SciLifeLab

Discovery and developmentof GRK2-biased beta 2-adrenergic receptor agonists for the treatment of metabolic disorders
2025-12-05 10:15 - 11:00 (Europe/Stockholm) | BMC Room C4:301, Husargatan 3, entrance C1, Uppsala, Sweden
Presenter: Dr Benjamin Pelcman, Atrogi AB

Atrogi AB is biotech company pioneering first-in-class treatments to revolutionize metabolic health. The talk will describe how targeting a novel GRK-biased b2-adrenergic receptor signaling pathway allows for the successful design of compounds useful in the treatment of disorders like type 2 diabetes (T2D), obesity and muscular wasting. The approach will be exemplified by the invention, selection and development of ATR-258, a b2-AR agonist that was developed for T2D and is about to enter phase 2 clinical trials. During the exploration of the chemical space, a diverse set of molecules were synthesized, and their effect on the downstream signaling will be discussed. In addition, the seminar will illustrate differences between drug development in Big Pharma and small biotech and the challenges of working in an environment with limited resources.

After receiving his Ph.D. in Organic Chemistry at KTH and a post doc session at Dartmouth College, NH, USA, Benjamin joined Astra Pain Control, first in Södertälje and then in Montreal, as a medicinal chemist. Benjamin has also held various positions at Pharmacia & Upjohn, Karo Bio, Biolipox and Orexo. After having started his own consultancy company, BeePCo, he came in contact with Atrogi where he was employed first as a CEO and later as Head of Chemistry and IP. Benjamin is now retired but is still working as a consultant for Atrogi and other small biotechs.

Campus Solna Seminar Series: Nona Struyf & Iva Sutevski
2025-12-04 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 Presentation of ongoing (unpublished) projects is strongly encouraged.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:

Nona Struyf

Brinton Seashore-Ludlow – alpha 4

FLT3 inhibitor response in AML is shaped by a progenitor-like cell state selectively targeted by SMAC mimetics

Iva Sutevski

Burcu Ayoglu – gamma 3

Leveraging spatial proteomics for molecular and single-cell insights into neurodegenerative diseases

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

3D Imaging in Health and Disease
2025-12-04 09:00 - 17:00 | Nobel Forum, Nobels väg 1, Solna, Sweden
Characterizing molecular and cellular complexities in 3D is an emerging field allowing to study biology in its true context.

In this symposium national and international experts will present developments and applications in 3D imaging aimed to improve health and disease analysis across scales

Please register by sending an e-mail to hans.blom@scilifelb.se

Program 3D symposiumDownload

User meeting for your multi-modal research projects
2025-12-04 09:00 - 10:30 | virtual event
Boost your research — Book a private SciLifeLab planning and feedback session for your multi-modal research projects!

Register here

Once we have received your registration, you will be sent the link to the online meeting.

Date: December 4, 9.00 – 10.30 Registration deadline: November 28

Multimodal molecular profiling and novel computational methods are transforming life science research, but also pose new challenges in study design, project resource planning and data management. SciLifeLab is a national resource of unique technologies and expertise available to life scientists, in areas such as biomedicine, ecology and evolution, aiming to bring scientists together across traditional boundaries and foster collaborations with industry, health care, public research organizations and international partners.

The first Thursday of every month at 9.00 (except July and August), SciLifeLab offers an opportunity to jointly meet with representatives across the SciLifeLab service platforms, to get feedback and help to plan, design, and refine new or ongoing multimodal research projects. Your project plans are discussed privately and remain confidential, and information will not be shared outside of the service platforms. Note that for most studies, follow-up meetings will be needed, but our aim for these meetings is to provide an easy-access entry point for an overarching planning of multimodal studies.

For studies focusing on a single technology only, please primarily contact our service platforms directly as described at the SciLifeLab homepage.

To make the best out of the allotted time, we ask you to provide some background information about your project, to help us ensure that the relevant experts are available to discuss your study.

The NIH NIAID Blueprint: A FAIR Implementation Approach for the Biomedical Sciences
2025-12-03 16:30 - 17:30 | Online event via Zoom
SciLifeLab Data Centre welcome you to join us for the webinar “The NIH NIAID Blueprint: A FAIR Implementation Approach for the Biomedical Sciences” presented by Christine Kirkpatrick. Head – GO FAIR US, Secretary General – CODATA, Principal Investigator – NIAID Data Landscaping and FAIRification, San Diego Supercomputer Center, UC San Diego

When: Wednesday Dec 3, 16:30-17:30 CET (Zoom)

register here

As organisations adopt the FAIR Principles, many face challenges FAIRifying not just datasets but entire ecosystems. The National Institute of Allergy and Infectious Diseases (NIAID), an Institute within the US National Institutes of Health (NIH), manages a diverse data landscape across infectious, allergic, and immunologic domains.

Its FAIRification project aims to improve discovery and reuse across repositories with varied architectures, metadata maturity, and timelines. This work culminated in the recently released, “A Blueprint for Including Digital Objects in the NIAID Data Ecosystem.

This presentation describes the GO FAIR US–led assessment of NIAID repositories, highlighting:

Customized FAIR assessment instruments

Evaluation of record-based (not just file-based) repositories

Common assessment and progress tracking

Impact-driven adoption of metadata standards and PIDs

Improving citation practices

Adapting to social and project constraints

The approach builds on prior FAIR frameworks (FAIRsFAIR, RDA DMM, EarthCube, GO FAIR Foundation) and uses stakeholder-informed questionnaires and interviews to capture repository practices. Combining qualitative assessment and FAIR Implementation Profiles, the method establishes a FAIR baseline, guides targeted improvement strategies, and enables cross-repository comparison to inform strategic planning and strengthen community buy-in.

Organiser: SciLifeLab Data Centre For more information or inquiries please contact: datacentre@scilifelab.se

This project has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. 75N91019D00024. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government.

Is high-throughput electrophysiology possible?
2025-12-02 13:00 - 14:00
Register here

On site seminar – Electrophysiology Infrastructure

Location: Jörgen Lehmann, Academicum, Medicinaregatan 3 and SciLifeLab Gothenburg

Presenters

Fredrik Elinder, Professor, Site director SciLifeLab Linköping, Chemical Biology Consortium Sweden (CBCS), and Department of Biomedical and Clinical Sciences (BKV), Linköping University

Nina Ottosson, Research Coordinator, Chemical Biology Consortium Sweden (CBCS), and Department of Biomedical and Clinical Sciences (BKV), Linköping University

The electrophysiology unit at Linköping University, part of Chemical Biology Consortium Sweden (CBCS) at SciLifeLab, visits site Gothenburg, and presents the infrastructure during a seminar.

During the day, 1-on-1 meetings with the presenters will be possible at The SciLifeLab office, Medicinaregatan 3. Take the chance to discuss how your research questions can be answered through analyses of ion channels. Request is added in the registration form.

The electrophysiology unit, a recent addition to SciLifeLab’s range of infrastructures, is equipped with automated patch-clamp instrumentation, and supports a wide range of electrophysiological studies involving both voltage-gated and ligand-gated ion channels, including pharmacological screening, cardiac safety assessments, and biophysical investigations.

WELCOME!

Fredrik Elinder and Nina Ottosson, Electrophysiologists

Josefine Sandström and Maria Smedh, SciLifeLab site coordinators Webpage of the CBCS Linköping node.

Introduction to the Module System on Berzelius
2025-12-02 10:00 - 11:30 | Zoom
This training offers a practical introduction to the module system on Berzelius. The session will cover:

how to find modules on Berzelius

load/unload modules

use modules in interactive or batch modes

create your own module

Participants will also gain hands-on experience with these commands. By the end of the session, you will be able to navigate the modules system Berzelius confidently and use them effectively for your research.-on experience with these commands. By the end of the session, you will be able to navigate Berzelius confidently and use its resources effectively for your research.

Date: December 2, 2025Time: 10:00–11:30

Target audience: The online event is open for all current and prospective Berzelius users. Please read the eligibility requirements for accessing Berzelius.Place: Online via Zoom (link provided upon registration)

registration

Preliminary Agenda

TimeSession TitleSpeaker(s)10:00–11:00Introduction to the Module System on BerzeliusSoumi Chaki11:00–11:30Open Q&A SessionBerzelius Application Expert

This event is a collaboration between National Supercomputer Centre (NSC) at Linköping University and SciLifeLab Data Centre.

For questions please contact soumi.chaki@liu.se (Soumi Chaki)

[The Svedberg seminar] - Genome organisation and patterns of molecular evolution
2025-12-01 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Jennifer James

Assistant Professor DDLS Fellow

Bio

Dr. Jennifer James did her PhD in population genetics with Adam Eyre-Walker at the University of Sussex. After a postdoctoral position at the University of Cambridge she moved to the US, where she worked as a postdoctoral researcher with Joanna Masel at the University of Arizona, which introduced her to the world of proteomics. She next moved to Uppsala and worked as a postdoctoral research fellow with Martin Lascoux prior to becoming a DDLS fellow and starting her own new research group in Molecular Evolution. Her group conducts research on patterns of molecular evolution both at the genome and proteome level, with a focus on understanding mutational robustness.

Genome organisation and patterns of molecular evolution

In my group, we try to understand patterns of phenotypic evolution at the proteome level, and molecular evolution across the genome. Key to this question is understanding how the genome is structured and organised. For example, how pleiotropic are the effects of genes on average, and how complex are gene networks? To give one case, if pleiotropy is universal, such that all genes affect all traits, we expect all new mutations to have the same effect on fitness. However, the extent of pleiotropy in real biological systems remains debated. In this seminar I will discuss our

Host: Siv Andersson siv.andersson@icm.uu.se, UU

Multimodal explorative testing in the ON-OFF ibrutinib trial in CLL
2025-11-28 09:00 - 09:30 | Online event via Zoom
Multimodal explorative testing in the ON-OFF ibrutinib trial in CLLRichard Rosenquist Brandell, Karolinska Institutet & Karolinska University Hospital

Chronic lymphocytic leukaemia (CLL) is the most common leukaemia in the Western World and displays substantial variability in clinical course, ranging from indolent disease requiring no therapy to highly aggressive forms with short survival despite treatment. Although the past decade has seen major advances in drug development, CLL remains incurable. Targeted therapies, particularly Bruton’s tyrosine kinase inhibitors (BTKi), have become central to CLL management. However, continuous long-term BTKi administration, such as with ibrutinib, is associated with considerable significant side-effects, including cardiac arrhythmias. Furthermore, despite its proven efficacy in both treatment-naïve and relapsed/refractory CLL, resistance to ibrutinib continues to challenge durable disease control. To address these limitations, we conducted a phase 1b/2 prospective, single-arm, multicenter study evaluating controlled treatment cessation as a strategy to preserve tolerability and maintain sensitivity to ibrutinib, while also improving cost-effectiveness. The study protocol incorporated serial blood sampling prior to treatment initiation and throughout on/off treatment periods. Here, we leverage this unique longitudinal sample collection to perform multimodal profiling, including genomic and transcriptomic sequencing as well as proteomics, to investigate mechanisms of drug response and resistance. We provide an update on the current status of the study and ongoing analyses.

registration

Biography

Richard Rosenquist Brandell is Professor of Clinical Genetics at the Department of Molecular Medicine and Surgery, Karolinska Institutet, and Senior Physician in Clinical Genetics at Karolinska University Hospital, Sweden. Focusing on hematological malignancies and utilizing high-throughput sequencing and other innovative technologies, his research team has identified novel prognostic and predictive biomarkers that have refined disease classification and significantly improved patient risk-stratification and clinical decision-making. Richard Rosenquist Brandell initiated and led the Clinical Genomics Unit within Science for Life Laboratory (SciLifeLab) in Uppsala (2013-2017) and was platform director for the Clinical Genomics platform (2016-2021) within SciLifeLab, which includes seven Clinical Genomics units across Sweden. He is currently Director of Genomic Medicine Sweden (GMS), a national infrastructure for implementation of precision medicine. Rosenquist Brandell is a member of the Nobel Assembly at Karolinska Institutet.

Campus Solna Seminar Series: Koen Jurgens & Alana Panzenhagen
2025-11-27 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:

Koen Jurgens

Marta Carroni – gamma 6

Structural basis for p97 and ataxin-3 interplay

Alana Panzenhagen

Ola Larsson – gamma 5

Uncovering mechanisms and organization underlying selective regulation of mRNA translation

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

NanoSIMS webinar series: Chemical bio-imaging using ToF-SIMS and OrbiSIMS
2025-11-26 15:00 - 16:00
This month’s Mass Spectrometry Imaging webinar will focus on chemical bio-imaging using ToF-SIMS and OrbiSIMS, what it is and where it is located, presented by Prof. David J. Scurr, the University of Nottingham, UK.

🕒 Time: 15:00–16:00 (presentation and discussion)☕ Followed by: Informal discussion with the speaker, 16:00–16:30📍 Format: Zoom

Zoom link

Meeting ID: 616 3655 5280Passcode: [REDACTED]

Speaker

Prof. David J. Scurr is a Principal Research Fellow at The University of Nottingham. He has pioneered the application of ToF-SIMS and OrbiSIMS in the field of pharmacy and biology. He obtained a BSc in Materials Science (2002) and PhD focusing upon materials characterisation (2005) at The University of Manchester. David’s research has a focus upon the implantation of novel data processing strategies, such as molecular formula prediction (MFP) [Edney et al. Anal. Chem. 2022].

His research highlights include the characterisation of biological samples using ToF-SIMS and OrbiSIMS, for example, breakthrough research into the in situ analysis of unlabelled proteins [Kotowska et al. Nature Comms, 2020] forming the basis of novel research in the development of proteomics / metabolomics, diseased tissue analysis and biomaterials at The University of Nottingham. Additionally, David’s research has demonstrated the ability of SIMS to characterise skin tissue and understand permeation mechanisms of xenobiotic chemistries (pharmaceutical, cosmetic, agrochemical and antibacterial) within complex tissues such as skin [Starr et al. PNAS, 2022].

[Spotlight Seminar Series] Molecular Mechanisms Underlying the Energy Currents of Life
2025-11-25 15:15 - 16:30 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Spotlight seminar series proudly welcomes Professor Vile R. I. Kaila to give a seminar at SciLifeLab Campus Solna.

Biography

Ville R. I. Kaila received his PhD in biochemistry in 2009 from University of Helsinki. After a postdoc at the US National Institutes of Health (NIH), he was appointed a professorship at the Technical University of Munich in 2013. In 2019, Kaila moved with his research group to Stockholm, where he is currently professor at the Department of Biochemistry and Biophysics at Stockholm University and a Wallenberg Scholar. His research focuses on elucidating mechanistic principles of bioenergetic enzyme complexes by development of integrative computational and experimental approaches. Read more at http://villekaila.com/

Abstract

Biological energy conversion is catalyzed by intricate protein complexes that transduce redox energy into proton currents across a biological membrane, powering the cellular energy metabolism. Yet, despite significant advances in recent years, the molecular principles of these reactions remain poorly understood and pose major scientific challenges. In this talk, I describe our integrative mechanistic exploration of complex bioenergetic machines, where we combine multiscale simulations and data-driven methods with biophysical experiments and structural (cryo-EM) studies to derive a molecular understanding of intricate long-range charge transfer reactions in biology on a broad range of timescales and spatial resolutions. I describe our recent work on understanding enzymes catalyzing long-range charge transfer reaction by intrinsic electric field effects. We find that mutations of key residues mediating these allosteric processes lead to perturbed coupling effects, and development of severe human diseases, with striking similarities in different biological systems.

Host: Marta Carroni marta.carroni@scilifelab.se

FAIR play: Mastering Metadata to Empower Life Scientists
2025-11-25 11:00 - 12:00 | https://uu-se.zoom.us/j/62780940554?from=addon
Unlock the potential of your research by mastering meta(data) management in and the FAIR Data Principles—Findable, Accessible, Interoperable, and Reusable. This session offers practical guidance tailored for life scientists, focusing on best practices to organise and share your data effectively. The talk will focus on how good metadata practices can enhance collaboration, ensure reproducibility, and align your work with Open Science principles, ultimately increasing the impact of your research.

Presenter: Parul Tewatia, PhD, project coordinator (FAIR metadata and semantic technologies), SciLifeLab Data Centre

Recording: https://youtu.be/mc4BOOoLTMASlides: https://doi.org/10.17044/scilifelab.28615511

More information

This event is part of the SciLifeLab Open Science seminar series, an event series by the SciLifeLab Data Centre and NBIS joint Data Management team.The goal of the events in this seminar series is to provide interesting interactive seminars around topics related to Research Data Management and Open Science in general, and to foster discussions around best practices.

Research Data Management (RDM) concerns the organization, storage, preservation, and sharing of data that is collected and analyzed during a research project. Proper planning and management of research data will make project management easier and more efficient while projects are being performed. It also facilitates sharing and allows others to validate as well as reuse the data.Open Science is a set of principles and practices that aim to make scientific research from all fields accessible to everyone for the benefits of scientists and society as a whole. Open science is about making sure not only that scientific knowledge is accessible but also that the production of that knowledge itself is inclusive, equitable and sustainable.

The events are open to everyone working at or affiliated with a Swedish research institute or university. We welcome all researchers, educational professionals, staff, RDM professionals, and others with an interest in life sciences, from all university levels. The events are informal and inclusive, so feel welcome to join and participate in our interesting discussions!

The events will be recorded and published openly after the seminars on the SciLifeLab YouTube channel. The slides will be made available at our SciLifeLab Data Repository. More information about SciLifeLab Data Centre and NBIS joint Open Science seminar series: https://www.scilifelab.se/data/scilifelab-data-management-seminar-series/

If you have suggestions for topics or presentations, please contact us at data-management@scilifelab.seFor more information or inquiries, please contact us at data-management@scilifelab.se

Rapid traversal of vast chemical space using machine learning-guided docking screens to accelerate drug discovery
2025-11-21 10:00 - 11:00 | Online event via Zoom
Speaker: Israel Cabeza de Vaca, Uppsala university (Jens Carlsson group).

NBIS and SciLifeLab Data Centre arrange an open SciLifeLab AI Seminar Series aimed at knowledge-sharing about Artificial Intelligence 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 presentation and 15 min discussion.

AbstractThe rapid expansion of make-on-demand chemical libraries now offers access to tens of billions of synthetically accessible molecules, creating unprecedented opportunities for structure-based drug discovery. However, screening such ultra-large libraries remains computationally prohibitive, even with state-of-the-art docking methods.In this presentation, I will describe a hybrid virtual screening strategy that integrates molecular docking with machine learning to efficiently navigate chemical space at the billion-compound scale. The workflow involves docking approximately one million compounds to a target protein and training a classification model to recognize high-scoring molecules. Using conformal prediction, the model guides compound selection from multi-billion-scale libraries, drastically reducing the number of molecules requiring explicit docking.Among several algorithms evaluated, CatBoost provided the best balance between accuracy and computational efficiency, enabling large-scale applications. When applied to a 3.5-billion-compound library, this approach reduced the computational cost of virtual screening by over three orders of magnitude. Experimental validation identified novel ligands for multiple G protein–coupled receptors, including compounds exhibiting designed multi-target activity.These results demonstrate how combining AI-based prediction with physics-based docking can make ultra-large-scale virtual screening a practical and powerful tool for modern drug discovery.

ContactFor questions, contact bengt.sennblad@scilifelab.se

zoom link

Powering Proteomics: Technologies, Insights, and Clinical Applications
2025-11-20 13:00 - 15:30
Join us for an engaging workshop on proteomics, exploring cutting-edge approaches in mass spectrometry and affinity-based methods. The event will feature external researchers sharing the latest developments and applications in protein analysis. Participants will gain insights into experimental strategies and see real-world examples highlighting how proteomics advances biomedical research and biomarker discovery.

Registration

Registration

You can join the Zoom meeting via the Confirmation email.

Program

Workshop on proteomicsDownload

13:00-13:05 Welcome

13:05-13:30 “Using mass spectrometry to characterize the airway proteome and treatment responses in cystic fibrosis”.

Presenter: Lisa Påhlman, Lund University

Host: Anahita Bakochi, Clinical Proteomics, Lund University

13:30-13:55 “Low Cell Proteomics resolves oncogenic molecular mechanisms in rare cell types”

Presenter: Pedro Moura, Karolinska Institute

Host: Henrik Johansson, Global Proteomics & proteogenomics, Karolinska Institute

13:55-14:20 “Applications of Proteomics in Steatotic Liver Disease”

Presenter: Tanmoy Dutta, Gothenburg University

Host: Carina Sihlbom Wallem, Glycoproteomics & MS Proteomics, Gothenburg University

14:20-14:45 “Shared and specific blood biomarkers for multimorbidity”

Presenter: Davide Liborio Vetrano, Karolinska Institute

Host: Claudia Fredolini, Affinity Proteomics-Stockholm, Royal Institute of Technology-KTH

14:45-15:10 “The circulating blood proteome of childhood acute leukemia”

Presenter Jessica Nordlund, Uppsala University

Host: Mikael Åberg, Affinity Proteomics Uppsala, Uppsala University

15:10:15:30 Questions and Final Remarks

Campus Solna Seminar Series: Charlotte Stadler
2025-11-20 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:

Charlotte Stadler

Spatial Proteomics – alpha 2

Current and future opportunities with Spatial Proteomics in discovery and translational research

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

[The Svedberg seminar] - Coagulation: Cancer's new best friend
2025-11-17 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Gareth Owen

Professor Pontificia Universidad Católica de Chile, Chile

Bio

Dr. Gareth Owen is currently visiting Professor in the lab of Dr Masood Kamali-Moghaddam, Department of Immunology, Genetics and Pathology, Uppsala University. He is a full professor in the Faculty of Biological Sciences and Faculty of Medicine at the Pontificia Universidad Catolica de Chile. Dr Owen did his BSc at King’s College London and has a PhD from the Royal Postgraduate Medical School, Hammersmith Hospital, London UK (Imperial College London). This was followed by a post-doctoral fellowships at the University of Colorado USA, and the Institute of Cancer Research (ICR-UK). Dr Owen is a PI in the Millennium Institute on Immunology and Immunotherapy Chile, and Board member of the Chilean National Cancer Forum.

Coagulation: Cancer’s new best friend

Coagulation is linked to cancer progression, with many patients exhibiting chronic hypercoagulability. Anticoagulant therapy has been associated with improved outcomes. Beyond hemostasis, the coagulation system can drive inflammation and metastasis, though the mechanisms remain unclear. Herein, we demonstrate that elevated levels of activated coagulation factor X (FXa) increase lung metastasis and that FXa promotes an immunosuppressive tumor microenvironment. Using a murine model of melanoma and in vitro assays, we found that FXa increased infiltration of regulatory T cells and Th17 cells, and upregulated PD-1 and CTLA-4 expression on CD4+ and CD8+ T cells. Co-treatment with the anti-FXa anticoagulant dalteparin abrogated these effects. Mechanistically, FXa in vitro suppressed macrophage M1 and Th1 differentiation through the Protease-Activated Receptor-1 (PAR1). The clinically approved PAR1 inhibitor Vorapaxar blocked FXa-induced tumor progression in vivo. These findings identify FXa or PAR1 inhibition as therapeutic strategies in cancer therapy.

Host: Masood Kamali-Moghaddam masood.kamali@igp.uu.se, UU

SwedNMR Meeting: Unravelling BioSolids mysteries by novel NMR approaches
2025-11-17 12:00 - 2025-11-18 09:00 | Stora Fokusrummet, KBC, Linnaeus väg 6, Umeå, 90736, Sweden
Join us on the 17th and 18th of November, the SwedNMR and its Umeå node will host a meeting were the current achievements will be highlighted and there will be a discussion in future directions in method development and new application areas

SwedNMR offers state-of-the-art NMR infrastructure and expertise to study a wide range of biosolids with atomic-level insight, including crystalline materials, drugs, biomembranes, protein aggregates, as well as plant and medical biopsies. SwedNMR via its Umeå node is the first word-wide to offer both ultra-fast solid-state MAS NMR and CryoMAS-NMR solid-state providing a new dimension in structural information and sensitivity for bioSolids. Together with the DNP facility at the NMR Centre in Gothenburg, SwedNMR provides world-wide unique structural and dynamic insights into complex biological solids and tiny intact biospecimens.

Registration

Registration

Sign up for the SwedNMR Meeting: Unravelling BioSolids mysteries by novel NMR approaches, a two day meeting starting on Monday the 17th of November at 12 pm

In the registration you can find more information about the program

If you have any further questions you can contact:

Ilona Dudka, ilona.dudka@umu.se

Gerhard Gröbner, gerhard.grobner@umu.se

Tobias Sparrman, tobias.sparrman@umu.se

DDLS Annual Conference 2025 workshops
2025-11-13 13:30 - 16:00 | Uppsala Konsert & Kongress, Vaksala torg 1, Uppsala, 75331, Sweden
During the second day of the DDLS Annual Conference 2025 held at Uppsala Kongress och Konsert (UKK) participants will have an opportunity to attend one of the workshops. The workshops are directed at researchers in data-driven life science in all career stages.

Please note that each workshop has a limited number of seats, on the first come first served basis. Those registered after the limit is reached will be placed on the waiting list. The workshops will take place in various rooms of the main venue of the conference –UKK All workshops start at 13:30 but end at various times. Coffee/tea and fika will be served during the workshops.

Feel free to email datacentre@scilifelab.se with any questions about workshop 1 and 2 and traininghub@scilifelab.se for workshop 3.

Workshops

Workshop 1. Automating life science & biomedical tasks with LLMs and beyond: practical guide

Held by: Ola Spjuth (UU, SciLifeLab AI Lead) and AI data engineers Mahbub Ul Alam and Johan Alfredéen at SciLifeLab Data Centre

Where and when: November 13, 2025 at 13:30-16:00, room K1 (36 seats) UKK

Registration

Description: We will explore how artificial intelligence (AI) can help make your research more productive. You will see how AI agents can help youcreate new, testable ideas. We will introduce modern agentic AI tools that can automatically handle many research tasks. These tools use powerful large language models (LLMs) to plan and perform complex jobs. You will learn how to apply them using several available cloudplatforms and open-source tools. The main goal is to show you how to use AI to speed up your work and discover new research questions.

Workshop participants can then choose from a number of hands-on exercises that they can complete on their own laptops. We will be available to help and answer questions.

Workshop 2. Open Source Software for Research – Sharing Code and Software the Right Way

Held by: Chris Erdmann (Head of Open Science, SciLifeLab) and coordinators Alma Nilsson, Suné Joubert and Parul Tewatia SciLifeLab Data Centre

Where and when: November 13, 2025 at 13:30-16:00, room K2 (20 seats) UKK

Registration

Description: Research depends on software, but without open and FAIR practices, reproducibility and reuse are limited. Open-source software means code that is not only available but also licensed for free use, modification, and sharing. This workshop provides an overview of open science policy related to software, and introduces the Open Science Software Checklist , showing how to apply it to make research code adhere to open science policies and guidelines. Speaker at the workshop include Malin Sandström from the Swedish Research Council (Vetenskapsrådet) and researchers from the SciLifeLab research community, as well as coordinators and data stewards from SciLifeLab Data Centre.

Participants should bring their own laptop and have a GitHub account. Having Visual Studio Code installed and connected to one’s GitHub is helpful but not required.

Workshop 3. Development of a Mastery Rubric for Data Driven Life Scientists

Held by: Jill Jaworski, SciLifeLab Training Hub

Where and when: November 13, 2025 at 13:30-16:00, room K3+K4 (90 seats) UKK

Registration

Description: What is a data-driven life scientist? What knowledge, skills and abilities do these individuals have and what core competencies do they share within their respective expertise-areas? What distinct characteristics set them apart from other life-scientists?

In this interactive workshop, through facilitated discussions and collaborative exercises, we will come to a shared understanding of what is required in this profession. We will create a Rubric that outlines the different knowledge, skill and ability areas of data-driven life scientists and map these competencies against beginner, intermediate and mastery levels.

In this way, we will help define the scope of data-driven life scientists and demonstrate what is needed for them to progress along learning paths from beginners to masters in their subject areas, thereby helping them understand how and where they can develop professionally. Amid quickly changing scientific landscapes, complex and pressing real-world issues, and growing mistrust in science, it is important to create a shared framework for what we mean when we describe data-driven life scientists, which will help bring credibility to the profession, trust, and clear guidance on how to professionally develop.

Participants will need to bring a laptop or tablet to this workshop to be able to fully participate.

Campus Solna Seminar Series: Keyi Geng
2025-11-13 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:

Keyi Geng

Claudia Kutter – gamma 5

tRNA gene deletion impairs cancer cell fitness

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

DDLS Annual Conference
2025-11-12 11:30 - 2025-11-13 13:30 | Uppsala Konsert & Kongress (UKK), Vaksala torg 1, Uppsala, 753 31, Sweden
We have reached full capacityWe are currently at full capacity with a waiting list. If you are no longer able to attend, please cancel your registration as soon as possible. This will allow us to accommodate others on the waiting list and ensure a smooth experience for all attendees. The Program in Hall B will be live-broadcast to SciLifeLab YouTube Talks & Training channel.

Live Stream

Live Stream – November 13

Live Stream – November 12

The Data-Driven Life Science (DDLS) program, funded by the Knut and Alice Wallenberg Foundation (KAW), warmly welcomes you to the fourth DDLS Annual Conference, taking place November 12–13, 2025, at Uppsala Konsert & Kongress (UKK).

Target Group: Anyone interested in data-driven life science is welcome to attend the Conference. You don´t need to be part of the SciLifeLab & Wallenberg National Program for Data-Driven Life Science, even though the conference focuses on achievements and highlights program activities.

This two-day, in-person event will highlight DDLS research and activities, showcase new technologies and services available to researchers across Sweden, and provide a forum for knowledge exchange and collaboration. Participants will have the opportunity to:

Share and discuss research findings

Explore ideas and insights across disciplines

Build networks for collaboration and career development

Gain perspectives beyond their own fields of expertise

The conference begins with a light lunch and registration on November 12 (11:30–12:30) and concludes with a networking lunch on November 13 (12:30–13:30).

YouTube live-broadcast

YouTube broadcast: The Program from Hall B will be live-broadcast on the YouTube SciLifeLab Talks & Training channel. Some speakers may share unpublished data that will be excluded from the live broadcast. You will find a YouTube embedded video player here on the event date.

Hosts & Moderators

The DDLS & SciLifeLab Director, Jan Ellenberg, will open the 2-day Conference. The DDLS Co-Directors, Erik Kristansson (Chalmers) and Carolina Wählby (Uppsala University), will moderate and guide you through the Program.

Confirmed speakers

Speaker Abstracts_DDLS Annual Conference 2025_v1Download

Invited speakers

Anna Kreshuk, EMBL
Title: Deep Learning for MicroscopyAffiliation: EMBL, HeidelbergBio: Anna Kreshuk is a group leader and a Senior Scientist in the Cell Biology and Biophysics Unit at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. She received a PhD in Computer Science from Heidelberg University in 2012. Following this, she worked as a PostDoc in the Heidelberg Collaboratory for Image Processing (HCI). She joined EMBL in July 2018, where her research group develops novel computer vision methods for the analysis of microscopy images. Beyond method development, she is also committed to the democratisation of machine learning for the life science community, contributing open source tools such as ilastik and PlantSeg. She is an ELLIS scholar and a scientific co-coordinator of the Horizon Europe project AI4Life.Abstract:

Daniel Tamarit, Utrecht University, the Netherlands
Title: The archaeal evolutionary origins of the eukaryotic cell

Affiliation: Utrecht University, the Netherlands

Bio: Daniel Tamarit is an Assistant professor at the Theoretical Biology and Bioinformatics (TBB) group, specialized in comparative and evolutionary genomics. He obtained his PhD at Uppsala University by studying the evolution of host-associated bacteria, and performed postdoctoral research at Wageningen University on major evolutionary transitions such as the origin of eukaryotes. Currently, his team uses evolutionary genomics to investigate fundamental questions in archaeal and bacterial biology, such as (i) what are the principles governing bacterial and archaeal genome architecture, (ii) what can the genomes of novel microbial lineages tell us about basic evolutionary processes, and (iii) what is the shape of the tree of life.

Abstract: The origin of eukaryotic cells was one of the most impactful transitions in evolution, setting the basis for the emergence of multicellular organisms such as animals, plants and fungi. Recent advances in genome-resolved metagenomics and phylogenomics have placed Asgard archaea at the heart of this transition, revealing that eukaryotes originated from within this group. Expanded genomic sampling and robust evolutionary modeling identify a lineage of Heimdallarchaeia, the Hodarchaeales, as the closest known relatives of eukaryotes. Reconstructions of ancestral gene repertoires, structure-based homology searches, and targeted experiments suggest that the archaeal progenitor of eukaryotes already possessed an enriched set of genes involved in cytoskeletal dynamics, membrane trafficking, and other functions that contribute to cellular complexity. This talk will showcase how integrating computational approaches is transforming our understanding of early cellular evolution and revealing the deep archaeal roots of eukaryotic life.

Ingemar André, Lund University
Title: Discovering patterns in the codon sequences of proteinsAffiliation: Center for Molecular Protein Science, Lund UniversityBio: Prof. André has a PhD in Biophysical Chemistry from Lund University. He joined the University of Washington for postdoctoral work before returning to Lund University to start his research group in 2009. He studies protein self-assembly to understand the mechanism behind the formation of large assemblies using experimental and computational methods. Large assemblies are also designed using computational protein design methods and artificial intelligence. His group also works on the design of conformational changes in proteins. Another direction is the study of codon adaptation in organisms and its effect on co-translational folding. Questions related to how protein structure has evolved are also addressed in research by the group using computational and experimental methods.Abstract: The genetic code defines how amino acid sequences are encoded in mRNA. Due to redundancy, this encoding is not unique, with up to six different codons specifying the same amino acid. Historically, synonymous mutations, changes between codons for the same amino acid, have been referred to as “silent.” However, it is now clear that codon choice can have significant functional consequences.

We investigated the effect of synonymous codons on protein folding efficiency in E. coli using a high-throughput experimental assay. Our results reveal a link between protein topology and the proportion of nascent proteins that emerge from the ribosome correctly folded, showing that even single synonymous substitutions can strongly influence co-translational protein folding.

Complementary bioinformatic analyses establish a relationship between codon usage and protein secondary structure. Furthermore, by training a large language model, we developed a predictive framework that identifies positions of rare codons within coding sequences, uncovers patterns explaining codon choice along the sequence, and highlights mRNA stability as an important determinant of codon usage.

Joakim Jaldén, KTH
Title: Restless bandits and self-driving microscopesAffiliation: KTH Royal Institute of TechnologyBio: Joakim Jaldén has a M.Sc. in electrical engineering and a Ph.D. in telecommunications from the KTH. Since his employment as a tenure-track faculty at KTH in 2009, he has increasingly devoted the group’s research efforts towards data analysis challenges in life science applications. Highlights include: The development of data association algorithms for single-cell tracking in time-lapse microscopy, in collaboration with the Blau lab at Stanford; Mathematical models and algorithms for cytokine movement and antibody interaction in immunoassay, which laid the foundation for patented technology behind the Mabtech AB analysis instruments for ELISpot and FluoroSpot, and most recently, multiplex assays; Algorithms and AI for long-read DNA basecalling from nanopore data, in collaboration with SciLifeLab. He has been a full professor at KTH since 2017, where he is now also deeply engaged in education.Abstract: The talk will focus on one result stemming from a first round of joint WASP-DDLS projects. The proposal envisioned the use of reinforcement learning as a tool to capture images of rare cell states in the context of automated microscopy. It will cover, at a conceptual level, the mathematical modeling decisions made to arrive at principled automation rules regarding what field of view to image and for how long, ending with empirical illustrations of the practically realizable gains.

Mark Ravinet, University of Oslo, Norway
Title: The evolutionary history of a commensal species: lessons from adapting to the AnthropoceneAffiliation: Centre for Ecological and Evolutionary Synthesis, University of OsloBio: Mark is an evolutionary biologist interested in understanding speciation and adaptation using a wide range of ecological and genomic techinques. He completed his PhD on local adaptation and speciation in three-spined sticklebacks at Queen’s University Belfast. Following that he was a JSPS Postdoctoral Fellow at the National Institute of Genetics, Japan, where he worked on the genomics of speciation in marine sticklebacks. He continued his work on the genomics of speciation and hybridisation, this time on Passer sparrows, at the University of Oslo as a Marie Curie fellow. It was here that his interest in understanding how human activity has shaped the evolution of other species began. He also has a strong interest in teaching genomics and bioinformatics to those beginning in the field. He has written several well-known resources and is co-author on the textbook Evolutionary Genetics: Concepts, Analysis and Practice. He is now an Associate Professor at the University of Oslo and his primary research focus is on using Passer sparrows as a model system for understanding how human activity might have driven adaptation, hybridisation and even potentially speciation in these charismatic little birds.Abstract: Human activity has altered the evolutionary trajectories and ecological circumstances of nearly every species on Earth. Commensal species are an extreme example to adaptation to anthropogenic niches, benefitting from a close association with human activity. What can the evolution of a commensal life history tell us about how species adapt to environmental change driven by humans?House sparrows (Passer domesticus) are a hugely successful human-commensal species, occurring on nearly every continent, largely due to human introductions. Despite its close association human society, surprisingly little is known about the evolutionary history of this species, how it has evolved to fit a tight anthropogenic niche and the evolutionary consequences of its rapid global spread. Our work has focused on addressing this.With resequencing data from over 1200 Passer sparrows, we first reconstructed the evolutionary history of the house sparrow. Our results suggest the species likely adapted to a human niche, potentially more than once, in Central Asia during the last 10,000 years. We used phenotypic data including micro-CT 3D scanning to compare skull morphology between human commensal and wild sparrow populations. We identified clear divergence in skull morphology, beak shape and an increased brain size in the commensal house sparrow populations. A major signature selective sweep in the house sparrow genome encompasses two major candidate genes; COL11A1 – which regulates craniofacial and skull development and AMY2A which is linked to adaptation to high-starch diets in humans and dogs. Functional analysis of COL11A1 confirms its role in skull development and we show evidence of copy number variation at AMY2A.Our next aim was to investigate the more recent global spread of the species. Native to Eurasia, the house sparrow was introduced to the Americas, Australasia and Sub-Saharan Africa in the 19th and 20th centuries. Using resequenced genome data from across this range, we have reconstructed the population genomic signatures of these introductions. Our findings point to introductions from two divergent lineages of house sparrow to different parts of the world as well as the rapid evolution of genetic differentiation among introduced populations. We further investigated adaptation to climatic variation across the introduced ranges of the species in North America and Australia. We identify several candidate genes linked to growth, thermoregulation and thermal tolerance, suggesting introduced populations have adapted to new environmental conditions in less than 150 generations.Our work identifies phenotypes and genes involved in rapid adaptation in parallel to anthropogenic change across the native and introduced range of the house sparrow. With a global distribution spanning a wide range of climatic conditions and a close association with human society, we suggest the house sparrow is an ideal model species for understanding adaptation in the Anthropocene.

Nicolai Birkbak, Aarhus University, Denmark
Title: T cell receptor diversity and immune health as a prognostic cancer biomarker

Affiliation: Department of Clinical Medicine, Aarhus University, Denmark

Bio: Nicolai Birkbak is Professor of Cancer Evolution and Bioinformatics at Aarhus University and Aarhus University Hospital, Denmark, where he leads an independent research group. His research focuses on the bioinformatic analysis of high-dimensional data to understand how the immune system interacts with cancer. By integrating genomic, transcriptomic, single-cell, and spatial data with medical imaging and liquid biopsy analyses, including circulating tumor DNA and T-cell receptor sequencing, his group develops holistic biomarkers that capture both tumor biology and host immune responses.

Nicolai trained in bioinformatics at the Technical University of Denmark and completed postdoctoral research at the Dana-Farber Cancer Institute and the Francis Crick Institute. At the Crick, he contributed to the TRACERx lung cancer evolution project, advancing understanding of how tumors evolve and evade immune surveillance. His work has also helped identify biomarkers of sensitivity to PARP inhibitors and elucidate mechanisms linking tumor evolution, immune modulation, and metastatic progression.

The overarching aim of his research is to translate these insights into precision medicine – enabling earlier detection, improved prediction of treatment response, and ultimately better outcomes for cancer patients.

Abstract: The adaptive immune system not only protects us against pathogens but also plays a crucial role in defending against cancer. Among its key components, T cells serve as central effectors in the endogenous anti-cancer response. Yet, the clinical significance of their quantity, diversity, and dynamics remains insufficiently understood.

We investigated the prognostic value of the T cell receptor (TCR) repertoire in patients with bladder cancer. In advanced-stage disease, we found that low pre-treatment peripheral TCR diversity was associated with poorer overall survival, particularly when combined with low circulating T cell fractions. These low-diversity repertoires were dominated by hyperexpanded clones that persisted throughout treatment and were frequently directed against chronic viral infections such as cytomegalovirus. Longitudinal analyses further revealed treatment-associated declines in TCR diversity, suggesting adverse effects on systemic immune health.

Together, these findings highlight that immune health biomarkers such as TCR diversity may provide new opportunities for precision medicine approaches aimed at improving cancer treatment outcomes.

Verónica Rendo, Uppsala University
Title: From tumor maps to new therapies for pediatric brain cancer

Affiliation: Department of Immunology, Genetics and Pathology; Uppsala University

Bio: Veronica studied Biology at Simon Bolivar University in Venezuela, and in 2013 moved to Sweden to pursue a PhD at Uppsala University. During this time, she worked under the mentorship of Prof. Tobias Sjöblom and studied how genomic losses in cancer could be exploited for therapy. In 2019, she moved to Boston (USA) to pursue a postdoc in Dr. Rameen Beroukhim’s lab at Dana-Farber Cancer Institute, affiliated with Harvard Medical School and the Broad Institute of MIT and Harvard. Here, Veronica focused on studying mechanisms of response and resistance associated with p53 reactivation in malignant brain tumors. She additionally continued her work on aneuploidy, describing a new class of therapeutic targets as ‘toxic genes’ – genes whose high-levels of expression are detrimental to cancer cell fitness. In 2025, Veronica became a Group Leader in Neuro-Oncology at the Department of Immunology, Genetics and Pathology at Uppsala University. Her lab investigates the genetic and adaptive mechanisms driving brain tumor evolution and therapy resistance, with the goal of identifying new treatment targets.

Abstract: In Sweden, cancer remains the leading cause of disease-related death among children, with brain tumors representing the most lethal subtype due to their limited treatment options and high relapse rates. One rare and aggressive subtype is atypical teratoid/rhabdoid tumors (AT/RT), an embryonal brain tumor which affects infants of under 2 years of age. The low incidence of AT/RT has hindered the establishment of a universal standard of care. Because these tumors primarily affect infants under two years of age, treatment is largely restricted to intensive chemotherapy regimens designed to avoid the harmful effects of radiation therapy. However, these high-dose regimens often yield only partial responses, underscoring the urgent need to elucidate mechanisms of chemoresistance and to identify novel therapeutic strategies. We aim to uncover the transcriptional cell states and genetic vulnerabilities associated with chemotherapy-persistent AT/RT, thereby revealing new targets that can enhance the efficacy of frontline treatments. To this end, we first employ cellular barcoding to track cancer cell populations at single-cell resolution before and after exposure to individual chemotherapeutic agents used in clinical AT/RT protocols. This approach enables comparison of treatment regimens and identification of overlapping mechanisms of resistance. To further dissect these mechanisms, we leverage CRISPR sensitizer screens to define targetable genes that potentiate chemotherapy response when depleted. Through our integrated transcriptomic and functional genomic analyses, we ultimately aim to uncover novel therapeutic targets in chemotherapy-persistent AT/RT cells and accelerate the development of more effective treatment strategies.

Jenny Frössling, Swedish Veterinary Agency

Karl Ståhl, Swedish Veterinary Agency

Erika Chenais, Swedish Veterinary Agency

Stefan Widgren, Swedish Veterinary Agency

Hyeyoung Kim, Swedish Veterinary Agency

Angela Fuentes Pardo, SciLifeLab Data Centre with Henrik Lantz, NBIS.

DDLS Fellows

Andrea Fossati, KI
Titel: Mapping infection at proteome scale: Toward mechanistic design of phage-based antimicrobialsAffiliation: Karolinska InstitutetAbstract: The rise of antimicrobial resistance (AMR) is outpacing the discovery of new antibiotics, creating an urgent need for alternative strategies. Bacteriophages (phages) offer a promising route to targeted antimicrobials, but their rational use is hindered by limited understanding of how they reprogram bacterial cells during infection. Our work addresses this by systematically mapping host–phage protein–protein interactions (PPIs) to uncover how viral proteins hijack essential bacterial complexes and redirect cellular physiology. Using next-generation interaction proteomics based on co-fractionation mass spectrometry (SEC-MS), we generated the first temporally resolved interactome of mycobacteriophage-infected cells. This approach captures native phage and host complexes without genetic tagging, enabling functional inference of phage proteins directly from their physical context. We identify hundreds of infection-specific assemblies, including viral inhibitors of essential bacterial machineries such as RNA polymerase and ribosomes. Structural modeling and comparative network analysis reveal conserved interface motifs and divergent strategies of complex remodeling across phage families. Integration of these data with CRISPRi perturbation and antibiotic susceptibility profiling provides a quantitative framework to predict infection outcomes and phage engineering.

Avlant Nilsson, KI
Title: Towards an interpretable deep learning model of cancerAffiliation: Karolinska InstitutetBio: Avlant Nilsson is a computational biologist and assistant professor in precision medicine at the department of Cell and Molecular Biology at Karolinska Institutet, Stockholm. He holds a MSc (2009-2014), and a PhD (2014-2019) degree in biological engineering from Chalmers University of Technology, where his thesis focused on the metabolism of growing cells, including liver cancer.In his postdoctoral work at Massachusetts Institute of Technology (2019-2023), he developed artificial neural network models to simulate signal transduction in immune cells.His lab at SciLifeLab is developing techniques to simulate cellular processes in cancer, aiming at identifying effective drug combinations, predicting resistance mechanisms, and understanding cell-cell interactions in the tumor microenvironment.Abstract: Deep learning offers new possibilities for understanding cancer using high throughput data. However, it can be challenging to translate predictive models into causal description of cellular responses. Our lab develops biologically informed neural networks that integrate omics data with prior knowledge of signaling, gene regulation, and metabolism. By constraining the models to only include physical molecular interactions, we are developing interpretable models for computer-aided design of personalized cancer medicine. With this approach we aim to answer questions such as why the same mutation yields different effects across cell types, unexpected signaling outcomes of drugs, and how genetic alterations may drive metabolic strategies.

Kelly Swarts, SLU Umeå
Title: Climate adaptation in natural forest treesAffiliation: Umeå Plant Sciences Centre, Swedish Agricultural UniversityAbstract: Conifers are ecologically dominant and economically important, but are succumbing to drought, disease, early-budding and other challenges globally because the climate has changed so that mature trees are no longer adapted to their environment. If we could predict how individual tree genotypes would respond to different environments, we could — given environmental predictions — plant the right tree in the right space. Standard agronomic approaches are effective but are less suitable for trees with long generation times and huge genetic diversity. We propose a system for quickly estimating adaptive responses for any forest tree. The key is tree increment core samples, which simultaneously provide DNA for genotyping and annual growth measurements, estimated from growth rings. For each genotype, we thus have a life-time’s worth of experienced year-environments. This allows us to partition growth variation into generalizable environmental responses for years with historical weather or biotic information, using quantitative, genomic and ecological approaches to control for correlated responses. We focus on the economically and ecologically important conifer Norway spruce (Picea abies) to 1) develop models and infrastructure to understand the fraction of annual growth that can be attributed to genotype, environment and genotype-by-environment interactions (GxE), 2) map the genetic basis of adaptive response using estimates for GxE as a response in genome-wide association studies (GWAS) and 3) predict genetic responses to novel environments. This approach enables estimation of the genetic basis of adaptive responses in any population, providing the means to evaluate a tree’s performance in any modeled environment. As environments shift under climate change, this provides a powerful tool to select parents for healthy, resilient forests.

Luisa W Hugerth, Uppsala University
Title: Bridging the last mile: microbiome-enhanced forecasting of pregnancy complications

Affiliation: Uppsala University

Bio: Luisa W. Hugerth trained both in biomedicine at Karolinska and in microbial ecology at KTH before combining these two interests by joining the Centre for Translatinal Microbiome Research. Since 2022 she is a DDLS fellow based at UU, where she leads the Human Microbial Ecology Lab, studying the microbiome as a modifiable risk factor in women’s health.

Abstract: Patients know a lot about themselves and their health, and asking the right questions will remain the key main strategy for taking clinical decisions. Still, there is always uncertainty in how an individual will react to an intervention. Leveraging large population-based pregnancy cohorts and combining questionnaires, registries, fecal and vaginal microbiome, we achieve improved accuracy in pregnancy complication predictions, including preterm birth, large-for-gestational age and small-for-gestational age infants.

Novelty, Excellence, Synergy, and Teams Projects (NEST)

TIMED: Time-Resolved Imaging and Multi-Channel Evaluation of Cellular Dynamics. Researchers: Rocio Mercado (CHT), Ola Spjuth (UU), Ashkan Panahi (CTH), Prashant Singh (UU) and Brinton Seashore-Ludlow (KI)

Learning 3D genome dynamics from heterogeneous data. Researchers: Thomas Schön (UU), Johan Elf (UU) and Magda Bienko (KI)

Multimodal AI-based Precision Diagnostics and Decision Support for Breast Cancer (AID4BC). Researchers: Claes Lundström (LiU), Mattias Rantalainen (KI), Sophia Zackrisson (LU) and Dave Zachariah (UU)

Research Data Community Projects (RDCP)

Microscopy Foundation Model & AI-Ready Data Hub for Smart Microscopy, Wei Ouyang, KTH. Presenting: Hanzhao Zhang, KTH

TissUUmaps Research Data Community Project, Carolina Wählby, Uppsala University

CRITICAL MICROBES – Comprehensive Research on InfecTIons Complications Across the Lifespan – MICROBiology Epidemiology in Sweden, Sara Kalucza, Umeå University

Swedish Metabarcoding Network (SMN), Tobias Andermann, Uppsala University

The Precision Medicine and Diagnostics and Cell and Molecular Biology parallel sessions will include selected short talks from submitted abstracts.

Registration

The Poster registration is closed! If you want to update or cancel your poster, please contact events@scilifelab.se.

We have reached full capacityWe are currently at full capacity with a waiting list. If you are no longer able to attend, please cancel your registration as soon as possible. This will allow us to accommodate others on the waiting list and ensure a smooth experience for all attendees. The Program in Hall B will be live-broadcast to SciLifeLab YouTube Talks & Training channel.

Register for the Waiting list

Registration and Poster Submission Deadline

We have 320 seats. The registration and poster submission close on October 21st. If you register after October 21st, you will need to write your name on a name tag at the on-site registration. Unfortunately, we cannot accommodate allergies or dietary preferences for those who register after the deadline.

Waiting List

To avoid empty seats, registration will remain open until the event begins. If we reach full capacity, a waiting list will be activated. Sign up for the waiting list, and you will automatically receive an email when a spot becomes available. You must accept to secure the spot. If you decline, the offer will go to the next person on the waiting list.

Cancellation

To minimize empty seats and especially food waste, you must cancel your registration if you are unable to attend the conference. If a waiting list is activated, your spot will go to someone else.

Poster session

Poster Abstracts

PostersA3Download

Poster Sessions, November 12

14:00 15:00 Hall C: Poster session I (odd numbers)

16:30 17:30 Hall C: Poster session II (even numbers)

Instructions:

1. Find your number in the POSTER LIST attached.

2. Hang your poster on the board indicating your number, starting at 11:00 in Hall C, to increase visibility during lunch on Day 1.

3. Please stand by your poster during your assigned session (odd or even numbers). Leave it displayed throughout the conference so everyone can see it.

The poster board area measures 103×143 cm. Bring a poster size you prefer.

DDLS Annual Poster Prize

The DDLS Poster Prize encourages PhD students and postdoctoral researchers to present high-quality work in data-driven life science. The award, decided by a Scientific Committee jury, includes a certificate and a travel grant of up to 5,000 SEK. Conditions apply. If you present a poster, please ensure you stay for the Poster Award Ceremony at 12:00 by the end of the Conference.

Map over UKK and the poster session (Hall C)

Map UKK Floor 3 with poster session in Hall CDownload

Program

The Plenary Program (excluding the Parallel Sessions) will be live-broadcast on the SciLifeLab YouTube channel. There might be some speakers sharing unpublished data that will be excluded from the live-broadcast.

Program DDLS Annual Conference 2025_v13Download

DDLS Annual Conference 2025 workshops

During the second day of the DDLS Annual Conference, participants will have an opportunity to attend one of three workshops. The workshops are designed for researchers in data-driven life sciences at all career stages.

Each workshop has a limited number of seats on a first-come, first-served basis. Those registered after the limit is reached will be placed on a waiting list. The workshops will take place in various rooms of the main conference venue, UKK. All workshops start at 13:30 but can end at various times. Coffee/tea and fika will be served during the workshops.

Feel free to email datacentre@scilifelab.se with any questions about workshop 1 and 2 and traininghub@scilifelab.se for workshop 3.

Read more about Workshops

Workshop 1. Automating life science & biomedical tasks with LLMs and beyond: practical guide

Workshop 2. Open Source Software for Research – Sharing Code and Software the Right Way

Workshop 3. Development of a Mastery Rubric for Data Driven Life Scientists

Practical information

Travel to Uppsala

The Venue, Uppsala Konsert & Kongress (UKK) is next to the Train station. MAP here! Travel centres, bus stops, parking and hotels are all located within walking distance from Uppsala Konsert & Kongress. Several train and bus lines connect Uppsala to the rest of the country and the region, and Arlanda Airport is only 18 minutes by train, Stockholm Central station is approx. 30 minutes by train.

Uppland public transport (UL) timetables and information: www.ul.seStockholm public transport (SL) timetables and information: www.sl.se SJ timestables and information: www.sj.se

Good to know, travelling to Uppsala.

Parking

The nearest parking garage is Centralgaraget. There is also parking available in Kvarnens parking garage, Svava, S:t Per Gallerians garage, Österplan, and several other locations in central Uppsala. For more information about parking in the area, please visit Uppsala Parkering.

Hotels in Uppsala

Find suggestions for accommodation in Uppsala here

Getting Started with Berzelius: Essential Commands
2025-11-11 10:00 - 11:30 | Zoom
Welcome to join this practical introduction to essential commands on Berzelius. The session will cover:

Logging in

Managing data

Setting up environments

Running and monitoring jobs

Participants will also gain hands-on experience with these commands. By the end of the session, you will be able to navigate Berzelius confidently and use its resources effectively for your research.

Date: Tuesday, November 11, 2025Time: 10:00–11:30

Target audience: The online event is open for all current and prospective Berzelius users. Please read the eligibility requirements for accessing Berzelius.Place: Online via Zoom (link provided upon registration)

Registration

Preliminary Agenda

TimeSession TitleSpeaker(s)10:00–11:00Getting Started with Berzelius: Essential CommandsXuan Gu11:00–11:30Open Q&A SessionBerzelius Application Expert

This event is a collaboration between National Supercomputer Centre (NSC) at Linköping University and SciLifeLab Data Centre.

For questions please contact xuan.gu@liu.se (Xuan Gu)

Epigenetic Diagnostic Classification of Cancer
2025-11-11 09:00 - 10:00 | Online event via Zoom
Use of DNA methylation to improve diagnosis of tumors in the clinical setting

Clinical Genomics Webinar Series

Clinical Genomics Linköping is hosting this webinar as part of the Clinical Genomics Platform webinar series

Join us on Zoom

There is increasing interest in using DNA methylation information from long-read sequencing to improve the classification of tumors, which has implications for surgical approach and treatment options. At Clinical Genomics Linköping we are exploring use of the NanoDx pipeline for classification of CNS tumors in collaboration with Dr. Eukirchen, who developed and implemented it in Berlin. We will present some background to the method, use on frozen tissue and liquid biopsy, as well as some user cases from both sites.

Everyone is welcome so feel free to spread the details with anyone who may be interested. Hope to see you there!

Host: Colum Walsh, Platform site director at Clinical Genomics Linköping

Invited speakers: Dr. Philipp Euskirchen, Charité University Hospital, Berlin and Dr. Małgorzata Łysiak, Clinical Genomics Linköping, Linköping University

BiG Talk – Best practices and common pitfalls in methylome sequencing analysis
2025-11-10 13:30 - 14:00 | Online event via Zoom
Abstract

Whole-genome methylation sequencing provides single-base resolution of DNA methylation but remains one of the most computationally challenging omics data types to process. Its complexity stems from bisulfite-induced sequence conversion, protocol-specific artifacts, and the large number of available software tools, making reproducible analysis and cross-study integration particularly difficult. To address this we systematically benchmarked ten complete computational workflows across five distinct profiling protocols using an experimental gold-standard reference. The results reveal substantial performance differences in accuracy, computational efficiency, and downstream analysis, particularly for low-input samples. Furthermore, we introduced a continuous, “living” benchmarking platform for future software developments. To further facilitate large-scale, standardized methylome analysis, we developed complementary R package for efficient storage, manipulation, and integration of genome-wide methylation data that also supports applications such as methylation-based clocks, or reference-based cell-type deconvolution enabling tissue composition inference from whole-genome methylomes. Together, these resources address the difficulties of processing, analyzing, and interpreting DNA methylation data at genomic scale to ease reproducible epigenome research.

Biography

Reka Toth is a computational biologist and group leader at the Luxembourg Institute of Health (LIH). She heads the Multi-omics Data Analysis Group in the Department of Cancer Research and drives omics initiatives within the Medical Informatics, Bioinformatics & AI Unit. Trained as a molecular biologist, she completed a PhD in genetic epidemiology at the University of Debrecen (Hungary) focused on chronic diseases and addiction, and later added Software Engineering to pivot into computational biology.

In 2013, Dr. Toth joined the National Center for Tumor Diseases in Heidelberg, where she led the Biostatistics and Bioinformatics Group on colorectal cancer. She then moved to the Epigenomics Division at the German Cancer Research Center (DKFZ), expanding her work in computational epigenomics across cancer types, with a particular emphasis on DNA methylation for prognosis and cell-of-origin. She joined LIH in 2021 and established her own group in 2025. Her research focuses on methylation as a diagnostic and prognostic biomarker and on integrative multi-omics to reveal complex biomarker signatures and mechanisms in cancer.

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

Broadcast link (live event): https://lu-se.zoom.us/j/62767371752

The talk is sponsored by the SciLifeLab Epigenomics Symposium.

A recording will also be available on the NBIS YouTube channel.

SciLifeLab Epigenomics Symposium
2025-11-10 09:00 - 17:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
Epigenomics is a cornerstone of modern genomics, providing crucial insights into gene regulation and cellular function. The study of epigenetic modifications, such as DNA methylation, histone modifications, and non-coding RNA expression, has revolutionized our understanding of gene activity across diverse biological systems. With advancements in sequencing technologies, researchers can now investigate these modifications at a genome-wide level, both in bulk tissues and at single-cell resolution. When integrated with genomic and transcriptomic data in a multimodal framework, epigenomics offers new perspectives on gene expression regulation with broad applications in ecology, developmental biology, and human health, including cancer and other diseases.

Welcome to a full-day symposium with presentations from leading experts in the epigenomics field.

This event is organized in collaboration with NGI, Clinical Genomics and NBIS.

Registration

The registration is closed.

Extra! Hands-on Course in Epigenomics

Following the symposium, a four-day hands-on course will be held November 11- 14. The course combines laboratory work, theory, and bioinformatics training, focused on the generation and analysis of DNA methylation data. Please visit the course page for more information and registration.

Read more

Confirmed speakers SciLifeLab Epigenomics Symposium

Philipp Euskirchen, Charité – Universitätsmedizin Berlin

Martí Duran-Ferrer, FRCB-IDIBAPS, Barcelona

Reka Toth, Luxembourg Institute of Health

Maja Jagodic, Karolinska Institutet

Angelica Maria Delgado-Vega, Karolinska Institutet

Sofie Degerman, Umeå University

Colum Walsh, Linköping University

Leif Andersson, Uppsala University

Carl-Johan Rubin, Uppsala University

Amanda Raine, Uppsala University

Katarzyna Dziasek, SLU

Program

SciLifeLab Epigenomics Symposium Agenda_251107Download

Contact for questions

Ulrika Liljedahl, Ulrika.Liljedahl@medsci.uu.se

Organizers

SciLifeLab Genomics NGI, Jessica Nordlund https://www.scilifelab.se/units/ngi/

SciLifeLab Clinical Genomics, Colum Walsh https://www.scilifelab.se/units/clinical-genomics/

National Bioinformatics Infrastructure, Louella Vasquez https://www.scilifelab.se/units/nbis/

With the kind support from:

Exploring long-read WGS in a clinical setting of Pediatric brain tumors
2025-11-07 11:00 - 12:00 | Online event via Zoom
Clinical Genomics Webinar Series

Clinical Genomics Gothenburg is hosting this webinar as part of the Clinical Genomics Platform webinar series

Join us on Zoom

The webinar will cover whole genome and whole transcriptome sequencing (WGS and WTS) analysis of childhood tumors in a clinical setting. Moreover, the seminar will cover specific research interest regarding fusion genes in childhood brain tumors and preliminary data from an ongoing study comparing long-read (ONT sequencing) to short-read WGS sequencing will be presented.

Everyone is welcome so feel free to spread the details with anyone who may be interested. Hope to see you there!

Host: Marcela Dávila, Head of Unit at Clinical Genomics Gothenburg

Invited speaker: Assoc. Prof. Frida Abel, University of Gothenburg

Campus Solna Seminar Series: Taras Sych
2025-11-06 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:

Taras Sych

Erdinc Sezgin – gamma 3

Membrane fluidity of nanosized biopartilces as metabolic disease biomarker

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

User meeting for your multi-modal research projects
2025-11-06 09:00 - 10:30 | virtual event
Boost your research — Book a private SciLifeLab planning and feedback session for your multi-modal research projects!

Register here

Once we have received your registration, you will be seny the link to the online meeting.

Date: November 6, 9.00 – 10.30 Registration deadline: October 31

Multimodal molecular profiling and novel computational methods are transforming life science research, but also pose new challenges in study design, project resource planning and data management. SciLifeLab is a national resource of unique technologies and expertise available to life scientists, in areas such as biomedicine, ecology and evolution, aiming to bring scientists together across traditional boundaries and foster collaborations with industry, health care, public research organizations and international partners.

The first Thursday of every month at 9.00 (except July and August), SciLifeLab offers an opportunity to jointly meet with representatives across the SciLifeLab service platforms, to get feedback and help to plan, design, and refine new or ongoing multimodal research projects. Your project plans are discussed privately and remain confidential, and information will not be shared outside of the service platforms. Note that for most studies, follow-up meetings will be needed, but our aim for these meetings is to provide an easy-access entry point for an overarching planning of multimodal studies.

For studies focusing on a single technology only, please primarily contact our service platforms directly as described at the SciLifeLab homepage.

To make the best out of the allotted time, we ask you to provide some background information about your project, to help us ensure that the relevant experts are available to discuss your study.

BAM Seminar: Scientific Storytelling
2025-11-06 09:00 - 10:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
As part of our “Biology At Most” seminar series we invite speakers from all types of life science career paths. They will share their visions, perspectives and expertise in their field in a informal environment.

Today’s guests are expert in the field of science communication

Our speakers will discuss the theory and practice your scientific presentations through storytelling!

We will have time for fika at the seminar and the pub will be open for networking & mingle after.

Register here

Speakers:

TBD – Update will come soon

Program

9.00-9.05

Welcome

9.05-9.55

TBD

9.55-10.00

Closing remarks (continue mingling at pub)

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

Nucleolar dysfunction: understanding its significance in human diseases
2025-11-05 15:00 - 16:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Welcome to a seminar with Dr. Dorthe Payne-Larsen, Danish Cancer Society Copenhagen, Nucleolar Stress Disease Group. We will meet up with individuals who do not have access to SciLifeLab in the reception at 14.50.

Speaker

Dr. Dorthe Payne-Larsen, Danish Cancer Society Copenhagen, Nucleolar Stress Disease Group

Host

Per Moberg, MBB
