EMBL Seminars

Abstract
Special Event! Don't miss the next Project Management Network event with Mark Sutton from Arm - a world-leading semiconductor company designing ultra-efficient processors that power billions of devices globally.

About the speaker
What: ‘Cultivating a Culture of Innovation in Project Management’ 

When: Wednesday 10^th September 2025 at 2PM-3PM(BST) / 3PM-4PM (CEST)

Where: Hybrid event:  EMBL-EBI Thornton Building - Dendron Seminar Suite or Zoom

Come and meet Mark Sutton a project management specialist with extensive expertise leading complex projects and programmes across diverse industries. Mark holds a degree in Manufacturing Systems Engineering, providing a strong technical foundation to support strategic execution and operational excellence. His career has been focused on Project and Programme delivery, and he currently serves as Senior Director of Engineering Operations in the Graphics Processor Unit (GPU) team at Arm, where he oversees high-impact initiatives, drive cross-functional collaboration and ensures delivery of world-class engineering solutions.

Mark will be delivering session on “Cultivating a Culture of Innovation in Project Management”. He will explore practical approaches for fostering a culture of openness and innovation within teams, focusing on how project managers can best share knowledge and experiences, build on spirit of innovation, and strengthen collaboration across the wider PM community to drive continuous improvement.

Connection details
Zoom*: [https://embl-org.zoom.us/j/93525595394?pwd=SI0yH2HbamxX3W571chnUa8JajbCnG.1&jst=2] (Meeting ID: [93525595394], Password: [034813])

Please note that the talk will be recorded.
*For the FAQ section, as a zoom participant, please use either the chat function (the host will read out your question) or the “raise your hand” function and turn on your microphone.

Abstract
Large Language Models (LLMs) like ChatGPT are transforming the way we do science and very prominently how we analyse scientific data. In this talk, I will introduce the fundamentals of LLMs and their emerging multimodal extensions, such as Vision-Language Models (VLMs). Computer scientists seek to enable analysis of biological images using VLMs, turning images into numbers and insights ideally directly. I will discuss current capabilities and limitations of these models for bio-image analysis and highlight the unique potential of LLMs for automating data analysis workflows through code-generation. Emphasizing practical examples, I will demonstrate how LLM-driven code-generation accelerates data exploration, preprocessing, and quantitative analysis in bio-image data science.

Abstract
[Strain-level variation within the human microbiome is a major determinant of functional capacity, pathogenic potential, and host interaction. However, resolving such variation remains a significant challenge. Sequencing-based methods, while powerful, require deep coverage, elaborate bioinformatics pipelines, and time-consuming workflows to achieve strain-level accuracy—making them costly and impractical for large-scale or time-sensitive applications.

We present DynaMAP, a rapid, sequencing-independent metagenomics platform based on high-density optical DNA mapping. By directly imaging fluorophore-labeled high-molecular-weight DNA extracted from human stool and other complex samples, DynaMAP generates long, single-molecule optical maps that preserve structural features specific to individual strains. These maps are matched against a curated reference database of nearly 20,000 microbial genomes, enabling strain-level identification up to 99.8% average nucleotide identity (ANI) resolution.

We benchmark DynaMAP on mock communities, standardized microbial panels, and real human fecal samples, and show that it achieves taxonomic profiles highly concordant with shotgun metagenomics, but with reduced complexity, same-day turnaround time, and affordable cost. Crucially, DynaMAP avoids the need for genome assembly or computationally intensive strain-calling algorithms, enabling accessible and scalable microbiome analysis.

Our results demonstrate that DynaMAP enables same-day, strain-resolved profiling of gut microbiota, with potential applications in clinical diagnostics, microbial infection monitoring, and routine microbiome monitoring in research and healthcare settings.].

About the speaker
[Arno Bouwens is the R&D Director at Perseus Biomics, a pioneering biotechnology company transforming microbiome analysis through optical mapping of metagenomic DNA. With a strong foundation in engineering, Arno brings deep expertise in the development of complex optical and electronic systems.

He earned his PhD in 2013 from the École Polytechnique Fédérale de Lausanne (EPFL), specializing in advanced biomedical imaging technologies. His postdoctoral research at KU Leuven, Université Libre de Bruxelles (ULB), and EPFL focused on DNA mapping techniques and optical implementations of machine learning.

Before joining Perseus Biomics, Arno worked as a senior systems engineer at a Belgian SME, where he developed optical metrology tools and satellite imaging hardware. Drawing on his multidisciplinary background in research, systems engineering, and data engineering, he now leads the development of high-precision, high-throughput data generation technologies tailored to life sciences applications.].

Connection details
Zoom*: [https://embl-org.zoom.us/j/93113530119?pwd=B5ifSphC0TrPbCO8uWMGmbIbbLVNoX.1] 

Abstract
Understanding how cells translate extracellular cues into specific patterns of gene expression is one of the major goals of modern neurobiology. Neurons are cells with a complex morphology, which maintain their cellular structure through the compartmentalized expression of proteins essential for growth and plasticity. Asymmetric localization of RNA is an evolutionarily conserved mechanism that allows spatial restriction of protein synthesis to specific cellular compartments. Incorrect processing and delivery of mRNA causes developmental defects and severe human neurological disorders. In neurons, mRNA transcripts are transported to both dendrites and axons where they are rapidly translated in response to stimuli. This talk will explore how transcripts localized in sympathetic neuron axons are transported, processed and translated in response to neurotrophins. Special emphasis will be given to the epigenetic modifications of the RNA of targeted axons and how they may determine the transcripts fate. I will also discuss our recent important findings indicating that at least some axonal RNA transcripts interact with the signalling endosomes and other organelles, generating a signalling mechanism that regulates the spatial expression of genes essential for neuronal survival and axon growth. 

Abstract
Memory formation relies on a bidirectional interplay between synaptic plasticity and nucleus-templated transcriptional programs, but how precisely this interplay is orchestrated by epigenetic mechanisms remains to a large extent unknown. In this talk, I will showcase our recent efforts to better understand this aspect from two angles. First, we have found that chromatin plasticity in the mouse brain is a key determinant for memory allocation, the process by which neurons become recruited into the memory trace: When we increased chromatin plasticity by enzymatic overexpression of histone acetyl transferases (HATs), neurons with elevated histone acetylation were preferentially recruited into the encoding ensemble and memory retention was enhanced, while optogenetic silencing of the epigenetically altered neurons prevented memory expression. Second, we have found that after learning, the epigenetic make-up of a single locus in the encoding ensemble is necessary and sufficient to bidirectionally alter memory performance across different phases of memory consolidation. Together, these findings stipulate that before and after memory encoding, epigenetic mechanisms play a pivotal role as molecular memory aids. 

Abstract
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About the speaker
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Attachments
[Link to a file (for example a pdf of the seminar’s programme) - the file can be uploaded on the intranet]

Connection details
Zoom*: [https://embl-org.zoom.us/j/96374261689?pwd=TnNxRWtQY2lyc2pSa2JpY3NGcDlhZz09] (Meeting ID: [963 7426 1689], Password: [DBU])

Please note that the talk will yes/not be recorded.
*For the FAQ section, as a zoom participant, please use either the chat function (the host will read out your question) or the “raise your hand” function and turn on your microphone.

Abstract

Epigenetic components regulate many biological phenomena during development and normal physiology. When dysregulated, epigenetic components can also accompany or drive diseases. One main class of epigenetic components are Polycomb group proteins. Originally, Polycomb proteins were shown to silence gene expression. We found that this function involves the regulation of 3D chromosome folding and we found that Polycomb components can induce the formation of long-distance interactions or chromatin loops that may play instructive roles in gene regulation as well as serve as scaffolding elements that contribute to enhancer-promoter specificity. Perturbation of Polycomb components is involved in human cancer and leads to tumorigenesis in flies. Surprisingly, even upon a transient depletion followed by restoration of the full Polycomb compendium, epithelial cells lose their normal differentiated fate, continue proliferating and establish aggressive tumors, demonstrating that cancer can have a fully epigenetic origin. Similarly, transient perturbation of histone acetylation in mouse ES cells and gastruloids shows that they can record chromatin changes and that this results in cellular memory of the perturbation states. The implication of these data will be discussed.