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DTSTART;TZID=Europe/Stockholm:20240918T080000
DTEND;TZID=Europe/Stockholm:20240919T170000
DTSTAMP:20260404T171237
CREATED:20240411T132838Z
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SUMMARY:Training Material made FAIR by Design
DESCRIPTION:This 2 day course is based on the FAIR training handbook and 10 simple rules to make material FAIR publication. All sessions are structured in a way that complement each other aiming to introduce participants with a theoretical & hands-on approach of how to design FAIR training material. \n\n\n\nPlease see the course website\, which will be updated regularly\, for more information \n\n\n\n \n\n\n\nTopics covered will include:\n\n\n\n\nFAIR vs OPEN training material\n\n\n\nTraining material documentation and reproducibility \n\n\n\n(ontology\, Learning Outcomes\,etc)\n\n\n\nIllustrations\, keeping it FAIR\n\n\n\nE-learning and videos\, challenges and solutions to keep it FAIR\n\n\n\nUnique identifiers and version control\n\n\n\n\nActivities are intended to increase the technical skills and critical thinking during the development of a new training course. From A to Z participants are going to be challenged to work in a group to build a FAIR lesson on a topic to be presented at the end of the course. Come inspired! \n\n\n\nImportant Dates\n\n\n\nApplication open: 11-April-2024Application closes: 23-August-2024 \n\n\n\nConfirmation to applicants 30-August-2024 \n\n\n\nRegistration\n\n\n\nCourse website\n\n\n\nNote: The course is highly interactive and hence it is important that you\, as a participant\, actively contribute to all sessions and elements of the course.  \n\n\n\nParticipants need to bring a laptop.There are no fees for this course. \n\n\n\nAll are welcome! Particularly interesting for trainers and instructors that design-develop-deliver short-format training. \n\n\n\nLearning Objectives\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\ncreate FAIR and open training material from the start\n\n\n\napply FAIR principles to all elements of training material\n\n\n\nuse AI tools in content creation of FAIR training material\n\n\n\n\nPrerequisites\n\n\n\nThe following is a list of skills required for being able to follow the course and complete the exercises: \n\n\n\n\nBe familiar with GitHub If not\, we advise you to have a look at the GitHub Skills pages and/or Github courses in Glittr.org in order to acquire the following:\n\nBasic knowledge: To be able to make commits\, create branches and issues\, make pull requests.\n\n\n\n\n\nDesirable\, but not essential skills increasing the output of the course include:\n\nPre-reading the FAIR Training Handbook\n\n\n\nPre-reading 10 simple rules to make material FAIR publication
URL:https://www.scilifelab.se/event/fair-training-material-by-design/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Course
ORGANIZER;CN="SciLifeLab Training Hub%2C NBIS%2C and VIB":MAILTO:traininghub@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240918T151500
DTEND;TZID=Europe/Stockholm:20240918T161500
DTSTAMP:20260404T171237
CREATED:20240829T065531Z
LAST-MODIFIED:20240829T065536Z
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SUMMARY:[The Svedberg seminar] - Leveraging innate immunity against epidemic and pandemic viruses
DESCRIPTION:Michael GaleProfessorThe University of Washington School of Medicine\, USA \n\n\n\n \n\n\n\n \n\n\n\n \n\n\n\n\n\n\n\nBio\n\n\n\nDr. Gale’s research program is focused on understanding the virus-host interactions that regulate innate immunity against virus infection. His group studies SARS-CoV-2\, CoVs\, HIV\, SIV\, hepatitis B virus\, hepatitis C virus\, influenza A virus\, hantaviruses\, West Nile virus\, Zika virus\, Dengue virus\, and other RNA viruses\, aiming to define the processes of virus recognition by the infected cell\, and how viruses control of innate immunity and immune programming to direct infection outcome. A major goal of the Gale laboratory is to define therapeutic targets to enhance immunity and vaccination outcomes against virus infection. Dr. Gale is a Principle Investigator (PI) of UWARN\, one of the NIH Centers for Research on Emerging Infectious Disease (CREID)\, and he also leads the NIH/DAIDS Nonhuman Primate Functional Genomics Core for HIV Vaccine Development. His group conducts functional genomics analyses of virus infection including assessment of preclinical HIV/SIV vaccines being tested in NIH-supported studies. These activities include bioinformatics/computational analyses of infection and vaccine responses and their linkage with mechanisms of action and disease or protection outcomes. Gale lab research is among the top 1% cited worldwide in the field of Microbiology since 2014. Dr. Gale teaches virology\, immunology\, infectious disease biology\, and public health to medical students and graduate students\, and is a member of the editorial board of several biomedical research journals. \n\n\n\nIn October 2024 Dr. Gale will relocate his lab to the University of Minnesota (UM) School of Medicine where he will be the Chair of the Department of Microbiology and Immunology\, and Director of the Institute on Infectious Disease. Contact: mgale@umn.edu \n\n\n\n \n\n\n\nLeveraging innate immunity against epidemic and pandemic viruses\n\n\n\nInnate immune defenses are essential for restricting virus replication and for programming the adaptive immune response against infection. Our studies are focused on defining the innate immune response to emerging viruses.  We have ongoing studies to define pathogen recognition receptor interactions and signaling events triggered by viral pathogen associated molecular patterns (PAMPs) across viral genera that drive innate antiviral immunity and program/enhance the adaptive immune response against infection\, with special focus on neuroinvasive flaviviruses\, SARS-CoV-2\, HIV\, and influenza A virus. We aim to translate our findings to build strategies for antiviral therapy and immune enhancement. This work has defined the RIG-I-like receptors\, including RIG-I\, MDA5\, and LGP2\, as critical factors in the recognition of RNA virus infection and immune protection against disease. We have identified distinct PAMP/RLR interactions that serve to program the outcome of infection and immunity. An overview of our emerging virus research program\, including SARS-CoV-2\, will be presented\, followed by an in-depth presentation of our work to define Zika virus infection\, immunity\, and disease. \n\n\n\n \n\n\n\n \n\n\n\n \n\n\n\n\n\n\n\nHost: Jan Komorowski jan.komorowski@icm.uu.se
URL:https://www.scilifelab.se/event/the-svedberg-seminar-michael-gale/
LOCATION:BMC Room C8:301\, Husargatan 3\, Uppsala\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/02/Picture1-The-Svedberg.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240919T120000
DTEND;TZID=Europe/Stockholm:20240919T130000
DTSTAMP:20260404T171237
CREATED:20240708T135643Z
LAST-MODIFIED:20240826T154057Z
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SUMMARY:Campus Solna Seminar Series: Simin Zhang & Adrià Sunyer
DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nPhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits\, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester. \n\n\n\nThis week:\n\n\n\n\n\n\nSimin Zhang\n\n\n\nSean Rudd – alpha 5 \n\n\n\nTailor antiviral therapy by targeting host nucleotide metabolism \n\n\n\n\n\nAdrià Sunyer\n\n\n\nJonathan Martin – gamma 5 \n\n\n\n \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-si-min-zhang-adria-sunyer/
LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna
CATEGORIES:Community
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ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240920T100000
DTEND;TZID=Europe/Stockholm:20240920T110000
DTSTAMP:20260404T171237
CREATED:20240815T085241Z
LAST-MODIFIED:20240909T135631Z
UID:10001322-1726826400-1726830000@www.scilifelab.se
SUMMARY:Variational inference for tumor phylogeny using single cell data
DESCRIPTION:Harald Melin\, KTH Royal institute of Technology \n\n\n\nMCMC has long been the gold standard for Bayesian inference in classical phylogenetics\, instantiated e.g. in popular softwares such as MrBayes and BEAST. This presentation focuses on an alternative Bayesian approach\, Variational Inference (VI)\, which has made recent advances in fields of classical and tumor phylogenetics. I will give an introduction to the method and how it is applied in classical phylogeny\, emphasising its strengths and limitations w.r.t. MCMC\, followed by how it facilitates Bayesian inference of copy number evolution in tumors using low coverage single cell whole-genome sequencing data\, based on our recent project VICTree. \n\n\n\n— \n\n\n\nNBIS arranges an open AI and IO Seminar Series aimed at knowledge-sharing about Artificial Intelligence and Integrative Omics (AI & IO) analysis and applications in the Life Science community. The seminar series is open to everyone. The seminar is run over Zoom on the third Friday of the month during academic terms\, typically between 10 and 11 am\, with approx. 45 min long presentation and 15 min discussion. 
URL:https://www.scilifelab.se/event/variational-inference/
LOCATION:Online event via Zoom
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240920T130000
DTEND;TZID=Europe/Stockholm:20240920T140000
DTSTAMP:20260404T171237
CREATED:20240902T120600Z
LAST-MODIFIED:20240902T120933Z
UID:10001344-1726837200-1726840800@www.scilifelab.se
SUMMARY:How does epigenetic mechanism impact Type 2 diabetes?
DESCRIPTION:Speaker: Dr. Charlotte Ling is a Professor at Lund University \n\n\n\nDr. Charlotte Ling is a Professor at Lund University and a principal investigator of the Epigenetics and Diabetes Unit at Lund University Diabetes Centre (LUDC). She obtained her PhD in Endocrinology at University of Gothenburg\, Sweden in 2002. After a postdoc at Lund University\, where she studied genetics of type 2 diabetes\, she dedicated her research to the study of epigenetic mechanisms causing type 2 diabetes and metabolic disease. Her research group has over the last two decades pioneered the field of epigenetics in type 2 diabetes. They have made several groundbreaking discoveries such as genome-wide epigenetic modifications in pancreatic islets\, skeletal muscle\, adipose tissue and the liver from patients with type 2 diabetes compared with non-diabetic control subjects. Dr. Ling’s research group has also shown that genetic and non-genetic factors such as SNPs\, exercise\, diet\, obesity and age alter the genome-wide epigenetic pattern in human primary tissues for type 2 diabetes.  More recently\, her group is trying to translate their epigenetic findings to biomarkers and novel therapies for precision medicine to improve prediction\, prevention and treatments of type 2 diabetes.  \n\n\n\nHost: Louella Vasquez\, NBIS (louella.vasquez@scilifelab.se) \n\n\n\nBroadcast link (live event):  https://lu-se.zoom.us/j/67681656100 \n\n\n\nThe talk will also be available afterwards on the NBIS YouTube channel.
URL:https://www.scilifelab.se/event/how-does-epigenetic-mechanism-impact-type-2-diabetes/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240924T100000
DTEND;TZID=Europe/Stockholm:20240924T110000
DTSTAMP:20260404T171237
CREATED:20240826T124908Z
LAST-MODIFIED:20251204T144518Z
UID:10001337-1727172000-1727175600@www.scilifelab.se
SUMMARY:Publish code\, software and workflows: Examples of why and how from SciLifeLab
DESCRIPTION:This seminar will highlight why code\, research software and computational workflows are important research assets and it will also showcase practical approaches to sharing\, citing and getting recognition for your work. The event opens with a presentation followed by a dynamic Q&A session to elaborate on the motivations and good practices based in examples from the SciLifeLab community. This is the first event in the SciLifeLab Data Management seminar series Autumn 2024. \n\n\n\nWhen: Tuesday September 24\, 10-11 CET (Zoom) \n\n\n\nSpeaker: Wolmar Nyberg Åkerström\, Data Steward\, NBIS \n\n\n\nSciLifeLab Data Management seminar series is an event series by the SciLifeLab Data Centre and NBIS joint Data Management team aimed at both the life science research community and infrastructure\, and others with an interest in research data management in life sciences. The events will showcase how to put the FAIR principles\, and good data management into practice. The goal of the events in this seminar series is to provide interesting seminars around topics related to research data management in general but also to foster discussions around best practices and how they can be improved. The events takes place virtually (over Zoom) and are open to everyone\, (researchers\, staff\, RDM professionals etc.) working at or affiliated with a Swedish research institute or university. Each event is scheduled for 60 minutes\, including 15 minutes for discussions and Q & A. The videos will be published openly after the seminars at the SciLifeLab YouTube channel.More information about SciLifeLab Data Centre and NBIS joint Data Management team: https://data-guidelines.scilifelab.se/ \n\n\n\nWelcome!Organisers: SciLifeLab Data Centre and NBIS National Bioinformatics Infrastructure SwedenFor more information or inquiries please contact: data-management@scilifelab.se
URL:https://www.scilifelab.se/event/publish-code-software-and-workflows-examples-of-why-and-how-from-scilifelab/
LOCATION:Online event via Zoom
CATEGORIES:Community
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2024/02/DC_seminar-series_background1-1.png
ORGANIZER;CN="Open Science Seminar Series":MAILTO:data-management@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240924T120000
DTEND;TZID=Europe/Stockholm:20240925T120000
DTSTAMP:20260404T171237
CREATED:20240507T151251Z
LAST-MODIFIED:20240925T061816Z
UID:10001257-1727179200-1727265600@www.scilifelab.se
SUMMARY:The Disruptive Role of Data and AI in the Life Sciences
DESCRIPTION:A Joint Conference between DDLS\, WASP and WASP-HS\n\n\n\n\n\nThe conference will focus on different aspects of research where collaboration over scientific domains is essential and will explore the following topics: \n\n\n\n\nHow data- and AI-driven research is shaping the future of life science\n\n\n\nDevelopment of new approaches to human-in-the-loop technologies and their use\n\n\n\nThe need for studies at the intersection of society\, AI\, and data driven life sciences\n\n\n\n\n\n\n\n\nParticipants will have the opportunity to network\, be inspired by excellent international keynotes\, and take part of the latest research in Sweden. In addition to plenary keynotes\, the program will offer parallel sessions\, panel discussions\, mingle and poster sessions. \n\n\n\nPractical Details\n\n\n\nDates and times  \n\n\n\nSeptember 24\, 12:00 – September 25\, 12:30Registration is open from 11:00 on September 24. \n\n\n\nVenue: Wallenberg Conference Center\, Medicinaregatan 20 A\, Gothenburg \n\n\n\nInformation for registered poster \n\n\n\n• size of poster 90x 120 cm portrait format• posters can be hung on the 24th of September from 11:00 and should be done by 12:00• poster should be removed after the end of the conference on the 25th. You are responsible for your poster. Forgotten posters will not be saved.During the poster session 17:15-19 on the 24th of September we would appreciate if you are available by your poster for discussions and questions. During the Magnet mingle on the 25th you are also welcome to be by your poster. \n\n\n\nRegistration to the Conference\n\n\n\nRegister here \n\n\n\nThe registration is open until September 6. \n\n\n\nContact: ddls@scilifelab.se or info@wasp-sweden.org \n\n\n\nProgram\n\n\n\n24 September\n\n\n\n11:00 Registration opensPosters are to be hung up from 11:00 and should be done by 12:00. \n\n\n\n12:00 – 13:00 Lunch \n\n\n\nStart of conference \n\n\n\n13:00 – 13:15 Opening Program DirectorsChristofer Edling\, WASP-HSOlli Kallioniemi\, DDLSAnders Ynnerman\, WASPChair\, Rebecka Jörnsten WASP \n\n\n\n13:15-14:00 Keynote speaker Sunduz KelesIntegrative Approaches to Single-Cell Genomics for Personalized MedicineChair\, Rebecka Jörnsten WASP \n\n\n\n14:05- 14:50 Keynote speaker Ross KingThe Automation of ScienceChair\, Rebecka Jörnsten WASP \n\n\n\n14:50-15:20 Coffee \n\n\n\n15:20-16:20 Project presentation WASP DDLS (4 *15 min)Christopher Sprague\, Incorporating Stability Into Flow MatchingBjörn Wallner\, Improved protein structure prediction by adding noise at  inferenceHedvig Kjällström\, Unraveling the secrets of nature’s high-performance fiberAlexander Schliep and Pär Mattsson Molecular simulation and machine learning to delineate target binding of therapeutic oligonucleotidesChair\, Päivi Östling \n\n\n\n16:20-17:05 Project presentation WASP-HS DDLS (3* 15 min)Harald Hammarström\, Linguistic Diversity Through the Prism of BiodiversityStanley Greenstein\, AI in the Health Care Sector – Legal ChallengesSonja Aits\, Mapping the Nexus of Biodiversity\, Climate Change\, Human Society and Health using Large Language Models and other Data Science ApproachesChair\, Stefan Larsson \n\n\n\n17:15: – 19:00 Finger food and poster session \n\n\n\n25 September\n\n\n\n08:30-9:30 Project presentation WASP DDLS (4*15 min)Ingrid Hotz\, Tino Ebbers\, Characterization and visualization of cardiac spectral imaging dataSebastian Westenhoff\, cryoSPHERE: Single-particle heterogeneousreconstruction from cryo EMAndreas Kerren\, Visual Analytics for Enhancing Quality and Trust in Genome-wide Expression Clustering and AnnotationMinh Hoang Vu\, Anonymization of Data in Precision Medicine ResearchChair\, Olli Kallioniemi \n\n\n\n09:30-10:45 Magnet mingle including coffeeChair\, Rebecka Jörnsten and Christofer Edling \n\n\n\n10:45-11:30 Keynote Speaker: Klaus HøyerAll the data from everywhere all at once: data integration\, AI imaginaries\, and their unpredictable outcomesChair\, Christofer Edling \n\n\n\n11:30-12:15 Panel on common research challengesSunduz Keles\, Ross King\, Klaus Hoyer\, Andreas Kerren\, Tino EbbersModerators\, Rebecka Jörnsten and Stefan Larsson \n\n\n\n12:15 Closing remarks\, Program DirectorsChristofer Edling\, WASP-HSOlli Kallioniemi\, DDLSRebecka Jörnsten WASP \n\n\n\n12:30 Lunch to go \n\n\n\nKeynote Speakers\n\n\n\nSunduz Keles\n\nTitle: Integrative Approaches to Single-Cell Genomics for Personalized MedicineBio: Dr. Keles obtained her Ph.D. in Biostatistics from the University of California at Berkeley. After a year-long postdoctoral appointment at UC Berkeley\, she joined the Department of Biostatistics and Medical Informatics and the Department of Statistics at the University of Wisconsin\, Madison. She has twenty years of experience in developing statistical and computational methods for genomics\, including serving as an ENCODE PI\, and pioneering foundational statistical models for leveraging multi-mapping reads in high throughput sequencing data analysis (ChIP-seq\, Hi-C). \n\n\nHer research interests span developing statistical and computational methods for denoising and signal extraction from sequencing data and modeling of high dimensional data. Her computational approaches led to fundamental contributions on how GATA factors mediate transcriptional regulation in HSPCs and erythroid cells. Dr. Keles is an elected fellow of the American Statistical Association. \n\n\n\n\n\nKlaus Lindgaard Høyer\nTitle: All the data from everywhere all at once: data integration\, AI imaginaries\, and their unpredictable outcomesBio: Klaus Hoeyer is professor of Medical Science and Technology Studies at the Centre for Medical Science and Technology Studies\, University of Copenhagen. His research focuses on the links between policy\, practice and experience in relations to medical research and clinical practice. In recent years\, he has focused mainly on what he calls intensified data sourcing in healthcare and how it interacts with and changes the health services. This research is primarily financed by the European Research Council. \n\n\n\n\nRoss D. King\nTitle: The automation of scienceBio: Ross D. King did his PhD on applying machine learning to predicting protein structure at the Turing Institute in Glasgow. He has joint positions at Chalmers Institute of Technology\, and the University of Cambridge. He is one of the most experienced machine learning researchers in Europe. \n\n\n\nHis main research interest is the interface between computer science and science. He originated the idea of a ‘Robot Scientist’: integrating AI and laboratory robotics to physically implement closed-loop scientific discovery. His Robot Scientist ‘Adam’ was the first machine to autonomously discover scientific knowledge. His Robot Scientist ‘Eve’ is currently searching for drugs against neglected tropical diseases\, and COVID.  His other core research interest is DNA computing. \n\n\n\n\nProject Presenters\n\n\n\nAlexander Schliep\nTitle: Molecular simulation and machine learning to delineate target binding of therapeutic oligonucleotides \n\n\n\nBio: Alexander Schliep is the chair for Medical Bioinformatics at the Faculty of Health Sciences Brandenburg at Brandenburg Technical University Cottbus-Senftenberg\, with a secondary appointment at the University of Gothenburg and member of the WASP (Wallenberg AI\, Autonomous Systems and Software Program) research collegium. \n\n\n\nHis current research program is focused on machine learning and algorithmics for analyses of genomic data and nucleic acid-based therapeutics\, including machine learning for pan-genome graph analyses\, efficient analysis algorithms for large genomic datasets\, and federated\, privacy-preserving methods for training ML/AI models for oligonucleotide therapeutics. \n\n\n\n\nAndreas Kerren\nTitle: Visual Analytics for Enhancing Quality and Trust in Genome-wide Expression Clustering and Annotation \n\n\n\nBio: Prof. Dr. Andreas Kerren received his PhD degree in Computer Science from Saarland University\, Saarbrücken\, Germany. In 2008\, he achieved his habilitation (docent competence) from Växjö University\, Sweden. \n\n\n\nDr. Kerren is currently a Full Professor of Information Visualization\, Linköping University (LiU) and Linnaeus University (LNU)\, Sweden. He holds the Chair of Information Visualization at LiU and is head of the research group Information and Software Visualization at LNU. In addition\, he is an ELLIIT professor supported by the Excellence Center at Linköping–Lund in Information Technology and key researcher of the Linnaeus University Centre for Data Intensive Sciences and Applications. \n\n\n\nHis main research interests include several areas of information visualization and visual analytics\, especially visual network analytics\, text visualization\, and the use of visual analytics for explainable AI. \n\n\n\nHe has been editorial board member of a number of journals such as Information Visualization or Computer Graphics Forum\, has served as organizer/program chair at numerous conferences such as IEEE VISSOFT 2013/2018 or GD 2018\, and has edited a number of successful books on human-centered visualization. Dr. Kerren has published more than 200 peer-reviewed papers\, articles\, and book chapters. \n\n\n\n\nBjörn Wallner\nTitle: Improved protein structure prediction by adding noise at inference \n\n\n\nBio: Björn Wallner has been a faculty member at Linköping University since 2011 and a Professor in Bioinformatics since 2019. He obtained his Ph.D. in Bioinformatics from Stockholm University in 2005 and did postdoctoral work at the University of Washington from 2006-2008. \n\n\n\nHis research interests include protein structure prediction\, protein-protein interactions\, protein function\, disorder\, flexibility\, and dynamics. \n\n\n\n\nChristopher Sprague\nTitle: Incorporating Stability Into Flow Matching \n\n\n\nBio: Christopher Iliffe Sprague is a postdoctoral researcher at KTH Royal Institute of Technology and SciLifeLab\, working with Arne Elofsson and Hossein Azizpour on deep learning approaches for protein-protein interactions. He earned his PhD in robotics from KTH\, where he focused on developing efficient and trustworthy AI for critical robotic systems. \n\n\n\nCurrently\, as a postdoc\, Christopher is leveraging his robotics expertise to enhance inductive biases in deep generative models\, particularly for equilibrium generation tasks like molecular docking. His research interests include flow-based generative models\, hybrid dynamical systems\, and drug design \n\n\n\n\nHarald Hammarström\nTitle: Linguistic Diversity Through the Prism of Biodiversity \n\n\n\nBio: Harald Hammarström is Professor of General Linguistics atUppsala University. He has a background in both Computer Science andLinguistics. \n\n\n\nHe has a very broad linguistic interest spanning allareas of the world but specializing in minority languages in Papua\,Africa and South America. His research activities span fromdocumentary fieldwork in Papua\, Indonesia\, classical linguisticanalytic work\, typological databases\, and NLP for lesser-knownlanguages. \n\n\n\nHe is currently focussing on large-scale empirical andcomputational approaches to linguistic diversity\, genealogical/arealrelationships and language universals. \n\n\n\n\nHedvig Kjellström \nTitel: Unraveling the secrets of nature’s high-performance fiber \n\n\n\nBio: Hedvig Kjellström is a Professor in the Division of Robotics\, Perception and Learning at KTH Royal Institute of Technology\, Sweden\, and also affiliated with Swedish University of Agricultural Sciences\, Swedish e-Science Research Centre\, and Max Planck Institute for Intelligent Systems\, Germany. She received an MSc in Engineering Physics and a PhD in Computer Science from KTH in 1997 and 2001\, respectively\, and thereafter worked at the Swedish Defence Research Agency\, before returning to a faculty position at KTH. Her present research focuses on methods for enabling artificial agents to interpret human and animal behavior. These ideas are applied in the study of human aesthetic bodily expressions such as in music and dance\, modeling and interpreting human communicative behavior\, and the understanding of animal behavior and experiences. In order to accomplish this\, methods are developed for agents to perceive the world and build representations of it through vision. \n\n\n\nHedvig has received several prizes for her research\, including the 2010 Koenderink Prize for fundamental contributions in computer vision. She has written around 150 papers in the fields of computer vision\, machine learning\, robotics\, information fusion\, cognitive science\, speech\, and human-computer interaction. She is mostly active within computer vision\, where she is an Editor-in-Chief for CVIU\, a Program Chair for CVPR 2025\, and regularly serves as Area Chair for the major conferences.  \n\n\n\n\nIngrid Hotz\nTitle: Characterization and visualization of cardiac spectral imaging data \n\n\n\nBio: Ingrid Hotz is a professor at Linköping University in Sweden\, leading the Scientific Visualization group in the Department of Science and Technology. She holds an M.S. in theoretical physics from Ludwig Maximilian University\, Munich\, and a Ph.D. in computer science from the University of Kaiserslautern. Hotz has held research positions at the Institute for Data Analysis and Visualization (IDAV) at UC Davis\, the Zuse Institute Berlin\, and the German Aerospace Center (DLR). Since 2015\, she has been a professor at Linköping University and was named the Dr. Ram Kumar IISc Distinguished Visiting Chair Professor at the Indian Institute of Science in 2022. \n\n\n\nHer research focuses on scientific visualization and topological data analysis\, aiming to develop advanced visual analysis tools for complex datasets across various fields\, including engineering\, physics\, chemistry\, and medicine. She integrates methods from computer science and mathematics\, such as computer graphics and computational topology\, with a participatory design approach to ensure practical and relevant solutions. \n\n\n\n\nMinh Hoang Vu\nTitle: Anonymization of Data in Precision Medicine Research \n\n\n\nBio: Minh Vu is a postdoctoral researcher at IceLab\, Umeå University\, working under the supervision of Martin Rosvall and Beatrice Melin. Their research focuses on anonymizing and visualizing biobank data to facilitate meaningful insights and discoveries in disease understanding and treatment development. \n\n\n\n\nPär Matsson\nTitle: Molecular simulation and machine learning to delineate target binding of therapeutic oligonucleotides \n\n\n\nBio: Pär Matsson is Professor of Pharmacokinetics at the Sahlgrenska Academy\, University of Gothenburg\, and Scientific Director of OligoNova Hub – the SciLifeLab infrastructure for development of therapeutic oligonucleotides. \n\n\n\nHis research is centered on elucidating the molecular mechanisms of cellular and subcellular drug disposition\, and how they influence therapeutic effect. A particular focus is on the cellular disposition and effects of non-traditional drug modalities\, including therapeutic oligonucleotides and targeted protein degraders (PROTACs). \n\n\n\n\nSonja Aits\nTitle: Mapping the Nexus of Biodiversity\, Climate Change\, Human Society and Health using Large Language Models and other Data Science Approaches \n\n\n\nBio: Sonja Aits leads the “Cell Death\, Lysosomes and Artificial Intelligence” group at the Faculty of Medicine\, Lund University\, which works at the intersection of data\, life and sustainability science. Her group develops computational tools such as large language models for scientific text mining and computer vision models for histology and high-content microscopy and uses them to identify biological pathways and disease mechanisms in humans and other species as well as intervention strategies that promote human health\, biodiversity and sustainability. \n\n\n\nSonja helps coordinate AI Lund\, Lund University’s umbrella organization for AI-related research\, outreach and education\, and the profile area “Nature-based future solutions”. In addition\, she serves as study director of the COMPUTE research school\, where she has developed the PhD course program “AI in Medicine and Life Science”. She is also deeply engaged in open education and public outreach. \n\n\n\n\nStanley Greenstein\nTitle: AI in the Health Care Sector – Legal Challenges \n\n\n\nBio: Stanley Greenstein (Jur. Dr.) is an Associate Professor (Docent) in Law and Information Technology\, Faculty of Law\, Stockholm University. He is Chairman of the Board\, Swedish Law and Informatics Research Institute (IRI\, https://irilaw.org/)\, Chairman of the Board\, Foundation for Legal Information (Stiftelsen för rättsinformation) and a Digital Futures faculty member (https://www.digitalfutures.kth.se/about/). \n\n\n\nStanley’s primary academic focus is cross-disciplinary in nature and addresses the regulation of emerging digital technologies\, especially artificial intelligence (AI). His teaching\, research and participation in externally funded projects has revolved around the subject areas of ethics\, data protection\, sustainability and legal design. \n\n\n\n\nTino Ebbers\nTitle: Characterization and visualization of cardiac spectral imaging data \n\n\n\nBio: Tino Ebbers is a professor of physiological measurements at Linköping University\, with a focus on cardiac imaging\, modeling\, and simulation. He holds an MSc in Electrical Engineering from the University of Twente and a PhD in Biomedical Engineering from Linköping University. After completing his PhD\, he worked at Philips Medical Systems before returning to academia. He also served as a visiting professor at the University of California\, San Francisco. \n\n\n\nWith over 100 publications in leading scientific journals and numerous contributions to international conferences\, Tino Ebbers has made a significant impact through his multidisciplinary approach to merging technical research with clinical applications. He is best known for pioneering 4D flow MRI\, a breakthrough technology now widely used to study cardiovascular blood flow in both research and clinical settings. His contributions have greatly advanced cardiovascular imaging and led to major innovations in the diagnosis\, treatment\, and management of cardiovascular diseases. \n\n\n\n\nBackground\n\n\n\nSince 2021 the Wallenberg AI\, Autonomous Systems and Software Program (WASP) and the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) are collaborating through joint research projects with the ultimate goal of solving ground-breaking research questions across disciplines. In line with this\, the programs will now host the first\, joint annual conference where common research topics are highlighted. Additionally\, the increasingly important humanity and societal aspects of the research will be addressed through participation of the WASP-HS program (Wallenberg AI\, Autonomous Systems and Software Program- Humanity and Society). Read more about the different research programs here: \n\n\n\nDDLS\n\n\n\nWASP\n\n\n\nWASP-HS \n\n\n\nOpen Calls\n\n\n\nThe conference is an opportunity to find collaborators for the two open calls: \n\n\n\nWASP-DDLS: NEST projects https://wasp-sweden.org/calls/call-for-joint-wasp-and-ddls-nests/  \n\n\n\nWASP-HS-DDLS: Research Initiation Grants for Data-Driven Life Sciences and Society https://wasp-hs.org/open-call-research-initiation-grants-for-data-driven-life-sciences-and-society/  \n\n\n\n \n\n\n\n \n\n\n\n\n\n\n\n \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n \n\n\n\nRead more\n\n\n\nRead more\n\n\n\nRead more
URL:https://www.scilifelab.se/event/the-disruptive-role-of-data-and-ai-in-the-life-sciences/
LOCATION:Conference Centre Wallenberg\, Medicinaregatan 20A\, Gothenburg\, 413 90\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2024/05/DDLS_WASP_WP-1536x864-1.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240925T100000
DTEND;TZID=Europe/Stockholm:20240925T110000
DTSTAMP:20260404T171237
CREATED:20240916T114029Z
LAST-MODIFIED:20240916T114244Z
UID:10001356-1727258400-1727262000@www.scilifelab.se
SUMMARY:DNA microscopy in two and three dimensions
DESCRIPTION:Speaker: Joshua Weinstein\, University of Chicago \n\n\n\nHost: Ian Hoffecker\, SciLifeLab \n\n\n\nThis lecture is open with no registration required. \n\n\n\nAbstract \n\n\n\nLymphatic\, nervous\, and tumoral tissues\, among others\, exhibit physiology that emerges from three-dimensional interactions between genetically unique cells. Technologies capable of volumetrically imaging transcriptomes\, genotypes\, and morphologies in a single de novo measurement can provide a critical lens into the biological complexity of living systems. We present on our experimental and computational work to develop DNA microscopy: a modality of imaging that captures physical images of specimen genetic content using a massive distributed network of DNA molecules inside it. We demonstrate DNA microscopy in two-dimensional cell cultures and genome-wide in intact zebrafish embryos. \n\n\n\nBiography \n\n\n\nJoshua Weinstein is a biophysicist and molecular technologist. He works on developing DNA-based technologies for high-throughput encoding and decoding of biological information with a view toward applications in biology and medicine. He has previously worked on applying massively parallel DNA sequencing to the study of immune receptor repertoires. Recently\, he invented DNA microscopy\, an imaging modality that uses DNA rather than light as an imaging medium in order to generate detailed pictures of how genetic diversity distributes spatially across biological specimens. Prof. Weinsten completed his undergraduate studies in physics and biophysics at the University of Pennsylvania\, and his PhD in biophysics at Stanford University in 2012 under the direction of Stephen Quake and Daniel Fisher. There\, he published the first global measurements of immune receptor sequence repertoires\, using the zebrafish as a model organism. Weinstein later applied repertoire-sequencing to immune development and human vaccine response. Weinsten completed his postdoctoral work at the Broad Institute/Massachusetts Institute of Technology\, under the joint-mentorship of Feng Zhang and Aviv Regev\, where he was supported by a Simons Fellowship from the Life Sciences Research Foundation. There\, he developed DNA microscopy\, enabling biological specimens to “image themselves” and thereby generating detailed spatio-genetic data sets\, which bypass the need for specialized equipment. In 2019\, Weinstein moved to his current position as assistant professor of molecular engineering and medicine in the section of genetic medicine at the University of Chicago.
URL:https://www.scilifelab.se/event/dna-microscopy/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Event
ORGANIZER;CN="Ian Hoffecker":MAILTO:ian.hoffecker@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240925T150000
DTEND;TZID=Europe/Stockholm:20240925T160000
DTSTAMP:20260404T171237
CREATED:20240904T115713Z
LAST-MODIFIED:20250409T200333Z
UID:10001495-1727276400-1727280000@www.scilifelab.se
SUMMARY:SciLifeLab Lund Seminar Series
DESCRIPTION:Welcome to the SciLifeLab Lund seminar series! \n\n\n\nThese seminars are designed to highlight SciLifeLab Lund\, our cutting-edge research infrastructure\, and the diverse resources available to the scientific community. \n\n\n\nAdditionally\, we aim to provide our users with a platform to showcase their projects and the results they have achieved through utilizing our services. \n\n\n\nIn the 1st seminar\, the site Director Markus Heidenblad\, the Data Science Coordinator Wojtek Potrzebowski\, and Site Coordinator Anabella Aguilera will introduce SciLifeLab Lund.   \n\n\n\nRegistration\n\n\n\nRegister for the next seminars!\n\n\n\n30th October 2024 | Swedish National Infrastructure for Biological Mass Spectrometry (BioMS) \n\n\n\nRegister Seminar October\n\n\n\n18th December 2024 | Center Translational Genomics within Clinical Genomics Lund \n\n\n\nRegister Seminar December\n\n\n\n29th January 2025 | CryoEM for Life Sciences at Lund University \n\n\n\nRegister Seminar January\n\n\n\n26th February 2025 | Display and Selection Technologies \n\n\n\nRegister Seminar February\n\n\n\n26th March 2025 | Lund University Bioimaging Centre (LBIC)  \n\n\n\nRegister Seminar March\n\n\n\n23rd April 2025 | Lund Protein Production Platform (LP3) \n\n\n\nRegister Seminar April\n\n\n\n28th May 2025 | National Bioinformatics Infrastructure (NBIS) \n\n\n\nRegister Seminar May\n\n\n\n18th June | Structural Proteomics \n\n\n\nRegister Seminar June
URL:https://www.scilifelab.se/event/scilifelab-lund-seminar-series/
LOCATION:Belfragesalen\, BMC D15\, Klinikgatan 32\, Lund\, Sweden
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240925T150000
DTEND;TZID=Europe/Stockholm:20240925T160000
DTSTAMP:20260404T171237
CREATED:20250224T130732Z
LAST-MODIFIED:20250224T131448Z
UID:10001346-1727276400-1727280000@www.scilifelab.se
SUMMARY:SciLifeLab Lund Seminar Series
DESCRIPTION:Welcome to the SciLifeLab Lund seminar series! \n\n\n\nThese seminars are designed to highlight SciLifeLab Lund\, our cutting-edge research infrastructure\, and the diverse resources available to the scientific community. \n\n\n\nAdditionally\, we aim to provide our users with a platform to showcase their projects and the results they have achieved through utilizing our services. \n\n\n\nIn the 1st seminar\, the site Director Markus Heidenblad\, the Data Science Coordinator Wojtek Potrzebowski\, and Site Coordinator Anabella Aguilera will introduce SciLifeLab Lund.   \n\n\n\nRegistration\n\n\n\nRegister for the next seminars!\n\n\n\n30th October 2024 | Swedish National Infrastructure for Biological Mass Spectrometry (BioMS) \n\n\n\nRegister Seminar October\n\n\n\n18th December 2024 | Center Translational Genomics within Clinical Genomics Lund \n\n\n\nRegister Seminar December\n\n\n\n29th January 2025 | CryoEM for Life Sciences at Lund University \n\n\n\nRegister Seminar January\n\n\n\n26th February 2025 | Display and Selection Technologies \n\n\n\nRegister Seminar February\n\n\n\n26th March 2025 | Lund University Bioimaging Centre (LBIC)  \n\n\n\nRegister Seminar March\n\n\n\n23rd April 2025 | Lund Protein Production Platform (LP3) \n\n\n\nRegister Seminar April\n\n\n\n28th May 2025 | National Bioinformatics Infrastructure (NBIS) \n\n\n\nRegister Seminar May\n\n\n\n18th June | Structural Proteomics \n\n\n\nRegister Seminar June
URL:https://www.scilifelab.se/event/scilifelab-lund-seminar-series-2/
LOCATION:Belfragesalen\, BMC D15\, Klinikgatan 32\, Lund\, Sweden
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Lund":MAILTO:lund@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240926T090000
DTEND;TZID=Europe/Stockholm:20240926T170000
DTSTAMP:20260404T171237
CREATED:20240610T130511Z
LAST-MODIFIED:20240924T143954Z
UID:10001274-1727341200-1727370000@www.scilifelab.se
SUMMARY:Data Driven Multi-omics Integration in Life Sciences
DESCRIPTION:The 10th RIKEN-KI-SciLifeLab Symposium \n\n\n\nLarge amounts of data are being generated in various omics disciplines such as genomics\, genetics\, transcriptomics\, proteomics\, metabolomics\, and epigenomics. Integrating these multi-dimensional omics datasets offers unprecedented opportunities to gain comprehensive insights into complex biological systems and their underlying mechanisms. This symposium on “Data Driven Multi-omics Integration in Life Sciences” brings together experts to explore the integration of multi-dimensional omics datasets. Speakers will specifically highlight the integrative aspect of their work and how it helped in understanding biology and medical sciences. \n\n\n\nRegistration\n\n\n\nProgram\n\n\n\n8:30Registration9:00Opening of SymposiumProf. Jan Ellenberg\, SciLifeLab DirectorProf. Annika Östman Wernerson\,KI PresidentProf. Kazuhiko Yamamoto (RIKEN Center IMS Director)Section 1: Transcriptomics/Genetics-centric integrationChair: Dr. Katsuyuki Yugi\, Dr. Chung-Chau Hon9:15Multi omics study on human immune systemProf. Kazuhiko Yamamoto (RIKEN IMS)9:45Mapping immune cell clonal dynamics within tissuesDr. Camilla Engblom (KI and SciLifeLab)10:05Integrating human genomics with population\, individual\, and single cell resolutionsDr. Yukinori Okada (RIKEN IMS)10:25Mobile element variation drives population-specific genome diversification\, gene regulation\, and disease riskDr. Kojima Sohei (RIKEN IMS)10:45Coffee BreakSpecial session: KI\, SciLifeLab and Japan11:15Introduction of JSPSJSPS Stockholm Office11:30RemarksProf. Per Nilsson (KI Japan Coordinator)11:30Section 2: Metabolomics/Proteomics-centric integrationChair: Dr. Chung-Chau Hon\, Dr. Katsuyuki Yugi11:35Bridging the gap between human genome and phenome with trans-omics networks of mouseDr. Katsuyuki Yugi (RIKEN IMS)11:55The new wave of interaction proteomics for mapping virus-host interactionsDr. Andrea Fossati (KI and SciLifeLab)12:15Decoding the cellular effects of pathogenic mutations through PTM and interaction proteomicsDr. Koshi Imami (RIKEN IMS)12:35Lunch BreakSection 3: Single-cell genomics-centric integrationChair: Dr. Carsten Daub\, Dr. Chung-Chau Hon13:45Spatial omics approaches for resolving stromal and neuro-immune interactions in osteoarthritisDr. Lea Mikkola (University of Turku)14:05Understanding disease heritability using single cell transcriptomics and deep learningDr. Chung-Chau Hon (RIKEN IMS)14:25Self-assembled surfaces for map-free spatial transcriptomicsDr. Erik Benson (KI and SciLifeLab)14:45Deciphering state-dependent immune features from multi-layer human omics at single-cell resolutionDr. Ryuya Edahiro (RIKEN IMS)15:05Genome-wide nutrition-induced ribosome frameshifts modulate transcriptome abundanceDr. Vicent Pelechano (KI and SciLifeLab)15:25Coffee Break (30 mins)Section 4: Large scale Data Integration/Artificial intelligenceChair: Dr. Carsten Daub\, Dr. Chung-Chau Hon15:55Use of AI in Biotechnology in Japan: Policy PerspectivesDr. Yusuke Mori (University of Tsukuba/Japan Embassy)16:15Autonomous Scientific Discovery by AIDr. Jun Seita (RIKEN IMS)16:35Predicting Drug Responses in Cancer with Interactome-Based AIDr. Avlant Nilsson (KI and SciLifeLab)16:55ClosingDr. Carsten Daub & Dr. Chung Chau Hon17:00Mingle & Pub\n\n\n\nSymposium History\n\n\n\nThis symposium series is organized between RIKEN in Japan\, and Karolinska Institutet and SciLifeLab in Sweden. The symposia alternate between RIKEN and SciLifeLab.  \n\n\n\nThe overall goals of the symposia are to  \n\n\n\n\nIdentify common scientific interests between RIKEN and SciLifeLab\, \n\n\n\nIdentify complementary skills and technologies for collaborations \n\n\n\nEncourage the exchange of Ph.D. students and postdocs between RIKEN and SciLifeLab/KI. \n\n\n\n\nSeveral collaborations between groups at KI\, SciLifeLab and RIKEN started based on first contact during one of the symposia. \n\n\n\nOrganizers\n\n\n\n\nDr. Kazuhiko Yamamoto (RIKEN IMS)\n\n\n\nDr. Carsten Daub (Karolinska Institutet/SciLifeLab)\n\n\n\nDr. Harukazu Suzuki (RIKEN IMS)\n\n\n\nDr. Chung-Chau Hon (RIKEN IMS)\n\n\n\n\n\n\n\n\n \n\n\n\n \n\n\n\n \n\n\n\nContact\n\n\n\nCarsten Daub\, KI/SciLifeLab \n\n\n\ncarsten.daub@scilifelab.se
URL:https://www.scilifelab.se/event/data-driven-multi-omics-integration-in-life-sciences-the-10th-riken-ki-scilifelab-symposium/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240926T113000
DTEND;TZID=Europe/Stockholm:20240926T133000
DTSTAMP:20260404T171237
CREATED:20240905T110109Z
LAST-MODIFIED:20240910T082704Z
UID:10001347-1727350200-1727357400@www.scilifelab.se
SUMMARY:Scalable\, Accessible Single Cell with Parse Biosciences' Evercode
DESCRIPTION:Join Us for a Seminar on Single-cell RNA Sequencing (scRNA-seq)\n\n\n\nSingle-cell RNA sequencing (scRNA-seq) has become a key tool in genomics\, offering researchers deep insights into cellular behavior. While droplet-based methods are commonly used\, they often come with limitations in flexibility\, cost\, and scalability. Parse Biosciences’ Evercode technology offers a solution\, enabling scalable single-cell sequencing without the need for specialized equipment. \n\n\n\nThis seminar\, co-hosted by Clinical Genomics Gothenburg (CGG) and Parse Biosciences\, will feature: \n\n\n\n\nIntroduction to Evercode Technology by Parse Biosciences\, including practical tips for sample preparation and analysis.\n\n\n\nUser Perspective Presentation by Joan Camuñas\, Dept of Medical Biochemistry and Cell biology\n\n\n\nResearch Support Overview by CGG\, where researchers can get support with experimental design\, lab work\, and data analysis for single-cell projects.\n\n\n\n\n\nMore information and registration\n\n\n\n\nLunch will be provided for onsite participation.Registration deadline: September 23 \n\n\n\nNo registration is required for online participation: \n\n\n\n\nZoom link
URL:https://www.scilifelab.se/event/scalable-accessible-single-cell-with-parse-biosciences-evercode/
LOCATION:Birgit Thilander Lecture Hall\, Medicinaregatan 3\, Göteborg
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240926T120000
DTEND;TZID=Europe/Stockholm:20240926T130000
DTSTAMP:20260404T171237
CREATED:20240708T135748Z
LAST-MODIFIED:20240926T080910Z
UID:10001296-1727352000-1727355600@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series: Qiuzhen Li & Luca Panconi
DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nPhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits\, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester. \n\n\n\nThis week:\n\n\n\n\n\n\nQiuzhen Li\n\n\n\nPatrick Bryant – alpha 2 \n\n\n\nDesign Peptide Binder Using Machine Learning \n\n\n\n\n\nLuca Panconi\n\n\n\nJuliette Grifflé – gamma 6 \n\n\n\nTowards computationally-optimised immunotherapy \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-qiuzhen-li-ines-cunha/
LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna
CATEGORIES:Community
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/IMG_20221103_123412496_HDR2-scaled.jpg
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240930T080000
DTEND;TZID=Europe/Stockholm:20241002T170000
DTSTAMP:20260404T171237
CREATED:20240521T064747Z
LAST-MODIFIED:20240521T064748Z
UID:10001263-1727683200-1727888400@www.scilifelab.se
SUMMARY:Metabolomics in Molecular Medicine - from idea to data interpretation
DESCRIPTION:A jointly organized workshop by the Swedish Metabolomics Centre (SMC) and FIMM’s Metabolomics Unit – University of Helsinki providing an introduction to different aspects of metabolomics\, from experimental design to data analysis. The programme consists of a public symposium on the first day and practical elements for workshop participants on days 2-3. Workshop participants are also expected to attend the symposium on the first day. \n\n\n\nRead more\n\n\n\nMetabolomics measures small molecules commonly known as metabolites that all together comprise a metabolome of a biological system. Since metabolome is a reflection of physiological status\, metabolomics helps us to understand molecular mechanisms such as drug responses and to find new indicators for diseases. \n\n\n\nThis workshop provides an introduction to mass spectrometry-based metabolomics with a special focus on its applications in molecular medicine. The workshop starts with a mini-symposium where the experts in the field discuss the recent advancements and applications in metabolomics research in life sciences. The following two days of practical training will cover the metabolomics workflow from the principles of experimental design\, sample preparation\, theory of chromatographic separation and mass spectrometry to data acquisition\, pre-processing\, analysis and interpretation. \n\n\n\nContact \n\n\n\nAnnika Johansson \n\n\n\nEmail \n\n\n\n+46 90 786 55 51
URL:https://www.scilifelab.se/event/metabolomics-in-molecular-medicine-from-idea-to-data-interpretation/
LOCATION:KBC Building Umeå\, Linneaus Väg 6\, Umeå
CATEGORIES:Event
ORGANIZER;CN="Swedish Metabolomics Centre (SMC)":MAILTO:annika.johansson01@umu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241001T080000
DTEND;TZID=Europe/Stockholm:20241003T170000
DTSTAMP:20260404T171237
CREATED:20240529T151443Z
LAST-MODIFIED:20240529T151527Z
UID:10001270-1727769600-1727974800@www.scilifelab.se
SUMMARY:Basic Course in Scanning and Transmission Electron Microscopy (SEM/TEM) for Life Sciences
DESCRIPTION:This course covers lectures and practical demonstrations in SEM and TEM techniques. The contents include principles of electron microscopy\, specimen preparation\, cryo-electron microscopy and correlative light-electron microscopy. The main focus will be on imaging biological samples\, but the course may also be suitable for material scientists interested in high-resolution electron microscopy. \n\n\n\nRead more\n\n\n\nApplication deadline:10 September 2024 \n\n\n\nLocation:Lectures at the KBC Building and laboratory demonstrations at UCEM. \n\n\n\nParticipants:18 persons \n\n\n\nInstructors:UCEM staff \n\n\n\nDuration:3 days \n\n\n\nBreaks/Refreshments:Coffee\, cookies and fruit. \n\n\n\nCosts:No course fee\, but full attendance is required! \n\n\n\nExamination/Credits:Oral and practical examinations are conducted during laboratory demonstrations. A course certificate will be given after participants attend all lectures and laboratory demonstrations for this 3-day course. UCEM recommends PhD program examiners to give 1 ECTS after successful participation.
URL:https://www.scilifelab.se/event/basic-course-in-scanning-and-transmission-electron-microscopy-sem-tem-for-life-sciences/
LOCATION:KBC Building Umeå\, Linneaus Väg 6\, Umeå
CATEGORIES:Course
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2024/05/241001_241003_Basic-TEM-SEM-Life-Sciences-2024.jpg
ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241001T090000
DTEND;TZID=Europe/Stockholm:20241001T170000
DTSTAMP:20260404T171237
CREATED:20230927T131415Z
LAST-MODIFIED:20240930T075234Z
UID:10000978-1727773200-1727802000@www.scilifelab.se
SUMMARY:Spatial Biology - The 2024 SciLifeLab Science Summit
DESCRIPTION:Spatial Biology is an emerging field driven by recent advances in Spatial Omics technologies. The aim of the summit is to present the spatial omics capabilities at SciLifeLab\, and examples of uses of such methods to address various research areas in Life Science. A lot of pioneering work in Spatial Biology originates from researchers associated with SciLifeLab\, and we hope to inspire more researchers to explore this approach and to join this growing spatial community. \n\n\n\nThe Annual Conference SciLifeLab Science Summit is a one-day symposium with a new topic each year. The topic for 2024 is Spatial Biology. \n\n\n\nWe warmly welcome international visitors to attend this free event. The conference also offers fantastic opportunities for networking and discussions with top academic researchers and industry leaders in spatial omics technology. \n\n\n\nWelcome! \n\n\n\nMats Nilsson\, Chair of the Scientific Committee\, Charlotte Stadler\, Per Andrén and Stefania Giacomello \n\n\n\n\n\n\n\nProgram\n\n\n\nScience Summit Program 2024Download\n\n\n\n\n\n\n\nPosters\n\n\n\nPoster Presentation Guidelines \n\n\n\nPoster Format \n\n\n\nThe poster screens are 103 cm wide and 143 cm high. Please ensure your poster fits within these measurements. \n\n\n\nMount your poster \n\n\n\nThe venue will be open from 8:45 AM. Please proceed to the 6th floor and hang your poster at your designated number. A numbered poster list will be provided closer to the event date. \n\n\n\nPoster sessions \n\n\n\nPoster Session I: During the morning coffee break\, from 10:55 AM to 11:35 AM\, presenters of posters with odd numbers (1\, 3\, 5\, 7…) should be present by their posters. \n\n\n\nPoster Session II: During the afternoon break\, from 3:15 PM to 3:55 PM\, presenters of posters with even numbers (2\, 4\, 6\, 8…) should be present by their posters. \n\n\n\nBest Poster Award \n\n\n\nAll poster presenters should attend the Best Poster Award ceremony at the end of the conference\, where the winners will be announced. The Scientific Committee will evaluate the posters throughout the day. \n\n\n\nDismount of posters \n\n\n\nPlease remove your poster immediately after the closing session at 5:00 PM. Poster screens will be collected at 5:30 PM\, and any remaining posters will be discarded. \n\n\n\nPoster List \n\n\n\nScience Summit Posterlist 2024Download\n\n\n\nAbstracts \n\n\n\nAbstracts Science Summit 2024 – PostersDownload\n\n\n\nRegistration\n\n\n\nFor late registrations (after September 13)\, we cannot guarantee lunch\, coffee\, nor can we accommodate any allergies or dietary requirements. These will be subject to availability. We appreciate your understanding. \n\n\n\nRegister here\n\n\n\nQuestions? If you have any inquiries regarding the event or your registration\, please contact events@scilifelab.se \n\n\n\nThe conference is free of charge; however\, if you do not attend and fail to cancel\, your department or organization will be charged a no-show fee of 500 SEK. \n\n\n\n\nImportant Notice Regarding Venue Regulations\n\n\n\nPlease be advised that for security reasons\, Uppsala Konsert & Kongress (UKK) has a strict policy regarding bags and outside clothing.  \n\n\n\nBags larger than A4 size and outside clothing (jackets\, coats etc.) are not permitted inside the auditorium.  \n\n\n\nHowever\, you are welcome to store these items in the venue’s cloakroom. Laptops can be brought into the auditorium in laptop sleeves. \n\n\n\nWe apologize for any inconvenience this may cause and appreciate your understanding and cooperation in adhering to the venue’s regulations. \n\n\n\n\nInvited Speakers – abstract and bio sketch\n\n\n\nClick on the arrow to read the speaker’s title\, abstract\, and bio. \n\n\n\nGonçalo Castelo-Branco\, Karolinska Institutet\, Sweden\nTalkOligodendroglia in Development and Multiple Sclerosis: Insights from Single-Cell and Spatial Omics \n\n\n\nAbstractOligodendroglia (OLG) mediate myelination of neurons\, a process that allows efficient electrical impulse transmission in the central nervous system. An autoimmune response in multiple sclerosis (MS) leads to OLG cell death\, loss of myelin and neuropathology. Using single cell transcriptomics\, we have previously identified disease-specific OLG populations in the EAE mouse model of MS and in human MS brain archival tissue\, characterized by the expression of immune genes.By assessing chromatin accessibility and the transcriptome simultaneously at the single cell level at different stages of the disease course\, we found that immune genes exhibit a primed chromatin state in mouse and human OLG in a non-disease context\, compatible with rapid transitions to immune-competent states in MS. Moreover\, we found dynamic and distinct transcriptomic and epigenomic responses of OLG subpopulations to the evolving environment in EAE mouse model of MS\, which might modulate their response to regenerative therapeutic interventions in MS.While single-cell genomics are powerful for investigating disease-specific cellular states\, these methods involve isolating the tissue under study from its niche\, leading to a loss of spatial information. Such information is essential for determining cell-to-cell communication in disease niches. We have applied in situ sequencing to investigate disease evolution in MS at a spatial level\, both in the EAE mouse model of MS and in human post-mortem MS samples. We annotated disease neighborhoods during lesion evolution and found centrifugal propagation of active lesions. We demonstrated that disease-associated (DA)-glia arise independently of lesions and are dynamically induced and resolved over the disease course.We have also applied dBIT-Seq\, a ligation-based method for deterministic barcoding in tissue\, to probe different histone modifications and chromatin accessibility in the mouse brain tissue sections\, either in an unimodal or simultaneously with transcriptomics. This spatial epigenome–transcriptome co-profiling has allowed us to identify cellular lineage progression and epigenomic priming events that precede transcription during development with spatial resolution. We are currently applying these methods to disease paradigms in MS\, to uncover how transitions to pathological cellular states occur at epigenomic and transcriptomic levels. \n\n\n\nBio \n\n\n\nGonçalo Castelo-Branco researches oligodendrocytes’ epigenetic states\, focusing on how transcription factors\, non-coding RNA\, and chromatin enzymes drive cell changes. His work has potential for multiple sclerosis therapies. \n\n\n\n\nRon Heeren\, Maastricht University\, The Netherlands\nTalk \n\n\n\nSpatial biology and translation life sciences \n\n\n\nAbstract \n\n\n\nModern molecular analytical technologies in the “omics” arena plays a crucial role in many scientific disciplines ranging from material sciences to clinical diagnostics. Technological advances have increased methodological sensitivity allowing researchers to acquire detailed molecular information of smaller and smaller samples. The biggest challenge is to put that concerted information in the context of the biological problem the samples originate from. This lecture describes how innovative mass spectrometry based molecular imaging technologies\, have impacted translational clinical research and beyond. Or: how a mass spectrometer can be used as a sensitive and selective molecular microscope in modern spatial biology. Targeted  and untargeted imaging technologies now offer new insights in the complexity that can be employed for systems medicine. Innovations in mass spectrometry based chemical microscopes have now firmly established themselves in translational molecular research. One key aspect of translational success is the ability to obtain this molecular information on thousands of molecules on a timescale relevant to translation. Single cells can be analyzed in great molecular detail and in the context of their native tissue. Combined this offers a true multi-omics approach that reveals contextual molecular complexity for systems medicine. \n\n\n\nBio \n\n\n\nProf. Dr. Ron M.A. Heeren obtained a PhD degree in technical physics in 1992 at the University of Amsterdam on plasma-surface interactions. He was the research group leader at FOM-AMOLF for macromolecular ion physics and biomolecular imaging mass spectrometry in the period 1995-2015. In 2001 he was appointed professor at the chemistry faculty of Utrecht University lecturing on the physical aspects of biomolecular mass spectrometry. In 2014 he was appointed as distinguished professor and Limburg Chair at the University of Maastricht. He is scientific director of M4I\, the Maastricht MultiModal Molecular Imaging institute and heads the division of imaging MS. He is the vice-president of the international mass spectrometry foundation and has been active in many professional societies to advance mass spectrometric research\, education and professionalization. His academic research interests are mass spectrometry based personalized medicine\, translational molecular imaging research\, high-throughput bioinformatics and the development and validation of new mass spectrometry based “omics” imaging techniques for the life sciences. \n\n\n\n \n\n\n\n\nArutha Kulasinghe\, The University of Queensland\, Australia\nTalk \n\n\n\nUncoupling Pathways Involved in Immunotherapy Resistance: Insights from Deep Tissue Profiling \n\n\n\nAbstract \n\n\n\nSpatially resolved multi-omic phenotyping is revolutionizing how we study tissue and immune responses to cancer treatments. In this talk\, we will describe our integrated approaches to characterizing the tumour microenvironment in head and neck\, lung\, and skin cancers using ultra high-plex spatial proteomics and transcriptomics\, benchmarking to ground truth\, and developing functionally characterised immuno-metabolic signatures associated with resistance and sensitivity to immunotherapy. \n\n\n\nBio \n\n\n\nDr. Arutha Kulasinghe is a Senior Research Fellow and leads the Clinical-oMx Lab at the University of Queensland. Dr Kulasinghe has pioneered spatial transcriptomics using digital spatial profiling approaches in the Asia-Pacific region\, contributing to world-first studies for lung cancer\, head and neck cancer\, skin cancer and COVID-19. His research aims to understand the underlying pathobiology by using an integrative multi-omics approach. \n\n\n\n\nCecilia Lindskog\, Uppsala University\, Sweden\nTalkA spatio-temporal single-cell type map of the human proteome based on transcriptomics\, high-resolution antibody-based imaging and artificial intelligenceAbstractFor a fundamental understanding of human health\, molecular medicine and targeted treatment\, it is necessary to map processes unique to each tissue and cell type. We here aimed to set up a stringent\, workflow for mapping human tissues at the single-cell type level\, and utilized this workflow to create high-resolution spatio-temporal maps of tissue or cell type-specific proteins in human tissues. One of these tissues is testis\, which is a complex organ with spermatogenesis involving thousands of genes and proteins activated or repressed through multiple cell states\, from spermatogonial stem cells to mature sperm. Understanding the intricate functions and mechanisms at each step of this process requires a multi-dimensional approach that integrates both quantitative and qualitative methods.Based on single-cell RNA sequencing data\, we identified 12 distinct cell types and subsets of germ cells in testis\, some of which cannot be distinguished by regular immunohistochemistry. Using a multiplex immunofluorescence pipeline\, we then built antibody panels specifically outlining each of these cell types. The fixed antibody panels were stained together with the candidate protein of interest\, one at a time\, to pinpoint the exact protein localization at a cellular and subcellular level. Using artificial intelligence\, the high-resolution images were quantified using an automated image analysis workflow. The integrated data allowed us to study temporal mRNA and protein expression gradients along with maturation processes and identify which mRNAs that are consistently translated into proteins from those that vary from a spatio-temporal aspect. We were also able to assign presumed functions to numerous uncharacterized proteins not previously described in the context of human reproduction.In summary\, we present a strategy for high-resolution spatio-temporal mapping of human tissues and cells\, presented as a single-cell type reference map of adult human testis. The data which is freely available on www.proteinatlas.org decodes the complexity of human germ cells and links quantitative data with tissue morphology\, and the validated workflow has the potential to be used for other tissues\, contributing to valuable insights into molecular function and processes linked to disease.BioDr. Lindskog is a research group leader and associate professor at the Department of Immunology\, Genetics and Pathology\, Cancer Precision Medicine unit\, Uppsala University\, Sweden. Her research group uses a multi-dimensional approach and combination of various qualitative and quantitative methods to generate high-resolution spatial maps of the human body at the single-cell type level. By combining scRNA-seq\, spatial technologies for mRNA and protein detection and machine learning\, she aims to link single cell type-specific expression profiles with molecular function and mechanisms of disease\, a first step towards precision medicine. Since 2006\, Dr. Lindskog is also affiliated with the Human Protein Atlas (HPA) project\, the largest biological database for spatial proteomics\, publicly available at www.proteinatlas.org. She received her PhD in Pathology at Uppsala University in 2013\, and since 2014 she has been director of the tissue-based efforts of the HPA project\, leading the team that generates the mRNA and protein expression data in human tissues. \n\n\n\n \n\n\n\n\nJoakim Lundeberg\, KTH\, Sweden\nTalk \n\n\n\nTissue ecosystems in time and space \n\n\n\nAbstract \n\n\n\nTools in spatial biology offer a wide range of technologies that quantify different types of biomolecules in tissue sections. These technologies provide information about distinct aspects of tissue anatomy\, such as its morphology\, genome\, transcriptome\, proteome\, and metabolome. Here\, several multiomics computational and experimental methodologies approaches that capture the tissue ecosystem from a single tissue section will be described. \n\n\n\nBio \n\n\n\nJoakim Lundeberg\, Ph.D.\, Professor in Molecular Biotechnology\, has\, during the most recent years\, focused on spatial transcriptomics\, which enables a detailed description of gene expression patterns in tissue sections. The methodology is now available worldwide through 10x Genomics Inc\, as Visium. The technology was also featured in Nature Methods as the Method of the Year 2020. Dr. Lundeberg has publications demonstrating technology development into several new spatial modalities and examples of its impact in biology. The current research focuses on expanding the spatial modalities and developing new tools and applications in human cell atlas\, neurology\, and cancer. \n\n\n\n\nSinem Saka\, EMBL\, Germany\nTalkA DNA toolbox for spatial biology from imaging to sequencingAbstractDNA is not only a fundamental constituent of cells\, but has also great capacity for information storage. We leverage the predictability of DNA hybridization kinetics and orthogonality of DNA sequences to utilize DNA oligos as tagging and barcoding tools for improving the major limitations of in situ visualization of molecules. We have previously developed multiplexed imaging approaches such as SABER-FISH and Immuno-SABER that utilize DNA barcoding and a flexible in situ signal amplification system for efficient visualisation of many protein\, DNA or RNA targets in cells and tissues. More recently\, we have implemented DNA barcoding for a new spatial transcriptomics approach\, Light-Seq\, which directly integrates fluorescence imaging and whole-transcriptome next-generation sequencing of the same cells in fixed biological samples. Light-Seq combines spatially-targeted\, rapid photocrosslinking of DNA barcodes onto cDNAs in situ with a novel one-step DNA stitching reaction to create pooled\, spatially-indexed sequencing libraries. This light-directed barcoding enables imaging-based in situ selection of multiple cell populations in intact fixed tissue samples for full transcriptome sequencing based on location\, morphology\, or protein stains\, without cellular dissociation. Applying Light-Seq to mouse retinal sections\, we discovered new biomarkers for a very rare neuronal subtype\, dopaminergic amacrine cells\, from only 4-8 individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next-generation sequencing of the same cells\, leaving the sample intact for further analysis post-sequencing. We are using these methods to directly link multi-dimensional and high-resolution microscopic phenotypes to transcriptomic profiles for diverse sample types. \n\n\n\nBio \n\n\n\nPhD in Molecular Biology\, 2013\, University of Göttingen/International Max Planck Research School\, Germany.Postdoctoral research at Wyss Institute for Biologically Inspired Engineering\, Harvard University\, USA.EMBO Postdoctoral Fellow 2016–2017.Human Frontier Science Program Fellow 2017–2020.Group leader at EMBL since December 2020. \n\n\n\n\nJeffrey Spraggins\, Vanderbilt University\, Nashville\, USA\nTalkBringing human disease into focus through integrated multimodal molecular imagingAbstractCellular interactions within tissue micro-environments form the basis of health and disease for all organisms. Exposure to nutrients\, toxins\, and neighboring cells triggers coordinated molecular responses that impact cellular function and metabolism in a beneficial\, adaptive\, or detrimental manner. Acquiring molecular information at cellular resolution is thus crucial for developing a comprehensive understanding of the biology of an organism. Matrix-assisted laser desorption/ionization (MALD) imaging mass spectrometry (IMS) addresses this need by combining the spatial fidelity of classical microscopy with the molecular specificity of a mass spectrometer. This presentation will highlight our work developing new\, high-performance technologies for improving the spatial resolution\, sensitivity\, and specificity of MALDI IMS for metabolite\, lipid\, and protein mapping. This will include the utilization of novel MALDI methods and development efforts using high spatial resolution Q-TOF platforms to address the molecular complexity associated with direct tissue analysis. Further\, I will describe recent advances in integrated\, multimodal methods that correlate molecular signals to specific biological tissue features and cell types. These technologies will be demonstrated through various biomedical research applications that include the construction of molecular atlases and understanding the molecular drivers of normal aging and disease.BioJeff Spraggins is an Associate Professor in the Department of Cell and Developmental Biology\, Director of the Biomolecular Multimodal Imaging Center (BIOMIC)\, and Director of the Mass Spectrometry Research Center at Vanderbilt University. He received his B.A. in Chemistry from the College of Wooster and his Ph.D. in Analytical Chemistry from the University of Delaware. Dr. Spraggins’ research program focuses on the development of next-generation imaging mass spectrometry (IMS) technologies to elucidate the molecular basis of health and disease. Modern instrumentation and computing capabilities have enabled researchers to move beyond reductionist biology and\, instead\, probe how the components of biological entities (e.g.\, molecules\, cells\, and tissues) interact to reveal the underlying biology of disease. This systems biology approach has been accelerated by advancements in high-throughput ‘omics’ technologies; however\, genetic and molecular information is only part of the story. The challenge lies in understanding how these parts interact and how perturbations to the system relate to disease. Molecular imaging effectively offers a ‘blueprint’ as to how biological components work together by providing spatial context to molecular information. Broadly\, Dr. Spraggins’ research falls into two categories: (1) Developing novel mass spectrometry technologies to maximize imaging performance\, enabling molecular histology at cellular resolution\, and (2) combining imaging mass spectrometry with a variety of other biomedical imaging technologies to create new integrated modalities capable of providing a systems biology view of tissue at cellular resolution. The Spraggins group applies these technologies to the construction of molecular atlases as part of the NIH Human Biomolecular Atlas Program (HuBMAP)\, the NIDDK Kidney Precision Medicine Project (KPMP)\, and the NCI Human Tumor Atlas Network (HTAN); and also\, to understanding the molecular drivers of Alzheimer’s\, kidney\, and infectious diseases. \n\n\n\n\nCarolina Wählby\, Uppsala University\, Sweden\nTalkMeasuring tissue morphology in spatial biologyAbstractSpatial omics has transformed our understanding of tissue architecture by preserving spatial context of gene expression patterns. Simultaneously\, advances in imaging AI have enabled extraction of morphological features describing the tissue. The intersection of spatial omics and imaging AI presents opportunities for a more holistic understanding: morphological features can be translated or integrated into spatial omics analyses. By translation we mean finding morphological features that spatially correlate with gene expression patterns with the purpose of predicting gene expression. Such features can be used to generate super-resolution gene expression maps or infer genetic information from clinical H&E-stained samples. By integration we mean finding morphological features that spatially complement gene expression patterns with the purpose of enriching information. Such features can be used to define spatial domains\, especially where gene expression has preceded morphological changes and where morphology remains after gene expression.BioCarolina Wählby is professor in Quantitative Microscopy at the Dept. of Information Technology\, Uppsala University\, and Scientific Director of the National SciLifeLab Bioimage Informatics facility. Her research lies in the intersection between life science and computational image analysis\, developing image analysis\, deep learning\, and visualization approaches for understanding the organization and dynamics of cells and tissue\, funded primarily by the ERC and the Swedish Foundation for Strategic research. She has a MSc in molecular biotechnology and a PhD in digital image analysis\, and carried out postdoc research within genetics and pathology. She was part of the Imaging Platform of the Broad Institute 2009-2015\, developing CellProfiler\, and became full professor at Uppsala University in 2014\, and is a member of the Royal Swedish Academy of Engineering Sciences. \n\n\n\n\n \n\n\n\nSpeaker abstracts 2024Download\n\n\n\nImportant dates\n\n\n\nOctober 1: Science Summit Opens at Uppsala Konsert & Kongress \n\n\n\nExhibitors\n\n\n\nMeet representatives from companies providing products and services in relevant fields. The following companies will be present during the day \n\n\n\n\n10x Genomics\n\n\n\nAkoya Biosciences\n\n\n\nBioNordika AB\n\n\n\nBruker (Canopy Biosciences and NanoStrings)\n\n\n\nLunaphore\n\n\n\nNavinci Diagnostics AB\n\n\n\nSaveen & Werner AB\n\n\n\nThermo Fisher Scientific\n\n\n\nVizgen Incorporated\n\n\n\n\nScientific Committee\n\n\n\nMats Nilsson\, Chair and Platform Director Spatial Biology\, SciLifeLab/Stockholm UniversityCharlotte Stadler\, Platform Co-Director Spatial Biology\, SciLifeLab/KTHPer Andrén\, SciLifeLab/Uppsala UniversityStefania Giacomello\, SciLifeLab/KTH \n\n\n\nProject leader Operations Office: Erika Bergqvist Erkstam \n\n\n\n\n\nSS24-Flyer_2Download
URL:https://www.scilifelab.se/event/scilifelab-science-summit/
LOCATION:Uppsala Konsert & Kongress\, Vaksala torg 1\, Uppsala\, 75331\, Sweden
CATEGORIES:Event
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DTSTART;TZID=Europe/Stockholm:20241002T150000
DTEND;TZID=Europe/Stockholm:20241002T153000
DTSTAMP:20260404T171237
CREATED:20240919T115545Z
LAST-MODIFIED:20240919T115655Z
UID:10001355-1727881200-1727883000@www.scilifelab.se
SUMMARY:CSI Seminar: Imposter Syndrome
DESCRIPTION:Dear Everyone\, \n\n\n\nWe are excited to host a new Coaching in Science Initiative (CSI) Seminar titled: ‘Imposter Syndrome’ \n\n\n\nImposter Syndrome is a common yet often overlooked challenge in academia\, affecting scholars at every stage—from graduate students to senior faculty. Despite your accomplishments\, do you often feel like you don’t belong or fear being “exposed” as a fraud? In this seminar\, we will examine what imposter syndrome is\, when and why it manifests\, and reflect on the deeper psychological and social factors that contribute to it. We will also provide practical strategies and tools to help you cope with these feelings of self-doubt\, overcome perfectionism\, and reclaim your confidence. \n\n\n\nDate: 02/10/2024 \n\n\n\nTime: 15:00 – 15:30 \n\n\n\nZoom link: https://kth-se.zoom.us/j/65426414592 \n\n\n\nOn-site location: Gamma 2 lunch room \n\n\n\nWe will begin with a ~ 20 min talk\, held in Solna and over zoom. Then proceed with a reflection and discussion held only on-site. We encourage other sites to form watch parties\, by listening in together to the talk and then hold their own discussion afterwards. Hopefully seeding many local chapters of CSI. \n\n\n\nTo help facilitate discussion and reflection\, consider the following starter questions: \n\n\n\nAwareness: where do we experience imposter syndrome in our lives? \n\n\n\nAnalysis: how do I currently interact with imposter thinking? \n\n\n\nAlternative: how could we relate to imposter syndrome\, in ourselves and others? \n\n\n\nAction: how will knowledge of imposter thinking change my decisions going forward? \n\n\n\nPlease forward this to friends and colleagues! \n\n\n\nYours sincerely\, \n\n\n\nThe CSI Team \n\n\n\n  \n\n\n\nWays to keep in touch with CSI \n\n\n\n  \n\n\n\n\nVisit our webpage for coaching material\, access to older seminars\, links to external resources and our events: https://www.thecoachinginscienceinitiative.org/\n\n\n\nWe will also post our events in the SciLifeLab event calendar: https://www.scilifelab.se/event\n\n\n\nOur seminars has/will be recorded and can be watch and re-used as workshops to raise awareness on this YouTube channel\, the first CSI seminar is already there: https://www.youtube.com/@TheCoachinginScienceInitiative\n\n\n\nIf you have a scilifelab e-mail\, find our channel in the scilifelab.slack.com workspace #coaching-in-science-initiative\n\n\n\nReach our committee thought our e-mail: csi@scilifelab.se\n\n\n\n\n 
URL:https://www.scilifelab.se/event/csi-seminar-imposter-syndrome/
LOCATION:Hybrid event in Gamma 2 lunchroom and zoom\, Tomtebodavägen 23 B\, Solna\, 17165\, Sweden
CATEGORIES:Event
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ORGANIZER;CN="Coaching in Science Initiative (CSI)":MAILTO:sami.saarenpaa@scilifelab.se
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DTSTART;TZID=Europe/Stockholm:20241002T160000
DTEND;TZID=Europe/Stockholm:20241002T170000
DTSTAMP:20260404T171237
CREATED:20240829T094923Z
LAST-MODIFIED:20240829T095938Z
UID:10001341-1727884800-1727888400@www.scilifelab.se
SUMMARY:Deciphering the mysteries of sleep: toward the molecular substrate for “sleepiness”
DESCRIPTION:KVA-JSPS lecture about orexins. Prof. Masashi Yanagisawa\, MD\, PhD\, International Institute for Integrative Sleep Medicine\, University of Tsukuba\, Japan\, \n\n\n\nProfessor Masashi Yanagisawa\, the discoverer of both endothelin and orexin\, which are extremely important peptides for blood pressure and sleep regulation\, will give a lecture in Uppsala\, H:son Holmdahlsalen\, Entrance 100\, Akademiska sjukhuset. His lecture will focus on the regulation of sleep and wakefulness. The Lecture will follow after a short presentation of JSPS. \n\n\n\nThe lecture is possible thanks to a travel grant from Japan Society for the Promotion of Science (JSPS). \n\n\n\nHost: Professor Dan Larhammar\, Department of Medical Cell Biology\, SciLifeLab affiliated group leader\, Uppsala University. Please contact Prof. Larhammar if you wish to meet with Prof. Yanagisawa during his visit to Uppsala.  \n\n\n\nAbstract\n\n\n\nAlthough sleep is a ubiquitous behavior in animal species with a nervous system\, many aspects in the neurobiology of sleep remain mysterious. Our discovery of orexin\, a hypothalamic neuropeptide involved in the maintenance of wakefulness\, has triggered intensive research examining the exact role of the orexinergic and other neuronal pathways in the regulation of sleep/wakefulness. Orexin receptor antagonists\, which specifically block the endogenous waking system\, have been approved as a new strategy to treat insomnia. Also\, since the sleep disorder narcolepsy-cataplexy is caused by orexin deficiency\, orexin receptor agonists are expected to provide mechanistic therapy for the disease; they will likely be also useful for treating excessive sleepiness due to other etiologies. \n\n\n\nEven though the executive neurocircuitry and neurochemistry for sleep/wake switching\, including the orexinergic system\, has been increasingly revealed in recent years\, the mechanism for homeostatic regulation of sleep\, as well as the neural substrate for “sleepiness” (sleep pressure)\, remains unknown. To crack open this black box\, we have initiated a large-scale forward genetic screen of sleep/wake phenotype in mice based on true somnographic (EEG/EMG) measurements. We have so far screened >10\,000 heterozygous ENU-mutagenized founders and established several pedigrees exhibiting heritable and specific sleep/wake abnormalities. By combining linkage analysis and the next-generation whole exome sequencing\, we have molecularly identified and verified the causal mutation in several of these pedigrees. Since these dominant mutations cause strong phenotypic traits\, we expect that the mutated genes will provide new insights into the elusive pathway regulating sleep/wakefulness. Indeed\, through a systematic cross-comparison of the SIK3 Sleepy mutants and sleep-deprived mice\, we have found that the cumulative phosphorylation state of a specific set of mostly synaptic proteins may represent the molecular substrate of sleep pressure. We have also found that the neuronal molecular pathway LKB1-SIK3-HDAC4/5 may represent the level of sleep pressure\, regulating the amount\, depth\, and timing of sleep by acting in different brain regions\, respectively (Kim et al. Nature 612: 512-518\, 2022; Zhou et al. Nature 612: 519-527\, 2022). \n\n\n\nBio sketch\n\n\n\nProf. Yanagisawa received his PhD at the University of Tsukuba where he discovered the powerful vasoconstrictor peptide endothelin. His group later identified a receptor for endothelin which is now an important target for treatment of hypertension. After moving to Texas Southwestern Medical Center in Dallas he identified the endothelin-converting enzyme and later described the role of the endothelin pathway in embryonic development. \n\n\n\nHis project to deorphanize G protein-coupled receptors resulted in the discovery of the hypothalamic neuropeptide orexin in 1998. The year after\, he showed that the sleep disorder narcolepsy is caused by orexin deficiency. This knowledge has resulted in orexin receptor antagonists approved for treatment of insomnia. An ongoing project in Tsukuba has led to identification of several new genes and molecular pathways that are importantly involved in the regulation of sleep amounts and the level of sleep need. \n\n\n\nProf. Yanagisawa has receved numerous honours and awards\, most recently the Breakthrough Prize in Life Sciences. He was elected to the U.S. National Academy of Sciences in 2003. Since 2012 he is the director for the International Institute for Integrative Sleep Medicine at the University of Tsukuba. \n\n\n\n\n\n\n\nAnnouncement Yanagisawa 2401002Download
URL:https://www.scilifelab.se/event/deciphering-the-mysteries-of-sleep-toward-the-molecular-substrate-for-sleepiness/
LOCATION:H:son Holmdahlsalen\, Entrance 100\, Akademiska sjukhuset\, Dag Hammarskjölds väg 8\, Uppsala
CATEGORIES:Event
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DTSTART;TZID=Europe/Stockholm:20241003T120000
DTEND;TZID=Europe/Stockholm:20241003T130000
DTSTAMP:20260404T171237
CREATED:20240708T140029Z
LAST-MODIFIED:20240926T081101Z
UID:10001297-1727956800-1727960400@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series: Linnea Påvenius
DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nPhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits\, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester. \n\n\n\nThis week:\n\n\n\n\n\n\n\n\n\n\n \n\n\n\n \n\n\n\n\n\nLinnea Påvenius\n\n\n\nHjalmar Brismar – gamma 3 \n\n\n\nLive-Imaging of mitochondrial dynamics in relation to metabolic flux. \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-alberto-arenas-molina-linnea-pavenius/
LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna
CATEGORIES:Community
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/12/IMG_4110-scaled.jpg
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241007T120000
DTEND;TZID=Europe/Stockholm:20241008T150000
DTSTAMP:20260404T171237
CREATED:20240620T093344Z
LAST-MODIFIED:20241003T140306Z
UID:10001284-1728302400-1728399600@www.scilifelab.se
SUMMARY:DDLS Symposium on Data-Driven Environmental Monitoring of Infectious Diseases
DESCRIPTION:The DDLS research area Epidemiology and Biology of Infection invites you to its second in-person symposium. (The event is fully in-person only). The symposium will focus on promoting and enhancing data-driven environmental assessment for infectious diseases (including antibiotic-resistant bacteria) across various settings using diverse approaches. \n\n\n\nThe symposium will feature both local and international high-profile speakers in the field and will cover topics ranging from sewage surveillance\, monitoring of airborne infectious agents\, as well as environmental and animal disease monitoring for pathogens\, antimicrobial resistance and harmful substances. The symposium will also include more technical aspects of implementations as well as data-driven advancements and challenges. \n\n\n\nThere will also be a possibility to submit abstracts for short talks! \n\n\n\nPlease join us for this one-and-a-half-day symposium on 7-8 October 2024\, in Navet\, SciLifeLab’s meeting place in Uppsala\, to meet the research area Fellows\, the Expert Group and excellent researchers of the area. Engage in discussions\, enjoy refreshments\, and network with experts across a range of infectious disease monitoring topics! \n\n\n\nWelcome! \n\n\n\nScientific committeeAnna Székely (SLU)Johan Bengtsson-Palme (Chalmers) \n\n\n\nRegistration\n\n\n\nDeadline for abstract submission: 23 September (Extended deadline)Deadline to register to attend: 25 September \n\n\n\nIf seats are available and you register after September 25\, we can not accommodate allergies or special requirements and you will write your name tag upon arrival to the venue.. \n\n\n\nRegistration\n\n\n\n\n\n\n\nProgram\n\n\n\nDDLS symposium EBI_PROGRAM_3Download\n\n\n\n\n\n\n\n\n\nMembers of The Data-driven Epidemiology and biology of infection expert group:\n\n\n\nTom Britton\, Stockholm UniversityJoakim Dillner\, Karolinska Institutet and Karolinska Univ. HospitalTove Fall\, Uppsala UniversityBirgitta Henriques-Normark\, Karolinska InstitutetErik Kristiansson\, Chalmers University of TechnologyPatrik Medstrand\, Lund UniversityStaffan Svärd\, Uppsala UniversityOliver Billker\, chair (DDLS SG member)
URL:https://www.scilifelab.se/event/ddls-symposium-on-data-driven-environmental-monitoring-of-infectious-diseases/
LOCATION:BMC Trippelrummet\, Husargatan 3\, entrance C11\, Uppsala\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/03/EBI_Icon.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241007T151500
DTEND;TZID=Europe/Stockholm:20241007T161500
DTSTAMP:20260404T171237
CREATED:20240920T145358Z
LAST-MODIFIED:20240920T145400Z
UID:10001364-1728314100-1728317700@www.scilifelab.se
SUMMARY:[The Svedberg seminar] - Patch-seq profiling of pancreatic islet cell types and cell-free RNA diagnostics
DESCRIPTION:Joan Camuñas-SolerAssistant ProfessorUniversity of Gothenburg\, Sweden \n\n\n\n \n\n\n\n \n\n\n\n\n\n\n\nJoan Camuñas\n\n\n\n\n\n\n\nBio\n\n\n\nDr. Camuñas-Soler is an Assistant Professor and Wallenberg Molecular Medicine Fellow at the University of Gothenburg since 2022. His current research focuses on data-driven genomics and precision medicine. Previously\, as a postdoctoral scholar at Stanford University\, he pioneered novel single-cell genomic techniques to study islet-cell function in health and diabetes. Additionally\, he developed liquid biopsy tools for the early prediction of pregnancy complications\, which led to the creation of a molecular diagnostics startup. His research is highly interdisciplinary\, combining approaches from molecular engineering\, biophysics\, and computational biology. His work has been recognized with several awards\, patents\, and prestigious establishment grants. \n\n\n\n \n\n\n\nPatch-seq profiling of pancreatic islet cell types and cell-free RNA diagnostics \n\n\n\nMethods to simultaneously profile transcriptome and cell function at the single-cell level are scarce. In this talk\, I will show that single-cell RNA sequencing (scRNAseq)\, in combination with electrophysiological measurements of exocytosis (patch-seq)\, can be used to study the connection between human endocrine physiology and transcriptomes at the single cell level. I will discuss the application of patch-seq to investigate normal physiology of pancreatic islet cells and their dysfunction in diabetes. \n\n\n\nUsing data from 1\,369 patch-seq cells from the pancreata of 34 human donors; I will show how this technology can be used to identify novel regulators of β-cell biology and transcriptomic alterations indicative of β-cell maladaptation and α-cell dysfunction in type 2 diabetes (T2D). Additionally\, I will introduce a complementary approach to measure the secretory capacity of these cells based in the use of fluorescent tracers of endocytic membrane retrieval\, which can then be combined with FACS sorting ad scRNAseq to characterize β-cell states associated with higher secretory capacity. \n\n\n\nIn the second part of this talk\, I will also discuss how sequencing of circulating RNA in the blood (cell-free RNA) can be used as a ‘liquid biopsy’ tool to monitor human physiology and disease. I will focus on the use of cell-free RNA to establish a molecular clock of pregnancy\, and as a tool to track autoimmune disorders with poorly understood pathophysiology. Some of this molecular diagnostics work is currently being translated into clinical validation. \n\n\n\nRead more: Camuñas-Soler Group   \n\n\n\n \n\n\n\n \n\n\n\n\n\n\n\nHost: Jessica Nordlund jessica.nordlund@medsci.uu.se
URL:https://www.scilifelab.se/event/the-svedberg-seminar-joan-camunas-soler/
LOCATION:BMC Room C8:301\, Husargatan 3\, Uppsala\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/02/Picture1-The-Svedberg.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241008T090000
DTEND;TZID=Europe/Stockholm:20241008T163000
DTSTAMP:20260404T171237
CREATED:20240523T131511Z
LAST-MODIFIED:20240913T130839Z
UID:10001265-1728378000-1728405000@www.scilifelab.se
SUMMARY:Stockholm Single Cell Genomics 2024 Symposium
DESCRIPTION:The National Genomics Infrastructure is pleased to announce the Stockholm Single Cell Genomics 2024 Symposium\, taking place on October 8th this fall. Join us for a day of engaging talks by experts in the field\, a chance to explore the latest technologies\, and networking opportunities. \n\n\n\nregister here\n\n\n\nConfirmed speakers:  \n\n\n\n\nGonçalo Castelo-Branco\, KI\, \n\n\n\nJessica Nordlund\, UU\, \n\n\n\nRickard Sandberg\, KI\, \n\n\n\nJoan Camuñas-Soler\, GU\, \n\n\n\nMartin Enge\, KI\, \n\n\n\nKasper Karlsson\, KI\, \n\n\n\nMohanraj Ramachandran\, UU\, \n\n\n\nTuuli Lappalainen\, KTH and \n\n\n\nAlexander Steemers\, Princess Maxima Center.\n\n\n\n\nSponsors: Scale Biosciences\, Pixelgen Technologies\, BioSkryb\, Techtum\, Parse Biosciences\, 10X Genomics\, Illumina\, Oxford Nanopore Technologies and BD Biosciences. \n\n\n\nCheck here to see any updates! 
URL:https://www.scilifelab.se/event/stockholm-single-cell-genomics-2024-symposium/
LOCATION:IVA Conference center\, Grev Turegatan 16\, Stockholm
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241009T090000
DTEND;TZID=Europe/Stockholm:20241011T163000
DTSTAMP:20260404T171237
CREATED:20240909T104734Z
LAST-MODIFIED:20240910T082733Z
UID:10001350-1728464400-1728664200@www.scilifelab.se
SUMMARY:Data-Driven Life Sciences Hackathon
DESCRIPTION:Join us at the DDLS Hackathon in person at SciLifeLab in Solna\, where participants will choose and collaborate on a range of provided projects. With the support of teaching assistants in a hands-on environment\, groups will innovate and develop solutions in the dynamic field of data-driven life science. \n\n\n\nDuring the three day hackathon\, participants will select a dataset and apply the skills and knowledge gained during the course (see link above for each module) to create AI models\, analyze the data\, and produce meaningful insights. At the end of the hackathon\, teams will present their achievements. \n\n\n\nEveryone affiliated with the DDLS programme or interested in data-driven life science is welcome to join–from PIs\, PhD students\, postdocs\, and facility experts/trainers. Participants will form pairs or small groups of 2-3 people on-site to work on projects\, exchange ideas and experiences\, and engage in pair programming. This collaborative environment will foster innovation and provide a unique opportunity to apply the concepts learned throughout the course to real-world problems in data-driven life sciences.  \n\n\n\nWhat will you gain attending the hackathon?If you are to be selected to participate you will get the opportunity not only to work hands-on on a data-driven life science project\, but also to network with experts within the field of data-driven life science\, researchers and research infrastructure experts \n\n\n\nRegistration deadline:Monday\, September 30th\, 2024 \n\n\n\n \n\n\n\nRegistration\n\n\n\nThis hackathon is part of the 2024 DDLS course and will gather data-driven life science researchers (MSc students\, PhD students\, post-docs\, staff-scientists\, experts and group leaders). \n\n\n\n \n\n\n\nFor questions\, contact Wei Ouyang at weio@kth.se or traininghub@scilifelab.se
URL:https://www.scilifelab.se/event/data-driven-life-sciences-hackathon/
LOCATION:Gamma 7 Lunchroom\, Tomtebodavägen 23A\, Solna\, 17121
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241010T120000
DTEND;TZID=Europe/Stockholm:20241010T130000
DTSTAMP:20260404T171237
CREATED:20240708T140138Z
LAST-MODIFIED:20241001T092646Z
UID:10001298-1728561600-1728565200@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series: Daniela Huhn & Mariya Mardamshina
DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nPhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits\, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester. \n\n\n\nThis week:\n\n\n\n\n\n\nDaniela Huhn\n\n\n\nOscar Fernandez-Capetillo – alpha 4 \n\n\n\nOne-Two punch approach for improved treatment of ERa+ Breast Cancer \n\n\n\n\n\nMariya Mardamshina\n\n\n\nEmma Lundberg – alpha 2 \n\n\n\nExpanding the limits: Measuring more proteins beyond current multiplexed imaging capabilities \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-daniela-huhn-varun-kumar-rajendran/
LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna
CATEGORIES:Community
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/IMG_20221103_124630107_HDR-scaled.jpg
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241011T100000
DTEND;TZID=Europe/Stockholm:20241011T160000
DTSTAMP:20260404T171237
CREATED:20240918T071315Z
LAST-MODIFIED:20240920T060502Z
UID:10001357-1728640800-1728662400@www.scilifelab.se
SUMMARY:Microsampling- New Avenues for Metabolomics in Precision Health
DESCRIPTION:The Metrabolomics Platform arranges a one day seminar on “Microsampling- New Avenues for Metabolomics in Precision Health” together with the Nordic Metabolomics Society.  \n\n\n\n\n\n\n\nProgram\n\n\n\n10.00Welcome\,Rikard Landberg (SciLifeLab& Chalmers) & Alex Dickens (Nordic Metabolomics Society10.10Microsampling in Metabolomics- Enabler of Precision Health?Timothy Garrett (University of Florida)10.40High-throughput NMR-based metabolmics on microsamplesPeter Würtz (Nightingale)11.10New microsampling techniquesNiclas Roxhed (KTH)11.30Evaluation of microsampling techniques for lipidomics and exposomicsTuulia Hyötyläinen (Örebro University)11.50Metabolomics and microsampling across labsAlex Dickens (University of Turku)12.10SciLife-platform microsampling project and the SCAPIS2-HOME studyRikard Landberg (Scilifelab & Chalmers)12.30Lunch13.30Microsampling devices for nontarget chemical exposomicsSolveigh Thiele (SciLifeLab & Stockholm University)13.50Microsampling in high-through proteomicsClaudia Fredolini (Scilifelab)14.10Pitches of available microsampling techniquesProducers/vendors of microsampling devices15.00Discussion focused on the way forward15.45Concluding remarks and the way forwardRikard Landberg (SciLifeLab& Chalmers\n\n\n\nRegistration\n\n\n\nHow to get there\n\n\n\nBusLine 3\, 6\, 77\, 507 from S:t Eriksplan. Get off at Karolinska Institutet\, Biomedicum.Line 53 and 72 från Odenplan. Get off at Karolinska Institutet west which is next to Berzeliuslaboratory.  \n\n\n\nSubwayNearest station is S:t Eriksplan (exit Torsgatan)\, from where it takes 15-20 min walking to the Berzelius laboratory Odenplan – take bus 53 och 72. \n\n\n\nCarIf you arrive by car\,  parkeringshuset Skruven is the closest partking to the Berzeliuslaboratory https://www.aimopark.se/stader/solna/campus-solna/ \n\n\n\nPlease note that the Main Entrance to Campus Solna is currently closed due to the construction of a new subway station. There are several options to enter the campus from Solnavägen for those who walk or cycle. For those coming by car\, you must come via Tomtebodavägen\, where the nearest parking garage in connection with the conference is also located. \n\n\n\n\n\n\n\n\n\n\n\n\n\nContact: Rikard Landberg rikard.landberg@chalmers.se
URL:https://www.scilifelab.se/event/microsampling-new-avenues-for-metabolomics-in-precision-health/
LOCATION:Andreas Vesalius Lecture Hall\, Karolinska Institutet\, Berzelius väg 3\, Solna\, 171 65\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2024/09/21A6061_frikopt-scaled.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241014T080000
DTEND;TZID=Europe/Stockholm:20241025T170000
DTSTAMP:20260404T171237
CREATED:20240617T081347Z
LAST-MODIFIED:20240617T081528Z
UID:10001279-1728892800-1729875600@www.scilifelab.se
SUMMARY:New Super-Resolution\, Light-Sheet\, and FCS-Methods at Scilifelab
DESCRIPTION:The Advanced Light Microscopy Facility\, ALM\, at Scilifelab gives a two-week PhD-level course on four new imaging and fluorescence spectroscopy techniques: \n\n\n\nDepletion-based Super-Resolution Imaging \n\n\n\n\nSTED-imaging\, 2D and 3D\, 30-50 nm resolution\n\n\n\nIn Living Cells – MoNaLISA\, 1-2 Hz\, 100 x 100 mm field of view\n\n\n\n\nMINFLUX \n\n\n\n\nImaging with 3 nm resolution\n\n\n\nTracking single molecules at 10 kHz\n\n\n\n\nLight-Sheet Imaging \n\n\n\n\nLong time-lapse imaging of live model organisms with low phototoxicity\n\n\n\nUltrafast volumetric imaging of cells with lattice light-sheet microscopy\n\n\n\n\nFCS-Methods \n\n\n\n\nMeasurements of concentrations\, diffusion coefficients\, molecular dynamics and interactions\, in solution or living cells\n\n\n\nCross-correlation\, FRET-\, STED-\, and line-scan-FCS are covered\n\n\n\n\nLecturers: \n\n\n\nSteven Edwards \n\n\n\nErdinc Sezgin \n\n\n\nAna Agostinho \n\n\n\nFrancesca Pennacchietti \n\n\n\nHans Blom \n\n\n\nStefan Wennmalm \n\n\n\nDates: Monday October 14th – Friday October 25th 2024 \n\n\n\nCredits: 3 hp for PhD students \n\n\n\nLocation: Gamma 3\, Scilifelab\, Solna \n\n\n\nRegistration: stewen@kth.se latest September 30th
URL:https://www.scilifelab.se/event/new-super-resolution-light-sheet-and-fcs-methods-at-scilifelab/
LOCATION:Gamma 3\, Tomtebodavägen 23 A\, Solna\, Sweden
CATEGORIES:Course
ORGANIZER;CN="Advanced Light Microscopy Unit":MAILTO:stewen@kth.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241014T090000
DTEND;TZID=Europe/Stockholm:20241018T170000
DTSTAMP:20260404T171237
CREATED:20240326T120939Z
LAST-MODIFIED:20240403T083011Z
UID:10001215-1728896400-1729270800@www.scilifelab.se
SUMMARY:Omics Integration and Systems Biology
DESCRIPTION:National course open for PhD students\, postdocs\, researchers\, and other employees in all Swedish universities\, in need of a general description of different approaches for working with multiple types of biological data. We also welcome applications from outside of Sweden and from the non-academic sector\, for more info contact us! \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2024-08-05 \n\n\n\nApplication closes: 2024-09-16 \n\n\n\nConfirmation to accepted students: 2024-09-23 \n\n\n\nCourse Leader and teachers: \n\n\n\nNikolay Oskolkov (Lund University\, course leader) \n\n\n\nRasool Saghaleyni (Chalmers University of Technology\, course leader) \n\n\n\nSergiu Netotea (Chalmers University of Technology\, course lecturer) \n\n\n\nJennifer Fransson (Uppsala University\, course lecturer) \n\n\n\nYuan Li (Lund University\, TA) \n\n\n\nNima Rafati (Uppsala University\, TA) \n\n\n\nIn case you miss information on any of the above dates\, please contact: \n\n\n\nNikolay Oskolkov\, nikolay.oskolkov@scilifelab.se \n\n\n\nRasool Saghaleyni\, rasools@chalmers.se \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\nCourse fee\n\n\n\nA course fee* of 3000 SEK for academic participants and 15 000 SEK for non-academic participants will be invoiced to accepted participants. The fee includes all coffee breaks\, all lunches and 1 course dinner. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse content\n\n\n\nThe aim of this workshop is to provide an integrated view of data-driven analysis of biological data through machine learning\, graph and network analysis as well as constraint-based modeling integration methods. A general description of different approaches for working with multiple layers of biological information\, i.e. Omics data (e.g. transcriptomics and genomics) will be presented with some of the lectures discussing their advantages and pitfalls. The techniques will be discussed in terms of their rationale and applicability. \n\n\n\nTopics covered will include: \n\n\n\n\nData pre-processing\, cleaning and feature selection prior to integration;\n\n\n\nApplication of key machine learning methods for multi-omics analysis including deep learning;\n\n\n\nMulti-omics factor analysis\, dimension reduction and clustering;\n\n\n\nSingle Cell and Spatial transcriptomics integration;\n\n\n\nBiological network inference\, community and topology analysis and visualization;\n\n\n\nCondition-specific and personalized modeling through Genome-scale Metabolic models for integration of transcriptomic\, proteomic\, metabolomic and fluxomic data;\n\n\n\nIdentification of key biological functions and pathways;\n\n\n\nIdentification of potential biomarkers and targetable genes through modeling and biological network analysis;\n\n\n\nApplication of network approaches in meta-analyses;\n\n\n\nSimilarity network fusion and matrix factorization techniques;\n\n\n\nIntegrated data visualization techniques\n\n\n\n\n\n\n\n\nLearning outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\nIdentify key methods for analysis and integration of omics data based on a given dataset;\n\n\n\nPerform  feature selection and dimension reduction techniques; \n\n\n\nUnderstand strengths and pitfalls of key machine learning techniques in multi-omic analysis;\n\n\n\nApply unsupervised and supervised machine learning data integration techniques;\n\n\n\nBuild biological networks based on different omics data including integrated multi-omics networks;\n\n\n\nPerform centrality and community analyses in graphs;\n\n\n\nApply network approaches in meta-analyses;\n\n\n\nApply similarity network fusion of patient data;\n\n\n\nCompare different cell-types or conditions through the application of different biological network analysis techniques;\n\n\n\nSimulate biological functions using constraint-based models and flux balance analysis;\n\n\n\nIdentify potential confounding factors and sources of bias.\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nThe following is a list of skills required for being able to follow the course and complete the exercises: \n\n\n\n\nBasic knowledge in R or Python;\n\n\n\nBasic understanding of frequentist statistics;\n\n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n\nExperience with NGS and omics analysis\n\n\n\nCompleting “Introduction to bioinformatics using NGS data” and “Introduction to biostatistics and machine learning” NBIS courses\n\n\n\n\n\n\n\n\nDue to limited space the course can accommodate a maximum of 35 participants. If we receive more applications\, participants will be selected based on selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/omics-integration-and-systems-biology/
LOCATION:Lund University\, Lund\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241015T100000
DTEND;TZID=Europe/Stockholm:20241015T110000
DTSTAMP:20260404T171237
CREATED:20240919T131404Z
LAST-MODIFIED:20251204T144057Z
UID:10001362-1728986400-1728990000@www.scilifelab.se
SUMMARY:Research involving human data - what do I need to think of as a researcher?
DESCRIPTION:This seminar will focus on collecting and using personal data in research. We will guide you through the different phases of a typical research project and discuss some commonly asked questions. We will\, for example\, talk about GDPR\, and secure management and sharing of sensitive data\, among others. \n\n\n\nWhen: Tuesday October 15\, 10-11 CET (Zoom) \n\n\n\nSpeaker: Markus Englund and Erik Hedman\, Data Steward\, NBIS \n\n\n\nSciLifeLab Data Management seminar series is an event series by the SciLifeLab Data Centre and NBIS joint Data Management team aimed at both the life science research community and infrastructure\, and others with an interest in research data management in life sciences. The events will showcase how to put the FAIR principles\, and good data management into practice. The goal of the events in this seminar series is to provide interesting seminars around topics related to research data management in general but also to foster discussions around best practices and how they can be improved. The events takes place virtually (over Zoom) and are open to everyone\, (researchers\, staff\, RDM professionals etc.) working at or affiliated with a Swedish research institute or university. Each event is scheduled for 60 minutes\, including 15 minutes for discussions and Q & A. The videos (excluding Q&A) will be published openly after the seminars at the SciLifeLab YouTube channel.More information about SciLifeLab Data Centre and NBIS joint Data Management team: https://data-guidelines.scilifelab.se/ \n\n\n\nWelcome! \n\n\n\nOrganisers: SciLifeLab Data Centre and NBIS National Bioinformatics Infrastructure SwedenFor more information or inquiries please contact: data-management@scilifelab.se
URL:https://www.scilifelab.se/event/research-involving-human-data-what-do-i-need-to-think-of-as-a-researcher/
LOCATION:Online event via Zoom
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2024/02/DC_seminar-series_background1-1.png
ORGANIZER;CN="Open Science Seminar Series":MAILTO:data-management@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241015T100000
DTEND;TZID=Europe/Stockholm:20241015T111500
DTSTAMP:20260404T171237
CREATED:20240902T120825Z
LAST-MODIFIED:20240902T120852Z
UID:10001345-1728986400-1728990900@www.scilifelab.se
SUMMARY:Deriving actionable insight from omics data – an industry perspective
DESCRIPTION:Speaker: Daniel Muthas\, Head of Data Science & Bioinformatics at AstraZeneca \n\n\n\nAbstract \n\n\n\nThis talk will focus on how advancement in omic analysis is enabling the realisation of precision medicine in chronic complex diseases. Large\, well phenotyped cohorts highlights the heterogeneity of disease and through single cell technologies we are able to study disease processes at unprecedented granularity\, but how do we take these insights into actionable and deployable applications? Here I will focus on how we employ a breadth of bioinformatic techniques of different modalities to bridge between populations\, patients\, and cellular level to identify novel targets\, biomarkers and patient populations. \n\n\n\nBackground \n\n\n\nDaniel’s team is working with applied bioinformatics across the whole drug discovery and development pipeline\, from target identification to indication expansion and exploratory biomarker analysis in clinical trials.   \n\n\n\nHost: Rasool Saghaleyni\, NBIS Chalmers University\, Gothenburg (rasool.saghaleyni@scilifelab.se) \n\n\n\nDate: October 15\, 10:00 – 11:15 CET online on zoom \n\n\n\nBroadcast link (live event): link\, pass: spd996 The talk will also be available afterwards on the SciLifeLab YouTube channel.More information about the Oimcs Integration and Systems Biology Workshop here.
URL:https://www.scilifelab.se/event/deriving-actionable-insight-from-omics-data-an-industry-perspective/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241015T110000
DTEND;TZID=Europe/Stockholm:20241015T120000
DTSTAMP:20260404T171237
CREATED:20240919T090941Z
LAST-MODIFIED:20240926T111646Z
UID:10001359-1728990000-1728993600@www.scilifelab.se
SUMMARY:Trade secrets for Academic Startups\, Pharma and Biotech Companies in the Life Sciences
DESCRIPTION:Welcome to this Drug Discovery Webinar\, organized by OligoNova and SciLifeLab Drug Discovery and Development\, to learn more about how academic and biotech interventions can be protected with the goal to benefit patients. \n\n\n\nThis webinar is an introduction to trade secrets as a form of intellectual property\, with a focus on its potential importance to a life sciences start up.   \n\n\n\nTrade secrets are often an overlooked form of intellectual property\, thought by many to be of little relevance in the life sciences.  However\, as part of a well-developed IP strategy\, trade secrets have an increasingly important role to play\, with the potential to not only supplement a patent-based strategy but\, in some cases\, to provide a more suitable alternative. \n\n\n\nIn this seminar\, we will discuss how trade secrets can be identified\, protected\, and used to increase value and support investment. \n\n\n\nregistration\n\n\n\nAgenda \n\n\n\n\nIntroduction – Fredrik Wångsell\, OligoNova\n\n\n\nTrade secrets in the Life Sciences – Fiona Hey\, Tony Proctor and Michel\, Pears Potter Clarkson\n\n\n\nQ&A and discussion\n\n\n\n\nWelcome \n\n\n\nSciLifeLab DDD and OligoNova \n\n\n\nOther Seminars\n\n\n\nOligaNova organizes three seminars during the fall 2024 \n\n\n\nTrade secrets in the Life Sciences\, October 15 \n\n\n\nMaximizing exclusivity in the Life Sciences\, November 6 \n\n\n\nIP Strategies in the Life Sciences\, December 18
URL:https://www.scilifelab.se/event/trade-secrets-in-the-life-sciences/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="OligoNova - Part of the Drug Discovery and Development Platform":MAILTO:par.matsson@oligonova.org
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