EMBL-EBI Industry Partnerships: Work with us to solve your data challenges

Partnering with industry has been a core part of EMBL-EBI’s mission right from the very beginning and a significant number of our users come from this sector. As we celebrate an incredible 25 years of industry collaboration next year, let’s hear from Andrew Leach, the new Head of Industry Partnerships at EMBL-EBI to find out a bit more.

Image: Dr Andrew Leach, joined EMBL-EBI in August 2016 following a 20 year career at GSK Research and Development. He took on the role as Head of Industry Partnerships in the summer this year, and will also continue as Head of Chemical Biology.

Industry Partnerships: What does this mean at EMBL-EBI?

Industry Partnerships at EMBL-EBI is about helping to connect public and industry science. We aim to foster and facilitate collaboration, knowledge exchange and networking between scientists and technologists at EMBL-EBI and their counterparts working in industry. We work across multiple sectors and with organisations from very large multinationals to very small start-ups.

Tell us more about the opportunities for scientists in industry to interact with EMBL-EBI.

EMBL-EBI’s Industry Programme is a subscription-based programme for global companies who are using EMBL-EBI’s data and resources as part of their research and development. Representatives from the member companies meet regularly in a forum where we share details of the latest innovations in EMBL-EBI’s services and research. The programme also organises a series of knowledge exchange workshops that explore new emerging areas for R&D. These events are open to any employee of the member companies. The programme also provides a great opportunity for scientists to meet their peers in a pre-competitive, science-oriented environment to discuss the latest developments.

We are always keen to hear of opportunities to explore new strategic partnerships with industry. Open Targets is an excellent example; this ground-breaking public-private consortium was established in 2014 with the overall goal of improving how we identify and prioritise drug targets. Open Targets currently involves six partners: EMBL-EBI, the Wellcome Sanger Institute, GlaxoSmithKline, Bristol Myers Squibb, Takeda and Sanofi.

We also have a proud history of research collaborations that bring together expertise from academia and industry to work on a common research problem or to address a particular data or technology challenge. One particular advantage of collaborating with EMBL-EBI is that we have tremendous flexibility in the way that collaborations can be set up, from small projects lasting a few months, to much larger projects. Key to success is active participation and commitment from everyone involved.

What about smaller companies? 

Every company has to start somewhere and we are committed to engage with small and medium-sized enterprises (SMEs) and start-up enterprises. These are very often the drivers of innovation, and we find that such organisations make extensive use of the resources available at EMBL-EBI. We actively work with organisations such as OneNucleus, the UK Trade and Investment agency (UKTI), the InnovateUK Bioinformatics knowledge-transfer network and the ELIXIR SME and Innovation Forum to showcase the opportunities at EMBL-EBI. Of course, we are also very keen to hear from any smaller company interested in collaborating more directly with us on a particular problem.

What can be achieved by connecting with industry?

Having worked in industry myself (for many years at GSK), I know that industry science is often just as cutting-edge as in traditional academic circles – but historically it has been much less visible due in part to commercial sensitivities together with the fact that publication was not seen as a key goal in industry. These attitudes are changing now; there is a real drive within industry to collaborate externally and especially with leading academic groups and institutions. Industry can bring “real world” applications of the resources and research that we do at the EMBL-EBI; it can be very rewarding to see how the work we do can translate into practical applications. Plus, it can be a way for students and post-docs to get some insights into what a career in industry looks like, and potentially for industry to identify potential recruits for the future!

What would you like to see in the future for Industry Partnerships at EMBL-EBI?

I would like to see our connections with industry continue to grow and strengthen. We have historically had very strong connections with the Pharma and biotech sectors and it would be good to see us strengthen our relationships in other areas of bioscience and also with relevant data science and technology sectors. Of course, we are always keen to create new large-scale strategic partnerships such as Open Targets but we also recognise that a smaller-scale, one-on-one collaboration for example between an SME and an EMBL-EBI Principle Investigator can be equally fruitful. We also want to make further steps to encourage entrepreneurs; this includes working with Jo Mills (Entrepreneurship and Innovation Centre Manager) who with her team is creating a new Startup School for genomics and biodata. This will support early-stage ideas and provide knowledge and confidence to develop them into future products or services.

We always welcome opportunities to explore new partnerships and ventures.

Find out moreGet in touch

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Best Poster Awards – Target Validation Using Genomics and Informatics

Meet Giovanni Spirito and Borja Gomez Ramos – the two poster prize winners at the recent EMBL – Wellcome Genome Campus Conference: Target Validation Using Genomics and Informatics (8 – 10 Dec 2019).

Identification and prioritization of candidate causal genomic variations from individuals affected by ASD

PHOTO: Giovanni Spirito

Authors: Giovanni Spirito (1), Diego Vozzi (2), Martina Servetti (3), Margherita Lerone (3), Maria Teresa Divizia (3), Giulia Rosti (3), Livia Pisciotta (4), Lino Nobili (4), Irene Serio (4), Stefano Gustincich (2), Remo Sanges (1)

Next generation sequencing (NGS) technologies enabled the extensive study of the genomics underlying human diseases. Namely whole exome sequencing (WES) represents a cost-efficient method which can lead to the detection of multiple classes of genomic variants and the discovery of novel disease-associated genes. One of the drawbacks of this approach however, is the large number of genomic variants detected in each analysis. Automated variant prioritization strategies are therefore required. This is particularly important in the case of complex disease such as ASD, whose genetic etiology is still poorly understood. To this aim we built a custom computational framework capable, from raw WES data, to automatically detect four classes of genomic variants (SNPs, indels, copy number variants and short tandem repeat variants) and prioritize them in regards to their relevance to a specific phenotype. We tested this framework on a selection of 29 trios including probands affected by severe and undiagnosed rare phenotypes and a small cohort of 10 trios all featuring healthy parents and one offspring affected by autism spectrum disorder (ASD). We were able to successfully detect rare and de novo high penetrance variants which have been validated and confirmed as causative among the undiagnosed probands. In the specific case of the ASD cohort we could highlight several genes which are not implicated in autism susceptibility, but nevertheless whose connections to genes relevant for ASD could suggest a possible involvement in the phenotype. Furthermore, our approach enabled us to detect several instances characterized by the presence of multiple candidate variants within genes belonging to the same canonical pathway in one proband. Our workflow allows to detect and prioritize multiple classes of genomic variants in order to both highlight rare high penetrance disease-causative mutation, and possibly reconstruct the genomics at the basis of complex ASD phenotypes.

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(1) SISSA, Italy, (2) IIT, Italy, (3) Gaslini Institute, Italy, (4) University of Genova, Italy


Omics data integration for the identification of cell-type-specific gene regulatory networks and regulatory variants in Parkinson’s disease

PHOTO: Borja Gomez Ramos

Authors: Borja Gomez Ramos (1,2), Jochen Ohnmacht (1,2), Nikola de Lange (2), Aurélien Ginolhac (1), Aleksandar Rakovic (5), Christine Klein (5), Roland Krause (2) , Marcel H. Schulz (6), Thomas Sauter (1), Rejko Krüger (2,3,4) and Lasse Sinkkonen (1)

Genome-Wide Association Studies (GWAS) have identified many variants associated with different diseases. However, it is still a challenge to make sense of this data as the majority of genetic variants are located in non-coding regions, complicating the understanding of their functionality. In the last few years, it has been found that non-coding genetic variants concentrate in regulatory regions in the genome, which are cell type and cell-stage specific. In this project, we seek to identify functional Parkinson’s disease GWAS non-coding genetic variants that could make carriers more prone to developing PD. To do so, we are using induced pluripotent stem cell (iPSC) technology to differentiate somatic cells into midbrain dopaminergic (mDA) neurons, astrocytes and microglia. Assessing their chromatin accessibility, active chromatin regions and transcriptome, we can identify crucial regulatory regions in the genome, key transcription factors and derive the gene regulatory networks for the three different cell types. Then, we will map the non-coding genetic variants to the different regulatory regions and predict their effect in silico for the subsequent validation in vitro. This innovative approach will also identify novel factors controlling cell fate and cell identity.

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(1) Life Sciences Research Unit, University of Luxembourg, Luxembourg, (2) Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, (3) Centre Hospitalier de Luxembourg (CHL), Luxembourg, (4) Luxembourg Institute of Health (LIH), Luxembourg, (5) Institute of Neurogenetics, University of Lübeck, Germany, (6) Institute for Cardiovascular Regeneration, Uniklinikum and Goethe University Frankfurt, Germany


Working on your own conference poster? Then check out 10 tips to create a scientific poster people want to stop by.

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