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Research

To perform fundamental research in molecular biology

EMBL’s research aims to understand the basis of life at a molecular level and in the context of different environments.

From genomes to organisms, EMBL is exploring the secrets of life. Its diverse research programme is pushing the limits of biological knowledge, with researchers developing innovative techniques and technologies as part of the process.

As noted on this page, seven research themes – molecular building blocks, multicellular dynamics, microbial ecosystems, infection biology, human ecosystems, planetary biology, and Theory@EMBL – offered significant, diverse findings and milestones in 2023.

“Now we have shown that this works, we are excited about making the software available to the research community. We hope that such deep-learning approaches will become established as a gold standard in cryo-electron tomography….”

— Julia Mahamid, EMBL Group Leader, on DeePiCt (Deep Picker in Context), an AI-based method to rapidly and efficiently annotate cellular structures in cryo-electron tomograms

Molecular building blocks

EMBL research delves into cellular function and subcellular components to systematically determine how responses to a changing environment are mediated at molecular levels. Among the many advances in this area this year, researchers created a deep-learning tool that speeds up analysis from cryo-electron tomography while gathering more detail about inner cell workings.

“This is a pioneering study for this kind of analysis in volume electron microscopy, and we want to generate many more such analyses. This is a new field that is just starting and visualisation tools such as MoBIE are critical to do the same for many more organisms in many different ways.”

— Detlev Arendt, EMBL Group Leader, on a collaboration started in 2018 to build a tool that would allow researchers across the world to share and view multifaceted datasets on simple computing systems

Multicellular dynamics

EMBL aims to unravel the impact of genetic and environmental variations in living systems and to understand responses at the single-cell and multicellular levels. Some of the highlights from this work in 2023 included new retinal research that will likely pave the way to prosthetic retinas of the future. Additionally, EMBL scientists continued to find new ways to push the frontiers of big data analysis in biological imaging.

New evidence on retinal function

The Asari group at EMBL Rome showed how retinal function in awake mice differed from isolated retinal samples – insights that could lead to future prosthetic replacements for retinas.

“With this knowledge and with artificial intelligence, I think it will be possible to develop completely new nature-inspired enzymes in the future, and make totally new products, such as new bioplastics.”

— Garo Antranikian, Hamburg University of Technology Group Leader, on a two-decade collaboration with Matthias Wilmanns at EMBL Hamburg

Microbial ecosystems

With an eye towards microbes that impact humans, the aim of this theme is to generate the foundational knowledge that will enable us to rationally modulate human microbial communities towards desired traits and compositions. In 2023 — amongst other work — scientists found new drug combinations to fight antimicrobial resistance as other researchers harnessed marine microbes to promote a circular bioeconomy.

“Previously, there have been studies on specific drug combinations, especially those commonly prescribed together in the clinic. However, we lacked systematic knowledge of how combinations of different classes of antibiotics, or combinations of antibiotics and non-antibiotic drugs, influence bacterial physiology, especially when considered independently of the host.”

— Elisabetta Cacace, former PhD student in EMBL Typas group, on how researchers systematically profiled over 10,000 drug combinations for their effectiveness against common multidrug-resistant bacteria

Infection biology

EMBL's Infection Biology theme aims to contribute to research on the biology and mechanisms of infection, as well as on diagnostics and treatment of infectious diseases. This past year's highlights included bioinformaticians developing a new tool that allows scientists to analyse millions of viral genomes all at once. Additionally, structural biologists shed light on the molecular activation of the final ‘switch’ that triggers inflammatory responses.

Switching off the cytokine storm

EMBL Grenoble and University of Geneva researchers shed light on molecular activation of the MAP kinase p38α, the final ‘switch’ triggering inflammatory responses.

“EMBL Rome has deep expertise in epigenetic inheritance research and in developing environmental exposure paradigms that can be studied in a systematic manner….Ultimately, this will help clarify the intricate relationship between environmental exposures and disease burden in human populations across generations.”

— Ana Boskovic, EMBL Rome Group Leader, on how scientists are investigating how basic traits are transmitted across generations with novel epigenetic mechanisms discovered in recent years

Human ecosystems

Within this theme, EMBL scientists take advantage of rapidly expanding human datasets to explore the gene–environment interplay and its effects on human phenotypes. Among other research in this area, a cancer cell ‘decathlon’ explored how to better predict tumour aggressiveness and metastasis. Additionally, other researchers developed new paradigms to study environmental impacts on reproduction in mammals and disease risks in their offspring.

The ‘long read’ for cancer

Looking to learn more from genomics sequencing about DNA mutations and cancer, researchers applied a long-read approach to get a broader genomic view.

“I believe we will be marking a new era in ecology. The beauty of BIOcean5D is also the large space left for fundamental research, exploration, and discovery. We are about to re-explore marine life, from viruses to whales, in water, sediments, and aerosols, along the entire European seascape from Finland to Crete (in collaboration with the TREC expedition).”

— Colomban de Varga, Research Director at CNRS/Sorbonne Université, and the BIOcean5D project deputy director and scientific project coordinator, at the inaugural meeting of BIOcean5D that has brought together 31 research partners to holistically explore marine biodiversity at molecular and organismal levels – from viruses to mammals – across space, time, and human scales

Planetary biology

This research theme aims to understand, from the molecular to the population level, how microbes, plants, and animals respond to each other and to their environment. To this end, TREC expedition launched in 2023, joining molecular biologists with other disciplines. Additionally, other EMBL researchers enlisted an unprecedented stem cell zoo to compare six different mammalian species’ developmental time.

BIOcean5D targets marine biodiversity

EMBL hosted the inaugural meeting for a major interdisciplinary project designed to explore marine biodiversity – from viruses to mammals – across space, time, and human scales.

“This is curiosity-driven fundamental information that will help us later in realising our full potential in any sort of field in which cells are the building blocks, such as tissue engineering or cellular therapeutics. This can be foundational work for anything we want to do that is cell-based.”

— Sarkis Tafnakaji, PhD Student in the Aulehla Group, EMBL Heidelberg, reflecting on the important role ‘time, timing, and transitions’ play in developmental biology

Theory@EMBL

A theory research programme has been promoting theory-guided paths to discovering, understanding, and conceptualising the underlying principles of complex and dynamic biological systems at all scales, from molecules to organisms to ecosystems. A good example of this in 2023 was the Barcelona Collaboratorium for Modelling and Predictive Biology, which continued to involve more researchers, promoting theory and mathematical modelling and strengthening interactions between disciplines.

Why time is of the essence in development

Developmental biologists explored the importance of time, timing, and transitions in living systems, employing modern technology able to reveal and manipulate oscillations in developing organisms.

EMBL Research in Numbers

Collaborative scientific publications

In 2023, EMBL researchers produced 701 publications and mostly in collaboration with scientists within EMBL member or associate member states, as shown on this chart.

From 701 total publications: 81 By EMBL 594 By EMBL in collaboration with organisations in member or associate member states 26 By EMBL in collaboration with organisations in non-member state locations only.

Collaborative grants

Beyond EMBL’s member state funding, external grants support activities often done in collaboration with scientists beyond EMBL. These charts broadly break down the type of grants EMBL held in 2023. 

474 grants: Total research grants: 321 Total infrastructure grants: 124 Total training and outreach grants: 29 177 By EMBL 260 By EMBL in collaboration with organisations in member or associate member states 37 By EMBL in collaboration with organisations in non-member state locations only

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