EMBL Seminars

At EMBL, experts from institutes throughout the world speak on a wide range of scientific and technical topics

Location
Type
Reset filters

5 June 2025, 10:30

Learning Cytometers: identifying critical cells beyond molecular markers

5 June 20252025External Faculty SpeakerEMBL Heidelberg, Virtual

Abstract Traditional flow cytometry has relied heavily on fluorescent molecular markers and investigator driven hypotheses to detect and sort cells of interest However suitable molecular markers are often unavailable or insufficient to distinguish biologically critical cell subpopulations effectively To address this we have developed a series of data centric AI based instruments termed... Abstract[Traditional flow cytometry has relied heavily on fluorescent molecular markers and investigator-driven hypotheses to detect and sort cells of interest. However, suitable molecular markers are often unavailable or insufficient to distinguish biologically critical cell subpopulations effectively. To address this, we have developed a series of data-centric AI-based instruments, termed Learning Cytometer, to find and sort critical cells by leveraging high-content, label-free optical data. I will first introduce Ghost Cytometry (Science, 2018; eLife, 2021), which enabled the first and fast “imaging" cell sorter. By combining label-free and fluorescence image data analyzed through supervised and unsupervised machine learning approaches, Ghost Cytometry identifies cells based on complex morphological signatures, particularly beneficial when molecular markers are unavailable...

Speaker(s): Sadao Ota, RCAST at University of Tokyo, ThinkCyte inc., Japan
Host: Beata Ramasz, Flow Cytometry Core Facility

Place: Small Operon

External Faculty Speaker

EMBL Heidelberg, Virtual

Additional information

Abstract
[Traditional flow cytometry has relied heavily on fluorescent molecular markers and investigator-driven hypotheses to detect and sort cells of interest. However, suitable molecular markers are often unavailable or insufficient to distinguish biologically critical cell subpopulations effectively. To address this, we have developed a series of data-centric AI-based instruments, termed Learning Cytometer, to find and sort critical cells by leveraging high-content, label-free optical data. 

I will first introduce Ghost Cytometry (Science, 2018; eLife, 2021), which enabled the first and fast “imaging" cell sorter. By combining label-free and fluorescence image data analyzed through supervised and unsupervised machine learning approaches, Ghost Cytometry identifies cells based on complex morphological signatures, particularly beneficial when molecular markers are unavailable or undesirable. Using several case studies, I will show the capabilities and applications of Ghost Cytometry in classifying diverse cell phenotypes and responses, highlighting its potential as a tool for unbiased, high-content cell analysis and sorting in biomedical research. 

Finally, as time permits, I will briefly introduce two recent advancements: Deep Nanometry (Nature Communications, 2025), a technology enabling ultrasensitive nanoparticle characterization, and another for time-lapse single-cell spectrometry (in submission).].

About the speaker
[Networked biophotonics and microfluidics
RCAST at Univ of Tokyo
ThinkCyte inc.].

Connection details
Zoom*: [https://embl-org.zoom.us/j/93633159006?pwd=AQjra4V7PEoZl5aEqp7bchjceOOSCZ.1] (Meeting ID: [93633159006]


6 June 2025, 13:00

The biology of sex in a divergent eukaryote – insights from systematic genetic screens in a malaria parasite

6 June 20252025Hamburg SpeakerEMBL Hamburg

...

Speaker(s): Oliver Billker, University of Umea, Sweden
Host: Matthias Wilmanns, EMBL Hamburg Unit, Hamburg

Place: Seminar Room 48e

Hamburg Speaker

EMBL Hamburg


13 June 2025, 13:00

Amyloids: from the origin to the end of life

13 June 20252025Hamburg SpeakerEMBL Hamburg

...

Speaker(s): Roland Riek, ETH Zurich Department of Chemistry and Applied Biosciences, Switzerland
Host: Meytal Landau

Place: Seminar Room 48e

Hamburg Speaker

EMBL Hamburg


16 June 2025, 11:00

Interview Skills: Hiring and Being Hired in Academia

16 June 20252025Career EventEMBL Heidelberg

...

Speaker(s): Ana Boskovic, Group Leader, European Molecular Biology Laboratory (EMBL), Italy, Italy | André Nadler, Senior Research Group Leader, Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) | Rafael Galupa, Group Leader, Centre de Biologie Intégrative (CBI)
Host: Fellows’ Skills and Career Development

Place: via Zoom VC (Join the VC)

Career Event

EMBL Heidelberg


16 June 2025, 12:10

Science & Society Conference "In Science We Trust?", 16-17 June 2025

16 June 20252025Science and SocietyEMBL Heidelberg

We live in an era of unprecedented scientific breakthroughs gene editing stem cell research AI driven discoveries and rapid vaccine development are revolutionizing our world Yet alongside these advancements misinformation ethical dilemmas and scientific scepticism have become more prominent raising crucial questions about trust in science How do we navigate a post truth society where... We live in an era of unprecedented scientific breakthroughs – gene editing, stem cell research, AI-driven discoveries, and rapid vaccine development are revolutionizing our world. Yet, alongside these advancements, misinformation, ethical dilemmas, and scientific scepticism have become more prominent, raising crucial questions about trust in science.How do we navigate a "post-truth" society where scientific credibility is constantly challenged? How can researchers, policymakers, and science communicators strengthen the bond between science and society?The 2025 Science & Society Conference "In Science We Trust?" is your opportunity to tackle these pressing issues head-on. Over two thought-provoking days, we’ll examine how public perception of science has evolved, explore the societal impact of trust in research, and discuss the role of scientists in fostering transparency and...

Speaker(s): Ralf Bartenschlager, Heidelberg University Hospital, Germany | Maura Hiney, University College Dublin, Ireland | Ulrike Beisiegel, University of Göttingen, Germany | Ben Bleasdale, Campaign for Science and Engineering, UK | Perihan Elif Ekmekci, TOBB University of Economics and Technology, Turkey | Caitjan Gainty, King’s College London, UK | Margaret Gold, Leiden University, The Netherlands | Giorgia Guglielmi, Freelance Science Journalist, Switzerland | Andreas Kosmider, Falling Walls Foundation, Germany | Resham Kotecha, Open Data Institute, UK | Mihalis Kritikos, European Parliament, Belgium | Rebecca Lawrence, F1000, UK | Marcus Munafo, University of Bristol, UK | Henriikka Mustajoki, Open Science, Finland | Malvika Sharan, The Alan Turing Institute, UK | Veli Vural Uslu, TAP (The Awesome Potatoes) Science Theater, Heidelberg | Victoria Tianjing Yan, EMBL Heidelberg, Germany | Hub Zwart, Erasmus School of Philosophy, The Netherlands
Host: Bioethics Services Office

Place: ATC Auditorium (Join the VC)

Science and Society

EMBL Heidelberg

Additional information

We live in an era of unprecedented scientific breakthroughs – gene editing, stem cell research, AI-driven discoveries, and rapid vaccine development are revolutionizing our world. Yet, alongside these advancements, misinformation, ethical dilemmas, and scientific scepticism have become more prominent, raising crucial questions about trust in science.

How do we navigate a "post-truth" society where scientific credibility is constantly challenged? How can researchers, policymakers, and science communicators strengthen the bond between science and society?

The 2025 Science & Society Conference "In Science We Trust?" is your opportunity to tackle these pressing issues head-on. Over two thought-provoking days, we’ll examine how public perception of science has evolved, explore the societal impact of trust in research, and discuss the role of scientists in fostering transparency and engagement. Through inspiring keynote speeches, lively panel discussions, and poster sessions, you’ll gain insights from leading experts and discuss together about the future of trust in science.

The conference welcomes not only life science researchers and students, but also professionals from different fields who are dedicated to fostering a trustworthy relationship between science and society. Whether you are a science communicator, educator, policy-maker, ombudsman or ethicist, this event is sure to be of interest to you!

 


2 July 2025, 10:30

CryoET data collection using SPACEtomo and processing in DECTRIS CLOUD

2 July 20252025Company RepresentativeEMBL Heidelberg

AbstractIn situ cryoET data collection requires experienced users and appreciable microscope time to carefully select targets for tilt series acquisition To facilitate full automation I developed smart parallel automated cryo electron tomography SPACEtomo a workflow using machine learning approaches for lamella detection and biological feature segmentation followed by automated target setup... AbstractIn situ cryoET data collection requires experienced users and appreciable microscope time to carefully select targets for tilt series acquisition. To facilitate full automation, I developed smart parallel automated cryo-electron tomography (SPACEtomo), a workflow using machine learning approaches for lamella detection and biological feature segmentation followed by automated target setup and parallel acquisition. This degree of automation will be essential for obtaining statistically relevant datasets and high-resolution structures of macromolecules in their native context. Such large datasets subsequently require careful data management and vast processing resources to obtain scientific insights. I will show how DECTRIS CLOUD can be leveraged to gain easy access to virtually unlimited cloud-based computing power for cryoEM and cryoET data processing. 

Speaker(s): Fabian Eisenstein, DECTRIS CLOUD, Switzerland
Host: Simone Mattei

Place: IC Lecture Hall

Company Representative

EMBL Heidelberg

Additional information

Abstract
In situ cryoET data collection requires experienced users and appreciable microscope time to carefully select targets for tilt series acquisition. To facilitate full automation, I developed smart parallel automated cryo-electron tomography (SPACEtomo), a workflow using machine learning approaches for lamella detection and biological feature segmentation followed by automated target setup and parallel acquisition. This degree of automation will be essential for obtaining statistically relevant datasets and high-resolution structures of macromolecules in their native context. Such large datasets subsequently require careful data management and vast processing resources to obtain scientific insights. I will show how DECTRIS CLOUD can be leveraged to gain easy access to virtually unlimited cloud-based computing power for cryoEM and cryoET data processing.

 


14 July 2025, 11:00

Deciphering the cis-regulatory sequence code of the human genome

14 July 20252025EMBL Distinguished Visitor LectureEMBL Rome

AbstractMy lab has developed lightweight robust and interpretable deep learning models that can predict diverse biochemical profiles spanning transcription factor binding chromatin accessibility nascent transcription steady state transcription and reporter assays Our models 1 detect learn and correct cryptic experimental biases 2 reveal underlying causal sequence syntax and its... AbstractMy lab has developed lightweight, robust and interpretable deep learning models that can predict diverse biochemical profiles spanning transcription factor binding, chromatin accessibility, nascent transcription, steady state transcription and reporter assays. Our models (1) detect, learn and correct cryptic experimental biases, (2) reveal underlying causal sequence syntax and its pleiotropy across biochemical and cellular contexts, (3) encode biophysical parameters and (4) predict effects of regulatory genetic variants. Our models match or surpass the performance of massive, multi-task supervised models and self-supervised DNA language models across a battery of carefully curated benchmarks, including molecular QTLs from diverse cell contexts and ancestries, reporter assays, CRISPR-based genome editing experiments, and fine mapped GWAS variants. By systematically...

Speaker(s): Anshul Kundaje, Stanford University, USA

Place: Conf Room/Building 14

EMBL Distinguished Visitor Lecture

EMBL Rome

Additional information

Abstract
My lab has developed lightweight, robust and interpretable deep learning models that can predict diverse biochemical profiles spanning transcription factor binding, chromatin accessibility, nascent transcription, steady state transcription and reporter assays. Our models (1) detect, learn and correct cryptic experimental biases, (2) reveal underlying causal sequence syntax and its pleiotropy across biochemical and cellular contexts, (3) encode biophysical parameters and (4) predict effects of regulatory genetic variants. Our models match or surpass the performance of massive, multi-task supervised models and self-supervised DNA language models across a battery of carefully curated benchmarks, including molecular QTLs from diverse cell contexts and ancestries, reporter assays, CRISPR-based genome editing experiments, and fine mapped GWAS variants. By systematically interpreting a foundational resource of ~5000 regulatory DNA sequence models trained on bulk and single cell datasets from diverse adult and fetal cellular contexts, we can begin unraveling the incredible complexity and context-specificity of regulatory sequence lexicons, syntax and genetic variation encoded in the human genome.

 

 


25 July 2025, 11:00

Decoding the transcription circuitry when the life begins

25 July 20252025EMBL Distinguished Visitor LectureEMBL Rome

AbstractDrastic epigenetic reprogramming occurs during mammalian early embryogenesis Deciphering the molecular events underlying these processes is crucial for understanding how epigenetic information is transmitted between generations and how life really begins Probing these questions was previously hindered by the scarce experimental materials that are available in early development By... AbstractDrastic epigenetic reprogramming occurs during mammalian early embryogenesis. Deciphering the molecular events underlying these processes is crucial for understanding how epigenetic information is transmitted between generations and how life really begins. Probing these questions was previously hindered by the scarce experimental materials that are available in early development. By developing a set of ultra-sensitive chromatin analysis technologies, we investigated chromatin reprogramming during early mouse development for chromatin accessibility, histone modifications, and 3D architecture. These studies unveiled highly dynamic and non-canonical chromatin regulation during maternal-to-zygotic transition and zygotic genome activation (ZGA). However, how ZGA is kickstarted and how the early development program is progressively driven by transcription factors (TFs) remain...

Speaker(s): Wei Xie, School of Life Sciences, Tsinghua University,, China
Host: Ana Boskovic

Place: Conf Room/Building 14

EMBL Distinguished Visitor Lecture

EMBL Rome

Additional information

Abstract
Drastic epigenetic reprogramming occurs during mammalian early embryogenesis. Deciphering the molecular events underlying these processes is crucial for understanding how epigenetic information is transmitted between generations and how life really begins. Probing these questions was previously hindered by the scarce experimental materials that are available in early development. By developing a set of ultra-sensitive chromatin analysis technologies, we investigated chromatin reprogramming during early mouse development for chromatin accessibility, histone modifications, and 3D architecture. These studies unveiled highly dynamic and non-canonical chromatin regulation during maternal-to-zygotic transition and zygotic genome activation (ZGA). However, how ZGA is kickstarted and how the early development program is progressively driven by transcription factors (TFs) remain enigmatic. Recently, we identified key TFs that act at the onset of ZGA, and those that connect ZGA to the first cell fate commitment. In this talk, I will discuss how TFs and epigenetic factors cooperatively establish embryonic program and restore the embryonic epigenomes when the life begins. 


12 September 2025, 11:00

How Large Language Models impact Bio-image Data Science

12 September 20252025External Faculty SpeakerEMBL Heidelberg

AbstractLarge 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... AbstractLarge 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. 

Speaker(s): Robert Haase, Universität Leipzig, Germany
Host: Christian Tischer

Place: Small Operon

External Faculty Speaker

EMBL Heidelberg

Additional information

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.

 


3 October 2025, 11:00

To be announced

3 October 20252025External Faculty SpeakerEMBL Rome

...

Speaker(s): Cyril Henry, University of Bordeaux, France
Host: Cornelius Gross

Place: Conf Room/Building 14

External Faculty Speaker

EMBL Rome


7 October 2025, 11:00

To be announced

7 October 20252025EMBL Distinguished Visitor LectureEMBL Rome

...

Speaker(s): Magdalena Götz, Helmholtz Zentrum München, Germany

Place: Conf Room/Building 14

EMBL Distinguished Visitor Lecture

EMBL Rome


17 October 2025, 11:00

To be announced

17 October 20252025EMBL - Sapienza LectureEMBL Rome

...

Speaker(s): Antonella Riccio, UCL Laboratory for Molecular Cell Biology, United Kingdom

Place: Sapienza Università di Roma - Aula Odeion - Museo dell'Arte Classica - P.le Aldo Moro, 5 - Roma

EMBL - Sapienza Lecture

EMBL Rome


24 October 2025, 11:00

Memory aids on the chromatin – Epigenetic mechanisms of memory encoding

24 October 20252025External Faculty SpeakerEMBL Rome

AbstractMemory 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... AbstractMemory 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...

Speaker(s): Johannes Graff, École Polytechnique Fédérale de Lausanne (EPFL), Switzerland

Place: Conf Room/Building 14

External Faculty Speaker

EMBL Rome

Additional information

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. 


7 November 2025, 11:00

To be announced

7 November 20252025EMBL Distinguished Visitor LectureEMBL Rome

...

Speaker(s): Stavros Lomvardas, Columbia University, USA

Place: Conf Room/Building 14

EMBL Distinguished Visitor Lecture

EMBL Rome


14 November 2025, 11:00

To be announced

14 November 20252025EMBL - Sapienza LectureEMBL Rome

...

Speaker(s): Andrea Ganna, Institute for Molecular Medicine Finland (FIMM), Finland

Place: Sapienza Università di Roma - Aula Odeion - Museo dell'Arte Classica - P.le Aldo Moro, 5 - Roma

EMBL - Sapienza Lecture

EMBL Rome


21 November 2025, 11:00

To be announced

21 November 20252025EMBL Distinguished Visitor LectureEMBL Rome

...

Speaker(s): Hongkui Zeng, Allen Institute for Brain Science, USA

Place: Conf Room/Building 14

EMBL Distinguished Visitor Lecture

EMBL Rome


4 December 2025, 14:30

To be announced

4 December 20252025External Faculty SpeakerEMBL Heidelberg

Abstract Text for abstract About the speaker Biographical information about the speaker Meet the speakerTo 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... Abstract[Text for abstract].About the speaker[Biographical information about the speaker].Meet the speakerTo 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 detailsZoom*: [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.

Speaker(s): Irene Miguel Aliaga, The Francis Crick Institute, United Kingdom

Place: Small Operon

External Faculty Speaker

EMBL Heidelberg

Additional information

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.