EMBL Seminars

Location: Room 301, Building D (3rd floor), Università della Sapienza di Roma - Viale Regina Elena 295

Abstract

Epigenetic mechanisms are invoked in many human diseases, typically involving assumptions about the mediation of environmental exposures, transcriptional reprogramming and the memory of past events. These assumptions are rooted in the complex history of the field, and in paradigmatic models that might not survive testing with modern approaches. In this presentation, the foundations for the field are critically re-examined, new frameworks are proposed, and ‘epigenetics’ is placed into a context of cell biology and genetics, aiming towards the practical goal of allowing more productive insights into human diseases.

Abstract

EMBL “Entrepreneurial Minds” is a  quarterly webinar series crafted to ignite entrepreneurial spirit and initiatives among all EMBL staff and fellows. Our speakers share practical insights into entrepreneurship, technology transfer, research commercialisation, and navigating start-up landscapes. Through engaging online webinars, attendees will explore success stories, learn from speaker experiences, and connect with industry experts including entrepreneurs, tech transfer professionals, and EMBL alumni. 

This event is open to all and will be livestreamed from EMBL Rome. Participants from EMBL Rome and other Monterotondo campus institutes are encouraged to attend in-person.

Please note - for our planning, we kindly ask both in-person and online participants to register at: https://embl-org.zoom.us/webinar/register/WN__n6yIi-wR4e0QhhNG8hYzQ 
Please note that the talk will be recorded.

About the speaker
In this seminar we will hear from Ilaria Ferlenghi, Global Scientific Leader and Associate Director at GSK.

Ilaria is an esteemed structural biologist and microscopy leader with over 30 years of expertise in cryo-electron microscopy (cryo-EM), AI/ML applications, and structural analysis, including more than 20 years dedicated to vaccine research and development. She was among the pioneers in introducing cryo-EM in the pharmaceutical industry to identify and characterize new vaccine candidates, contributing significantly to its adoption as a transformative tool in vaccine R&D. In this context, she played a key role in the design and development of the BEXSERO vaccine.

As Global Scientific Leader and Associate Director at GSK, she leads scientific vision and strategic direction across therapeutic areas, driving innovation in structural vaccinology. Ilaria developed the GEMINI AI/ML-based platform, which integrates structural biology with artificial intelligence to accelerate the identification of antigens as potential vaccine candidates.

Her career spans leadership roles at GSK and Novartis, with deep specialization in advanced microscopy techniques and vaccine R&D. She holds a PhD in Structural Biology and Biophysics from the University of Heidelberg, followed by postdoctoral research at HHMI (Boston) and CNRS (France). Widely recognized for fostering impactful collaborations between academia and industry, Ilaria continues to drive scientific innovation at the intersection of structural biology, digital technologies, and global health.

She serves as a member of nine scientific advisory boards worldwide, contributing her expertise to advance innovation and translational science in vaccine development and beyond. She is also the co-founder of the WeInspireBio initiative, a global effort dedicated to inspiring and supporting the next generation of scientists.

Abstract
Dear EMBL colleagues,
We are pleased to invite you to the 7th session of the EMBL Entrepreneurial Minds Webinar Series! This event will feature Ilaria Ferlenghi, a former EMBL predoc and Global Scientific Leader and Associate Director at GSK, whose career spans structural biology, advanced microscopy, vaccine R&D and scientific innovation.

Event details
•    Location: EMBL Rome seminar room and online via Zoom 
•    Registration (for both in-person and online attendance): link 
Registration is open to all EMBL fellows and staff.

We look forward to your participation!
Kind regards,
Laurène and Rachel 

Global views of development

The interplay between transcription factors and chromatin accessibility regulates spatiotemporal gene expression and cell type diversification. However, comprehensive atlases and gene regulatory networks underlying these processes have remained elusive. I will present our recent efforts in single-cell multiomics and spatial transcriptomics to address this challenge. We generated a single-cell multiomics atlas of RNA expression and chromatin accessibility during zebrafish embryogenesis and developed DeepDanio, a deep learning model to dissect cis-regulatory interactions. In parallel, we developed a whole-embryo imaging platform to quantify the expression of hundreds of genes at subcellular resolution. Integration with the single-cell multiomics data generated an atlas detailing the expression of ~25,000 genes and the accessibility of ~300,00 chromatin regions, as well as the online browser MERFISHEYES. I will discuss how exploration of the atlas and the gene regulatory network identified instant differentiation as a novel mode of cell differentiation and how changes in gene expression generate sharp boundaries during gastrulation. 

Abstract
Animals have evolved within the framework of microbes and are constantly exposed to diverse microbiota. Eukaryotic organisms are therefore metaorganisms: consortia of zygote-derived host cells and associated microorganisms, including bacteria, archaea, fungi, protists, and viruses. Hosts and microbes are deeply interconnected, often co-evolving and shaping one another’s fitness.

Over the past decades, microbiome research has shown that microbial communities are essential for normal animal development, physiology, and reproduction. Microbial signals also become integrated into neural circuits, influencing behaviour across evolution—from simple reflexes in Hydra to associative learning in honey bees and emotional regulation in mammals. Yet how animals perceive, transmit, and integrate these signals remains largely unknown.

Using the ancestral metazoan Hydra as a model, I will argue that animal development and behaviour are not autonomous processes, but emerge through transient and persistent interactions with the microbial world. Symbiotic microbes provide developmental and behavioural signals that contribute directly to phenotype formation. Integrating the microbiome into our understanding of development and evolution therefore reveals a more complete picture of how organisms function, adapt, and evolve—and of the very fabric of life itself.

About the speaker
Thomas is a leading researcher in host–microbe interactions and the biology of metaorganisms. Using the freshwater polyp Hydra as a model, his group has transformed our understanding of how microbial communities shape animal development, nervous-system function, and behaviour. His seminar will offer a fascinating perspective on animals as deeply integrated partnerships between hosts and microbes, with broad implications for development, behaviour, and evolution.