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DTSTART;TZID=Europe/Stockholm:20230918T151500
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DTSTAMP:20260404T132244
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SUMMARY:[The Svedberg seminar] - Female sex hormones and the human microbiome
DESCRIPTION:Luisa Hugerth \n\n\n\nAssistant ProfessorDDLS FellowDepartment of Medical Biochemistry and Microbiology\, UU \n\n\n\n \n\n\n\n\n\n\n\nBio\n\n\n\n\n\n\n\nLuisa Hugerth has a background in molecular biology and biomedicine\, but got her PhD in 2016 at KTH Royal Institute of Technology with an analysis of microbial community time-series in the Baltic Sea. After that\, Dr. Hugerth spent 6 years at the Centre for Translational Microbiome Research in Karolinska Institutet\, where she studied the human microbiome in functional bowel disorders\, before becoming deeply involved in research on the microbiome of pregnant and non-pregnant women. Since 2022\, she is a DDLS fellow in epidemiology and biology of infection at Uppsala University’s Department of Medical Biochemistry and Microbiology\, Imbim \n\n\n\n \n\n\n\nFemale sex hormones and the human microbiome\n\n\n\nEstrogen and progesterone have pleitropic effects throughout the body. This includes mucosal surfaces and the diverse microbial communities that inhabit them. Microbiota can enhance or dampen these effects\, thereby acting as risk mediating factors for various diseases\, most notably gynecologic and periodontal inflammation. The vaginal microbiota has been epidemiologically linked to various outcomes\, from STI acquisition to preterm birth. The oral microbiota has also been causally linked to as disparate outcomes as preterm birth and newly onset depression. Here\, I will present ongoing work on the interplay between endogenous and exhogenous hormones on the oral\, vaginal and gut microbiome\, in women with a regular menstrual cycle as well as pregnant women. Additionally\, since both sex hormones and the gut microbiome are implicated in mood disorders\, I will touch upon the gut-brain axis in relation to pregnancy nausea and perinatal depression. \n\n\n\n\n\n\n\n\n\n\n\nHost: Mikael Sellin mikael.sellin@imbim.uu.se\, UU
URL:https://www.scilifelab.se/event/the-svedberg-seminar-luisa-hugerth/
LOCATION:BMC Room C8:301\, Husargatan 3\, Uppsala\, Sweden
CATEGORIES:Event
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ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230919T140000
DTEND;TZID=Europe/Stockholm:20230919T143000
DTSTAMP:20260404T132244
CREATED:20230829T081621Z
LAST-MODIFIED:20230830T083907Z
UID:10000960-1695132000-1695133800@www.scilifelab.se
SUMMARY:Neurodiversity in communication\, relationships\, academia & life
DESCRIPTION:We are excited to host a new Coaching in Science Initiative (CSI) Seminar titled:\n‘Neurodiversity in communication\, relationships\, academia & life’ \n\n\n\nNeurodiversity; to be outside of the category of people who are considered cognitive ‘normal’. But what is ‘normal’ really? And how broadly can we extend the concept of neurodiversity? On a personal level\, perhaps it is more helpful to ask ourselves\, what neurodiverse traits do I have in general\, or in this particular group of people? Could they be different depending on whom I’m socializing with at work and at home? \n\n\n\nApplying the CSI coaching model and our core values\, we will explore who we are in relation to others\, raise awareness of how we are different\, learn more about the biology behind our emotional regulation and what to do when we find ourselves in difficult social interactions. \n\n\n\nDate: 19/9/2023\nTime: 14:00\nOn-site location: Gamma 2 lunch room\nZoom link: https://kth-se.zoom.us/j/65001858940 \n\n\n\nWe will begin with a 15-20 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 follow starter questions:\nAwareness: where do we experience neurodiversity in our lives already?\nAnalysis: how well do I currently interact with neurodiversity?\nAlternative: how can we relate to neurodiversity\, in ourselves and others?\nAction: how will knowledge of neurodiversity change my decisions going forward?
URL:https://www.scilifelab.se/event/neurodiversity-in-communication-relationships-academia-life/
LOCATION:Gamma 2 Lunchroom\, SciLifeLab\, Tomtebodavägen 23\, Solna\, Sweden
CATEGORIES:Event
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ORGANIZER;CN="Coaching in Science Initiative (CSI)":MAILTO:sami.saarenpaa@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230920T090000
DTEND;TZID=Europe/Stockholm:20230920T170000
DTSTAMP:20260404T132244
CREATED:20221120T085632Z
LAST-MODIFIED:20230919T143955Z
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SUMMARY:SciLifeLab Science Summit 2023
DESCRIPTION:Genomics of Biodiversity and Evolution\n\n\n\nIn an era characterized by extinction and habitat loss\, it is crucial to explore biological diversity on our planet and understand the evolutionary processes that generate it. Genome sequencing has generated numerous insights into how species form and how they adapt to their environments\, which is vital to understand in a changing world. As sequencing technologies improve and become less expensive it becomes feasible to produce high-quality genome assemblies and analyze genetic diversity in a huge number of species\, which has led to a number of ambitious projects including the Earth BioGenome Project to sequence all known Eukaryotes. \n\n\n\nSwedish scientists and SciLifeLab are at the forefront of this field\, with genome projects including spruce\, herring\, Arctic fox and 240 mammals\, advancing knowledge of topics including population genetics\, adaptation\, speciation\, convergent evolution\, and functional constraint. \n\n\n\nIn this SciLifeLab Science Summit\, we have gathered several leading researchers who use genomics to learn about the diversity of life! \n\n\n\nWe invite you to Stockholm and Aula Magna for a full-day conference program with ample time for discussions\, mingling\, and networking. \n\n\n\nThis event is open to anyone interested in the topic and is free of charge. \n\n\n\nRegistration closed If you are interested in participating\, please send an email to events@scilifelab.se.  \n\n\n\n\n\n\n\nPoster session\, Flash Talk & Best Poster Award\n\n\n\nRegistration opens at 08:45. Please hang your poster on the poster boards upon arrival and in time before the Conference starts at 09:30. Pins are available. There are two poster sessions. Please remove your poster from the poster board after the second session or at 17:00. Any remaining posters after 17:15 will be discarded. The Scientific Committee´s Poster jury will nominate the Science Summit 2023 Best Poster and award the winner a 5 000 SEK Travel Grant. You must stay for the prize ceremony at the end of the conference. \n\n\n\nSciLifeLab Science Summit 2023 Poster ListDownload\n\n\n\nFour (4) submitted poster abstracts will be selected for Flash Talks à 5 minutes on stage.  \n\n\n\nThe selected Flash Talks speakers are  \n\n\n\nCynthia Perez Estrada. Three-dimensional genome architecture persists in a 52\,000-year-old woolly mammoth skin sample \n\n\n\nPatrik Rödin Mörch. The Role of Population History in Shaping the Mutational Load of Structural Variants Relative to SNPs\, in Distinct Island versus Continental Lagopus Lineages \n\n\n\nAndreas Wallberg. New insights into the evolutionary history and adaptive potential of World Ocean krill using comparative population transcriptomics \n\n\n\nQiaoling Deng. Genetic parallelism and adaptation to brackish water bodies in sprat (Sprattus sprattus) and Atlantic herring (Clupea harengus) \n\n\n\n  \n\n\n\n\n\n\n\nImportant dates \n\n\n\nSept 1. Registration deadline for posters! Poster submission closes\, and the selection of Flash Talks will be made. \n\n\n\nSept 4. Poster submission approval email. \n\n\n\nSept 11. Invitation email to selected Flash talk speakers. \n\n\n\nSept 11 at 12:00. Registration for the SciLifeLab Science Summit closes \n\n\n\nSept 11. Poster Abstracts published as a PDF on the website \n\n\n\n\n\n\n\nFree bus transportation\n\n\n\nWe offer free bus transportation from Uppsala (BMC Campus) at 08:00 to Aula Magna\, (SU Campus Frescati) in the morning and back after the Conference at 17:00 and after the mingle at 18:30. Reserve your seat when filling in the registration form.  \n\n\n\n \n\n\n\n\n \n\n\n\nSatellite Symposium:Computational Methods in Evolution and Biodiversity\n\n\n\nOn September 21\, the Data-Driven Life Science Expert group invites you to a full-day satellite symposium and workshop\, “Computational Methods in Evolution and Biodiversity“ \n\n\n\nRead more\n\n\n\n \n\n\n\n \n\n\n\n\n\n\n\n\nSpeakers\n\n\n\n\nLeif Andersson\, Uppsala University\, SWE\n\n\n\nRichard Durbin\, Wellcome Sanger Institute\, UK\n\n\n\nTom Gilbert\, University of Copenhagen\, DK\n\n\n\nElinor Karlsson\, University of Massachusetts Medical School & Broad Institute\, USA\n\n\n\nKarin Norén\, Stockholm University\, SWE\n\n\n\nKarin Rengefors\, Lund University\, SWE\n\n\n\nTanja Slotte\, Stockholm University\, SWE\n\n\n\nTom van der Valk\, Swedish Museum of Natural History\, SWE\n\n\n\n\nPlease\, see the abstracts below the Program \n\n\n\nProgram\n\n\n\nProgram Science Summit 2023Download\n\n\n\n08:00Bus from BMC Uppsala to Aula Magna08:45Registration and coffee\, hanging posters09:30Welcome WordsYlva Engström\, Chair of the SciLifeLab BoardIntroduction to the ConferenceKerstin Lindblad-Toh\, Chair of the Scientific CommitteeSession I: Moderator Kerstin Lindblad-Toh09:45Investigating mammalian evolution and human disease through comparative genomics in hundreds of speciesElinor Karlsson\, UMass Chan Medical School and Broad Institute\, USA10:15A Million-Year-Old Journey: Exploring Mammoth Speciation and Adaptive Evolution through timeTom van der Valk\, Swedish Museum of Natural History10:40Coffee break and Poster session ISession II: Moderator Leif Andersson11:20Insights from high quality genome sequencing across the tree of lifeRichard Durbin\, University of Cambridge\, UK11:55Conservation genomics of the Scandinavian Arctic foxKarin Norén\, Stockholm University12:20Lunch break and mingle\, exhibitionsSession III: Moderator Love Dalén13:40Domestication hologenomics – what are we missing without taking this approach?Tom Gilbert\, University of Copenhagen\, DK14:15Sequencing the supergene that governs Darwin’s different forms of flowersTanja Slotte\, Stockholm University14:40Flash Talks from Junior researchers (selected from submitted abstracts) 5-minute talk/researcher15:05Coffee break and Poster session IISession IV: Moderator Matthew Webster15:45The remarkable population structure of Atlantic and Baltic herring – selection\, selection\, selectionLeif Andersson\, Uppsala University16:20Why cyanobacterial blooms produce toxins – unravelling the underlying genetic diversity in the microcystin gene clusterKarin Rengefors\, Lund University16:45Best Poster Award ceremonyClosing words17:00End of ConferenceMeet the speakers and mingle; snacks and free beveragesBus to Uppsala departs at 17:00 and at 18:30\n\n\n\nSpeaker abstracts\n\n\n\nScience Summit speaker abstracts 2023Download\n\n\n\nAbstract Leif Andersson – The remarkable population structure of Atlantic and Baltic herring – selection\, selection\, selection\nInitial genetic studies with a handful of neutral markers revealed no genetic differentiation among populations of Atlantic herring\, not even between Atlantic and Baltic herring classified as distinct subspecies by Linnaeus. Whole genome sequencing has totally changed the picture. Atlantic herring can now be divided into many subpopulations (ecotypes). It is an adaptive radiation with incomplete reproductive isolation between ecotypes. We find strong genetic differentiation at loci under selection but minute genetic differentiation at neutral loci. The explanation for this is the huge population sizes minimizing drift\, high fecundity allowing effective selection\, a homing behavior but with gene flow. Herring is a broadcast spawner and it is probably no strong selection for prezygotic reproductive isolation. Ecological adaptation in Atlantic herring is related to a diversity of environmental conditions including salinity\, temperature and light conditions as well as behavioral traits such as timing of reproduction and migration. Recently we used SNP-chip analysis to explore the population structure of Baltic herring in the Bothnian Sea. This analysis revealed two major subgroups: spring- and autumn-spawning Baltic herring. However\, a third genetically distinct population was present among the spring-spawners. This ecotype had a three-fold larger body size than other populations spawning in the same area at the same time implying a marked difference in feeding behavior. This illustrates the adaptive differentiation occurring in the herring. The results have important implications for fishery management of the herring in the Baltic Sea and elsewhere. \n\n\n\nDr. Leif Andersson is a specialist in genetics and genome biology. He and his group have made ground-breaking studies on the relationship between genetic and phenotypic variation. He has been working on comparative genomics using domestic animals as models for phenotypic evolution. This has resulted in discoveries of genotype-phenotype relationships such as mutations affecting pigmentation\, gaits in horses\, comb morphology in chickens and muscle growth in pigs. He has also studied the genetic basis for domestication of rabbits\, chickens and pigs. The research program has been expanded to natural populations as exemplified by studies of the evolution of Darwin’s finches and their beaks\, a supergene controlling male mating strategies in the ruff and genetic basis of ecological adaptation in Atlantic herring. Leif Andersson is professor in Functional Genomics at Uppsala University and in Animal Genomics at Texas A&M University. He was awarded the Wolf prize in Agriculture 2014. \n\n\n\n\nAbstract Richard Durbin – Insights from high quality genome sequencing across the tree of life\nI will discuss progress in scaling up the generation of high quality reference genome sequences\, and some of the insights that we have obtained from them.  Using high accuracy PacBio CCS reads and paired end Illumina Hi-C data we are now obtaining essentially complete\, high contiguity chromosomal assemblies at an increasing rate and decreasing cost\, with more than a thousand assemblies completed within the Tree of Life programme at the Wellcome Sanger Institute.  Because in most cases even heterochromatic repeat DNA is well assembled\, we have been able to characterise turnover of centromere-associated repeates which are some of the most rapidly evolving seqence in the genome\, observing repeated transitions in plants between satellite tandem repeats and transposon cluster patterns.  Furthermore\, by selection of very high confidence bases from the individual CCS sequencing reads\, we are able to identify signatures of somatic mutations across a very wide range of species\, suggesting previously unobserved mutational processes. \n\n\n\nRichard Durbin works in computational genomics.  He has been leader or co-leader of multiple large collaborative projects\, including the 1000 Genomes Project\, and more recently has worked on genome assembly and contributed to the Vertebrate Genomes Project and the Earth Biogenome Project.  He has also introduced multiple bioinformatic methods and data structures\, including bwa for read mapping and the BAM format for genomic data\, and worked on evolutionary genomics in non-model vertebrate systems\, and understanding human history from ancient and modern DNA data. Richard is a Fellow of the Royal Society of London (2004)\, a Member of EMBO (2009) and a Foreign Member of the American Academy of Arts and Sciences (2019).  \n\n\n\n\nAbstract Tom Gilbert – Domestication hologenomics – what are we missing without taking this approach?\nAnalyses that compare the genomes of contemporary domestic animals and plants with those of their wild relatives have provided a wealth of insights into not only when and where our ancestors started the process\, but also what specific genetic variants are key to modern phenotypes. Furthermore\, once coupled to palaeogenomic data\, such datasets can also even reveal the order in which such variants arose\, shedding further insights into the process itself. However while there is no doubt that we have learnt much about domestication in general\, and indeed for most domestic species we can clearly document the genetic basis of why the end product differs from the start\, I argue that there may be certain processes that were involved that have been largely overlooked\, in particular related to the so-called hologenome. \n\n\n\nTom Gilbert is Professor of Palaeogenomics at the University of Copenhagen\, Professor II at NTNU University Museum\, and Director of the DNRF Center for Evolutionary Hologenomics. He holds a PhD in the study of ancient DNA from the University of Oxford\, and has been active in both trying to develop methods to both expand the potential of ancient DNA to our understanding of the past\, as well as more recently leading research aimed at revisiting our understanding of ecological and evolutionary processes using hologenomic techniques – ie the integrative approach of combining host genomes with those of their microbiome. \n\n\n\n\nAbstract Elinor Karlsson – Investigating mammalian evolution and human disease through comparative genomics in hundreds of species\nA major challenge in genomics is discerning which bases among billions alter organismal phenotypes and affect health and disease risk. The Zoonomia project compared 240 different placental mammal species to detect which individual bases in the genome are exceptionally conserved (constrained) and likely to be functionally important. Eighty percent of the most constrained bases are outside protein-coding exons\, and half have no functional annotations in the ENCODE project.  By pairing Zoonomia’s genomic resources with phenotype annotations\, we find genomic elements associated with phenotypes that differ between species\, including olfaction\, hibernation\, brain size\, and vocal learning. Comparative genomics is advancing human health today by identifying functionally important in both coding and noncoding regions. Exploring the genomic basis of phenotype diversity that has emerged across 100 millions of years of placental mammal evolution is a powerful tool for discovering the next generation of biotechnological advances.  \n\n\n\nElinor Karlsson\, PhD\, is associate professor in Bioinformatics and Integrative Biology at the UMass Chan Medical School\, and director of Vertebrate Genomics at the Broad Institute of MIT and Harvard. Her research combines new technology\, community science and genomics to investigate diseases and discover the origins of exceptional mammalian traits.  Dr. Karlsson’s research includes the Zoonomia project\, an international effort to compare the genomes of over 240 mammals (from the African Yellow-spotted Rock Hyrax to the Woodland Dormouse)\, to identify segments of DNA that are important for survival and health.  Dr. Karlsson has a special interest in dog and wolf genetics\, and her international Darwin’s Ark project invites all dog owners to enroll their dogs in an open data research project exploring the genetic basis of behavior\, as well as diseases such as cancer.   \n\n\n\nElinor received her B.A. in biochemistry/cell biology and her B.F.A. (Bachelor of Fine Arts) from Rice University\, and earned her Ph.D. in bioinformatics from Boston University. She was a postdoctoral fellow with Pardis Sabeti at Harvard University before starting her research group at UMass Chan in 2014. \n\n\n\n\nAbstract Karin Norén – Conservation genomics of the Scandinavian Arctic fox\nOver the past decade\, whole genome sequencing has generated important insights about key processes in conservation genetics\, e.g. inbreeding depression\, genomic erosion and genetic rescue in small and threatened populations. The Scandinavian Arctic fox (Vulpes lagopus) was on the verge of extinction in the late 1990s. In response to efficient conservation actions\, the population has increased\, but studies have documented that the bottleneck\, geographic fragmentation and long-term low population size resulted inbreeding depression and loss of genetic variation. To explore the dynamics of inbreeding\, accumulation of deleterious genetic variation and genetic rescue\, we assembled a draft reference genome and resequencing data of >80 complete Arctic fox genomes. We found alternating levels of genomic inbreeding and a short-term genetic rescue effect\, operating over different time scales. An immigration event resulted in an increased mutational load where immigrant offspring displayed higher proportion of loss of function mutations compared to native individuals. Further\, we established a link between deleterious genetic variation and individual fitness. The results from these studies play a fundamental role for making informed decisions in conservation of this particular population\, but also make important contributions for conservation of other small and threatened populations and species. \n\n\n\nKarin Norén is a researcher and docent in animal ecology at Department of Zoology\, Stockholm University. She received a PhD from Stockholm University in 2011. Thereafter\, she spent three years as a post-doctoral researcher at University of California\, Davis. She is currently a PI in the Swedish Arctic Fox Project and her research is focused on conservation genomics\, especially in carnivores\, and genetic processes in fluctuating populations in northern ecosystems. \n\n\n\n\nAbstract Karin Rengefors – Why cyanobacterial blooms produce toxins – unravelling the underlying genetic diversity in the microcystin gene cluster\nCyanobacterial blooms are a global threat to freshwater ecosystems since they produce cyanotoxins that are poisonous to humans\, wildlife\, and livestock. Microcystin is the most common and toxic among the cyanotoxins and induces liver failure and tumor promotion in mammals. However\, its function in cyanobacteria is still contested.  In Microcystis spp.\, the most common microcystin-producing genus\, microcystin-producing and non microcystin-producing strains co-exist within populations. Moreover the proportions of the strain types vary in time and space. Microcystin is biosynthesized by the constitutively expressed mcy gene cluster consisting of ten modular genes (mcyA-J). Previous studies have suggested that non-producers lack the entire cluster. In the field\, toxigenic strains are quantified using quantitative PCR targeting one of the genes in the microcystin gene cluster (usually mcyB or E). However\, the number of gene copies are not always correlated with microcystin in the water. To better understand the underlying genotypes of microcystin producers and non-producers we sequenced the genomes of strains of Microcystis isolated from a single bloom. At the same time\, the strains were phenotyped to determine microcystin variants.  Unexpectedly\, non microcystin-producing strains displayed a range of genotypes yet with a common pattern of mostly lacking mcyF\, G\, and J. Other genes in the cluster were either present or had partial hits against our custom-made microcystin gene database. We suggest that non microcystin-producing Microcystis are genotypically and phenotypically diverse and that genotype composition varies among populations. I will also discuss potential causes of mcy gene-loss and the way forward to unravel the function of microcystin. \n\n\n\nDr. Karin Rengefors is a professor of limnology at the Biology Department of Lund University\, and her research interest is on phytoplankton ecology and evolution\, with focus on freshwater harmful algal blooms. Currently her research group focuses on understanding the population dynamics and genetic diversity of toxin-producing cyanobacteria. Another research topic is investigating the processes underlying population differentiation and speciation in phytoplankton. Dr. Rengefors also has a strong interest in doctoral education and took the lead in developing and running GENECO\, the Graduate Research School in Genomic Ecology at Lund university 2008-2013. For this work she was awarded the Lund University Pedagogical prize in 2012. She has also been a co-director of the internationally renowned Workshop on Genomics in Cesky Krumlow. Dr. Rengefors did her BSc as well as her PhD at Uppsala University\, followed by two years postdoc at the Woods Hole Oceanographic Institution\, USA. In 2001\, she landed an Assistant Professorship at Lund University\, and in 2005 a University Lecturer position. She was promoted full professor in 2008\, thus becoming the first female professor in limnology in Sweden. \n\n\n\n\nAbstract Tanja Slotte – Sequencing the supergene that governs Darwin’s different forms of flowers\nSupergenes are genomic regions containing sets of tightly linked genes that control multi-trait phenotypic polymorphisms. Although supergenes are responsible for a wide variety of balanced polymorphisms in nature\, our understanding of the origins and evolution of supergenes remains incomplete. We aim to fully characterize and study evolutionary processes at one of the first described supergenes\, the S-locus that governs a floral polymorphism called distyly. We are doing so in Linum\, wild flaxseed species\, a system where Darwin himself described this floral polymorphism\, but where its genetic basis remained unknown. To generate a genomic framework for the study of distyly\, we assembled high-quality genomes of a diverse set of Linum species. We then identified the distyly supergene and showed that it harbors indel variation and not inversions\, which is typical for many other supergenes. Our results have important implications for the evolution and breakdown of distyly supergenes\, and shed light on the genetic architecture and evolution of the classic supergene that governs Darwin’s “different forms of flowers”. \n\n\n\nTanja Slotte is a professor in the Department of Ecology\, Environment and Plant Sciences at Stockholm University. Her group works on the evolution of supergenes and plant mating systems primarily using evolutionary genomic analyses. A population geneticist by training\, she received her PhD from Uppsala University\, followed by a postdoc at the University of Toronto\, Canada before starting her own group at Uppsala University. In 2014 she moved to Stockholm University to take up a SciLifeLab Fellow position and since 2022 she is Professor in Ecological Genomics at Stockholm University. \n\n\n\n\nAbstract Tom van der Valk – A Million-Year-Old Journey: Exploring Mammoth Speciation and Adaptive Evolution through time\nIn this presentation\, I will share our efforts over the past years in recovering genome-wide data from woolly mammoths and discuss how the genomic insights have advanced our understanding of evolutionary processes such as speciation and long-term adaptive evolution. Our research involved sequencing specimens from the Early and Middle Pleistocene subepochs\, including some of the last surviving woolly mammoths. This work led to the identification of a previously unknown mammoth lineage\, evidence of hybridization between different mammoth species\, and the finding that most protein-coding changes linked to cold adaptation in woolly mammoths were already present one million years ago. I will show that the woolly mammoths had acquired a diverse array of positively selected genes associated with among others hair and skin development and fat storage at the time of its origin. Our research also identified genes that underwent recent positive selection\, including those related to skeletal morphology\, body size\, and a gene potentially responsible for the small ear size observed in Late Quaternary woolly mammoths. Overall\, our findings highlight the potential of palaeogenomics in enriching our understanding of speciation and long-term adaptive evolution. \n\n\n\nTom completed his doctoral studies at Uppsala University\, Sweden\, with his thesis “Genomics of population decline\,” which investigated the genomic consequences of rapid population declines in endangered mammals. He then worked as Postdoctoral Researcher at the Centre for Palaeogenetics in Stockholm\, focusing on the computational analysis of ancient and historical genomes of multiple extinct and endangered species. He then served as a Bioinformatician at the National Bioinformatics Infrastructure Sweden\, working on a large-scale conifer genome project. As of 2022\, Tom is a Data-Driven-Life-Science fellow at the Centre for Palaeogenetics\, where his research group focusses on the development of computational methods to analyze complex samples\, with a priority on identifying the presence of species from minute amounts of DNA. \n\n\n\n \n\n\n\n\n\n\n\n\nScience-Summit-Poster-abstracts-2023Download\n\n\n\nScientific Committee\n\n\n\nKerstin Lindblad-Toh (chair)\, Leif Andersson\, Matt Webster\, Love Dalén. \n\n\n\nOperations office project leader: Erika Bergqvist Erkstam. Team: Maria Bäckström\, David Gotthold\, Isolde Palombo and Hampus Persson. \n\n\n\n\n\n\nSciLifeLab Science Summit – Proposal for topic 2024\n\n\n\nThe SciLifeLab Science Summit is a one-day symposium\, each year with a new topic. The Science Summit aims to create awareness about SciLifeLab research and researchers\, promote collaborations within life science in Sweden\, and be a day for the SciLifeLab community to meet and interact. \n\n\n\nTo SciLifeLab Group Leaders\, Platform Directors and Head of Units\,\n\n\n\nIs your research the theme for SciLifeLab Science Summit in 2024? Send in your proposal now and take part as the scientific committee! \n\n\n\nRead more
URL:https://www.scilifelab.se/event/scilifelab-science-summit-2023/
LOCATION:Aula Magna\, Frescativägen 6\, Stockholm\, 114 18 Stockholm\, Sweden
CATEGORIES:Event
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230921T090000
DTEND;TZID=Europe/Stockholm:20230921T170000
DTSTAMP:20260404T132244
CREATED:20230426T155028Z
LAST-MODIFIED:20230922T130208Z
UID:10000871-1695286800-1695315600@www.scilifelab.se
SUMMARY:Computational Methods in Evolution and Biodiversity
DESCRIPTION:This symposium and workshop will showcase the latest computational methods for analysing big data in evolution and biodiversity and provide an opportunity for participants to gain hands-on experience in these methods. Two keynote speakers will discuss a) new advances in using image recognition to analyse biodiversity and b) population genomics approaches to understand the effects of climate adaptation on genetic diversity. In addition\, there will be three parallel computer workshops focused on the application of computational and machine learning methods to genome variation and biodiversity data. Participants should bring their own computers to join these workshops. This symposium is organised by the DDLS Evolution and Biodiversity expert group in conjunction with the SciLifeLab summit on Genomics of Biodiversity and Evolution. \n\n\n\nPost-symposium material from the Workshops\n\n\n\nWe have the workshop leaders’ permission to share links to the material for the workshops in the DDLS symposium Computational Methods in Evolution and Biodiversity. Feel free to do tutorials from the other workshops than the one you attended. \n\n\n\nTobias Andermann’s workshop (slides\, tutorial\, and data): https://github.com/tandermann/ai_workshop \n\n\n\nPer Unneberg’s workshop: https://percyfal.github.io/workshop-biodiversity-summit/lab/index.html \n\n\n\nMarcin Kierczak’s workshop: https://github.com/mkierczak/autoencoders_workshop \n\n\n\n\n\n\n\n\n\n\n\nProgram\n\n\n\n09:00Welcome and introduction09:10Challenges in Fine-Grained Image Analysis. Keynote speaker: Serge Belongie\, Pioneer Center for AI\, Denmark09:50Computational methods give insight into paradigms and paradoxes in landscape genomics. Keynote speaker: Katie E. Lotterhos Northeastern University\, USA10:30CoffeeIntroduction to Workshop x 311:00Looking at population structure from a machine learning perspective\, Marcin Kierczak11:25Neural Networks for biodiversity research: challenges and opportunities\, Tobias Andermann11:50Inference of ancestral recombination graphs for population genomics\, Per Unneberg12:15Lunch13:30Workshop x 3; parallel sessions:Room P232\, P224\, P216. (Guidance on site)From PCA to Generative Deep Learning Models for better understanding population structure\, Marcin KierczakBuilding your own customized neural network model (bring your own data if you want)\, Tobias AndermannIntroduction to whole genome tree sequence inference with tsinfer\, Per Unneberg17:00End of DayVenue: Vivi Täckholmsalen (Q-salen)\, NPQ-huset\, Svante Arrhenius väg 20\, Stockholm University\n\n\n\n\n\n\n\nAbstract Serge Belongie\, Pioneer Center for AI\, Denmark\nChallenges in Fine-Grained Image Analysis\n\n\n\nFine-grained image analysis (FGIA) is a longstanding and fundamental problem in computer vision and pattern recognition\, and underpins a diverse set of real-world applications. The task of FGIA is concerned with visual objects from subordinate categories\, e.g.\, species of birds or models of cars. The small inter-class and large intra-class variation inherent to fine-grained image analysis makes it a challenging problem. Capitalizing on advances in deep learning\, in recent years we have witnessed remarkable progress in deep learning powered FGIA. In this talk we review representative examples in the context of recognition\, retrieval\, and generation/synthesis. In addition\, we also review other key issues of FGIA\, such as publicly available benchmark datasets\, related domain-specific applications\, and connections with other modalities including text and audio. We conclude by highlighting several research directions and open problems. \n\n\n\n\nAbstract Katie E. Lotterhos\, Northeastern University\, USA\nComputational methods give insight into paradigms and paradoxes in landscape genomics \n\n\n\nPredicting organisms’ vulnerabilities to rapid and multivariate climate change is a major scientific challenge. A hurdle to addressing this challenge arises from evolution in multivariate environments. This talk will highlight how adaptation in multivariate environments can lead to unexpected patterns at the alleles under selection\, which has implications for the inference of the genetic basis of adaptation and for predicting vulnerability to environmental change.  \n\n\n\n\n\n\n\n\nWorkshop\n\n\n\nFrom PCA to Generative Deep Learning Models for better understanding population structure\, Marcin Kierczak \n\n\n\nThe workshop will focus on looking at different ways of modelling and visualising population structure based on genomic kinship. Starting from more traditional approaches like PCs or MDS as a benchmark\, we will build more complex deep learning-based models and discuss when such approach can be beneficial. Finally\, we will see how deep learning can potentially be used to augment original input data with some artificially-generated individuals with desired pre-defined kinship relations. Throughout this workshop\, we will be using Python and keras interface to Tensorflow. \n\n\n\nBuilding your own customized neural network model (bring your own data if you want)\, Tobias Andermann \n\n\n\nIn this workshop we will cover some computational and data processing tools that will come in handy when working with neural network models. The workshop is focused on implementing your own custom-built neural network model for a chosen task. The provided examples will be from the field of biodiversity research\, but you can apply the tools we cover during the workshop to problems in other research fields. In general this is an easy to follow and hands-on introduction to using neural network models. The workshop requires very basic familiarity with Python\, as the model will be implemented using the Python tensorflow library. \n\n\n\nIntroduction to whole genome tree sequence inference with tsinfer\, Per Unneberg \n\n\n\nIn this workshop\, we will introduce tree sequence (a.k.a. ARG) inference using the tsinfer library. We will build tree sequences from input variation data and look at some applications and analyses using the resulting tree sequences. As the exercises will be performed in jupyter notebooks in Python\, basic familiarity with Python is required. \n\n\n\n \n\n\n\n\n\n\n\nScientific Committee\n\n\n\n\nFredrik Ronquist\, NRM\n\n\n\nTanja Slotte\, SU\n\n\n\nMatthew Webster\, UU\n\n\n\n\n\n\nData-driven Evolution and biodiversity\n\n\n\nThe DDLS subject area concerns research that takes advantage of the massive data streams offered by techniques such as high-throughput sequencing of genomes and biomes\, continuous recording of video and audio in the wild\, high-throughput imaging of biological specimens\, and large-scale remote monitoring of organisms or habitats. This research subject area aims to lead the development or application of novel methods relying on machine learning\, artificial intelligence\, or other computational techniques to analyze these data and take advantage of such methods in addressing major scientific questions in evolution and biodiversity. \n\n\n\nThe research area Expert Group arranges symposia and workshops and welcomes interested to join the activities. More information about  the research area Evolution and Biodiversity here.
URL:https://www.scilifelab.se/event/computational-methods-in-evolution-and-biodiversity/
LOCATION:Vivi Täckholmsalen (Q-salen)\, NPQ-huset\, Stockholm University\, Svante Arrhenius väg 20\, Stockholm\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/03/EB_Icon.png
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DTSTART;TZID=Europe/Stockholm:20230921T120000
DTEND;TZID=Europe/Stockholm:20230921T130000
DTSTAMP:20260404T132244
CREATED:20230829T082158Z
LAST-MODIFIED:20230829T082159Z
UID:10000941-1695297600-1695301200@www.scilifelab.se
SUMMARY:Metabolomics for the masses
DESCRIPTION:Metabolites reflect the interaction between the gene cascade and surrounding exposures and are therefore essential components in all living organisms. Metabolites can be used to identify biomarkers of both health conditions and environmental exposures. The SciLifeLab Metabolomics platform offers a range of services\, which will be presented during this talk\, for researchers interested in metabolomics. \n\n\n\nThe presenter\, Otto Savolainen\, is head of the Swedish Metabolomics Centre (SMC)\, which offers small molecule\, lipid and metabolomics analysis in biological tissues and fluids using mass spectrometry methods\, in Gothenburg.  The SciLifeLab site in Gothenburg includes units at both the University of Gothenburg and Chalmers University of Technology and has a strong connection to Sahlgrenska University Hospital. The SMC unit in Gothenburg is part of the Chalmers Mass Spectrometry Infrastructure (CMSI). \n\n\n\nA light lunch will be offered for those attending onsite. \n\n\n\nregistration\n\n\n\nDeadline for registration is 19/9.
URL:https://www.scilifelab.se/event/metabolomics-for-the-masses/
LOCATION:Birgit Thilander Lecture Hall\, Medicinaregatan 3\, Göteborg
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Gothenburg":MAILTO:gothenburg@scilifelab.se
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230925T100000
DTEND;TZID=Europe/Stockholm:20230925T110000
DTSTAMP:20260404T132244
CREATED:20230816T080428Z
LAST-MODIFIED:20230816T080740Z
UID:10000953-1695636000-1695639600@www.scilifelab.se
SUMMARY:Dissecting peripheral protein-membrane interfaces
DESCRIPTION:Speaker: Nathalie Reuter\, Department of Chemistry and Computational Biology Unit\, University of Bergen \n\n\n\nHost: Arne Elofsson \n\n\n\nAbstract \n\n\n\nPeripheral membrane proteins (PMPs) are soluble proteins that bind transiently to the surface of cell membranes. Peripheral membrane proteins include a wide variety of proteins including membrane-targeting domains such as C1\, C2\, FYVE\, PH\, PX\, ENTH and GLA\, enzymes involved in lipid metabolism such as phospholipases\, membrane remodeling. machines such as BAR domains or ESCRTIII\, and lipid-transfer proteins to name a few. Having the ability to exist in both a soluble and a membrane-bound form their membrane-binding region is constrained to retain a fine balance of polar and hydrophobic character\, which makes it difficult to distinguish it from the rest of their surface. As a result peripheral membrane-binding sites are notoriously difficult to predict. \n\n\n\nWe collected and curated a dataset containing 2500 structures and compared their membrane-binding sites to the rest of their solvent-accessible surfaces\, in order to reveal features of PMPs’membrane-binding sites. We find that\, among positively charged amino acids\, lysines are significantly more present than arginines. Protruding hydrophobes are a landmark of the interfacial binding sites of ca. 2/3 of peripheral membrane binding proteins\, indicating that a majority of PMPs takes advantage of the hydrophobic effect while a non-negligeable minority (1/3) most likely relies on electrostatics interactions or other mechanisms. The IBS of peripheral membrane proteins contain significantly more glycines than the rest of their surface. Furthermore the analysis of 9 superfamilies revealed amino acid distribution patterns in agreement with their known functions and membrane-binding mechanisms. \n\n\n\nThese findings and the collected dataset will be useful for the development of prediction models for membrane-binding sites of PMPs.
URL:https://www.scilifelab.se/event/dissecting-peripheral-protein-membrane-interfaces/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230925T151500
DTEND;TZID=Europe/Stockholm:20230925T161500
DTSTAMP:20260404T132244
CREATED:20230831T123645Z
LAST-MODIFIED:20230901T121318Z
UID:10000958-1695654900-1695658500@www.scilifelab.se
SUMMARY:[The Svedberg seminar] - Targeting Non-Coding RNAs Using Synthetic Small Molecules: Original Targets for Innovative Therapies
DESCRIPTION:Dr Maria Duca \n\n\n\nCNRS Research Director\, Université Côte d’Azur\, FranceWebsite: icn.univ-cotedazur.fr/tna \n\n\n\nHost: Duc Duy Vo duc.duy.vo@kemi.uu.se\, UU \n\n\n\nBio\n\n\n\nDr. Maria Duca is head of Targeting of Nucleic Acids research group in the Institute of Chemistry of Nice (Université Côte d’Azur – CNRS). After undergraduate studies in Pharmacy and Medicinal Chemistry (Faculty of Pharmacy\, University of Bologna\, Italy)\, she obtained her PhD in Molecular Biochemistry under the supervision of Dr. Paola B. Arimondo (National Natural History Museum\, Paris\, France) working on topoisomerase II inhibitors. A 2-year post-doctoral training in Sydney Hecht’s lab (Department of Chemistry\, University of Virginia\, USA) allowed her to pursue the study of nucleic acids working on targeted protein mutagenesis. After CNRS recruitment as a Research Scientist in 2008 and promotion to Director of Research in 2022\, her research activities focus on the targeting of non-coding RNAs using synthetic small molecules toward innovative therapeutic approaches for anticancer\, antiviral and antimicrobial applications. She has been awarded the Michel Delalande award from the Académie de Pharmacie as well as national and international grants including H2020 grants. She is Associate Editor for RSC Medicinal Chemistry journal\, chair of the Chemical Biology Initiative of EFMC as well as vice-president of the French medicinal chemistry society. \n\n\n\n \n\n\n\nTargeting Non-Coding RNAs Using Synthetic Small Molecules: Original Targets for Innovative Therapies\n\n\n\nRNA is one of the most intriguing and promising biological targets for the discovery of innovative drugs in a large number of pathologies and various biologically relevant RNAs that could serve as drug targets have already been identified.1 Among the most important ones\, it is worth to mention prokaryotic ribosomal RNA which is the target of a number of currently employed antibiotics\, viral RNAs such as TAR\, RRE and DIS RNA of HIV-1 or oncogenic microRNAs that are tightly involved in the development and progression of various cancers.2 However\, difficulties in the rational design of strong and specific small-molecule ligands renders this kind of molecules relatively rare. \n\n\n\nIn this presentation\, the structure-based design of new RNA ligands targeting oncogenic RNAs will be illustrated together with the identification of new compounds bearing a promising biological activity.3 Also\, it will be shown how the active binders can be employed as chemical tools for a better understanding of the formed interactions toward the design of optimized compounds.4 Finally\, the use of RNA binders for the validation of new antibacterial targets against resistant bacterial strains will be described to highlight the potential of the small-molecule approach in RNA targeting. \n\n\n\nReferences \n\n\n\n[1] J. Childs-Disney\, X. Yang\, Q. Gibaut\, Y. Tong\, R. Batey\, M. Disney\, Nat. Rev. Drug. Discov. 2022\, 21\, 736. \n\n\n\n[2] J. Falese\, A. Donlic\, A. Hargrove\, Chem. Soc. Rev. 2021 50\, 2224. \n\n\n\n[3] D. D. Vo\, C. Becquart\, T. Tran\, A. Di Giorgio\, F. Darfeuille\, C. Staedel\, M. Duca\, Org. Biomol. Chem. 2018 16\, 6262; C. Staedel\, T. Tran\, J. Giraud\, F. Darfeuille\, A. Di Giorgio\, N. Tourasse\, F. Salin\, P. Uriac\, M. Duca\, Sci. Rep. 2018 8\, 1667. \n\n\n\n[4] Maucort\, C.\, Vo\, D.D.\, Aouad\, S.\, Charrat\, C.\, Azoulay\, S.\, Di Giorgio\, A.\, Duca\, M. ACS Med. Chem. Lett. 2021 12\, 899; Tran\, T.P.A.\, Poulet\, S.\, Pernak\, M.\, Rayar\, A.\, Azoulay\, S.\, Di Giorgio A.\, Duca\, M. RSC Med. Chem. 2022 13\, 311; Scheheoleva I.\, Fernandez-Remacha\, D.\, Estrada-Tejedor\, R.\, Duca\, M.\, Michelet\, V. Chem. Eur. J. 2023 doi.org/10.1002/chem.202300825
URL:https://www.scilifelab.se/event/the-svedberg-seminar-maria-duca/
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
ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230926T140000
DTEND;TZID=Europe/Stockholm:20230926T153000
DTSTAMP:20260404T132244
CREATED:20230904T110830Z
LAST-MODIFIED:20230922T152355Z
UID:10000964-1695736800-1695742200@www.scilifelab.se
SUMMARY:FAIRPoints 'Ask Me Anything' webinar on Equitable and transparent access to information
DESCRIPTION:Welcome to join SciLifeLab Data Centre for this virtual FAIRPoints ‘Ask Me Anything’ event. The theme of this session is “FAIRPoints ‘Ask Me Anything’ on Equitable and transparent access to information“. A discussion about the role of infrastructure for open and equitable access of information\, how this reflects in design decisions and how open and FAIR relate to or mean to the rest of the world.  \n\n\n\nSpeakers: Sharif Islam; DiSSCo (Distributed System of Scientific Collections)\, and Karl Meyer; GÉANT. The event is moderated by Emma Wilson. \n\n\n\nWhen: Sept 26th 14.00-15.30 CEST virtual event.  \n\n\n\nThis event is hosted by SciLifeLab Data Centre in collaboration with FAIRPoints\, RDA\, EOSC and FDO.  \n\n\n\n\nRegister\n\n\n\n\n \n\n\n\nFor more information or inquiries please contact: Sara El-Gebali\, SciLifeLab Data Centre\, Project leader\, Metadata and curation\, sara.elgebali@scilifelab.uu.se  or fairpoints@protonmail.com \n\n\n\nLearn more about FAIRPoints\, an event series highlighting pragmatic measures developed by the community towards the implementation of the FAIR (Findable\, Accessible\, Interoperable\, Reusable) data principles here.
URL:https://www.scilifelab.se/event/fairpoints-ask-me-anything-webinar/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230927T100000
DTEND;TZID=Europe/Stockholm:20230927T110000
DTSTAMP:20260404T132244
CREATED:20230810T123528Z
LAST-MODIFIED:20230829T092737Z
UID:10000944-1695808800-1695812400@www.scilifelab.se
SUMMARY:Blending Chemistry and Biology to Enable Systems Pharmacology
DESCRIPTION:Patrick Aloy\, Prof.\, Institute for Research in Biomedicine (IRB Barcelona) \n\n\n\n \n\n\n\nOrganizers \n\n\n\nCBCS-KI and PhenoTarget Research Community Program \n\n\n\nJoin the seminar on Zoomhttps://ki-se.zoom.us/j/64473979770 \n\n\n\nAbstract \n\n\n\nBig Data analytical techniques and AI have the potential to transform drug discovery\, as they are reshaping other areas of science and technology\, but we need to blend biology and chemistry in a format that is amenable for modern machine learning. In this talk\, I will present the Chemical Checker (CC)\, a resource that provides processed\, harmonized and integrated bioactivity data on small molecules. The CC divides data into five levels of increasing complexity\, ranging from the chemical properties of compounds to their clinical outcomes. In between\, it considers targets\, off-targets\, perturbed biological networks and several cell-based assays such as gene expression\, growth inhibition and morphological profiles. I will also present the Bioteque\, a resource of unprecedented size and scope that contains pre-calculated biomedical embeddings around 11 biological entities (e.g. genes\, cells\, tissues\, disease\, etc)\, derived from a gigantic knowledge graph\, so that each entity can be described considering different contexts (e.g. interactions\, expression\, etc). With small molecule and biological bioactivity descriptors in hand\, we now face a new scenario for chemical and biological entities where they both are translated into a common numerical format. In this computational framework\, complex connections between entities can be unveiled by means of simple arithmetic operations. Indeed\, we demonstrate and experimentally validate that these descriptors can be used to reverse and mimic biological signatures of disease models and genetic perturbations in vitro and in vivo\, options that are otherwise impossible using chemical information alone.ReferencesDuran-Frigola et al. Extending the small molecule similarity principle to all levels of biology with the Chemical Checker. 2020. Nat Biotechnol. 38: 1087-1096. \n\n\n\nBertoni et al. Bioactivity descriptors for uncharacterized chemical compounds. 2021. Nat Commun. 12: 3932. \n\n\n\nPauls et al. Identification and drug-induced reversion of molecular signatures of Alzheimer’s disease onset and progression in AppNL-G-F\, AppNL-F\, and 3xTg-AD mouse models. 2021. Genome Med. 13:168. \n\n\n\nFernández-Torras et al. Connecting chemistry and biology through molecular descriptors. 2022. Curr Opin Chem Biol\, 66: 102090. \n\n\n\nFernández-Torras et al. Integrating and formatting biomedical data in the Bioteque\, a comprehensive repository of pre-calculated knowledge graph embeddings. 2022. Nat Commun. 13: 5304.
URL:https://www.scilifelab.se/event/blending-chemistry-and-biology-to-enable-systems-pharmacology/
LOCATION:Gamma 2 Lunchroom\, SciLifeLab\, Tomtebodavägen 23\, Solna\, Sweden
CATEGORIES:Event
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230928T080000
DTEND;TZID=Europe/Stockholm:20230928T170000
DTSTAMP:20260404T132244
CREATED:20230313T112118Z
LAST-MODIFIED:20230926T140525Z
UID:10000833-1695888000-1695920400@www.scilifelab.se
SUMMARY:SciLifeLab Day Lund
DESCRIPTION:SciLifeLab has launched four new sites across Sweden in 2022. The sites\, located in Gothenburg\, Linköping\, Lund\, and Umeå\, will be crucial in promoting scientific research and research infrastructure nationally\, while also strengthening the collaboration between all Swedish universities. \n\n\n\nThe expansion of SciLifeLab’s network will provide researchers across Sweden with state-of-the-art research infrastructure and technology\, enabling them to perform cutting-edge research in areas such as genomics\, proteomics\, and bioinformatics. This will not only help to advance scientific knowledge but also contribute to the development of innovative solutions to pressing societal challenges. \n\n\n\nThe launch of the national sites\, in addition to existing ones in Stockholm and Uppsala\, will also contribute to the development of a stronger research environment\, crucial for attracting talented researchers and investment to the country\, further cementing Sweden’s position as a leader in scientific research. \n\n\n\nThroughout this year\, each site arrange a whole day program to highlight the national and local perspectives of SciLifeLab.  \n\n\n\nConference proceedings\n\n\n\nSciLifeLab-Day-Lund-Booklet-finalDownload\n\n\n\nProgram\n\n\n\nSciLifeLab-Day-in-Lund-ProgrammeDownload\n\n\n\n\n\n\n\nContact\n\n\n\n\n\n lund@scilifelab.se \n\n\n\n\n\nEsther González-PadillaLund UniversitySite Coordinator SciLifeLab Lundesther.gonzalez-padilla@scilifelab.se (+46) 76-517 38 35\n\n\n\n\n\nVenue\n\n\n\n\n\n\n\nSciLifeLab Days on the national sites\n\n\n\n\nGothenburg\, April 17\n\n\n\nUmeå\, September 11\n\n\n\nLund\, September 28\n\n\n\nLinköping\, October 10
URL:https://www.scilifelab.se/event/scilifelab-day-lund/
LOCATION:Forum Medicum\, Fernströmsalen\, Sölvegatan 19\, Lund\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/05/SciLifeLab-Day-Lund-Registration-with-QR.png
ORGANIZER;CN="SciLifeLab Lund":MAILTO:lund@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230929T100000
DTEND;TZID=Europe/Stockholm:20230929T110000
DTSTAMP:20260404T132244
CREATED:20230816T080214Z
LAST-MODIFIED:20230922T144940Z
UID:10000952-1695981600-1695985200@www.scilifelab.se
SUMMARY:Computational Enzymology - Identifying Catalytic Modules and predicting Mechanisms
DESCRIPTION:Speaker: Janet Thornton\, EBI \n\n\n\nComputational Enzymology: Towards using knowledge of structure and function to predict enzyme transformations and mechanisms. \n\n\n\nJM Thornton\, AJM Ribeiro\, Ioannis Riziotis\, JD Tyzack\, Neera Borkakoti\, Roman Laskowski. European Bioinformatics Institute (EMBL-EBI)\, Wellcome Genome Campus\, Cambridge CB10 1SD\, UK \n\n\n\nEnzymes catalyse most of the chemical reactions which are essential for life. They are powerful catalysts that have evolved over millions of years to perform the functions in an organism that are necessary for survival. Using structural data and computational biology we seek to understand and predict how enzymes work and how they evolve to perform new enzyme functions. In this talk I will present our ongoing work to ‘perform catalysis’ in the computer. Using methods developed in cheminformatics\, combined with information derived from 3D enzyme structures\, we are developing tools to predict transformations and mechanisms.  \n\n\n\nHost: Arne Elofsson \n\n\n\nDame Janet M Thornton has contributed significantly to structural bioinformatics by increasing our fundamental understanding of the structure and function of proteins and how they contribute to disease and ageing. She has uniquely combined the analysis of structural features with the development of prediction methods. Together with Christine Orengo\, the popular database CATH was developed. Her studies of sidechain conformation and stereochemistry were developed with Roman Laskowski into a tool\,  PROCHECK\, widely used for evaluating the quality of experimentally defined protein structures. With Orengo and David Jones she developed methods for protein structure prediction. She was the director of the European Bioinformatics Institute from 2001 to 2015 and initiated the European infrastructure ELIXIR.
URL:https://www.scilifelab.se/event/computational-enzymology-identifying-catalytic-modules-and-predicting-mechanisms/
LOCATION:Gamma 2 Lunchroom\, SciLifeLab\, Tomtebodavägen 23\, Solna\, Sweden
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231003T090000
DTEND;TZID=Europe/Stockholm:20231005T150000
DTSTAMP:20260404T132244
CREATED:20230919T150816Z
LAST-MODIFIED:20230928T094717Z
UID:10000972-1696323600-1696518000@www.scilifelab.se
SUMMARY:Exhibition in Navet at BMC
DESCRIPTION:On October 3-5\, between 09.00-15.00\, you have a new opportunity to visit our exhibition in Navet at BMC. This is a chance to receive information and updates from 30 of the leading life science companies in Sweden. The entrance to Navet will be open between 09:00-10:00 and 13:00-14:00 for external visitors. \n\n\n\n\n\n\n\n\n\nTuesday\, Oct 3 \n\n\n\nAH DiagnosticsWe help laboratories within life science and diagnostics to reach optimal performance by providing innovative quality products and full workflow solutions. \n\n\n\nBio-TechneBio-Techne´s family of brands includes R&D Systems\, Novus Biologicals\, Tocris\, Protein Simple\, ACD and Exosome Dx\, creating a unique portfolio of products & services to empower researchers in Life Science & Clinical Diagnostics. \n\n\n\nBioNordika \n\n\n\nEppendorfEppendorf in the house\, Navet October 3rd! \n\n\n\nMove-it pipettes\, first centrifuge with “green cooling”\, lab consumables made from recycled cooking oils\, new PCR and competitions. \n\n\n\nKem-En-Tec Nordic \n\n\n\nSENSE Multilabel Plate Reader\, Mirus Transfection reagents Efficient\, Low Toxic\, Instant Coomasie Stain 15 min w/o washes\, Antibodies and ELISA kits\, Metabolomic kits\, DNA/RNA extraction kits \n\n\n\nMercodiaFocuses on the development and manufacturing of immunoassays for research and clinical diagnostics\, as well as offering bioanalytical services to pharma- and biotech companies. \n\n\n\nMicromedicMicromedic provides a range of products for microscopy. The portfolio includes brands like Leica Microsystems (microscopes)\, Ibidi (consumable for live cell imaging) and SunJinLab (clearing reagents). \n\n\n\nNordic BioLabsDistributor representing e.g. Promega (enzymes\, reagents)\, Active Motif (epigenetics)\, Lexogen (RNA-seq)\, Invitek (kits)\, Biosearch Technologies (enzymes\, competent cells)\, Cytiva and Capricorn (cell culture) \n\n\n\nPeproTech \n\n\n\nRAMCON ABKombinerar globala produkter och expertis med lokal kunskap för att garantera att våra kunder uppnår bättre resultat på kortare tid. Vi riktar oss till forskare och tillverkare inom industrin\, läkemedel\, kemi och bioteknik. \n\n\n\nThermo Fisher Scientific \n\n\n\n \n\n\n\n\n\nWednesday\, Oct 4 \n\n\n\nAkoya BiosciencesAkoya Biosciences offers comprehensive single-cell imaging solutions that allow researchers to phenotype cells with spatial context and visualize how they organize and interact to influence disease progression and response to therapy. \n\n\n\nBeckman Coulter \n\n\n\nDedicated to developing and providing advanced technologies and equipment for research and discovery to explore new treatment methods. \n\n\n\n \n\n\n\nBecton DickinsonBD Biosciences provides high-quality single cell multiomics (scM) instruments\, reagents\, and bioinformatics tools for reliable\, reproducible scM data \n\n\n\nHyperfine studiosHyperfine Studios\, an animation\, video and illustration production studio. We produce visuals that are scientifically correct and visually appealing. The studio possesses expertise in both science and visual communication. \n\n\n\nMeso Scale \n\n\n\nMettler Toledo \n\n\n\nNordic BioSiteNordic BioSite is a supplier of products for research & diagnostics throughout the Nordics. Let’s talk about your workflow for Genomics and Transcriptomics\, antibodies available in BULK\, and services. \n\n\n\nQiagenQIAGEN delivers Sample to Insight solutions for molecular testing and offers products and services that enable our customers to gain valuable insights from any biological sample – from basic research to clinical healthcare. \n\n\n\nScience ImagingDistributes selected Life Science Products mainly in Scandinavia and Finland. Our goal is to offer comprehensive solutions to the image related problems faced by today’s research communities \n\n\n\nTecan NordicTecan is a Swiss company founded in 1980\, a world-leading provider of automated solutions for laboratories. We develop\, manufacture and distribute our own products worldwide\, with production in Switzerland\, Austria and the USA. \n\n\n\n\n\nThursday\, Oct 5 \n\n\n\nBio-WorksWe supply the biopharmaceutical and biotech industry with WorkBeadsTM chromatography resins and GoBio™ prepacked columns for the purification of a wide range of biomolecules\, e.g. proteins and peptides. \n\n\n\nGenScriptGenscript biotech is global CRO provider of genes\, protein\, peptides and antibodies as a products and services for research and clinical use \n\n\n\nHamilton Nordic \n\n\n\nIntegrated DNA Technologies \n\n\n\nLabLife NordicExciting news for cell- and molecular biosciences\, Label-free cell characterization and sorting\, NGS & single cell sample prep and target enrichment panels\,Oligo synthesis\, Cell assay sample prep\, Cleanup and extraction\, Western blot \n\n\n\nNavinciNavinci is a Swedish biotech company that specializes in developing innovative solutions for the study of protein interactions based on our proprietary proximity ligation technology – Bringing Precision to Spatial Proteomics. \n\n\n\nPacific BiosciencesPacBio is a life science technology company that is providing advanced sequencing solutions that enable scientists to improve their understanding of the genome and ultimately\, resolve genetically complex problems. \n\n\n\nShimadzuShimadzu Sweden provides a broad range of analytical instruments indispensable for research\, development\, and quality control in a variety of fields. \n\n\n\nTakara Bio \n\n\n\nCommitted to helping scientists break new ground with innovative technologies. Our extensive portfolio offers solutions to support advancements across many areas of research\, diagnostics\, & clinical applications \n\n\n\nTechtum LabA distributor of cutting-edge laboratory equipment and solutions for molecular biology research will exhibit at BMC Navet October 5. Live demos of a selection of our instruments!
URL:https://www.scilifelab.se/event/exhibition-in-navet-at-bmc-2/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/03/Navet.jpg
ORGANIZER;CN="SciLifeLab Navet":MAILTO:lokalbokning@scilifelab.uu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231004T090000
DTEND;TZID=Europe/Stockholm:20231005T170000
DTSTAMP:20260404T132244
CREATED:20230220T151823Z
LAST-MODIFIED:20231002T130421Z
UID:10000814-1696410000-1696525200@www.scilifelab.se
SUMMARY:6th CryoNET Symposium in Stockholm
DESCRIPTION:We are very much looking forward to seeing you all in Stockholm on Wednesday. We’ll have a full house of around 200 participants\, some 50 posters and a bunch of exciting speakers. It will be two intense and\, we hope\, enjoyable days! \n\n\n\nCryoNet is a Nordic network in Cryo-electron microscopy that aims to promote collaboration and knowledge sharing across national borders. A main goal is to help establish state-of-the-art cryo-electron microscopy as a strong pillar of Nordic life science research. \n\n\n\nThe core of the network is formed by the Cryo-EM facilities at the University of Copenhagen\, Aarhus University\, Stockholm University and Umeå University. The network also reaches out to Cryo-EM sites in Norway and Finland. \n\n\n\nThe 6th CryoNET Symposium will take place October 4-5 2023 at Stockholm University. Take the opportunity to hear from world leaders in the field and network with students and researchers!  \n\n\n\nParticipation in the symposium is free of charge and includes two days of lectures and a symposium dinner on October 4. We will start at 9:00 on Wednesday 4 October and finish 16:30 on Thursday 5 October. \n\n\n\nWe strongly encourage students and postdocs to submit an abstract about their research project. A number of abstracts will be selected for short talks and there will be a poster session for everyone during the symposium. \n\n\n\nOrganizersGunnar von Heijne\, Marta Carroni\, Arne Elofsson och Xiaodong ZouContact: Gunnar von Heine \n\n\n\n\n\n\n\nProgram & Abstracts\n\n\n\nCryonet_program_abstracts_finalDownload\n\n\n\n \n\n\n\nKeynote Speakers\n\n\n\n\nTamir Gonen\, UCLA\, USA\n\n\n\nEllen Zhong\, Princeton University\, USA\n\n\n\n\nConfirmed Speakers\n\n\n\n\nHenriette Autzen\, Univ. Copenhagen\, Denmark\n\n\n\nTristan Croll\, Altos Labs\, Cambridge\, UK\n\n\n\nFriedrich Förster\, Utrecht Bioinformatic Center\, The Netherlands\n\n\n\nEmil Kristoffersen\, Aarhus University\n\n\n\nKarin Lindkvist\, Lund University\, Sweden\n\n\n\nMisha Kudryashev\, Max Delbrück Center\, Berlin\, Germany\n\n\n\nShintaro Aibara\, AstraZeneca\, UK\n\n\n\nVille Paavilainen\, University of Helsinki\, Finland  \n\n\n\nAnastassis Perrakis\, NKI\, Amsterdam\, The Netherlands\n\n\n\nSuparna Sanyal\, Uppsala University\, Sweden \n\n\n\nLudovic Sauguet\, Institut Pasteur\, Paris\, France\n\n\n\nSuyang Zhang\, LMB-MRC\, Cambridge UK
URL:https://www.scilifelab.se/event/6th-cryonet-symposium-in-stockholm/
LOCATION:Arrhenius Laboratory\, Stockholm University\, Svante Arrhenius väg 16C\, Stockholm
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/02/ClpCP_Carroni.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231006T110000
DTEND;TZID=Europe/Stockholm:20231006T120000
DTSTAMP:20260404T132244
CREATED:20230816T080538Z
LAST-MODIFIED:20231005T084643Z
UID:10000954-1696590000-1696593600@www.scilifelab.se
SUMMARY:From sequences to structures\, from structures to biology - On homo-oligomers and co-translational assembly
DESCRIPTION:Speaker: Emmanuel Levy\, Weizmann \n\n\n\nHost: Arne Elofsson \n\n\n\nIn this talk\, I will provide an overview of our research\, emphasizing two recent pieces of work. The first goes from sequences to structures\, with the development of an atlas of homo-oligomerization spanning proteomes and lineages (https://www.biorxiv.org/content/10.1101/2023.06.09.544317v1). The second goes from structures to biology\, leveraging protein complexes’ structures to crack the code of co-translational assembly.
URL:https://www.scilifelab.se/event/from-sequences-to-structures-from-structures-to-biology-on-homo-oligomers-and-co-translational-assembly/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231010T080000
DTEND;TZID=Europe/Stockholm:20231010T170000
DTSTAMP:20260404T132244
CREATED:20230313T112350Z
LAST-MODIFIED:20231009T112407Z
UID:10000834-1696924800-1696957200@www.scilifelab.se
SUMMARY:SciLifeLab Day Linköping
DESCRIPTION:This event is a kick-off for the national SciLifeLab site in Linköping.\n\n\n\nLearn more about the services and capabilities that are offered from SciLifeLab\, both nationally and locally\, and how you can participate in the activities. \n\n\n\nWelcome to the SciLifeLab Day in Linköping. Here\, life-science researchers will have a unique opportunity to meet experts in research infrastructure\, participate in discussions on societal challenges and learn about what SciLifeLab have to offer both locally and nationally. \n\n\n\nExhibition\, poster session\, and mingle\n\n\n\nShow your research in a poster and take the opportunity to discuss how you can implement SciLifeLab’s advanced technologies with the infrastructure experts and visit the exhibitions or posters from the infrastructure units to learn what services they can offer you. \n\n\n\nRead more and find the program\n\n\n\nSciLifeLab etablerar nytt forskningssäte i Linköping\n\n\n\nProgram\n\n\n\nDetailed-program-SciLifeLab-Day-LinkopingDownload\n\n\n\n\n\n\n\nContact\n\n\n\n\n\nlinkoping@scilifelab.se \n\n\n\n\n\nJosefine SandströmLinköping UniversitySite Coordinator SciLifeLab Linköpingjosefine.sandstrom@liu.se\n\n\n\n\n\nSciLifeLab Days on the national sites\n\n\n\n\nGothenburg\, April 17\n\n\n\nUmeå\, September 11\n\n\n\nLund\, September 28\n\n\n\nLinköping\, October 10
URL:https://www.scilifelab.se/event/scilifelab-day-linkoping/
LOCATION:Campus US\, Linköping University\, Lasarettsgatan 20\, Linköping\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/08/1691583487328.jpg
ORGANIZER;CN="SciLifeLab Link%C3%B6ping":MAILTO:linkoping@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231011T120000
DTEND;TZID=Europe/Stockholm:20231011T130000
DTSTAMP:20260404T132244
CREATED:20231003T063653Z
LAST-MODIFIED:20231003T063813Z
UID:10000979-1697025600-1697029200@www.scilifelab.se
SUMMARY:Metabolomics at speed – can direct analysis fingerprinting metabolomics be used for rapid sample screening?
DESCRIPTION:On-line seminar by Alastair Ross\, Senior researcher/Metabolomics team lead at AgResearch\, New Zealand. \n\n\n\nArranged by Otto Savolainen\, Head of Unit\, Chalmers Mass Spectrometry Infrastructure (CMSI)\, Metabolomics Platform. \n\n\n\nRegistration
URL:https://www.scilifelab.se/event/metabolomics-at-speed-can-direct-analysis-fingerprinting-metabolomics-be-used-for-rapid-sample-screening/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Gothenburg":MAILTO:gothenburg@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231019T100000
DTEND;TZID=Europe/Stockholm:20231019T110000
DTSTAMP:20260404T132244
CREATED:20230906T070555Z
LAST-MODIFIED:20230907T142252Z
UID:10000966-1697709600-1697713200@www.scilifelab.se
SUMMARY:Using containers to simplify ML training on Berzelius and other supercomputers: beginner-friendly introduction
DESCRIPTION:This webinar is part of the Tools for AI/ML research in life sciences event series arranged by the SciLifeLab Data Centre. \n\n\n\nTitle: Using containers to simplify ML training on Berzelius and other supercomputers: beginner-friendly introduction \n\n\n\nSpeakers: AI engineers from the SciLifeLab Data Centre and application experts from Berzelius (NSC\, LiU). \n\n\n\nWhere and when: October 19\, 2023 at 10:00-11:00 Stockholm time\, online. Registration is open till Oct 18 at 24.00.  \n\n\n\nAbstract: A common approach to train machine learning models is to first create a prototype using a small dataset on a local machine to verify that it works and thereafter use a large scale compute infrastructure such as Berzelius for the full-scale training. One of the challenges with this approach however is incompatible systems in terms of differences in available software packages\, versions\, etc. An effective way to solve this issue is to use a container solution. Using a container environment allows a highly portable workflow and reproducible results between systems as diverse as a laptop\, Berzelius or EuroHPC resources such as LUMI for instance. During this beginner-friendly event\, we will introduce and demonstrate how to work with containers on Berzelius (Apptainer and Enroot) using an example from life sciences\, starting from raw data and finishing with a trained model. During the Q&A session\, the Berzelius life science support team will answer your questions. \n\n\n\nRegister to join the event\n\n\n\nMore about the event series: \n\n\n\nTools for AI/ML research in life sciences is an event series by the SciLifeLab Data Centre aimed at life science researchers who use machine learning methods in their work. The goal of the events in this series is to provide introductions to different tools for ML research but also to foster discussions around our practices and how they can be improved. The events takes place virtually (over Zoom) and are open to researchers in Sweden and beyond. Each event is scheduled for 60 minutes\, consisting of a talk and an extended discussion. Follow the page of the event series to learn about future seminars. \n\n\n\nFor questions about the events please contact the organizing team by emailing  serve@scilifelab.se  \n\n\n\n \n\n\n\nScientific lead: Prof. Ola Spjuth\, SciLifeLab Data Centre and Uppsala University \n\n\n\nContact information: serve@scilifelab.se
URL:https://www.scilifelab.se/event/using-containers-berzelius/
LOCATION:Online event via Zoom
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231023T151500
DTEND;TZID=Europe/Stockholm:20231023T161500
DTSTAMP:20260404T132244
CREATED:20231006T134540Z
LAST-MODIFIED:20231006T140206Z
UID:10000993-1698074100-1698077700@www.scilifelab.se
SUMMARY:[The Svedberg seminar] - Peptide nucleic acid (PNA)-mediated pretargeting for radionuclide therapy
DESCRIPTION:Amelie Karlström \n\n\n\nProfessor of Molecular BiotechnologyDepartment of Protein Science\, KTH \n\n\n\n \n\n\n\n\n\n\n\nBio\n\n\n\nAmelie Eriksson Karlström is Professor of Molecular Biotechnology at the Department of Protein Science\, KTH\, where her research group is focused on protein engineering\, affinity technologies and bioconjugation chemistry for diagnostic and therapeutic applications. Amelie Eriksson Karlström has a background in solid phase peptide synthesis methodology from PhD studies at the Department of Neurochemistry and Neurotoxicology at Stockholm University. She did postdoctoral studies at the Scripps Research Institute\, La Jolla\, CA\, working on catalytic antibodies and display technologies with Profs. Richard A. Lerner and Carlos Barbas\, III\, before starting her independent research at KTH \n\n\n\n \n\n\n\nPeptide nucleic acid (PNA)-mediated pretargeting for radionuclide therapy\n\n\n\nTargeted radionuclide therapy utilizes tumor-specific radiolabeled molecules to deliver cytotoxic radiation to tumor cells. To avoid unwanted exposure of non-tumor organs\, a pretargeting strategy can be used\, where the tumor-targeting step is uncoupled from the delivery of the toxic radionuclide. The primary agent is administered first and the secondary\, radiolabeled agent is administered after the primary agent has accumulated in the tumor and cleared from non-tumor tissue. We have developed and evaluated a system for pretargeting based on the high selectivity and high affinity of peptide nucleic acid (PNA) hybridization. We have demonstrated that the PNA-based pretargeting system gives high tumor-to-normal tissue contrast in vivo both using affibody molecules and monoclonal antibodies as the tumor-targeting agents.  \n\n\n\nIn this seminar\, the molecular design and technological aspects of the PNA-based pretargeting system will be discussed. Results from preclinical evaluation of the PNA-based pretargeting strategy will be presented.  \n\n\n\n \n\n\n\n\n\n\n\n\n\n\n\nHost: Abhimanyu Thakur\,UU
URL:https://www.scilifelab.se/event/the-svedberg-seminar-amelie-karlstrom/
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
ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231024T090000
DTEND;TZID=Europe/Stockholm:20231024T190000
DTSTAMP:20260404T132244
CREATED:20231018T073920Z
LAST-MODIFIED:20231024T071000Z
UID:10001002-1698138000-1698174000@www.scilifelab.se
SUMMARY:SciLifeLab Campus Solna Science Talks
DESCRIPTION:We would hereby like to warmly welcome you to take part in this year’s Campus Solna Science Talks symposium on October 24th – a meeting for everyone in the community to learn more about ongoing research and activities at SciLifeLab’s Campus Solna\, which aims to bring the community together\, inspire exchange and new collaborations. \n\n\n\nResearch presentations will be given by group leaders and junior researchers (selected with consideration for balance in topics\, presenters’ career stages\, and affiliations) as part of a plenary session between 9:00 and 16:00 (including lunch)\, and the event will conclude with a poster session\, mingle and food in Campus Solna’s meeting place Delta.  \n\n\n\nWe invite all Campus Solna research groups to be represented with at least 1 poster (and maximum 3). Furthermore\, we want to encourage all infrastructure units and committees (The Diversity\, Equity and Inclusion-committee\, the Public Engagement-committee\, the CSI and the PhD- & Postdoc-council) to partake with posters! \n\n\n\nList of Posters (titles & numbering) \n\n\n\n\n\n\n\n \n\n\n\n\n\n\n\nProgram\n08:30Arrival\, registration and coffeeJacob Berzelius hall\, Karolinska Institutet09:00Welcome and opening of symposiumScientific Committee & Per LjungdahlSession I. Moderator Yerma Pareja09:15Mapping B and T cell receptors using spatial transcriptomicsCamilla Engblom09:30Use the Flow\, Leukocyte: ion and water fluxes are required for T cell migrationLeon de Boer09:45B cell repertoire analysis of SARS-CoV-2-infected individualsGunilla Karlsson Hedestam10:15Coffee BreakSession II. Moderator Marcel Tarbier10:45agoTRIBE detects microRNA-target interactions transcriptome-wide in single cellsVaishnovi Sekar11:00Single cell-resolution in situ sequencing elucidates spatial dynamics of multiple sclerosis lesion and disease evolutionChristoffer Mattsson Langseth11:15Beyond the host’s spatial transcriptomeStefania Giacomello11.30Machine learning of immune escape dynamics from single cell and spatial tumor transcriptomicsJakob Rosenbauer11.45LunchSession III. Moderator Ute Hoffmann13:00Female sex hormones and the human microbiomeLuisa Hugherth13:15Environmental genomics for broadscale studies on aquatic microbial diversity and evolutionKrzysztof Jurdzinski13:30Interaction proteomics to explore protein regulation in photosynthetic organismsAnna Karlsson13:45Developmental Gene TranscriptionMattias Mannervik14:15Coffee BreakSession IV. Moderator Erdinc Sezgin14:45Modelling Glut1 Deficiency Syndrome (Glut1DS) for therapeutics and drug discoveryRekha Tripathi15:00Multiplexed high-content screening of drug and immune sensitivity in microwellsValentina Carannante15:15Dynamics at the molecular scale from cells to STARSSIlaria Testa15:45Concluding RemarksPer Ljungdahl16:00Poster SessionSciLifeLab DeltaMingle\, pub and light food\n\n\n\n \n\n\n\n \n\n\n\n\n\n\n\n\nPoster Session\nEach group/unit is welcome to bring up to 3 posters to the grand Poster Session that will follow the talks. Submit the poster titles in the registration form. Please coordinate within your research group/unit beforehand who should bring a poster. Poster session will take place in the Delta building in SciLifeLab Solna. \n\n\n\nPoster dimensions: 70×100 \n\n\n\n \n\n\n\n\n\n\n\n\nScientific Committee\nThis event has been made possible through the hard work of the Scientific committee. \n\n\n\nScientific Committee \n\n\n\n\nErdinc Sezgin\n\n\n\nMarcel Tarbier\n\n\n\nUte Hoffman\n\n\n\nStefania Giacomello\n\n\n\nKristoffer Sahlin\n\n\n\nPer Ljungdahl\n\n\n\n\nOperations Office representatives \n\n\n\n\nIsolde Palombo\n\n\n\nDisa Larsson Hammarlöf
URL:https://www.scilifelab.se/event/scilifelab-campus-solna-science-talks-2/
LOCATION:Jacob Berzelius salen\, KI\, Berzelius väg 3\, Solna\, 171 65\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/07/181A6885-Danish-Saroee_frikopt-scaled.jpg
ORGANIZER;CN="SciLifeLab Event":MAILTO:events@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231031T130000
DTEND;TZID=Europe/Stockholm:20231031T160000
DTSTAMP:20260404T132244
CREATED:20231010T074915Z
LAST-MODIFIED:20231020T074900Z
UID:10000996-1698757200-1698768000@www.scilifelab.se
SUMMARY:I Forskningens Framkant - Fortbildning för Gymnasielärare
DESCRIPTION:Välkommen till en fortbildning där du får uppleva delar av det nationella forskningscentret för molekylära biovetenskaper i Stockholm. \n\n\n\nDenna eftermiddag får du möta fyra forskare som berättar om sin forskning och så gör vi en rundvandring på SciLifelab. Fortbildningen avslutas med mingel med tilltugg. \n\n\n\nProgram12:30-13:00 Kaffe13:00-14:30 Föreläsningar – fyra forskare från SciLifeLab14:30-15:00 Visning av labb15:00-16:00 Mingel med tilltugg \n\n\n\nPlats: SciLifeLab\, Tomtebodavägen 23\, SolnaKarta: Google Maps \n\n\n\nVälkommen med din anmälan! \n\n\n\nRegistrering\n\n\n\nFrom Genes to Proteins: The Power of the Human Protein AtlasFredrik Edfors\, SciLifeLab/KTHFramtidens målsökande läkemedelStefan Ståhl\, SciLifeLab/KTHKlinisk GenomikAnna Lyander\, SciLifeLab/Karolinska InstitutetMikrobernas samhällenAnders Andersson\, SciLifeLab/KTH14:00-15:00 Rundvandring i lokalerna15:00-16:00 Mingel med tilltugg \n\n\n\n \n\n\n\nFrom Genes to Proteins: The Power of the Human Protein AtlasFredrik Edfors\, SciLifeLab/KTH \n\n\n\nHuman Protein Atlas (HPA) som finansieras av Knut och Alice Wallenbergs stiftelse är ett svenskt projekt som är baserat på SciLifeLab\, en nationell samarbetsplattform för molekylär biologi som drivs av KTH\, Karolinska Institutet\, Stockholms universitet och Uppsala universitet. Människan har cirka 20 000 gener som kodar för proteiner\, och HPA hjälper till att identifiera olika kombinationer av proteiner som är avgörande för mänsklig biologi. HPA strävar efter att systematiskt kartlägga det mänskliga genomet på proteinnivå och på www.proteinatlas.org presenteras dessa nivåer inom flera olika fokusområden. Dessa inkluderar bland annat inkluderar proteinuttryck i vävnader\, hjärna\, cell-linjer eller nivåer blod och hur dessa skiljer sig mellan olika sjukdomstillstånd. Förutom att stödja andra forskare är atlasen också en värdefull utbildningsresurs för ämnen som rör den mänskliga kroppen\, cellbiologi och molekylärbiologi.  \n\n\n\nFramtidens målsökande läkemedelStefan Ståhl\, SciLifeLab/KTH \n\n\n\nSmå bindarproteiner kan med hjälp av riktad evolution fås att binda till sjukdomsrelaterade proteiner\, så kallade biomarkörer\, som kan utnyttjas som måltavlor för nya typer av proteinläkemedel. Som exempel kan cancertumörceller målsökas på detta sätt. Dessa målsökande bindarproteinerna kan “beväpnas”\, t.ex. med cellgifter eller lämpliga radioisotoper som dödar tumörcellerna\, med minimal påverkan på frisk vävnad. \n\n\n\nKlinisk GenomikAnna Lyander\, SciLifeLab/Karolinska Institutet \n\n\n\nClinical Genomics är en infrastrukturplattform vid Scilifelab. Plattformen arbetar med avancerade genomikmetoder\, olika typer av sekvenseringsteknologier och dataanalysverktyg\, för att stötta forskning och sjukvård. Clinical Genomics erbjuder en helhetslösning inom next generation sequencing för translationella forskningsprojekt och kliniska studier\, och bidrar till att optimera tekniker så att de kan användas inom precisionsmedicin. Plattformen arbetar också inom ramen för Genomic Medicine Sweden för att harmonisera precisionsmedicin i Sverige vilket banar väg för bättre diagnostik\, vård och behandling i hela landet. \n\n\n\nMikrobernas samhällenAnders Andersson\, SciLifeLab/KTH
URL:https://www.scilifelab.se/event/i-forskningens-framkant-fortbildning-for-gymnasielarare/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Event":MAILTO:events@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231106T100000
DTEND;TZID=Europe/Stockholm:20231107T170000
DTSTAMP:20260404T132244
CREATED:20230509T092633Z
LAST-MODIFIED:20231020T075809Z
UID:10000882-1699264800-1699376400@www.scilifelab.se
SUMMARY:21st Swedish Bioinformatics Workshop 2023 in Stockholm
DESCRIPTION:We’re pleased to invite you to the 21st Swedish Bioinformatics Workshop (SBW) that will take place in Stockholm on November 6th – 7th (Mo-Tu). SBW is an annual event that is hosted by different universities across Sweden. This year\, the event will take place at Karolinska Sjukhuset Solna at the Sune Bergström’s Aula. \n\n\n\nAs is tradition\, SBW will be a chance for PhD students and postdocs as well as all researchers working with bioinformatics or computational biology to present their work\, discuss the latest developments in the field\, and improve their bioinformatic skills through different workshops. In addition\, the program includes lectures from invited speakers\, participant presentations\, and poster sessions. \n\n\n\nThis year SBW is part of the Nordic Computational Biology Week. It features SBW (6th-7th of Nov.\, Mo-Tu)\, the Danish Bioinformatics Symposium (8th-9th of Nov.\, We-Th) and the Finish Symposium on Computational Biology (10th of Nov.\, Fr). More information can be found under: bit.ly/ncb-week-2023 \n\n\n\nMore information regarding SBW will be updated on the website: sbw2023.eu. On-site registration is closed\, but you can still sign up for free for virtual attendance. There you can also sign up for the other events that are part of the Nordic Computational Biology Week. If you have any questions\, feel free to reach out to sbw2023@scilifelab.se. \n\n\n\nWelcome to the Swedish Bioinformatics Workshop 2023!
URL:https://www.scilifelab.se/event/swedish-bioinformatics-workshop-2023/
LOCATION:Sune Bergström Aula\, BioClinicum\, New Karolinska University Hospital\, Solnavägen 30\, Stockholm\, 17164\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/05/SBW2023_logo_green_tb1-1024x327-1.png
ORGANIZER;CN="Swedish Bioinformatics Workshop 2023":MAILTO:sbw2023@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231107T130000
DTEND;TZID=Europe/Stockholm:20231107T140000
DTSTAMP:20260404T132244
CREATED:20231030T125153Z
LAST-MODIFIED:20231030T132952Z
UID:10001009-1699362000-1699365600@www.scilifelab.se
SUMMARY:Discovery of SARS-CoV-2 Main Protease inhibitors at the DDD platform
DESCRIPTION:Pandemic preparedness and the generation of SARS-CoV-2 inhibitors – A new exit from SciLifeLab Drug Discovery and Development platform \n\n\n\nDDD Exit Event 2023-11-07\, zoomcast 13.00 \n\n\n\n \n\n\n\nPresenters\n\n\n\nDr. Ulf Ribacke. Dept. of Microbiology\, Tumor and Cell Biology\, Karolinska InstitutetTel: +46 70 497 5196\, Email: ulf.ribacke@ki.se \n\n\n\nProf. Jens Carlsson\, Dept. of Cell and Molecular Biology\, Uppsala UniversityTel: +46 72 227 7976\, Email: jens.carlsson@icm.uu.se \n\n\n\nAbstract\n\n\n\nSciLifeLab has been commissioned by the government to build laboratory capacity to assist in future pandemics through research and competence and technology development. Hear more about the SciLifeLab Pandemic Laboratory Preparedness program from Ulf Ribacke\, (SciLifeLab and Karolinska Institutet) and groundbreaking research performed by researchers at Uppsala University that led to discovery of potent main protease SARS-CoV-2 inhibitors. \n\n\n\nJens Carlsson\, Helena Danielson\, Anja Sandström and Lindon Moodie have recently signed an agreement for international partnering of a project focusing on development of drugs for treatment of COVID-19 (DP_JC_188). \n\n\n\nThe project was funded by the National COVID-19 Research Program initiated by the Knut and Alice Wallenberg Foundation. Hit compounds identified by virtual screening were published in 2022 by Luttens et al. (https://doi.org/10.1021/jacs.1c08402). Hit-to-lead generation was then performed together with the Drug Discovery and Development Platform in the DP_JC_188 project. Lead optimization and preclinical development of assets are now supported by an international pharmaceutical company. \n\n\n\nShort speakers biography:\n\n\n\nUlf Ribacke: Ulf is scientific co-director of the SciLifeLab Pandemic Laboratory Preparedness program and heads two research labs located at Karolinska Institutet and Uppsala University\, both dedicated to resolve how malaria parasites adapt to evade cellular stress with the ultimate goal to identify targets for new interventions. \n\n\n\nJens Carlsson: Jens is a Professor of Computational Biochemistry at Uppsala University\, where his group uses computational models to understand protein function at the molecular level and develops strategies for drug discovery.For more information\, visit http://www.carlssonlab.org/. \n\n\n\nUlf RibackeKarolinska InstitutetScientific Lead – Pandemic Laboratory Preparedness at SciLifeLabulf.ribacke@ki.se\n\n\n\nJens CarlssonUppsala Universityjens.carlsson@icm.uu.se
URL:https://www.scilifelab.se/event/discovery-of-sars-cov2-mpro-inhibitors-at-the-ddd-platform/
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231109T100000
DTEND;TZID=Europe/Stockholm:20231109T153000
DTSTAMP:20260404T132244
CREATED:20231009T132350Z
LAST-MODIFIED:20231026T114542Z
UID:10000995-1699524000-1699543800@www.scilifelab.se
SUMMARY:The Spatial Biology Tour 2023 - the Spatial Proteomics Unit and Lunaphore
DESCRIPTION:The Spatial Proteomics Unit at SciLifeLab hosts the Lunaphore Spatial Biology Tour at SciLifeLab Solna.  \n\n\n\nTake the opportunity to learn more about the COMET platform for automated sequential immunofluorescence and how you can work with the Spatial Proteomics Unit to generate highly multiplexed imaging data for your research project.  \n\n\n\nThe Spatial Proteomics Unit was an early beta tester of the COMET platform in 2021 and since 2022 offer the COMET platform as a service in their unit. You will also get the chance to see the instrument live in the Spatial Proteomics unit. \n\n\n\nRead more and register here\n\n\n\n\n\n\n\nMultiplexed image of a colon FFPE sample generated on the COMET platform\n\n\n\n \n\n\n\nProgram\n\n\n\n10:00Welcome and registration10.15Spatial cell profiling with hyperplex immunofluorescenceAngelo Da Rosa11.00COMET – opportunities in the Spatial Proteomics FacilityCharlotte Stadler11.45RNAscope™: Single-molecule RNA in situ hybridization. ANY Gene. ANY Species. ANY tissue.Joan Raouf12.15Lunch and networking13.00COMET™ on-site instrument demonstration14.15Refreshment and networking
URL:https://www.scilifelab.se/event/the-spatial-biology-tour-2023-the-spatial-proteomics-unit-and-lunaphore/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/10/COMET-colon.png
ORGANIZER;CN="Spatial Proteomics Unit":MAILTO:spatial.proteomics@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231115T123000
DTEND;TZID=Europe/Stockholm:20231116T123000
DTSTAMP:20260404T132244
CREATED:20230119T182051Z
LAST-MODIFIED:20231114T233510Z
UID:10000792-1700051400-1700137800@www.scilifelab.se
SUMMARY:DDLS Annual Conference 2023; The emerging role of AI in data-driven life science
DESCRIPTION:Image generated with DALL-E 3\n \n\n\n\n\n\n\n\n\nThis DDLS Annual Conference brings together the data-driven community in Life Science\, introduces newly appointed DDLS fellows\, and provides opportunities for networking across the research community and SciLifeLab infrastructures. The theme for 2023 is “the emerging role of AI in data-driven life science”\, and we are excited to welcome Prof. Dr. Fabian Theis\, Director of the Computational Health Center and Director of the Institute for Computational Biology and Rocio Mercado\, WASP Fellow\, Chalmers University of Technology as Keynote speakers. There will be presentations from DDLS fellows\, and invited speakers on how they use AI in their research and their future visions. The conference also features two pre-conference introductory lectures on AI for imaging and natural language processing and a post-conference workshop on AI model serving. \n\n\n\nTarget group: All scientists interested in data-driven research are welcome to join the 2-day lunch-to-lunch Conference in Stockholm. \n\n\n\nRegistration\n\n\n\nThe onsite event has reached total capacity. Please register as a Zoom participant to get access to the Zoom link. Feel free to add yourself to the waiting list\, and you will be notified by email if a place becomes available. \n\n\n\nRegistration for zoom link\n\n\n\n\n\n\n\nPoster session\n\n\n\nPoster session\, Flash Talk & Best Poster Award (click to open)\nPoster list \n\n\n\nPoster-List-DDLS-Annual-conference-2023Download\n\n\n\nPoster booklet\, including abstracts \n\n\n\nPoster-Booklet-DDLS-Annual-conference-2023Download\n\n\n\nThe DDLS Annual Conference Best Poster Award\, encourages the submission and exhibition of high-quality posters carried out by young scientists\, including Ph.D. students\, post-doctoral researchers\, etc. The poster should be on a topic related to data-driven life science. The Prize\, which is based upon the decision of a Scientific Committee-appointed Jury\, consists of a certificate and a travel grant of up to 5 000 SEK. The travel must be booked and ordered through the DDLS Support team and follow regular University travel policy. The trip should be completed before 2024-12-31. \n\n\n\nThe Best Poster Award winner for 2022 was Adelina Rabenius\, KTH\, and we are proud to support her attendance at an EMBO conference this summer. \n\n\n\nOrganizer: SciLifeLab\, host of SciLifeLab & Wallenberg National Program for Data-Driven Life Science\, on behalf of the DDLS Steering group. \n\n\n\n\nPre-conference introductory lectures \n\n\n\nIn the morning of the first conference day\, there will be two introductory lectures; one on AI within image analysis (by Anna Klemm from Bioimage Informatics Facility\, SciLifeLab) and one on large-language models (by Magnus Sahlgren from AI Sweden). The purpose of these lectures is to cover the basics and emerging role of AI within these two active fields. No prior knowledge of the fields is required. \n\n\n\nPost-conference activities\n\n\n\nNote! The Post-conference workshop and different DDLS stakeholder meetings will be handled separately and require separate registrations. \n\n\n\nWorkshop\n\n\n\nBuilding and sharing machine learning demo applications within life sciences: a practical tutorial. This event is now full\, you can register for the wait list only (in case we receive a cancellation). November 16\, at 13:30 – 15:30. SciLifeLab Campus Solna\, Tomtebodavägen 23. Meet-up in the Lobby. Room Gamma 2 Lunchroom.  Participant list here \n\n\n\nStakeholder meetings\n\n\n\nDDLS Fellows meeting (DDLS Fellows only). November 16\, at 13:30 – 15:30. Biomedicum\, Solnavägen 9. Room B0317. Participant list here \n\n\n\nDDLS Fellows PhD & Postdocs meeting (for the PhD and Postdoc members of the DDLS Fellows research groups). November 16\, at 13:30 – 15:30. Biomedicum\, Solnavägen 9. Room B0313. Participant list here \n\n\n\nDDLS Cell and Molecular Biology Expert group meeting (for the CMB Expert group and the CMB Data Science Node). November 16\, at 15:30 – 17:30. SciLifeLab Campus Solna\, Tomtebodavägen 23. Room Earth \n\n\n\n\nDDLS Research area Cell and Molecular Biology Symposium\, Nov 17\n\n\n\nThe DDLS research area\, Cell and molecular biology\, invites you to the first in-person symposium on November 17 from 9 to 14. The day will be an introduction to the research area Fellows and Expert Group.  \n\n\n\nMore information here\n\n\n\n\nProgram\n\n\n\nNovember 15\n\n\n\n09:30Venue: Jacob Berzeliussalen\, Berzelius väg 3\, SolnaRegistration is open from 09:30. Hang your poster from 09:30 to 12:30.10:00Pre-conference introductory lecture: AI in bioimage analysisAnna Klemm\, Uppsala University10:45Pre-conference introductory lecture: Large Language ModelsMagnus Sahlgren\, AI Sweden11:30Lunch12:30WelcomeOla Spjuth\, chair of Scientific Committee DDLS Annual ConferenceModerator: Ola Spjuth\, Uppsala University12:35Data-driven Life ScienceOlli Kallioniemi\, Director SciLifeLab13:00Blood proteome is a powerful tool to monitor human health and diseaseWen Zhong\, DDLS Fellow\, Linköping University 13:20Artificial intelligence-based computational pathology for precision diagnostics in breast cancerMattias Rantalainen\, KI13:40Coffee break 14:10Keynote: Generative AI for modeling single-cell state and responseFabian J. Theis\, Helmholtz Munich\, Technical University of Munich15:00Short breakModerator: Fredrik Johansson\, Chalmers15:155 x Flash Talks à 5 min per selected poster1. Gonzalo Uribarr2. Melisa Maidana Capitan3. Marcel Tarbier4. Sheng Joevenller5. Philipp Rentzsch 15:45Poster session with snacks and drinks17:30End of Day 117:30Speakers Dinner. Invited only. Speakers\, DDLS Steering Group\, DDLS Fellows\, Organizing committee\n\n\n\nNovember 16\n\n\n\n08:30CoffeeModerator: Laura Carroll\, Umeå University09:00From super resolution microscopy to modelling: how proteins spatial distribution regulates cellular processesJuliette Griffé\, DDLS Fellow\, Stockholm University09:20Multi-omics data integration with robust penalized regression identifies context-dependent signaling networksCemal Erdem\, DDLS Fellow\, Umeå University09:40AICell Lab: Laying the AI Foundation for Data-Driven Whole-Cell ModelingWei Ouyang\, DDLS Fellow\, KTH10:00Data Centre – capabilities and collaborationsJohan Rung\, SciLifeLab Data centre10:20Coffee break10:45Announcement of Best Poster Award10:50Keynote: Transforming Biomolecular Engineering Through AIRocio Mercado\, WASP Fellow\, Chalmers University of Technology Moderator: Johan Bengtsson-Palme\, Chalmers11:45Panel discussion about the emerging role of AI in DDLS12:30Lunch and end of DDLS Annual Conference13:30Post-Conference activities (separate registration)Building and sharing machine learning demo applications within life sciences: a practical tutorial. The event is fully booked.SciLifeLab Campus Solna\, Tomtebodavägen 23A. Room Gamma lunch room.DDLS Fellows meetingBiomedicum\, Solnavägen 9. Room B0317.DDLS Fellows PhD & Postdoc meetingBiomedicum\, Solnavägen 9. Room B0313.15:30End of Post-Conference activities15:30DDLS Cell and Molecular Biology Expert group meetingSciLifeLab Campus Solna\, Tomtebodavägen 23A. Room Earth.\n\n\n\nAbstracts\n\n\n\nPre-Conference Lectures\n\n\n\nAnna Klemm – AI in bioimage analysis\nIn this introductory lecture I will present how AI is used in bioimage analysis. The lecture will start with examples of “classical” image analysis to then explain the concepts of machine learning and AI-techniques in bioimage analysis. In the lecture I will give examples of life science projects in which we have trained convolutional neural networks to segment and classify structures of interest in the images\, or encode entire images. I will explain why we chose AI-based methods over classical image analysis and will also point to resources of the growing landscape of workflows\, pre-trained networks\, and repositories of freely available bioimage data + their annotations. \n\n\n\n\n\n\n\nExample of using a CNN for image segmentation on H&E-stained sections of mouse salivary glands. Segmentation starting from manually generated ground-truth\, using a Xception network model. Source: https://biifsweden.github.io/projects/2023/08/07/EduardoVillablanca2023-1/\, Xenia Tolstoy\, Christophe Avenel (BIIF) \n\n\n\n\nMagnus Sahlgren – Large Language Models\nThis presentation gives an introduction to and overview of the currently dominating trend in AI with Large Language Models (LLMs). We cover the theoretical background\, basic architectures\, training methodologies\, and capabilities of LLMs\, spotlighting models like the GPT series\, as well as Sweden’s national initiative GPT-SW3. We will touch upon diverse applications of LLMs in both the public and private sectors\, and address various considerations and challenges related to LLMs\, including biases\, transparency\, and societal implications. \n\n\n\n\nConference\n\n\n\nMartin Eklund – Prediction models and artificial intelligence for improving prostate cancer diagnostics and treatment\nProstate cancer diagnostics and treatment suffer from inefficient use of information for clinical decision making\, leading to high rates of overdiagnosis and overtreatment of indolent disease at the same time as prostate cancer is the leading cause of cancer death among men. We will in our presentation discuss how we are systematically trying to develop and clinically implement prediction models and artificial intelligence (AI) systems to address these inefficiencies. We will for example discuss the combination of the Stockholm3 test with MRI to improve prostate cancer diagnostics (Eklund et al. NEJM\, 2021; Nordström et al. Lancet Oncology\, 2021)\, and show results from the development of an AI-system for diagnosis and grading of prostate cancer in biopsies (Ström et al. Lancet Oncology\, 2020; Bulten et al. Nature Medicine\, 2022; Olsson et al. Nature Communications 2022)\, which we have demonstrated can performs on par with internationally leading uro-pathologist. We will also discuss the link between AI and clinical trials and how clinical trials can be transformed into continuous learning systems\, which we will exemplify with the ongoing ProBio trial for improving treatment for men with metastatic prostate cancer (Crippa et al. Trials\, 2020; De Laere et al. European Urology Focus\, 2022). \n\n\n\n\nCemal Erdem – Multi-omics data integration with robust penalized regression identifies context-dependent signaling networks\nCells integrate signals from different external stimuli to decide their fate\, such as growth or death. The “context” of a cell -the extracellular and intracellular environments- dictates the structure of signaling networks that determine such cellular responses. Identifying context-specific edges is vital for predicting and understanding cell decision-making logic. However\, robust identification of context-dependent network structures remains a broadly unsolved problem. Here\, I will talk about a pipeline we built previously to integrate multi-omics datasets using machine learning algorithms in a central-dogmatic view. Applying this pipeline to publicly available datasets\, we showed that it could pinpoint differentially activated pathways: (i) in response to two highly similar sister cytokines in breast epithelial cells and (ii) in breast tumor subtypes. I will conclude my talk with a vignette showing how such knowledge can further be utilized to explore new gene regulatory mechanisms. \n\n\n\n\nJuliette Griffié – From super resolution microscopy to modelling: how proteins spatial distribution regulates cellular processes\nSingle Molecule Localisation Microscopy (SMLM) is a fluorescence super-resolution microscopy technique which allows to image fluorophores in cells with unprecedented resolution (typically 10-30nm). It produces lists of localisations from which fundamental information about key cellular processes can be extracted. We will focus here on how SMLM data sets can be used as input to design dynamic models on cellular membrane biophysics. We will apply these data-driven models to reliably recapitulate and predict the nanoscale requirements for immune cells activation as well as to control and modify cellular signalling in the context of diseases. \n\n\n\n\nRocío Mercado – Transforming Biomolecular Engineering Through AI\nAI’s lightning-paced advancements are ushering in a new era of scientific research\, and the realm of molecular engineering stands as a prime beneficiary of this transformation. This talk explores the growing integration of AI in the life sciences\, with a primary emphasis on therapeutic discovery\, shedding light on the current state-of-the-art for molecular discovery and future prospects. We delve into the evolution of deep generative models and their practical applications in molecular engineering\, giving a few key examples of reinforcement learning and synthesizability-constrained design in this domain. Moreover\, we share recent progress in challenging application areas\, such as targeted protein degradation and synthesis prediction. With adaptive AI models\, capable of learning from vast datasets in real time\, we can streamline computational and experimental resources\, improving efficiency as we search through the complex chemical space. The talk will conclude with an overview of leading developments in AI which have yet to see widespread application in the life sciences\, offering new horizons for scientists exploring data-driven life science research. These innovative methodologies hold the potential to reshape conventional practices and bridge the gap between scientific exploration and AI-driven innovation. \n\n\n\n\nWei Ouyang – AICell Lab: Laying the AI Foundation for Data-Driven Whole-Cell Modeling\nAs part of the Data-Driven Life Science fellows program at SciLifeLab\, AICell Lab is actively laying the groundwork for a future powered by AI in cellular and molecular biology. With a focus on long-term strategic planning\, the lab is investing in state-of-the-art automated imaging farms\, complete with advanced microscopes\, robotic arms\, liquid handlers\, and automatic incubators. \n\n\n\nIn addition\, AICell Lab is developing specialized AI software to augment real-time microscopic imaging\, enable smart acquisition\, facilitate robotic control\, integrate multi-omics data\, and power AI-driven cell simulators\, among other functionalities. These preparatory steps align with the lab’s long-term vision to build large-scale\, comprehensive models of human cells\, utilizing both existing multi-omics datasets and new data generated in-house. \n\n\n\nThrough this focused preparation and investment\, AICell Lab aims to redefine in-silico cellular research and drug discovery\, contributing to a unified and systematic understanding of human cellular biology. \n\n\n\n\nFabian J. Theis – Generative AI for modeling single-cell state and response\nAdvances in single cell genomics nowadays allow the large scale construction of organ atlases. These can be used to study perturbations such as signaling\, drugs or diseases\, with large-scale access to state changes on the multi-omic and spatial level. This provides an ideal application area for machine learning methods to understand cellular response. With generative AI revolutionizing many fields of science by allowing researchers to explore uncharted territories\, generate novel hypotheses\, and simulate complex phenomena\, we ask how it has been enabling modeling single cell variation\, potentially towards a single cell foundation model. \n\n\n\nAfter reviewing deep generative representation learning approaches to identify the gene expression manifold\, I will shortly outline some applications on cell atlas building. Then I will discuss interpretable modeling of perturbations on this manifold\, in particular effect of drug responses as well as multiscale readouts such as disease state across patients\, and how to learn organism-wide cell type predictors. I will finish with extensions towards temporal and spatial observations. \n\n\n\n\nWen Zhong – Blood proteome is a powerful tool to monitor human health and disease\nThe rise of high throughput molecular technologies has shed lights on the development of next-generation molecular diagnostics and biomarkers for patient stratifications in the precision medicine era. There is an urgent need to develop new systematic tools to combine multi-omics data and link genotype to phenotype to expand our knowledge of complex traits of human diseases. Our research group mainly focuses on the integration of multi-omics\, the interplay between genetics and phenotypes\, and the development of data-driven strategies/tools for precision medicine. The aim is to investigate the molecular biomarkers for the estimation of disease risks\, early diagnosis of disease\, stratification of drug treatment response\, disease progression monitoring and the stratification of patients.  \n\n\n\n\nWorkshop \n\n\n\nBuilding and sharing machine learning demo applications within life sciences: a practical tutorial\nIt is becoming increasingly popular to share machine learning models with the community as web applications with an easy-to-use interface. Users can then adjust parameters or submit their own input and see the predictions generated by the underlying model. This tutorial is aimed at researchers working within life sciences who work with machine learning models but do not have the skills to build applications for web. During the tutorial we will start from a trained model and demonstrate step by step how you can create a graphical user interface for your application\, prepare it for deployment\, and make it available on the web with a URL. We will demonstrate the use of specific tools which make this process easy and doable within a couple of hours. \n\n\n\nThe workshop will last for 2 hours with a break in the middle. We have room to accept 30 participants\, on the first come first served basis. Those registered after that will be placed on the waiting list. \n\n\n\nNote that registration for the workshops is separate from the registration for the conference. Please see the workshop page for information on registration. \n\n\n\n \n\n\n\n\nScientific Committee\n\n\n\n\nChair: Ola Spjuth\, Uppsala University\n\n\n\nJohan Bengtsson-Palme\, Chalmers\n\n\n\nLaura Carroll\, Umeå University\n\n\n\nFredrik Johansson\, WASP\, Chalmers\n\n\n\n\nProject leader\n\n\n\n\nErika Erkstam\, Operations office
URL:https://www.scilifelab.se/event/ddls-annual-conference-2023/
LOCATION:Jacob Berzelius salen\, KI\, Berzelius väg 3\, Solna\, 171 65\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/DDLS_cropped-Liten.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231116T093000
DTEND;TZID=Europe/Stockholm:20231116T170000
DTSTAMP:20260404T132244
CREATED:20231004T141040Z
LAST-MODIFIED:20231109T155333Z
UID:10000989-1700127000-1700154000@www.scilifelab.se
SUMMARY:New Horizons for Swedish Sciences: World-unique (Bio)Solids Capabilities at the national UMU NMR facility
DESCRIPTION:Inauguration of world-unique combined solid-state NMR equipment (MAS CryoNMR Probe + Ultrafast MAS NMR Probe) for the next application level in sciences ranging from bio and medical sciences to novel material and environment. Equipment is installed at the Umeå University KBC NMR core facility\, a national SciLifeLab and VR-RFI (SwedNMR) node. \n\n\n\nRead more\n\n\n\nProgram \n\n\n\nProgramInaugurationNMR20231116finalDownload
URL:https://www.scilifelab.se/event/new-horizons-for-swedish-sciences-world-unique-biosolids-capabilities-at-the-national-umu-nmr-facility/
LOCATION:Carl Kempe-salen\, KBC Building\, Umeå University\, Umeå\, Sweden
CATEGORIES:Event
ORGANIZER;CN="Swedish NMR Centre":MAILTO:info@nmr.gu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231116T133000
DTEND;TZID=Europe/Stockholm:20231116T153000
DTSTAMP:20260404T132244
CREATED:20231017T130803Z
LAST-MODIFIED:20231101T115949Z
UID:10001003-1700141400-1700148600@www.scilifelab.se
SUMMARY:Building and sharing machine learning demo applications within life sciences: a practical tutorial
DESCRIPTION:This workshop is part of the DDLS Annual Conference 2023: The emerging role of AI in data-driven life science. This event is also part of Tools for AI/ML research in life sciences event series arranged by the SciLifeLab Data Centre. \n\n\n\nTitle: Building and sharing machine learning demo applications within life sciences: a practical tutorial \n\n\n\nOrganizer: AI Data Engineers from the SciLifeLab Serve team. \n\n\n\nWhere and when: November 16\, 2023 at 13:30-15:30 at SciLifeLab Solna (Tomtebodavägen 23A\, Solna) \n\n\n\nAbstract: It is becoming increasingly popular to share machine learning models with the community as web applications with an easy-to-use interface. Users can then adjust parameters or submit their own input and see the predictions generated by the underlying model. This tutorial is aimed at researchers working within life sciences who work with machine learning models but do not have the skills to build applications for web. During the tutorial we will start from a trained model and demonstrate step by step how you can create a graphical user interface for your application\, prepare it for deployment\, and make it available on the web with a URL. We will demonstrate the use of specific tools which make this process easy and doable in under an hour. \n\n\n\nThe workshop will last for 2 hours with a break in the middle.  We have room to accept 30 participants\, on the first come first served basis. Those registered after that will be placed on the waiting list. \n\n\n\nSince there is a limited number of spots in this workshop please sign up only if you intend to attend. \n\n\n\nThis event is now full\, you can register for the waiting list only (in case we received a cancellation). We will organize similar workshops in the future\, it will be announced in the same event series. \n\n\n\nRegister to join the event\n\n\n\nMore about the event series: \n\n\n\nTools for AI/ML research in life sciences is an event series by the SciLifeLab Data Centre aimed at life science researchers who use machine learning methods in their work. The goal of the events in this series is to provide introductions to different tools for ML research but also to foster discussions around our practices and how they can be improved. The events takes place virtually (over Zoom) and are open to researchers in Sweden and beyond. Each event is scheduled for 60 minutes\, consisting of a talk and an extended discussion. Follow the page of the event series to learn about future seminars. \n\n\n\nFor questions about the events please contact the organizing team by emailing  serve@scilifelab.se  \n\n\n\n \n\n\n\nScientific lead: Prof. Ola Spjuth\, SciLifeLab Data Centre and Uppsala University \n\n\n\nContact information: serve@scilifelab.se
URL:https://www.scilifelab.se/event/building-and-sharing-machine-learning-demo-applications-within-life-sciences-a-practical-tutorial/
LOCATION:SciLifeLab Campus Solna\, Tomtebodavägen 23 A\, Solna\, Sweden
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231117T090000
DTEND;TZID=Europe/Stockholm:20231117T141000
DTSTAMP:20260404T132244
CREATED:20230830T210018Z
LAST-MODIFIED:20231112T090520Z
UID:10000962-1700211600-1700230200@www.scilifelab.se
SUMMARY:Cell and Molecular Biology Symposium
DESCRIPTION:The DDLS research area\, Cell and molecular biology\, invites you to the first in-person symposium. The day will be an introduction to the research area Fellows and Expert Group. \n\n\n\nRegistration\n\n\n\nWe have a limited number of seats (52p). All participants must register (including the speakers i.e.\, DDLS Fellows and research area Expert group). Participant list here  If you register after Nov 7\, we offer fika and lunch but can’t accommodate food preferences.  \n\n\n\nRegistration\n\n\n\nAgenda\n\n\n\n08:45Registration\, check-in and Coffee09:00Introduction to Data-driven Life Science program and the Cell and molecular biology research areaMargit Mahlapuu\, Chair of the DDLS CMB Expert groupPresentations of fellows\, Expert group members\, and Data science node09:15Title TBAJuliette Griffie\, DDLS Fellow09:40Making it work in reality – bridging the gap between curated proof of concept tests and real world deployment of biomedical image based deep learningIda-Maria Sintorn\, DDLS Expert group  09:55AICell Lab: Towards AI-powered Data-driven Whole-cell ModelingWei Ouyang\, DDLS Fellow10:20Title TBAErik Lindahl\, DDLS Expert group10:35Coffee break 10:50Time-resolved structural studies of photoactive proteinsSebastian Westenhoff\, DDLS Expert group11:05From model systems to global surveillance programs for infectious diseases: Some challenges and the road aheadJohan Bengtsson-Palme\, DDLS Fellow11:30The DDLS Data Science Node – status report towards supporting the national CMB research communityThomas Svensson\, Sverker Holmgren\, Data Science node12:00RNA insights from extinct animals and single cellsMarc Friedländer\, DDLS Expert group12:15Understanding intestinal diseases with spatial transcriptomicEduardo Villablanca\, DDLS Expert group12:30Lunch13:15“Weak\, noisy and uninteresting”: subtle features of macromolecular structuresNicholas Pearce\, DDLS Fellow13:40Metabolic Liver Disease: Molecular Mechanisms and Novel TargetsMargit Mahlapuu\, DDLS Expert group13:55Wrap-up and Action item summaryMargit Mahlapuu14:10End of the day
URL:https://www.scilifelab.se/event/cell-and-molecular-biology-symposium/
LOCATION:Biomedicum\, room Peter Reichard\, Solnavägen 9\, Stockholm\, 171 65
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/03/CMB_Icon-1.png
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231121T150000
DTEND;TZID=Europe/Stockholm:20231121T160000
DTSTAMP:20260404T132244
CREATED:20220829T115023Z
LAST-MODIFIED:20231120T151621Z
UID:10000656-1700578800-1700582400@www.scilifelab.se
SUMMARY:SciLifeLab Data Platform- how we support data-driven life science research
DESCRIPTION:The SciLifeLab Data Management seminar series next event is focused on the SciLifeLab Data Platform which is a hub for data-driven life science research. The SciLifeLab Data Platform aims to act as a ‘one-stop shop’ for data-driven life science in Sweden. It includes services (e.g. tools and databases)\, materials related to community building (e.g. jobs and events pages)\, and resources aimed at promoting data-driven life science research (e.g. data highlights). Presentations from the Liane Hughes\, SciLifeLab Data Centre Platform team lead\, will give you an overview of about the services\, resources\, and community building of the Platform\, suggestions on how you can contribute\, as well as a quick guide to hosting your data on the Platform.  \n\n\n\nWhen: Nov 21\, 3.00-4.00 PM CET.Where:  Zoom  \n\n\n\nRegister before Nov 21 at 3PM ( Zoom link will be sent out to registered participants.) \n\n\n\n\nRegister\n\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\, consisting of a presentation and an also gives time to discussion and questions from the participants. The videos will be published openly after the seminars at the SciLifeLab YouTube channel. \n\n\n\nMore 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 Sweden   \n\n\n\nContact us\, data-management@scilifelab.se
URL:https://www.scilifelab.se/event/data-platform-how-we-support-data-driven-life-science/
CATEGORIES:Event
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LOCATION:https://www.scilifelab.se/event/data-platform-how-we-support-data-driven-life-science/
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DTSTART;TZID=Europe/Stockholm:20231122T100000
DTEND;TZID=Europe/Stockholm:20231122T120000
DTSTAMP:20260404T132244
CREATED:20230921T093726Z
LAST-MODIFIED:20231120T152126Z
UID:10000974-1700647200-1700654400@www.scilifelab.se
SUMMARY:Data Management Plans in practise - research funder perspectives and practical demos
DESCRIPTION:Join SciLifeLab Data Centre and NBIS in collaboration with Uppsala University Library and Umeå University Library for a joint virtual event “Data Management Plans in practise – research funder perspectives and practical demos“. The first hour is focused on Data Management Plans (DMPs) from the perspective of Swedish research funders.  \n\n\n\nPart 1 – Data Management Plans (DMPs) from the perspective of Swedish research fundersToday\, many research funders require or recommend that researchers write DMPs for the research projects that they fund. What is the purpose of DMPs from the research funder´ s perspective? What would the funder like to achieve with the DMPs? Major Swedish research funders present their perspective as stakeholders\, followed by a panel discussion about how DMPs can help researchers and funders conduct research more effectively and to improve the quality of the research outputs. \n\n\n\nPart 2 – Demonstration of DMPonline and Data Stewardship WizardMany researchers and PhD students perceive writing a DMPs as a difficult task. A common mistake that researchers make when they write their first DMPs is copying content from their research plan. This is usually not going to work well because data management plans address different questions than research plans. A data management plan is not about scientific questions but about work with information and how this information can be preserved and shared with other stake holders. This webinar offers interested participants an opportunity to see how tools for writing DMPs look like\, what guidance they give and how one can use question-based templates to write a data management plan in a short time. The demonstrations cover the tools DMPonline and Data Stewardship Wizard. DMPonline is a general tool that researchers can use to write DMPs or all disciplines. Data Stewardship Wizard has a different design and SciLifeLab offers an instance focused on research in life sciences. \n\n\n\nWhen: Nov 22nd 2023.  10.00-12.00 (Stockholm time) on Zoom \n\n\n\nTarget group: Researchers and PhD students from all research fields and everybody else who works with research data. \n\n\n\nRegister by Nov 22\, at 10.00 \n\n\n\n\nRegister\n\n\n\n\n \n\n\n\nPart 1: Data Management Plans – the perspective of Swedish research funders \n\n\n\n10:00 – 10:05 Welcome\, Christer Lagvik\, Uppsala University Library \n\n\n\n10:05 – 10:35 Presentations from Sanja Halling\, Swedish Research Council\, Eva Stensköld\, Riksbankens Jubileumsfond and Andreas Björke\, Forte.  \n\n\n\n10:35 – 10:55 Panel discussion Sanja Halling\, Swedish Research Council\, Eva Stensköld\, Riksbankens Jubileumsfond\, Andreas Björke\, Forte and Siv Andersson\, Knut and Alice Wallenberg Foundation. Moderator: Niclas Jareborg\, NBIS \n\n\n\nPart 2. Demos of tools for writing DMPs \n\n\n\n11:05 – 11:35 Demonstration of DMPonline using a question-based template\, Theresa Kieselbach\, Umeå University Library. \n\n\n\n11:35 – 12:00 Demonstration of Data Stewardship Wizard at SciLifeLab\, Elin Kronanser\, NBIS.  \n\n\n\nWelcome! \n\n\n\nThis event is a collaboration between SciLifeLab Data Centre\, NBIS\, Uppsala University Library and Umeå University Library. For questions please contact SciLifeLab Data Centre  datacentre@scilifelab.se
URL:https://www.scilifelab.se/event/data-management-plans-in-practise/
CATEGORIES:Event
LOCATION:
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231122T141500
DTEND;TZID=Europe/Stockholm:20231122T150000
DTSTAMP:20260404T132244
CREATED:20231115T101836Z
LAST-MODIFIED:20231115T150503Z
UID:10001028-1700662500-1700665200@www.scilifelab.se
SUMMARY:Launch of calls for DDLS PhD projects
DESCRIPTION:The SciLifeLab & Wallenberg National Program for Data-Driven Life Science announces calls for PhD projects within academia and industry. The calls will be open for researchers in Sweden who are interested to act as supervisor for a PhD student. The aim is to fund 20 projects for academic PhD students and 7 for industrial. Join this online event for detailed information about the calls and the possibility to ask questions. \n\n\n\nAGENDA \n\n\n\nInformation about calls – Olli Kallioniemi\, DDLS director \n\n\n\nQ & A session \n\n\n\n\nRegister here\n\n\n\n\nWebpage: https://www.scilifelab.se/data-driven/ddls-research-school/
URL:https://www.scilifelab.se/event/call-for-ddls-phd-projects/
LOCATION:Online event via Zoom
CATEGORIES:Event
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