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: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 BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20240331T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20241027T010000 END:STANDARD END:VTIMEZONE BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230622T120000 DTEND;TZID=Europe/Stockholm:20230622T130000 DTSTAMP:20260404T014606 CREATED:20230101T220709Z LAST-MODIFIED:20230614T120309Z UID:10000779-1687435200-1687438800@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Marianna Tampere and Guillaume Minet 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 Presentation of ongoing (unpublished) projects is strongly encouraged.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\nMarianna Tampere\n\n\n\nPäivi Östling – alpha 4 \n\n\n\nMulti-layered drug profiling for repurposing medicines in infectious diseases – how infrastructure supports research \n\n\n\n\n\nGuillaume Minet\n\n\n\nIlaria Testa – gamma 3 \n\n\n\nModular parallelized RESOLFT setup for live-cell imaging \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-jun-22/ 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_120135408_HDR-scaled.jpg ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230628T110000 DTEND;TZID=Europe/Stockholm:20230628T120000 DTSTAMP:20260404T014606 CREATED:20230616T074651Z LAST-MODIFIED:20230616T074652Z UID:10000917-1687950000-1687953600@www.scilifelab.se SUMMARY:Call for new drug discovery pilot projects at SciLifeLab DDD with special emphasis on biologics and antibiotics DESCRIPTION:The DDD platform at SciLifeLab supports academic drug discovery project with expertise and technical capabilities. We have\, for example\, platforms to develop small molecule drugs\, therapeutic antibodies\, oligonucleotide therapeutics\, proximity-inducing agents such as bispecific antibodies and PROTACs.  \n\n\n\nIn this call\, the Drug Discovery and Development Platform (DDD) at SciLifeLab is looking for new pilot project proposals for drug discovery. All therapeutic modalities outlined above are of interest. Of special interest are new project ideas for (multispecific) biologics\, and in collaboration with ENABLE2 https://www.ilk.uu.se/enable2/\, small molecule projects for discovery of new antibiotics. \n\n\n\nNote that small projects for selections in phage display libraries for antibodies\, selections in DNA encoded chemical libraries for small molecules or limited screening for antisense or siRNA molecules can be considered.  \n\n\n\nA description of new modalities in drug discovery research can be found here: https://pubs.acs.org/doi/10.1021/acsmedchemlett.9b00582 \n\n\n\nIf you have questions about the call please contact DDD by email (dddprojectproposal@scilifelab.se). This call is open for scientists with a doctoral degree at a Swedish university or higher institution. English should be used when filling out this application. You are responsible for ensuring that the application is complete. Incomplete applications will not be processed. \n\n\n\nProgram\n\n\n\n11.00 Introduction to Anubis call for DDD pilot-projects\, Per Arvidsson \n\n\n\n11.05 Oligonucleotide therapeutics through OligoNova HUB at DDD\, Pär Matsson \n\n\n\n11.30 Questions & Answers \n\n\n\n11.45 End with a video about collaboration with SciLifeLab DDD featuring Marika Nestor\, Uppsala University \n\n\n\n \n\n\n\nWelcome!\n\n\n\nRegistration\n\n\n\nMore About the call\n\n\n\nLink to Online Event URL:https://www.scilifelab.se/event/call-for-new-drug-discovery-pilot-projects-at-scilifelab-ddd-with-special-emphasis-on-biologics-and-antibiotics/ CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230628T130000 DTEND;TZID=Europe/Stockholm:20230628T140000 DTSTAMP:20260404T014606 CREATED:20230529T134540Z LAST-MODIFIED:20230622T091701Z UID:10000898-1687957200-1687960800@www.scilifelab.se SUMMARY:Nya verktyg för att säkra biologisk mångfald i en föränderlig värld – vilken väg ska Sverige välja? DESCRIPTION:SciLifeLab i Almedalen\n\n\n\nUnder Almedalsveckan 2023 arrangerar SciLifeLab ett antal seminarier för att visa hur och debattera kring hur forskning och forskningsinfrastruktur kan bidra till att möta samhälleliga utmaningar vara för att fortsatt vara en ledande life science nation.Varmt välkommen att delta! \n\n\n\nOm du vill ha kontakt med projektteamet för SciLifeLab Almedalsveckan – kontakta Per Lek \n\n\n\n \n\n\n\nBeskrivning av samhällsfrågan\n\n\n\nJorden genomgår en biodiversitetskris. För att sätta in verksamma motåtgärder behöver vi en effektivare övervakning av biologisk mångfald än observationsstudier. En lösning är att göra DNA-analyser av miljöprover för att få information om arters närvaro och variation. Kan det vara vägen framåt? \n\n\n\nläs mer\n\n\n\nUtökad information om evenemanget:\n\n\n\nVår jord genomgår en biodiversitetskris. Arter förloras i ett allt högre tempo som en direkt följd av mänsklighetens expansion och påverkan på våra ekosystem och klimatet. För att motverka denna alarmerande utveckling måste vi kartlägga olika arters utbredning\, status och prognos. Här finns en utmaning: detta är resurskrävande och därför övervakar vi bara ett mindre urval arter vilket är otillräckligt för att utforma effektiva förvaltningsåtgärder. En väg framåt är att dra nytta av de nya analysmetoder som skapat förutsättningar för human precisionsmedicin. Samma utveckling är möjlig för att diagnostisera tillståndet i vår natur! Teknikutvecklingen går snabbt. DNA från miljöprov kan ge oss information om vilka arter som finns i närområdet samt kartlägga förekomsten av smittämnen och invasiva arter. Fördelarna och möjligheterna är många\, men finns det också en baksida? Vi bjuder in till diskussion om förutsättningar och risker med denna nya molekylära precisionsövervakning av miljön. \n\n\n\nMedverkande:\n\n\n\nStefan Bertilsson\, Professor\, Sveriges LantbruksuniversitetOlga Vinnere Pettersson\, PhD\, Uppsala UniversitetMikael Dahl\, Göteborg Universitet / IVL Svenska miljöinstitutetMats Svensson\, Avdelningschef\, Havs och Vatten myndighetenMathilda Karlsson\, Expert\, WWF SwedenGunilla Rosenqvist\, Projektledare\, Naturresurser och Hållbar utveckling\, Uppsala Universitet URL:https://www.scilifelab.se/event/nya-verktyg-for-att-sakra-biologisk-mangfald-i-en-foranderlig-varld-vilken-vag-ska-sverige-valja/ LOCATION:B-huset\, Campus Gotland\, Cramérgatan 3\, Visby\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/05/Almedalen-2022-platsen_JLG-1-scaled.jpg ORGANIZER;CN="SciLifeLab i Almedalen":MAILTO:events@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230629T120000 DTEND;TZID=Europe/Stockholm:20230629T130000 DTSTAMP:20260404T014606 CREATED:20230101T221012Z LAST-MODIFIED:20230530T095916Z UID:10000780-1688040000-1688043600@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Maximilian Senftleben 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\nTBC\n\n\n\nHåkan Jönsson – alpha 4 \n\n\n\n \n\n\n\n\n\nMaximilian Senftleben\n\n\n\nHjalmar Brismar – gamma 3 \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-jun-29/ 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:20230629T130000 DTEND;TZID=Europe/Stockholm:20230629T140000 DTSTAMP:20260404T014606 CREATED:20230529T142924Z LAST-MODIFIED:20230531T101906Z UID:10000899-1688043600-1688047200@www.scilifelab.se SUMMARY:Bättre sjukvård och forskning tack vare Europasatsning på säker storskalig lösning för genomikdata DESCRIPTION:SciLifeLab i Almedalen\n\n\n\nUnder Almedalsveckan 2023 arrangerar SciLifeLab ett antal seminarier för att visa hur och debattera kring hur forskning och forskningsinfrastruktur kan bidra till att möta samhälleliga utmaningar vara för att fortsatt vara en ledande life science nation.Varmt välkommen att delta! \n\n\n\nOm du vill ha kontakt med projektteamet för SciLifeLab Almedalsveckan – kontakta Per Lek \n\n\n\n \n\n\n\nBeskrivning av samhällsfrågan\n\n\n\nFör att förbättra sjukvården (precisionsmedicin) och öka kunskapen om genetisk variation samt i framtiden möjliggöra förebyggande behandlingar arbetar Europa tillsammans för att på ett säkert sätt skall ge forskare och läkare tillgång till viktiga genomikdata. \n\n\n\nläs mer\n\n\n\nUtökad information om evenemanget:\n\n\n\nSverige leder tillsammans med Finland utvecklingen av infrastrukturen inom EU-projektet GDI (Genomic Data Infrastructure). Målet är att GDI redan år 2026 skall vara i drift i 15 länder. För att projektet skall nå sina mål behövs en bakomliggande datahantering som uppfyller de stora säkerhetskrav som ställs på denna typ av data. Vid seminariet kommer vi att informera om det pågående arbetet samt diskutera de möjligheter projektet ger för framtidens sjukvård och forskning\, de legala och tekniska utmaningar som finns\, och hur vi på bästa sätt engagerar oss från svensk sida. Arbetet i GDI är en del av det stora arbetet med att tillgängliggöra hälsodata inom Europa (EHDS\, European Health Data Space). \n\n\n\nMedverkande:\n\n\n\nBengt Persson\, Prof.\, Uppsala Universitet\, SciLifeLab\, ELIXIRRichard Rosenqvist Brandell\, Prof.\, Genomic Medicine SwedenAnna Hagwall\, Projektledare\, Nationell BioinformatikInfrastruktur SverigeManólis Nymark\, Jurist\, European 1+ Million Genome project URL:https://www.scilifelab.se/event/battre-sjukvard-och-forskning-tack-vare-europasatsning-pa-saker-storskalig-losning-for-genomikdata/ LOCATION:B-huset\, Campus Gotland\, Cramérgatan 3\, Visby\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/05/Almedalen-2022-platsen_JLG-1-scaled.jpg ORGANIZER;CN="SciLifeLab i Almedalen":MAILTO:events@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230629T160000 DTEND;TZID=Europe/Stockholm:20230629T170000 DTSTAMP:20260404T014606 CREATED:20230529T143138Z LAST-MODIFIED:20230627T064700Z UID:10000900-1688054400-1688058000@www.scilifelab.se SUMMARY:Hur ska Sverige hänga med i den snabba globala utvecklingen inom precisionsmedicin? DESCRIPTION:SciLifeLab i Almedalen\n\n\n\nUnder Almedalsveckan 2023 arrangerar SciLifeLab ett antal seminarier för att visa hur och debattera kring hur forskning och forskningsinfrastruktur kan bidra till att möta samhälleliga utmaningar vara för att fortsatt vara en ledande life science nation.Varmt välkommen att delta! \n\n\n\nOm du vill ha kontakt med projektteamet för SciLifeLab Almedalsveckan – kontakta Per Lek \n\n\n\n \n\n\n\nSverige har en hög ambition att vara världsledande inom life science och precisionsmedicin/hälsa. Hur skapar vi ett globalt konkurrenskraftigt Sverige som säkerställer att nya teknologier\, datadriven diagnostik\, individanpassad behandling och prevention kommer patienter och samhället till nytta? \n\n\n\nläs mer\n\n\n\nUtökad information om evenemanget:\n\n\n\nNya teknologier och datadriven vård möjliggör vassare diagnostik\, individanpassad behandling och sjukdomsprevention. SciLifeLab är en nationell infrastruktur som erbjuder spjutspetsteknologier och avancerad dataanalys och fungerar som ett drivhus för utveckling av nya diagnostiska verktyg. Parallellt arbetar Genomic Medicine Sweden (GMS) med implementering av genomikbaserad precisionsmedicin och möjliggör datadelning nationellt. Hur ska Sverige fortsätta att effektivt utveckla och integrera nya metoder i vården\, bedriva klinisk forskning och säkerställa att precisionsmedicin kommer till nytta för patienter? En sammanhållen organisation för precisionsmedicin mellan akademi\, sjukvård och industri skulle göra Sverige mer attraktivt för kliniska studier och för rekrytering av viktig kompetens. Vad är statens och regionernas ansvar för att säkerställa långsiktig finansiering och likvärdig tillgång till precisionsmedicin i Sverige? Och hur står vi oss i den allt hårdare globala konkurrensen? \n\n\n\nMedverkande:\n\n\n\n\nAcko Ankarberg Johansson\, Sjukvårdsminister\, Regeringen\n\n\n\nBeatrice Melin\, Professor\, Umeå universitet och FoUI direktör\, Region Västerbotten\n\n\n\nRichard Rosenquist Brandell\, Professor\, Karolinska Institutet\, överläkare i klinisk genetik\, Karolinska Universitetssjukhuset och föreståndare GMS\n\n\n\nJanne Lehtiö\, Professor\, Karolinska Institutet och vetenskaplig ledare för precisionsmedicin\, SciLifeLab\n\n\n\nEva Tiensuu Janson\, Professor\, Uppsala universitet\n\n\n\nMia Phillipson\, moderator\, Professor\, Uppsala universitet och bitr. föreståndare\, SciLifeLab\n\n\n\nSuzanne Håkansson\, Chef Samhällskontakter\, AstraZeneca URL:https://www.scilifelab.se/event/hur-ska-sverige-hanga-med-i-den-snabba-globala-utvecklingen-inom-precisionsmedicin/ LOCATION:B-huset\, Campus Gotland\, Cramérgatan 3\, Visby\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/05/Almedalen-2022-platsen_JLG-1-scaled.jpg ORGANIZER;CN="SciLifeLab i Almedalen":MAILTO:events@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230630T143000 DTEND;TZID=Europe/Stockholm:20230630T153000 DTSTAMP:20260404T014606 CREATED:20230529T143449Z LAST-MODIFIED:20230620T144921Z UID:10000901-1688135400-1688139000@www.scilifelab.se SUMMARY:Pandemisk laboratorieberedskap - vad hände\, vad gör vi och vad behöver vi göra till nästa gång DESCRIPTION:SciLifeLab i Almedalen\n\n\n\nUnder Almedalsveckan 2023 arrangerar SciLifeLab ett antal seminarier för att visa hur och debattera kring hur forskning och forskningsinfrastruktur kan bidra till att möta samhälleliga utmaningar vara för att fortsatt vara en ledande life science nation.Varmt välkommen att delta! \n\n\n\nOm du vill ha kontakt med projektteamet för SciLifeLab Almedalsveckan – kontakta Per Lek \n\n\n\n \n\n\n\nBeskrivning av samhällsfrågan\n\n\n\nVi kommer att drabbas av nya pandemier och vi behöver beredskap för det. Tidigt under COVID-19 pandemin blev det uppenbart att Sverige hade begränsade resurser att analysera prover och det påverkade kontrollen av pandemin. Vad var problemen? Hur löstes dem? Vad ska vi göra till nästa pandemi? \n\n\n\nläs mer\n\n\n\nUtökad information om evenemanget:\n\n\n\nFrågor rörande pandemisk laboratorieberedskap kommer att diskuteras i ett rundabordssamtal mellan experter inom området från Folkhälsomyndigheten\, de stora mikrobiologiska laboratorierna\, SciLifeLab och universiteten som alla var iblandade i hanteringen av prover från COVID-19 infekterade patienter men även forskning som behövdes för att förstå och kunna kontrollera pandemin. Tanken är att belysa vad som av problematiskt samt vad man bör göra inför nästa pandemin\, något som vi vet kommer att ske men inte när? \n\n\n\nMedverkande:\n\n\n\n\nMia Phillipson\, Professor\, Uppsala Universitet och SciLifeLab\n\n\n\nJohan Lindh\, Docent\, Sektionschef\, Akademiska sjukhuset\n\n\n\nKarin Tegmark Wisell\, Generaldirektör\, Folkhälsomyndigheten\n\n\n\nJessica Alm\, Enhetschef\, National Pandemic Center\, Karolinska Institutet\n\n\n\nPeter Nilsson\, Professor\, KTH/SciLifeLab URL:https://www.scilifelab.se/event/pandemisk-laboratorieberedskap-vad-hande-vad-gor-vi-och-vad-behover-vi-gora-till-nasta-gang/ LOCATION:D-huset\, Campus Gotland\, Kaserngatan 1\, Visby\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/05/Almedalen-2022-platsen_JLG-1-scaled.jpg ORGANIZER;CN="SciLifeLab i Almedalen":MAILTO:events@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230730T133000 DTEND;TZID=Europe/Stockholm:20230731T140000 DTSTAMP:20260404T014606 CREATED:20230425T131158Z LAST-MODIFIED:20230516T152015Z UID:10000869-1690723800-1690812000@www.scilifelab.se SUMMARY:Advances in mRNA translation and protein synthesis DESCRIPTION:The symposium is a satellite meeting of the European Biophysical Societies’ Association conference. It will start on 30 July and finish on 31 July. The symposium will highlight the latest discoveries in the field of translation and protein synthesis. Translation occurs on ribosomes that form hubs of a proteome and nucleic acids\, which are intricate in the range of functions and their structural dynamics. Those ribosomal hubs involve multiple cofactors and are implicated in disorders\, which makes them key drug targets. Since translation requires coordination and rapid exchange between multiple factors\, tracking such a system is a laborious task. In this respect\, recent developments in imaging techniques have had a major impact on our understanding of translational systems. Therefore\, alongside presentations of biological results\, there will be methodological advances. \n\n\n\nThere will be options to present your work in a short talk or a poster. \n\n\n\nTwelve talks will be selected from abstracts submitted before June 10. Please apply for oral presentation before June 10 (extended deadline). \n\n\n\nImportant information\n\n\n\nDate: July 30 13:30 to July 31st 14:00Location: Lecture hall at BMC\, Uppsala University (more details to be announced). \n\n\n\nConference fee: The Conference fee is 650 SEK\, including dinner on July 30th and lunch on July 31st. An invoice will be sent to your Department. Payments shall be made by Departments or Organizations only (no private bank account or private address will be approved). Participants from businesses and organizations with VAT numbers within the EU can claim the VAT back from their local tax authority. More information is on the EU website.  \n\n\n\nA maximum of 60 participants will be accommodated\, with participation being confirmed on a first-come-first-serve basis. \n\n\n\nRegistration\n\n\n\n\n\n\n\n\n\n\n\nInvited speakers\n\n\n\n\n\n\n\n\n\nAxel Innis\, University of Bordeaux. \n\n\n\n\n\n\n\n\n\nDanny Nedialkova\, Max Planck Institute of Biochemistry\, Martinsried. \n\n\n\n\n\n\n\n\n\nSophia Rudorf\, Leibniz University Hannover. \n\n\n\n\n\nAxel Innis\, University of Bordeaux \n\n\n\nWe are interested in how ribosomes make proteins\, how they are regulated in response to different stimuli\, and how small molecules block these molecular machines. The focus is on the bacterial ribosome and how it is affected by nascent proteins known as arrest peptides\, antimicrobial peptides\, and antibiotics. In order to study the underlying molecular mechanisms\, we use a combination of structural biology\, high-throughput functional characterization and biochemistry. \n\n\n\nDanny Nedialkova\, Max Planck Institute of Biochemistry\, Martinsried \n\n\n\nOur research seeks to define how distinct proteomes are established and maintained in eukaryotic cells\, with the long-term goal of understanding why some cell types are selectively vulnerable to dysregulated protein homeostasis in disease. To address these questions at a systems level\, we develop and apply quantitative genome-wide techniques and combine these with functional genomics in diverse eukaryotic model systems. \n\n\n\nSophia Rudorf\, Leibniz University Hannover \n\n\n\nWe employ computational\, bioinformatic\, and mathematical approaches to model and analyze biomolecular processes. Our primary focus lies on studying protein biosynthesis across various organisms and in-vitro expression systems. \n\n\n\nOrganizers\n\n\n\nMaria Selmer\, Suparna Sanyal\, Magnus Johansson\, Uppsala University. Alexey Amunts\, SciLifeLab \n\n\n\nFor any organizational inquiries\, please contact Maria Selmer. \n\n\n\nwith support from\n\n\n\nEBSASciLifeLabEMBO URL:https://www.scilifelab.se/event/advances-in-mrna-translation-and-protein-synthesis/ CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230731T080000 DTEND;TZID=Europe/Stockholm:20230804T170000 DTSTAMP:20260404T014606 CREATED:20230224T093112Z LAST-MODIFIED:20230522T142749Z UID:10000821-1690790400-1691168400@www.scilifelab.se SUMMARY:EBSA Congress 2023 DESCRIPTION:Welcome to EBSA 2023! \n\n\n\nAn EBSA congress in Sweden is timely. In 1986\, the first EBSA Workshop was hosted by the Swedish Biophysical Society and Professor Anders Ehrenberg\, the first president of EBSA. In 2023\, after a series of great EBSA meetings around Europe\, the Swedish Society for Biochemistry\, Biophysics and Molecular Biology (SFBBM) is again\, jointly with EBSA and Protein Society\, proud to host the 14th EBSA congress at Stockholm University\, supported by the Swedish National Committee for Molecular Biosciences (of the Royal Swedish Academy of Sciences). In this meeting\, we are honored to also collaborate with the Biophysical Society\, IUPAB and SciLifeLab.In Biophysics\, we investigate properties of time\, force\, and motion in biomolecular assemblies and processes – from single molecules to cells and tissues – and relate these to biological function. Biophysics has evolved dramatically since 1986\, and many Nobel prizes have been awarded to biophysicists to previous EBSA Plenary Lecturers in the past\, and Nobel Prize winners will also participate in the upcoming congress. The EBSA-2023 will be held at the Aula Magna at Stockholm University\, which is also known for hosting the Nobel Lectures in Physics and Chemistry. \n\n\n\nEBSA-2023 will offer a creative meeting ground for investigating how the most novel experimental\, theoretical and computational approaches in Biophysics can be synergistically tailored to improve our understanding of biological function\, and thereby build an even stronger scientific bridge between physics\, biology and medicine. \n\n\n\nWe are much looking forward to learning more about your most recent findings at EBSA-2023\, and to jointly enjoy novel breakthroughs in this wide and exciting field. \n\n\n\nRead more\n\n\n\n\n\n\n\nChair \n\n\n\nDr Maria Sunnerhagen\, Professor of Structural Biology\, Linköping University \n\n\n\nCo-Chairs \n\n\n\n\nDr Erik Lindahl\, Professor of Biophysics\, Stockholm University and SciLifeLab\n\n\n\nDr Lena Mäler\, Professor of Biochemistry\, Stockholm University\n\n\n\nDr Jerker Widengren\, Professor of Biomolecular Physics\, KTH Royal Institute of Technology\, Stockholm URL:https://www.scilifelab.se/event/ebsa-congress-2023/ LOCATION:Aula Magna\, Frescativägen 6\, Stockholm\, 114 18 Stockholm\, Sweden CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230816T100000 DTEND;TZID=Europe/Stockholm:20230816T104500 DTSTAMP:20260404T014606 CREATED:20230621T114415Z LAST-MODIFIED:20230815T130146Z UID:10000919-1692180000-1692182700@www.scilifelab.se SUMMARY:Project support in chemical biology and drug discovery DESCRIPTION:The chemical biology unit (CBCS) and the Drug discovery and development (DDD) platform at SciLifeLab have calls out for projects. \n\n\n\nCBCS is looking for projects in Chemical Biology which includes assay development for small molecule screening and profiling\, as well as enabling chemistry. For more information\, please visit www.cbcs.se. \n\n\n\nThe DDD platform has a call looking for new project proposals for drug discovery. All therapeutic modalities that can be developed in collaboration with the DDD platform at SciLifeLab are of interest\, including small molecules\, antibodies\, oligonucleotides and new modalities. \n\n\n\nSome users and projects are at the intersection between chemical biology and drug discovery. This webinar aims to guide users to the call that best suits the needs of their project. \n\n\n\nregister here to receive link\n\n\n\nDocumentation\n\n\n\nDDD Call for Projects \n\n\n\nCBCS Large Projects Call 2023 \n\n\n\nWebinar Slides CBCS \n\n\n\nWebinar Slides DDD URL:https://www.scilifelab.se/event/project-support-in-chemical-biology-and-drug-discovery-2/ LOCATION:Online event via Zoom CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230823T080000 DTEND;TZID=Europe/Stockholm:20230824T163000 DTSTAMP:20260404T014606 CREATED:20230608T150625Z LAST-MODIFIED:20230818T114821Z UID:10000909-1692777600-1692894600@www.scilifelab.se SUMMARY:Integrated Structural Biology workshop DESCRIPTION:Structural Biology comprises studies of proteins and nucleic acids\, how they interact and how they appear in solution. The answer provides insight in to the function of the macromolecules and can explain diseases\, basic functions or be used to understand mechanisms and in the longer perspective aim in drug design to name a few of the important areas where the techniques contributes. \n\n\n\nImportant techniques for structural biology include Cryo-EM\, Nuclear Magnetic Resonance and Structural Proteomics and all of these are available through SciLifeLab. For a structural biology project\, there is a pipeline starting with the gene and the end goal information is how and where the encoded protein functions or interacts with the surround. \n\n\n\nIt has become clear over the years that no technique alone can provide a full insight into a biological problem. Thus an integrated approach where different techniques are combined is often necessary. The aim for us working with structural biology at SciLifeLab is to be a partner along the whole way\, from gene to final answer. \n\n\n\nProgram\n\n\n\nIntegrated-Structural-Biology-Workshop-1Download\n\n\n\nDay 1\n\n\n\nWe will hear from Swedish infrastructures\, covering the whole pipeline from gene to 3D protein structure and the subsequent functional analysis\, in addition to computational aspects including AlphaFold. \n\n\n\nDay 2\n\n\n\nDay 2 will contain a general overview of structural biology and available techniques. There will also be a few presentations from participants that are given the chance to discuss and get feedback on their own project from participants but also from the infrastructure representatives. We will also have a time slot to discuss the availability of infrastructures in Sweden and if there are missing parts or suggestions for changes from the users. \n\n\n\nregistration URL:https://www.scilifelab.se/event/integrated-structural-biology-workshop/ LOCATION:Online event via Zoom CATEGORIES:Event ORGANIZER;CN="Integrated Structural Biology Platform at SciLifeLab":MAILTO:cecilia.persson@nmr.gu.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230823T090000 DTEND;TZID=Europe/Stockholm:20230824T170000 DTSTAMP:20260404T014606 CREATED:20230425T082831Z LAST-MODIFIED:20230425T083359Z UID:10000868-1692781200-1692896400@www.scilifelab.se SUMMARY:Forum for the Future of Neuroscience DESCRIPTION:What will the next 10 years of Neuroscience look like?\n\n\n\n \n\n\n\nThe global coronavirus pandemic has disproportionately affected early career researchers. This meeting is a symposium geared toward young neuroscience investigators embarking on their own research programs. Bringing together young investigators from diverse subdisciplines of neuroscience in a single venue\, where they can freely discuss the issues and future directions of their respective fields without the influence of more senior investigators\, has the potential to shape the trajectory of neuroscience in the coming decade. \n\n\n\nOn the symposium’s first day\, the event will take place at the Nobel Forum\, located close to the Karolinska Institutet in Stockholm. The Nobel Forum is where the Nobel Assembly meets to select the annual Nobel laureates in physiology or medicine \n\n\n\nOn the symposium’s second day\, the venue will shift to a more secluded location at the Swedish Collegium for Advanced Study in Uppsala. This venue\, built in 1787 to house Linneaus’s botanical collection\, is known for its peaceful and serene surroundings\, which are conducive to scholarly and intellectual pursuits. \n\n\n\n\n\n\n\nConfirmed speakers:\n\n\n\n\nJustus Kebschull JOHN HOPKINS UNIVERSITY\n\n\n\nGioele La Manno EPFL\n\n\n\nAnnegret Falkner PRINCETON UNIVERSITY\n\n\n\nTalmo Pereira SALK INSTITUTE\n\n\n\nKatharina Schmack FRANCIS CRICK INSTITUTE\n\n\n\nAshley Juavinett UNIVERSITY OF SAN DIEGO\n\n\n\nSulagna Das EMORY UNIVERSITY\n\n\n\nArkarup Banerjee CSHL\n\n\n\nNikos Konstantinides INSTITUTE JACQUES MONOD\n\n\n\nSam Golden UNIVERSITY OF WASHINGTON\n\n\n\nAlessandro Furlan KAROLINSKA INSTITUTET\n\n\n\nMarek Bartosovic STOCKHOLM UNIVERSITY\n\n\n\n\n\n\n\n\nOrganizing committee:\n\n\n\nArkarup Banerjee\, Cold Spring Harbor LaboratoryAnnegret Falkner\, Princeton UniversityAlessandro Furlan\, Karolinska InstituteDaniel Fürth\, SciLifeLab/Uppsala UniversityContact for questions: Daniel Fürthfurth@scilifelab.uu.se \n\n\n\nEvent Website: https://triplef.life/ \n\n\n\nThis event is sponsored by:\n\n\n\nMarcus Wallenberg Foundation for International Scientific CollaborationWenner-Gren FoundationsSciLifeLab URL:https://www.scilifelab.se/event/forum-for-the-future-of-neuroscience/ CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/04/Skarmavbild-2023-04-25-kl.-10.27.13.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230901T085000 DTEND;TZID=Europe/Stockholm:20230901T092500 DTSTAMP:20260404T014606 CREATED:20230822T125503Z LAST-MODIFIED:20230829T115842Z UID:10000956-1693558200-1693560300@www.scilifelab.se SUMMARY:Open online lecture by Prof. Edward Holmes: Metagenomics at the human-animal interface DESCRIPTION:The PLP (Pandemic Laboratory Preparedness) program\, started in 2021\, acts to meet society’s need for efficient use of resources\, training and education\, to propagate skills and setting up technologies and equipment to be better prepared for new pandemics. \n\n\n\nDuring the upcoming PLP program retreat\, on Friday September 1 at 08:50\, we are honored to welcome Professor Edward Holmes for an online lecture\, open for everyone to join. \n\n\n\n\n\n\n\n\n\nEdward (Eddie) Holmes is an evolutionary biologist distinguished for his work on the emergence and evolution of viruses. He has used genomic and phylogenetic approaches to reveal the major mechanisms of virus evolution and determined the genetic and epidemiological processes that explain how viruses jump species boundaries and spread in new hosts.His work has revealed the origin\, evolution and molecular epidemiology of important human pathogens including influenza\, HIV and dengue\, and enabled more accurate assessments of what types of virus are most likely to emerge in human populations and whether they will evolve human-to-human transmission. His recent research has provided fundamental insights into the breadth and biodiversity of the viral world.Eddie is currently a Professor in the School of Medical Sciences at the University of Sydney. In 2015 he was elected a Fellow of the Australian Academy of Science and in 2017 he was elected a Fellow of the Royal Society. In 2021 he received the Australian Prime Minister’s prize for science. \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nZoom link URL:https://www.scilifelab.se/event/open-online-lecture-by-prof-edward-holmes-metagenomics-at-the-human-animal-interface/ LOCATION:Online event via Zoom CATEGORIES:Event ORGANIZER;CN="SciLifeLab Event":MAILTO:events@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230904T151500 DTEND;TZID=Europe/Stockholm:20230904T161500 DTSTAMP:20260404T014606 CREATED:20230822T111554Z LAST-MODIFIED:20230822T112432Z UID:10000957-1693840500-1693844100@www.scilifelab.se SUMMARY:[The Svedberg seminar] - Toward Multidimensional Spectral Flow Cytometry: Entering the Quantum Cytometry Domain DESCRIPTION:J. Paul Robinson\, Professor \n\n\n\nDistinguished Professor of Cytometry \n\n\n\nProfessor of Biomedical Engineering \n\n\n\nPurdue University\, USA \n\n\n\n \n\n\n\n \n\n\n\nBio\n\n\n\n\n\n\n\nDr. Robinson received his early education at the University of NSW\, Sydney Australia where he received a B.Sc. (Hons)\, M.Sc. and Ph.D. degrees. He was a postdoctoral fellow in the University of Michigan Medical School then a junior faculty in the School of Pathology prior to moving to Purdue University where he was promoted to full professor in 1993. \n\n\n\nDr. Robinson is currently a Distinguished Professor of Cytometry\, and Professor of Biomedical Engineering in the Weldon School of Biomedical Engineering. He also holds appointment in the Purdue Polytechnic Institute\, School of Computer and Information Technology and IU School of Medicine. Dr. Robinson is a Fellow of the American Institute for Medical and Biological Engineering\, a Fellow of the American Association for the Advancement of Science\, a Fellow of the National Academy of Inventors and a Fellow of the Royal Microscipal Society.  Dr. Robinson is a past president of the International Society for Advancement of Cytometry and is the past Editor-in-Chief of Current Protocols in Cytometry. \n\n\n\nHe is an accomplished researcher with over 210 peer-reviewed papers\, over 400 conference presentations\, 10 books\, 15 CDs or DVDs published and over 160 invited international keynote lectures and over 20 issued patents. He formed the Purdue Cytometry Electronic Discussion list in 1989 (http://cyto.purdue.edu/hmarchiv/index.htm) and it continues today with 4500 participants. \n\n\n\nDr. Robinson is the inventor of the key patent on spectral flow cytometry that has been commercialized and morphed into one of the most significant technologies in the field of fluorescence-based single cell detection. In this regard\, together with his colleague Masanobu Yamamoto\, they recently developed the most sensitive\, highest speed single photon detector technology that is likely to have future impact on the field.  He has also worked for many years on detection technologies in the area of food borne pathogens. More recently his group has been focused on developing new approaches to toxin and pathogen detection using laser induced breakdown spectroscopy (LIBS). By combining lanthanide conjugated antibodies as target molecules for toxins\, it is possible to create a rapid detection assay that can be highly multiplexed. \n\n\n\nDr. Robinson is an accomplished mountaineer having summited several of the world’s most difficult mountains including Everest\, (8\,849m\, May 23\, 2009); Manaslu (8\,163m\, Oct 3\, 2008); and McKinley (6\,191m\, Jul 1\, 2008). In 2006 he formed the not-for-profit foundation “Cytometry for Life” (www.cytometyforlife.org) as a mechanism to promote low-cost diagnostics and education primarily in Africa and this organization continues working today to expand education and training in Africa in conjunction with AIBBC (https://www.aibbc-society.org). \n\n\n\n \n\n\n\nToward Multidimensional Spectral Flow Cytometry: Entering the Quantum Cytometry Domain\n\n\n\nFor decades flow cytometry has been a go-to technology for single cell analysis. There are clear advantages for analysis of complex suspensions of cells\, particularly when considering blood cell analysis. The principles for the latest iteration for flow cytometry technology is a spectral approach with is now 2 decades old since we first developed this approach in 2001-2003. Spectral flow cytometry has become the driving technology in the field over the past 5-7 years. What spectral cytometry has brought to the field is a vast increase in multiparameter assay capability now approaching 50 simultaneous fluorescent probes. \n\n\n\nHowever\, what we see as the future of cytometry is often based on our current view of what we presently have. And the question arises can we envisage a technology that is different from what we currently understand and use? This is a difficult question as most of us can’t exactly predict the future! What we do know is there are new tools out there that can become integrated into the field. \n\n\n\nThere is a potential for a 2nd generation spectral technology that we have been working on that may provide many more features that we currently consider when we design our experiments. This presentation will discuss the engineering developments in both current spectral analyzers and spectral cell sorters and outline the next-generation technology that will open up new frontiers in biotechnology research in both research and clinical diagnostics.  The focus will be around how do we approach quantum cytometry? Can we move from the analog world to the digital world – that is to the world where we deal with single photons – the photon being the ultimate digital event?  This requires new sensors for high-speed detection. New sensors require better optics  – more advanced diffraction approaches for light collection than currently available. High-speed sensors demand high speed electronics moving from the megahertz to the gigahertz domain. In all\, moving to quantum cytometry means redefining most of the technology that we have been using for decades.  There is a saying that “you cannot put new wine into old wine skins”! The technical demands for quantum cytometry are far more stringent that current systems allow. However\, when you meet these criteria\, the opportunities for biological detection approaches expands enormously. This presentation will outline a new sensor technology\, new laser/electronics technology and how this will generate datasets that require advanced analytical toolsets demanding AI for potentially automated diagnostics. \n\n\n\n\n\n\n\n\n\n\n\nHost: Masood Kamali-Moghaddam masood.kamali@igp.uu.se\, UU URL:https://www.scilifelab.se/event/the-svedberg-paul-robinson/ 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:20230906T090000 DTEND;TZID=Europe/Stockholm:20230906T170000 DTSTAMP:20260404T014606 CREATED:20230320T105854Z LAST-MODIFIED:20230901T113534Z UID:10000842-1693990800-1694019600@www.scilifelab.se SUMMARY:Emerging data-driven approaches to cancer DESCRIPTION:Welcome to the second in-person symposium in data-driven precision medicine and diagnostics (PMD) research area. Listen to leading experts in this area\, including Data-Driven Life Science (DDLS)\, and expand your network with international and national colleagues. \n\n\n\nThis meeting brings together the community in precision medicine and diagnostics and researchers who implemented artificial intelligence and machine learning applications in their research in PMD to improve human health and diagnostics\, introduces newly appointed DDLS fellows in the PMD research area\, and provides opportunities for networking across the research community and the SciLifeLab infrastructures. Thematically\, this meeting will focus on emerging approaches to cancer research\, ranging from both cutting-edge basic science to promising translational developments of AI. \n\n\n\nWe are excited to host international keynote speakers and welcome the community to join us. Hopefully\, this event will inspire you on the potentials of data-driven precision medicine and diagnostics in Sweden. \n\n\n\nTarget group: We welcome all researchers interested in the DDLS program and data-driven precision medicine and diagnostics. This is an onsite event only. The event will not be recorded as the speakers might share their unpublished results. \n\n\n\nDeadline for registration to guarantee fika and lunch: August 30. Note; to minimize food waste\, we ask you kindly to cancel your participation before August 30\, if you can´t participate. \n\n\n\nSpeakers\n\n\n\n\nAbhishek Niroula\, DDLS Fellow\, University of Gothenburg\n\n\n\nAvlant Nilsson\, DDLS Fellow\, Karolinska Institutet\n\n\n\nBeatrice Melin\, Umeå University\n\n\n\nBjörn Nilsson\, Lund University\n\n\n\nFredrik Strand\, Karolinska Institutet\n\n\n\nIda Larsson\, Uppsala University\n\n\n\nHannah Muti\, University Hospital RWTH Aachen\n\n\n\nKarin Forsberg Nilsson\, Uppsala University\n\n\n\nMichael Mints\, Weizmann Institute of Science\n\n\n\nNina Linder\, Uppsala University\n\n\n\nOlli Kallioniemi\, Director SciLifeLab and DDLS\n\n\n\nVeronica Rendo\, Uppsala University\n\n\n\n\n\n\n\n\nRegister here\n\n\n\nWhen the event is fully booked\, add yourself to the waiting list. You will be notified by email if a place becomes available. We kindly ask participants to cancel if they can´t come so the seat can become available to someone else. Thank you! \n\n\n\n\n\n\n\nProgram\n\n\n\nH:son Holmdahlsalen\, Ing 100/101\, 2 tr. Akademiska sjukhuset\, Uppsala. \n\n\n\n08:45Registration 08:45 – Please be seated at 09:1509:15Welcome and Introduction to Precision Medicine and Diagnostics Research AreaBasic science 1: Tumor heterogenetity and dynamics. Moderator: Sven Nelander\, SciLifeLab\, Uppsala University09:30Data-Driven Hallmarks (DDHMs) for Cancer Diagnostics and Precision Therapy\, Olli Kallioniemi\, SciLifeLab\, KI09:50Precision Medicine in Head and Neck Cancer Powered through Single-cell RNA Sequencing\, Michael Mints\, Weizmann Institute of Science\, Israel10:15Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers\, Ida Larsson\, Uppsala University10:35Coffee breakBasic science 2: Pushing the envelope on cancer genetics. Moderator Janne Lehtiö\, SciLifeLab\, KI10:55Genetic variation exposes regulators of hematopoietic stem and progenitor cells in vivo in humans\, Björn Nilsson\, Lund University11:15Using Evolutionary Constraint to Define Novel Candidate genes in Brain Tumors\, Karin Forsberg Nilsson\, Uppsala University11:35Understanding brain tumors; machine learning meets epidemiology\, Beatrice Melin\, Umeå University11:55Identification and exploration of toxic genes in human cancer\, Veronica Rendo\, Uppsala University12:15Lunch and network13:15DDLS Precision Medicine and Data Science Node\, Janne Lehtiö\, SciLifeLab\, KI13:25Panel discussion with all the speakers. Moderator: Janne Lehtiö\, SciLifeLab\, KIAI\, cancer\, and precision medicine. Moderator: Päivi Östling\, SciLifeLab\, KI14:05Artificial intelligence cervical cancer diagnostics at the point-of-care\, Nina Linder\, Uppsala University14:25AI for Breast Cancer Risk Prediction\, Fredrik Strand\, KI14:45The use of artificial intelligence in gastrointestinal oncology – past\, present and future\, Hannah Sophie Muti\, University Hospital Dresden\, Germany and EKFZ Institute for Digital Health\, Technical University Dresden\, Germany15:10Coffee breakDDLS Fellows session. Moderator: Åsa Johansson\, SciLifeLab\, Uppsala University15:30Pre-malignant clonal hematopoiesis stratifies risk of hematologic cancers\, Abhishek Niroula\, DDLS Fellow\, University of Gothenburg15:50A deep learning model of cellular networks\, Avlant Nilsson\, DDLS Fellow\, KI16:10Closing\, Sven Nelander\, Uppsala University 16:15The symposium ends\n\n\n\n\n\n\n\nFind your way to the Venue! \n\n\n\nEvent coordinator: Fulya Taylan\, DDLS RA coordination and Erika Erkstam\, Operations office\, SciLifeLab. \n\n\n\n\n\n\n\nMembers of The Data-driven Precision Medicine & Diagnostics expert group:\n\n\n\nGunnar Cedersund\, Linköping UniversitySven Nelander\, Uppsala UniversityLars Klareskog\, Karolinska InstitutetJohan Trygg\, Umeå UniversityPatrik Georgii-Hemming\, Karolinska InstitutetPäivi Östling\, KI (adj. SciLifeLab Precision Medicine Capability lead)Francis Lee (adj. WASP-HS representative in DDLS)David Gisselsson Nord (adjunct as GMS representant)Janne Lehtiö\, chair (DDLS SG member) \n\n\n\nAbstracts\n\n\n\nKarin Forsberg Nilsson Using Evolutionary Constraint to Define Novel Candidate Genes in Brain Tumors\nCurrent knowledge of cancer genomics remains biased against non-coding mutations. To systematically search for regulatory non-coding mutations\, we assessed mutations in conserved positions in the genome under the assumption that these are more likely to be functional than mutations in positions with low conservation. To this end\, we use whole-genome sequencing data from the International Cancer Genome Consortium (ICGC) and combined it with evolutionary constraint inferred from 240 mammals\, to identify genes enriched in non-coding constraint mutations (NCCMs)\, mutations likely to be regulatory in nature. We compare medulloblastoma (MB)\, which is malignant\, to pilocytic astrocytoma (PA)\, a primarily benign tumor\, and find highly different NCCM frequencies between the two\, in agreement with the fact that malignant cancers tend to have more mutations. In PA\, a high NCCM frequency only affects the BRAF locus\, which is the most commonly mutated gene in PA. In contrast\, in MB\, >500 genes have high levels of NCCMs. Intriguingly\, several loci with NCCMs in MB are associated with different age of onset\, such as the HOXB cluster in young MB patients. NCCMs in this locus were found to alter expression of HOXB2\, HOXB5 and HOXB9 in MB cells. In adult patients\, NCCMs occurred in e.g. the WASF-2/AHDC1/FGR locus. One of these NCCMs led to increased expression of the SRC kinase FGR\, and augmented responsiveness of MB cells to dasatinib\, a SRC kinase inhibitor. Our analysis thus points to different molecular pathways in different patient groups. These newly identified putative candidate driver genes may aid in patient stratification in MB\, and could be valuable for future selection of personalized treatment options. \n\n\n\nKarin Forsberg Nilsson is Professor of Stem Cell Research at the Department of Immunology\, Genetics and Pathology\, Uppsala\, and Dean of the Faculty of Medicine\, University. She is SciLifeLab Faculty\, and has a position as Guest Professor at the University of Nottingham\, UK. Karin Forsberg Nilsson obtained her PhD in 1992 from Uppsala University and did a postdoc 1994-1996 at the National Institutes of Health\, MD\, USA. She has held leadership positions in both pharmaceutical industry and academia. The focus of her lab is brain tumor biology and genetics. \n\n\n\n\nOlli Kallioniemi Data-Driven Hallmarks (DDHMs) for Cancer Diagnostics and Precision Therapy\nTranslating complex multi-level molecular profiling data into actionable insights for cancer diagnosis and therapy poses a formidable challenge. We propose here a paradigm for analyzing and interpreting in-depth multi-omics and functional drug response data derived from acute myeloid leukemia (AML)\, aiming at practical applications in precision clinical oncology. Our approach is based on Data-Driven Hallmarks (DDHMs)\, drawing inspiration from the Weinberg-Hanahan cancer hallmark concept (Hanahan\, 2022). While the original cancer hallmark concept provides a useful theoretical framework for understanding cancer\, it is not applicable for processing\, interpreting\, and translating molecular profiling data for precision diagnostics and therapy in individual patients. \n\n\n\nWe first acquired and integrated genomics\, transcriptomics\, epigenetics\, and proteomics data alongside ex-vivo drug response data for over 500 drugs across 150 AML samples\, resulting in nearly 100 million data points (Erkers et al.\, 2023). Subsequently\, we identified 11 dimensions of variability across the entire dataset\, referred here as DDHMs of AML. DDHMs intertwine specific multi-omics molecular features (potential diagnostic biomarkers) with distinct vulnerabilities to individual drugs (potential cancer treatments). DDHMs show proficiency in predicting high-risk AML and determining the effective drugs for each AML sample. The strategy of assembling drugs targeting active hallmarks in each patient offers a promising avenue for tailoring effective drug combinations. \n\n\n\nIn summary\, we showcase the conversion of millions of complex multi-omics research data into a manageable set of DDHMs\, which are based on specific biomarkers and linked drug vulnerabilities and provide an opportunity for tailoring drug treatments and drug combinations for individual patients. This approach aligns well with current practices and guidelines in translational\, clinical\, regulatory\, and industrial setting and could expedite bringing the benefits of data-driven precision medicine research to cancer patients. \n\n\n\nReferences: \n\n\n\n\nHanahan\, D. (2022). Hallmarks of Cancer: New Dimensions. Cancer Discov 12\, 31-46.\n\n\n\nErkers T\, Struyf N\, James T…. Orre L\, Jafari R\, Pawitan Y\, Seashore-Ludlow B\, Lehtiö J\, Lehmann S\, Östling P\, Kallioniemi O. Data-driven hallmarks of acute myeloid leukemia\, submitted\, 2023.\n\n\n\n\nOlli Kallioniemi\, M.D.\, Ph.D. is director of the Science for Life Laboratory (www.SciLifeLab.se)\, a national infrastructure for life sciences in Sweden and also a professor in Molecular Precision Medicine at the Karolinska Institutet (2015-present). He also directs the national SciLifeLab program on Data-Driven Life Science (DDLS). Olli Kallioniemi was previously the founding director of FIMM – the Institute for Molecular Medicine Finland at the University of Helsinki\, as part of the Nordic EMBL partnership in Molecular Medicine (2007-2015) Olli Kallioniemi is a member of European Molecular Biology Organization (EMBO)\, European Academy of Cancer Sciences\, the Nobel Assembly at the Karolinska Institutet and the Royal Swedish Academy of Sciences. \n\n\n\n\nIda Larsson Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers\nNervous system cancers contain a large spectrum of transcriptional cell states\, reflecting processes active during normal development\, injury response and growth. However\, we lack a good understanding of these states’ regulation and pharmacological importance. Here\, we describe the integrated reconstruction of such cellular regulatory programs and their therapeutic targets from extensive collections of single-cell RNA sequencing data (scRNA-seq) from both tumors and developing tissues. Our method\, termed single-cell Regulatory-driven Clustering (scRegClust)\, predicts essential kinases and transcription factors in little computational time thanks to a new efficient optimization strategy. Using this method\, we analyze scRNA-seq data from both adult and childhood brain cancers to identify transcription factors and kinases that regulate distinct tumor cell states. In adult glioblastoma\, our model predicts that blocking the activity of PDGFRA\, DDR1\, ERBB3 or SOX6\, or increasing YBX1 -activity\, would potentiate temozolomide treatment. We further perform an integrative study of scRNA-seq data from both cancer and the developing brain to uncover the regulation of emerging meta-modules. We find a meta-module regulated by the transcription factors SPI1 and IRF8 and link it to an immune-mediated mesenchymal-like state. Our algorithm is available as an easy-to-use R package and companion visualization tool that help uncover the regulatory programs underlying cell plasticity in cancer and other diseases. \n\n\n\nIda Larsson studied medical biotechnology at the Royal Institute of Technology in Stockholm and received her MScEng in 2018. She then continued as a PhD student in computational systems biology at Uppsala University\, where her research has focused on the brain tumor glioblastoma and developing methods for analyzing single-cell RNA sequencing data. She defended her PhD in 2023 and is now starting as a postdoctoral fellow at Dana-Farber Cancer Institute in Boston. Her research interests revolve around intratumoral heterogeneity and plasticity in neural cancers. \n\n\n\n\nNina Linder Artificial intelligence cervical cancer diagnostics at the point-of-care\nOur research group has developed and conducted proof-of-concept studies of a novel method that combines artificial intelligence (AI) and mobile digital microscopy for cell-based cervical cancer screening in resource-limited settings. The mobile microscopes are wirelessly connected via mobile networks for AI-based analysis and provide access to diagnostics where there is a lack of medical experts. We are now assessing the use of the new diagnostic method in the form of a validation studies in Kenya and Tanzania with the aim of detecting premalignant changes for the purpose of cervical cancer prevention. Cervical smears are collected at the point-of-care and digitized with mobile microscope scanners and premalignant cells detected with an AI-algorithm. Suspected abnormal cells are verified by a pathologist and treated. The method’s diagnostic accuracy\, technical feasibility\, cost and time per test\, and acceptance of the AI method is evaluated and compared to conventional diagnostics. Throughout the project\, opportunities for larger scale implementation of the diagnostic platform in East Africa are evaluated\, with the ultimate goal of achieving sustainable solutions for low-resource settings.The methods have great potential to improve equitable and sustainable access to high-quality diagnostics for cervical cancer screening among women residing in low- and middle income countries\, carrying the highest cervical cancer burden globally. \n\n\n\nNina Linder is a physician by training and received her MD and PhD from the University of Helsinki\, Finland and is an Associate Professor at Uppsala University\, Sweden as well the Institute for Molecular Medicine\, University of Helsinki\, Finland. Nina Linder’s current research involves the development of novel artificial intelligence-based solutions for cancer and infectious disease diagnostics. Linder is co-heading projects developing artificial intelligence-based tools for point-of-care diagnostics in a global setting. The overall goal of Linder’s research is to promote the implementation of innovative decision-support solutions for precision medicine to improve the translation from basic medical research to the doctor and patient at the clinic. \n\n\n\n\nBeatrice Melin Understanding brain tumors; machine learning meets epidemiology\nThe causes of glioma\, the most malignant brain tumor\, is in most cases unknown. Common environmental factors such as alcohol and smoking has not been linked to brain tumors. High doses of ionizing radiation are associated with increased risk\, but it explains very few cases. Therefore\, one assumption could be\, that glioma is an endogenous disease that is caused by a stochastic effect initiated by a complex inheritance and subsequent biological cascades leading to tumor development. To discover which biological parameters that are associated with glioma risk\, several factors need to be taken in consideration. Taking glioma as an example\, important factors when collecting data and samples and biostatistical considerations will be presented\, giving corner stones for how we have been able to harvest and find true association through data driven analyses. \n\n\n\nBeatrice Melin is MD\, PHD and Professor of Oncology at Umeå University and Director of Research Development and Innovation at Region Västerbotten. Professor Melin has worked in the field of brain tumor research for 25 years and published on both cohort\, blood tumor and registry studies. \n\n\n\n\nMichael Mints Precision Medicine in Head and Neck Cancer Powered through Single-cell RNA Sequencing\nHead and neck cancer (HNC) can be divided into two biologically distinct entities based on human papillomavirus (HPV) status. In HPV-negative HNC\, the main challenge remains finding treatments to improve survival rates and decrease recurrence\, while HPV-positive patients need better stratification methods to avoid morbidity from overtreatment. Intra-tumour heterogeneity (ITH) is a major feature in both types of HNC and a barrier to successful patient stratification and treatment. Despite its significance\, ITH remains poorly understood. \n\n\n\nWe posit that HNC tumours consist of a vast\, diverse ecosystem of cell types with different roles. In order to improve patient-tailored treatment\, our goal is to\, through single-cell RNA sequencing\, characterize these populations\, their biological and clinical significance and their roles in responses to various treatments. \n\n\n\nWe report firstly\, the identification of a novel population of cancer cells with undetectable HPV expression in HPV+ tumours. These cells are less proliferative\, more invasive and respond poorly to treatment. Validating these findings through TCGA\, we found that decreased HPV expression levels are linked to poor prognosis in HPV-positive oropharyngeal cancer. \n\n\n\nSecondly\, we show that malignant cells in HPV- oral cavity cancer express antigen-presentation genes\, and that expression of these genes together with an interferon signal across multiple cell types strongly predicts response to neoadjuvant PD-1 inhibition. \n\n\n\nFinally\, through collecting a dataset comprising > 120 HNC patients and one million cells\, we were able to find diverse recurrent cancer cell states and microenvironmental co-expression patterns. Notably\, we found a rare subset of cancer cells that undergo a full\, rather than partial epithelial-mesenchymal transition (EMT). These cells are linked to depletion of CD8+ T-cells and increased numbers of fibroblasts and macrophages in the microenvironment\, as well as poor outcomes. \n\n\n\nIn summary\, we have created a comprehensive atlas of the HNC ecosystem at previously unseen scale and resolution. We identify rare cell populations responsible for cancer hallmarks such as senescence\, proliferation and metastasis and show how subpopulations change in response to HPV infection\, radiotherapy and immunotherapy. This knowledge will greatly advance personalised treatment of head and neck cancer through guiding patient stratification\, drug development and treatment selection. \n\n\n\nMichael Mints studied medicine at Karolinska Institutet through the clinician-scientist training programme. He received his MD in 2013 and his PhD in 2015 at the Department of Oncology-Pathology. After clinical work in Umeå and a physician-researcher internship in Östersund he started a postdoc in Itay Tirosh’s lab at the Weizmann Institute in 2019. There\, his work focuses on leveraging single-cell RNA sequencing and computational methods in order to understand head and neck cancer heterogeneity with the goal of personalizing head and neck cancer treatment. \n\n\n\n\nHannah Sophie Muti The use of artificial intelligence in gastrointestinal oncology – past\, present and future\nArtificial intelligence (AI) can infer information from data in a way that exceeds human capacity to do so. Especially in clinical oncology\, scientists use AI to generate biomarkers\, find correlations or extract prognostic or predictive information. This talk will give you an idea of how it started\, how it’s going and what the future might hold for cancer researchers in an era of paradigm-shifting technological advances. \n\n\n\nHannah Muti is a Clinician/Scientist with interests in precision medicine in gastrointestinal oncology and visceral surgery. Her research covers the use of artificial intelligence to investigate gastrointestinal cancers in the context of precision oncology. She simultaneously works in the Department for Visceral\, Thoracic and Vascular Surgery at the University Hospital Dresden to obtain her specialization in visceral surgery.  \n\n\n\n\nAvlant Nilsson A deep learning model of cellular networks\nThe activity of human cells depends on interactions between molecules in molecular networks. Disruptions to these networks are common in disease\, e.g. it can drive unrestricted growth in cancer cells. Simulations of these processes could predict disease mechanisms and identify suitable drug targets. However\, these networks consist of thousands of different molecules with tens of thousands of interactions\, and it has been challenging to parametrize systems-wide models using traditional approaches. We have developed recurrent neural network models of the networks that use molecules as hidden nodes with connections constrained to known molecular interactions. These models predict unseen test-data from living cells\, e.g. we predict gene expression in macrophages in response to different ligands and we use the models to infer causative signaling cascades. Currently\, we are expanding the framework to integrate signaling\, metabolism\, and gene regulation for a more complete mechanistic description of cellular activities. \n\n\n\nAvlant Nilsson is a computational biologist and assistant professor in precision medicine at Karolinska Institutet\, Stockholm. He holds a MSc (2009-2014)\, and a PhD (2014-2019) degree in biological engineering from Chalmers University of Technology\, where his thesis focused on the metabolism of growing cells. In his postdoctoral work at Massachusetts Institute of Technology (2019-2023)\, he developed artificial neural network models to simulate signal transduction in immune cells. His new lab at Karolinska will be using these techniques to simulate cellular processes in cancer\, aiming at identifying effective drug combinations\, predicting resistance mechanisms\, and understanding cell-cell interactions in the tumor microenvironment. \n\n\n\n\nBjörn Nilsson Genetic variation exposes regulators of hematopoietic stem and progenitor cells in vivo in humans\nStem cell transplantation is a cornerstone in the treatment of blood malignancies. The most common method to harvest stem cells for transplantation is by leukapheresis\, requiring mobilization of CD34+ hematopoietic stem and progenitor cells (HSPCs) from the bone marrow into the blood. Identifying the genetic factors that control blood CD34+ cell levels could reveal new drug targets for HSPC mobilization. Here we report the first large-scale\, genome-wide association study on blood CD34+ cell levels. Across 13 167 individuals\, we identify 9 significant and 2 suggestive associations\, accounted for by 8 loci (PPM1H\, CXCR4\, ENO1-RERE\, ITGA9\, ARHGAP45\, CEBPA\, TERT\, and MYC). Notably\, 4 of the identified associations map to CXCR4\, showing that bona fide regulators of blood CD34+ cell levels can be identified through genetic variation. Further\, the most significant association maps to PPM1H\, encoding a serine/threonine phosphatase never previously implicated in HSPC biology. PPM1H is expressed in HSPCs\, and the allele that confers higher blood CD34+ cell levels downregulates PPM1H. Through functional fine-mapping\, we find that this downregulation is caused by the variant rs772557-A\, which abrogates an MYB transcription factor-binding site in PPM1H intron 1 that is active in specific HSPC subpopulations\, including hematopoietic stem cells\, and interacts with the promoter by chromatin looping. Furthermore\, PPM1H knockdown increases the proportion of CD34+ and CD34+90+ cells in cord blood assays. Our results provide the first large-scale analysis of the genetic architecture of blood CD34+ cell levels and warrant further investigation of PPM1H as a potential inhibition target for stem cell mobilization. \n\n\n\n\nAbhishek Niroula Pre-malignant clonal hematopoiesis stratifies risk of hematologic cancers\nClonal hematopoiesis (CH) is a pre-malignant condition characterized by the expansion of genetically distinct blood cell clones in healthy individuals. CH with cancer driver variations is common in the elderly population and is associated with a 10-fold higher risk of blood cancer. A number of genes recurrently mutated in CH are known (e.g.\, DNMT3A\, TET2\, and ASXL1); however\, these gene variants only account for <30% of CH clones in elderly individuals. To identify new genetic drivers of CH\, we analyzed exome sequencing data from peripheral blood samples of >50\,000 individuals. We identified CH with genetic variants in several genes previously not linked to CH. Further\, we grouped CH into myeloid and lymphoid based on the mutated genes\, which stratified the risk of incident myeloid and lymphoid malignancies. Integrating the genetic data with clinical measurements allowed identification of individuals at high risk of developing hematologic malignancies. Currently\, we are developing methods to analyze somatic variants across the whole genome to characterize CH and identify new genetic regulators of CH. \n\n\n\nI am a DDLS Fellow in precision medicine and diagnostics at the University of Gothenburg. I obtained my PhD from Lund University and did a postdoc at the Broad Institute\, Cambridge MA. My research background is on bioinformatics and human genomics\, focusing on the effects of genetic variants in human diseases including cancer. As a DDLS Fellow\, my research focuses on the study of clonal hematopoiesis (CH)\, a pre-cancer of blood. We utilize large-scale genomic data from population cohorts to understand the origin and evolution of CH and its malignant transformation. \n\n\n\n\nVeronica Rendo Identification and exploration of toxic genes in human cancer\nChromosomal gains are one of the most common somatic genetic alterations found in cancer. While the impact of sustained oncogene expression has been extensively studied\, the effects of copy number gains on “bystander” genes\, which are collaterally amplified\, remain less understood in terms of cellular fitness. To shed light on this\, we integrated the expression and copy number profiles of over 8\,000 TCGA tumors and CCLE cell lines\, along with the viability effect of gene overexpression from 17 human cancer ORF screens. Through this comprehensive and data-driven analysis\, we identified a group of genes termed ‘Amplification-Related Gain Of Sensitivity’ (ARGOS) genes. ARGOS genes are situated in frequently amplified regions of the genome\, and their expression level is reduced compared to their copy number status. However\, when overexpressed upon gain\, they prove to be toxic to the cell. Our compensation and toxicity analyses revealed five frequently amplified ARGOS genes. Notably\, one candidate showed a mechanism of toxicity involving altered DNA damage and innate immune signaling responses upon gene overexpression. This study represents a significant effort to better understand the toxicity effects associated with gene overexpression in human cancers. \n\n\n\nVeronica studied Biology at Simon Bolivar University in Venezuela\, and then moved to Sweden to pursue a PhD at Uppsala University. During this time\, she worked under the mentorship of Prof. Tobias Sjoblom and studied how genomic losses occurring in colorectal cancer can be exploited for therapy. In 2019\, she moved to Boston (USA) to pursue a postdoc in Dr. Rameen Beroukhim’s lab at Dana-Farber Cancer Institute\, affiliated with Harvard Medical School and the Broad Instititute of MIT and Harvard. Veronica’s research focused on studying therapeutic vulnerabilities associated with aneuploidy\, including predictors of resistance to clinically relevant p53 reactivation strategies in brain tumors and negative selection against amplifications in cancer. In 2023\, Veronica left the Beroukhim lab to start her own laboratory at the Department of Immunology\, Genetics and Pathology at Uppsala University. Here\, she combines descriptive and functional genomic approaches to understand how brain tumors respond and evolve during treatment. This includes continued exploration of how aneuploidy creates vulnerabilities that can be therapeutically exploited. \n\n\n\n\nFredrik Strand AI for Breast Cancer Risk Prediction\nAmong women attending screening\, 30% of their cancer is missed by current mammography-based screening. We have trained AI models to assess specific aspects of the mammography images to measure when a negative exam is less reliable. After retrospective validation we are conducting a randomized clinical trial selecting around 7% of women from screening to be offered MRI. \n\n\n\nFredrik Strand is a Swedish breast radiologist and associate professor at Karolinska Institutet\, Stockholm. He holds an MD\, PhD and MSc degrees\, and has prior experience as a strategy consultant and leading a start-up company. Fredrik is head of the research and education committee at the Swedish society of breast imaging. His academic research evolves around exploring AI for breast imaging. He and his team are involved in retrospective validation of AI algorithms\, prospective clinical trials\, and in developing new machine-learning algorithms for breast cancer detection and supplemental MRI imaging. URL:https://www.scilifelab.se/event/ddls-pmd-minisymposium-2023/ LOCATION:Martin H:son Holmdahlsalen\, Dag Hammarskjöldsväg 8\, Entrance 100\, Akademiska sjukhuset\, Uppsala CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/03/PMD_Icon.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230907T090000 DTEND;TZID=Europe/Stockholm:20230907T140000 DTSTAMP:20260404T014606 CREATED:20230821T130137Z LAST-MODIFIED:20230822T092439Z UID:10000959-1694077200-1694095200@www.scilifelab.se SUMMARY:Spatial Biology Symposium. From the Facilities to the user DESCRIPTION:Spatially resolved omics technologies (to visualize biomolecules within intact tissue specimens) have emerged during the last years. The Spatial Biology platform covers cutting-edge technologies for spatial profiling of transcripts\, proteins\, DNA\, and small molecules. Learn more about the services and capabilities that are offered from Spatial Biology Platform. Meet with researchers and national infrastructures experts from Spatial Transcriptomics\, In Situ Sequencing\, Spatial proteomics and Spatial Mass Spectrometry unit . Learn about our technologies and how other users have used to reach their goals. 10 of you will have the opportunity to visit our facilities and see the cutting-edge equipment\, meet the facility staff and discuss your potential projects. \n\n\n\nProgram\n\n\n\n09:00Registration09:10Spatial Biology overviewCharlotte Stadler09:30Spatial TranscriptomicsAnja Mezger09:50In situ sequencingKatarina Tiklova10:30Spatial ProteomicsCharlotte Stadler10:50Spatial Mass SpectrometryAnna Nilsson11:10User presentationSpatial Multimodal Analysis of Transcriptomes and Metabolomes in TissuesMarco Vicari11:30Lunch & mingle12:30Visit to Lab facilities4 groups with 5 persons max12:45Visit to Lab facilities4 groups with 5 persons max\n\n\n\nRegistration URL:https://www.scilifelab.se/event/spatial-biology-symposium-from-the-facilities-to-the-user/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Event ORGANIZER;CN="Spatial Proteomics and Spatial Transcriptomics facilities":MAILTO:carolina.oses@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230907T120000 DTEND;TZID=Europe/Stockholm:20230907T130000 DTSTAMP:20260404T014606 CREATED:20230711T112315Z LAST-MODIFIED:20230829T075641Z UID:10000925-1694088000-1694091600@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Fitz Gerald Silao & Michael Hawgood 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\nFitz Gerald Silao\n\n\n\nPer Ljungdahl – alpha 3 \n\n\n\nAn acid-test of alkalization: Diverse mechanisms control amino acid-dependent environmental alkalization in Candida albicans \n\n\n\n\n\nMichael Hawgood\n\n\n\nBennie Lemmens – alpha 5 \n\n\n\nInvestigating novel inhibitors on genome instability \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-sept-7/ 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:20230908T100000 DTEND;TZID=Europe/Stockholm:20230908T110000 DTSTAMP:20260404T014606 CREATED:20230626T102011Z LAST-MODIFIED:20230828T055235Z UID:10000920-1694167200-1694170800@www.scilifelab.se SUMMARY:Modelling life science data in big pharma\, academia\, and startups DESCRIPTION:Join the NEW event series arranged by the SciLifeLab Data Centre focused on tools for AI/ML research in life sciences. \n\n\n\nTitle: Modelling life science data in big pharma\, academia\, and startups – Differences\, Examples\, and Some Learnings \n\n\n\nSpeaker: Andreas Bender\, Professor of Molecular Informatics\, University of Cambridge \n\n\n\nWhere and when: September 8\, 2023 at 10:00-11:00 Stockholm time\, online. Registration is open till Sept 7 at 24.00. \n\n\n\nAbstract: Life science data\, modelling methods\, and organizational environments in which they are implemented vary widely – from big pharma\, to academia\, and start-up environments (and beyond). This presentation will partly cover science and modelling\, but there will be an additional focus on the differences between the above environments (all of which the presenter has worked in)\, and how they influence the approaches\, as well as the eventual result and product to be delivered. \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/modelling-life-science-data/ LOCATION:Online event via Zoom CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230908T110000 DTEND;TZID=Europe/Stockholm:20230908T120000 DTSTAMP:20260404T014606 CREATED:20230808T131008Z LAST-MODIFIED:20230829T082636Z UID:10000943-1694170800-1694174400@www.scilifelab.se SUMMARY:Overview of compute and storage resources in data-driven life science DESCRIPTION:Compute and storage resources available to the life science field in Sweden are provided by several different organisations. SciLifeLab and the DDLS program are in various ways providing access to infrastructure\, new data services\, and support to existing ones. We work towards improved coordination and accessibility. \n\n\n\nAt this event on September 8\, representatives for SciLifeLab Data Centre\, National Bioinformatics Infrastructure Sweden (NBIS)\, National Academic Infrastructure for Super­computing in Sweden (NAISS) and National Supercomputer Centre at Linköping University (NSC) will give an overview of who does what and how to access different services\, and how to interact regarding input\, feedback or suggested new services. There will also be time for a Q & A. \n\n\n\nAgenda \n\n\n\n11:00-11.05  Introduction\, Johan Rung \n\n\n\n11:05-11:15 Overview of SciLifeLab resources\, Jonas Svensson\, Liane Hughes\, Konstantin Dossis \n\n\n\n11:15-11:25 Overview of NAISS resources\, Johan Raber \n\n\n\n11:25-11:35 Overview of NSC resources (Berzelius)  Soumi Chaki\, Xuan Gu \n\n\n\n11:35-11:45 Overview of NBIS & UPPMAX resources\, Marcus Lundberg \n\n\n\n11.45.-11:50 Summary \n\n\n\n11:50-12:00 Q & A- ways of working \n\n\n\n \n\n\n\n12:00-12.30 For follow-up questions in four breakout rooms: SciLifeLab\, NBIS-UPPMAX\, NAISS\, or NSC. \n\n\n\nDate: Sept 8\, 11:00-12:00 CEST on Zoom\, followed by 30 min break-out rooms for additional questions to the respresentatives from SciLifeLab\, NBIS-UPPMAX\, NAISS\, and NSC. \n\n\n\nTarget group: Researchers\, research staff and others interested in compute and storage resources in life science. \n\n\n\n\nRegister here\n\n\n\n\nWelcome! \n\n\n\nFor questions about the event please contact SciLifeLab Data Centre on email datacentre@scilifelab.se For more information about services for data-driven life science research see SciLifeLab Data Platform URL:https://www.scilifelab.se/event/overview-of-compute-and-storage-resources-in-data-driven-life-science/ CATEGORIES:Event ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se LOCATION: END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230913T080000 DTEND;TZID=Europe/Stockholm:20230915T170000 DTSTAMP:20260404T014606 CREATED:20230421T112659Z LAST-MODIFIED:20230421T112843Z UID:10000866-1694592000-1694797200@www.scilifelab.se SUMMARY:ELIXIR-GOBLET Train-the-Trainer DESCRIPTION:Course Content\n\n\n\nThis course offers guidance\, ideas and tips for designing training/teaching\, development and delivery on training activities\, all based on research-driven educational principles. This course will cover 4 main topics: \n\n\n\n\nLearning principles and how they apply to training and teaching\n\n\n\nDesign and plan session\, course\, materials\n\n\n\nTeaching techniques to enhance learner engagement and participation\n\n\n\nAssessment and feedback in training and teaching\n\n\n\n\nThis course will be delivered through Canvas learning management system. You can find a link to the course pages here. \n\n\n\nNote! The course is highly interactive and hence it is important that you\, as a participant\, actively contribute to all sessions and elements of the course. \n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-04-21 \n\n\n\nApplication closes: 2023-08-21 \n\n\n\nConfirmation to accepted students: 2023-08-25 \n\n\n\nCourse Leaders and teachers: Jessica Lindvall and Nina Norgren \n\n\n\nIn case you miss information on any of the above dates\, please contact: Nina Norgren (traininghub@scilifelab.se) \n\n\n\n\nCOURSE WEBSITE AND PROGRAM\n\n\n\nREGISTRATION\n\n\n\n\nLearning Objectives\n\n\n\n\nTo get acquainted with Learning principles and how they apply to training\n\n\n\nTo be able to select and use training techniques that can help enhance learner engagement and participation\n\n\n\nTo learn how to use assessment and feedback in training\n\n\n\nTo learn about session\, course\, and materials design\n\n\n\n\nLearning Outcomes\n\n\n\nBy the end of this course\, learners will be able to: \n\n\n\n\nName learning principles that a good teacher/instructor should have in mind\n\n\n\nDescribe at least three training techniques\, drawing on learning principles\n\n\n\nDesign a training session and a course\n\n\n\nDevelop assessment questionnaires\n\n\n\nEnumerate types of materials needed for each part of a training session or course\n\n\n\n\nEntry requirements\n\n\n\nWhoever is interested in becoming a trainer/instructor\, or improving your training skills. If you have questions like the following ones\, this course may be very helpful to you. \n\n\n\n\nHow learning works?\n\n\n\nHow do I use learning principles and theories to improve my teaching/training?\n\n\n\nHow do I make my teaching/training more engaging and effective?\n\n\n\nHow should I adjust my teaching/training to different types of learners?\n\n\n\nHow do I ensure learning progress?\n\n\n\nHow can I assess whether my students are actually understanding my lessons? Are they actually learning?\n\n\n\nWhat is the best balance between theory and practice?\n\n\n\nHow can I best assess whether learning is occurring and/or has occurred?\n\n\n\nWhat works in a classroom and what doesn’t?\n\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 selection criteria: Priority will be given to applicants from SciLifeLab infrastructures\, institutes and organisations across the Nordic research community\, and to participants from Nordic ELIXIR nodes. \n\n\n\nCourse fee \n\n\n\nA course fee* of 2000 SEK will be invoiced to accepted participants. The fee includes lunches\, coffee and fikas\, and a course dinner. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nNote! If you are accepted and decide not to attend without communicating the reason for the no-show with us latest on the 8th of September\, we will invoice a no-show-fee of 2000 SEK. \n\n\n\nThe invoicing information needs to be included in the registration in order to guarantee your spot in the training event\, if you are to be accepted. By giving the invoice information you hereby confirm that the group leader/PI/manager has given a consent regarding your possible participation in the Training event. URL:https://www.scilifelab.se/event/elixir-goblet-train-the-trainer/ LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden CATEGORIES:Course ORGANIZER;CN="NBIS & Training Hub":MAILTO:traininghub@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230914T080000 DTEND;TZID=Europe/Stockholm:20230914T170000 DTSTAMP:20260404T014606 CREATED:20230829T153916Z LAST-MODIFIED:20230831T122645Z UID:10000961-1694678400-1694710800@www.scilifelab.se SUMMARY:Beyond pharmacological inhibition of DNA repair DESCRIPTION:A Mini-Symposium dedicated to the boosting and reprogramming of DNA repair as a novel technology and its implications in the treatment of human disease.Come and learn more about exciting opportunities in modulating DNA repair\, discuss with experts and enjoy a classic swedish Fika. \n\n\n\nregistration for on-site participation\n\n\n\nregistration for on-line participation\n\n\n\nInvitationDownload URL:https://www.scilifelab.se/event/beyond-pharmacological-inhibition-of-dna-repair/ LOCATION:Atrium\, Karolinska Institutet\, Nobels väg 12\, Solna\, Sweden CATEGORIES:Event ORGANIZER;CN="Maurice Michel":MAILTO:maurice.grube@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230914T120000 DTEND;TZID=Europe/Stockholm:20230914T130000 DTSTAMP:20260404T014606 CREATED:20230711T113326Z LAST-MODIFIED:20230907T123740Z UID:10000926-1694692800-1694696400@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Christian Sommerauer & Robin Ebbestad 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\nChristian Sommerauer\n\n\n\nClaudia Kutter – gamma 5 \n\n\n\nEstrogen receptor activation remodels TEAD1 gene expression to alleviate nonalcoholic fatty liver disease \n\n\n\n\n\nRobin Ebbestad\n\n\n\nHjalmar Brismar – gamma 3 \n\n\n\nHigh-resolution imaging and deep learning-based segmentation of glomerular pathologies in the kidney \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-sept-14/ LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna CATEGORIES:Community ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/IMG_20221103_120135408_HDR-scaled.jpg ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230918T080000 DTEND;TZID=Europe/Stockholm:20230922T170000 DTSTAMP:20260404T014606 CREATED:20230510T125126Z LAST-MODIFIED:20230510T131009Z UID:10000883-1695024000-1695402000@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: 2023-09-04 \n\n\n\nConfirmation to accepted students: 2023-09-08 \n\n\n\n\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\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\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\n\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\n\nData processing and analyses for differential DNA methylation with Illumina EPIC arrays and Bisulfite-seq;\n\n\n\nChIP-seq: peak calling\, peak independent / dependent quality metrics\, differential binding analysis; DNA motif enrichment;\n\n\n\nATAC-seq: peak calling\, peak independent / dependent quality metrics\, differential accessibility analysis;\n\n\n\nQuantitative ChIP-seq using spike-ins;\n\n\n\nCUT&Tag / CUT&RUN: Novel methods to investigate protein-chromatin interactions;\n\n\n\nFunctional analysis\, including finding nearest genes and custom features\, GO terms and Reactome pathways enrichment;\n\n\n\nBasic multi-omics exploration and integration;\n\n\n\nVisualisations of epigenomics datasets;\n\n\n\nIntroduction to analysis of single cell functional genomics data (scATAC-seq);\n\n\n\nIntroduction to nf-core pipelines for processing and analysis of epi- and functional genomics data : Methylseq\, ChIP-seq\, ATAC-seq.\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the workshop and complete the computer exercises: \n\n\n\n\nBYOL\, bring your own laptop with R and RStudio installed;\n\n\n\nBasic knowledge in Linux;\n\n\n\nBasic programming experience\, preferably in R.\n\n\n\n\n\n\n\n\nDesirable \n\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;\n\n\n\nPrevious experience with NGS data analyses;\n\n\n\nCompleting NBIS workshops “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists” or equivalent.\n\n\n\n\n\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-3/ 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:20230918T151500 DTEND;TZID=Europe/Stockholm:20230918T161500 DTSTAMP:20260404T014606 CREATED:20230831T123817Z LAST-MODIFIED:20230904T061932Z UID:10000963-1695050100-1695053700@www.scilifelab.se 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 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:20230919T140000 DTEND;TZID=Europe/Stockholm:20230919T143000 DTSTAMP:20260404T014606 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 ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/08/CSI_logo_text_mail-1.png 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:20260404T014606 CREATED:20221120T085632Z LAST-MODIFIED:20230919T143955Z UID:10000736-1695200400-1695229200@www.scilifelab.se 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 ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/11/Screen-shot-Science-Summit-2023.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230921T090000 DTEND;TZID=Europe/Stockholm:20230921T170000 DTSTAMP:20260404T014606 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 END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230921T120000 DTEND;TZID=Europe/Stockholm:20230921T130000 DTSTAMP:20260404T014606 CREATED:20230711T113450Z LAST-MODIFIED:20230907T123846Z UID:10000927-1695297600-1695301200@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Irene Stevens & Charlotta Heningson 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\nIrene Stevens\n\n\n\nVicente Pelechano – gamma 5 \n\n\n\nThe co-translational degradome provides a readout of Fluconazole response in Candida albicans \n\n\n\n\n\nCharlotta Heningson\n\n\n\nIskra Pollak Dorocic – gamma 5 \n\n\n\nThe effect of SSRIs on the spatio-molecular organization of the serotonin system \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-sept-21/ LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna CATEGORIES:Community ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/IMG_20221103_123412496_HDR2-scaled.jpg ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230921T120000 DTEND;TZID=Europe/Stockholm:20230921T130000 DTSTAMP:20260404T014606 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 END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230925T100000 DTEND;TZID=Europe/Stockholm:20230925T110000 DTSTAMP:20260404T014606 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 END:VCALENDAR