and crystallographic data analysis into continuous workflows operated via the web. These pipelines are currently used by hundreds of scientists worldwide and are based on the CrystalDirect technologies and CRIMS software, which we have contributed to develop. Recently, we have implemented a fully automated pipeline for ligand and fragment screening to support structure guided drug design. EMBL Grenoble is co-located with the European Synchrotron Radiation Facility (ESRF) in Grenoble, which produces some of the world’s most brilliant X-ray beams worldwide. EMBL and ESRF jointly operate six crystallography beamlines one of which is the fully automated MASSIF-1 whose operation is highly integrated with the operations at EMBL’s HTX Lab. Our interdisciplinary team offers opportunities for scientists, engineers and software developers to work in one of the leading infrastructures for structural biology within the areas of protein crystallography, drug desing, automation, and large-scale scientific data management and analysis. Currently, we are particularly interested in profiles in structural biology or computer science orientated towards one or several of the following areas: fragment screening, structure guided drug design, cloud computing, machine learning and artificial intelligence.

Maria J. Martin

Team Leader | Protein Function Development

EMBL-EBI, Hinxton, UK

Technology fields: AI and machine learning, bioinformatics, data management

Life Science fields: bioinformatics research, computational biology

Read more Our work focuses on developing technologies for the delivery of scalable and robust data infrastructures for protein data (SQL and NoSQL databases, programming languages, Graph Knowledgebases, Apache Lucene and Solr search engines, clustering algorithms) as well as developing novel data mining methods for protein function prediction and large-scale data analysis. The team use Deep Learning algorithms for extracting knowledge from biological data and recommendation systems.

Simone Mattei

Team Leader | Structural and Computational Biology Unit

EMBL Heidelberg, Germany

Technology fields: automation, image analysis, imaging, microscopy

Life Science fields: biophysics, cell biology, structural biology

Read more Our team is part of the EMBL Imaging Centre, a new service unit with the mission to make the cutting-edge electron and light microscopy technologies available to the scientific international user community, including academically developed methods not yet commercially available. We develop methods and software supporting cryogenic correlative light and electron microscopy (cryo-CLEM) and high-throughput fully automated pipelines to tackle the current challenges in cryo-EM sample preparation and screening.

Andrew McCarthy

Team Leader | Synchrotron Crystallography Team

EMBL Grenoble, France

Technology fields: automation, chemistry and chemical biology, data management, software development

Life Science fields: biophysics, drug design, structural biology

Read more The McCarthy team is composed of engineers and scientists who provide operational and user support on seven high brilliance X-ray based structural biology beamlines with proven expertise in developing automated data collection instruments and methods in collaboration with our colleagues at the European Synchrotron Radiation Facility (ESRF). We will continue to optimise data collection protocols and analyses methods as well as develop and expand the experimental instruments and techniques currently available in order to realise the scientific potential of the recently completed ESRF-Extremely Brilliant Source upgrade for the European structural biology community.

Ellen Mcdonagh

Open Targets Informatics Science Director

EMBL-EBI, Hinxton, UK

Technology fields: bioinformatics, data management, data science and big data

Life Science fields: disease modelling, drug design, genome biology

Read more In the past, I worked closely with bioinformaticians, developers, scientific curators and clinicians to create an open source crowdsourcing knowledgebase for rare disease gene evaluation, which is utilised within a genome analysis service at Genomics England for patient diagnosis with the NHS, as well as by researchers and clinicians worldwide. In my current role, the open source Open Targets Platform, Genetics Portal and COVID-19 target prioritisation tool provide aggregated data, visualisations and tools to inform evidence-based prioritisation of targets and therapeutic hypothesis generation for drug discovery for external and internal scientists worldwide.

Johanna McEntyre

Associate Director of EMBL-EBI Services

Head of Literature Services

EMBL-EBI, Hinxton, UK

Technology fields: AI and machine learning, data management, data science and big data, software development

Life Science fields: bioinformatics research, computational biology

Read more Using machine learning to find information buried in the research literature promises to change the way we do literature searching and more specifically at EMBL-EBI, will help curators add key information to data resources such as UniProt, the PDB, IntAct, and Reactome. The Europe PMC publications database provides a rich data source for the development of text mining techniques to extract key entities or assertions, rank article results, or article classification, in collaboration with one more curated data resources at the EBI.

Christoph Müller

Head of Structural and Computational Biology Unit

Group Leader | Structural and Computational Biology Unit

EMBL Heidelberg, Germany

Technology fields: automation, data management, imaging, microscopy

Life Science fields: biophysics, drug design, structural biology

Read more Our group is pioneering the use of single-particle cryo-EM in the drug discovery process. Through the ARISE program we plan to develop a stable workflow for the high-throughput screening of ligand binding to drug targets by single-particle cryo-EM. Critical elements of the workflow comprise sample tracking throughout the workflow, automated EM grid dispensing, automated cryo-EM sample evaluation and HTP processing.

Irene Papatheodorou

Team Leader | Gene Expression

EMBL-EBI, Hinxton, UK

Technology fields: AI and machine learning, bioinformatics, software development

Life Science fields: bioinformatics research, computational biology

Read more Cellular and organismal phenotypes are described via EMBL-EBI’s resources: Expression and Single Cell Expression Atlas, for gene expression; PRIDE, for protein expression. Integration in a single platform of gene and protein expression data is quite challenging, requiring novel analysis (including e.g. artificial intelligence approaches) and/or visualisation techniques for biologists to take full advantage to having gene and protein expression side by side and uncover relationships between gene and protein expression within and across different species, in baseline or diseased conditions.

Gergely Papp

Team Leader | Instrumentation Team

EMBL Grenoble, France

Technology fields: automation, image analysis, software development

Life Science fields: drug design, structural biology

Read more

Over the two past decades, the instrumentation team has developed instruments for neutron and x-ray scattering experiments with constant objectives of supporting the most challenging structural biology experiments and making the instruments available to the scientific community worldwide through services provided by synchrotron beamlines and high throughput crystallization facilities.

As an example, our CrystalDirect automated harvesting technology is used at ALPX, an EMBL spinoff company (https://www.embl.org/news/lab-matters/alpx/), which provides MX services for drug design. Relying on patent applications, and technology transfers, most of the instruments used in Macromolecular Crystallography are commercialized worldwide (CrystalDirect™ automatic crystal harvester, HC-Lab crystal Humidity Controller, MD2S and MD3 X-ray Micro diffractometer families, BioSAXS sample changers). A similar strategy is being developed for our automated Cryo-EM sample grids preparation system.

Rainer Pepperkok

Director of Scientific Core Facilities and Scientific Services

Head of Advanced Light Microscopy Facility

EMBL Heidelberg, Germany

Technology fields: automation, image analysis, imaging, microscopy, microfluidics

Life Science fields: bioinformatics research, biophysics, cell biology

Read more The ALMF and Pepperkok Team at EMBL Heidelberg develop and provide a service in advanced light microscopy and image analysis methods to EMBL scientists and external users from and beyond EMBL member states. Currently we are working on projects developing technology to provide a service in spatial multi-omics/phenomics to integrate automated phenotype recognition in complex biological samples by advanced light microscopy and online image analysis to sort the phenotypes for subsequent (single cell) multi-omics analyses.

Robert Prevedel

Group Leader | Cell Biology and Biophysics Unit

EMBL Heidelberg, Germany

Technology fields: automation, imaging, microscopy, software development

Life Science fields: biophysics, developmental biology, neurobiology

Read more We are developing advanced optical imaging methods that are based on multi-photon microscopy, active wave-front shaping, photo-acoustics as well as high-resolution spectroscopy. Our aim is to establish our new approaches as disruptive technologies in the life sciences and to further engineer and automate our prototypes for routine service provision.

Jonas Ries

Group leader | Cell Biology and Biophysics Unit

EMBL Heidelberg, Germany

Technology fields: image analysis, imaging, microscopy, software development

Life Science fields: biophysics, cell biology, structural biology

Read more The Ries group develops superresolution microscopy methods based on single-molecule localization microscopy (SMLM) and MINFLUX. With new optical and computational approaches, we push the resolution of microscopy towards the nanometer scale to enable imaging the structure and dynamics of multi-protein machines in cells.

Jim Sawitzke

Head of Genetic & Viral Engineering Facility

EMBL Rome, Italy

Technology fields: genetic engineering, virology, molecular biology

Life Science fields: biotechnology, neurobiology, genome engineering

Read more For internal and external clients the Genetic & Viral Engineering Facility design and construct new viral cargos which can be delivered to cells or mice for labelling, gene editing, epigenetic modification or gene therapy. We are also developing new technologies and methodologies using these viral tools to more rapidly, accurately, and at a higher frequency create targeted DNA changes in a way that is more accessible to a wide range of researchers.

Thomas Schneider

Joint Head of Research Infrastructures

Group Leader

EMBL Hamburg, Germany

Technology fields: software development

Life Science fields: biophysics, structural biology

Read more EMBL Hamburg is operating synchrotron beamlines for macromolecular crystallography for several, decades. Currently, we are using radiation from PETRA III for which an upgrade to the next generation synchrotron technology is in the planning. For making synchrotron radiation usable for scientific user community we are constantly developing software for controlling high-rate and high-volume data acquisition, automated sample handling, data flows and data evaluation. A large part of this work takes place in international consortia.

Yannick Schwab

Team Leader | Cell Biology and Biophysics Unit

Head of Electron Microscopy Core Facility

EMBL Heidelberg, Germany

Technology fields: automation, imaging, microscopy, software development

Life Science fields: cell biology

Read more The Electron Microscopy Core Facility at EMBL is committed to provide access to state of the art methods in cellular electron microscopy to a large user baser from EMBL, its member states and beyond. Besides advanced methods for ultrastructural analysis, the EMCF is specialized in CLEM, in volume SEM and has recently developed workflows for high throughput TEM tomography data collection.

Jim Swoger

Head of Mesoscopic Imaging Facility

EMBL Barcelona, Spain

Technology fields: imaging, microscopy, optical instrumentation development

Life Science fields: developmental biology, tissue biology

Read more The Mesoscopic Imaging Facility develops technologies such as Selective Plane Illumination Microscopy (SPIM), Optical Projection Tomography (OPT), and related sample handling protocols that allow optical characterization of meso-scale biological samples. Our developments are made available through the Facility to scientists both within EMBL and in the international research community.

Vikas Trivedi

Group Leader | Tissue Biology and Disease Modelling Unit

EMBL Barcelona, Spain

Technology fields: automation, high-precision mechanics, robotics

Life Science fields: biotechnology, translational research, tissue engineering

Read more Trained as an engineer (focus: mechanical engineering and bioengineering), I switched to optics and instrumentation during my PhD where I developed 2-photon light sheet imaging based methods for deep and fast imaging. Current technological focus of my group is development of novel embryonic organoids and high-throughput, long term monitoring of such in vitro systems and therefore demands automated systems for protocol optimization and molecular characterization through staining, all of which can be provided as services to labs both within and outside EMBL as well as in industry.

Sameer Velankar

Team Leader | Protein Data Bank in Europe

EMBL-EBi, Hinxton, UK

Technology fields: AI and machine learning, data science and big data, information retrieval & relevance ranking

Life Science fields: bioinformatics research, structural biology, translational research

Read more Our work is focused on developing a scalable, state-of-the-art, integrated data management and delivery infrastructure for structural biology data (SQL databases, programming languages, Graph Knowledgebases, Apache Lucene and Solr search engines, clustering algorithms). We are keen on deploying machine learning and AI approaches for deriving knowledge from our integrated structural biology knowledge base. Our technology development work also involves better information retrieval and ranking systems and multiscale structural data visualisation tools (https://github.com/molstar) to enable scientific research in both academic and industry settings.

Juan Antonio Vizcaino

Team Leader | Proteomics resources and tools

EMBL-EBi, Hinxton, UK

Technology fields: bioinformatics, data science and big data, software development

Life Science fields: bioinformatics research, computational biology, proteomics

Read more Improving PRIDE’s functionality as the world-leading proteomics data repository, and the integration of proteomics data with other omics data types are two key aspects for the team in the near future. This offers the possibility for the fellow to work in different topics (e.g. data analysis, data visualisation, infrastructure, data management practises, etc), depending their background. In the context of data integration, this would involve different data types such as gene and protein expression information (together with Expression Atlas), post-translational modifications (UniProt), and (meta)proteomics data and (meta)genomics sequences (Ensembl, MGnify). Additionally, support in PRIDE for additional proteomics data types (e.g. top down proteomics, non-mass spectrometry methods) is also a key aspect in our future work.

Daniel Zerbino

Team Leader | Functional annotation of sequence variants and non-genic regions

EMBL-EBi, Hinxton, UK

Technology fields: AI and machine learning, bioinformatics, data science and big data

Life Science fields: bioinformatics research, computational biology, epigenetics

Read more My group focuses on the gene expression regulation mechanisms that guide the behaviour of cells as they differentiate and adjust to local conditions. We describe the genome's promoters and their enhancers by aggregating large arrays of multi-omic datasets (ChIP-Seq, DNAseI Hypersensitivity, ATAC-Seq, single-cell assays, eQTLs etc) into a structured Ensembl database, using a diversity of machine learning and visualisation approaches.

Michael Zimmermann

Group Leader | Structural and Computational Biology Unit

EMBL Heidelberg, Germany

Technology fields: chemistry and chemical biology, data science and big data, software development

Life Science fields: computational biology

Read more In combination with EMBL’s Chemical Biology Core Facility (CBCF) our laboratory combines high-throughput screening and computational approaches to develop tools and pipelines to investigate the mutual interactions between environmental contaminants and biological systems. In this context we are currently establishing a platform available to EMBL and Non-EMBL researchers that involves chemical libraries, screening pipelines together with computational tools, software, and data resources that will enable integrative analyses of the impact of environmental toxins on organisms at the molecular level.

Timo Zimmermann

Team Leader | Cell Biology and Biophysics Unit

EMBL Heidelberg, Germany

Technology fields: image analysis, imaging, microscopy

Life Science fields: biophysics, cell biology

Read more In the new EMBL Imaging Centre the Zimmermann Team will provide a wide range of light microscopy instrumentation that is not yet commonly available to external researchers. We also aim to efficiently connect highest resolution LM approaches (including cryo-fluorescence) to the corresponding EM technology offer of the Imaging Centre.

ARISE partner organisations

ARISE has a number of partner organisations that will support training of the ARISE fellows by providing the opportunity for long- or short-term secondments at their premises. Partner organisations are from both academic and non-academic sectors.

Academic (service-providing and technology-developing) organisations (alphabetically sorted)

Biology Center of the Czech Academy of Sciences, České Budějovice, Czech Republic

Center for Ecotoxicological Research, CETI, Podgorica, Montenegro

Center for Genomics Research, CRG, Barcelona, Spain

Center of Excellence for Biomedical Research, Montenegro

Central European Institute at Masaryk University, Brno, Czech Republic

Charles University, Faculty of Science, Prague, Czech Republic

Jessenius Faculty of Medicine, Comenius University Bratislava, Bratislava, Slovakia

Comenius University Bratislava, Slovakia

ETH Zurich, Functional Genomics Center, Zurich, Switzerland

European Synchrotron Radiation Facility, Grenoble, France

Fraunhofer Gesellschaft – Institute for Manufacturing and Production, Stuttgart, Germany

Friedrich Miescher Institute, Basel, Switzerland

German Cancer Research Center (DKFZ), Heidelberg, Germany

Heinrich-Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany

Institute of Structural Biology, IBS, CNRS, Grenoble, France

Institut Pasteur, Paris, France

Institut Curie, Paris, France

Instituto Gulbenkian de Ciência (IGC), Lisbon, Portugal

Institute of Advanced Biosciences, Grenoble, France

Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic

Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic

Institute of Molecular Genetics of the Czech Academy of Sciences, IMG,Prague, Czech Republic

KU Leuven, Leuven, Belgium

L-Università ta'Malta, Department of Applied Biomedical Sciences, Malta

Palacky University Olomouc, Faculty of Medicine and Dentistry, Olomouc, Czech Republic

UiT The Arctic University of Norway, Tromsø, Norway

The Francis Crick Institute, London, UK

Umeå University, Umeå, Sweden

University of Gothenburg, Centre for Cellular Imaging, Gothenburg, Sweden

Universität Hamburg (University of Hamburg), Hamburg, Germany

University of Heidelberg, Heidelberg, Germany

University of Montenegro, Podgorica, Montenegro

Vlaams Instituut voor Biotechnologie, VIB, Gent, Belgium

Vienna Biocenter Core Facilities GmbH, Vienna, Austria

Non-academic organisations (alphabetically sorted)

ARINAX Scientific Instrumentation, Grenoble, France,

Bayer AG, Division Crop Sciences, Monheim am Rhine, Germany

The Charité, Universitätsmedizin Berlin, Department of Urology, Berlin, Germany

CelGene Institute for Translational Research Europe, Seville, Spain

CrestOptics, Rome, Italy

Eli Lilly and Company Limited, Surrey, England, UK

European X-Ray Free-Electron Laser Company GmbH, EuXFEL, Schenefeld, Germany

F. Hoffmann-La Roche, Basel, Switzerland

Leica Microsystems GmbH, Wetzlar, Germany

Luxendo, a Bruker Company, Heidelberg, Germany

LyncéeTec SA, Lausanne, Switzerland

Merck Sharp & Dohme Corp (MSD), London, UK

New England BioLabs, NEB, Ipswitch, Massachusetts, USA

Novartis Institute for Biomedical Research Informatics, NIBR, Basel, Switzerland

Octapharma Biopharmaceuticals GmbH, Heidelberg, Germany

Olympus Europa SE & Co KG, Hamburg, Germany

SciBite Ltd., Cambridge, UK

Syngenta, Jealott's Hill International Research Center, Bracknell, UK

XtalConcepts GmbH, Hamburg, Germany


Learn more

Further information on the programme can be found in the following sections.

ARISE

An introduction to the ARISE Programme.

Programme overview

Develop skills uniquely required by Research Infrastructure Scientists.

How to apply

The ARISE Programme is open to experienced STEM professionals from the whole world.

Contacts

Who to contact and how to get in touch.

ARISE project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 945405.

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