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EMBL Heidelberg

This course will teach the biological researchers how to analyse biological data sets using open-source software. Most of the analysis will be performed with docker4seq and rCASC packages, which was developed to facilitate the use of computing demanding applications in the field of NGS data analysis. Docker4seq and rCASC packages use docker containers that embed demanding computing tasks (e.g. short reads mapping) into isolated containers. This approach provides multiple advantages: the user does not need to install all the software on its local server, the results generated by different containers can be organised in pipelines and reproducible research is guarantee by the possibility of sharing the docker images used for the analysis. Computers for hands-on exercises will be provided along with demo data sets.

EMBL Events;     Email: events@embl.de

Data Analysis and Bioinformatics,

EMBL Heidelberg

Ageing is often considered a complex phenotype that affects multiple organs and tissues in a time-dependent manner. This may result in the aged population consuming a myriad of medications, each aimed to treat, but not cure, the affected tissue. Recent studies have demonstrated that the “Primary Hallmarks of Ageing” are a set of five molecular mechanisms that malfunction, independent of tissue type, and drive ageing. Hence, focusing on these five hallmarks simplifies the efforts to understand ageing-associated disease. This, the second edition of this symposium will bring together an all-new, international line-up of speakers to continue the exchange on the basic/mechanistic aspects of chromosome biology with the applied and emerging field of ageing sciences. As more and more interventions and supplements flood the market, claiming to attenuate aging processes, it is critical that we investigate genomic changes during the ageing process. To keep the symposium fresh, in 2025 there will be new emphasis on the importance of chromatin changes and telomere dysfunction, nonetheless keeping in mind how they also affect DNA damage and repair responses

This symposium will bring together many diverse fields across topics including the below, and tie them together with the field of ageing biology and its relevant models of ageing.

Sophie Dutzi;     Email: sophie.dutzi@embl.de

Cell Biology and Biophysics

EMBL Heidelberg

This practical course teaches the basics of multicellular modelling to any researcher wishing to enter the field, particularly experimentalists with no prior experience of computational modelling. It is a “hands-on” course with 60% of the time devoted to students working on laptops performing exercises designed to give a practical familiarity with different types of computational modelling. The course focuses on the dynamics of multicellular systems- from embryos to organoids, covering both the molecular side (how gene regulatory networks perform pattern formation) and also the mechanical side in 2D and 3D (how the movements and activities of many cells together leads to tissue-level morphogenesis and organisation). A carefully-chosen variety of modelling tools will be introduced, which cover the core approaches of vertex models, finite element models (FEM), and agent-based models (ABM). Attendees will also work through the week in small groups on group projects, which will be presented on the last day to the whole class. Each day will end with a keynote lecture by a prominent researcher in the field, putting the topic of the day into context through an example of relevant biological research.

Julia Patricia Nohle;     Email: julia.nohle@embl.de

EMBL Heidelberg

In the last 20 years, genomics has revolutionised our understanding of genome organisation and its regulation. It led to near complete annotation of the genome and the factors regulating expression of our genes. Yet, almost all of this knowledge arises from experiments that sample millions of regulatory events to create an average static picture that fails to capture the mechanistic steps and the dynamics that underlie these complex processes. The last decade has seen the independent emergence in the field of microscopy and genomics of technologies able to study gene regulatory processes at the resolution of individual DNA molecules. Joining the power of these orthogonal approaches promise to bring us towards a molecular understanding of gene regulation mechanisms in vivo.

EMBL Events;     Email: events@embl.de

EMBL Heidelberg

Spatial biology is a rapidly evolving scientific topic with frequent and novel technological advances that have powerful application potential in the context of basic and translational research. The aim of the course is to provide participants a comprehensive conceptual introduction and intensive hands-on practical training on the main techniques of Imaging-based spatial-omics, i.e. multiplex immunofluorescence and spatial transcriptomics. We will provide a general overview of the field through lectures from scientific experts, assist the participants on how to choose and implement the right method for their scientific needs, and finally also share practical tips and experience of developing these techniques thanks to the presence of the original developers of such methods. Through hands-on practicals and computer sessions, the course will teach participants how to carry out open-source imaging-based methods for cost-effective spatial transcriptomics (hybridization in situ sequencing) and multiplex immunofluorescence (immune-SABER and IBEX).

Iva Gavran;     Email: iva.gavran@embl.de

Data Analysis and Bioinformatics, Genome Biology, Transcription, Translation, Technology, Imaging, Methods, #EMBOSpatialOmics

EMBL Heidelberg

We live in an era characterised by dazzling scientific and technological progress on an unprecedented scale. From the application of new gene editing techniques, pioneering stem cell research, or rapid vaccine development to emerging technologies such as AI or organoid research, advances in life sciences offer a myriad of potential benefits to society. However, these scientific endeavours exist against a backdrop of misinformation and disinformation in the scientific arena, which have the potential to cast a shadow on the public perception of science. From attitudes surrounding scientific issues in the pandemic, highly publicised cases of scientific fraud and misconduct, or ethical issues in research which may cross into the realms of science fiction, the issue of societal trust in science is never far from the public consciousness.

EMBL Events;     Email: events@embl.de

EMBL Heidelberg

This symposium is the seventh edition of a successful series started in 2013 and held biannually since, establishing itself as a must-attend fixture in the calendar for scientists working with bacteria and new technologies. The meeting covers a broad range of cutting-edge topics in microbiology, featuring diverse research. Emphasis is placed on novel approaches and technologies (from systems-based to single-cell) that drive each field or have the potential to revolutionize future research in microbiology. The meeting is always oversubscribed and manages to bring together scientists from different areas, who normally don’t meet, creating a highly interactive and dynamic atmosphere.

EMBL Events;     Email: events@embl.de

European Molecular Biology Organization (EMBO)

Schloss Dagstuhl - Leibniz-Zentrum für Informatik GmbH

In proteomics, novel algorithms are drivers of innovation, enhancing extraction of actionable insights from collected data and thereby advancing the field. We have identified three highly interesting computational challenges (and thus opportunities) that have come to the foreground in recent years: First is the application of machine learning in proteomics, which is already contributing to advancements in data analysis and interpretation in areas such as protein identification, functional annotations, and personalized medicine. Second is the rapidly growing field of glycoproteomics, which links to therapeutics as many therapeutic proteins are glycosylated. The focus here will lie on the characterization of the glycan moieties attached to proteins, the analysis of which poses specific computational challenges. Third is a cross-cutting topic at the interface between proteomics and other omics in the context of translational research. This includes both mass spectrometry and new approaches to generate, interrogate, and integrate data related to proteins, their transcripts and related metabolites. These topics are at the forefront of arising technologies and require novel solutions to emerging, highly complex problems.

EMBL Heidelberg

Mechanisms that shape cellular proteomes are critical for life. This conference focuses on the process of protein synthesis, from the molecular and structural understanding of the translational machinery to its regulation, its implications in cell and organismal biology, and its alteration in disease. The regulation of mRNA translation is critical to maintaining cell homeostasis and mediates cellular responses to environmental, physiological, and pathological cues. Given the central importance of protein synthesis, it is unsurprising that dysregulation or defects in mRNA translation are widely linked to disease, including cancer, neurological or metabolic disorders, and viral infection. In recent years, technical advances have challenged hitherto established dogmas, uncovered new quality control mechanisms, expanded the breadth of translation regulators, enhanced our understanding of the dynamics of translation in living cells, and revealed unexpected interconnections with other cellular processes such as metabolism. Advances in these aspects of mRNA translation will be featured, as well as new insights into translation regulation in physiology and disease.

Charlotte Courtney;     Email: charlotte.courtney@embl.de

The European Association for Cancer Research (EACR)

The 6th edition of this conference will focus on cancer models that span in vitro investigations to in vivo cancer biology. It will emphasise how targeting the mechanisms that control tissue assembly – including the interactions with multiple epithelial cell types and the immune system – affects cancer progression and treatment response. Emerging topics also being discussed include mechanobiology, the immune response, how the extracellular matrix controls cell architecture, and how cell fate transitions underpin tissue morphogenesis and the metastatic cascade. The target audience for this conference is scientists, postdocs, and graduate students interested in the latest generation of engineered ex vivo models of tissue biology, in vivo cancer biology, and the use of these mechanobiological concepts for the development of cancer therapeutics. It will also be highly relevant for industry scientists interested in cutting-edge models of cancer and journal editors interested in ex vivo to in vivo models of biology and cancer.

Conference Officer Hannah Barrs;     Tel.: [N/A];     Email: hannah.barrs@eacr.org

cancer research, oncology, in vitro models of cancer, ex vivo models of cancer, in vivo models of cancer, the extracellular matrix, cancer cell architecture, mechanobiology, immune response to cancer, tissue morphogenesis, the metastatic cascade, cancer immunotherapies, advanced imaging technologies, organoids, microtissue platforms, spatial transcriptomics, cell fate transitions, homeostasis, cancer progression, cancer therapeutic developments.

Onkologie,    Immunologie und Allergie

EMBL Heidelberg

Karoline Wolkersdorfer;     Email: karoline.wolkersdorfer@embl.de

Course overview This course will focus on the latest state-of-the-art novel library preparation protocols. We will start with experimental design, focusing on hands-on library preparation (including best practices, standards, and potential pitfalls), concluding with sequencing of libraries, bioinformatic evaluation & best practices. Multiomic data in scientific projects have become more and more important. NicE-Seq is a novel method enabling detection of open chromatin in fixed low numbers of cells without any additional instrumentation. Combining open chromatin with transcriptome information is crucial for interpretation of cellular states. Therefore, the course participants will also prepare mRNA libraries from the same cell populations. Participants will carry out a complete workflow, from isolation of DNA & RNA from fixed cells, library preparation for both applications and shallow sequencing. The course will discuss alternative novel approaches, various cell fixatives and their impact on analysis. In addition, we will cover basic bioinformatic tools required for data processing, quality control and initial data analysis. Beside the practical exercises, lectures and discussion sessions, the course will offer the opportunity to learn more about transferring the knowledge gained during the course to the participants’ home institu

EMBL Heidelberg

The molecular processes of life are naturally dynamic in space and time from the atomic to the organismal level. The rapid development of imaging methods across the full scale of biological organisation is revolutionising our ability to visualise the inner workings of macromolecular complexes, organelles, cells, tissues, organs and whole organisms. Being able to see biological processes unfold in real time allows us to understand the mechanisms of life as well as disease. The symposium will bring together the leading developers of imaging methods with cutting-edge applications that illustrate how imaging can answer biological questions. We will emphasize methods that can capture the dynamics of life, spanning the whole range from molecular resolution to imaging of whole organisms. From its beginning in 2011, ‘Seeing is believing’ has embraced novel imaging technologies that open new windows for biological discovery, including single-molecule and super-resolution, light sheet and correlative light electron microscopy.

Iva Gavran;     Email: iva.gavran@embl.de

EMBL Heidelberg

There is an increasing interest and need to analyse biomarkers in liquid biopsies, including basic research and clinical applications. Liquid biopsies have several advantages including being minimally invasive, allowing repeated sampling and sampling is often clinical routine. This course will provide an overview of the several techniques to detect and analyse liquid biopsy-based analytes such as circulating tumour cells, cell-free tumor-DNA (ctDNA), miRNA, extracellular vesicles, mRNA, carbohydrates and proteins. Participants will be introduced to all aspects ranging from proper sampling through analyte analysis and final data analysis. Experimentally, we will demonstrate ultrasensitive ctDNA analysis using sequencing and digital PCR. In addition, targeted miRNA profiling and flow cytometry with single-cell analysis will be highlighted. We will cover aspects of other analytes by lectures and we will have a strong focus on applications, especially cancer applications. Aspects of biobanking and clinical implementation will also be highlighted.

EMBL Events;     Email: events@embl.de

EMBL Heidelberg

The ability to grow tissues from stem cells in 3D culture to generate so-called organoids has revolutionised the study of tissue biology, especially human biology. This exciting technology has great potential for drug discovery and regenerative medicine. Because organoids model a variety of tissues with remarkably high fidelity, they allow for new discoveries in human development, homeostasis, regeneration, and disease. This symposium will bring together the leading researchers in this field, representing the premier conference for this research community, and providing a much-anticipated program that demonstrates how this field is truly pushing the boundaries for our understanding of tissue biology. This, the fifth edition of this established meeting will again bring together researchers from different fields to enhance our understanding of how organoids can be formed and maintained and their biomedical applications, from how they can be exploited to study disease to eventually use them to regenerate and replace human tissues. An aim for the 2025 edition of the symposium is the incorporation of more complementary technologies, such as multiomics, engineered embryo models and bioengineering as well as increased representation of the topic of cancer.

Inna Bösselmann;     Email: inna.boesselmann@embl.de

EMBL Heidelberg

The regulation of the transcriptome is key to cellular processes that underpin cell biology, development and tissue function. All classes of cellular RNA are subject to post-transcriptional modification, be it by direct chemical modification, editing or non-templated nucleotide additions. Now in its fourth edition, the ‘Epitranscriptome’ meeting first held at EMBL in 2016 (and repeated in 2018 then in 2022 as a virtual conference) was the first RNA modification-dedicated meeting with the focus on mammalian systems. It is now established that biochemical modifications of nucleotides regulate RNA metabolism, modulate cell functions and contribute to severe human diseases including cancer and metabolic disorders. Moreover, the power of single, chemically modified nucleotides to alter the electrostatic charge, base pairing and stability of RNA molecules is exploited for clinical use of stable artificial RNA transcripts such as mRNA vaccines or synthetic small RNA molecules to increase or decrease the expression of therapeutic proteins.

EMBL Events;     Email: events@embl.de

EMBL Heidelberg

Disparaged as “selfish DNA” for decades, it’s now clear that transposable elements (TEs) underlie the remarkably dynamic nature of bacterial, plant, and animal genomes. This conference builds on the highly successful 2021 and 2023 Mobile Genome EMBO workshops and has emerged as the major European venue in this ever-growing cross-disciplinary research field. The 2025 Mobile Genome conference will assemble recognized experts from diverse disciplines (e.g., genomics, epigenetics, structural biology, evolutionary biology, and developmental biology), as well as the next generation of scientists who will become leaders in the field, to discuss the broad impact of TEs on organismal biology. A dedicated discussion session focused on technological and conceptual advances will augment the program to provide a forum for cross-disciplinary interaction among attendees with the goal of catalyzing collaborative opportunities to address new questions and challenges in TE research.

Julia Patricia Nohle;     Email: julia.nohle@embl.de

EMBL Heidelberg

Flow cytometry is a highly effective method for analysing individual cells that has become widely used in the fields of life sciences and medicine. By utilising flow cytometry, researchers can accurately identify and measure specific cell populations within complex mixtures, as well as assess cell cycle progression, proliferation status, and expression of fluorescent markers. Our course aims to provide a comprehensive understanding of the underlying principles of flow cytometry, while also emphasising practical considerations related to the most frequently used assays. Through a combination of theoretical instruction and hands-on training, students will gain the knowledge and skills necessary to effectively design, execute, and interpret flow cytometry experiments.

EMBL Events;     Email: events@embl.de

EMBL Heidelberg

This meeting will provide an opportunity to learn about and keep up to date with the rapidly progressing area of cancer genomics. We aim to bring together scientists from across several disciplines connected with cancer research, for a unique opportunity to interact and stimulate further integration of these efforts.

EMBL Events;     Email: events@embl.de

EMBL Heidelberg

The nucleus lies at the literal and figurative heart of the cell – as the one organelle that all eukaryotes share, it is over 2 billion years old and integrated with every aspect of cellular function, from mechanosensing and genome regulation to membrane trafficking and cell division. Although the role of the nucleus in organising, housing and protecting the genome frequently takes centre stage, much remains to be discovered about the cellular physiology of this unique organelle studied in its own right rather than just as a passive scaffold for chromatin. This meeting will bring together a group of scientists spanning the fields of biochemistry, membrane trafficking, cytoskeletal dynamics, cell division control and cellular biophysics to address the cellular roles of the nuclear compartment from a diversity of angles.

EMBL Heidelberg

The rapid evolution of computational structural biology, driven by AI, continues to revolutionise our understanding of biomolecular structures, functions, and interactions. This follow-up to the 2023 first edition of the workshop responds to the field’s swift advancements and the pressing need for a forum that not only aligns with these progresses but also foresees future shifts. The conference aims to advance computational structural biology, promote the adoption of innovative methodologies, and enhance interdisciplinary research and collaborations. Capturing the latest advancements in this vibrant field, this second edition of the meeting is set to provide a pivotal platform for disseminating these breakthroughs and charting future directions in computational structural biology.

EMBL Events;     Email: events@embl.de

EMBL Heidelberg

This course will provide training in genome editing and cell engineering in mammalian cells and mouse embryos using the highly efficient CRISPR/Cas9 system. Participants will learn design of CRISPR targets using bioinformatics tools, generation of gene knock-outs/knock-ins, and target validation using the most current technologies. The course will be split into two groups (mammalian cells OR mice) based on participants’ expertise. Please note that all participants are expected to engage in all sessions. Participants should plan for approximately 1 hour extra per day for self paced learning modules.

EMBL Events;     Email: events@embl.de

Genomforschung und Bioinformatik,    Biologie