InterPro version 95.0 and InterProScan 5.63-95.0 are now available!

InterPro now features hundreds of new methods integrated from partner databases, and InterProScan draws on over 39000 entries.

InterPro version 95.0 – new features include:

• The addition of 413 InterPro entries.

• An update to NCBIfam (12.0).

• Integration of 424 new methods from the CDD (157), NCBIfam (259), PANTHER (5), Pfam (2), SFLD (1) databases.

InterPro 95.0 covers 81.7% of UniProt Knowledgebase release 2023_03. It predicts Gene Ontology (GO) terms for over 144 million UniProt proteins via the InterPro2GO pipeline.

The new release includes an update to UniParc (uniparc_match.tar.gz) matches to InterPro methods. You can find this file on the InterPro ftp.

For full details, see the latest InterPro Release Notes.

## InterProScan 5.63-95.0

InterProScan 5.63-95.0 uses data from the newly released InterPro 95.0, which contains 39,227 entries.

You can find the full release notes on the InterProScan documentation.

If you need help with InterPro or InterProScan, please contact us using the InterPro helpdesk.

A collaboration between the Márquez group at EMBL Grenoble and Italian researchers from the European Biomedical Research Institute of Salerno (EBRIS) has led to the development and characterisation of a novel small molecule inhibitor, which shows promising activity against three SARS-CoV-2 variants.

In a publication in the European Journal of Medicinal Chemistry, the scientists describe a generation of compounds that would act against the main protease of SARS-CoV-2. One of these compounds is currently a clinical candidate for the development of an intranasal spray against SARS-CoV-2. Moreover, due to the highly conserved amino acid sequence of the active site of targeted enzymes among coronaviruses, this inhibitor could treat infections from different coronavirus species.

The Italian research group, led by Simone Di Micco, began studying SARS-CoV-2 in early 2020. Already interested in the design of new bioactive molecules, they quickly adapted their previous research on celiac disease towards this new direction. While Di Micco’s team could use in silico methodology to design new compounds that would target one of the key enzymes of the virus, they didn’t have a way to figure out the real-life binding interactions between the molecules and their biological target.

Structural biology is an essential discipline in molecular biology used in drug development. By obtaining the atomic structure of a molecule interacting with its biological target, structural biologists can give important insights about its mode of binding and use this information to design new molecules with improved affinity and specificity. The fully-automated X-ray crystallography pipelines developed and operated jointly by EMBL Grenoble and ESRF are especially suited for this, as they allow rapid screening of compound libraries and can be used to identify small molecules that bind the biological target.

However, Di Micco’s group had no prior expertise in structural biology, nor the equipment to perform the experiments. It was at this point that Di Micco attended a webinar hosted by Instruct-ERIC, a structural biology research infrastructure that supports European researchers by providing them with access to high-end technologies and methods. 

José Márquez, Head of the Crystallisation Facility at EMBL Grenoble, was one of the speakers and presented the automated protein-to-structure pipelines they developed in Grenoble based on the CrystalDirect technology and the CRIMS software. “I contacted the Márquez lab after the workshop and this is how our collaboration began,” said Di Micco.

Besides delivering high-quality science, EMBL’s structural biology services support the external research community across Europe by offering a range of approaches and infrastructures often based on unique technologies developed at EMBL.

The High-Throughput Crystallisation Laboratory (HTX Lab), operated by the Márquez team, is one of the most important facilities for high-throughput nano volume and crystallisation screening in Europe. These pipelines use the CrystalDirect technology for automated crystal harvesting and cryocooling. They combine this approach with the use of EMBL’s Crystallographic Information Management System (CRIMS), a web-based software suite providing interfaces for online design and evaluation of crystallographic experiments, with real-time access to results and experimental parameters.

With this system, scientists all over the world can mail in their samples and follow each step from the crystallisation to X-ray diffraction experiments and structure solution, obtaining the information needed remotely. “This is what makes HTX Lab different from other laboratories that perform crystallography,” said Rahila Rahimova, a postdoctoral fellow in the Márquez Team.

Rahimova, together with research technician Léa Mammri and José Márquez, supported Di Micco with their expertise in structural biology and biophysical methods, and performed X-ray crystallography studies to characterise the molecular interaction between the new compound and the SARS-CoV-2 main protease.

This interdisciplinary collaboration soon yielded results. The structural studies performed at EMBL Grenoble revealed how the compound binds to and inhibits the SARS-CoV-2 main protease, which is essential for the virus life cycle. Moreover, this provided important feedback to the Di Micco group who could then use it to further refine the drug design process. This resulted in a compound with very low cellular toxicity, reducing the risk of side effects.

“I would like to stress the importance of collaboration in science. In our case, it was also possible to obtain access to EMBL Grenoble facilities, services, equipment, and expertise thanks to ISIDORe.” said Di Micco. The Integrated Services For Infectious Disease Outbreak Research (ISIDORe) provides scientists studying infectious disease with access to European facilities, services, equipment, and expertise.

This research also ties into the Infection Biology transversal theme, part of EMBL’s 2022-26 Programme ‘Molecules to Ecosystems’. This theme aims to contribute to research on infectious diseases and the biology of their mechanisms, diagnostics, and treatment.

The next step for Di Micco is to test this molecule in a clinical trial, since this compound could pave the way towards the development of new treatments against COVID-19. “The infection’s highest concentration is in the nose at the beginning: before it goes to the upper airways and then in the lungs. An intranasal spray would simplify the administration of drugs without the assistance of nurses or doctors, or the need to go to the hospital,” he said.

Facilitare la scoperta di farmaci contro il COVID-19

Una collaborazione tra l’EMBL di Grenoble e gli scienziati dell’ EBRIS ha portato alla caratterizzazione di un nuovo composto con un’attività promettente contro le varianti del SARS-CoV-2

Una collaborazione tra il gruppo di Márquez dell’EMBL di Grenoble e i ricercatori italiani dello European Biomedical Research Institute of Salerno (EBRIS) ha portato allo sviluppo e alla caratterizzazione di una piccola molecola ad attività inibitoria, che mostra una buona efficacia contro tre varianti del SARS-CoV-2.

In una pubblicazione sull’European Journal of Medicinal Chemistry, gli scienziati hanno descritto un gruppo di composti che agirebbero contro la proteasi principale del SARS-CoV-2. Uno di questi composti è attualmente in fase di sperimentazione per lo sviluppo di uno spray intranasale contro SARS-CoV-2. Inoltre, grazie alla sequenza aminoacidica altamente conservata del sito attivo delle proteasi dei coronavirus, questo inibitore potrebbe agire contro le infezioni da diverse specie di coronavirus.

Il gruppo di ricerca italiano, guidato da Simone Di Micco, ha iniziato a studiare SARS-CoV-2 all’inizio del 2020. Già interessati alla progettazione di nuove molecole bioattive, hanno rapidamente adattato la loro precedente ricerca sulla celiachia a questa nuova direzione. Sebbene il team di Di Micco fosse in grado di progettare in silico nuovi composti in grado di colpire uno degli enzimi chiave del virus, le tecnologie a loro disposizione non consentivano di studiare le interazioni tra le molecole e il loro bersaglio biologico.

La biologia strutturale è una disciplina essenziale della biologia molecolare utilizzata nello sviluppo di farmaci. Ottenendo la struttura atomica di una molecola che interagisce con il suo bersaglio biologico, i biologi strutturali possono fornire importanti indicazioni sulle sue modalità di legame e utilizzare queste informazioni per progettare nuove molecole con maggiore affinità e specificità. I processi di cristallografia a raggi X completamente automatizzati, sviluppati e gestiti congiuntamente dall’EMBL di Grenoble e dall’ESRF, sono particolarmente adatti a questo scopo, in quanto consentono uno screening rapido di numerosi composti per identificare le molecole che si legano ad un determinato bersaglio biologico.

 Il gruppo di Di Micco non aveva precedente esperienza in biologia strutturale, né le attrezzature per eseguire gli esperimenti. Di Micco ha dunque partecipato a un webinar organizzato da Instruct-ERIC, un’infrastruttura di ricerca in biologia strutturale che sostiene i ricercatori europei fornendo loro l’accesso a tecnologie e metodi di alto livello.

José Márquez, responsabile della struttura di cristallizzazione dell’EMBL di Grenoble, era uno dei relatori e ha presentato le pipeline automatizzate da proteina a struttura sviluppate a Grenoble sulla base della tecnologia CrystalDirect e del software CRIMS. “Ho contattato il laboratorio di Márquez dopo il workshop ed è così che è iniziata la nostra collaborazione”, ha detto Di Micco.

Oltre a produrre dati scientifici di alta qualità, i servizi di biologia strutturale dell’EMBL sostengono la comunità scientifica in tutta Europa offrendo una serie di approcci e infrastrutture spesso basati su tecnologie uniche sviluppate all’EMBL.

Il laboratorio di cristallizzazione ad alto rendimento (HTX Lab), gestito dal team di Márquez, è una delle strutture più importanti in Europa per lo screening ad alto rendimento di nano volumi e cristallizzazioni. Queste pipeline utilizzano la tecnologia CrystalDirect per la raccolta e il raffreddamento automatico dei cristalli. L’approccio viene combinato all’uso del Crystallographic Information Management System (CRIMS) dell’EMBL, un software che fornisce interfacce per la progettazione e la valutazione online degli esperimenti cristallografici, con accesso in tempo reale ai risultati e ai parametri sperimentali.

Con questo sistema, gli scienziati di tutto il mondo possono spedire i loro campioni e seguire ogni fase, dalla cristallizzazione agli esperimenti di diffrazione dei raggi X e alla soluzione della struttura, ottenendo le informazioni necessarie a distanza. “Questo è ciò che rende l’HTX Lab diverso dagli altri laboratori che eseguono cristallografia”, ha dichiarato Rahila Rahimova, ricercatrice postdoc del team Márquez.

Rahimova, insieme al tecnico di ricerca Léa Mammri e a José Márquez, ha supportato Di Micco grazie alla sua esperienza in biologia strutturale e in metodi biofisici, e ha eseguito studi di cristallografia a raggi X per caratterizzare l’interazione molecolare tra il nuovo composto e la proteasi principale del SARS-CoV-2.

Questa collaborazione interdisciplinare ha dato presto i risultati sperati. Gli studi strutturali eseguiti all’EMBL di Grenoble hanno rivelato come il composto si leghi e inibisca la proteasi principale del SARS-CoV-2, essenziale per il ciclo vitale del virus. Il gruppo di Di Micco ha utilizzato queste informazioni per affinare ulteriormente il processo di progettazione del nuovo composto bioattivo. Il risultato è stato una molecola con una tossicità cellulare molto bassa, che ha ridotto il rischio di effetti collaterali.

“Vorrei sottolineare l’importanza della collaborazione nella scienza. Nel nostro caso, grazie a ISIDORe è stato possibile ottenere l’accesso alle strutture, ai servizi, alle attrezzature e alle competenze dell’EMBL di Grenoble” ha dichiarato Di Micco. L’Integrated Services For Infectious Disease Outbreak Research (ISIDORe) offre agli scienziati che studiano le malattie infettive l’accesso a strutture, servizi, attrezzature e competenze europee.

Questa ricerca si inserisce anche nel tema trasversale Infection Biology, che fa parte del programma 2022-26 dell’EMBL “Molecules to Ecosystems”. Questo tema mira a contribuire alla ricerca sulle malattie infettive e sulla biologia dei loro meccanismi, della diagnostica e del trattamento.

Il prossimo passo di Di Micco è testare questa molecola in uno studio clinico, poiché questo composto potrebbe aprire la strada allo sviluppo di nuovi trattamenti contro la COVID-19. “La concentrazione più alta dell’infezione si trova nel naso all’inizio, prima che passi alle vie aeree superiori e poi ai polmoni. Uno spray intranasale semplificherebbe la somministrazione di farmaci senza l’assistenza di infermieri o medici, o la necessità di andare in ospedale”, ha detto.

Single-cell RNA sequencing data are useful for studying cell phenotypes and function. However, deciphering the clonal relationships of cells is critical to understanding the patterns of cell migration during development and tissue growth, and to studying the relationship between genomic mutations and cell function. 

Mapping clonal relationships to cell phenotypes can be achieved by detecting somatic mutations in single cells. Until now, detecting somatic mutations in individual cells remained technically challenging because single-cell RNA data are sparse by definition – meaning only a small fraction of the data is captured – and have many sequencing errors. 

EMBL’s European Bioinformatics Institute (EMBL-EBI) has developed a new algorithm able to detect somatic mutations in single-cell profiling data without requiring a reference sample, such as matched genome sequencing data. This can be done at cell type and single-cell resolution. 

The algorithm, called SComatic, allows researchers to study cancer evolution and patterns of mutations in healthy cells within tissues. It can also be used to study a number of fundamental biological processes, including: 

• clonal mosaicism – where subpopulations of cells in a tissue have slightly different genetic information than the rest due to the accumulation of somatic mutations 
• cell plasticity – a cell’s ability to change its phenotypes in response to environmental factors, without changes in the genotype
• cancer evolution and intra-tumour heterogeneity
• tissue architecture and patterns of cell migration during development 

SComatic also allows researchers to answer questions such as what mutation events have taken place in a specific cell, or how many mutations there are in a specific cell or cell type compared to others. More widely, SComatic allows scientists to map genotype to phenotype at single-cell resolution. This is particularly useful for scientific initiatives analysing single-cell data, such as the Human Cell Atlas. 

“SComatic is specifically designed for de novo detection of somatic mutations in high throughput single-cell profiling data,” said Francesc Muyas Remolar, Postdoctoral Fellow at EMBL-EBI. “It’s at least five times more precise than other somatic detection algorithms, enabling scientists to study topics that were inaccessible before, such as the cell of origin from which some cancers and diseases originate. I look forward to seeing how colleagues apply SComatic to address diverse research questions.”

“Being able to bypass the need for a reference sample in this context is a major technical advancement,” said Isidro Cortes-Ciriano, Research Group Leader at EMBL-EBI. ”We can now harness the large collections of existing and upcoming single-cell data sets to study somatic mutations at unprecedented resolution.” 

The European Molecular Biology Laboratory (EMBL) and ZEISS have entered a long-term strategic partnership. The collaboration aims to close the gap between early-stage imaging technology development and its application in life science research.

Through this collaborative approach, users of the EMBL Imaging Centre and related EMBL imaging services will have access to the latest microscopy technologies and expertise from ZEISS. At the same time, the research carried out at EMBL and projects by Imaging Centre users will provide ZEISS with invaluable insights into new applications and opportunities for market-testing their most recent technology developments.

Continuous collaboration

The new agreement, negotiated with support from EMBL’s technology transfer arm EMBLEM, is based on the long-term collaborative interaction between EMBL and ZEISS and previous project-based partnerships. For example, ZEISS recently supported the initial equipment for operations in the EMBL Imaging Centre and generously provided microscopy instruments for the EMBL mobile laboratories for field research.

“EMBL and ZEISS have been working together fruitfully on multiple microscopy projects for decades, and we are excited to take the next step in our relations and give it a strategic perspective in this new framework agreement,” said Jan Ellenberg, Head of the EMBL Imaging Centre.

The long-term collaboration will allow the users of the Imaging Centre to get early access to the latest microscopy innovations from ZEISS. At the same time, regular strategic discussions will provide a unique opportunity for EMBL and ZEISS to engage in joint technology development, thereby making sure life scientists’ future needs for imaging technologies are taken into account for the development of the next generation of commercial microscopes.

The EMBL Imaging Centre’s core mission is to provide access to and training in cutting-edge imaging technologies and to stimulate the ongoing development of these technologies. This offers a unique opportunity to take the partnership with ZEISS to a new level. Michael Albiez, Head of ZEISS Research Microscopy Solutions, stated: “This collaboration is creating new ways for both EMBL and ZEISS to interact and work together. The cutting-edge research performed in the EMBL Imaging Centre and EMBL as a whole will be an ideal testing and development environment for our next generation of imaging technologies.”

Enabling future life science applications

EMBL and ZEISS work together to make new technologies available as early as possible to users of the Imaging Centre and related EMBL services and thereby guide their development for future applications in the life sciences. The collaboration focuses on three areas: the joint development and application testing of new imaging technologies, joint activities in Open Data, and training.

The DECIPHER website and database, which are used globally by researchers and clinicians to interpret and share phenotypic and genotypic data from rare disease patients, are moving to EMBL’s European Bioinformatics Institute (EMBL-EBI). The team behind this resource is now based at the organisation. 

DECIPHER stores and shares phenotype-linked candidate diagnostic variants from people with rare disease. Where consent for open sharing has been given, this data is shared globally. Genomic variants are often difficult to interpret, making clinical diagnosis challenging. It can take many years for patients to obtain a rare disease diagnosis and this diagnostic odyssey is arduous for patients and their families. Sharing rare disease data helps clinicians to identify the genotype-phenotype correlations underpinning these disorders and assists in diagnosis. The wealth of resources in DECIPHER can give insight into potential therapeutic targets or highlight where management guidelines or treatments are available.

DECIPHER is an interactive website that incorporates a suite of bioinformatics tools designed to aid in the interpretation of genomic variants for rare disease research. The project was founded in 2004 at the Wellcome Sanger Institute and now holds data from over 46,000 patients from all over the world. 

“The DECIPHER project enables the global sharing of rare disease patient data to help progress rare disease research,” said Matthew Hurles, Director of the Wellcome Sanger Institute. “Seeing the project move to EMBL-EBI is a huge step forward and will allow closer collaborations with EMBL-EBI’s world-leading biodata resources that will further strengthen the platform.”

Harnessing research data for patient benefit

The DECIPHER project has always benefited from EMBL-EBI data, displaying information from many of the institute’s data resources to assist in variant interpretation. These include data from Ensembl, the Ensembl Variant Effect Predictor (VEP), UniProt, Protein Data Bank in Europe (PDBe), and Gene2Phenotype. Moving to EMBL-EBI will help the project to strengthen these connections and further improve the user experience.

“DECIPHER allows clinicians and researchers to push the boundaries of gene–disease associations,” said Julia Foreman, DECIPHER Project Leader at EMBL-EBI. “The database is accessible and allows users to find new phenotypes and genetic variants associated with a particular disease.”

Phenotype linked variant data is deposited by clinical genetic centres from across the world. These centres obtain patient consent, which complies with the applicable laws and regulations in the depositing centres’ jurisdiction, to allow the data to be shared openly. This makes a patient’s rare disease variant discoverable globally so they can be offered the opportunity to participate in research or therapeutic trials and contribute to advancing knowledge. DECIPHER’s mission aligns with EMBL-EBI’s scientific and responsible data sharing strategies and will benefit from the institute’s expertise and data management skills. 

Driving diagnostics

DECIPHER is a powerful resource for genomic medicine. The website is continually being developed and updated to ensure that the most up-to-date genotypic and phenotypic data is presented, which is essential in this fast-moving field. DECIPHER’s browser views make it possible to see how gene function might be disrupted by a given variant. Simply by searching based on a patient’s genomic variant, clinicians can quickly access a wealth of information about a potential diagnosis. 

“When I’m reviewing patients in the clinic, DECIPHER gives me a snapshot of what is currently known about a variant, enabling me to quickly assess whether it explains a patient’s symptoms and whether new knowledge has emerged since it was reported,” said Helen Firth, Consultant Clinical Geneticist and Hon. Professor of Clinical Genomics at Cambridge University Hospitals. “This is crucial to ensure that patients receive the most up-to-date, high-quality advice in such a fast-moving field.” 

Researchers can evaluate genotypes and phenotypes to help in the understanding of new disorders. DECIPHER data has been used in over 3,000 publications, a testament to its importance in data-sharing and catalysing collaborations in rare disease research.

“Open genomic data is helping to diagnose and treat thousands of rare disease patients around the world,” said Andy Yates, Team Leader of Genomics Technology Infrastructure at EMBL-EBI. “It is truly a game-changer for the field and DECIPHER is among the key open data resources enabling this.”

EMBL’s European Bioinformatics Institute (EMBL-EBI) has launched the Pathogens Portal – an online platform that enables researchers, clinicians, and policymakers to access the most comprehensive collection of biomolecular data about pathogens. The portal features data spanning over 200,000 pathogen species and strains and is set to become a key tool for infection biology and pathogen surveillance. 

The list of pathogens featured in the portal was collated using the UK’s Health and Safety Executive’s list of approved biological agents and the WHO’s global priority pathogens list. It includes well-known pathogens that affect humans, including HIV, influenza, Hepatitis B, and the malaria parasite Plasmodium falciparum. It also covers lesser-known pathogens affecting humans, such as Lassa mammarenavirus, the cause of Lassa hemorrhagic fever, which can lead to deafness and even death in severe cases. The portal also contains hundreds of pathogens that affect other animals, which makes it a useful tool for food security and biodiversity. 

The Pathogens Portal currently contains nucleotide sequences, raw genomic data, sample metadata, and relevant scientific literature. The intention is to integrate additional data types, including protein sequence and structure and chemistry data from other public data resources. 

“The unique feature of the Pathogens Portal is that it brings together different data types, which are currently scattered in lots of different places,” explained Guy Cochrane, Team Leader at EMBL-EBI. “This new approach enables researchers, clinical scientists, and public health agencies to access all publicly-available data about their pathogen of interest with just one quick search. The portal also contains intuitive tools for discovery, which make it easy for users to refine their searches.”

“The Pathogens Portal is an important step in preparing for the next pandemic,” said Marion Koopmans Head of the Erasmus Medical Centre’s Department of Viroscience. “Pulling together multiple open biological data resources for a breadth of pathogens is a key knowledge base to ready ourselves for future pandemics.”

Pandemic preparedness

“The COVID-19 pandemic demonstrated that having robust and easy-to-use data sharing structures in place can save lives because these enable a quick and informed public health response,” explained Marianna Ventouratou, Data Platform Manager at EMBL-EBI. “Building on the lessons learned from COVID-19 pandemic, EMBL-EBI and partners have now developed the Pathogens Portal, which researchers and public health authorities around the world can use to enhance global pathogen surveillance efforts.”

Importantly, the data accessible through the Pathogens Portal is open and FAIR (Findable, Accessible, Interoperable, and Reusable), meaning it is available to anyone with an internet connection. This approach is particularly valuable during a public health emergency, when data sharing speed is of the essence.  

“It is invaluable to have a data portal like the Pathogens Portal, which represents the pathogen world beyond viruses, and takes a much more holistic and flexible view of where the next threatening pathogen may come from,” explained Frank Møller Aarestrup, Head of Genomic Epidemiology at the Technical University of Denmark.

Private data and cohort data

There is also a key component, called the Data Hubs system, which allows researchers and health agencies to keep their data private in the first instance. This is operated from EMBL-EBI’s existing infrastructure, including the European Nucleotide Archive (ENA). This is an important functionality for countries and researchers who wish to keep their data private before publication, but still want to be able to analyse them alongside other public records available through the portal. 

Another exciting feature of the portal is the cohort browser, which contains highly sought-after clinical-epidemiological data from patient cohorts. There is currently only one pilot study focusing on SARS-CoV-2 available in the browser, provided through the ReCoDID project by the Erasmus Medical Centre, with the help of the University Hospital Heidelberg. The Pathogen Portal team is actively encouraging researchers to submit more cohort data. 

“The Cohort Browser interoperates genomic data with clinical epidemiological data, which enables deep interrogation of disease data by linking information on the pathogen and the host it directly infected,” said Lauren Maxwell, Group Leader at the Universitätsklinikum Heidelberg. 

Building on success

The Pathogens Portal is built on the same framework as the European COVID-19 Data Portal, which EMBL-EBI and collaborators set up during the COVID-19 pandemic to support international data sharing essential for the pandemic response. Since launch, the COVID-19 Data Portal has been accessed by almost 300,000 users in 187 countries and geographical areas. 

Already, three EMBL-EBI resources feed data into the Pathogens Portal, with more coming soon. 

• European Nucleotide Archive (ENA), which provides a comprehensive record of the world’s nucleotide sequencing information, covering raw sequencing data, sequence assembly information, and functional annotation.
• BioSamples, which stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry.
• Europe PMC, which provides comprehensive access to over 40 million life sciences publications from trusted sources. 

The Pathogens Portal is a part of EMBL’s Infection Biology transversal theme, within EMBL’s Scientific Programme Molecules to Ecosystems. The theme enhances our understanding of the biology and mechanisms of infection, as well as diagnostics and treatment of infectious diseases. 

The Pathogens Portal is a community-driven initiative, and users are invited to submit feedback and questions to the project team on ena-path-collabs@ebi.ac.uk.

Supporting projects

The Pathogens Portal is supported by European Union funding through the RECODID (Horizon 2020 no. 825746), VEO (Horizon 2020 no. 874735) and BY-COVID (Horizon Europe no. 101046203) projects.

It builds on infrastructure developed and funded by ELIXIR-CONVERGE (Horizon 2020 no. 871075), EOSC-Life (Horizon 2020 no. 824087), COMPARE (Horizon 2020 no. 643476), CORBEL (Horizon 2020, no. 654248), and EMBL core funding.

Open Targets has appointed David Hulcoop as its new Executive Director, following the retirement of Ian Dunham. Hulcoop will build on the programme’s existing capabilities to maximise Open Targets’s impact on drug discovery decision making.

Open Targets, a public-private partnership founded in 2014, aims to use the information generated by genome sequencing and genetics studies to systematically improve the identification and prioritisation of drug targets for safe and effective medicines. Founding partners EMBL’s European Bioinformatics Institute (EMBL-EBI), the Wellcome Sanger Institute, and GSK have since been joined by Bristol Myers Squibb, Sanofi, Pfizer, and Genentech, a member of the Roche Group.

Emanuele de Rinaldis, VP, Global Head of Precision Medicine and Computational Biology at Sanofi, and Laurent Debussche, VP, Global Head of Tumor Biology and External Partnerships Lead Oncology Research at Sanofi, said: “Our collaboration with Open Targets and our integration within the research programme has changed the way we think about target selection. David Hulcoop has been key to helping us get the most from the partnership and bringing the benefits of membership to life within Sanofi; we are thrilled to continue working with him in this next stage of his career.”

New leadership 

Hulcoop became Acting Director of Open Targets when Ian Dunham retired at the end of June, and will take the helm officially on 4 October as an EMBL-EBI faculty member. Before joining Open Targets, Hulcoop led complex R&D projects to develop processes for large-scale production of pharmaceutical compounds at GSK, and worked for the Office of the CEO in the Future Strategy Group. Since joining Open Targets in 2017 as Strategy and Operations Director, he has been instrumental in growing the partnership from two to five industry partners, and providing a key role in bridging academic and industry viewpoints.

“Open Targets has built a strong foundation in target identification and prioritisation and has brought industry and academia together around a unique ecosystem of projects that wouldn’t exist otherwise,” said David Hulcoop. “We are excited about how we can further harness cutting-edge technologies to explore more granular aspects of disease states and mechanisms towards our ultimate goal of helping our partners and the community to envision safe and effective medicines. As we enter our 10th year, we are focussing on the real world impact of our work – the translation of our research to drug discovery decision making.”

Shaping the future of Open Targets

“Open Targets has done wonders for drug target identification, validation, and prioritisation under the leadership of Ian Dunham,” said Ewan Birney, Deputy Director General of EMBL and Director of EMBL-EBI. “We are certain David will continue on this innovative path, and bring his own vision to the endeavour. Open Targets’s unique, pre-competitive, highly-collaborative, and cross-disciplinary approach has developed indispensable resources and tools for the community and showcased that public-private collaborations are not only possible, but profoundly advantageous.”

Hulcoop will be supported in his role by the Open Targets Executive team. Gosia Trynka will take on the role of Scientific Director to lead the overarching scientific direction of the consortium and deputise for the Director as required. Ellen McDonagh will take on the role of Translational Informatics Director to lead integrated informatics and data science strategies across projects, platforms, and core teams.

“In this new role, David combines his extensive strategic experience at Open Targets and industry with fresh ideas and new ways of working across the consortium,” said Ellen McDonagh. “I’m excited to work closely together with David and Gosia, our team, and partners, as we shape the future of Open Targets.”

This was originally published on the Open Targets website. 

EMBL’s 2022 Annual Report is now available online, including a downloadable ‘Year in Review’ with additional information. EMBL switched to a digital-first annual report last year as part of its commitment to more sustainable, cost-effective operations. The digital-first format eliminates the need for at least 210,000 printed pages each year and enables us to reach wider and more diverse audiences.

With highlights from all of EMBL’s key missions – research, services, training, innovation and translation, and integration of European life sciences – as well as our people and operations, the annual report is a record of the first year of EMBL’s newest scientific programme, Molecules to Ecosystems, including the introduction of new research transversal themes and the final pilot expedition for the Traversing European Coastlines (TREC) expedition. You can follow TREC’s current progress on our website. 

Wolfgang Huber, Julia Mahamid, and Oliver Stegle, who all lead research groups at EMBL Heidelberg, are among 69 life scientists elected to membership of the European Molecular Biology Organization (EMBO). Recognised for their contributions to and leadership within the scientific community, they join the organisation’s community of more than 2,000 leading life scientists.

Wolfgang Huber and his group develop statistical and bioinformatics models for the analysis of different datasets. With applications from multi-omics to quantitative imaging, his work contributes to understanding complex biological systems.

Huber said about his election: “EMBO is one of the scientific organisations I respect the most. I am deeply honoured by the membership and excited to make contributions to its work. I particularly appreciate EMBO’s role in building a pan-European research landscape, furthering mobility, personal interactions, training, and careers of junior scientists, based on excellence.”

The Mahamid group applies cryo-electron tomography to reveal the 3D structure and function of macromolecular complexes in intact cells. She also recently received the 2023 EMBO Gold Medal for exceptional achievements in structural cell biology and developing powerful techniques to visualise cellular machinery in situ.

“I am delighted to join this group of outstanding scientists to support EMBO’s activities in promoting fundamental research in the life sciences. I am especially appreciative of EMBO’s efforts in advancing early-career researchers, training activities through support of practical courses on cutting-edge methods that enable frontier research, and knowledge exchange through the support of conferences,” Mahamid said about her election.

Oliver Stegle, who is an associate group leader at EMBL and leads the department of computational genomics and systems genetics at the German Cancer Research Centre (DKFZ) in Heidelberg, develops and applies machine learning methods for deciphering molecular variation across individuals, space, and time.

“It’s a great honour to see our work on computational biology being recognised in this way. EMBO is a unique organisation, providing young scientists the foundation to make important discoveries. I look forward to contributing to EMBO and working together with the community to maximise the utility of machine learning and AI in modern biology,” said Stegle.

Six EMBL alumni are also among the 69 scientists elected to EMBO membership this year. They are Florence Besse (Staff Scientist, EMBL Heidelberg, 2003-2008), Paul Dupree (Postdoctoral Fellow, EMBL Heidelberg, 1991-1993), Gáspár Jékely (Postdoctoral Fellow, EMBL Heidelberg, 2000-2007), Gaëlle Legube (Postdoctoral Fellow, EMBL Heidelberg, 2003-2006), Anastassis Perrakis (Staff Scientist, EMBL Grenoble and Hamburg, 1993-2000), and Eugenia Piddini (Predoctoral Fellow, EMBL Heidelberg, 1997-2002).

EMBO Members are involved in the organisation’s activities in different ways, for example, by serving on EMBO Council, Committees, and Advisory Boards, evaluating applications, and mentoring early-career scientists. For more information, visit the EMBO website.

EMBL is gearing up for its 50th anniversary, with plans to recognise the milestone via a two-day exciting scientific symposium. This colloquium, ‘From atoms to ecosystems – a new era in life sciences’, will be held both virtually and in-person at Heidelberg on 4-5 July 2024. The event celebrates the foresight 10 member nations had when they ratified a proposal to bring a world-class life sciences laboratory to Europe, resulting in the creation of EMBL.

The symposium will explore the foundational science and technology EMBL has fostered and is helping to advance. 

“EMBL’s staff and alumni can be proud of their contributions that have improved human and planetary health over the past 49 years. But we never stand still, and the best way to honour this landmark moment is to look forward to the next 50 years of achievement in research, services, and training,” said Edith Heard, EMBL’s Director General. “The anniversary provides an opportunity to celebrate the EMBL spirit – past, present, and future.”

Each symposium session will include presentations from a former EMBL group leader, a former EMBL PhD student or postdoctoral fellow, and a current EMBL group leader. 

The first day’s sessions will look at research from cells to tissues, genome biology, developmental biology, and protein structures and complexes. On the second day, the focus will turn to sessions on bioinformatics, the expansive scope of EMBL’s research programme ‘Molecules to Ecosystems’, and technological advances past and present. The day will conclude with a panel discussion.

“This inspiring two-day symposium will showcase EMBL’s pioneering scientific contributions over the last 50 years and highlight how these continue to evolve to address topics of global importance,” said Jürgen Deka, Head of EMBL External Scientific Training. “Many impactful scientific careers have started at EMBL and the symposium will highlight EMBL’s strong collaborations with many life science institutes worldwide through alumni.”

The event will also include presentations of EMBL’s two alumni awards in 2024: the John Kendrew Award and the Lennart Philipson Award, as well as a tribute to EMBL’s alumni. 

Further details are forthcoming, including how to register for this event. Additionally, over the next 12 months, EMBL will highlight key moments from its history through articles in its web newsfeed, as well as on an upcoming, new section of the EMBL website that will reflect the many voices that continue to make EMBL a world-class research institution.