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DTSTART;TZID=Europe/Stockholm:20250306T100000
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DTSTAMP:20260501T092551
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SUMMARY:Automation of research processes with LLMs and AI
DESCRIPTION:SciLifeLab is thrilled to invite you to the symposium ‘Automation of research processes with LLMs and AI’\, to be held on March 6 at Eva & Georg Klein lecture hall\, Biomedicum\, Karolinska Institutet Campus Solna. \n\n\n\nThe purpose of the symposium is practical knowledge sharing\, inspiration\, and reflection on the future of scientific processes in life sciences and health research. Academic\, healthcare\, and industry researchers working within the broad life sciences are welcome to attend. \n\n\n\nMore and more AI-based tools are currently being integrated in scientific research processes\, from simple academic text editing tools to automated labs empowered by large language models (LLMs) running experiments and making scientific conclusions. For researchers in life sciences and health\, developments in the AI technologies are important because of the high potential\, large monetary investments\, but also expectations about future breakthroughs.This one-day event offers an opportunity for the researchers to hear about specific examples of incorporating Large Language Models (LLMs) and other recent developments in foundational AI models in research workflows as well as to discuss the future of scientific research processes with this new technology present. \n\n\n\nWe will start the morning with inspirational talks about new advances in research workflow automation. During lunch\, there will be a possibility to network and discuss different perspectives with other attendees. After lunch we plan to have interactive sessions where the audience will have an opportunity to share and discuss visions and expectations\, including spontaneous flash/pop-up talks by the attendees. \n\n\n\nThe talks will be livestreamed through Zoom. The rest of the event is on-site in Biomedicum only. \n\n\n\nRegistration\n\n\n\nRegistration \n\n\n\nParticipation is free of charge on the first-come first-served basis. Refreshments and lunch will be served for the on-site participants. Unfortunately\, we cannot accommodate allergies or dietary preferences for those who register after March 1. If you register to listen to livestreamed talks on Zoom\, you will receive a link on the day of the event. The talks will not be recorded and saved\, only streamed live on the day. \n\n\n\nRegister to attend\n\n\n\nWaiting List \n\n\n\nTo avoid empty seats\, registration will remain open until the event begins. If we reach full capacity\, a waiting list will be activated. Sign up for the waiting list\, and you will automatically receive an email when a spot becomes available. You must accept to secure the spot. If you decline\, the offer will go to the next person on the waiting list. \n\n\n\nCancellation \n\n\n\nTo minimize empty seats and especially food waste\, you must cancel your registration if you are unable to attend the event. If a waiting list is activated\, your spot will go to someone else. Otherwise\, your cancellation will result in us covering the cost of your refreshments and lunch. \n\n\n\nIf you have questions\, please contact datacentre@scilifelab.se \n\n\n\n\n\n\n\n\n\n\n\nSpeakers\n\n\n\nOlli Kallioniemi (KI/FIMM) – AI-Empowered Life Science: How Can You Benefit Today and in the Future?\nNobel prizes\, huge tech investments\, generative AI and AI agents\, multidisciplinary expertise\, expectations on emerging superhuman intelligence\, and 1\,000+ AI-powered approved medical devices all highlight AI’s transformative potential for life scientists. Yet\, many researchers remain unaware or skeptical\, often due to limited exposure. This talk will cover AI’s current and future impact in life sciences\, highlighting how it can empower every scientist\, boost research productivity\, and foster innovative approaches. \n\n\n\nOlli Kallioniemi is the Founding Director of the SciLifeLab & Wallenberg Data-Driven Life Science (DDLS) Program and served as Director of SciLifeLab from 2015 to 2024. He is a Professor of Molecular Precision Medicine at Karolinska Institute (OnkPat) and holds a joint appointment at the Institute for Molecular Medicine Finland (FIMM) at the University of Helsinki. He has recently focused on exploring and explaining the opportunities that AI offers for life science research and how AI can benefit every researcher. \n\n\n\n\nMelissa Harrison (EMBL-EBI) – How Europe PMC uses and supports LLM development for research workflows\nEurope PubMed Central (Europe PMC)\, developed by EMBL-EBI\, is a free\, open-access literature database containing over 45 million life science literature outputs; over 10 million of which are full text. This includes almost a million preprints from 34 different servers. Associated research outputs\, such as data\, are linked to the literature\, which is also enriched with additional persistent identifiers\, text mined funding information\, and text mined annotations of the articles and supplementary files. Annotations are dictionary-based and are being transitioned to a machine learning approach. This talk will discuss the potential of this transition and will explore how Europe PMC plans to leverage machine learning in the future while maintaining the community’s trust in its curated\, open dataset as a reliable resource for scientific research. Words of caution about AI and ghost workers\, including biocurators\, will also be mentioned. \n\n\n\nMelissa Harrison is the Lead of Literature Services at EMBL’s European Bioinformatics Institute (EMBL-EBI). After completing a biology degree at King’s College London she worked in scientific publishing for two decades. In her previous role at eLife she honed her skills in open science policy and implementation and has been instrumental in the propagation of open persistent identifiers and metadata. \n\n\n\n\n Aasa Feragen (DTU) – AI fairness — it doesn’t have to be hard\nAasa Feragen is a Professor in Medical Image Analysis at the Technical University of Denmark (DTU).  \n\n\n\n\nMartin Eklund (KI) – Limitations of foundation models for achieving optimal performance\nFoundation models are undoubtedly highly useful. But are they a panacea for advancing performance of deep learning systems? If not\, what are their limitations? In the presentation\, we explore these questions using large and rich digitized prostate pathology data as an example. \n\n\n\nMartin Eklund is professor of epidemiology at the Department of Medical Epidemiology and Biostatistics where he focusses his research on reducing the mortality of prostate cancer as well as the negative side effects of today’s imprecise diagnostics and treatment selection. He works a lot on development of AI systems for clinical decision making. \n\n\n\n\nPrashant Singh (UU) – AI and Optimization for Science: Principles and Pitfalls\nData-driven science has emerged as a modern pillar of science\, complementing theory\, experiments and computational approaches. Scientific workflows – from design of experiments to data analysis\, have greatly benefited from tools and techniques from various fields including optimization\, statistics\, computational science\, etc. In this talk\, we will motivate principled approaches for various stages of the scientific research pipeline\, from traditional foundations such as optimization\, to recent AI-based advances such as large-language models. \n\n\n\nPrashant is an Assistant Professor\, and a SciLifeLab fellow hosted at the Department of Information Technology\, Science for Life Laboratory\, Uppsala University. His research interests involve developing machine learning and optimization methods to enable fast\, data-efficient analysis and processing of scientific data\, particularly in the domain of life sciences. \n\n\n\n\nPhil Ewels (Seqera) – Building and testing scientific workflows with LLMs and AI agents\nNextflow has become the leading tool for scientific workflows in bioinformatics\, but writing workflows can be challenging. This talk introduces Seqera AI\, a new tool that helps generate Nextflow pipelines either from scratch\, from existing scripts\, or even other workflow languages. I’ll discuss how Seqera AI is able to generate best-practice DSL2 code that follows nf-core guidelines\, and how we go beyond just code generation: creating and running test suites with AI agents\, streamlining development while improving code quality and validation. \n\n\n\nPhil Ewels is Senior Product Manager for Open Source at Seqera\, working with Nextflow\, MultiQC\, nf-core and Wave. Before joining Seqera in 2022\, Phil worked at the National Genomics Infrastructure (NGI) at SciLifeLab in Stockholm\, Sweden. It was through this work that Phil became involved with Nextflow and eventually co-founded the nf-core community. Phil’s career has spanned many disciplines from lab work and bioinformatics research in epigenetics\, through to software development and community engagement. He is the author of MultiQC\, SRA-Explorer\, QCFail.com\, and has a PhD in Molecular Biology from the University of Cambridge\, UK. \n\n\n\n\nProgram\n\n\n\nAutomation_of_research_workflows_March_6_programmeDownload
URL:https://www.scilifelab.se/event/automation/
LOCATION:Eva & Georg Klein lecture hall\, Biomedicum\, Solnavägen 9\, 171 65 Solna\, Solna\, 171 65\, Sweden
CATEGORIES:Event
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DTSTART;TZID=Europe/Stockholm:20250317T120000
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SUMMARY:Imaging in Cell and Molecular Biology
DESCRIPTION:The DDLS research area symposia series aims to engage and build a strong national scientific community around the DDLS research themes. Each of the four areas arranges two symposia per year. Everyone interested in data-driven research is welcome to take part. We want to bring together researchers\, industry\, and healthcare to foster collaboration and push the frontiers of data-driven life science. \n\n\n\nThe DDLS research area Expert Group in Cell and Molecular Biology invites all interested in Data-driven life science to meet\, present\, interact\, and discuss Imaging in Cell and Molecular Biology.  \n\n\n\nThe event will take place at Ångström Laboratory in Uppsala and will include presentations from international and national invited speakers and selected abstracts. The event is free of charge.  \n\n\n\nDate: March 17 – 18\, 2025 \n\n\n\nStart: at 12:00 on March 17\, with lunch and registration.  \n\n\n\nEnd: with lunch 12:20-13:15 on March 18. \n\n\n\nVenue: Room Heinz-Otto Kreiss\, Ångström Laboratory\, Lägerhyddsvägen 1\, 752 37 Uppsala. Find your way – Maze map link here!  \n\n\n\nFind your way: From Uppsala Central Station\, take buss № 4 (place B4) to Polacksbacken (find timetables for Uppsala City buses here). \n\n\n\nPoster session\n\n\n\nThe poster session starts at 17:10 with networking and refreshments. Find the poster list and abstracts below. \n\n\n\nFor accepted Posters\, if you have registered for: \n\n\n\n\nPaper/canvas poster: Hang your poster during the coffee break in Room 101136 (Evelyn Sokolowski). \n\n\n\nDigital poster: Display your presentation in Room 101142 (next to Evelyn Sokolowski).\n\n\n\n\nPins will be available\, and the poster boards will be marked with poster numbers.  \n\n\n\nList Posters Abstract v6Download\n\n\n\nCompany Exhibition\n\n\n\nYou will have the opportunity to meet with the following companies during the symposia: \n\n\n\n\nCarl Zeiss AB\n\n\n\nBioNordika AB\n\n\n\nTdB Labs AB\n\n\n\nMicromedic AB\n\n\n\nBruker Nordic AB\n\n\n\n10x Genomics Sweden\n\n\n\n\nCompany contact Erika Erkstam\, erika.erkstam@SciLifeLab.uu.se. \n\n\n\nIn compliance with GDPR regulations\, conference participants may not be added to company newsletters\, mailing lists\, or similar subscriptions without their explicit consent. \n\n\n\nRegistration\n\n\n\nThe registration deadline is March 3. To avoid empty seats\, registration will remain open until the event begins\, BUT registering after March 3 requires you to write your name on a name tag at the on-site registration. Unfortunately\, we cannot accommodate allergies or dietary preferences for those who register after March 3. \n\n\n\nMarch 4: The event has reached full capacity\, so a waiting list has been activated. If you sign up for the waiting list\, you will automatically receive an email when a spot becomes available. You must accept within 24 hours to secure the spot. If you decline\, the offer will go to the next person on the waiting list.  \n\n\n\nRegistration\n\n\n\nCancellation\n\n\n\nTo minimize empty seats and food waste\, you must cancel your registration if you are unable to attend the symposia. Cancel via the Confirmation email or send an email to events@scilifelab.se. \n\n\n\n\n\n\n\nInvited speakers\n\n\n\nDownload the Speaker abstracts: \n\n\n\nDDLS CMB SpeakersDownload\n\n\n\nMarta Carroni\, SU\nTitle of talk: Structural basis for bacterial protein disaggregation and proteolysis  \n\n\n\nAbstract: Protein homeostasis is meticulously maintained across all cells\, spanning from archaea to humans. Any deviation from the equilibrium of the proteome\, induced by stress or cellular aging\, leads to the accumulation of misfolded proteins\, contributing to cellular toxicity. A complex proteostasis network actively manages misfolded proteins through processes such as refolding\, degradation\, or sequestration into intracellular inclusions. Integral to this protein quality control system are ATPases from the AAA+ superfamily (ATPases Associated to a variety of cellular Activities). \n\n\n\nThese AAA+ proteins\, universally present in organisms\, share a common structural fold for ATP hydrolysis\, but each possesses distinct function-specific domains\, enabling specialization in particular cellular activities and interactions with regulatory protein partners. \n\n\n\nOur work focuses on the structural investigation of bacterial Hsp100 AAA+ chaperones involved in protein quality control. We aim at understanding their fine-tuned regulation\, which is absolutely required by the bacterium to survive harsh environment conditions and useful for us in the effort of killing pathogenic bacterial strains. Using cryo-EM in combination with biochemical functional assays\, we can describe the molecular tuning mechanisms used by bacteria to assure the disaggregation or proteolysis of toxic protein species only\, while leaving intact functional protein molecules. \n\n\n\nBio: Marta Carroni is the Head of the Swedish National Cryo-EM Facility at SciLifeLab in Stockholm\, whose start and development she drove since its institution in 2016. She is a trained structural biologist and more specifically an expert in cryo electron microscopy (cryo-EM)\, technique on which she received extensive training since 2007 first at Imperial College London and then at Birkbeck College London\, under the supervision of Helen Saibil. Marta Carroni has initiated and trained in electron microscopy and image processing a large number of researchers in Sweden and abroad; she is often invited as teacher at cryoEM symposia and workshops. For this contribution\, she has been named one of the female innovators by the Italian Association of Women Inventors and Innovators in 2018 and awarded the Hugo Theorell price in 2023. Since 2020\, she is also the director of the Cellular and Molecular Imaging platform at SciLifeLab where she oversees the integration between different imaging modalities. Since 2022\, thanks to fundings form KAW\, SSF and support from Stockholm University\, she can run independent research projects with her group\, composed of 2 PhD students and 2 postdocs\, mainly looking at AAA+ molecular motors and their regulatory mechanisms in bacterial and human systems. The group often hosts master and Erasmus students and\, while developing an independent research path\, fosters many collaborations in Sweden and abroad.  \n\n\n\n\nJan Ellenberg\, Director SciLifeLab\nTitle of talk: Quantitative Imaging of Protein Networks and Genome Structure in Single Human Cells and an Outlook on Alpha Cell \n\n\n\nAbstract: The rapid development of new imaging technologies allows unprecedented insights into the molecular machinery inside living cells and organisms. For the first time\, light and electron microscopy have molecular sensitivity and resolving power in situ\, and\, if used together\, can connect structural detail with molecular dynamics of the whole cell. Aided by machine learning driven image analysis powered by open sharing of image data\, this provides unprecedented opportunities for new insights into the molecular mechanisms that drive life’s core functions at the scale of the cell. \n\n\n\nI will present the progress we have made to study one of life’s most fundamental functions\, cell division\, by mapping the dynamic protein network\, assembly of individual protein complexes and genome re-folding that drive it. Our work has studied cell division in human cancer cells and early mammalian embryos using advanced cross-scale imaging methods\, including light-sheet\, quantitative fluorescence correlation spectroscopy (FCS)-calibrated\, super-resolution and correlative light and electron microscopy. The quantitative integrated molecular data that these new technologies deliver\, allow us to better understand how the molecular machinery functions in space and time to ensure faithful cell division and prevent the errors that underlie congenital disease\, infertility and cancer. \n\n\n\nBio: Since July 2024\, Professor Ellenberg is appointed Director of SciLifeLab. Jan Ellenberg is distinguished for many contributions to the cell biology and imaging field. The majority of these were made at the European Molecular Biology Laboratory (EMBL) where he is Senior Scientist and Head of the Cell Biology and Biophysics Unit. His major research contributions cover several aspects of the cell division cycle and nuclear organization\, including systematic analysis of mitosis\, nuclear pore complex structure and assembly\, as well as chromatin organization and formation and segregation of mitotic and meiotic chromosomes.His goal has been to obtain structural and functional measures of the required molecular machinery inside cells using quantitative 4D imaging\, single molecule spectroscopy\, as well as light sheet and super-resolution microscopy\, which his group is constantly developing and automating to address all molecular components comprehensively. \n\n\n\n\nAnja Hauser\, DRFZ\, Germany\nTitle of talk: Functional\, multidimensional optical microscopy to analyze the function of myeloid cells during bone regeneration \n\n\n\nAbstract: Focusing on bone regeneration after injury\, we aim to understand how the tissue microenvironment affects the metabolism of myeloid cells in the bone marrow over time\, and how that impacts on cell function. We previously demonstrated that CX3CR1+ myeloid cells act as trailblazers for osteogenic type H vessels in the bone marrow. In order to analyze this process in 3D\, we developed a tissue clearing\, staining and light sheet fluorescence microscopy imaging pipeline called MarShie\, optimized to image the entire intact femur at subcellular resolution down to the deepest bone marrow regions. To analyze the three-dimensional dataset\, we applied a machine learning approach\, enabling us to segment thousands of cells. We find that during homeostasis CX3CR1+ myeloid cells localize in perivascular niches\, whereas CD169+ myeloid cells are dispersed in the parenchyma. After injury\, CX3CR1+ myeloid cells relocate and sequester the injury site prior to vascularization. Analysis of the femur after full osteotomy reveals that vessel sprouting is initiated at periosteal regions.Phenotypes and functions of immune cells are tightly linked to their metabolic profiles\, which in turn is affected by changes in the tissue microenvironment. We developed a lens implant for longitudinal intravital imaging of the mouse femur\, to enable micro-endoscopic fluorescence lifetime imaging (FLIM) for metabolic profiling at the same tissue region over the whole time course of bone healing. Using a reference system of fluorescence lifetimes derived from the ubiquitous metabolic co-enzymes NADH and NADPH (NAD(P)H)\, we can determine enzymatic activities in vivo. This approach allows us to identify a high degree of dynamics in dominant metabolic pathways for energy production. Additionally\, we distinguish pathways associated to cellular function and cellular state\, i.e. oxidative burst (NADPH oxidase activity) and dormancy or death. Under in vivo conditions\, myeloid cells with various metabolic profiles\, i.e. using other pathways for energy production than the anaerobic pathway associated with pro-inflammatory cells\, perform the oxidative burst necessary for phagocytosis. This demonstrates that a high metabolic flexibility of myeloid cells in vivo. \n\n\n\nBio: Anja Hauser holds the Professorship for Immune Dynamics at Charité – Universitätsmedizin Berlin\, and is head of Program Area “Cell and Tissue Immunology” at Deutsches Rheuma-Forschungszentrum Berlin\, Germany.Anja is a trained veterinarian who received her degree at the Tierärztliche Hochschule Hannover\, Germany. During her PhD thesis\, she investigated microenvironmental conditions that promote plasma cell longevity in tissues and became interested in the spatial organization of immune cells. Her postdoctoral work at Yale University School of Medicine focused on the dynamics of germinal center B cells\, which she analyzed by intravital microscopy. Since founding her own laboratory\, she has broadened her focus from the analysis of B cells to other adaptive and innate immune cells\, with a particular focus on the analysis of immune-stroma interactions and the signals that maintain chronic inflammation.Thus\, her work is centered around the basic concept that the immune system is organized in a spatial and temporal manner. To that end\, she develops and applies advanced imaging technologies. Anja is founding member of the European Society for Spatial Biology. \n\n\n\n \n\n\n\n \n\n\n\n\nSverker Holmgren\, Data Science Node\, Chalmers\nTitle of talk: National Data Services for Imaging in Cell and Molecular Biology \n\n\n\nAbstract: The Gothenburg DDLS Data Science Node is developing and deploying national services for managing and analyzing images in CMB. The node works together with the SciLifeLab Data Center\, and the areas covered are selected jointly with the DDLS Expert Group in CMB. Currently\, a national Open Microscopy Environment service (OMERO) for image data management and storage is being deployed\, and this will be connected to High Performance Computing resources for analysis\, using e.g. AI models\, and later also to image repositories for preservation and open sharing. In the next phase\, the underlying work setting up this national service is used to develop and deploy two other sets of prioritized services. \n\n\n\nBio: Sverker Holmgren is the Director of Chalmers e-Commons at Chalmers University of Technology\, where he is also a Professor of Scientific Computing. Chalmers e-Commons is Chalmers’ digital infrastructure for research\, providing integrated support to Chalmers researchers with a focus on data management\, analysis\, and data publication. Together with Chalmers Facility for Computational Systems Biology\, Chalmers e-Commons hosts the Gothenburg DDLS Data Science Node in Cell and Molecular Biology. Chalmers e-Commons is also the Chalmers node in other selected national and international digital infrastructures and initiatives\, e.g. the National Academic Infrastructure for Supercomputing (NAISS)\, the Swedish National Data Service (SND)\, and the National Research Infrastructure for Data Visualization (InfraVis). \n\n\n\nHolmgren has a long history of engaging in data and large-scale computing infrastructures locally\, nationally\, and internationally. Besides leading the local effort at Chalmers\, he is a member of national and international reference groups and initiatives on data management. Holmgren is a permanent Expert in the Swedish Delegation to the European Strategic Forum for Research Infrastructure (ESFRI)\, a member of the ESFRI IG\, and a Swedish Delegate in the European e-Infrastructure Reflections Group (e-IRG). Earlier\, Holmgren held a professorship at Uppsala University where he also served as the Dean of Mathematics and Computer Science for six years. \n\n\n\n\nRasmus Krogh Norrild\, DTU\, Denmark\nTitle of talk: High-throughput experimental approaches for quantifying the thermodynamics of biomolecular condensate formation \n\n\n\nAbstract: Biomolecular condensates (BMCs) are phase-separated and membraneless compartments enriched in specific biomolecules\, playing key roles in biological function and disease. Understanding how BMC formation depends on solution conditions\, amino acid sequence\, and nucleotide sequence is crucial\, particularly for applications in drug discovery. High-throughput methods are therefore highly valuable for large-scale screening and for elucidating the fundamental driving forces of condensate formation. In this seminar\, I will present Condensate Partitioning by mRNA-Display (CPmD)\, a novel high-throughput approach based on mRNA display (Norrild et al.\, bioRxiv 2024). CPmD enables the simultaneous analysis of partitioning behaviour for tens of thousands of peptides and their corresponding synthetic mRNAs within BMCs\, offering new insights into the thermodynamics of condensate formation. To validate CPmD\, we employed two microfluidics-based methods\, Capflex (Stender\, Ray\, Norrild et al.\, Nat. Commun. 2021) and TDIPS (Norrild et al.\, Angew. Chem. Int. Ed. 2024)\, both leveraging the commercially available FIDA1 microcapillary system. These methods demonstrate how proteome-scale CPmD data on peptide partitioning can directly inform on biomolecular condensate formation of the proteins from which the peptides originate. \n\n\n\nBio: I am a postdoctoral researcher at the Technical University of Denmark (DTU)\, specializing in protein biophysics. I have a MSc in Biochemistry from the University of Copenhagen and I did my PhD in Biophysics at DTU on Biophysics. My research focuses on understanding how protein structure\, stability\, and phase behavior contribute to cellular function and disease. I combine experimental and data-driven computational approaches to study and engineer dynamic proteins\, especially intrinsically disordered regions of these. My goal is to integrate quantitative biophysics with cell biology to uncover new insights into protein function in complex biological systems. \n\n\n\n\nWei Ouyang\, DDLS Fellow\, KTH\nTitle of talk: Unleash the Power of Generative AI for Data-Driven Cell Biology \n\n\n\nAbstract: This talk presents the ongoing work of AICell Lab (https://aicell.io) focusing on developing generative AI\, diffusion models for human cell modeling\, and AI-driven automation in microscopy and robotics. We focus on the development of the REEF Microscopy Imaging Farm\, which aims to create fully automated imaging systems that generate high-quality datasets for cell simulation. We are also building scalable platforms like ImJoy and Hypha\, which power the BioImage Model Zoo—a community-driven repository enabling easy AI model testing. Additionally\, our BioImage Chatbot\, an AI agent built on a bioimaging knowledge base\, is being extended for automated scientific discovery. These efforts converge in the Hypha platform\, connecting hardware\, AI models\, and users to advance whole-cell modeling and redefine in-silico research and drug discovery. \n\n\n\n\nErdinc Sezgin\, KI\nTitle of talk: Physical properties of cells and nanoscale bioparticles as new biomarkers of health and disease \n\n\n\nAbstract: Remodelling of our cells as response to environmental changes is essential for their survival and function. Although numerous studies aimed at finding protein markers during such cellular processes\, there is a major gap in our understanding of how collective biophysical properties of the cells (such as stiffness\, membrane fluidity\, viscosity etc) alter during these crucial biological processes. Similarly\, our understanding of how biophysical properties of cells change in diseases is also limited. To gain a thorough mechanistic perception of cellular processes and diseases\, it is essential to fill this gap and have a clear and quantitative picture of biophysical remodelling of the cells.We and others have made extensive effort to unravel the biophysical aspects of cells in a quantitative manner. To achieve this\, we developed advanced imaging approaches that could reveal the molecular details with very high spatiotemporal resolution. These technologies allowed us to see how biophysical properties of cells play crucial roles for signalling from molecular to cellular level. Although these technologies were extremely useful to study biophysical aspects of cellular life at the molecular level\, their low sampling (one cell at a time) has been a major obstacle to apply them to medical problems that require measuring thousands of cells. This can be overcome with high throughput methodologies that can robustly report on the ensemble biophysical properties of cells which require reliable reporters and instruments. Thus\, while developing advanced instrumentation\, we also develop reliable probes to quantify different biophysical properties of cells. Here\, I will discuss our approach from probe development to high throughput biophysical analysis \n\n\n\nBio: Erdinc Sezgin studied Genetics and Bioengineering at the Yeditepe University\, Istanbul Turkey. He next joined International Max Planck Research School for PhD in Dresden\, Germany. After graduation\, he obtained EMBO\, Marie Curie and Newton fellowships to perform his postdoctoral research in immunology and imaging at University of Oxford. Since 2020\, he has been leading his independent lab as an Associate Professor at Karolinska Institutet and SciLifeLab. He is currently an EMBO Young Investigator and a Visiting Faculty at University of Oxford. \n\n\n\n\nEduardo Villablanca\, KI\nTitle of talk: Unraveling the Molecular Architecture of the Intestinal Barrier: Insights from Spatial Transcriptomics \n\n\n\nAbstract: The complex cellular network that constitutes the intestinal barrier is crucial for maintaining health and preventing diseases. In this talk\, I will present the remarkable capabilities of spatial transcriptomics (ST) in unveiling the molecular organization of the entire colonic tissue during mucosal healing and tumorigenesis. By leveraging ST\, we revealed a previously undiscovered regionalization of the colon’s transcriptomic landscape under steady state conditions\, which undergoes dramatic changes during mucosal healing. We identified spatially organized transcriptional programs that define compartmentalized mucosal healing\, including regions exhibiting dominant wired pathways. Furthermore\, I will discuss the translational potential of our findings by mapping transcriptomic modules associated with human diseases. \n\n\n\nBio: Dr. Villablanca is a developmental biologist turned immunologist with expertise in cell migration and mucosal immunology. He began his research using zebrafish as an in vivo model before shifting his focus to immunology during his PhD in Molecular Medicine at San Raffaele University in Milan\, Italy. His interest in intestinal leukocyte trafficking led him to Harvard Medical School\, where he trained as a postdoctoral fellow in Dr. Rodrigo Mora’s lab. After four years\, he was promoted to Instructor in Medicine and joined Dr. Xavier’s lab to study inflammatory bowel disease (IBD) risk genes and their role in intestinal immune homeostasis.In late 2014\, Dr. Villablanca was recruited to establish his own laboratory at the Karolinska Institute’s Division of Immunology and Respiratory Medicine in Sweden. Now a Professor of Gastrointestinal Immunology\, Wallenberg Fellow\, and ERC awardee\, he leads a research team integrating developmental biology\, mucosal immunology\, and systems biology to uncover how intestinal homeostasis is maintained and how its disruption contributes to disease.Visit the Villablanca lab webpage here or watch the research video summary here.BsKy: @ejvillablanca.bsky.social \n\n\n\n\nFor questions about the Program\, please contact the Scientific Committee: \n\n\n\n\nIda-Maria Sintorn\, UU\n\n\n\nMarc Friedländer\, SU\n\n\n\n\nAbout the event\, please contact Project leader: Erika Erkstam\, Operations office\, SciLifeLab \n\n\n\nProgram\n\n\n\nDDLS-Symposium-PROGRAM-NY2Download\n\n\n\nMore information about the Data-driven Life Science Research area\n\n\n\n\n\n\n\nDDLS Cell and Molecular Biology
URL:https://www.scilifelab.se/event/imaging-in-cell-and-molecular-biology/
LOCATION:Ångström Laboratory\, Lägerhyddsvägen 1\, Uppsala\, Sweden
CATEGORIES:Event
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DTSTART;TZID=Europe/Stockholm:20250318T150000
DTEND;TZID=Europe/Stockholm:20250321T140000
DTSTAMP:20260501T092552
CREATED:20250109T082032Z
LAST-MODIFIED:20250318T173404Z
UID:10001427-1742310000-1742565600@www.scilifelab.se
SUMMARY:DDLS Research School Annual Meeting
DESCRIPTION:The first DDLS Research School Annual Meeting for PhDs and PIs\, including DDLS fellows. This meeting is by invitation only. DDLS PhD students are invited to participate the entire duration of the meeting (18-21 March)\, while their supervisors are invited to participate 18-19 March (afternoon-to-lunch) \n\n\n\n \n\n\n\nProgram\n\n\n\nTuesday March 18: \n\n\n\n14:30-15:30Registration and coffeeLilla Kongressen15:30-16:30Welcome and introduction to the DDLS Research SchoolLilla Kongressen16:30-17:15– PIs: meeting with DDLS Research School Directors                               – PhD students: group activity– Room 7E – Lilla Kongressen17:30-18:3017:30-19:00– PIs: questions and answers with DDLS RS Directors – PhD students: Social activity – Lilla Kongressen– House 9\, Stora Kongressen19:00Welcome drinkLobby\, main building19:30DinnerRestaurant\, main building\n\n\n\n\n\n\n\nWednesday March 19:  \n\n\n\n07:00   Breakfast opens08:30-10:10PI presentations: CMB & EBI Stora Kongressen10:10-10:40Coffee with Group PhotoStora Kongressen10:40-12:30PI presentations: EB & PMD Stora Kongressen12:45– Lunch – Set up your poster in Stora KongressenMain building13:45Bus departure for PIs Outside main building14:00-16:30 Workshop led by Maja Neiman\, SwedenBioStora Kongressen16:30-18:30Poster session with refreshmentsStora Kongressen19:00  Dinner Restaurant\, main building\n\n\n\n\n\n\n\nThursday March 20:     \n\n\n\n08:30-17:00Course: Open science in the Swedish contextLilla Kongressen11:30LunchRestaurant\, main building17:00-18:30Free time18:30 Dinner Restaurant\, main building20:00 Music quiz House 9\, Bar\n\n\n\n\n\n\n\nFriday March 21:    \n\n\n\n09:00-10:00Introduction to upcoming DDLS Research School coursesLilla Kongressen10:00-10:30CoffeeLilla Kongressen10:30-11:30Group work: future courses in the DDLS Research SchoolLilla Kongressen11:30-12:00Summary of the Annual Meeting [RS directors]Lilla Kongressen12:00 Lunch. Annual Meeting ends.Restaurant\, main building13:15 Bus departureOutside main building\n\n\n\n\n\n\n\nBustransfer\n\n\n\nDetails regarding bus transfer will be sent by email to those who have signed up for bus in their registration \n\n\n\n18 March Bus from Uppsala at 13:15from Stockholm at 13:00 \n\n\n\n19 March From Djurönäset to Stockholm and Uppsala 13:45 \n\n\n\n21 March From Djurönäset to Stockholm and Uppsala 13:15
URL:https://www.scilifelab.se/event/ddls-research-school-annual-meeting/
LOCATION:Djurönäset\, Seregårdsvägen 1\, Djurhamn
CATEGORIES:Community
END:VEVENT
END:VCALENDAR