SciLifeLab

Variational inference for tumor phylogeny using single cell data
2024-09-20 10:00 - 11:00 (Europe/Stockholm) | Online event via Zoom
Harald Melin, KTH Royal institute of Technology

MCMC has long been the gold standard for Bayesian inference in classical phylogenetics, instantiated e.g. in popular softwares such as MrBayes and BEAST. This presentation focuses on an alternative Bayesian approach, Variational Inference (VI), which has made recent advances in fields of classical and tumor phylogenetics. I will give an introduction to the method and how it is applied in classical phylogeny, emphasising its strengths and limitations w.r.t. MCMC, followed by how it facilitates Bayesian inference of copy number evolution in tumors using low coverage single cell whole-genome sequencing data, based on our recent project VICTree.

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NBIS arranges an open AI and IO Seminar Series aimed at knowledge-sharing about Artificial Intelligence and Integrative Omics (AI & IO) analysis and applications in the Life Science community. The seminar series is open to everyone. The seminar is run over Zoom on the third Friday of the month during academic terms, typically between 10 and 11 am, with approx. 45 min long presentation and 15 min discussion.

How does epigenetic mechanism impact Type 2 diabetes?
2024-09-20 13:00 - 14:00 | Online event via Zoom
Speaker: Dr. Charlotte Ling is a Professor at Lund University

Dr. Charlotte Ling is a Professor at Lund University and a principal investigator of the Epigenetics and Diabetes Unit at Lund University Diabetes Centre (LUDC). She obtained her PhD in Endocrinology at University of Gothenburg, Sweden in 2002. After a postdoc at Lund University, where she studied genetics of type 2 diabetes, she dedicated her research to the study of epigenetic mechanisms causing type 2 diabetes and metabolic disease. Her research group has over the last two decades pioneered the field of epigenetics in type 2 diabetes. They have made several groundbreaking discoveries such as genome-wide epigenetic modifications in pancreatic islets, skeletal muscle, adipose tissue and the liver from patients with type 2 diabetes compared with non-diabetic control subjects. Dr. Ling’s research group has also shown that genetic and non-genetic factors such as SNPs, exercise, diet, obesity and age alter the genome-wide epigenetic pattern in human primary tissues for type 2 diabetes. More recently, her group is trying to translate their epigenetic findings to biomarkers and novel therapies for precision medicine to improve prediction, prevention and treatments of type 2 diabetes.

Host: Louella Vasquez, NBIS (louella.vasquez@scilifelab.se)

Broadcast link (live event): https://lu-se.zoom.us/j/67681656100

The talk will also be available afterwards on the NBIS YouTube channel.

The Disruptive Role of Data and AI in the Life Sciences
2024-09-24 12:00 - 2024-09-25 12:00 | Conference Centre Wallenberg, Medicinaregatan 20A, Gothenburg, 413 90, Sweden
A Joint Conference between DDLS, WASP and WASP-HS

The conference will focus on different aspects of research where collaboration over scientific domains is essential and will explore the following topics:

How data- and AI-driven research is shaping the future of life science

Development of new approaches to human-in-the-loop technologies and their use

The need for studies at the intersection of society, AI, and data driven life sciences

Participants will have the opportunity to network, be inspired by excellent international keynotes, and take part of the latest research in Sweden. In addition to plenary keynotes, the program will offer parallel sessions, panel discussions, mingle and poster sessions.

Practical Details

Dates and times

September 24, 12:00 – September 25, 12:30Registration is open from 11:00 on September 24.

Venue: Wallenberg Conference Center, Medicinaregatan 20 A, Gothenburg

Information for registered poster

• size of poster 90x 120 cm portrait format• posters can be hung on the 24th of September from 11:00 and should be done by 12:00• poster should be removed after the end of the conference on the 25th. You are responsible for your poster. Forgotten posters will not be saved.During the poster session 17:15-19 on the 24th of September we would appreciate if you are available by your poster for discussions and questions. During the Magnet mingle on the 25th you are also welcome to be by your poster.

Registration to the Conference

Register here

The registration is open until September 6.

Contact: ddls@scilifelab.se or info@wasp-sweden.org

Program

24 September

11:00 Registration opensPosters are to be hung up from 11:00 and should be done by 12:00.

12:00 – 13:00 Lunch

Start of conference

13:00 – 13:15 Opening Program DirectorsChristofer Edling, WASP-HSOlli Kallioniemi, DDLSAnders Ynnerman, WASPChair, Rebecka Jörnsten WASP

13:15-14:00 Keynote speaker Sunduz KelesIntegrative Approaches to Single-Cell Genomics for Personalized MedicineChair, Rebecka Jörnsten WASP

14:05- 14:50 Keynote speaker Ross KingThe Automation of ScienceChair, Rebecka Jörnsten WASP

14:50-15:20 Coffee

15:20-16:20 Project presentation WASP DDLS (4 *15 min)Christopher Sprague, Incorporating Stability Into Flow MatchingBjörn Wallner, Improved protein structure prediction by adding noise at inferenceHedvig Kjällström, Unraveling the secrets of nature’s high-performance fiberAlexander Schliep and Pär Mattsson Molecular simulation and machine learning to delineate target binding of therapeutic oligonucleotidesChair, Päivi Östling

16:20-17:05 Project presentation WASP-HS DDLS (3* 15 min)Harald Hammarström, Linguistic Diversity Through the Prism of BiodiversityStanley Greenstein, AI in the Health Care Sector – Legal ChallengesSonja Aits, Mapping the Nexus of Biodiversity, Climate Change, Human Society and Health using Large Language Models and other Data Science ApproachesChair, Stefan Larsson

17:15: – 19:00 Finger food and poster session

25 September

08:30-9:30 Project presentation WASP DDLS (4*15 min)Ingrid Hotz, Tino Ebbers, Characterization and visualization of cardiac spectral imaging dataSebastian Westenhoff, cryoSPHERE: Single-particle heterogeneousreconstruction from cryo EMAndreas Kerren, Visual Analytics for Enhancing Quality and Trust in Genome-wide Expression Clustering and AnnotationMinh Hoang Vu, Anonymization of Data in Precision Medicine ResearchChair, Olli Kallioniemi

09:30-10:45 Magnet mingle including coffeeChair, Rebecka Jörnsten and Christofer Edling

10:45-11:30 Keynote Speaker: Klaus HøyerAll the data from everywhere all at once: data integration, AI imaginaries, and their unpredictable outcomesChair, Christofer Edling

11:30-12:15 Panel on common research challengesSunduz Keles, Ross King, Klaus Hoyer, Andreas Kerren, Tino EbbersModerators, Rebecka Jörnsten and Stefan Larsson

12:15 Closing remarks, Program DirectorsChristofer Edling, WASP-HSOlli Kallioniemi, DDLSRebecka Jörnsten WASP

12:30 Lunch to go

Keynote Speakers

Sunduz Keles

Title: Integrative Approaches to Single-Cell Genomics for Personalized MedicineBio: Dr. Keles obtained her Ph.D. in Biostatistics from the University of California at Berkeley. After a year-long postdoctoral appointment at UC Berkeley, she joined the Department of Biostatistics and Medical Informatics and the Department of Statistics at the University of Wisconsin, Madison. She has twenty years of experience in developing statistical and computational methods for genomics, including serving as an ENCODE PI, and pioneering foundational statistical models for leveraging multi-mapping reads in high throughput sequencing data analysis (ChIP-seq, Hi-C).

Her research interests span developing statistical and computational methods for denoising and signal extraction from sequencing data and modeling of high dimensional data. Her computational approaches led to fundamental contributions on how GATA factors mediate transcriptional regulation in HSPCs and erythroid cells. Dr. Keles is an elected fellow of the American Statistical Association.

Klaus Lindgaard Høyer
Title: All the data from everywhere all at once: data integration, AI imaginaries, and their unpredictable outcomesBio: Klaus Hoeyer is professor of Medical Science and Technology Studies at the Centre for Medical Science and Technology Studies, University of Copenhagen. His research focuses on the links between policy, practice and experience in relations to medical research and clinical practice. In recent years, he has focused mainly on what he calls intensified data sourcing in healthcare and how it interacts with and changes the health services. This research is primarily financed by the European Research Council.

Ross D. King
Title: The automation of scienceBio: Ross D. King did his PhD on applying machine learning to predicting protein structure at the Turing Institute in Glasgow. He has joint positions at Chalmers Institute of Technology, and the University of Cambridge. He is one of the most experienced machine learning researchers in Europe.

His main research interest is the interface between computer science and science. He originated the idea of a ‘Robot Scientist’: integrating AI and laboratory robotics to physically implement closed-loop scientific discovery. His Robot Scientist ‘Adam’ was the first machine to autonomously discover scientific knowledge. His Robot Scientist ‘Eve’ is currently searching for drugs against neglected tropical diseases, and COVID. His other core research interest is DNA computing.

Project Presenters

Alexander Schliep
Title: Molecular simulation and machine learning to delineate target binding of therapeutic oligonucleotides

Bio: Alexander Schliep is the chair for Medical Bioinformatics at the Faculty of Health Sciences Brandenburg at Brandenburg Technical University Cottbus-Senftenberg, with a secondary appointment at the University of Gothenburg and member of the WASP (Wallenberg AI, Autonomous Systems and Software Program) research collegium.

His current research program is focused on machine learning and algorithmics for analyses of genomic data and nucleic acid-based therapeutics, including machine learning for pan-genome graph analyses, efficient analysis algorithms for large genomic datasets, and federated, privacy-preserving methods for training ML/AI models for oligonucleotide therapeutics.

Andreas Kerren
Title: Visual Analytics for Enhancing Quality and Trust in Genome-wide Expression Clustering and Annotation

Bio: Prof. Dr. Andreas Kerren received his PhD degree in Computer Science from Saarland University, Saarbrücken, Germany. In 2008, he achieved his habilitation (docent competence) from Växjö University, Sweden.

Dr. Kerren is currently a Full Professor of Information Visualization, Linköping University (LiU) and Linnaeus University (LNU), Sweden. He holds the Chair of Information Visualization at LiU and is head of the research group Information and Software Visualization at LNU. In addition, he is an ELLIIT professor supported by the Excellence Center at Linköping–Lund in Information Technology and key researcher of the Linnaeus University Centre for Data Intensive Sciences and Applications.

His main research interests include several areas of information visualization and visual analytics, especially visual network analytics, text visualization, and the use of visual analytics for explainable AI.

He has been editorial board member of a number of journals such as Information Visualization or Computer Graphics Forum, has served as organizer/program chair at numerous conferences such as IEEE VISSOFT 2013/2018 or GD 2018, and has edited a number of successful books on human-centered visualization. Dr. Kerren has published more than 200 peer-reviewed papers, articles, and book chapters.

Björn Wallner
Title: Improved protein structure prediction by adding noise at inference

Bio: Björn Wallner has been a faculty member at Linköping University since 2011 and a Professor in Bioinformatics since 2019. He obtained his Ph.D. in Bioinformatics from Stockholm University in 2005 and did postdoctoral work at the University of Washington from 2006-2008.

His research interests include protein structure prediction, protein-protein interactions, protein function, disorder, flexibility, and dynamics.

Christopher Sprague
Title: Incorporating Stability Into Flow Matching

Bio: Christopher Iliffe Sprague is a postdoctoral researcher at KTH Royal Institute of Technology and SciLifeLab, working with Arne Elofsson and Hossein Azizpour on deep learning approaches for protein-protein interactions. He earned his PhD in robotics from KTH, where he focused on developing efficient and trustworthy AI for critical robotic systems.

Currently, as a postdoc, Christopher is leveraging his robotics expertise to enhance inductive biases in deep generative models, particularly for equilibrium generation tasks like molecular docking. His research interests include flow-based generative models, hybrid dynamical systems, and drug design

Harald Hammarström
Title: Linguistic Diversity Through the Prism of Biodiversity

Bio: Harald Hammarström is Professor of General Linguistics atUppsala University. He has a background in both Computer Science andLinguistics.

He has a very broad linguistic interest spanning allareas of the world but specializing in minority languages in Papua,Africa and South America. His research activities span fromdocumentary fieldwork in Papua, Indonesia, classical linguisticanalytic work, typological databases, and NLP for lesser-knownlanguages.

He is currently focussing on large-scale empirical andcomputational approaches to linguistic diversity, genealogical/arealrelationships and language universals.

Hedvig Kjellström
Titel: Unraveling the secrets of nature’s high-performance fiber

Bio: Hedvig Kjellström is a Professor in the Division of Robotics, Perception and Learning at KTH Royal Institute of Technology, Sweden, and also affiliated with Swedish University of Agricultural Sciences, Swedish e-Science Research Centre, and Max Planck Institute for Intelligent Systems, Germany. She received an MSc in Engineering Physics and a PhD in Computer Science from KTH in 1997 and 2001, respectively, and thereafter worked at the Swedish Defence Research Agency, before returning to a faculty position at KTH. Her present research focuses on methods for enabling artificial agents to interpret human and animal behavior. These ideas are applied in the study of human aesthetic bodily expressions such as in music and dance, modeling and interpreting human communicative behavior, and the understanding of animal behavior and experiences. In order to accomplish this, methods are developed for agents to perceive the world and build representations of it through vision.

Hedvig has received several prizes for her research, including the 2010 Koenderink Prize for fundamental contributions in computer vision. She has written around 150 papers in the fields of computer vision, machine learning, robotics, information fusion, cognitive science, speech, and human-computer interaction. She is mostly active within computer vision, where she is an Editor-in-Chief for CVIU, a Program Chair for CVPR 2025, and regularly serves as Area Chair for the major conferences.

Ingrid Hotz
Title: Characterization and visualization of cardiac spectral imaging data

Bio: Ingrid Hotz is a professor at Linköping University in Sweden, leading the Scientific Visualization group in the Department of Science and Technology. She holds an M.S. in theoretical physics from Ludwig Maximilian University, Munich, and a Ph.D. in computer science from the University of Kaiserslautern. Hotz has held research positions at the Institute for Data Analysis and Visualization (IDAV) at UC Davis, the Zuse Institute Berlin, and the German Aerospace Center (DLR). Since 2015, she has been a professor at Linköping University and was named the Dr. Ram Kumar IISc Distinguished Visiting Chair Professor at the Indian Institute of Science in 2022.

Her research focuses on scientific visualization and topological data analysis, aiming to develop advanced visual analysis tools for complex datasets across various fields, including engineering, physics, chemistry, and medicine. She integrates methods from computer science and mathematics, such as computer graphics and computational topology, with a participatory design approach to ensure practical and relevant solutions.

Minh Hoang Vu
Title: Anonymization of Data in Precision Medicine Research

Bio: Minh Vu is a postdoctoral researcher at IceLab, Umeå University, working under the supervision of Martin Rosvall and Beatrice Melin. Their research focuses on anonymizing and visualizing biobank data to facilitate meaningful insights and discoveries in disease understanding and treatment development.

Pär Matsson
Title: Molecular simulation and machine learning to delineate target binding of therapeutic oligonucleotides

Bio: Pär Matsson is Professor of Pharmacokinetics at the Sahlgrenska Academy, University of Gothenburg, and Scientific Director of OligoNova Hub – the SciLifeLab infrastructure for development of therapeutic oligonucleotides.

His research is centered on elucidating the molecular mechanisms of cellular and subcellular drug disposition, and how they influence therapeutic effect. A particular focus is on the cellular disposition and effects of non-traditional drug modalities, including therapeutic oligonucleotides and targeted protein degraders (PROTACs).

Sonja Aits
Title: Mapping the Nexus of Biodiversity, Climate Change, Human Society and Health using Large Language Models and other Data Science Approaches

Bio: Sonja Aits leads the “Cell Death, Lysosomes and Artificial Intelligence” group at the Faculty of Medicine, Lund University, which works at the intersection of data, life and sustainability science. Her group develops computational tools such as large language models for scientific text mining and computer vision models for histology and high-content microscopy and uses them to identify biological pathways and disease mechanisms in humans and other species as well as intervention strategies that promote human health, biodiversity and sustainability.

Sonja helps coordinate AI Lund, Lund University’s umbrella organization for AI-related research, outreach and education, and the profile area “Nature-based future solutions”. In addition, she serves as study director of the COMPUTE research school, where she has developed the PhD course program “AI in Medicine and Life Science”. She is also deeply engaged in open education and public outreach.

Stanley Greenstein
Title: AI in the Health Care Sector – Legal Challenges

Bio: Stanley Greenstein (Jur. Dr.) is an Associate Professor (Docent) in Law and Information Technology, Faculty of Law, Stockholm University. He is Chairman of the Board, Swedish Law and Informatics Research Institute (IRI, https://irilaw.org/), Chairman of the Board, Foundation for Legal Information (Stiftelsen för rättsinformation) and a Digital Futures faculty member (https://www.digitalfutures.kth.se/about/).

Stanley’s primary academic focus is cross-disciplinary in nature and addresses the regulation of emerging digital technologies, especially artificial intelligence (AI). His teaching, research and participation in externally funded projects has revolved around the subject areas of ethics, data protection, sustainability and legal design.

Tino Ebbers
Title: Characterization and visualization of cardiac spectral imaging data

Bio: Tino Ebbers is a professor of physiological measurements at Linköping University, with a focus on cardiac imaging, modeling, and simulation. He holds an MSc in Electrical Engineering from the University of Twente and a PhD in Biomedical Engineering from Linköping University. After completing his PhD, he worked at Philips Medical Systems before returning to academia. He also served as a visiting professor at the University of California, San Francisco.

With over 100 publications in leading scientific journals and numerous contributions to international conferences, Tino Ebbers has made a significant impact through his multidisciplinary approach to merging technical research with clinical applications. He is best known for pioneering 4D flow MRI, a breakthrough technology now widely used to study cardiovascular blood flow in both research and clinical settings. His contributions have greatly advanced cardiovascular imaging and led to major innovations in the diagnosis, treatment, and management of cardiovascular diseases.

Background

Since 2021 the Wallenberg AI, Autonomous Systems and Software Program (WASP) and the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) are collaborating through joint research projects with the ultimate goal of solving ground-breaking research questions across disciplines. In line with this, the programs will now host the first, joint annual conference where common research topics are highlighted. Additionally, the increasingly important humanity and societal aspects of the research will be addressed through participation of the WASP-HS program (Wallenberg AI, Autonomous Systems and Software Program- Humanity and Society). Read more about the different research programs here:

DDLS

WASP

WASP-HS

Open Calls

The conference is an opportunity to find collaborators for the two open calls:

WASP-DDLS: NEST projects https://wasp-sweden.org/calls/call-for-joint-wasp-and-ddls-nests/

WASP-HS-DDLS: Research Initiation Grants for Data-Driven Life Sciences and Society https://wasp-hs.org/open-call-research-initiation-grants-for-data-driven-life-sciences-and-society/

Read more

Read more

Read more

DNA microscopy in two and three dimensions
2024-09-25 10:00 - 11:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Speaker: Joshua Weinstein, University of Chicago

Host: Ian Hoffecker, SciLifeLab

This lecture is open with no registration required.

Abstract

Lymphatic, nervous, and tumoral tissues, among others, exhibit physiology that emerges from three-dimensional interactions between genetically unique cells. Technologies capable of volumetrically imaging transcriptomes, genotypes, and morphologies in a single de novo measurement can provide a critical lens into the biological complexity of living systems. We present on our experimental and computational work to develop DNA microscopy: a modality of imaging that captures physical images of specimen genetic content using a massive distributed network of DNA molecules inside it. We demonstrate DNA microscopy in two-dimensional cell cultures and genome-wide in intact zebrafish embryos.

Biography

Joshua Weinstein is a biophysicist and molecular technologist. He works on developing DNA-based technologies for high-throughput encoding and decoding of biological information with a view toward applications in biology and medicine. He has previously worked on applying massively parallel DNA sequencing to the study of immune receptor repertoires. Recently, he invented DNA microscopy, an imaging modality that uses DNA rather than light as an imaging medium in order to generate detailed pictures of how genetic diversity distributes spatially across biological specimens. Prof. Weinsten completed his undergraduate studies in physics and biophysics at the University of Pennsylvania, and his PhD in biophysics at Stanford University in 2012 under the direction of Stephen Quake and Daniel Fisher. There, he published the first global measurements of immune receptor sequence repertoires, using the zebrafish as a model organism. Weinstein later applied repertoire-sequencing to immune development and human vaccine response. Weinsten completed his postdoctoral work at the Broad Institute/Massachusetts Institute of Technology, under the joint-mentorship of Feng Zhang and Aviv Regev, where he was supported by a Simons Fellowship from the Life Sciences Research Foundation. There, he developed DNA microscopy, enabling biological specimens to “image themselves” and thereby generating detailed spatio-genetic data sets, which bypass the need for specialized equipment. In 2019, Weinstein moved to his current position as assistant professor of molecular engineering and medicine in the section of genetic medicine at the University of Chicago.

SciLifeLab Lund Seminar Series
2024-09-25 15:00 - 16:00 | Belfragesalen, BMC D15, Klinikgatan 32, Lund, Sweden
Welcome to the SciLifeLab Lund seminar series!

These seminars are designed to highlight SciLifeLab Lund, our cutting-edge research infrastructure, and the diverse resources available to the scientific community.

Additionally, we aim to provide our users with a platform to showcase their projects and the results they have achieved through utilizing our services.

In the 1st seminar, the site Director Markus Heidenblad, the Data Science Coordinator Wojtek Potrzebowski, and Site Coordinator Anabella Aguilera will introduce SciLifeLab Lund.

Registration

Register for the next seminars!

30th October 2024 | Swedish National Infrastructure for Biological Mass Spectrometry (BioMS)

Register Seminar October

18th December 2024 | Center Translational Genomics within Clinical Genomics Lund

Register Seminar December

29th January 2025 | CryoEM for Life Sciences at Lund University

Register Seminar January

26th February 2025 | Display and Selection Technologies

Register Seminar February

26th March 2025 | Lund University Bioimaging Centre (LBIC)

Register Seminar March

23rd April 2025 | Lund Protein Production Platform (LP3)

Register Seminar April

28th May 2025 | National Bioinformatics Infrastructure (NBIS)

Register Seminar May

18th June | Structural Proteomics

Register Seminar June

Data Driven Multi-omics Integration in Life Sciences
2024-09-26 09:00 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
The 10th RIKEN-KI-SciLifeLab Symposium

Large amounts of data are being generated in various omics disciplines such as genomics, genetics, transcriptomics, proteomics, metabolomics, and epigenomics. Integrating these multi-dimensional omics datasets offers unprecedented opportunities to gain comprehensive insights into complex biological systems and their underlying mechanisms. This symposium on “Data Driven Multi-omics Integration in Life Sciences” brings together experts to explore the integration of multi-dimensional omics datasets. Speakers will specifically highlight the integrative aspect of their work and how it helped in understanding biology and medical sciences.

Registration

Program

8:30Registration9:00Opening of SymposiumProf. Jan Ellenberg, SciLifeLab DirectorProf. Annika Östman Wernerson,KI PresidentProf. Kazuhiko Yamamoto (RIKEN Center IMS Director)Section 1: Transcriptomics/Genetics-centric integrationChair: Dr. Katsuyuki Yugi, Dr. Chung-Chau Hon9:15Multi omics study on human immune systemProf. Kazuhiko Yamamoto (RIKEN IMS)9:45Mapping immune cell clonal dynamics within tissuesDr. Camilla Engblom (KI and SciLifeLab)10:05Integrating human genomics with population, individual, and single cell resolutionsDr. Yukinori Okada (RIKEN IMS)10:25Mobile element variation drives population-specific genome diversification, gene regulation, and disease riskDr. Kojima Sohei (RIKEN IMS)10:45Coffee BreakSpecial session: KI, SciLifeLab and Japan11:15Introduction of JSPSJSPS Stockholm Office11:30RemarksProf. Per Nilsson (KI Japan Coordinator)11:30Section 2: Metabolomics/Proteomics-centric integrationChair: Dr. Chung-Chau Hon, Dr. Katsuyuki Yugi11:35Bridging the gap between human genome and phenome with trans-omics networks of mouseDr. Katsuyuki Yugi (RIKEN IMS)11:55The new wave of interaction proteomics for mapping virus-host interactionsDr. Andrea Fossati (KI and SciLifeLab)12:15Decoding the cellular effects of pathogenic mutations through PTM and interaction proteomicsDr. Koshi Imami (RIKEN IMS)12:35Lunch BreakSection 3: Single-cell genomics-centric integrationChair: Dr. Carsten Daub, Dr. Chung-Chau Hon13:45Spatial omics approaches for resolving stromal and neuro-immune interactions in osteoarthritisDr. Lea Mikkola (University of Turku)14:05Understanding disease heritability using single cell transcriptomics and deep learningDr. Chung-Chau Hon (RIKEN IMS)14:25Self-assembled surfaces for map-free spatial transcriptomicsDr. Erik Benson (KI and SciLifeLab)14:45Deciphering state-dependent immune features from multi-layer human omics at single-cell resolutionDr. Ryuya Edahiro (RIKEN IMS)15:05Genome-wide nutrition-induced ribosome frameshifts modulate transcriptome abundanceDr. Vicent Pelechano (KI and SciLifeLab)15:25Coffee Break (30 mins)Section 4: Large scale Data Integration/Artificial intelligenceChair: Dr. Carsten Daub, Dr. Chung-Chau Hon15:55Use of AI in Biotechnology in Japan: Policy PerspectivesDr. Yusuke Mori (University of Tsukuba/Japan Embassy)16:15Autonomous Scientific Discovery by AIDr. Jun Seita (RIKEN IMS)16:35Predicting Drug Responses in Cancer with Interactome-Based AIDr. Avlant Nilsson (KI and SciLifeLab)16:55ClosingDr. Carsten Daub & Dr. Chung Chau Hon17:00Mingle & Pub

Symposium History

This symposium series is organized between RIKEN in Japan, and Karolinska Institutet and SciLifeLab in Sweden. The symposia alternate between RIKEN and SciLifeLab.

The overall goals of the symposia are to

Identify common scientific interests between RIKEN and SciLifeLab,

Identify complementary skills and technologies for collaborations

Encourage the exchange of Ph.D. students and postdocs between RIKEN and SciLifeLab/KI.

Several collaborations between groups at KI, SciLifeLab and RIKEN started based on first contact during one of the symposia.

Organizers

Dr. Kazuhiko Yamamoto (RIKEN IMS)

Dr. Carsten Daub (Karolinska Institutet/SciLifeLab)

Dr. Harukazu Suzuki (RIKEN IMS)

Dr. Chung-Chau Hon (RIKEN IMS)

Contact

Carsten Daub, KI/SciLifeLab

carsten.daub@scilifelab.se

Scalable, Accessible Single Cell with Parse Biosciences' Evercode
2024-09-26 11:30 - 13:30 | Birgit Thilander Lecture Hall, Medicinaregatan 3, Göteborg
Join Us for a Seminar on Single-cell RNA Sequencing (scRNA-seq)

Single-cell RNA sequencing (scRNA-seq) has become a key tool in genomics, offering researchers deep insights into cellular behavior. While droplet-based methods are commonly used, they often come with limitations in flexibility, cost, and scalability. Parse Biosciences’ Evercode technology offers a solution, enabling scalable single-cell sequencing without the need for specialized equipment.

This seminar, co-hosted by Clinical Genomics Gothenburg (CGG) and Parse Biosciences, will feature:

Introduction to Evercode Technology by Parse Biosciences, including practical tips for sample preparation and analysis.

User Perspective Presentation by Joan Camuñas, Dept of Medical Biochemistry and Cell biology

Research Support Overview by CGG, where researchers can get support with experimental design, lab work, and data analysis for single-cell projects.

More information and registration

Lunch will be provided for onsite participation.Registration deadline: September 23

No registration is required for online participation:

Zoom link

Metabolomics in Molecular Medicine - from idea to data interpretation
2024-09-30 08:00 - 2024-10-02 17:00 | KBC Building Umeå, Linneaus Väg 6, Umeå
A jointly organized workshop by the Swedish Metabolomics Centre (SMC) and FIMM’s Metabolomics Unit – University of Helsinki providing an introduction to different aspects of metabolomics, from experimental design to data analysis. The programme consists of a public symposium on the first day and practical elements for workshop participants on days 2-3. Workshop participants are also expected to attend the symposium on the first day.

Read more

Metabolomics measures small molecules commonly known as metabolites that all together comprise a metabolome of a biological system. Since metabolome is a reflection of physiological status, metabolomics helps us to understand molecular mechanisms such as drug responses and to find new indicators for diseases.

This workshop provides an introduction to mass spectrometry-based metabolomics with a special focus on its applications in molecular medicine. The workshop starts with a mini-symposium where the experts in the field discuss the recent advancements and applications in metabolomics research in life sciences. The following two days of practical training will cover the metabolomics workflow from the principles of experimental design, sample preparation, theory of chromatographic separation and mass spectrometry to data acquisition, pre-processing, analysis and interpretation.

Contact

Annika Johansson

Email

+46 90 786 55 51

Spatial Biology - The 2024 SciLifeLab Science Summit
2024-10-01 09:00 - 17:00 | Uppsala Konsert & Kongress, Vaksala torg 1, Uppsala, 75331, Sweden
Spatial Biology is an emerging field driven by recent advances in Spatial Omics technologies. The aim of the summit is to present the spatial omics capabilities at SciLifeLab, and examples of uses of such methods to address various research areas in Life Science. A lot of pioneering work in Spatial Biology originates from researchers associated with SciLifeLab, and we hope to inspire more researchers to explore this approach and to join this growing spatial community.

The Annual Conference SciLifeLab Science Summit is a one-day symposium with a new topic each year. The topic for 2024 is Spatial Biology.

We warmly welcome international visitors to attend this free event. The conference also offers fantastic opportunities for networking and discussions with top academic researchers and industry leaders in spatial omics technology.

Welcome!

Mats Nilsson, Chair of the Scientific Committee, Charlotte Stadler, Per Andrén and Stefania Giacomello

Program

Science Summit Program 2024Download

Posters

Poster Presentation Guidelines

Poster Format

The poster screens are 103 cm wide and 143 cm high. Please ensure your poster fits within these measurements.

Mount your poster

The venue will be open from 8:45 AM. Please proceed to the 6th floor and hang your poster at your designated number. A numbered poster list will be provided closer to the event date.

Poster sessions

Poster Session I: During the morning coffee break, from 10:55 AM to 11:35 AM, presenters of posters with odd numbers (1, 3, 5, 7…) should be present by their posters.

Poster Session II: During the afternoon break, from 3:15 PM to 3:55 PM, presenters of posters with even numbers (2, 4, 6, 8…) should be present by their posters.

Best Poster Award

All poster presenters should attend the Best Poster Award ceremony at the end of the conference, where the winners will be announced. The Scientific Committee will evaluate the posters throughout the day.

Dismount of posters

Please remove your poster immediately after the closing session at 5:00 PM. Poster screens will be collected at 5:30 PM, and any remaining posters will be discarded.

Poster List

Science Summit Posterlist 2024Download

Abstracts

Abstracts Science Summit 2024 – PostersDownload

Registration

For late registrations (after September 13), we cannot guarantee lunch, coffee, nor can we accommodate any allergies or dietary requirements. These will be subject to availability. We appreciate your understanding.

Register here

Questions? If you have any inquiries regarding the event or your registration, please contact events@scilifelab.se

The conference is free of charge; however, if you do not attend and fail to cancel, your department or organization will be charged a no-show fee of 500 SEK.

Important Notice Regarding Venue Regulations

Please be advised that for security reasons, Uppsala Konsert & Kongress (UKK) has a strict policy regarding bags and outside clothing.

Bags larger than A4 size and outside clothing (jackets, coats etc.) are not permitted inside the auditorium.

However, you are welcome to store these items in the venue’s cloakroom. Laptops can be brought into the auditorium in laptop sleeves.

We apologize for any inconvenience this may cause and appreciate your understanding and cooperation in adhering to the venue’s regulations.

Invited Speakers – abstract and bio sketch

Click on the arrow to read the speaker’s title, abstract, and bio.

Gonçalo Castelo-Branco, Karolinska Institutet, Sweden
TalkOligodendroglia in Development and Multiple Sclerosis: Insights from Single-Cell and Spatial Omics

AbstractOligodendroglia (OLG) mediate myelination of neurons, a process that allows efficient electrical impulse transmission in the central nervous system. An autoimmune response in multiple sclerosis (MS) leads to OLG cell death, loss of myelin and neuropathology. Using single cell transcriptomics, we have previously identified disease-specific OLG populations in the EAE mouse model of MS and in human MS brain archival tissue, characterized by the expression of immune genes.By assessing chromatin accessibility and the transcriptome simultaneously at the single cell level at different stages of the disease course, we found that immune genes exhibit a primed chromatin state in mouse and human OLG in a non-disease context, compatible with rapid transitions to immune-competent states in MS. Moreover, we found dynamic and distinct transcriptomic and epigenomic responses of OLG subpopulations to the evolving environment in EAE mouse model of MS, which might modulate their response to regenerative therapeutic interventions in MS.While single-cell genomics are powerful for investigating disease-specific cellular states, these methods involve isolating the tissue under study from its niche, leading to a loss of spatial information. Such information is essential for determining cell-to-cell communication in disease niches. We have applied in situ sequencing to investigate disease evolution in MS at a spatial level, both in the EAE mouse model of MS and in human post-mortem MS samples. We annotated disease neighborhoods during lesion evolution and found centrifugal propagation of active lesions. We demonstrated that disease-associated (DA)-glia arise independently of lesions and are dynamically induced and resolved over the disease course.We have also applied dBIT-Seq, a ligation-based method for deterministic barcoding in tissue, to probe different histone modifications and chromatin accessibility in the mouse brain tissue sections, either in an unimodal or simultaneously with transcriptomics. This spatial epigenome–transcriptome co-profiling has allowed us to identify cellular lineage progression and epigenomic priming events that precede transcription during development with spatial resolution. We are currently applying these methods to disease paradigms in MS, to uncover how transitions to pathological cellular states occur at epigenomic and transcriptomic levels.

Bio

Gonçalo Castelo-Branco researches oligodendrocytes’ epigenetic states, focusing on how transcription factors, non-coding RNA, and chromatin enzymes drive cell changes. His work has potential for multiple sclerosis therapies.

Ron Heeren, Maastricht University, The Netherlands
Talk

Spatial biology and translation life sciences

Abstract

Modern molecular analytical technologies in the “omics” arena plays a crucial role in many scientific disciplines ranging from material sciences to clinical diagnostics. Technological advances have increased methodological sensitivity allowing researchers to acquire detailed molecular information of smaller and smaller samples. The biggest challenge is to put that concerted information in the context of the biological problem the samples originate from. This lecture describes how innovative mass spectrometry based molecular imaging technologies, have impacted translational clinical research and beyond. Or: how a mass spectrometer can be used as a sensitive and selective molecular microscope in modern spatial biology. Targeted and untargeted imaging technologies now offer new insights in the complexity that can be employed for systems medicine. Innovations in mass spectrometry based chemical microscopes have now firmly established themselves in translational molecular research. One key aspect of translational success is the ability to obtain this molecular information on thousands of molecules on a timescale relevant to translation. Single cells can be analyzed in great molecular detail and in the context of their native tissue. Combined this offers a true multi-omics approach that reveals contextual molecular complexity for systems medicine.

Bio

Prof. Dr. Ron M.A. Heeren obtained a PhD degree in technical physics in 1992 at the University of Amsterdam on plasma-surface interactions. He was the research group leader at FOM-AMOLF for macromolecular ion physics and biomolecular imaging mass spectrometry in the period 1995-2015. In 2001 he was appointed professor at the chemistry faculty of Utrecht University lecturing on the physical aspects of biomolecular mass spectrometry. In 2014 he was appointed as distinguished professor and Limburg Chair at the University of Maastricht. He is scientific director of M4I, the Maastricht MultiModal Molecular Imaging institute and heads the division of imaging MS. He is the vice-president of the international mass spectrometry foundation and has been active in many professional societies to advance mass spectrometric research, education and professionalization. His academic research interests are mass spectrometry based personalized medicine, translational molecular imaging research, high-throughput bioinformatics and the development and validation of new mass spectrometry based “omics” imaging techniques for the life sciences.

Arutha Kulasinghe, The University of Queensland, Australia
Talk

Uncoupling Pathways Involved in Immunotherapy Resistance: Insights from Deep Tissue Profiling

Abstract

Spatially resolved multi-omic phenotyping is revolutionizing how we study tissue and immune responses to cancer treatments. In this talk, we will describe our integrated approaches to characterizing the tumour microenvironment in head and neck, lung, and skin cancers using ultra high-plex spatial proteomics and transcriptomics, benchmarking to ground truth, and developing functionally characterised immuno-metabolic signatures associated with resistance and sensitivity to immunotherapy.

Bio

Dr. Arutha Kulasinghe is a Senior Research Fellow and leads the Clinical-oMx Lab at the University of Queensland. Dr Kulasinghe has pioneered spatial transcriptomics using digital spatial profiling approaches in the Asia-Pacific region, contributing to world-first studies for lung cancer, head and neck cancer, skin cancer and COVID-19. His research aims to understand the underlying pathobiology by using an integrative multi-omics approach.

Cecilia Lindskog, Uppsala University, Sweden
TalkA spatio-temporal single-cell type map of the human proteome based on transcriptomics, high-resolution antibody-based imaging and artificial intelligenceAbstractFor a fundamental understanding of human health, molecular medicine and targeted treatment, it is necessary to map processes unique to each tissue and cell type. We here aimed to set up a stringent, workflow for mapping human tissues at the single-cell type level, and utilized this workflow to create high-resolution spatio-temporal maps of tissue or cell type-specific proteins in human tissues. One of these tissues is testis, which is a complex organ with spermatogenesis involving thousands of genes and proteins activated or repressed through multiple cell states, from spermatogonial stem cells to mature sperm. Understanding the intricate functions and mechanisms at each step of this process requires a multi-dimensional approach that integrates both quantitative and qualitative methods.Based on single-cell RNA sequencing data, we identified 12 distinct cell types and subsets of germ cells in testis, some of which cannot be distinguished by regular immunohistochemistry. Using a multiplex immunofluorescence pipeline, we then built antibody panels specifically outlining each of these cell types. The fixed antibody panels were stained together with the candidate protein of interest, one at a time, to pinpoint the exact protein localization at a cellular and subcellular level. Using artificial intelligence, the high-resolution images were quantified using an automated image analysis workflow. The integrated data allowed us to study temporal mRNA and protein expression gradients along with maturation processes and identify which mRNAs that are consistently translated into proteins from those that vary from a spatio-temporal aspect. We were also able to assign presumed functions to numerous uncharacterized proteins not previously described in the context of human reproduction.In summary, we present a strategy for high-resolution spatio-temporal mapping of human tissues and cells, presented as a single-cell type reference map of adult human testis. The data which is freely available on www.proteinatlas.org decodes the complexity of human germ cells and links quantitative data with tissue morphology, and the validated workflow has the potential to be used for other tissues, contributing to valuable insights into molecular function and processes linked to disease.BioDr. Lindskog is a research group leader and associate professor at the Department of Immunology, Genetics and Pathology, Cancer Precision Medicine unit, Uppsala University, Sweden. Her research group uses a multi-dimensional approach and combination of various qualitative and quantitative methods to generate high-resolution spatial maps of the human body at the single-cell type level. By combining scRNA-seq, spatial technologies for mRNA and protein detection and machine learning, she aims to link single cell type-specific expression profiles with molecular function and mechanisms of disease, a first step towards precision medicine. Since 2006, Dr. Lindskog is also affiliated with the Human Protein Atlas (HPA) project, the largest biological database for spatial proteomics, publicly available at www.proteinatlas.org. She received her PhD in Pathology at Uppsala University in 2013, and since 2014 she has been director of the tissue-based efforts of the HPA project, leading the team that generates the mRNA and protein expression data in human tissues.

Joakim Lundeberg, KTH, Sweden
Talk

Tissue ecosystems in time and space

Abstract

Tools in spatial biology offer a wide range of technologies that quantify different types of biomolecules in tissue sections. These technologies provide information about distinct aspects of tissue anatomy, such as its morphology, genome, transcriptome, proteome, and metabolome. Here, several multiomics computational and experimental methodologies approaches that capture the tissue ecosystem from a single tissue section will be described.

Bio

Joakim Lundeberg, Ph.D., Professor in Molecular Biotechnology, has, during the most recent years, focused on spatial transcriptomics, which enables a detailed description of gene expression patterns in tissue sections. The methodology is now available worldwide through 10x Genomics Inc, as Visium. The technology was also featured in Nature Methods as the Method of the Year 2020. Dr. Lundeberg has publications demonstrating technology development into several new spatial modalities and examples of its impact in biology. The current research focuses on expanding the spatial modalities and developing new tools and applications in human cell atlas, neurology, and cancer.

Sinem Saka, EMBL, Germany
TalkA DNA toolbox for spatial biology from imaging to sequencingAbstractDNA is not only a fundamental constituent of cells, but has also great capacity for information storage. We leverage the predictability of DNA hybridization kinetics and orthogonality of DNA sequences to utilize DNA oligos as tagging and barcoding tools for improving the major limitations of in situ visualization of molecules. We have previously developed multiplexed imaging approaches such as SABER-FISH and Immuno-SABER that utilize DNA barcoding and a flexible in situ signal amplification system for efficient visualisation of many protein, DNA or RNA targets in cells and tissues. More recently, we have implemented DNA barcoding for a new spatial transcriptomics approach, Light-Seq, which directly integrates fluorescence imaging and whole-transcriptome next-generation sequencing of the same cells in fixed biological samples. Light-Seq combines spatially-targeted, rapid photocrosslinking of DNA barcodes onto cDNAs in situ with a novel one-step DNA stitching reaction to create pooled, spatially-indexed sequencing libraries. This light-directed barcoding enables imaging-based in situ selection of multiple cell populations in intact fixed tissue samples for full transcriptome sequencing based on location, morphology, or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we discovered new biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only 4-8 individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next-generation sequencing of the same cells, leaving the sample intact for further analysis post-sequencing. We are using these methods to directly link multi-dimensional and high-resolution microscopic phenotypes to transcriptomic profiles for diverse sample types.

Bio

PhD in Molecular Biology, 2013, University of Göttingen/International Max Planck Research School, Germany.Postdoctoral research at Wyss Institute for Biologically Inspired Engineering, Harvard University, USA.EMBO Postdoctoral Fellow 2016–2017.Human Frontier Science Program Fellow 2017–2020.Group leader at EMBL since December 2020.

Jeffrey Spraggins, Vanderbilt University, Nashville, USA
TalkBringing human disease into focus through integrated multimodal molecular imagingAbstractCellular interactions within tissue micro-environments form the basis of health and disease for all organisms. Exposure to nutrients, toxins, and neighboring cells triggers coordinated molecular responses that impact cellular function and metabolism in a beneficial, adaptive, or detrimental manner. Acquiring molecular information at cellular resolution is thus crucial for developing a comprehensive understanding of the biology of an organism. Matrix-assisted laser desorption/ionization (MALD) imaging mass spectrometry (IMS) addresses this need by combining the spatial fidelity of classical microscopy with the molecular specificity of a mass spectrometer. This presentation will highlight our work developing new, high-performance technologies for improving the spatial resolution, sensitivity, and specificity of MALDI IMS for metabolite, lipid, and protein mapping. This will include the utilization of novel MALDI methods and development efforts using high spatial resolution Q-TOF platforms to address the molecular complexity associated with direct tissue analysis. Further, I will describe recent advances in integrated, multimodal methods that correlate molecular signals to specific biological tissue features and cell types. These technologies will be demonstrated through various biomedical research applications that include the construction of molecular atlases and understanding the molecular drivers of normal aging and disease.BioJeff Spraggins is an Associate Professor in the Department of Cell and Developmental Biology, Director of the Biomolecular Multimodal Imaging Center (BIOMIC), and Director of the Mass Spectrometry Research Center at Vanderbilt University. He received his B.A. in Chemistry from the College of Wooster and his Ph.D. in Analytical Chemistry from the University of Delaware. Dr. Spraggins’ research program focuses on the development of next-generation imaging mass spectrometry (IMS) technologies to elucidate the molecular basis of health and disease. Modern instrumentation and computing capabilities have enabled researchers to move beyond reductionist biology and, instead, probe how the components of biological entities (e.g., molecules, cells, and tissues) interact to reveal the underlying biology of disease. This systems biology approach has been accelerated by advancements in high-throughput ‘omics’ technologies; however, genetic and molecular information is only part of the story. The challenge lies in understanding how these parts interact and how perturbations to the system relate to disease. Molecular imaging effectively offers a ‘blueprint’ as to how biological components work together by providing spatial context to molecular information. Broadly, Dr. Spraggins’ research falls into two categories: (1) Developing novel mass spectrometry technologies to maximize imaging performance, enabling molecular histology at cellular resolution, and (2) combining imaging mass spectrometry with a variety of other biomedical imaging technologies to create new integrated modalities capable of providing a systems biology view of tissue at cellular resolution. The Spraggins group applies these technologies to the construction of molecular atlases as part of the NIH Human Biomolecular Atlas Program (HuBMAP), the NIDDK Kidney Precision Medicine Project (KPMP), and the NCI Human Tumor Atlas Network (HTAN); and also, to understanding the molecular drivers of Alzheimer’s, kidney, and infectious diseases.

Carolina Wählby, Uppsala University, Sweden
TalkMeasuring tissue morphology in spatial biologyAbstractSpatial omics has transformed our understanding of tissue architecture by preserving spatial context of gene expression patterns. Simultaneously, advances in imaging AI have enabled extraction of morphological features describing the tissue. The intersection of spatial omics and imaging AI presents opportunities for a more holistic understanding: morphological features can be translated or integrated into spatial omics analyses. By translation we mean finding morphological features that spatially correlate with gene expression patterns with the purpose of predicting gene expression. Such features can be used to generate super-resolution gene expression maps or infer genetic information from clinical H&E-stained samples. By integration we mean finding morphological features that spatially complement gene expression patterns with the purpose of enriching information. Such features can be used to define spatial domains, especially where gene expression has preceded morphological changes and where morphology remains after gene expression.BioCarolina Wählby is professor in Quantitative Microscopy at the Dept. of Information Technology, Uppsala University, and Scientific Director of the National SciLifeLab Bioimage Informatics facility. Her research lies in the intersection between life science and computational image analysis, developing image analysis, deep learning, and visualization approaches for understanding the organization and dynamics of cells and tissue, funded primarily by the ERC and the Swedish Foundation for Strategic research. She has a MSc in molecular biotechnology and a PhD in digital image analysis, and carried out postdoc research within genetics and pathology. She was part of the Imaging Platform of the Broad Institute 2009-2015, developing CellProfiler, and became full professor at Uppsala University in 2014, and is a member of the Royal Swedish Academy of Engineering Sciences.

Speaker abstracts 2024Download

Important dates

October 1: Science Summit Opens at Uppsala Konsert & Kongress

Exhibitors

Meet representatives from companies providing products and services in relevant fields. The following companies will be present during the day

10x Genomics

Akoya Biosciences

BioNordika AB

Bruker (Canopy Biosciences and NanoStrings)

Lunaphore

Navinci Diagnostics AB

Saveen & Werner AB

Thermo Fisher Scientific

Vizgen Incorporated

Scientific Committee

Mats Nilsson, Chair and Platform Director Spatial Biology, SciLifeLab/Stockholm UniversityCharlotte Stadler, Platform Co-Director Spatial Biology, SciLifeLab/KTHPer Andrén, SciLifeLab/Uppsala UniversityStefania Giacomello, SciLifeLab/KTH

Project leader Operations Office: Erika Bergqvist Erkstam

SS24-Flyer_2Download

CSI Seminar: Imposter Syndrome
2024-10-02 15:00 - 15:30 | Hybrid event in Gamma 2 lunchroom and zoom, Tomtebodavägen 23 B, Solna, 17165, Sweden
Dear Everyone,

We are excited to host a new Coaching in Science Initiative (CSI) Seminar titled: ‘Imposter Syndrome’

Imposter Syndrome is a common yet often overlooked challenge in academia, affecting scholars at every stage—from graduate students to senior faculty. Despite your accomplishments, do you often feel like you don’t belong or fear being “exposed” as a fraud? In this seminar, we will examine what imposter syndrome is, when and why it manifests, and reflect on the deeper psychological and social factors that contribute to it. We will also provide practical strategies and tools to help you cope with these feelings of self-doubt, overcome perfectionism, and reclaim your confidence.

Date: 02/10/2024

Time: 15:00 – 15:30

Zoom link: https://kth-se.zoom.us/j/65426414592

On-site location: Gamma 2 lunch room

We will begin with a ~ 20 min talk, held in Solna and over zoom. Then proceed with a reflection and discussion held only on-site. We encourage other sites to form watch parties, by listening in together to the talk and then hold their own discussion afterwards. Hopefully seeding many local chapters of CSI.

To help facilitate discussion and reflection, consider the following starter questions:

Awareness: where do we experience imposter syndrome in our lives?

Analysis: how do I currently interact with imposter thinking?

Alternative: how could we relate to imposter syndrome, in ourselves and others?

Action: how will knowledge of imposter thinking change my decisions going forward?

Please forward this to friends and colleagues!

Yours sincerely,

The CSI Team

Ways to keep in touch with CSI

Visit our webpage for coaching material, access to older seminars, links to external resources and our events: https://www.thecoachinginscienceinitiative.org/

We will also post our events in the SciLifeLab event calendar: https://www.scilifelab.se/event

Our seminars has/will be recorded and can be watch and re-used as workshops to raise awareness on this YouTube channel, the first CSI seminar is already there: https://www.youtube.com/@TheCoachinginScienceInitiative

If you have a scilifelab e-mail, find our channel in the scilifelab.slack.com workspace #coaching-in-science-initiative

Reach our committee thought our e-mail: csi@scilifelab.se

Deciphering the mysteries of sleep: toward the molecular substrate for “sleepiness”
2024-10-02 16:00 - 17:00 | H:son Holmdahlsalen, Entrance 100, Akademiska sjukhuset, Dag Hammarskjölds väg 8, Uppsala
KVA-JSPS lecture about orexins. Prof. Masashi Yanagisawa, MD, PhD, International Institute for Integrative Sleep Medicine, University of Tsukuba, Japan,

Professor Masashi Yanagisawa, the discoverer of both endothelin and orexin, which are extremely important peptides for blood pressure and sleep regulation, will give a lecture in Uppsala, H:son Holmdahlsalen, Entrance 100, Akademiska sjukhuset. His lecture will focus on the regulation of sleep and wakefulness. The Lecture will follow after a short presentation of JSPS.

The lecture is possible thanks to a travel grant from Japan Society for the Promotion of Science (JSPS).

Host: Professor Dan Larhammar, Department of Medical Cell Biology, SciLifeLab affiliated group leader, Uppsala University. Please contact Prof. Larhammar if you wish to meet with Prof. Yanagisawa during his visit to Uppsala.

Abstract

Although sleep is a ubiquitous behavior in animal species with a nervous system, many aspects in the neurobiology of sleep remain mysterious. Our discovery of orexin, a hypothalamic neuropeptide involved in the maintenance of wakefulness, has triggered intensive research examining the exact role of the orexinergic and other neuronal pathways in the regulation of sleep/wakefulness. Orexin receptor antagonists, which specifically block the endogenous waking system, have been approved as a new strategy to treat insomnia. Also, since the sleep disorder narcolepsy-cataplexy is caused by orexin deficiency, orexin receptor agonists are expected to provide mechanistic therapy for the disease; they will likely be also useful for treating excessive sleepiness due to other etiologies.

Even though the executive neurocircuitry and neurochemistry for sleep/wake switching, including the orexinergic system, has been increasingly revealed in recent years, the mechanism for homeostatic regulation of sleep, as well as the neural substrate for “sleepiness” (sleep pressure), remains unknown. To crack open this black box, we have initiated a large-scale forward genetic screen of sleep/wake phenotype in mice based on true somnographic (EEG/EMG) measurements. We have so far screened >10,000 heterozygous ENU-mutagenized founders and established several pedigrees exhibiting heritable and specific sleep/wake abnormalities. By combining linkage analysis and the next-generation whole exome sequencing, we have molecularly identified and verified the causal mutation in several of these pedigrees. Since these dominant mutations cause strong phenotypic traits, we expect that the mutated genes will provide new insights into the elusive pathway regulating sleep/wakefulness. Indeed, through a systematic cross-comparison of the SIK3 Sleepy mutants and sleep-deprived mice, we have found that the cumulative phosphorylation state of a specific set of mostly synaptic proteins may represent the molecular substrate of sleep pressure. We have also found that the neuronal molecular pathway LKB1-SIK3-HDAC4/5 may represent the level of sleep pressure, regulating the amount, depth, and timing of sleep by acting in different brain regions, respectively (Kim et al. Nature 612: 512-518, 2022; Zhou et al. Nature 612: 519-527, 2022).

Bio sketch

Prof. Yanagisawa received his PhD at the University of Tsukuba where he discovered the powerful vasoconstrictor peptide endothelin. His group later identified a receptor for endothelin which is now an important target for treatment of hypertension. After moving to Texas Southwestern Medical Center in Dallas he identified the endothelin-converting enzyme and later described the role of the endothelin pathway in embryonic development.

His project to deorphanize G protein-coupled receptors resulted in the discovery of the hypothalamic neuropeptide orexin in 1998. The year after, he showed that the sleep disorder narcolepsy is caused by orexin deficiency. This knowledge has resulted in orexin receptor antagonists approved for treatment of insomnia. An ongoing project in Tsukuba has led to identification of several new genes and molecular pathways that are importantly involved in the regulation of sleep amounts and the level of sleep need.

Prof. Yanagisawa has receved numerous honours and awards, most recently the Breakthrough Prize in Life Sciences. He was elected to the U.S. National Academy of Sciences in 2003. Since 2012 he is the director for the International Institute for Integrative Sleep Medicine at the University of Tsukuba.

Announcement Yanagisawa 2401002Download

DDLS Symposium on Data-Driven Environmental Monitoring of Infectious Diseases
2024-10-07 12:00 - 2024-10-08 15:00 | BMC Trippelrummet, Husargatan 3, entrance C11, Uppsala, Sweden
The DDLS research area Epidemiology and Biology of Infection invites you to its second in-person symposium. (The event is fully in-person only). The symposium will focus on promoting and enhancing data-driven environmental assessment for infectious diseases (including antibiotic-resistant bacteria) across various settings using diverse approaches.

The symposium will feature both local and international high-profile speakers in the field and will cover topics ranging from sewage surveillance, monitoring of airborne infectious agents, as well as environmental and animal disease monitoring for pathogens, antimicrobial resistance and harmful substances. The symposium will also include more technical aspects of implementations as well as data-driven advancements and challenges.

There will also be a possibility to submit abstracts for short talks!

Please join us for this one-and-a-half-day symposium on 7-8 October 2024, in Navet, SciLifeLab’s meeting place in Uppsala, to meet the research area Fellows, the Expert Group and excellent researchers of the area. Engage in discussions, enjoy refreshments, and network with experts across a range of infectious disease monitoring topics!

Welcome!

Scientific committeeAnna Székely (SLU)Johan Bengtsson-Palme (Chalmers)

Registration

Deadline for abstract submission: 23 September (Extended deadline)Deadline to register to attend: 25 September

If seats are available and you register after September 25, we can not accommodate allergies or special requirements and you will write your name tag upon arrival to the venue..

Registration

Program

DDLS symposium EBI_PROGRAM_3Download

Members of The Data-driven Epidemiology and biology of infection expert group:

Tom Britton, Stockholm UniversityJoakim Dillner, Karolinska Institutet and Karolinska Univ. HospitalTove Fall, Uppsala UniversityBirgitta Henriques-Normark, Karolinska InstitutetErik Kristiansson, Chalmers University of TechnologyPatrik Medstrand, Lund UniversityStaffan Svärd, Uppsala UniversityOliver Billker, chair (DDLS SG member)

[The Svedberg seminar] - Patch-seq profiling of pancreatic islet cell types and cell-free RNA diagnostics
2024-10-07 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Joan Camuñas-SolerAssistant ProfessorUniversity of Gothenburg, Sweden

Joan Camuñas

Bio

Dr. Camuñas-Soler is an Assistant Professor and Wallenberg Molecular Medicine Fellow at the University of Gothenburg since 2022. His current research focuses on data-driven genomics and precision medicine. Previously, as a postdoctoral scholar at Stanford University, he pioneered novel single-cell genomic techniques to study islet-cell function in health and diabetes. Additionally, he developed liquid biopsy tools for the early prediction of pregnancy complications, which led to the creation of a molecular diagnostics startup. His research is highly interdisciplinary, combining approaches from molecular engineering, biophysics, and computational biology. His work has been recognized with several awards, patents, and prestigious establishment grants.

Patch-seq profiling of pancreatic islet cell types and cell-free RNA diagnostics

Methods to simultaneously profile transcriptome and cell function at the single-cell level are scarce. In this talk, I will show that single-cell RNA sequencing (scRNAseq), in combination with electrophysiological measurements of exocytosis (patch-seq), can be used to study the connection between human endocrine physiology and transcriptomes at the single cell level. I will discuss the application of patch-seq to investigate normal physiology of pancreatic islet cells and their dysfunction in diabetes.

Using data from 1,369 patch-seq cells from the pancreata of 34 human donors; I will show how this technology can be used to identify novel regulators of β-cell biology and transcriptomic alterations indicative of β-cell maladaptation and α-cell dysfunction in type 2 diabetes (T2D). Additionally, I will introduce a complementary approach to measure the secretory capacity of these cells based in the use of fluorescent tracers of endocytic membrane retrieval, which can then be combined with FACS sorting ad scRNAseq to characterize β-cell states associated with higher secretory capacity.

In the second part of this talk, I will also discuss how sequencing of circulating RNA in the blood (cell-free RNA) can be used as a ‘liquid biopsy’ tool to monitor human physiology and disease. I will focus on the use of cell-free RNA to establish a molecular clock of pregnancy, and as a tool to track autoimmune disorders with poorly understood pathophysiology. Some of this molecular diagnostics work is currently being translated into clinical validation.

Read more: Camuñas-Soler Group

Host: Jessica Nordlund jessica.nordlund@medsci.uu.se

Stockholm Single Cell Genomics 2024 Symposium
2024-10-08 09:00 - 16:30 | IVA Conference center, Grev Turegatan 16, Stockholm
The National Genomics Infrastructure is pleased to announce the Stockholm Single Cell Genomics 2024 Symposium, taking place on October 8th this fall. Join us for a day of engaging talks by experts in the field, a chance to explore the latest technologies, and networking opportunities.

register here

Confirmed speakers:

Gonçalo Castelo-Branco, KI,

Jessica Nordlund, UU,

Rickard Sandberg, KI,

Joan Camuñas-Soler, GU,

Martin Enge, KI,

Kasper Karlsson, KI,

Mohanraj Ramachandran, UU,

Tuuli Lappalainen, KTH and

Alexander Steemers, Princess Maxima Center.

Sponsors: Scale Biosciences, Pixelgen Technologies, BioSkryb, Techtum, Parse Biosciences, 10X Genomics, Illumina, Oxford Nanopore Technologies and BD Biosciences.

Check here to see any updates!

Data-Driven Life Sciences Hackathon
2024-10-09 09:00 - 2024-10-11 16:30 | Gamma 7 Lunchroom, Tomtebodavägen 23A, Solna, 17121
Join us at the DDLS Hackathon in person at SciLifeLab in Solna, where participants will choose and collaborate on a range of provided projects. With the support of teaching assistants in a hands-on environment, groups will innovate and develop solutions in the dynamic field of data-driven life science.

During the three day hackathon, participants will select a dataset and apply the skills and knowledge gained during the course (see link above for each module) to create AI models, analyze the data, and produce meaningful insights. At the end of the hackathon, teams will present their achievements.

Everyone affiliated with the DDLS programme or interested in data-driven life science is welcome to join–from PIs, PhD students, postdocs, and facility experts/trainers. Participants will form pairs or small groups of 2-3 people on-site to work on projects, exchange ideas and experiences, and engage in pair programming. This collaborative environment will foster innovation and provide a unique opportunity to apply the concepts learned throughout the course to real-world problems in data-driven life sciences.

What will you gain attending the hackathon?If you are to be selected to participate you will get the opportunity not only to work hands-on on a data-driven life science project, but also to network with experts within the field of data-driven life science, researchers and research infrastructure experts

Registration deadline:Monday, September 30th, 2024

Registration

This hackathon is part of the 2024 DDLS course and will gather data-driven life science researchers (MSc students, PhD students, post-docs, staff-scientists, experts and group leaders).

For questions, contact Wei Ouyang at weio@kth.se or traininghub@scilifelab.se

Microsampling- New Avenues for Metabolomics in Precision Health
2024-10-11 10:00 - 16:00 | Andreas Vesalius Lecture Hall, Karolinska Institutet, Berzelius väg 3, Solna, 171 65, Sweden
The Metrabolomics Platform arranges a one day seminar on “Microsampling- New Avenues for Metabolomics in Precision Health” together with the Nordic Metabolomics Society.

Program

10.00Welcome,Rikard Landberg (SciLifeLab& Chalmers) & Alex Dickens (Nordic Metabolomics Society10.10Microsampling in Metabolomics- Enabler of Precision Health?Timothy Garrett (University of Florida)10.40High-throughput NMR-based metabolmics on microsamplesPeter Würtz (Nightingale)11.10New microsampling techniquesNiclas Roxhed (KTH)11.30Evaluation of microsampling techniques for lipidomics and exposomicsTuulia Hyötyläinen (Örebro University)11.50Metabolomics and microsampling across labsAlex Dickens (University of Turku)12.10SciLife-platform microsampling project and the SCAPIS2-HOME studyRikard Landberg (Scilifelab & Chalmers)12.30Lunch13.30Microsampling devices for nontarget chemical exposomicsSolveigh Thiele (SciLifeLab & Stockholm University)13.50Microsampling in high-through proteomicsClaudia Fredolini (Scilifelab)14.10Pitches of available microsampling techniquesProducers/vendors of microsampling devices15.00Discussion focused on the way forward15.45Concluding remarks and the way forwardRikard Landberg (SciLifeLab& Chalmers

Registration

How to get there

BusLine 3, 6, 77, 507 from S:t Eriksplan. Get off at Karolinska Institutet, Biomedicum.Line 53 and 72 från Odenplan. Get off at Karolinska Institutet west which is next to Berzeliuslaboratory.

SubwayNearest station is S:t Eriksplan (exit Torsgatan), from where it takes 15-20 min walking to the Berzelius laboratory Odenplan – take bus 53 och 72.

CarIf you arrive by car, parkeringshuset Skruven is the closest partking to the Berzeliuslaboratory https://www.aimopark.se/stader/solna/campus-solna/

Please note that the Main Entrance to Campus Solna is currently closed due to the construction of a new subway station. There are several options to enter the campus from Solnavägen for those who walk or cycle. For those coming by car, you must come via Tomtebodavägen, where the nearest parking garage in connection with the conference is also located.

Contact: Rikard Landberg rikard.landberg@chalmers.se

Research involving human data - what do I need to think of as a researcher?
2024-10-15 10:00 - 11:00 | Online event via Zoom
This seminar will focus on collecting and using personal data in research. We will guide you through the different phases of a typical research project and discuss some commonly asked questions. We will, for example, talk about GDPR, and secure management and sharing of sensitive data, among others.

When: Tuesday October 15, 10-11 CET (Zoom)

Speaker: Markus Englund and Erik Hedman, Data Steward, NBIS

SciLifeLab Data Management seminar series is an event series by the SciLifeLab Data Centre and NBIS joint Data Management team aimed at both the life science research community and infrastructure, and others with an interest in research data management in life sciences. The events will showcase how to put the FAIR principles, and good data management into practice. The goal of the events in this seminar series is to provide interesting seminars around topics related to research data management in general but also to foster discussions around best practices and how they can be improved. The events takes place virtually (over Zoom) and are open to everyone, (researchers, staff, RDM professionals etc.) working at or affiliated with a Swedish research institute or university. Each event is scheduled for 60 minutes, including 15 minutes for discussions and Q & A. The videos (excluding Q&A) will be published openly after the seminars at the SciLifeLab YouTube channel.More information about SciLifeLab Data Centre and NBIS joint Data Management team: https://data-guidelines.scilifelab.se/

Welcome!

Organisers: SciLifeLab Data Centre and NBIS National Bioinformatics Infrastructure SwedenFor more information or inquiries please contact: data-management@scilifelab.se

Deriving actionable insight from omics data – an industry perspective
2024-10-15 10:00 - 11:15 | Online event via Zoom
Speaker: Daniel Muthas, Head of Data Science & Bioinformatics at AstraZeneca

Abstract

This talk will focus on how advancement in omic analysis is enabling the realisation of precision medicine in chronic complex diseases. Large, well phenotyped cohorts highlights the heterogeneity of disease and through single cell technologies we are able to study disease processes at unprecedented granularity, but how do we take these insights into actionable and deployable applications? Here I will focus on how we employ a breadth of bioinformatic techniques of different modalities to bridge between populations, patients, and cellular level to identify novel targets, biomarkers and patient populations.

Background

Daniel’s team is working with applied bioinformatics across the whole drug discovery and development pipeline, from target identification to indication expansion and exploratory biomarker analysis in clinical trials.

Host: Rasool Saghaleyni, NBIS Chalmers University, Gothenburg (rasool.saghaleyni@scilifelab.se)

Date: October 15, 10:00 – 11:15 CET online on zoom

Broadcast link (live event): link, pass: spd996 The talk will also be available afterwards on the SciLifeLab YouTube channel.More information about the Oimcs Integration and Systems Biology Workshop here.

Trade secrets for Academic Startups, Pharma and Biotech Companies in the Life Sciences
2024-10-15 11:00 - 12:00 | Online event via Zoom
Welcome to this Drug Discovery Webinar, organized by OligoNova and SciLifeLab Drug Discovery and Development, to learn more about how academic and biotech interventions can be protected with the goal to benefit patients.

This webinar is an introduction to trade secrets as a form of intellectual property, with a focus on its potential importance to a life sciences start up.

Trade secrets are often an overlooked form of intellectual property, thought by many to be of little relevance in the life sciences. However, as part of a well-developed IP strategy, trade secrets have an increasingly important role to play, with the potential to not only supplement a patent-based strategy but, in some cases, to provide a more suitable alternative.

In this seminar, we will discuss how trade secrets can be identified, protected, and used to increase value and support investment.

registration

Agenda

Introduction – Fredrik Wångsell, OligoNova

Trade secrets in the Life Sciences – Fiona Hey, Tony Proctor and Michel, Pears Potter Clarkson

Q&A and discussion

Welcome

SciLifeLab DDD and OligoNova

Other Seminars

OligaNova organizes three seminars during the fall 2024

Trade secrets in the Life Sciences, October 15

Maximizing exclusivity in the Life Sciences, November 6

IP Strategies in the Life Sciences, December 18

SciLifeLab Uppsala Site Day
2024-10-17 09:00 - 17:00 | University Main Building, Biskopsgatan 3, Uppsala, 75310
The SciLifeLab site in Uppsala welcomes you to a full day of vibrant and inspiring science. During this event, SciLifeLab Uppsala will highlight the research and infrastructure located in Uppsala.

Experience the wide variety of research infrastructures at SciLifeLab Uppsala. Listen to talks from SciLifeLab/DDLS fellows. Join the panel discussion with the nationwide capability programs in Planetary Biology, Precision Medicine, and Pandemic Laboratory Preparedness. Enjoy poster sessions and exhibitions from SciLifeLab facilities.

The SciLifeLab Uppsala Site Day aims to foster discussions and interaction among participants. The event will be held exclusively on-site in Sal X, which has a seating capacity of 221 people, and will be streamed to Sal IX, which can accommodate 141 people. Since the seats are limited, remember to cancel if you cannot attend.

All attendees are invited to enjoy fika, lunch, and mingling sessions. Please note that no Zoom link will be available.

Registration

Registration closes on October 14 at 09:00.

Registration

If you have questions, please contact events@scilifelab.se

Program

SciLifeLab Day Uppsala_Program_v4.0Download

Exhibition List

U-Print, 3D printing facility Paul O’Callaghan

DanioReadout Beata Filipek-Gorniok

NMR-UppsalaRuisheng Xiong

MicrofluidicsMaria Tenje

Affinity Proteomics UppsalaMikael Åberg

Genomics PlatformSusanne Hellstedt Kerje

BioImage Informatics Anna KlemmBioinformatics (NBIS/ELEXIR-SE),Bengt Persson

Chemical Biology Consortium Sweden Uppsala Jordi Carreras Puigvert

Clinical Genomics UppsalaMalin Melin

Drug Discovery and Development Platform Rebecka Klintenberg

Spatial Mass SpectrometryAnna Nilsson

Uppsala International HubCharlotte Walker

Testa CenterAlexandra Patriksson

SciLifeLab CapabilitiesPrecision Medicine Capability, Eva Berglund. Pandemic Laboratory Preparedness Capability, Alice Sollazzo. Planetary Biology Capability, Anabella Aguilera

EATRIS Ulrika BäckmanInnovation coaching Kerstin Ekelöf, UU Innovation, Liza Nilsson, UU Innovation

Uppsala Clinical Research Center (UCR), Maria Sörby

SciLifeLab Data Centre and Data Science Node in Evolution and Biodiversity, Angela Fuentes Pardo

SciLifeLab, Training Hub, Data-driven Life Science Program (DDLS) supported by KAW and SciLifeLab, Hampus Pehrsson Ternström

Posters and Flash Talks
We have reserved space for selected SciLifeLab/DDLS fellow PhD students, eSSENCE PhD students to bring a scientific poster. Four submitted abstracts have been selected for a 5-minute Flash Talk. The selected Flash Talks are highlighted.

Instructions

Mount your poster during the Coffee & Registration at 08:30-09:00, poster presentation during the lunch mingle.

The poster screens are portrait oriented, 103×143 cm.

Poster #Poster title and presenter1Investigating Islet Vasculature Alterations in Type I DiabetesCasian-Simon Aioanei – FLASH TALK2Optimal effect estimation in genome-wide association studies with censored biomarker measurements in large-scale biobanksYaqi Deng – FLASH TALK3Loss of chromogranin A and catestatin affect islet composition and neurotransmitters in the pancreasDali Epremidze – FLASH TALK4Chemoselective Primer Extension for Sequencing in Fixed and Living CellsChengxiang Yuan5Unraveling the Alzheimer’s Puzzle: The Role of ApoE4, Mitochondria, and Lipid Metabolism in neuronal settingSona Hakhverdyan6Adaptive Robust Learning using Latent Bernoulli VariablesAleksandr Karakulev7Deep Learning with Big Data for Genetic EpidemiologyMax Kovalenko8Strained Cyclooctynes with Photocages for Subcellular 3D Photolithographic BarcodingAlfred Larsson9The evolution of gene CNVs in C. rubellaFreja Lindstedt10Variational Approaches for Simulation-Based InferenceMayank Nautiyal11Deep Learning-driven Survival Prediction In Non-small Cell Lung Cancer Using Multiplex Immunofluorescent ImagingLove Nordling12Detection of protein-protein interactions by bio-orthogonal fluorogenic proximity probesAndreas Torell – FLASH TALK13Copy number variations and adaptation along environmental gradients in Picea abies and P. obovataQiujie Zhou

Organizers

Eva Tiensuu Janson, chair SciLifeLab Uppsala committee, Integration Director

Aristidis Moustakas, SciLifeLab Uppsala committee

Mikael Widersten, SciLifeLab Uppsala committee

Jenny Alfredsson, SciLifeLab Uppsala committee

Anna Dimberg, SciLifeLab Uppsala committee

Titti Ekegren, project coordinator, SciLifeLab Uppsala committee

Generation of context-specific genome-scale metabolic models using single-cell RNA-Seq data
2024-10-17 13:00 - 14:15 | Online event via Zoom
Johan Gustafsson, Postdoc researcher, Broad Institute, USA

Abstract

The metabolic networks in cells vary across tissues and cell types, and to accurately model the metabolism of cells, the full generic metabolic network defined in the genome needs to be reduced to a context-specific network representing the network expressed specifically in the cells of interest. Single-cell RNA-Seq promises to provide the information needed for such a reduction, but noise in the form of data sparsity is a challenge. Here, we present methods to handle data sparsity and estimate the uncertainty of modeling results.

Biography

Johan is an expert in modeling cancer metabolism and analyzing single-cell RNA/DNA sequencing data, aiming to uncover vulnerabilities in cancer. With a background in both computer science and biochemistry, Johan has completed a PhD in metabolic modeling at Chalmers University of Technology and now works as a postdoc in the Getz lab at the Broad Institute, focusing on CLL/Richter’s syndrome and hypoxia in solid tumors.

Host: Rasool Saghaleyni, NBIS Chalmers University, Gothenburg (rasool.saghaleyni@scilifelab.se)

Date: October 17, 13:00 – 14:15 CET online on zoom

Broadcast link (live event): link, pass:spd996The talk will also be available afterwards on the SciLifeLab YouTube channel.More information about the Oimcs Integration and Systems Biology Workshop here.

Conformal prediction enables disease course prediction and allows individualized diagnostic uncertainty in multiple sclerosis
2024-10-18 10:00 - 11:00 | Online event via Zoom
Accurate assessment of progression and disease course in multiple sclerosis (MS) is vital for timely and appropriate clinical intervention. The transition from relapsing-remitting MS (RRMS) to secondary progressive MS (SPMS) is gradual and diagnosed retrospectively with a typical delay of three years. To address this diagnostic delay, we developed a predictive model that is able to distinguish between RRMS and SPMS with high accuracy, trained on data from electronic health records collected at routine hospital visits obtained from the Swedish MS Registry containing 22,748 patients with 197,227 hospital visits. To be useful within a clinical setting, we applied conformal prediction to deliver valid measures of uncertainty in predictions at the level of the individual patient. We showed that the model was theoretically and empirically valid, having the highest efficiency at a 92% confidence level, and demonstrated on an external test set that it enables effective prediction of the clinical course of a patient with individual confidence measures. We applied the model to a set of patients who transitioned from RRMS to SPMS during the cohort timeframe and showed that we can accurately predict when patients transition from RRMS to SPMS. We also identified new patients who, with high probability, are in the transition phase from RRMS to SPMS but have not yet received a clinical diagnosis. We conclude that our methodology can assist in monitoring MS disease progression and proactively identify patients undergoing transition to SPMS. An anonymized, publically accessible version of the model is available at https://msp-tracker.serve.scilifelab.se/.

A preprint is available here: https://www.medrxiv.org/content/10.1101/2024.03.01.24303566v1

Kim Kultima, Uppsala University

NBIS arranges an open AI and IO Seminar Series aimed at knowledge-sharing about Artificial Intelligence and Integrative Omics (AI & IO) analysis and applications in the Life Science community. The seminar series is open to everyone. The seminar is run over Zoom on the third Friday of the month during academic terms, typically between 10 and 11 am, with approx. 45 min long presentation and 15 min discussion.

Long-Read Sequencing Uppsala Meeting 2024
2024-10-21 09:00 - 2024-10-23 17:00 | Universitetsaulan, Biskopsgatan 3, Uppsala, Sweden
In recent years, long-read DNA sequencing has replaced short-read technologies as the gold standard solution for a wide range of genomics applications. In addition to producing high-quality de novo genome assembly, long-read technologies can be used to study complex structural variation, full-length RNA isoforms, detection of epigenetic signals, and much more. The adaptation of long-read sequencing is sweeping through several areas of the life sciences, including agricultural, environmental, and medical research.

Join us in Uppsala for a three-day international event to catch up with the latest developments in long-read sequencing technologies and their applications, get inspired by peers presenting their research, and enjoy discussions with leading experts and company representatives.

Read more

Registration

Exhibition in Navet at BMC
2024-10-22 09:00 - 2024-10-24 15:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
On October 22-24, between 09.00-15.00, you have a new opportunity to visit our exhibition in Navet at BMC. This is a chance to receive information and updates from 30 of the leading life science companies in Sweden. The entrance to Navet will be open between 09:00-15:00 for external visitors.

Drips and SliPS and Retirees, Oh My!
2024-10-22 15:15 - 16:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Speaker: Jonathan Wilson Yewdell

Chief, Cellular Biology Section Laboratory of Viral DiseasesNational Institute of Allergy and Infectious Diseases (NIAID)National Institute of Health (NIH)Bethesda, MD, USA

Biography:

Jon Yewdell graduated from Princeton University in 1975 with an AB in biochemistry and received MD and immunology PhD degrees from the University of Pennsylvania in 1981. After a post-doctoral fellowship at Imperial College in London with David Lane, he spent 4 years as an Assistant Professor at the Wistar Institute in Philadelphia. In 1987 he joined NIAID. His lab uses influenza A, SARS-CoV2, vaccinia and other viruses to explore basic elements of cell biology, virology, and immunology, and has contributed to understanding how peptides are generated for CD8+ T cell immunosurveillance.

Title: Drips and SliPS and Retirees, Oh My!

Abstract for the talk:

MHC class I molecules present short peptides derived from biosynthesized proteins, enabling CD8+ T cell immunosurveillance of tumors, viruses and intracellular microbes. Many cellular peptides, and likely nearly all viral peptides, derive from rapidly degraded proteins, which consist of defective ribosomal products (DRiPs) and short-lived proteins (SLiPs). I will describe the nature of a number of influenza virus DRiPs and how ribosome profiling facilitates the identification of peptides derived from non-canonically translated cellular DRiPs. I will also discuss how cells with ribosomes lacking individual protein subunits demonstrate either enhanced or decreased peptide generation in a subunit-specific manner and how this can be exploited by cancer cells to escape immunosurveillance. I will present a model to explain how peptide generation avoids the law of mass action to generate a highly diverse peptide repertoire (immunopeptidome) that enables pathogen and tumor recognition. This talk will illustrate how, in over 4 decades of research, cell biology, virology, and immunology can be combined to dissect a medically important immune effector mechanism.

Host: Adnane Achour, adnane.achour@scilifelab.se

Discover services for data-driven life science
2024-10-24 10:00 - 12:30 | https://uu-se.zoom.us/j/63809262140
Welcome to join SciLifeLab Data Centre and SciLifeLab Data Management for “Discover services for data-driven life science“- an overview of data-driven services, tools, and support aimed at the fellows community. The event will also include a feedback session to help SciLifeLab Data Centre best support your specific research needs. Share your views about your current and future research needs, e.g. state-of-the-art services that would further your research or the general research of your field, currently not available on the SciLifeLab Data Platform.

When: Oct 24, 10-12.30 CET (Zoom)Target group: Scilifelab Fellows, DDLS Fellows, and interested participants

Agenda

10.00-10.10 Welcome Johan Rung, Head of SciLifeLab Data Centre

10.10-10.35 Open Science 101 Chris Erdmann, Head of Open Science

10.35-11.00 SciLifeLab Data Management services and support Angela Fuertes-Pardo, Data Steward, SciLifeLab Data Centre

11.00-11.05 Coffee break

11.05-11.30 How to get access to Compute, Storage, and Hosting to support your research, speaker TBA

11.30-12.30 Feedback session: Share your needs for data-driven life science services and tools. Moderators: Johan Rung, Head of SciLifeLab Data Centre, and Niclas Jareborg, NBIS

For additional information please contact SciLifeLab Data Centre at datacentre@scilifelab.se

Lund: Building and sharing machine learning demo applications within life sciences
2024-10-24 10:00 - 13:00 | BMC Hus E, room Rådslaget, Sölvegatan 19, Lund, 223 62, Sweden
This event is open to everyone at Lund University. It consists of a workshop followed by a free lunch for participants. During the lunch the participants will have an opportunity to informally chat with AI data engineers from the SciLifeLab Data Centre to discuss the needs for services and research infrastructure in life science research using machine learning methods.

Title: Building and sharing machine learning demo applications within life sciences: a practical tutorial.

Organizer: AI Data Engineers from the SciLifeLab Serve team.

Where and when: October 24, 2024 at 10:00-13:00 at room Rådslaget, BMC Hus E (Sölvegatan 19, 223 62 Lund)

Agenda:10:00-12:00: Workshop12:00-13:00: Lunch

Abstract: It is becoming increasingly popular to share machine learning models with the community as web applications with an easy-to-use interface. Users can then adjust parameters or submit their own input and see the predictions generated by the underlying model. This tutorial is aimed at researchers working within life sciences who work with machine learning models but do not have the skills to build applications for web. During the tutorial we will start from a trained model and demonstrate step by step how you can create a graphical user interface for your application, prepare it for deployment, and make it available on the web with a URL. We will demonstrate the use of specific tools which make this process easy and doable in under an hour.

The workshop will last for 2 hours with a break in the middle. We have room to accept 35 participants, on the first come first served basis. Those registered after that will be placed on the waiting list.

After the workshop all participants are invited for lunch.

Since there is a limited number of spots in this workshop please sign up only if you intend to attend.

Register to join the event

More about the event series:

Tools 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.

For questions about the events please contact the organizing team by emailing serve@scilifelab.se

Scientific lead: Prof. Ola Spjuth, SciLifeLab Data Centre and Uppsala University

Contact information: serve@scilifelab.se

Precision Omics Initiative Sweden (PROMISE) Symposium
2024-10-28 08:30 - 2024-10-29 13:00 | Lecture Hall X, Uppsala University Main Building, Biskopsgatan 3, Uppsala, Sweden
Sweden is uniquely positioned to advance medical research and implement precision medicine on a national scale, benefiting its entire population. Integration of cutting-edge biomedical research technologies with Sweden’s uniform healthcare system has the potential to position our country as a global frontrunner, leading the development of precision medicine in this new technological era. However, data fragmentation and data isolation currently hinder the Swedish ability to fully capitalize on its potential and maximize the use of already available infrastructure and prior investments.

Precision Omics Initiative Sweden (PROMISE) is a new transformative initiative that will be centered around SciLifeLab and Genomic Medicine Sweden (GMS) to completely integrate medical research with the healthcare system in Sweden.

PROMISE will have three major focus areas: 1) Generate extensive multi-omics data from both patients and the general population in Sweden, 2) Develop a strong and effective infrastructure to integrate healthcare generated multi-omics data for research applications, improve data sharing and data accessibility across Sweden, 3) Develop legal and regulatory frameworks for better alignment with modern capabilities, for maximum utilization of Sweden’s great potential.

Register for the PROMISE symposium, October 28-29 2024, to contribute to further developing the scientific foundation and design of this transformative initiative.

registration

Program

PROMISE Symposium Uppsala October 28-29_FINALDownload

Organizing committee

Anna Clareborn

Sanna Gudmundsson

Bo Jacobsson

Åsa Johansson

Anders Kämpe

Tuuli Lappalainen

Kerstin Lindblad-Toh

Anna Lindstrand

Bengt Persson

Richard Rosenquist Brandell

Tobias Sjöblom

Colum Walsh

I Forskningens Framkant – Fortbildning för Gymnasielärare
2024-10-29 13:00 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Eventet är inställt

Microbes are a girl’s best friend: en introduktion till människans mikrobiota och hur den kan påverka vår reproduktiv hälsa

Luisa Hughert

Alla ytor i och på människokroppen är täckta i mikrober. Deras gemensamma arvsmassa är mer än hundra gånger större än människans och de har därför tillgång till betydligt flera metabola vägar. I den här föreläsningen undersöker vi hur våra könshormoner samspelar med våra mikrober, och vilket nytta eller skada de kan göra.

Framtidens målsökande läkemedel

Stefan Ståhl

Intensiv forskning pågår för att utveckla läkemedel som kan målsöka sjuk vävnad, t.ex. cancertumörer. Detta möjliggör att man kan koppla “tumördödande” substanser till målsökaren, för att minska risk för biverkningar. Utmaningen är dock att måltavlan, den s.k. biomarkören, för målsökaren inte bara finns på tumören, utan även i frisk vävnad. Därför eftersträvar man idag att utveckla målsökare som aktiverar sin “tumördödande” substans enbart i närhet av cancertumören.

En nål i en höstack- att kartlägga immunceller i tumörer

Camilla Engblom

Genteknisk modifiering av alger och växter för att förbättra fotosyntes

Paul Hudson

Plats: SciLifeLab, Tomtebodavägen 23, SolnaKarta: Google Maps

Välkommen med din anmälan!

Anmälan

Organiseras av SciLifeLab tillsammans med Vetenskapens Hus.
