SciLifeLab

Campus Solna Seminar Series: Josefin Kenrick & Carlos Santolaria
2024-10-31 12:00 - 13:00 (Europe/Stockholm) | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

PhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester.

This week:

Josefin Kenrick

Fredrik Edfors – gamma 6

Profiling the Blood Proteome in Autoimmune Disease Using Proximity Extension Assay

Carlos Santolaria

Vicent Pelechano – gamma 5

Mapping the Allosteric Regulation sites in Metabolism and Gene Expression

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

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.

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

Campus Solna Seminar Series: Alberto Arenas Molina & Kiana Hosseinpour Moghaddam
2024-10-24 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

PhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester.

This week:

Alberto Arenas Molina

Simon Elsässer – alpha 4

Translating the untranslated: Microproteins encoded by “non-coding” regions and their role in tumorigenesis

Kiana Hosseinpour Moghaddam

Ola Larsson – gamma 5

Di-codon organization orchestrates the malignant proteome

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

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

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

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

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.

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

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.

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.

Campus Solna Seminar Series: Quentin Verron & Annika Bendes
2024-10-17 12:00 - 13:00 | Milkyway SciLifeLab Solna, Tomtebodavägen 23, Solna
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

PhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester.

This week:

Quentin Verron

Magda Bienko – alpha 4

Exploring the Role of Trans-Interacting Intronic RNAs in Neuronal Genome Organization

Annika Bendes

Jochen Schwenk – alpha 2

Insights from highly frequent microsampling of the circulating proteome — A study of virus induced diabetes in mice

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

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

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

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.

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

Omics Integration and Systems Biology
2024-10-14 09:00 - 2024-10-18 17:00 | Lund University, Lund, Sweden
National course open for PhD students, postdocs, researchers, and other employees in all Swedish universities, in need of a general description of different approaches for working with multiple types of biological data. We also welcome applications from outside of Sweden and from the non-academic sector, for more info contact us!

Important dates and information

Application opens: 2024-08-05

Application closes: 2024-09-16

Confirmation to accepted students: 2024-09-23

Course Leader and teachers:

Nikolay Oskolkov (Lund University, course leader)

Rasool Saghaleyni (Chalmers University of Technology, course leader)

Sergiu Netotea (Chalmers University of Technology, course lecturer)

Jennifer Fransson (Uppsala University, course lecturer)

Yuan Li (Lund University, TA)

Nima Rafati (Uppsala University, TA)

In case you miss information on any of the above dates, please contact:

Nikolay Oskolkov, nikolay.oskolkov@scilifelab.se

Rasool Saghaleyni, rasools@chalmers.se

Application

Course website

Course fee

A course fee* of 3000 SEK for academic participants and 15 000 SEK for non-academic participants will be invoiced to accepted participants. The fee includes all coffee breaks, all lunches and 1 course dinner.

*Please note that NBIS cannot invoice individuals

Course content

The aim of this workshop is to provide an integrated view of data-driven analysis of biological data through machine learning, graph and network analysis as well as constraint-based modeling integration methods. A general description of different approaches for working with multiple layers of biological information, i.e. Omics data (e.g. transcriptomics and genomics) will be presented with some of the lectures discussing their advantages and pitfalls. The techniques will be discussed in terms of their rationale and applicability.

Topics covered will include:

Data pre-processing, cleaning and feature selection prior to integration;

Application of key machine learning methods for multi-omics analysis including deep learning;

Multi-omics factor analysis, dimension reduction and clustering;

Single Cell and Spatial transcriptomics integration;

Biological network inference, community and topology analysis and visualization;

Condition-specific and personalized modeling through Genome-scale Metabolic models for integration of transcriptomic, proteomic, metabolomic and fluxomic data;

Identification of key biological functions and pathways;

Identification of potential biomarkers and targetable genes through modeling and biological network analysis;

Application of network approaches in meta-analyses;

Similarity network fusion and matrix factorization techniques;

Integrated data visualization techniques

Learning outcomes

Upon completion of this course, you will be able to:

Identify key methods for analysis and integration of omics data based on a given dataset;

Perform feature selection and dimension reduction techniques;

Understand strengths and pitfalls of key machine learning techniques in multi-omic analysis;

Apply unsupervised and supervised machine learning data integration techniques;

Build biological networks based on different omics data including integrated multi-omics networks;

Perform centrality and community analyses in graphs;

Apply network approaches in meta-analyses;

Apply similarity network fusion of patient data;

Compare different cell-types or conditions through the application of different biological network analysis techniques;

Simulate biological functions using constraint-based models and flux balance analysis;

Identify potential confounding factors and sources of bias.

Entry requirements

The following is a list of skills required for being able to follow the course and complete the exercises:

Basic knowledge in R or Python;

Basic understanding of frequentist statistics;

Desirable, but not essential, skills increasing the output of the course, include:

Experience with NGS and omics analysis

Completing “Introduction to bioinformatics using NGS data” and “Introduction to biostatistics and machine learning” NBIS courses

Due to limited space the course can accommodate a maximum of 35 participants. If we receive more applications, participants will be selected based on selection criteria, including (but not limited to) correct entry requirements, motivation to attend the course, as well as gender and geographical balance.

New Super-Resolution, Light-Sheet, and FCS-Methods at Scilifelab
2024-10-14 08:00 - 2024-10-25 17:00 | Gamma 3, Tomtebodavägen 23 A, Solna, Sweden
The Advanced Light Microscopy Facility, ALM, at Scilifelab gives a two-week PhD-level course on four new imaging and fluorescence spectroscopy techniques:

Depletion-based Super-Resolution Imaging

STED-imaging, 2D and 3D, 30-50 nm resolution

In Living Cells – MoNaLISA, 1-2 Hz, 100 x 100 mm field of view

MINFLUX

Imaging with 3 nm resolution

Tracking single molecules at 10 kHz

Light-Sheet Imaging

Long time-lapse imaging of live model organisms with low phototoxicity

Ultrafast volumetric imaging of cells with lattice light-sheet microscopy

FCS-Methods

Measurements of concentrations, diffusion coefficients, molecular dynamics and interactions, in solution or living cells

Cross-correlation, FRET-, STED-, and line-scan-FCS are covered

Lecturers:

Steven Edwards

Erdinc Sezgin

Ana Agostinho

Francesca Pennacchietti

Hans Blom

Stefan Wennmalm

Dates: Monday October 14th – Friday October 25th 2024

Credits: 3 hp for PhD students

Location: Gamma 3, Scilifelab, Solna

Registration: stewen@kth.se latest September 30th

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

Campus Solna Seminar Series: Daniela Huhn & Mariya Mardamshina
2024-10-10 12:00 - 13:00 | Milkyway SciLifeLab Solna, Tomtebodavägen 23, Solna
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

PhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester.

This week:

Daniela Huhn

Oscar Fernandez-Capetillo – alpha 4

One-Two punch approach for improved treatment of ERa+ Breast Cancer

Mariya Mardamshina

Emma Lundberg – alpha 2

Expanding the limits: Measuring more proteins beyond current multiplexed imaging capabilities

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

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

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!

[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

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)

Campus Solna Seminar Series: Linnea Påvenius
2024-10-03 12:00 - 13:00 | Milkyway SciLifeLab Solna, Tomtebodavägen 23, Solna
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

PhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester.

This week:

Linnea Påvenius

Hjalmar Brismar – gamma 3

Live-Imaging of mitochondrial dynamics in relation to metabolic flux.

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

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

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

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

Basic Course in Scanning and Transmission Electron Microscopy (SEM/TEM) for Life Sciences
2024-10-01 08:00 - 2024-10-03 17:00 | KBC Building Umeå, Linneaus Väg 6, Umeå
This course covers lectures and practical demonstrations in SEM and TEM techniques. The contents include principles of electron microscopy, specimen preparation, cryo-electron microscopy and correlative light-electron microscopy. The main focus will be on imaging biological samples, but the course may also be suitable for material scientists interested in high-resolution electron microscopy.

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Application deadline:10 September 2024

Location:Lectures at the KBC Building and laboratory demonstrations at UCEM.

Participants:18 persons

Instructors:UCEM staff

Duration:3 days

Breaks/Refreshments:Coffee, cookies and fruit.

Costs:No course fee, but full attendance is required!

Examination/Credits:Oral and practical examinations are conducted during laboratory demonstrations. A course certificate will be given after participants attend all lectures and laboratory demonstrations for this 3-day course. UCEM recommends PhD program examiners to give 1 ECTS after successful participation.

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.

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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
