EMBL Seminars

Ibrahim Cemel (ONT): Oxford Nanopore update

Tobias Rausch (EMBL): Decoding the consequences of structural variants with long-read genomics

Isabel S. Naarman-de Vries (University of Heidelberg): Detection of RNA modifications with nanopore platform – Elucidating the potential interplay of different modifications

Claudio Asencio (EMBL, GSK-Cellzome): RNAkinet- a novel approach to study kinetics of mRNA turnover

Maximilian Schönung (NCT & DKFZ): Rapid multi-omics leukemia diagnostics using nanopore sequencing

Abstract
 

To understand the function of the brain and how its dysfunction leads to brain diseases, it is essential to uncover the cell type composition of the brain, how the cell types are connected with each other and what their roles are in circuit function. At the Allen Institute, we generated a comprehensive and high-resolution transcriptomic and spatial cell type atlas for the whole adult mouse brain, including >5,300 clusters that are hierarchically organized. Extending from this foundational reference atlas, we have investigated the dynamic changes of transcriptomic profiles of specific cell types in the developing and aging brain. In the aging mouse brain, through brain-wide single-cell transcriptomic profiling, we uncovered cell-type specific transcriptomic signatures of decreased neuronal structure and function and increased immune response and inflammation. We further identified a potential hotspot for aging involving specific hypothalamic cell types regulating energy homeostasis that exhibit both decreased neuronal function and increased immune response, suggesting a connection among metabolism, neuroinflammation, and aging. As a first deep characterization of brain development, we generated a transcriptomic and epigenomic cell type atlas of the developing mouse visual cortex, with dense temporal sampling from E11.5 to P28. We reconstructed a transcriptomic developmental trajectory map of all excitatory, inhibitory, and non-neuronal cell types in the visual cortex, which reveals continuous cell type diversification throughout the pre- and postnatal stages of cortical development. We also conducted an in-depth analysis of the transcriptomic and spatial organization of GABAergic neuron types (>1,000 clusters) in all regions of the mouse telencephalon and their developmental origins. We found that long-distance migration and dispersion is a common characteristic of nearly all these neuron types. In contrast to cortical and striatal GABAergic neurons which undergo extensive postnatal diversification, septal, preoptic and most pallidal GABAergic neuron types emerge in a burst during the embryonic stage with limited postnatal diversification, suggesting distinct cell-type development mechanisms in different brain regions. 

Zoom details: https://www.embl.org/internal-information/updates/distinguished-visitor-lecture-hongkui-zeng/ 

In this webinar, two professionals from small and medium-sized enterprises (SMEs) in the IT and software sector will discuss their career paths and share insights with researchers. Following the speakers' introductory presentations, participants will have the opportunity to ask questions during a panel discussion.

Please register for this zoom webinar: https://embl-org.zoom.us/webinar/register/WN_zEAB_TYGTKuKWuPFKrqOdw#/registration

Please note that the webinar will be recorded.
*For the FAQ section, as a zoom participant, please use  the chat function (the host will read out your question).

Abstract
Quantifying the dynamics of particle suspensions is a widespread interest in soft matter. For instance, probing the motion of cells or larger organisms can help us understand biological behavior. When multiple particles interact, they perform collective dynamics, which visually translates into a zoology of effects. Yet, available analysis techniques face challenges reconstructing trajectories in dense or heterogeneous suspensions where accurately labelling particles is difficult.

Inspired by Smoluchowski, we introduce a broadly applicable analysis technique, that probes particle dynamics based on a simple principle: counting the fluctuating number of particles in finite observation boxes of an image. Through colloidal experiments, simulations, and theory, we demonstrate the practical benefits of analyzing fluctuating counts. We can determine equilibrium motion properties, such as self-diffusion coefficients. Moreover, by increasing the observation box size, we can naturally probe collective diffusion coefficients. Out-of-equilibrium features also manifest in such fluctuating counts: for instance, our framework is sensitive to self-propulsion velocities and can distinguish between different reorientation dynamics. Beyond, by correlating nearby boxes we demonstrate how to map out flow field maps.

Both in dense or heterogeneous states, by simply counting particles, we overcome some of the challenges of trajectory reconstruction; and, more importantly open up the possibility of systematically linking individual and collective behavior, with broad perspectives in soft and statistical physics.

Abstract
AVITI24 combines single cell, spatial co-detection of RNA, protein, and morphology, and next-generation sequencing into one integrated system - all powered by the groundbreaking Avidite Base Chemistry™ (ABC™). AVITI24 empowers seeing more in every experiment, from drug response pathway deconvolution and genetic perturbation screens to immune profiling and dynamic cell state analysis. It also enables direct in sample sequencing and custom protein detection.

doi: 10.1101/2025.05.03.651997v1, doi: 10.1101/2025.10.11.681797v1

Connection details
Zoom*: [https://embl-org.zoom.us/j/91525609229?pwd=KtKI5bx7yB4ftsRqADrPlLLpHmp6rd.1] (Meeting ID: [91525609229]

Abstract
EMBL “Entrepreneurial Minds” is a dynamic 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.  Whether you are refining a startup concept, exploring ways to translate research into societal impacts, seeking insights into industry and commercial careers, or considering future opportunities as a founder, the “EMBL Entrepreneurial Minds Series” equips you with ideas, knowledge and networks to advance your entrepreneurial journey.

About the speaker
Fay Christodoulou is a distinguished molecular biologist and entrepreneur based in San Francisco. Born in Greece, she pursued her undergraduate studies at Sussex University in the UK and earned her PhD in evolutionary developmental biology from the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. In 2014, she co-founded Miroculus, leading the development of innovative digital microfluidics technology that automates sample preparation for next generation sequencing (NGS) as Chief Scientific Officer.

In 2023, Miroculus was acquired by INTEGRA Biosciences, where Fay now serves as Chief Scientific Officer in Microfluidics. Her expertise continues to drive advancements in biotechnology, focusing on integrating microfluidics into laboratory workflows. Fay is an Endeavor Entrepreneur, a mentor at QB3 Berkeley early-stage mentoring program and is passionate about advocating for women's representation in STEM.

Registration details - please register to attend in-person or online
https://embl-org.zoom.us/webinar/register/WN_Dazq-sR7SYKOivqB7YVzFg#/registration

Please note that the talk will be recorded.
*For the FAQ section, as a zoom participant, please use  the chat function (the host will read out your question).

Abstract
[Text for abstract].

About the speaker
[Biographical information about the speaker].

Meet the speaker
To meet with the speaker informally after the talks,sign up here [add link]. We especially encourage predocs and postdocs to take advantage of this opportunity.

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.