BEGIN:VCALENDAR VERSION:2.0 PRODID:-//SciLifeLab - ECPv6.15.18//NONSGML v1.0//EN CALSCALE:GREGORIAN METHOD:PUBLISH X-WR-CALNAME:SciLifeLab X-ORIGINAL-URL:https://www.scilifelab.se X-WR-CALDESC:Events for SciLifeLab REFRESH-INTERVAL;VALUE=DURATION:PT1H X-Robots-Tag:noindex X-PUBLISHED-TTL:PT1H BEGIN:VTIMEZONE TZID:Europe/Stockholm BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20210328T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20211031T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20220327T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20221030T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20230326T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20231029T010000 END:STANDARD END:VTIMEZONE BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221111T090000 DTEND;TZID=Europe/Stockholm:20221111T093000 DTSTAMP:20260403T225555 CREATED:20220923T085744Z LAST-MODIFIED:20220928T154812Z UID:10000687-1668157200-1668159000@www.scilifelab.se SUMMARY:[Clinical Talks] Combining AI and in situ sequencing to explore the tumor micro-environment DESCRIPTION:Carolina Wählby\n\n\n\nProfessor in quantitative microscopy\, SciLifeLab and Dept. IT\, Uppsala University \n\n\n\n\n\n\n\nCarolina Wählby is professor in Quantitative Microscopy at the Dept. of Information Technology\, Uppsala University\, and Scientific Director of the National SciLifeLab Bioimage Informatics Unit. Her research is focused on developing computational approaches for extracting information from image data with focus on precision medicine and life science. Methods include traditional image analysis as well as AI and deep learning for understanding dynamics of cancer tissue\, antibiotics susceptibility and spatial transcriptomics\, funded primarily by the ERC TissUUmaps project and the Swedish Foundation for Strategic research. She received the SBI2 President’s innovation award in 2014 for her work on in situ sequencing\, and the Thuréus prize in 2015 for development of open tools for image analysis. She is a member of the Royal Society of Sciences at Uppsala and the Royal Swedish Academy of Engineering Sciences. She has a MSc in molecular biotechnology and a PhD in digital image analysis\, and carried out postdoc research within genetics and pathology. She was part of the Imaging Platform of the Broad Institute of Harvard and MIT in 2009-2015 and became full professor at Uppsala University in 2014. She is a member of the steering group of a 300M€ effort on Data Driven Life Science\, funded by the Knut and Alice Wallenberg Foundation\, with the ambitious goal of training the next generation of life scientists. Her heart lies in the intersection between life science and computational image analysis\, and she is intrigued by the possibilities of technological developments and convergence of the scientific fields. \n\n\n\nregister to receive zoom link\n\n\n\nModerator: Päivi Östling\, SciLifeLab \n\n\n\n\n\n\n\n \n\n\n\nClinical Talks\n\n\n\nClinical Talks is back for more! With a brand new and shiny Season 6. After successfully completing 5 seasons with > 70 enthusiastic Clinical Talkers to our record\, we have barely scratched the surface of all the amazing work our clinical\, academic and industry Life Science community has to offer. More about the upcoming events is available here. \n\n\n\nThese events are co-organized by Karolinska Institutet Innovations AB and SciLifeLab\, and brought to you by Colibri Ventures. URL:https://www.scilifelab.se/event/clinical-talks-combining-ai-and-in-situ-sequencing-to-explore-the-tumor-micro-environment/ LOCATION:Online event via Zoom CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/08/Square-500x500-Clinical-Talks@4x.png ORGANIZER;CN="Clinical Talks":MAILTO:precisionmedicine@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221109T080000 DTEND;TZID=Europe/Stockholm:20221109T170000 DTSTAMP:20260403T225555 CREATED:20221003T134428Z LAST-MODIFIED:20221031T094134Z UID:10000703-1667980800-1668013200@www.scilifelab.se SUMMARY:Workshop on biomolecular simulations DESCRIPTION:The main focus of ‘Biomoelcular simulations workshop’ is on molecular dynamics simulations of biomolecular systems. The target audience of this workshop is the researchers working in Sweden on biomolecular simulations. The goal of this workshop is to bring together all the researchers from Sweden interested in biomolecular simulations and to provide an opportunity to junior researchers in the field to present their work. This will be a single day event with some talks by other researchers from abroad and ample opportunities for discussion and interactions among the people in the field. \n\n\n\nConfirmed speakers\n\n\n\nSimon Olsson\, Chalmers\, GothenburgMilosz Wieczor\, IRB BarcelonaMercedes Alfonso-Prieto\, Forschungszentrum Jülich\n\n\n\n\n\n\n\nProgram and abstracts are collapsible items – click to expand. \n\n\n\nProgram\n09:30Morning Coffee\, MingleInghesalen\, Karolinska Institutet09:55Welcome from organizersOrganizing Committee10:00Multiscale simulations to study proton transfer: from enzymes to membrane proteinsMercedes Alfonso-Prieto\, Forschungszentrum Jülich\, Germany10:40Exploring the selectivity profile of plant UDP dependent glycosyl transferases (UGTs) by computational and experimental studiesJunhao Li\, Uppsala University11:00Multi-scale Modeling of Axonal Injury (coupling of finite element analysis with molecular dynamics simulations)Maryam Majdolhosseini\, KTH Royal Institute of Technology11:20Coffee Break11:40A Machine-Learned Atomistic Force Field for Nucleic AcidsMiłosz Wieczór\, IRB Barcelona12:20Combining evolution and physics with coevolution-powered machine learningDarko Mitrovic\, KTH Royal Institute of Technology12:40Lipid-ethanol mixtures for topical drug delivery applications: A molecular dynamics and NMR studyAmanda Quinones Vallin\, Stockholm University13:00Lunch14:00Machine learning to reconcile experiment and simulationSimon Olsson\, Chalmers University of Technology14:40Effective Molecular Dynamics from Neural-Network Based Structure Prediction ModelsAlexander Jussupow\, Stockholm University15:00Opportunities and Challenges in GPCR SBDD: Finding the Sweet SpotsPierre Matricon\, Sosei Heptares15:20Wrap up\, Thank youOrganizing Committee\n\n\n\n\nMultiscale simulations to study proton transfer: from enzymes to membrane proteins\nMercedes Alfonso-Prieto\, Assistant Professor\, Forschungszentrum Jülich\, Germany \n\n\n\nProton transfer (PT) is one the most common processes in biology. Studying PT at the molecular level is a challenging task\, due to the intrinsic complexity of proteins\, including their functional dynamics and the presence of several titratable residues. Therefore\, combination of experimental and computational techniques is needed to obtain a more comprehensive picture. Recent methodological and software advancements have enabled the efficient application of quantum mechanics/molecular mechanics (QM/MM) simulations to (large) biological systems. This multiscale approach allows treating the region of the protein where PT takes place at the QM level\, while including the effect of the rest of the protein and its environment at the MM level. In this talk\, I will show some examples of QM/MM simulations applied to PT processes in different systems\, from enzymes to membrane proteins. Such hybrid simulations have provided atomistic insights complementary to experiments. \n\n\n\n\nA Machine-Learned Atomistic Force Field for Nucleic Acids\nMiłosz Wieczór\, Postdoctoral fellow\, IRB Barcelona \n\n\n\nWe present a new paradigm for the parametrization of nonbonded interactions in molecular force fields directly from quantum chemical data. The proposed machine-learned force field (ML-FF) accurately reproduces well-validated quantum chemical interaction energies\, as well as allows for the systematic incorporation of experimental data such as measured affinity constants. Contrary to many recently published general ML-FFs\, our force field ensures stability in molecular dynamics simulations thanks to a combination of regularization and active learning\, and permits gradual upgrades should issues arise in previously untested systems. Meanwhile\, a simple embedding scheme allows the parameters learned from minimal methyl-nucleobase systems to be employed in simulations of large biomacromolecules at virtually no computational overhead. We also present several key directions for the future evolution of our force field\, both in terms of accuracy and applicability. \n\n\n\n\nMachine learning to reconcile experiment and simulation\nSimon Olsson\, Assistant Professor\, Chalmers University of Technology \n\n\n\nLong-time-scale and enhanced sampling molecular dynamics simulations reveal the approximations of classical molecular dynamics force fields disagreeing with experimental data. However\, under ideal conditions\, experiments and simulations observe the same process — consequently\, by optimally balancing experimental and simulation data\, we may build models extracting helpful information from both. In this talk\, I will overview efforts in this direction and talk about Augmented Markov models\, and their recent extension dynamic Augmented Markov models. \n\n\n\n\n\n\n\n\nRegistration URL:https://www.scilifelab.se/event/workshops-on-biomolecular-simulations/ LOCATION:Inghesalen\, Tomtebodavägen 18a\,\, Solna\, 171 65 171 65\, Sweden CATEGORIES:Event ORGANIZER;CN="Biomolecular Simulations Network":MAILTO:lucie.delemotte@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221108T120000 DTEND;TZID=Europe/Stockholm:20221108T130000 DTSTAMP:20260403T225555 CREATED:20220927T104558Z LAST-MODIFIED:20220927T104712Z UID:10000696-1667908800-1667912400@www.scilifelab.se SUMMARY:NBIS - Bioinformatics and data support at SciLifeLab DESCRIPTION:NBIS – Bioinformatics and data support at SciLifeLab\n\n\n\nThomas Svensson \n\n\n\nNBIS\, National Bioinformatics Infrastructure Sweden\, is a distributed national research infrastructure. We are the SciLifeLab bioinformatics platform and the Swedish node in Elixir\, a European intergovernmental organisation bringing together life science resources from across Europe. We offer bioinformatics support\, infrastructure and training. \n\n\n\nSciLifeLab is a national infrastructure within life science with a wide range of advanced technology and expertise. The newly started 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. \n\n\n\nA light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available\, please click the zoom-link below to join the event at the appointed time. \n\n\n\nVenue\n\n\n\nAssembly Room Birgit Thilander\, Medicinaregatan 3 URL:https://www.scilifelab.se/event/nbis-bioinformatics-and-data-support-at-scilifelab/ LOCATION:Birgit Thilander Lecture Hall\, Medicinaregatan 3\, Göteborg CATEGORIES:Event ORGANIZER;CN="SciLifeLab Gothenburg":MAILTO:gothenburg@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221108T110000 DTEND;TZID=Europe/Stockholm:20221108T120000 DTSTAMP:20260403T225555 CREATED:20221107T151644Z LAST-MODIFIED:20221107T151703Z UID:10000726-1667905200-1667908800@www.scilifelab.se SUMMARY:SciLifeLab Uppsala PhD&Postdoc Online Seminar Series - Immunology Theme DESCRIPTION:Welcome back to the SciLifeLab Uppsala PhD&Postdoc seminar series!\n\nThis seminar will take place on Tuesday November 8th from 11h to 11:50h on Zoom (https://uu-se.zoom.us/j/66489618700)\n\nFor this occasion the speakers will be:\n\n1. Tiarne van de Walle\, PhD Student at Anna Dimberg and Magnus Essand’s Labs (Vascular Biology & Cancer Immunotherapy)\, Dept. of Immunology\, Genetics and Pathology\, Uppsala University\n\nTitle: Shining the LIGHT on Glioblastoma\n\nSummary:\nGlioblastoma is the most aggressive primary brain cancer and is resistant to immunotherapy\, which is largely due to poor T cell infiltration. Here\, we screened a panel of lymphoneogenic cytokines\, from which we selected LIGHT/TNFSF14 as the most promising candidate for treatment of glioma. Then\, we utilized a brain endothelial cell-targeted vector to express LIGHT on the glioma vasculature. Systemic treatment with this novel therapeutic agent resulted in prolonged survival\, and promoted efficient T cell infiltration and anti-tumour immune responses. As such\, our work demonstrates that tailoring the vascular phenotype through vessel-targeted expression of LIGHT is a promising therapeutic strategy\, which has broader implications for treatment of other immunotherapy-resistant cancers.\n\n \n\n\n2. Miguel Vizoso Patiñoi\, Researcher at Mia Phillipson’s Lab (Immunology)\, Dept. of Medical Cell Biology\, Uppsala University\n\nTitle: Uncovering the role of the innate immune cells in vascular remodeling during menstruation and associated pathologies\n\nSummary:\nMore than 10% of women worldwide suffer from abnormal uterine bleeding (AUB). Current standardized therapies for AUB include ovulation blockade and hysterectomy\, which both are highly aggressive and interfere with fertility. Thus\, there is an unmet clinical need for more effective and non-invasive treatments. The scarcity of efficient therapies is at least partly due to the lack of reproductive experimental models\, as well as that the underlying mechanisms resulting in AUB are largely unknown. However\, innate immune cells have been documented to be actively recruited to the endometrium during physiological menstrual cycle and pregnancy. Based on our recent discoveries of a pro-angiogenic subpopulation of neutrophils\, in addition to novel functions of macrophages important for blood-vessel maturation\, I will in this project\, define the contribution of innate immune cells in the vascular phenotype of AUB. The main goals addressed by 2 work packages (WPs) are:\n\n\nTo develop the first humanized murine uterus to characterize how human endometrial epithelial cells (hEECs) participate of the vascular network remodeling in vivo. To this end\, EECs from healthy and AUB donors will be orthotopically transplanted in immunocompromised mice and its impact on vasculature remodeling will be measurable in real time by intravital microscopy upon menstrual cycle induction. Samples will be also submitted for scRNAseq to reveal the transcriptomic networks connecting the epithelium (human-origin) and stroma/endothelium (murine-origin) compartments at different time points of the menstrual cycle.\nTo assess whether the role of the innate immune cells in endometrial angiogenesis and vascular pruning differs depending on their interaction with healthy or pathogenic (AUB) derived hEECs.\n\nThus\, this project will provide a novel model to study endometrial human physiology in vivo\, to enable the discovery of new mechanisms involved in AUB. Generated insights will then be used to pursue opportunities to translate the findings into clinical practice and provide non-invasive therapies to treat AUB disorders. URL:https://www.scilifelab.se/event/scilifelab-uppsala-phdpostdoc-online-seminar-series-immunology-theme/ LOCATION:Online event via Zoom CATEGORIES:Community ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/11/SciLifeLab-PhDPostdoc-conuncil-poster_landscape_November_08.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221108T080000 DTEND;TZID=Europe/Stockholm:20221109T170000 DTSTAMP:20260403T225555 CREATED:20221019T150314Z LAST-MODIFIED:20221019T150316Z UID:10000717-1667894400-1668013200@www.scilifelab.se SUMMARY:KBC DAYS 2022 DESCRIPTION:We cordially invite you to join us for the Celebration of the 15th anniversary of KBC on 8 November and to attend the KBC DAYS 2022 conference with the main theme “Big data” on 8-9 November! \n\n\n\nWhen: Tuesday\, 8 November – Wednesday\, 9 November 2022 \n\n\n\nWhere: Carl Kempe salen (KB.E3.03) (MAP) and other locations at KBC \n\n\n\nWe invite you to participate in the KBC DAYS\, an annual interdisciplinary conference\, which will be back to a physical format this year after two years of digital events! Our aim is to foster collaborations between different departments and research centres affiliated with the Chemical Biological Centre\, KBC\, including departments from two faculties from Umeå University as well as from the Faculty of Forest Sciences from SLU. \n\n\n\nA scientific focus this year will be on “Big Data“. We welcome you to listen to the plenary lectures and other presentations discussing different aspects\, advantages and challenges of analysing\, interpreting and handling big data. \n\n\n\nUpdate yourself about the research infrastructures available in Umeå\, get to know more about their services and join the guided tours to their facilities! \n\n\n\nCome and listen to exciting scientific talks from new faculty members of the KBC environment\, awardees and researchers that received major grants in the last year\, presentations by PhD students and selected talks by young researchers from the Umeå Postdoc Society (UPS)! \n\n\n\nWe invite postdoctoral researchers from Umeå University and SLU Umeå to give a scientific talk during this year’s KBC DAYS. We especially encourage submissions from research related to this year’s topic\, Big Data. We have a total of four 15-minutes slots (12 minutes talk + 3 minutes Q&A). Interested in presenting your work? Fill in the form and hit submit (before 20 October): https://forms.office.com/r/YFHYHXDuyF \n\n\n\nThis year\, two special events will be dedicated to celebrating the 15th anniversary of KBC! Join for the panel discussion with those who contributed to the establishment and development of KBC to reminisce about how it all started\, highlight what has been achieved\, and discuss future visions for research and collaboration at KBC! The celebration gala dinner will be held on the evening of 8 November (more details and the program will be announced later). \n\n\n\nIn the frame of the celebration activities\, we open a photo contest\, “KBC is…” and invite you to express in 1-3 photos and share your vision of what KBC is for you. \n\n\n\nCheck your photo archives or shoot new ones and submit your photo(s) already now but no later than Monday\, 7 November (23:59h) following this link: https://pollunit.com/polls/kbc_photo_contest_2022. You will also find detailed rules of the contest on this webpage. \n\n\n\nThe voting will take place\, and the winner will be announced during the KBC DAYS\, 8-9 November. \n\n\n\nThe contest is open to the participants of the KBC DAYS and everyone else related to the KBC environment! \n\n\n\nIf you have more photos related to the KBC history and past events in your archives\, we will be more than happy to use these photos in a slide show during the KBC anniversary celebration! Please send these photos to info.kbc@umu.se! URL:https://www.scilifelab.se/event/kbc-days-2022/ LOCATION:Carl Kempe-salen\, KBC Building\, Umeå University\, Umeå\, Sweden CATEGORIES:Event ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221107T151500 DTEND;TZID=Europe/Stockholm:20221107T161500 DTSTAMP:20260403T225555 CREATED:20221025T140529Z LAST-MODIFIED:20221103T114505Z UID:10000721-1667834100-1667837700@www.scilifelab.se SUMMARY:[The Svedberg] - Studying microRNA functions at the single-cell level DESCRIPTION:MicroRNAs are gene regulatory molecules that play important roles in numerous biological processes including human health. The function of a given microRNA is defined by its selection of target transcripts\, yet current state-of-the-art experimental methods to identify microRNA targets are laborious and require millions of cells – hampering the entry of the microRNA field into the single-cell era. We have overcome these limitations by fusing the microRNA effector protein Argonaute2 to the RNA editing domain of ADAR2\, allowing for the first time the detection of microRNA targets transcriptome-wide in single cells. Our agoTRIBE method reports functional microRNA targets which are additionally supported by evolutionary sequence conservation. As a proof-of-principle\, we study microRNA interactions in single cells\, and find substantial differential targeting across the cell cycle. In addition to presenting this single-cell project\, I will talk about our recent efforts to sequence RNA fragments from ancient animal samples that are preserved in the Siberian permafrost. \n\n\n\nMarc Friedländer is an associate professor at Stockholm University\, Department of Molecular Biosciences. He graduated from his master’s thesis under the supervision of Anders Krogh in Copenhagen and his PhD in the group of Nikolaus Rajewsky in Berlin. He founded his own lab in Stockholm with funding from a SciLifeLab Fellowship and an ERC starting grant. His team is balanced between wet-lab and dry-lab biologists\, and they develop and apply experimental and computational methods to understand gene regulation – with particular emphasis on microRNAs. His lab has studied these molecules in the context of space exposure (a collaboration with NASA); in ancient animal samples preserved in permafrost; and in mammalian single cells. \n\n\n\nWebpage: www.friedlanderlab.org URL:https://www.scilifelab.se/event/the-svedberg-marc-friedlander-assoc-prof/ 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:20221103T120000 DTEND;TZID=Europe/Stockholm:20221103T130000 DTSTAMP:20260403T225555 CREATED:20220912T093644Z LAST-MODIFIED:20221107T171023Z UID:10000673-1667476800-1667480400@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Sami Saarenpää and Vaishnovi Sekar DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nThis week:\n\n\n\n\n\n\nSami Saarenpää\n\n\n\nStefania Giacomello – alpha 3 \n\n\n\nSpatially resolved host-bacteria-fungi interactomes via spatial metatranscriptomics \n\n\n\n\n\nVaishnovi Sekar\n\n\n\nMarc Friedländer – gamma 5 \n\n\n\nagoTRIBE detects miRNA-target interactions in single cells \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page. URL:https://www.scilifelab.se/event/campus-solna-seminar-series-nov-3/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Community ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/IMG_20221103_124630107_HDR-scaled.jpg ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221101T120000 DTEND;TZID=Europe/Stockholm:20221101T130000 DTSTAMP:20260403T225555 CREATED:20220927T104420Z LAST-MODIFIED:20220927T104528Z UID:10000695-1667304000-1667307600@www.scilifelab.se SUMMARY:Bioinformatics and Data Center - A bioinformatics hub supporting biomedical and clinical research DESCRIPTION:Bioinformatics and Data Center – A bioinformatics hub supporting biomedical and clinical research\n\n\n\nMarcela Davila / Per Sikora \n\n\n\nIn this seminar\, we will present the new setup for bioinformatics and infrastructure support at Core Facilities. The Bioinformatics and Data Centre provides high-throughput techniques for biomedical\, clinical and pre-clinical research; a wide range of support in bioinformatics and statistics is available – from short term consulting to long term project support and training; general consulting and support for HPC hardware and software infrastructure development and storage for “big data”. \n\n\n\nSciLifeLab is a national infrastructure within life science with a wide range of advanced technology and expertise. The newly started 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. \n\n\n\nA light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available\, please click the zoom-link below to join the event at the appointed time. \n\n\n\nVenue\n\n\n\nAssembly Room Birgit Thilander\, Medicinaregatan 3 URL:https://www.scilifelab.se/event/bioinformatics-and-data-center-a-bioinformatics-hub-supporting-biomedical-and-clinical-research/ LOCATION:Birgit Thilander Lecture Hall\, Medicinaregatan 3\, Göteborg CATEGORIES:Event ORGANIZER;CN="SciLifeLab Gothenburg":MAILTO:gothenburg@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221031T080000 DTEND;TZID=Europe/Stockholm:20221102T170000 DTSTAMP:20260403T225555 CREATED:20220323T160943Z LAST-MODIFIED:20220906T102510Z UID:10000566-1667203200-1667408400@www.scilifelab.se SUMMARY:Long-Read Sequencing Uppsala Meeting 2022 DESCRIPTION:In recent years\, long-read DNA sequencing has replaced short-read technologies as the gold standard solution for a wide range of genomics applications. In addition to producing high quality de novo genome assembly\, long-read technologies can be used to study complex structural variation\, full-length RNA isoforms\, detection of epigenetic signals\, and much more. The adaptation of long-read sequencing is sweeping through several areas of the life sciences including agricultural\, environmental\, and medical research. \n\n\n\nJoin us in Uppsala for a three-day event to catch up with the latest developments in long-read sequencing technologies and their applications\, get inspired by peers presenting their research\, and enjoy discussions with leading experts and company representatives. \n\n\n\nRead more URL:https://www.scilifelab.se/event/long-read-sequencing-uppsala-meeting-2022/ LOCATION:Universitetsaulan\, Biskopsgatan 3\, Uppsala\, Sweden CATEGORIES:Event ORGANIZER;CN="National Genomics Infrastructure (NGI)":MAILTO:support@ngisweden.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221028T102000 DTEND;TZID=Europe/Stockholm:20221028T110000 DTSTAMP:20260403T225555 CREATED:20221020T111054Z LAST-MODIFIED:20221020T111433Z UID:10000719-1666952400-1666954800@www.scilifelab.se SUMMARY:Seminar: Single cell and spatially resolved epigenomics DESCRIPTION:Spatial omics has emerged as a new frontier of biological and biomedical research. In particular\, spatial transcriptomics has enabled genome-scale gene expression mapping with spatial resolution in tissue sections. So far\, the ability to capture spatial epigenetic information at the cellular level and genome scale has been lacking. This talk will describe recent advances in spatial epigenomics (ATAC-seq\, CUT&Tag)\, single cell epigenomics\, and how they can be applied to study multiple sclerosis. \n\n\n\n\n\n\n\nSpeaker\n\n\n\nProf. Gonçalo Castelo-Branco is the Professor of Glial Cell Biology at the Department of Medical Biochemistry and Biophysics at Karolinska Institutet\, Stockholm\, Sweden. Prof. Castelo-Branco received his PhD in Medical Biochemistry in 2005\, working on development of dopaminergic neurons and neural stem differentiation. He completed post-doctoral fellowships first at the Karolinska Institutet and then at the University of Cambridge\, United Kingdom\, working in neural and pluripotent stem cells and chromatin. Prof. Castelo-Branco started his research group in 2012\, focusing on the molecular mechanisms defining the epigenetic state of cells of the oligodendrocyte lineage. The main focus of Prof. Castelo-Branco’s research group is to investigate how distinct epigenetic states within the oligodendrocyte lineage are established\, by identifying key transcription factors\, chromatin modifying complexes and non-coding RNAs that are involved in epigenetic transitions\, using technologies such as RNA-Seq (single-cell and bulk)\, quantitative proteomics and epigenomics\, among others. The long term aim of this research group to design epigenetic based-therapies to induce regeneration (remyelination) in demyelinating diseases\, such as multiple sclerosis. \n\n\n\nLab website \n\n\n\n\n\n\n\n\n\nZOOM link\n\n\n\n\n\nContact: Jakub Westholm\, SciLifeLab Bioinformatics Long-term Support URL:https://www.scilifelab.se/event/seminar-single-cell-and-spatially-resolved-epigenomics/ LOCATION:Online event via Zoom CATEGORIES:Event ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221027T153000 DTEND;TZID=Europe/Stockholm:20221027T170000 DTSTAMP:20260403T225555 CREATED:20221003T150502Z LAST-MODIFIED:20221003T150536Z UID:10000704-1666884600-1666890000@www.scilifelab.se SUMMARY:Developing therapies for the inherited bone marrow failure syndrome diamond-blackfan anemia DESCRIPTION:Johan Flygare \n\n\n\nDocent\, MD and PhD\, Department of Laboratory Medicine\, Lund University \n\n\n\n \n\n\n\nHost: Mikael Lindström\, Docent and PhD \n\n\n\nOctober 27 at 3.30 pm \n\n\n\nSeminar room: Air & Fire \n\n\n\nOrganizers: CBCS-KI and PhenoTarget Research Community Program URL:https://www.scilifelab.se/event/developing-therapies-for-the-inherited-bone-marrow-failure-syndrome-diamond-blackfan-anemia/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221027T120000 DTEND;TZID=Europe/Stockholm:20221027T130000 DTSTAMP:20260403T225555 CREATED:20220830T081254Z LAST-MODIFIED:20221013T072640Z UID:10000660-1666872000-1666875600@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Kathleen Watt and Mateusz Garbulowski DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nThis week:\n\n\n\n\n\n\nKathleen Watt\n\n\n\nOla Larsson – gamma 5 \n\n\n\nHypoxia-induced transcription start site switching remodels 5’UTRs driving translational reprogramming in breast cancer \n\n\n\n\n\nMateusz Garbulowski\n\n\n\nErik Sonnhammer – gamma 7 \n\n\n\nGene regulatory network inference of RNA binding proteins \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page. URL:https://www.scilifelab.se/event/campus-solna-seminar-series-oct-27/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Community ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/08/logo_PhD_Postdoc_Council.png ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221027T080000 DTEND;TZID=Europe/Stockholm:20221028T170000 DTSTAMP:20260403T225555 CREATED:20220920T125029Z LAST-MODIFIED:20220920T125030Z UID:10000685-1666857600-1666976400@www.scilifelab.se SUMMARY:Swedish Bioinformatics Workshop DESCRIPTION:This year SBW will take place at Umeå University\, October 27-28. The two days will be filled with inspiring talks\, including keynote talks by Kerstin Lindblad-Toh (Uppsala University/Broad Institute)\, Debora S. Marks (Harvard University)\, and Simon Anders (Heidelberg University). There will also be three parallel hands-on workshops\, a poster session\, and a social event.  \n\n\n\nThe target group is traditionally PhD students and postdocs working with any kind of bioinformatics and computational biology. This workshop aims to bring together talented students and young researchers across faculties and universities from throughout the country.  \n\n\n\nVisit sbw2022.com to register and view the programme. Registration will be open until 23rd September. \n\n\n\nRead more URL:https://www.scilifelab.se/event/swedish-bioinformatics-workshop/ LOCATION:Naturvetarhuset\, Umeå University\, Umeå CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/09/Skärmavbild-2022-09-20-kl.-14.49.52.png ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221026T120000 DTEND;TZID=Europe/Stockholm:20221028T120000 DTSTAMP:20260403T225555 CREATED:20220707T120240Z LAST-MODIFIED:20220831T073649Z UID:10000641-1666785600-1666958400@www.scilifelab.se SUMMARY:6th Uppsala Transposon Symposium DESCRIPTION:We are excited to announce that the 6th Uppsala Transposon Symposium – integrating transposon and virus identification into evolution and disease research will be on October 26-28 in Uppsala. This year\, we have an in-person symposium with abstract submission\, a livestream for virtual attendance + questions\, and an interactive workshop with tool developers. Day 3 will be dedicated to a tools and database workshop. This will be a unique opportunity to discuss ideas\, meet experts\, and showcase contributions. Tool developers from RepeatModeler/Masker\, Repbase\, dfam\, TE-hub\, etc. will all be in Uppsala! \n\n\n\nVirtual attendants can ask written questions that the chair will read out for the in-person audience. You will have the chance for networking with fellow virtual attendants during the coffee breaks. \n\n\n\nAbstract submission deadline is September 23\, and we encourage especially early-career transposon researchers to submit an abstract for regular talk or lightning talk with poster. \n\n\n\nAs previously for this symposium\, registration will be free of charge\, and especially early-career scientists are encouraged to submit an abstract for a regular talk or poster with lightning talk. The free in-person attendance includes coffee/tea/snacks + >1 meal\, (and other meals at a student-friendly price). \n\n\n\nPlease follow the link for a detailed program\, more information and to register! The registration is open. \n\n\n\n#UppTransposon2022 \n\n\n\nEvent webpage more Information\n\n\n\n\n\n\n\nIf you are looking for a second reason (apart from Uppsala October weather) to travel to Uppsala\, note that the Long-Read Uppsala meeting (Oct 31-Nov 02) will be directly after the Uppsala Transposon Symposium. Abstract submission deadline for LRUA2022 is September 01. \n\n\n\n\n\n\n\nConfirmed speakers:\n\n\n\nIrina Arkhipova (Marine Biological Laboratory) [keynote 1]John Coffin (Tufts University) [keynote 2]Kenji Kojima (Genetic Information Research Institute)Alice Eunjung Lee (Harvard University)Gayle McEwen (Leibniz Institute for Zoo and Wildlife Research)Arian Smit (Institute for Systems Biology)Björn Nystedt (SciLifeLab)\n\n\n\nOrganizing committee:\n\n\n\nAlexander Suh (University of East Anglia and Uppsala University)Claudia Kutter (Karolinska Institute)Patric Jern (Uppsala University)\n\n\n\n\n\n\n\nContact us: transposonsymposium@gmail.com URL:https://www.scilifelab.se/event/6th-uppsala-transposon-symposium/ LOCATION:Friessalen\, Evolutionary Biology Centre\, Norbyvägen 14\, ground floor\, Uppsala\, 75236\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/07/logo_2ndte_only-logo_red_frame.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221025T120000 DTEND;TZID=Europe/Stockholm:20221025T130000 DTSTAMP:20260403T225555 CREATED:20221011T110651Z LAST-MODIFIED:20221021T085311Z UID:10000713-1666699200-1666702800@www.scilifelab.se SUMMARY:XPS Platform: Nobel prized technique to study surface and interfaces DESCRIPTION:In the frame of the “SciLifeLab Site Umeå / KBC Infrastructure Seminar Series”\, the seminars will be organised every second Tuesday during autumn 2022. The seminars will be held in a hybrid format IRL in Glasburen\, KBC\, and online via Zoom. Take the chance to get information on facilities\, possibilities and services that infrastructure\, both SciLifeLab-associated and local\, can offer! Learn more about the seminar series and the schedule for autumn 2022 here: https://www.umu.se/en/research/infrastructure/medicinska-fakulteten/u/umea-centre-for-electron-microscopy-ucem/scilifelab-in-umea/scilifelab-site-umea–kbc-infrastructure-seminar-series/ \n\n\n\nOn October 25th\, 12:00-13:00\, you are welcome to participate in the seminar \n\n\n\nXPS Platform: Nobel prized technique to study surface and interfaces \n\n\n\nby Andrey Shchukarev\, manager of the XPS Platform and research fellow at the Department of Chemistry\, Umeå University \n\n\n\nMore information about the infrastructure: https://www.umu.se/en/research/infrastructure/xps/ \n\n\n\nSeminar description: XPS Platform seminar covers the basics of X-ray Photoelectron Spectroscopy (XPS or ESCA) and focuses on XPS applications to probe real surfaces and interfaces in nature and life. \n\n\n\nRead more\n\n\n\n \n\n\n\nRegistration deadline: Monday\, 24 October\, 10:00. \n\n\n\nOnline attendance: You can also join the seminar on Zoom\, https://umu.zoom.us/j/63138997026 (registration is not required) \n\n\n\nOrganisers: SciLifeLab Site Umeå and Chemical Biological Centre (KBC) URL:https://www.scilifelab.se/event/xps-platform-nobel-prized-technique-to-study-surface-and-interfaces/ LOCATION:Glasburen Seminar Room\, Chemical Biological Centre (KBC) Building\, Umeå University\, Umeå\, 901 87\, Sweden CATEGORIES:Event ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221024T120000 DTEND;TZID=Europe/Stockholm:20221024T130000 DTSTAMP:20260403T225555 CREATED:20220927T104249Z LAST-MODIFIED:20220927T104546Z UID:10000694-1666612800-1666616400@www.scilifelab.se SUMMARY:Swedish NMR Centre - NMR in life sciences DESCRIPTION:Swedish NMR Centre – NMR in life sciences\n\n\n\nGöran Karlsson\, Swedish NMR Centre\, SciLifeLab Göteborg \n\n\n\nThe Swedish NMR Centre is a national research infrastructure offering metabolomics\, protein-drug interaction studies and protein structure and dynamics characterization. \n\n\n\nSciLifeLab is a national infrastructure within life science with a wide range of advanced technology and expertise. The newly started 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. \n\n\n\nA light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available\, please click the zoom-link below to join the event at the appointed time. \n\n\n\nVenue\n\n\n\nAssembly Room Birgit Thilander\, Medicinaregatan 3 URL:https://www.scilifelab.se/event/swedish-nmr-centre-nmr-in-life-sciences/ LOCATION:Birgit Thilander Lecture Hall\, Medicinaregatan 3\, Göteborg CATEGORIES:Event ORGANIZER;CN="SciLifeLab Gothenburg":MAILTO:gothenburg@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221024T090000 DTEND;TZID=Europe/Stockholm:20221028T170000 DTSTAMP:20260403T225555 CREATED:20220516T122403Z LAST-MODIFIED:20220516T122509Z UID:10000607-1666602000-1666976400@www.scilifelab.se SUMMARY:Epigenomics Data Analysis: from Bulk to Single Cell (ONLINE) DESCRIPTION:National workshop open for PhD students\, postdocs\, researchers and other employees within Swedish academia. This course is run by the National Bioinformatics Infrastructure Sweden (NBIS). \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication opens:  now \n\n\n\nApplication closes: 2022-09-23 \n\n\n\nConfirmation to accepted students: 2022-09-30 \n\n\n\nResponsible teachers\n\n\n\nAgata Smialowska\, Jakub Orzechowski Westholm\, Vincent van Hoef \n\n\n\nPlease contact edu.epigenomics@nbis.se for course specific questions. \n\n\n\n\n\n\n\n\nCOURSE WEBSITE\n\n\n\nAPPLICATION\n\n\n\n\n\n\n\n\nWorkshop fee\n\n\n\nThis online training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2000 SEK.  \n\n\n\n*Please note that NBIS cannot invoice individuals. \n\n\n\nWorkshop content\n\n\n\nThis workshop aims to introduce the best practice bioinformatics methods for processing\, analyses\, visualisation and integration of epigenomics and functional genomics data. \n\n\n\nTopics covered include: \n\n\n\nData processing and analyses for differential DNA methylation with Illumina EPIC arrays and Bisulfite-seq;ChIP-seq: peak calling\, peak independent / dependent quality metrics\, differential binding analysis; DNA motif enrichment;ATAC-seq: peak calling\, peak independent / dependent quality metrics\, differential accessibility analysis;Quantitative ChIP-seq using spike-ins;CUT&Tag / CUT&RUN: Novel methods to investigate protein-chromatin interactions;Functional analysis\, including finding nearest genes and custom features\, GO terms and Reactome pathways enrichment;Basic multi-omics exploration and integration;Visualisations of epigenomics datasets;Introduction to analysis of single cell functional genomics data (scATAC-seq);Introduction to nf-core pipelines for processing and analysis of epi- and functional genomics data : Methylseq\, ChIP-seq\, ATAC-seq.\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the workshop and complete the computer exercises: \n\n\n\nBYOL\, bring your own laptop with R and RStudio installed;Basic knowledge in Linux;Basic programming experience\, preferably in R.\n\n\n\n\n\n\n\nDesirable \n\n\n\nExperience working on the SNIC center Uppmax or another HPC. We encourage participants to run the linked Uppmax tutorial before the workshop;Previous experience with NGS data analyses;Completing NBIS workshops “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists” or equivalent.\n\n\n\nDue to limited capacity the workshop can accommodate maximum of 25 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. \n\n\n\nPlease note that NBIS training events do not provide any formal university credits. \n\n\n\nThis training content is estimated to correspond to a 1.5 HPs\, however the estimated credits are just guidelines. If formal credits are crucial\, participants need to confer with the home department whether the course is valid for formal credits. URL:https://www.scilifelab.se/event/epigenomics-data-analysis-from-bulk-to-single-cell-online-2/ LOCATION:Online event via Zoom CATEGORIES:Course ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221021T110000 DTEND;TZID=Europe/Stockholm:20221021T120000 DTSTAMP:20260403T225555 CREATED:20221004T164130Z LAST-MODIFIED:20221004T164133Z UID:10000706-1666350000-1666353600@www.scilifelab.se SUMMARY:3D-Equivariant Graph Neural Networks for Refining and Evaluating Protein Structures DESCRIPTION:Speaker: \n\n\n\nJianlin Cheng\, Department of Electrical Engineering and Computer Science at the University of Missouri\, Columbia\, USA. \n\n\n\nTitle3D-Equivariant Graph Neural Networks for Refining and Evaluating Protein Structures \n\n\n\nAbstract \n\n\n\nDeep learning is revolutionizing the prediction of protein structure and is close to solve this grand challenge hanging over the scientific world for many years. In this talk\, I will describe how this technology emerged in the field\, how it overcame various technical hurdles to reach a high accuracy of predicting protein structures as demonstrated by AlphaFold2\, and where it is going now. I will present our latest work of applying 3D-equivariant graph neural networks with self- attention to evaluate and refine protein structural models. Our experiments demonstrate that 3D-equivariant graph network networks that are robust against the rotation and translation of 3D objects can evaluate and improve the quality of protein structures more effectively than the existing methods. URL:https://www.scilifelab.se/event/3d-equivariant-graph-neural-networks-for-refining-and-evaluating-protein-structures/ LOCATION:Online event via Zoom CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221021T090000 DTEND;TZID=Europe/Stockholm:20221021T093000 DTSTAMP:20260403T225555 CREATED:20220831T154039Z LAST-MODIFIED:20220928T142401Z UID:10000664-1666342800-1666344600@www.scilifelab.se SUMMARY:[Clinical Talks] Stanford Ignite: Lessons learned from teaching entrepreneurs DESCRIPTION:Yossi Feinberg\n\n\n\nThe Adams Distinguished Professor of Management and Professor of Economics at Stanford Graduate School of Business (GSB) \n\n\n\n\n\n\n\nYossi Feinberg received his PhD in Mathematics from the Hebrew University in Jerusalem in 1997. His thesis studied how differing prior beliefs of decision makers can be expressed by their disagreement on current (posterior) events. After completing his dissertation under the supervision of Nobel Laureate Professor Robert J. Aumann\, Yossi began teaching economics at Kellogg Graduate School of Management. Yossi joined Stanford GSB in 1998. \n\n\n\nYossi’s teaching interests include Economics of Organization\, Managerial Economics\, Strategy\, Information Markets\, Game Theory and Applied Decision Making. In 2003 he received the MBA distinguished teaching award. \n\n\n\nYossi’s recent research interests include\, for example\, the analysis and implication of strategic decision making in the face of unawareness. He has modeled games with unawareness and their solutions. In these games each decision maker can reason about the extent to which others may only have a limited perception of the full scale of the economic interaction at hand. Yossi was an Associate Editor of the Journal of Economic Theory and is serving as a referee for all major microeconomics journals. He has given numerous invited seminars as well as multiple plenary talks at academic conferences. \n\n\n\nHe has been consulting in a wide range of industries including hi-tech\, media and healthcare as well as giving invited talks on topics such as pricing\, the sub-prime crisis\, in-house vs. outsourcing\, allocating decision power in organizations and strategic interactions. \n\n\n\nHe is the faculty director of Stanford Ignite\, a global innovation program running on the Stanford Campus. \n\n\n\nregister to receive zoom link\n\n\n\nStanford Ignite\n\n\n\nStanford Ignite grew out of a new kind of entrepreneurial educational program initiated in 2006 and spearheaded by Professor Yossi Feinberg. In aggregate\, about 1\,600 past participants have started more than 100 successful companies since the program was introduced. \n\n\n\nStanford Ignite is a certificate program that provides the business fundamentals necessary to succeed at any entrepreneurial or intrapreneurial venture. Business concepts learned in the classroom span core business skills and functional skills\, and are reinforced through practical application with team venture projects\, where participants work by project-based learning approach\, in teams of five or six to develop a new product or service for an existing organization or a new venture.Previous participants include graduate students currently pursuing a master’s\, MD\, PhD\, or post-doc program in a nonbusiness field\, with a strong representation from the Life Sciences area. A key attribute to of the success of the program is the close academic experience it offers. Participants engage directly with the same renowned faculty that teach in the Stanford MBA Program. Participation in real-time lectures\, case evaluations\, Q&A sessions\, small group discussions\, workshops\, panels\, and team projects. The program also features guest speakers from leading companies\, many of whom become venture-project mentors. \n\n\n\nKey Benefits\n\n\n\nStanford Ignite –is a certificate program that provides the business fundamentals to succeed at any entrepreneurial ventures. \n\n\n\nLearn fundamental business concepts from core business frameworks to tactical skills.Reinforce and apply lessons learned by working on a team to develop a new product or service.Improve communication\, elevator pitch\, and presentation skills in a daylong communications bootcamp.Present your idea and get robust feedback from venture capitalists\, angel investors\, industry experts\, and experienced entrepreneurs.\n\n\n\n \n\n\n\nClinical Talks\n\n\n\nClinical Talks is back for more! With a brand new and shiny Season 6. After successfully completing 5 seasons with > 70 enthusiastic Clinical Talkers to our record\, we have barely scratched the surface of all the amazing work our clinical\, academic and industry Life Science community has to offer. More about the upcoming events is available here. \n\n\n\nThese events are co-organized by Karolinska Institutet Innovations AB and SciLifeLab\, and brought to you by Colibri Ventures. URL:https://www.scilifelab.se/event/clinical-talks-yossi-feinberg/ LOCATION:Online event via Zoom CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/08/Square-500x500-Clinical-Talks@4x.png ORGANIZER;CN="Clinical Talks":MAILTO:precisionmedicine@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221020T120000 DTEND;TZID=Europe/Stockholm:20221020T130000 DTSTAMP:20260403T225555 CREATED:20220830T081026Z LAST-MODIFIED:20221006T141414Z UID:10000659-1666267200-1666270800@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Simin Zhang DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nThis week:\n\n\n\n\n\n\nSimin Zhang\n\n\n\nSean Rudd – alpha 5 \n\n\n\nTargeting nucleotide catabolic enzymes to improve chemotherapies \n\n\n\n\n\n\n\n\n\n \n\n\n\n \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page. URL:https://www.scilifelab.se/event/campus-solna-seminar-series-oct-20/ LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna CATEGORIES:Community ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/08/logo_PhD_Postdoc_Council.png ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221020T093000 DTEND;TZID=Europe/Stockholm:20221020T163000 DTSTAMP:20260403T225555 CREATED:20220620T082646Z LAST-MODIFIED:20221020T060635Z UID:10000629-1666258200-1666283400@www.scilifelab.se SUMMARY:The 8th RIKEN-KI-SciLifeLab Symposium DESCRIPTION:Preparing for the next pandemic \n\n\n\n\n\nCOVID-19 pandemic responses were organized by countries according to their needs. The preparations for responses to potential future pandemics are currently addressed by organizations including RIKEN\, Karolinska Institutet and SciLifeLab with prominent roles in Japan and Sweden\, respectively. This symposium event\, which is part of the RIKEN-KI-SciLifeLab Symposium Series\, addresses the political\, organizational and practical aspects of preparedness for potentially upcoming pandemics with focus on Japan and Sweden.  \n\n\n\nThis symposium is co-organized and sponsored by JSPS Stockholm Office. \n\n\n\n\n\n\n\nDate and location 2022-10-20 (THU)  \n\n\n\n09:30-16:30 Symposium  \n\n\n\n16:30-18:00 Social mingle  \n\n\n\n \n\n\n\n\n\n\n\n\nDownload Program (PDF)\n\n\n\n\n\n\n\n\nRegistration\n\n\n\n\n\n\n\nSymposium history\n\n\n\nEach symposium of the series is centered on one specific topic. Topics from previous years are: Molecular Imaging and Genomics (2014)\, Structural Biology for Drug Discovery (2015)\, Decoding Health and Disease with a) Imaging & Disease\, b) RNA & Disease\, c) Single\, Rare and Stem cells & Disease (2016)\, Life Science Frontiers in Health\, Disease and Aging\, with sessions a) Gene Expression in Disease and Aging\, b) Neural Function\, Disease and Therapy\, c) Molecular Aspects of Health\, Disease and Aging\, d) Visualizing Health\, Disease and Aging\, e) Molecular Network Control (2017)\, Artificial Intelligence meet Life Sciences (2018)\, and Biomedical Data for Artificial Intelligence (2019\, 2020). URL:https://www.scilifelab.se/event/the-8th-riken-ki-scilifelab-symposium/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/06/IMG_6802.jpeg END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221018T120000 DTEND;TZID=Europe/Stockholm:20221018T130000 DTSTAMP:20260403T225555 CREATED:20221011T110401Z LAST-MODIFIED:20221011T110403Z UID:10000712-1666094400-1666098000@www.scilifelab.se SUMMARY:The Protein Expertise Platform - a Core Facility at the KBC and a node of PPS DESCRIPTION:In the frame of the “SciLifeLab Site Umeå / KBC Infrastructure Seminar Series”\, the seminars will be organised every second Tuesday during autumn 2022. The seminars will be held in a hybrid format IRL in Glasburen\, KBC\, and online via Zoom. Take the chance to get information on facilities\, possibilities and services that infrastructure\, both SciLifeLab-associated and local\, can offer! Learn more about the seminar series and the schedule for autumn 2022 here: https://www.umu.se/en/research/infrastructure/medicinska-fakulteten/u/umea-centre-for-electron-microscopy-ucem/scilifelab-in-umea/scilifelab-site-umea–kbc-infrastructure-seminar-series/ \n\n\n\nOn October 18th\, 12:00-13:00\, you are welcome to participate in the seminar \n\n\n\nThe Protein Expertise Platform – a Core Facility at the KBC and a node of PPS \n\n\n\nby Uwe Sauer\, Associate professor\, PEP coordinator\, Department of Chemistry\, Umeå University \n\n\n\nRead more\n\n\n\nSeminar description: Proteins play a central role for most cellular processes. In order to study such processes\, Swedish Life-Science researchers rely on high-quality protein reagents for their research. At the Protein Expertise Platform (PEP) at the Dept. of Chemistry and the KBC\, we work with the custom production of recombinant proteins in E. coli and plant cell suspensions. We have teamed up with six other Swedish protein production platforms and\, since 2022\, are part of Protein Production Sweden (PPS)\, a national research infrastructure for protein production (www.gu.se/pps) funded by VR and the local Universities. PPS provides expert competence in a variety of expression systems\, including E. coli\, insect cells\, P. pastoris\, plant cells and cell-free translation. The PPS nodes collaborate in the form of a national distributed research infrastructure and provide expertise in gene and vector design\, production and purification of the proteins\, as well as methods for quality control. PPS can also produce proteins with different labels. \n\n\n\nResearchers can apply for project support through a common application portal found on the PPS website. \n\n\n\nRegistration: To register your physical attendance and reserve your free sandwich\, please go to the registration Link: https://www.umu.se/en/chemical-biological-centre/kbc_events/registration-form-infrastructure-seminar/ \n\n\n\nRegistration deadline: Monday\, 17 October\, 10:00. \n\n\n\nOnline attendance: You can also join the seminar on Zoom\, https://umu.zoom.us/j/63138997026 (registration is not required) \n\n\n\nMore information about PEP: https://www.umu.se/en/research/infrastructure/pep/ \n\n\n\nOrganisers: SciLifeLab Site Umeå and Chemical Biological Centre (KBC) URL:https://www.scilifelab.se/event/the-protein-expertise-platform-a-core-facility-at-the-kbc-and-a-node-of-pps/ LOCATION:Glasburen Seminar Room\, Chemical Biological Centre (KBC) Building\, Umeå University\, Umeå\, 901 87\, Sweden CATEGORIES:Event ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221017T151500 DTEND;TZID=Europe/Stockholm:20221017T161500 DTSTAMP:20260403T225555 CREATED:20221009T184510Z LAST-MODIFIED:20221009T185208Z UID:10000710-1666019700-1666023300@www.scilifelab.se SUMMARY:[The Svedberg] - Manfred Schartl DESCRIPTION:Developmental Biochemistry\, University of Würzburg\, Germany \n\n\n\nTime: 15:15Venue: C8:305\, BMC\, Uppsala \n\n\n\nHost: Leif Andersson\, Uppsala University \n\n\n\nTitle of the talk: Evolution of sex determination and sex chromosomes in fish \n\n\n\nBio: Prof. Manfred Schartl studied Biology and Chemistry at the University of Giessen\, Germany\, and graduated in Genetics. After postdoctoral research in Giessen and at the NIH in Bethesda he was team leader of a research group from 1985 to 1991 at the Gene Center of the Max Planck Institute for Biochemistry in Martinsried\, Germany. Until 2019 he was full professor and chairman of Physiological Chemistry at the Biocenter of the University of Würzburg. Currently\, he heads a research group as senior professor at the Biocenter and works as scholar in residence at the Xiphophorus Genetic Stock Center at Texas State University in San Marcos. He is member of the German Academy of Sciences\, Leopoldina\, and the European Academy of Sciences\, Academia Europea. He holds an honorary doctorate from the University of Bergen\, Norway.He uses the small aquarium fish biomedical models Xiphophorus and Medaka to understand molecular processes of organ development and their malfunction in disease with a focus on pigment cells and melanoma and another one on sex determination and gonad development. Key to his research is taking an evolutionary perspective to answer these questions on the basis of comparative genomics and molecular biology experimental studies. \n\n\n\nAbstract: Sex determination (SD) is unique biological process in showing an astonishing plasticity of mechanisms. Fish present the greatest variability of SD amongst vertebrates. In the case of genetic SD this is linked to a similarly high variability of sex chromosome differentiation. While in a handful of species with genetic SD the master SD genes have been identified\, their molecular function in directing the development of the bipotential gonad primordium towards testis or ovary is unclear in many cases or incompletely known in the others. To obtain a deeper understanding of this diversity we need a better knowledge of the molecular basis of SD mechanisms and the structure and genetic organization of sex chromosomes across a broad diversity of fish. To identify sex chromosomes and primary SD genes\, we use high throughput RAD-tag marker mapping\, transcriptomics\, Pool-Seq and whole genome sequencing to identify sex-specific chromosomal regions and candidate SD genes in sharks\, sturgeons and teleosts. This led to the identification of sex-specific markers\, allowing to delineate the extent of recombination suppression\, which turned out to be highly variable between species. We identified several species with clear cut XX/XY or ZZ/ZW monofactorial systems but also species with more complex sex-determination systems including species with a mix of genetic SD and environmental SD and species with potential polygenic systems. In species with available genomic resources\, sex-specific markers could be used to assign scaffolds to regions that are supposed to contain the primary SD gene. We identified candidate genes in several species and find that most of them belong to already known factors of the primary SD regulatory network including candidate genes that have not been found so far as being SD genes. We also find that many species harbor very poorly differentiated sex-chromosomes. The SD variety does not follow a phylogenetic pattern\, and turnovers of the genetic SD system from male to female heterogamety and vice versa are frequent in some groups\, making the evolutionary instability of SD a spectacular trait whose biological meaning is not yet understood. URL:https://www.scilifelab.se/event/the-svedberg-manfred-schartl/ 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:20221017T100000 DTEND;TZID=Europe/Stockholm:20221018T140000 DTSTAMP:20260403T225555 CREATED:20220622T085908Z LAST-MODIFIED:20221128T095930Z UID:10000634-1666000800-1666101600@www.scilifelab.se SUMMARY:Facility Forum DESCRIPTION:Facility Forum is a two-day event exclusively for the SciLifeLab infrastructure community\, including platform and unit leadership\, staff\, and administrative personnel\, as well as central management and support teams. \n\n\n\nThe event aims to bring everyone updated on what is cooking at SciLifeLab\, promote cross-platform and cross-unit interactions\, and enable discussions on urgent topics related to infrastructure operations. We offer inspiring talks\, network activities\, discussions in parallel sessions\, and dinner with entertainment in the evening on day one. The second day is devoted to platform-wise activities and ends with a joint lunch. We have a maximum number of participants (400p). \n\n\n\nYour participation includes the following: \n\n\n\n\nBus from/to Cityterminalen\, Tomtebodavägen Solna or BMC Uppsala\n\n\n\nConference program\n\n\n\nLunches and coffee breaks\n\n\n\nTeamwork activity\n\n\n\nConference dinner\n\n\n\nOvernight stay in a single/double room (only for participants of Day 1+2)\n\n\n\n\n\n\n\n\nBus transport to Djurönäset\, Oct 17\n\n\n\nDeparture from BMC Uppsala at exactly 07:15 \n\n\n\nDeparture from Tomtebodavägen 23\, Solna at exactly 08:00 \n\n\n\nDeparture from Cityterminalen\, Stockholm at exactly 08:30(Gate number is shown on the digital screens inside the terminal building\, 30 minutes before departure) \n\n\n\nBus transport from Djurönäset\, Oct 18\n\n\n\n14:00 Busses to Cityterminalen\, BMC Uppsala\, and Tomtebodavägen departs from Djurönäset \n\n\n\n\n\n\n\nBus transport to Fågelbrohus\, evening Oct 17 and morning Oct 18\n\n\n\nThe event is fully booked\, and accommodation (single room) at Fågelbrohus (about 10 minutes by bus) has been arranged for the latest registered participants. The Fågelbrohus residents are welcome to use the SPA at Djurönäset before dinner. \n\n\n\n22:00 Bus departs to Fågelbrohus \n\n\n\n23:30 Bus departs to Fågelbrohus \n\n\n\n08:30 Bus departs to Djurönäset from Fågelbrohus \n\n\n\n\n\n\n\nProgram\n\n\n\n\nDownload Program\n\n\n\n\n\n\n\n\nProgram\nOctober 17\n\n\n\n09:00Coffee\, sandwich\, and registration10:00Welcome. SciLifeLab talk show with guests\, Stora KongressenShort break 11:00-11:30 and 12:00-12:10 12:45Conference lunch13:45Drop-in Poster session and coffee\, Stora Kongressen14:30Teamwork activity\, instructions from the stage\, Stora KongressenCoffeeCheck-in15:30Parallel sessions (see Workshops A-G below) 17:00Free time\, SPA available18:15Aperitif and music\, Lounge\, main building19:00Conference dinner and entertainment\n\n\n\nOctober 18\n\n\n\n09:00Platform-wise program09:00 Platform-wise programClinical Genomics\, House 7\, Room Lilla KongressenOperations office/SISU\, Room 1K+1ASpatial and Single Cell Biology\, Room 2AGenomics\, Room 3ADDD\, Room\, 4ABioinformatics\, Room 5AClinical Proteomics and Immunomonitoring\, Room 6ACBGE\, Room 1ECellular and Molecular Imaging\, Room 2EIntegrated Structural Biology\, Room 3EMetabolomics\, Room 4EData center\, Room 5E09:30Coffee is served in the lounge\, outside the meeting rooms from 09:30-11:00. Special requirements in House 6.12:45Conference lunch14:00Bus transfer\n\n\n\n \n\n\n\n\n\n\n\n\nWorkshops\n\n\n\nSciLifeLab Training Hub\nMeet the team for the SciLifeLab Training Hub to discuss how training\, courses\, lifelong learning\, and education of the infrastructure users should be organized in a nationally coordinated model to optimally serve both the platforms and the Swedish life science research community. \n\n\n\nLocation: ROOM 6A \n\n\n\nWorkshop leader\n\n\n\nJessica Lindvall \n\n\n\n\nHow do you reach out? – Improve your communication skills\nReflections and advice on reaching out to target groups outside science with a focus on presentation techniques. \n\n\n\nContents include \n\n\n\n\nFive core principles of effective communication\n\n\n\nPopularizing science – some hands-on advice\n\n\n\nThe Five Ps: Planning\, Preparing and Performing Persuasive Presentations\n\n\n\nPreparing an elevator pitch – a walkthrough\n\n\n\nPractical advice for connecting with the audience\n\n\n\n\nLocation: ROOM 2A \n\n\n\nWorkshop leader\n\n\n\nOlle Bergman \n\n\n\n\nHow to serve academic vs non-academic infrastructure users and the work towards harmonized SciLifeLab models\nMeet the SciLifeLab External Relations Office and SciLifeLab/KTH lawyer to discuss models to interact with different user categories\, user fee policies\, priorities\, contracts\, legal aspects\, and intellectual property rights. \n\n\n\nLocation: ROOM 4A \n\n\n\nWorkshop Leader\n\n\n\nJosefin Lundgren Gawell \n\n\n\n\nIT and data management services for SciLifeLab infrastructure\nMeet representatives from SciLifeLab Data Centre to find out about services available for your platform/unit and to discuss future needs. Learn about the Data Centre plans and how to get involved in testing of upcoming systems and services. \n\n\n\nLocation: ROOM 3A \n\n\n\nWorkshop leader\n\n\n\nHanna Kultima \n\n\n\n\nPrecision medicine at SciLifeLab\nHow can the infrastructure contribute to implementation of precision medicine into routine clinical care in Sweden? An interactive workshop and discussion with representatives from the SciLifeLab Precision Medicine team. \n\n\n\nLocation: ROOM LILLA KONGRESSEN\, 7A \n\n\n\nWorkshop leader\n\n\n\nÅsa Johansson \n\n\n\n\nQuality aspects of infrastructure operations\, data handling and scientific output\nIn the light of the recommendations from our International Advisory Board\, this workshop will focus on discussions on how to increase the quality of the research that is facilitated by the infrastructure. This involves among other things aspects of the service repertoire\, modes of operation\, cross-platform interactions\, and data handling. \n\n\n\nLocation: ROOM 1A \n\n\n\nWorkshop leader\n\n\n\nAnnika Jenmalm Jensen \n\n\n\n\nPlanetary Biology – understanding ecosystems from molecular to planetary scale\nMeet the scientific leads of the recently launched Planetary Biology capability at SciLifeLab and find out more about the mission and vision. Brainstorm with us about what technologies and methods in the SciLifeLab infrastructure toolbox could be of value to the target research community in visionary and forward-looking discussions. \n\n\n\nLocation: ROOM 5A \n\n\n\nWorkshop Leaders\n\n\n\nStefan Bertilsson & Olga Vinnare Pettersson \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nImportant information\n\n\n\nRegistration: Registration has closed\, and we have a waiting list. We have 400 p. registered for Facility Forum. \n\n\n\nCancellations: In the unfortunate case that you need to cancel your participation\, send an email to infra@scilifelab.se ASAP so we can have someone from the waiting list take your place. \n\n\n\nParallel sessions: All the participants have been granted their first choice of workshop. \n\n\n\nOvernight stay: Only participants of Day 2 are allowed the overnight stay. We have exceeded the number of rooms available at Djurönäset\, så the last registered persons will stay at Hotel Fågelbrohus. A bus transfer from/to Djurönäset (about 10 minutes) will be provided in the evening and the morning. We have used the first-come-first-served principle\, and a large number of people are accommodated with a roommate. All double rooms have separate beds. If you can stay in a double room\, let us know your room mate. \n\n\n\nConference dinner: If necessary\, priority will be given to people participating for two days. \n\n\n\nGetting there by public transport: Visit www.sl.se and make a query for your journey – e.g. from T-centralen to Djurönäset. Bus 433 and bus 434 departs regularly from Slussen to Djurönäset. \n\n\n\nFor questions about Facility Forum\, please contact infra@scilifelab.se \n\n\n\n \n\n\n\nOrganizing committee\n\n\n\nChair: Annika Jenmalm Jensen\, SciLifeLab Infrastructure Director \n\n\n\nOperations office: Erika Bergqvist Erkstam\, project leader\, Maria Bäckström\, David Gotthold\, Lars Johansson\, Alice Sollazzo\, Samuel Avraham\, Charlotte Stadler\, Björn Nystedt\, and with fantastic support from the Platform Coordination Officers. URL:https://www.scilifelab.se/event/facility-forum/ LOCATION:Djurönäset\, Seregårdsvägen 1\, Djurhamn CATEGORIES:Community ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/06/ff_temabild-scaled.jpg ORGANIZER;CN="Operations office":MAILTO:events@SciLifeLab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221014T153000 DTEND;TZID=Europe/Stockholm:20221014T170000 DTSTAMP:20260403T225555 CREATED:20221010T171937Z LAST-MODIFIED:20221010T172151Z UID:10000711-1665761400-1665766800@www.scilifelab.se SUMMARY:The Dark Side of Science: Misconduct in Biomedical Research DESCRIPTION:Researchers in all stages of their career are welcome to attend and could find the talk useful. Kindly feel free to extend the invitation to your home universities.  \n\n\n\nFlyer-BAM-Elisabeth-BikDownload\n\n\n\nScience builds upon science. Even after peer-review and publication\, science papers could still contain images or other data of concern. If not addressed post-publication\, papers containing incorrect or even falsified data could lead to wasted time and money spent by other researchers trying to reproduce those results. Several high-profile science misconduct cases have been described\, but many more cases remain undetected. Elisabeth Bik is an image forensics detective who left her paid job in industry to search for and report biomedical articles that contain errors or data of concern. She has done a systematic scan of 20\,000 papers in 40 journals and found that about 4% of these contained inappropriately duplicated images. In her talk she will present her work and show several types of inappropriately duplicated images and other examples of research misconduct. In addition\, she will show how to report scientific papers of concern\, and how journals and institutions handle such allegations. \n\n\n\nElisabeth Bik\, PhD is a Dutch-American microbiologist who has worked for 15 years at Stanford University and 2 years in industry. Since 2019\, she is a science integrity volunteer and consultant who scans the biomedical literature for images or other data of concern and has reported over 6\,000 scientific papers.  Her work has resulted in over 900 retracted and almost 1\,000 corrected papers.  \n\n\n\nWho the event is aimed at i.e.\, who will attend:  Researchers in all stages of their career are welcome to attend and could find the talk useful. Kindly feel free to extend the invitation to your home universities.  \n\n\n\nSpeakers: Dr. Elisabeth Bik URL:https://www.scilifelab.se/event/the-dark-side-of-science-misconduct-in-biomedical-research/ LOCATION:Online event via Zoom CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/08/logo_PhD_Postdoc_Council.png ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221013T151500 DTEND;TZID=Europe/Stockholm:20221013T163000 DTSTAMP:20260403T225555 CREATED:20221005T112555Z LAST-MODIFIED:20221005T113202Z UID:10000707-1665674100-1665678600@www.scilifelab.se SUMMARY:[The Svedberg seminar] Prof. Jay Hinton DESCRIPTION:University of Liverpool\, UK \n\n\n\nTime: 15:15Venue: C8:305\, BMC\, Uppsala \n\n\n\nHost: Siv Andersson\, Uppsala University \n\n\n\nProf. Jay Hinton is Professor of Microbial Pathogenesis at the University of Liverpool. Prof. Prof. Hinton has developed RNA-seq-based approaches for studying gene expression of in vitro-grown and intra-macrophage bacteria. He is currently using functional genomics methods to understand how new Salmonella pathovariants are causing endemic bloodstream infections across sub-Saharan Africa. This disease has killed around 500\,000 people over the last decade. \n\n\n\nTitle of the talk: How has Salmonella become so dangerous in Africa?\n\n\n\nWith 3.4 million infections each year\, invasive non-Typhoidal Salmonella (iNTS) is a major cause of illness worldwide. In Sub-Saharan Africa\, bloodstream infections involving iNTS Salmonella enterica serovar Typhimurium are causing ~49\,000 deaths annually. Co-infection with HIV or malaria in adults\, and a young age (<5 years) are known risk factors. The main causative agent of iNTS is a pathovariant of Salmonella Typhimurium called ST313\, which is multi-drug resistant and closely-related to the ST19 type of Salmonella responsible for gastroenteritis globally. \n\n\n\nUsing a combination of comparative genomics and comparative transcriptomics\,we discovered phenotypic differences that distinguish African from global Salmonella pathovariants (Canals et al.\, 2019; Honeycutt et al.\, 2020). \n\n\n\nOur analysis led us to identify a single core genome SNP responsible for the up-regulation of a single promoter in strain D23580 that controlled the expression of a Salmonella virulence factor (Hammarlöf et al.\, 2018)\, and offers part of the explanation of the pan-African epidemic of bloodstream infection.All of the Salmonella transcriptomic data we have generated are now available online in a user-friendly website that allows intra-strain and inter-strain comparisons of gene expression between African and global pathovariants ofS. Typhimurium: https://tinyurl.com/SalComD23580 \n\n\n\nMost recently\, we used the combined power of genomics and epidemiology and thousands of historical and contemporary Salmonella isolates to understand the precise evolutionary trajectory of the S. Typhimurium ST313 pathogen in Africa. We identified a series of novel genome degradation events that impacted upon the function of Salmonella genes required for colonisation of the mammalian gut\, providing evidence of niche adaptation and the continuing evolution of ST313 (Pulford et al.\, 2021). \n\n\n\nI will summarise the evolutionary pathway of invasive S. Typhimurium across Africa\, and explain the value of an integrated functional genomic analysis for understanding how bacterial pathogens cause disease. \n\n\n\nReferencesCanals et al. (2019) Adding function to genome of African Salmonella Typhimurium ST313. PLoS Biology 17(1): e3000059. DOI: 10.1371/journal.pbio.3000059 \n\n\n\nHammarlöf et al. (2018) Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella. PNAS 115: E2614 – E2623. \n\n\n\nDOI: 10.1073/pnas.1714718115 \n\n\n\nHoneycutt et al. Genetic variation in the MacAB-TolC efflux pump influences pathogenesis of invasive Salmonella isolates from Africa. PLoS Pathog. 2020 16:e1008763. DOI: 10.1371/journal.ppat.1008763 \n\n\n\nPulford et al. (2021) Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. Nature Microbiology 6: 327–338. \n\n\n\nDOI:10.1038/s41564-020-00836-1 URL:https://www.scilifelab.se/event/the-svedberg-seminar-prof-jay-hinton/ 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:20221013T150000 DTEND;TZID=Europe/Stockholm:20221013T160000 DTSTAMP:20260403T225555 CREATED:20221005T141602Z LAST-MODIFIED:20221005T141605Z UID:10000708-1665673200-1665676800@www.scilifelab.se SUMMARY:Structural proteogenomics analyses of circulating antibody repertoires DESCRIPTION:We showcase a novel structural proteogenomics workflow to decipher the properties of circulating antibody repertories relating to immunity against bacteria and viruses. \n\n\n\nProf. Johan Malmström\, Lund University \n\n\n\nOctober 13th\, 15:00-16:00 SciLifeLab Gamma-2 lunchroom URL:https://www.scilifelab.se/event/structural-proteogenomics-analyses-of-circulating-antibody-repertoires/ LOCATION:Gamma 2 Lunchroom\, SciLifeLab\, Tomtebodavägen 23\, Solna\, Sweden CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221013T120000 DTEND;TZID=Europe/Stockholm:20221013T130000 DTSTAMP:20260403T225555 CREATED:20220830T080828Z LAST-MODIFIED:20220927T110646Z UID:10000658-1665662400-1665666000@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Aditi Shenoy and Jean Froment DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nThis week:\n\n\n\n\n\n\nAditi Shenoy\n\n\n\nArne Elofsson – alpha 6 \n\n\n\nEvaluation of AlphaFold-Multimer predictions – edge cases and exploring its utility for binding-site prediction \n\n\n\n\n\nJean Froment\n\n\n\nJonathan Martin – gamma 5 \n\n\n\nWhy is the air toxic? Virtual effects-directed analysis (vEDA) of fine particulate matter (PM2.5) \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page. URL:https://www.scilifelab.se/event/campus-solna-seminar-series-oct-13/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Community ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/08/logo_PhD_Postdoc_Council.png ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221011T120000 DTEND;TZID=Europe/Stockholm:20221011T130000 DTSTAMP:20260403T225555 CREATED:20220927T104040Z LAST-MODIFIED:20220927T104229Z UID:10000693-1665489600-1665493200@www.scilifelab.se SUMMARY:Clinical Genomics Gothenburg - Infrastructure and Research services DESCRIPTION:Clinical Genomics Gothenburg – Infrastructure and Research services\n\n\n\nMeena Kanduri\, Clinical Genomics\, SciLifeLab Göteborg \n\n\n\nJoin us to learn more about the NGS-based services and the bioinformatic support that we offer at Clinical Genomics Gothenburg (CGG) unit with a focus towards translational and clinical research. \n\n\n\nSciLifeLab is a national infrastructure within life science with a wide range of advanced technology and expertise. The newly started SciLifeLab site in Gothenburg includes units at both the University of Gothenburg and Chalmers University of Technology and has a strongconnection to Sahlgrenska University Hospital. This seminar series is started with an overview of the site\, followed by presentations by the individual units. \n\n\n\nA light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available\, please click the zoom-link below to join the event at the appointed time. \n\n\n\nVenue\n\n\n\nAssembly Room Birgit Thilander\, Medicinaregatan 3 URL:https://www.scilifelab.se/event/clinical-genomics-gothenburg-infrastructure-and-research-services/ LOCATION:Birgit Thilander Lecture Hall\, Medicinaregatan 3\, Göteborg CATEGORIES:Event ORGANIZER;CN="SciLifeLab Gothenburg":MAILTO:gothenburg@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20221011T090000 DTEND;TZID=Europe/Stockholm:20221013T170000 DTSTAMP:20260403T225555 CREATED:20220621T074909Z LAST-MODIFIED:20220831T075512Z UID:10000630-1665478800-1665680400@www.scilifelab.se SUMMARY:Introduction to Data Management Practices DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees within all Swedish universities. This course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. \n\n\n\nNote: We follow the recommendations and guidelines from Swedish authorities and Folkhälsomyndigheten. The course is designed to be an interactive face-to-face event. However\, we follow the situation carefully and will deliver the course online if needed. \n\n\n\nContact: edu.intro-dm@nbis.se \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication opens:  open now \n\n\n\nApplication closes:  2022-09-09 \n\n\n\nConfirmation to accepted students:  2022-09-13 \n\n\n\n\n\n\n\n\n\nCourse Website\n\n\n\n\n\nApplication\n\n\n\n\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\n1500 SEK paid by invoice to NBIS. This includes lunches\, coffee and snacks. Please note that NBIS cannot invoice individuals. \n\n\n\nDue to limited space the course can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\n\n\n\n\nCourse content\n\n\n\nTopics covered will include \n\n\n\n• Open Science and FAIR in practice \n\n\n\n• Organising data\, files and folders in research projects \n\n\n\n• Versioning data\, documents and scripts with Git \n\n\n\n• Describing data with metadata \n\n\n\n• Cleaning tabular data and metadata with OpenRefine \n\n\n\n• Submitting data to public data repositories \n\n\n\n• Writing basic recipes for data analysis and visualisation with R \n\n\n\n\n\n\n\nLearning objectives \n\n\n\n• To get acquainted with\, and reflect upon\, the principles of Open Science and FAIR \n\n\n\n• To understand the importance of metadata\, and how it affects “FAIRness” \n\n\n\n• To learn how to organise files to make project work more efficient \n\n\n\n• To learn to clean up messy tabular data and metadata \n\n\n\n• To learn how to find\, and submit to\, relevant public repositories for data publication \n\n\n\n• To learn to apply simple version control practices on files \n\n\n\n• To learn to start using R to analyse data \n\n\n\n\n\n\n\nEntry requirements\n\n\n\nNo previous programming experience is required but you are required to bring your own laptop with the required software pre-installed. Installation instructions will be provided before the course starts. URL:https://www.scilifelab.se/event/introduction-to-data-management-practices-3/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Course ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT END:VCALENDAR