Pandemisk laboratorieberedskap - vad hände, vad gör vi och vad behöver vi göra till nästa gång
2023-06-30 14:30 - 15:30 (Europe/Stockholm) | D-huset, Campus Gotland, Kaserngatan 1, Visby, Sweden
SciLifeLab i Almedalen

Under Almedalsveckan 2023 arrangerar SciLifeLab ett antal seminarier för att visa hur och debattera kring hur forskning och forskningsinfrastruktur kan bidra till att möta samhälleliga utmaningar vara för att fortsatt vara en ledande life science nation.Varmt välkommen att delta!

Om du vill ha kontakt med projektteamet för SciLifeLab Almedalsveckan – kontakta Per Lek

Beskrivning av samhällsfrågan

Vi kommer att drabbas av nya pandemier och vi behöver beredskap för det. Tidigt under COVID-19 pandemin blev det uppenbart att Sverige hade begränsade resurser att analysera prover och det påverkade kontrollen av pandemin. Vad var problemen? Hur löstes dem? Vad ska vi göra till nästa pandemi?

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Utökad information om evenemanget:

Frågor rörande pandemisk laboratorieberedskap kommer att diskuteras i ett rundabordssamtal mellan experter inom området från Folkhälsomyndigheten, de stora mikrobiologiska laboratorierna, SciLifeLab och universiteten som alla var iblandade i hanteringen av prover från COVID-19 infekterade patienter men även forskning som behövdes för att förstå och kunna kontrollera pandemin. Tanken är att belysa vad som av problematiskt samt vad man bör göra inför nästa pandemin, något som vi vet kommer att ske men inte när?

Medverkande:

Mia Phillipson, Professor, Uppsala Universitet och SciLifeLab

Johan Lindh, Docent, Sektionschef, Akademiska sjukhuset

Karin Tegmark Wisell, Generaldirektör, Folkhälsomyndigheten

Jessica Alm, Enhetschef, National Pandemic Center, Karolinska Institutet

Peter Nilsson, Professor, KTH/SciLifeLab

Advances in mRNA translation and protein synthesis
2023-07-30 13:30 - 2023-07-31 14:00
The symposium is a satellite meeting of the European Biophysical Societies’ Association conference. It will start on 30 July and finish on 31 July. The symposium will highlight the latest discoveries in the field of translation and protein synthesis. Translation occurs on ribosomes that form hubs of a proteome and nucleic acids, which are intricate in the range of functions and their structural dynamics. Those ribosomal hubs involve multiple cofactors and are implicated in disorders, which makes them key drug targets. Since translation requires coordination and rapid exchange between multiple factors, tracking such a system is a laborious task. In this respect, recent developments in imaging techniques have had a major impact on our understanding of translational systems. Therefore, alongside presentations of biological results, there will be methodological advances.

There will be options to present your work in a short talk or a poster.

Twelve talks will be selected from abstracts submitted before June 10. Please apply for oral presentation before June 10 (extended deadline).

Important information

Date: July 30 13:30 to July 31st 14:00Location: Lecture hall at BMC, Uppsala University (more details to be announced).

Conference fee: The Conference fee is 650 SEK, including dinner on July 30th and lunch on July 31st. An invoice will be sent to your Department. Payments shall be made by Departments or Organizations only (no private bank account or private address will be approved). Participants from businesses and organizations with VAT numbers within the EU can claim the VAT back from their local tax authority. More information is on the EU website.

A maximum of 60 participants will be accommodated, with participation being confirmed on a first-come-first-serve basis.

Registration

Invited speakers

Axel Innis, University of Bordeaux.

Danny Nedialkova, Max Planck Institute of Biochemistry, Martinsried.

Sophia Rudorf, Leibniz University Hannover.

Axel Innis, University of Bordeaux

We are interested in how ribosomes make proteins, how they are regulated in response to different stimuli, and how small molecules block these molecular machines. The focus is on the bacterial ribosome and how it is affected by nascent proteins known as arrest peptides, antimicrobial peptides, and antibiotics. In order to study the underlying molecular mechanisms, we use a combination of structural biology, high-throughput functional characterization and biochemistry.

Danny Nedialkova, Max Planck Institute of Biochemistry, Martinsried

Our research seeks to define how distinct proteomes are established and maintained in eukaryotic cells, with the long-term goal of understanding why some cell types are selectively vulnerable to dysregulated protein homeostasis in disease. To address these questions at a systems level, we develop and apply quantitative genome-wide techniques and combine these with functional genomics in diverse eukaryotic model systems.

Sophia Rudorf, Leibniz University Hannover

We employ computational, bioinformatic, and mathematical approaches to model and analyze biomolecular processes. Our primary focus lies on studying protein biosynthesis across various organisms and in-vitro expression systems.

Organizers

Maria Selmer, Suparna Sanyal, Magnus Johansson, Uppsala University. Alexey Amunts, SciLifeLab

For any organizational inquiries, please contact Maria Selmer.

with support from

EBSASciLifeLabEMBO

EBSA Congress 2023
2023-07-31 08:00 - 2023-08-04 17:00 | Aula Magna, Frescativägen 6, Stockholm, 114 18 Stockholm, Sweden
Welcome to EBSA 2023!

An EBSA congress in Sweden is timely. In 1986, the first EBSA Workshop was hosted by the Swedish Biophysical Society and Professor Anders Ehrenberg, the first president of EBSA. In 2023, after a series of great EBSA meetings around Europe, the Swedish Society for Biochemistry, Biophysics and Molecular Biology (SFBBM) is again, jointly with EBSA and Protein Society, proud to host the 14th EBSA congress at Stockholm University, supported by the Swedish National Committee for Molecular Biosciences (of the Royal Swedish Academy of Sciences). In this meeting, we are honored to also collaborate with the Biophysical Society, IUPAB and SciLifeLab.In Biophysics, we investigate properties of time, force, and motion in biomolecular assemblies and processes – from single molecules to cells and tissues – and relate these to biological function. Biophysics has evolved dramatically since 1986, and many Nobel prizes have been awarded to biophysicists to previous EBSA Plenary Lecturers in the past, and Nobel Prize winners will also participate in the upcoming congress. The EBSA-2023 will be held at the Aula Magna at Stockholm University, which is also known for hosting the Nobel Lectures in Physics and Chemistry.

EBSA-2023 will offer a creative meeting ground for investigating how the most novel experimental, theoretical and computational approaches in Biophysics can be synergistically tailored to improve our understanding of biological function, and thereby build an even stronger scientific bridge between physics, biology and medicine.

We are much looking forward to learning more about your most recent findings at EBSA-2023, and to jointly enjoy novel breakthroughs in this wide and exciting field.

Read more

Chair

Dr Maria Sunnerhagen, Professor of Structural Biology, Linköping University

Co-Chairs

Dr Erik Lindahl, Professor of Biophysics, Stockholm University and SciLifeLab

Dr Lena Mäler, Professor of Biochemistry, Stockholm University

Dr Jerker Widengren, Professor of Biomolecular Physics, KTH Royal Institute of Technology, Stockholm

Project support in chemical biology and drug discovery
2023-08-16 10:00 - 10:45 | Online event via Zoom
The chemical biology unit (CBCS) and the Drug discovery and development (DDD) platform at SciLifeLab have calls out for projects.

CBCS is looking for projects in Chemical Biology which includes assay development for small molecule screening and profiling, as well as enabling chemistry. For more information, please visit www.cbcs.se.

The DDD platform has a call looking for new project proposals for drug discovery. All therapeutic modalities that can be developed in collaboration with the DDD platform at SciLifeLab are of interest, including small molecules, antibodies, oligonucleotides and new modalities.

Some users and projects are at the intersection between chemical biology and drug discovery. This webinar aims to guide users to the call that best suits the needs of their project.

register here to receive link

Documentation

DDD Call for Projects

CBCS Large Projects Call 2023

Webinar Slides CBCS

Webinar Slides DDD

Integrated Structural Biology workshop
2023-08-23 08:00 - 2023-08-24 16:30 | Online event via Zoom
Structural Biology comprises studies of proteins and nucleic acids, how they interact and how they appear in solution. The answer provides insight in to the function of the macromolecules and can explain diseases, basic functions or be used to understand mechanisms and in the longer perspective aim in drug design to name a few of the important areas where the techniques contributes.

Important techniques for structural biology include Cryo-EM, Nuclear Magnetic Resonance and Structural Proteomics and all of these are available through SciLifeLab. For a structural biology project, there is a pipeline starting with the gene and the end goal information is how and where the encoded protein functions or interacts with the surround.

It has become clear over the years that no technique alone can provide a full insight into a biological problem. Thus an integrated approach where different techniques are combined is often necessary. The aim for us working with structural biology at SciLifeLab is to be a partner along the whole way, from gene to final answer.

Program

Integrated-Structural-Biology-Workshop-1Download

Day 1

We will hear from Swedish infrastructures, covering the whole pipeline from gene to 3D protein structure and the subsequent functional analysis, in addition to computational aspects including AlphaFold.

Day 2

Day 2 will contain a general overview of structural biology and available techniques. There will also be a few presentations from participants that are given the chance to discuss and get feedback on their own project from participants but also from the infrastructure representatives. We will also have a time slot to discuss the availability of infrastructures in Sweden and if there are missing parts or suggestions for changes from the users.

registration

Forum for the Future of Neuroscience
2023-08-23 09:00 - 2023-08-24 17:00
What will the next 10 years of Neuroscience look like?

The global coronavirus pandemic has disproportionately affected early career researchers. This meeting is a symposium geared toward young neuroscience investigators embarking on their own research programs. Bringing together young investigators from diverse subdisciplines of neuroscience in a single venue, where they can freely discuss the issues and future directions of their respective fields without the influence of more senior investigators, has the potential to shape the trajectory of neuroscience in the coming decade.

On the symposium’s first day, the event will take place at the Nobel Forum, located close to the Karolinska Institutet in Stockholm. The Nobel Forum is where the Nobel Assembly meets to select the annual Nobel laureates in physiology or medicine

On the symposium’s second day, the venue will shift to a more secluded location at the Swedish Collegium for Advanced Study in Uppsala. This venue, built in 1787 to house Linneaus’s botanical collection, is known for its peaceful and serene surroundings, which are conducive to scholarly and intellectual pursuits.

Confirmed speakers:

Justus Kebschull JOHN HOPKINS UNIVERSITY

Gioele La Manno EPFL

Annegret Falkner PRINCETON UNIVERSITY

Talmo Pereira SALK INSTITUTE

Katharina Schmack FRANCIS CRICK INSTITUTE

Ashley Juavinett UNIVERSITY OF SAN DIEGO

Sulagna Das EMORY UNIVERSITY

Arkarup Banerjee CSHL

Nikos Konstantinides INSTITUTE JACQUES MONOD

Sam Golden UNIVERSITY OF WASHINGTON

Alessandro Furlan KAROLINSKA INSTITUTET

Marek Bartosovic STOCKHOLM UNIVERSITY

Organizing committee:

Arkarup Banerjee, Cold Spring Harbor LaboratoryAnnegret Falkner, Princeton UniversityAlessandro Furlan, Karolinska InstituteDaniel Fürth, SciLifeLab/Uppsala UniversityContact for questions: Daniel Fürthfurth@scilifelab.uu.se

Event Website: https://triplef.life/

This event is sponsored by:

Marcus Wallenberg Foundation for International Scientific CollaborationWenner-Gren FoundationsSciLifeLab

Open online lecture by Prof. Edward Holmes: Metagenomics at the human-animal interface
2023-09-01 08:50 - 09:25 | Online event via Zoom
The PLP (Pandemic Laboratory Preparedness) program, started in 2021, acts to meet society’s need for efficient use of resources, training and education, to propagate skills and setting up technologies and equipment to be better prepared for new pandemics.

During the upcoming PLP program retreat, on Friday September 1 at 08:50, we are honored to welcome Professor Edward Holmes for an online lecture, open for everyone to join.

Edward (Eddie) Holmes is an evolutionary biologist distinguished for his work on the emergence and evolution of viruses. He has used genomic and phylogenetic approaches to reveal the major mechanisms of virus evolution and determined the genetic and epidemiological processes that explain how viruses jump species boundaries and spread in new hosts.His work has revealed the origin, evolution and molecular epidemiology of important human pathogens including influenza, HIV and dengue, and enabled more accurate assessments of what types of virus are most likely to emerge in human populations and whether they will evolve human-to-human transmission. His recent research has provided fundamental insights into the breadth and biodiversity of the viral world.Eddie is currently a Professor in the School of Medical Sciences at the University of Sydney. In 2015 he was elected a Fellow of the Australian Academy of Science and in 2017 he was elected a Fellow of the Royal Society. In 2021 he received the Australian Prime Minister’s prize for science.

Zoom link

[The Svedberg seminar] - Toward Multidimensional Spectral Flow Cytometry: Entering the Quantum Cytometry Domain
2023-09-04 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
J. Paul Robinson, Professor

Distinguished Professor of Cytometry

Professor of Biomedical Engineering

Purdue University, USA

Bio

Dr. Robinson received his early education at the University of NSW, Sydney Australia where he received a B.Sc. (Hons), M.Sc. and Ph.D. degrees. He was a postdoctoral fellow in the University of Michigan Medical School then a junior faculty in the School of Pathology prior to moving to Purdue University where he was promoted to full professor in 1993.

Dr. Robinson is currently a Distinguished Professor of Cytometry, and Professor of Biomedical Engineering in the Weldon School of Biomedical Engineering. He also holds appointment in the Purdue Polytechnic Institute, School of Computer and Information Technology and IU School of Medicine. Dr. Robinson is a Fellow of the American Institute for Medical and Biological Engineering, a Fellow of the American Association for the Advancement of Science, a Fellow of the National Academy of Inventors and a Fellow of the Royal Microscipal Society. Dr. Robinson is a past president of the International Society for Advancement of Cytometry and is the past Editor-in-Chief of Current Protocols in Cytometry.

He is an accomplished researcher with over 210 peer-reviewed papers, over 400 conference presentations, 10 books, 15 CDs or DVDs published and over 160 invited international keynote lectures and over 20 issued patents. He formed the Purdue Cytometry Electronic Discussion list in 1989 (http://cyto.purdue.edu/hmarchiv/index.htm) and it continues today with 4500 participants.

Dr. Robinson is the inventor of the key patent on spectral flow cytometry that has been commercialized and morphed into one of the most significant technologies in the field of fluorescence-based single cell detection. In this regard, together with his colleague Masanobu Yamamoto, they recently developed the most sensitive, highest speed single photon detector technology that is likely to have future impact on the field. He has also worked for many years on detection technologies in the area of food borne pathogens. More recently his group has been focused on developing new approaches to toxin and pathogen detection using laser induced breakdown spectroscopy (LIBS). By combining lanthanide conjugated antibodies as target molecules for toxins, it is possible to create a rapid detection assay that can be highly multiplexed.

Dr. Robinson is an accomplished mountaineer having summited several of the world’s most difficult mountains including Everest, (8,849m, May 23, 2009); Manaslu (8,163m, Oct 3, 2008); and McKinley (6,191m, Jul 1, 2008). In 2006 he formed the not-for-profit foundation “Cytometry for Life” (www.cytometyforlife.org) as a mechanism to promote low-cost diagnostics and education primarily in Africa and this organization continues working today to expand education and training in Africa in conjunction with AIBBC (https://www.aibbc-society.org).

Toward Multidimensional Spectral Flow Cytometry: Entering the Quantum Cytometry Domain

For decades flow cytometry has been a go-to technology for single cell analysis. There are clear advantages for analysis of complex suspensions of cells, particularly when considering blood cell analysis. The principles for the latest iteration for flow cytometry technology is a spectral approach with is now 2 decades old since we first developed this approach in 2001-2003. Spectral flow cytometry has become the driving technology in the field over the past 5-7 years. What spectral cytometry has brought to the field is a vast increase in multiparameter assay capability now approaching 50 simultaneous fluorescent probes.

However, what we see as the future of cytometry is often based on our current view of what we presently have. And the question arises can we envisage a technology that is different from what we currently understand and use? This is a difficult question as most of us can’t exactly predict the future! What we do know is there are new tools out there that can become integrated into the field.

There is a potential for a 2nd generation spectral technology that we have been working on that may provide many more features that we currently consider when we design our experiments. This presentation will discuss the engineering developments in both current spectral analyzers and spectral cell sorters and outline the next-generation technology that will open up new frontiers in biotechnology research in both research and clinical diagnostics. The focus will be around how do we approach quantum cytometry? Can we move from the analog world to the digital world – that is to the world where we deal with single photons – the photon being the ultimate digital event? This requires new sensors for high-speed detection. New sensors require better optics – more advanced diffraction approaches for light collection than currently available. High-speed sensors demand high speed electronics moving from the megahertz to the gigahertz domain. In all, moving to quantum cytometry means redefining most of the technology that we have been using for decades. There is a saying that “you cannot put new wine into old wine skins”! The technical demands for quantum cytometry are far more stringent that current systems allow. However, when you meet these criteria, the opportunities for biological detection approaches expands enormously. This presentation will outline a new sensor technology, new laser/electronics technology and how this will generate datasets that require advanced analytical toolsets demanding AI for potentially automated diagnostics.

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

Emerging data-driven approaches to cancer
2023-09-06 09:00 - 17:00 | Martin H:son Holmdahlsalen, Dag Hammarskjöldsväg 8, Entrance 100, Akademiska sjukhuset, Uppsala
Welcome to the second in-person symposium in data-driven precision medicine and diagnostics (PMD) research area. Listen to leading experts in this area, including Data-Driven Life Science (DDLS), and expand your network with international and national colleagues.

This meeting brings together the community in precision medicine and diagnostics and researchers who implemented artificial intelligence and machine learning applications in their research in PMD to improve human health and diagnostics, introduces newly appointed DDLS fellows in the PMD research area, and provides opportunities for networking across the research community and the SciLifeLab infrastructures. Thematically, this meeting will focus on emerging approaches to cancer research, ranging from both cutting-edge basic science to promising translational developments of AI.

We are excited to host international keynote speakers and welcome the community to join us. Hopefully, this event will inspire you on the potentials of data-driven precision medicine and diagnostics in Sweden.

Target group: We welcome all researchers interested in the DDLS program and data-driven precision medicine and diagnostics. This is an onsite event only. The event will not be recorded as the speakers might share their unpublished results.

Deadline for registration to guarantee fika and lunch: August 30. Note; to minimize food waste, we ask you kindly to cancel your participation before August 30, if you can´t participate.

Speakers

Abhishek Niroula, DDLS Fellow, University of Gothenburg

Avlant Nilsson, DDLS Fellow, Karolinska Institutet

Beatrice Melin, Umeå University

Björn Nilsson, Lund University

Fredrik Strand, Karolinska Institutet

Ida Larsson, Uppsala University

Hannah Muti, University Hospital RWTH Aachen

Karin Forsberg Nilsson, Uppsala University

Michael Mints, Weizmann Institute of Science

Nina Linder, Uppsala University

Olli Kallioniemi, Director SciLifeLab and DDLS

Veronica Rendo, Uppsala University

Register here

When the event is fully booked, add yourself to the waiting list. You will be notified by email if a place becomes available. We kindly ask participants to cancel if they can´t come so the seat can become available to someone else. Thank you!

Program

H:son Holmdahlsalen, Ing 100/101, 2 tr. Akademiska sjukhuset, Uppsala.

08:45Registration 08:45 – Please be seated at 09:1509:15Welcome and Introduction to Precision Medicine and Diagnostics Research AreaBasic science 1: Tumor heterogenetity and dynamics. Moderator: Sven Nelander, SciLifeLab, Uppsala University09:30Data-Driven Hallmarks (DDHMs) for Cancer Diagnostics and Precision Therapy, Olli Kallioniemi, SciLifeLab, KI09:50Precision Medicine in Head and Neck Cancer Powered through Single-cell RNA Sequencing, Michael Mints, Weizmann Institute of Science, Israel10:15Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers, Ida Larsson, Uppsala University10:35Coffee breakBasic science 2: Pushing the envelope on cancer genetics. Moderator Janne Lehtiö, SciLifeLab, KI10:55Genetic variation exposes regulators of hematopoietic stem and progenitor cells in vivo in humans, Björn Nilsson, Lund University11:15Using Evolutionary Constraint to Define Novel Candidate genes in Brain Tumors, Karin Forsberg Nilsson, Uppsala University11:35Understanding brain tumors; machine learning meets epidemiology, Beatrice Melin, Umeå University11:55Identification and exploration of toxic genes in human cancer, Veronica Rendo, Uppsala University12:15Lunch and network13:15DDLS Precision Medicine and Data Science Node, Janne Lehtiö, SciLifeLab, KI13:25Panel discussion with all the speakers. Moderator: Janne Lehtiö, SciLifeLab, KIAI, cancer, and precision medicine. Moderator: Päivi Östling, SciLifeLab, KI14:05Artificial intelligence cervical cancer diagnostics at the point-of-care, Nina Linder, Uppsala University14:25AI for Breast Cancer Risk Prediction, Fredrik Strand, KI14:45The use of artificial intelligence in gastrointestinal oncology – past, present and future, Hannah Sophie Muti, University Hospital Dresden, Germany and EKFZ Institute for Digital Health, Technical University Dresden, Germany15:10Coffee breakDDLS Fellows session. Moderator: Åsa Johansson, SciLifeLab, Uppsala University15:30Pre-malignant clonal hematopoiesis stratifies risk of hematologic cancers, Abhishek Niroula, DDLS Fellow, University of Gothenburg15:50A deep learning model of cellular networks, Avlant Nilsson, DDLS Fellow, KI16:10Closing, Sven Nelander, Uppsala University 16:15The symposium ends

Find your way to the Venue!

Event coordinator: Fulya Taylan, DDLS RA coordination and Erika Erkstam, Operations office, SciLifeLab.

Members of The Data-driven Precision Medicine & Diagnostics expert group:

Gunnar Cedersund, Linköping UniversitySven Nelander, Uppsala UniversityLars Klareskog, Karolinska InstitutetJohan Trygg, Umeå UniversityPatrik Georgii-Hemming, Karolinska InstitutetPäivi Östling, KI (adj. SciLifeLab Precision Medicine Capability lead)Francis Lee (adj. WASP-HS representative in DDLS)David Gisselsson Nord (adjunct as GMS representant)Janne Lehtiö, chair (DDLS SG member)

Abstracts

Karin Forsberg Nilsson Using Evolutionary Constraint to Define Novel Candidate Genes in Brain Tumors
Current knowledge of cancer genomics remains biased against non-coding mutations. To systematically search for regulatory non-coding mutations, we assessed mutations in conserved positions in the genome under the assumption that these are more likely to be functional than mutations in positions with low conservation. To this end, we use whole-genome sequencing data from the International Cancer Genome Consortium (ICGC) and combined it with evolutionary constraint inferred from 240 mammals, to identify genes enriched in non-coding constraint mutations (NCCMs), mutations likely to be regulatory in nature. We compare medulloblastoma (MB), which is malignant, to pilocytic astrocytoma (PA), a primarily benign tumor, and find highly different NCCM frequencies between the two, in agreement with the fact that malignant cancers tend to have more mutations. In PA, a high NCCM frequency only affects the BRAF locus, which is the most commonly mutated gene in PA. In contrast, in MB, >500 genes have high levels of NCCMs. Intriguingly, several loci with NCCMs in MB are associated with different age of onset, such as the HOXB cluster in young MB patients. NCCMs in this locus were found to alter expression of HOXB2, HOXB5 and HOXB9 in MB cells. In adult patients, NCCMs occurred in e.g. the WASF-2/AHDC1/FGR locus. One of these NCCMs led to increased expression of the SRC kinase FGR, and augmented responsiveness of MB cells to dasatinib, a SRC kinase inhibitor. Our analysis thus points to different molecular pathways in different patient groups. These newly identified putative candidate driver genes may aid in patient stratification in MB, and could be valuable for future selection of personalized treatment options.

Karin Forsberg Nilsson is Professor of Stem Cell Research at the Department of Immunology, Genetics and Pathology, Uppsala, and Dean of the Faculty of Medicine, University. She is SciLifeLab Faculty, and has a position as Guest Professor at the University of Nottingham, UK. Karin Forsberg Nilsson obtained her PhD in 1992 from Uppsala University and did a postdoc 1994-1996 at the National Institutes of Health, MD, USA. She has held leadership positions in both pharmaceutical industry and academia. The focus of her lab is brain tumor biology and genetics.

Olli Kallioniemi Data-Driven Hallmarks (DDHMs) for Cancer Diagnostics and Precision Therapy
Translating complex multi-level molecular profiling data into actionable insights for cancer diagnosis and therapy poses a formidable challenge. We propose here a paradigm for analyzing and interpreting in-depth multi-omics and functional drug response data derived from acute myeloid leukemia (AML), aiming at practical applications in precision clinical oncology. Our approach is based on Data-Driven Hallmarks (DDHMs), drawing inspiration from the Weinberg-Hanahan cancer hallmark concept (Hanahan, 2022). While the original cancer hallmark concept provides a useful theoretical framework for understanding cancer, it is not applicable for processing, interpreting, and translating molecular profiling data for precision diagnostics and therapy in individual patients.

We first acquired and integrated genomics, transcriptomics, epigenetics, and proteomics data alongside ex-vivo drug response data for over 500 drugs across 150 AML samples, resulting in nearly 100 million data points (Erkers et al., 2023). Subsequently, we identified 11 dimensions of variability across the entire dataset, referred here as DDHMs of AML. DDHMs intertwine specific multi-omics molecular features (potential diagnostic biomarkers) with distinct vulnerabilities to individual drugs (potential cancer treatments). DDHMs show proficiency in predicting high-risk AML and determining the effective drugs for each AML sample. The strategy of assembling drugs targeting active hallmarks in each patient offers a promising avenue for tailoring effective drug combinations.

In summary, we showcase the conversion of millions of complex multi-omics research data into a manageable set of DDHMs, which are based on specific biomarkers and linked drug vulnerabilities and provide an opportunity for tailoring drug treatments and drug combinations for individual patients. This approach aligns well with current practices and guidelines in translational, clinical, regulatory, and industrial setting and could expedite bringing the benefits of data-driven precision medicine research to cancer patients.

References:

Hanahan, D. (2022). Hallmarks of Cancer: New Dimensions. Cancer Discov 12, 31-46.

Erkers T, Struyf N, James T…. Orre L, Jafari R, Pawitan Y, Seashore-Ludlow B, Lehtiö J, Lehmann S, Östling P, Kallioniemi O. Data-driven hallmarks of acute myeloid leukemia, submitted, 2023.

Olli Kallioniemi, M.D., Ph.D. is director of the Science for Life Laboratory (www.SciLifeLab.se), a national infrastructure for life sciences in Sweden and also a professor in Molecular Precision Medicine at the Karolinska Institutet (2015-present). He also directs the national SciLifeLab program on Data-Driven Life Science (DDLS). Olli Kallioniemi was previously the founding director of FIMM – the Institute for Molecular Medicine Finland at the University of Helsinki, as part of the Nordic EMBL partnership in Molecular Medicine (2007-2015) Olli Kallioniemi is a member of European Molecular Biology Organization (EMBO), European Academy of Cancer Sciences, the Nobel Assembly at the Karolinska Institutet and the Royal Swedish Academy of Sciences.

Ida Larsson Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers
Nervous system cancers contain a large spectrum of transcriptional cell states, reflecting processes active during normal development, injury response and growth. However, we lack a good understanding of these states’ regulation and pharmacological importance. Here, we describe the integrated reconstruction of such cellular regulatory programs and their therapeutic targets from extensive collections of single-cell RNA sequencing data (scRNA-seq) from both tumors and developing tissues. Our method, termed single-cell Regulatory-driven Clustering (scRegClust), predicts essential kinases and transcription factors in little computational time thanks to a new efficient optimization strategy. Using this method, we analyze scRNA-seq data from both adult and childhood brain cancers to identify transcription factors and kinases that regulate distinct tumor cell states. In adult glioblastoma, our model predicts that blocking the activity of PDGFRA, DDR1, ERBB3 or SOX6, or increasing YBX1 -activity, would potentiate temozolomide treatment. We further perform an integrative study of scRNA-seq data from both cancer and the developing brain to uncover the regulation of emerging meta-modules. We find a meta-module regulated by the transcription factors SPI1 and IRF8 and link it to an immune-mediated mesenchymal-like state. Our algorithm is available as an easy-to-use R package and companion visualization tool that help uncover the regulatory programs underlying cell plasticity in cancer and other diseases.

Ida Larsson studied medical biotechnology at the Royal Institute of Technology in Stockholm and received her MScEng in 2018. She then continued as a PhD student in computational systems biology at Uppsala University, where her research has focused on the brain tumor glioblastoma and developing methods for analyzing single-cell RNA sequencing data. She defended her PhD in 2023 and is now starting as a postdoctoral fellow at Dana-Farber Cancer Institute in Boston. Her research interests revolve around intratumoral heterogeneity and plasticity in neural cancers.

Nina Linder Artificial intelligence cervical cancer diagnostics at the point-of-care
Our research group has developed and conducted proof-of-concept studies of a novel method that combines artificial intelligence (AI) and mobile digital microscopy for cell-based cervical cancer screening in resource-limited settings. The mobile microscopes are wirelessly connected via mobile networks for AI-based analysis and provide access to diagnostics where there is a lack of medical experts. We are now assessing the use of the new diagnostic method in the form of a validation studies in Kenya and Tanzania with the aim of detecting premalignant changes for the purpose of cervical cancer prevention. Cervical smears are collected at the point-of-care and digitized with mobile microscope scanners and premalignant cells detected with an AI-algorithm. Suspected abnormal cells are verified by a pathologist and treated. The method’s diagnostic accuracy, technical feasibility, cost and time per test, and acceptance of the AI method is evaluated and compared to conventional diagnostics. Throughout the project, opportunities for larger scale implementation of the diagnostic platform in East Africa are evaluated, with the ultimate goal of achieving sustainable solutions for low-resource settings.The methods have great potential to improve equitable and sustainable access to high-quality diagnostics for cervical cancer screening among women residing in low- and middle income countries, carrying the highest cervical cancer burden globally.

Nina Linder is a physician by training and received her MD and PhD from the University of Helsinki, Finland and is an Associate Professor at Uppsala University, Sweden as well the Institute for Molecular Medicine, University of Helsinki, Finland. Nina Linder’s current research involves the development of novel artificial intelligence-based solutions for cancer and infectious disease diagnostics. Linder is co-heading projects developing artificial intelligence-based tools for point-of-care diagnostics in a global setting. The overall goal of Linder’s research is to promote the implementation of innovative decision-support solutions for precision medicine to improve the translation from basic medical research to the doctor and patient at the clinic.

Beatrice Melin Understanding brain tumors; machine learning meets epidemiology
The causes of glioma, the most malignant brain tumor, is in most cases unknown. Common environmental factors such as alcohol and smoking has not been linked to brain tumors. High doses of ionizing radiation are associated with increased risk, but it explains very few cases. Therefore, one assumption could be, that glioma is an endogenous disease that is caused by a stochastic effect initiated by a complex inheritance and subsequent biological cascades leading to tumor development. To discover which biological parameters that are associated with glioma risk, several factors need to be taken in consideration. Taking glioma as an example, important factors when collecting data and samples and biostatistical considerations will be presented, giving corner stones for how we have been able to harvest and find true association through data driven analyses.

Beatrice Melin is MD, PHD and Professor of Oncology at Umeå University and Director of Research Development and Innovation at Region Västerbotten. Professor Melin has worked in the field of brain tumor research for 25 years and published on both cohort, blood tumor and registry studies.

Michael Mints Precision Medicine in Head and Neck Cancer Powered through Single-cell RNA Sequencing
Head and neck cancer (HNC) can be divided into two biologically distinct entities based on human papillomavirus (HPV) status. In HPV-negative HNC, the main challenge remains finding treatments to improve survival rates and decrease recurrence, while HPV-positive patients need better stratification methods to avoid morbidity from overtreatment. Intra-tumour heterogeneity (ITH) is a major feature in both types of HNC and a barrier to successful patient stratification and treatment. Despite its significance, ITH remains poorly understood.

We posit that HNC tumours consist of a vast, diverse ecosystem of cell types with different roles. In order to improve patient-tailored treatment, our goal is to, through single-cell RNA sequencing, characterize these populations, their biological and clinical significance and their roles in responses to various treatments.

We report firstly, the identification of a novel population of cancer cells with undetectable HPV expression in HPV+ tumours. These cells are less proliferative, more invasive and respond poorly to treatment. Validating these findings through TCGA, we found that decreased HPV expression levels are linked to poor prognosis in HPV-positive oropharyngeal cancer.

Secondly, we show that malignant cells in HPV- oral cavity cancer express antigen-presentation genes, and that expression of these genes together with an interferon signal across multiple cell types strongly predicts response to neoadjuvant PD-1 inhibition.

Finally, through collecting a dataset comprising > 120 HNC patients and one million cells, we were able to find diverse recurrent cancer cell states and microenvironmental co-expression patterns. Notably, we found a rare subset of cancer cells that undergo a full, rather than partial epithelial-mesenchymal transition (EMT). These cells are linked to depletion of CD8+ T-cells and increased numbers of fibroblasts and macrophages in the microenvironment, as well as poor outcomes.

In summary, we have created a comprehensive atlas of the HNC ecosystem at previously unseen scale and resolution. We identify rare cell populations responsible for cancer hallmarks such as senescence, proliferation and metastasis and show how subpopulations change in response to HPV infection, radiotherapy and immunotherapy. This knowledge will greatly advance personalised treatment of head and neck cancer through guiding patient stratification, drug development and treatment selection.

Michael Mints studied medicine at Karolinska Institutet through the clinician-scientist training programme. He received his MD in 2013 and his PhD in 2015 at the Department of Oncology-Pathology. After clinical work in Umeå and a physician-researcher internship in Östersund he started a postdoc in Itay Tirosh’s lab at the Weizmann Institute in 2019. There, his work focuses on leveraging single-cell RNA sequencing and computational methods in order to understand head and neck cancer heterogeneity with the goal of personalizing head and neck cancer treatment.

Hannah Sophie Muti The use of artificial intelligence in gastrointestinal oncology – past, present and future
Artificial intelligence (AI) can infer information from data in a way that exceeds human capacity to do so. Especially in clinical oncology, scientists use AI to generate biomarkers, find correlations or extract prognostic or predictive information. This talk will give you an idea of how it started, how it’s going and what the future might hold for cancer researchers in an era of paradigm-shifting technological advances.

Hannah Muti is a Clinician/Scientist with interests in precision medicine in gastrointestinal oncology and visceral surgery. Her research covers the use of artificial intelligence to investigate gastrointestinal cancers in the context of precision oncology. She simultaneously works in the Department for Visceral, Thoracic and Vascular Surgery at the University Hospital Dresden to obtain her specialization in visceral surgery.

Avlant Nilsson A deep learning model of cellular networks
The activity of human cells depends on interactions between molecules in molecular networks. Disruptions to these networks are common in disease, e.g. it can drive unrestricted growth in cancer cells. Simulations of these processes could predict disease mechanisms and identify suitable drug targets. However, these networks consist of thousands of different molecules with tens of thousands of interactions, and it has been challenging to parametrize systems-wide models using traditional approaches. We have developed recurrent neural network models of the networks that use molecules as hidden nodes with connections constrained to known molecular interactions. These models predict unseen test-data from living cells, e.g. we predict gene expression in macrophages in response to different ligands and we use the models to infer causative signaling cascades. Currently, we are expanding the framework to integrate signaling, metabolism, and gene regulation for a more complete mechanistic description of cellular activities.

Avlant Nilsson is a computational biologist and assistant professor in precision medicine at Karolinska Institutet, Stockholm. He holds a MSc (2009-2014), and a PhD (2014-2019) degree in biological engineering from Chalmers University of Technology, where his thesis focused on the metabolism of growing cells. In his postdoctoral work at Massachusetts Institute of Technology (2019-2023), he developed artificial neural network models to simulate signal transduction in immune cells. His new lab at Karolinska will be using these techniques to simulate cellular processes in cancer, aiming at identifying effective drug combinations, predicting resistance mechanisms, and understanding cell-cell interactions in the tumor microenvironment.

Björn Nilsson Genetic variation exposes regulators of hematopoietic stem and progenitor cells in vivo in humans
Stem cell transplantation is a cornerstone in the treatment of blood malignancies. The most common method to harvest stem cells for transplantation is by leukapheresis, requiring mobilization of CD34+ hematopoietic stem and progenitor cells (HSPCs) from the bone marrow into the blood. Identifying the genetic factors that control blood CD34+ cell levels could reveal new drug targets for HSPC mobilization. Here we report the first large-scale, genome-wide association study on blood CD34+ cell levels. Across 13 167 individuals, we identify 9 significant and 2 suggestive associations, accounted for by 8 loci (PPM1H, CXCR4, ENO1-RERE, ITGA9, ARHGAP45, CEBPA, TERT, and MYC). Notably, 4 of the identified associations map to CXCR4, showing that bona fide regulators of blood CD34+ cell levels can be identified through genetic variation. Further, the most significant association maps to PPM1H, encoding a serine/threonine phosphatase never previously implicated in HSPC biology. PPM1H is expressed in HSPCs, and the allele that confers higher blood CD34+ cell levels downregulates PPM1H. Through functional fine-mapping, we find that this downregulation is caused by the variant rs772557-A, which abrogates an MYB transcription factor-binding site in PPM1H intron 1 that is active in specific HSPC subpopulations, including hematopoietic stem cells, and interacts with the promoter by chromatin looping. Furthermore, PPM1H knockdown increases the proportion of CD34+ and CD34+90+ cells in cord blood assays. Our results provide the first large-scale analysis of the genetic architecture of blood CD34+ cell levels and warrant further investigation of PPM1H as a potential inhibition target for stem cell mobilization.

Abhishek Niroula Pre-malignant clonal hematopoiesis stratifies risk of hematologic cancers
Clonal hematopoiesis (CH) is a pre-malignant condition characterized by the expansion of genetically distinct blood cell clones in healthy individuals. CH with cancer driver variations is common in the elderly population and is associated with a 10-fold higher risk of blood cancer. A number of genes recurrently mutated in CH are known (e.g., DNMT3A, TET2, and ASXL1); however, these gene variants only account for <30% of CH clones in elderly individuals. To identify new genetic drivers of CH, we analyzed exome sequencing data from peripheral blood samples of >50,000 individuals. We identified CH with genetic variants in several genes previously not linked to CH. Further, we grouped CH into myeloid and lymphoid based on the mutated genes, which stratified the risk of incident myeloid and lymphoid malignancies. Integrating the genetic data with clinical measurements allowed identification of individuals at high risk of developing hematologic malignancies. Currently, we are developing methods to analyze somatic variants across the whole genome to characterize CH and identify new genetic regulators of CH.

I am a DDLS Fellow in precision medicine and diagnostics at the University of Gothenburg. I obtained my PhD from Lund University and did a postdoc at the Broad Institute, Cambridge MA. My research background is on bioinformatics and human genomics, focusing on the effects of genetic variants in human diseases including cancer. As a DDLS Fellow, my research focuses on the study of clonal hematopoiesis (CH), a pre-cancer of blood. We utilize large-scale genomic data from population cohorts to understand the origin and evolution of CH and its malignant transformation.

Veronica Rendo Identification and exploration of toxic genes in human cancer
Chromosomal gains are one of the most common somatic genetic alterations found in cancer. While the impact of sustained oncogene expression has been extensively studied, the effects of copy number gains on “bystander” genes, which are collaterally amplified, remain less understood in terms of cellular fitness. To shed light on this, we integrated the expression and copy number profiles of over 8,000 TCGA tumors and CCLE cell lines, along with the viability effect of gene overexpression from 17 human cancer ORF screens. Through this comprehensive and data-driven analysis, we identified a group of genes termed ‘Amplification-Related Gain Of Sensitivity’ (ARGOS) genes. ARGOS genes are situated in frequently amplified regions of the genome, and their expression level is reduced compared to their copy number status. However, when overexpressed upon gain, they prove to be toxic to the cell. Our compensation and toxicity analyses revealed five frequently amplified ARGOS genes. Notably, one candidate showed a mechanism of toxicity involving altered DNA damage and innate immune signaling responses upon gene overexpression. This study represents a significant effort to better understand the toxicity effects associated with gene overexpression in human cancers.

Veronica studied Biology at Simon Bolivar University in Venezuela, and then moved to Sweden to pursue a PhD at Uppsala University. During this time, she worked under the mentorship of Prof. Tobias Sjoblom and studied how genomic losses occurring in colorectal cancer can be exploited for therapy. In 2019, she moved to Boston (USA) to pursue a postdoc in Dr. Rameen Beroukhim’s lab at Dana-Farber Cancer Institute, affiliated with Harvard Medical School and the Broad Instititute of MIT and Harvard. Veronica’s research focused on studying therapeutic vulnerabilities associated with aneuploidy, including predictors of resistance to clinically relevant p53 reactivation strategies in brain tumors and negative selection against amplifications in cancer. In 2023, Veronica left the Beroukhim lab to start her own laboratory at the Department of Immunology, Genetics and Pathology at Uppsala University. Here, she combines descriptive and functional genomic approaches to understand how brain tumors respond and evolve during treatment. This includes continued exploration of how aneuploidy creates vulnerabilities that can be therapeutically exploited.

Fredrik Strand AI for Breast Cancer Risk Prediction
Among women attending screening, 30% of their cancer is missed by current mammography-based screening. We have trained AI models to assess specific aspects of the mammography images to measure when a negative exam is less reliable. After retrospective validation we are conducting a randomized clinical trial selecting around 7% of women from screening to be offered MRI.

Fredrik Strand is a Swedish breast radiologist and associate professor at Karolinska Institutet, Stockholm. He holds an MD, PhD and MSc degrees, and has prior experience as a strategy consultant and leading a start-up company. Fredrik is head of the research and education committee at the Swedish society of breast imaging. His academic research evolves around exploring AI for breast imaging. He and his team are involved in retrospective validation of AI algorithms, prospective clinical trials, and in developing new machine-learning algorithms for breast cancer detection and supplemental MRI imaging.

Spatial Biology Symposium. From the Facilities to the user
2023-09-07 09:00 - 14:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Spatially resolved omics technologies (to visualize biomolecules within intact tissue specimens) have emerged during the last years. The Spatial Biology platform covers cutting-edge technologies for spatial profiling of transcripts, proteins, DNA, and small molecules. Learn more about the services and capabilities that are offered from Spatial Biology Platform. Meet with researchers and national infrastructures experts from Spatial Transcriptomics, In Situ Sequencing, Spatial proteomics and Spatial Mass Spectrometry unit . Learn about our technologies and how other users have used to reach their goals. 10 of you will have the opportunity to visit our facilities and see the cutting-edge equipment, meet the facility staff and discuss your potential projects.

Program

09:00Registration09:10Spatial Biology overviewCharlotte Stadler09:30Spatial TranscriptomicsAnja Mezger09:50In situ sequencingKatarina Tiklova10:30Spatial ProteomicsCharlotte Stadler10:50Spatial Mass SpectrometryAnna Nilsson11:10User presentationSpatial Multimodal Analysis of Transcriptomes and Metabolomes in TissuesMarco Vicari11:30Lunch & mingle12:30Visit to Lab facilities4 groups with 5 persons max12:45Visit to Lab facilities4 groups with 5 persons max

Registration

Campus Solna Seminar Series: Fitz Gerald Silao & Michael Hawgood
2023-09-07 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 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

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

This week:

Fitz Gerald Silao

Per Ljungdahl – alpha 3

An acid-test of alkalization: Diverse mechanisms control amino acid-dependent environmental alkalization in Candida albicans

Michael Hawgood

Bennie Lemmens – alpha 5

Investigating novel inhibitors on genome instability

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

Modelling life science data in big pharma, academia, and startups
2023-09-08 10:00 - 11:00 | Online event via Zoom
Join the NEW event series arranged by the SciLifeLab Data Centre focused on tools for AI/ML research in life sciences.

Title: Modelling life science data in big pharma, academia, and startups – Differences, Examples, and Some Learnings

Speaker: Andreas Bender, Professor of Molecular Informatics, University of Cambridge

Where and when: September 8, 2023 at 10:00-11:00 Stockholm time, online. Registration is open till Sept 7 at 24.00.

Abstract: Life science data, modelling methods, and organizational environments in which they are implemented vary widely – from big pharma, to academia, and start-up environments (and beyond). This presentation will partly cover science and modelling, but there will be an additional focus on the differences between the above environments (all of which the presenter has worked in), and how they influence the approaches, as well as the eventual result and product to be delivered.

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

Overview of compute and storage resources in data-driven life science
2023-09-08 11:00 - 12:00
Compute and storage resources available to the life science field in Sweden are provided by several different organisations. SciLifeLab and the DDLS program are in various ways providing access to infrastructure, new data services, and support to existing ones. We work towards improved coordination and accessibility.

At this event on September 8, representatives for SciLifeLab Data Centre, National Bioinformatics Infrastructure Sweden (NBIS), National Academic Infrastructure for Supercomputing in Sweden (NAISS) and National Supercomputer Centre at Linköping University (NSC) will give an overview of who does what and how to access different services, and how to interact regarding input, feedback or suggested new services. There will also be time for a Q & A.

Agenda

11:00-11.05 Introduction, Johan Rung

11:05-11:15 Overview of SciLifeLab resources, Jonas Svensson, Liane Hughes, Konstantin Dossis

11:15-11:25 Overview of NAISS resources, Johan Raber

11:25-11:35 Overview of NSC resources (Berzelius) Soumi Chaki, Xuan Gu

11:35-11:45 Overview of NBIS & UPPMAX resources, Marcus Lundberg

11.45.-11:50 Summary

11:50-12:00 Q & A- ways of working

12:00-12.30 For follow-up questions in four breakout rooms: SciLifeLab, NBIS-UPPMAX, NAISS, or NSC.

Date: Sept 8, 11:00-12:00 CEST on Zoom, followed by 30 min break-out rooms for additional questions to the respresentatives from SciLifeLab, NBIS-UPPMAX, NAISS, and NSC.

Target group: Researchers, research staff and others interested in compute and storage resources in life science.

Register here

Welcome!

For questions about the event please contact SciLifeLab Data Centre on email datacentre@scilifelab.se For more information about services for data-driven life science research see SciLifeLab Data Platform

ELIXIR-GOBLET Train-the-Trainer
2023-09-13 08:00 - 2023-09-15 17:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
Course Content

This course offers guidance, ideas and tips for designing training/teaching, development and delivery on training activities, all based on research-driven educational principles. This course will cover 4 main topics:

Learning principles and how they apply to training and teaching

Design and plan session, course, materials

Teaching techniques to enhance learner engagement and participation

Assessment and feedback in training and teaching

This course will be delivered through Canvas learning management system. You can find a link to the course pages here.

Note! The course is highly interactive and hence it is important that you, as a participant, actively contribute to all sessions and elements of the course.

Important dates and information

Application opens: 2023-04-21

Application closes: 2023-08-21

Confirmation to accepted students: 2023-08-25

Course Leaders and teachers: Jessica Lindvall and Nina Norgren

In case you miss information on any of the above dates, please contact: Nina Norgren (traininghub@scilifelab.se)

COURSE WEBSITE AND PROGRAM

REGISTRATION

Learning Objectives

To get acquainted with Learning principles and how they apply to training

To be able to select and use training techniques that can help enhance learner engagement and participation

To learn how to use assessment and feedback in training

To learn about session, course, and materials design

Learning Outcomes

By the end of this course, learners will be able to:

Name learning principles that a good teacher/instructor should have in mind

Describe at least three training techniques, drawing on learning principles

Design a training session and a course

Develop assessment questionnaires

Enumerate types of materials needed for each part of a training session or course

Entry requirements

Whoever is interested in becoming a trainer/instructor, or improving your training skills. If you have questions like the following ones, this course may be very helpful to you.

How learning works?

How do I use learning principles and theories to improve my teaching/training?

How do I make my teaching/training more engaging and effective?

How should I adjust my teaching/training to different types of learners?

How do I ensure learning progress?

How can I assess whether my students are actually understanding my lessons? Are they actually learning?

What is the best balance between theory and practice?

How can I best assess whether learning is occurring and/or has occurred?

What works in a classroom and what doesn’t?

Due to limited space the course can accommodate a maximum of 25 participants. If we receive more applications, participants will be selected based on selection criteria: Priority will be given to applicants from SciLifeLab infrastructures, institutes and organisations across the Nordic research community, and to participants from Nordic ELIXIR nodes.

Course fee

A course fee* of 2000 SEK will be invoiced to accepted participants. The fee includes lunches, coffee and fikas, and a course dinner.

*Please note that NBIS cannot invoice individuals

Note! If you are accepted and decide not to attend without communicating the reason for the no-show with us latest on the 8th of September, we will invoice a no-show-fee of 2000 SEK.

The invoicing information needs to be included in the registration in order to guarantee your spot in the training event, if you are to be accepted. By giving the invoice information you hereby confirm that the group leader/PI/manager has given a consent regarding your possible participation in the Training event.

Beyond pharmacological inhibition of DNA repair
2023-09-14 08:00 - 17:00 | Atrium, Karolinska Institutet, Nobels väg 12, Solna, Sweden
A Mini-Symposium dedicated to the boosting and reprogramming of DNA repair as a novel technology and its implications in the treatment of human disease.Come and learn more about exciting opportunities in modulating DNA repair, discuss with experts and enjoy a classic swedish Fika.

registration for on-site participation

registration for on-line participation

InvitationDownload

Campus Solna Seminar Series: Christian Sommerauer & Robin Ebbestad
2023-09-14 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 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

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

This week:

Christian Sommerauer

Claudia Kutter – gamma 5

Estrogen receptor activation remodels TEAD1 gene expression to alleviate nonalcoholic fatty liver disease

Robin Ebbestad

Hjalmar Brismar – gamma 3

High-resolution imaging and deep learning-based segmentation of glomerular pathologies in the kidney

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

Epigenomics Data Analysis: from Bulk to Single Cell (ONLINE)
2023-09-18 08:00 - 2023-09-22 17:00 | Online event via Zoom
National workshop open for PhD students, postdocs, researchers and other employees within Swedish academia. This course is run by the National Bioinformatics Infrastructure Sweden (NBIS).

Important dates

Application opens: now

Application closes: 2023-09-04

Confirmation to accepted students: 2023-09-08

Responsible teachers

Agata Smialowska, Jakub Orzechowski Westholm, Vincent van Hoef

Please contact edu.epigenomics@nbis.se for course specific questions

Application

Course website

Workshop fee

This online training event has no fee. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2000 SEK.

*Please note that NBIS cannot invoice individuals.

Workshop content

This workshop aims to introduce the best practice bioinformatics methods for processing, analyses, visualisation and integration of epigenomics and functional genomics data.

Topics covered include:

Data processing and analyses for differential DNA methylation with Illumina EPIC arrays and Bisulfite-seq;

ChIP-seq: peak calling, peak independent / dependent quality metrics, differential binding analysis; DNA motif enrichment;

ATAC-seq: peak calling, peak independent / dependent quality metrics, differential accessibility analysis;

Quantitative ChIP-seq using spike-ins;

CUT&Tag / CUT&RUN: Novel methods to investigate protein-chromatin interactions;

Functional analysis, including finding nearest genes and custom features, GO terms and Reactome pathways enrichment;

Basic multi-omics exploration and integration;

Visualisations of epigenomics datasets;

Introduction to analysis of single cell functional genomics data (scATAC-seq);

Introduction to nf-core pipelines for processing and analysis of epi- and functional genomics data : Methylseq, ChIP-seq, ATAC-seq.

Entry requirements

Required for being able to follow the workshop and complete the computer exercises:

BYOL, bring your own laptop with R and RStudio installed;

Basic knowledge in Linux;

Basic programming experience, preferably in R.

Desirable

Experience working on the SNIC center Uppmax or another HPC. We encourage participants to run the linked Uppmax tutorial before the workshop;

Previous experience with NGS data analyses;

Completing NBIS workshops “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists” or equivalent.

Due to limited capacity the workshop can accommodate maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance.

Please note that NBIS training events do not provide any formal university credits.

This training content is estimated to correspond to a 1.5 HPs, however the estimated credits are just guidelines. If formal credits are crucial, participants need to confer with the home department whether the course is valid for formal credits.

[The Svedberg seminar] - Female sex hormones and the human microbiome
2023-09-18 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Luisa Hugerth

Assistant ProfessorDDLS FellowDepartment of Medical Biochemistry and Microbiology, UU

Bio

Luisa Hugerth has a background in molecular biology and biomedicine, but got her PhD in 2016 at KTH Royal Institute of Technology with an analysis of microbial community time-series in the Baltic Sea. After that, Dr. Hugerth spent 6 years at the Centre for Translational Microbiome Research in Karolinska Institutet, where she studied the human microbiome in functional bowel disorders, before becoming deeply involved in research on the microbiome of pregnant and non-pregnant women. Since 2022, she is a DDLS fellow in epidemiology and biology of infection at Uppsala University’s Department of Medical Biochemistry and Microbiology, Imbim

Female sex hormones and the human microbiome

Estrogen and progesterone have pleitropic effects throughout the body. This includes mucosal surfaces and the diverse microbial communities that inhabit them. Microbiota can enhance or dampen these effects, thereby acting as risk mediating factors for various diseases, most notably gynecologic and periodontal inflammation. The vaginal microbiota has been epidemiologically linked to various outcomes, from STI acquisition to preterm birth. The oral microbiota has also been causally linked to as disparate outcomes as preterm birth and newly onset depression. Here, I will present ongoing work on the interplay between endogenous and exhogenous hormones on the oral, vaginal and gut microbiome, in women with a regular menstrual cycle as well as pregnant women. Additionally, since both sex hormones and the gut microbiome are implicated in mood disorders, I will touch upon the gut-brain axis in relation to pregnancy nausea and perinatal depression.

Host: Mikael Sellin mikael.sellin@imbim.uu.se, UU

Neurodiversity in communication, relationships, academia & life
2023-09-19 14:00 - 14:30 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
We are excited to host a new Coaching in Science Initiative (CSI) Seminar titled:
‘Neurodiversity in communication, relationships, academia & life’

Neurodiversity; to be outside of the category of people who are considered cognitive ‘normal’. But what is ‘normal’ really? And how broadly can we extend the concept of neurodiversity? On a personal level, perhaps it is more helpful to ask ourselves, what neurodiverse traits do I have in general, or in this particular group of people? Could they be different depending on whom I’m socializing with at work and at home?

Applying the CSI coaching model and our core values, we will explore who we are in relation to others, raise awareness of how we are different, learn more about the biology behind our emotional regulation and what to do when we find ourselves in difficult social interactions.

Date: 19/9/2023
Time: 14:00
On-site location: Gamma 2 lunch room
Zoom link: https://kth-se.zoom.us/j/65001858940

We will begin with a 15-20 min talk, held in Solna and over zoom. Then proceed with a reflection and discussion held only on-site. We encourage other sites to form watch parties, by listening in together to the talk and then hold their own discussion afterwards. Hopefully seeding many local chapters of CSI.

To help facilitate discussion and reflection, consider the follow starter questions:
Awareness: where do we experience neurodiversity in our lives already?
Analysis: how well do I currently interact with neurodiversity?
Alternative: how can we relate to neurodiversity, in ourselves and others?
Action: how will knowledge of neurodiversity change my decisions going forward?

SciLifeLab Science Summit 2023
2023-09-20 09:00 - 17:00 | Aula Magna, Frescativägen 6, Stockholm, 114 18 Stockholm, Sweden
Genomics of Biodiversity and Evolution

In an era characterized by extinction and habitat loss, it is crucial to explore biological diversity on our planet and understand the evolutionary processes that generate it. Genome sequencing has generated numerous insights into how species form and how they adapt to their environments, which is vital to understand in a changing world. As sequencing technologies improve and become less expensive it becomes feasible to produce high-quality genome assemblies and analyze genetic diversity in a huge number of species, which has led to a number of ambitious projects including the Earth BioGenome Project to sequence all known Eukaryotes.

Swedish scientists and SciLifeLab are at the forefront of this field, with genome projects including spruce, herring, Arctic fox and 240 mammals, advancing knowledge of topics including population genetics, adaptation, speciation, convergent evolution, and functional constraint.

In this SciLifeLab Science Summit, we have gathered several leading researchers who use genomics to learn about the diversity of life!

We invite you to Stockholm and Aula Magna for a full-day conference program with ample time for discussions, mingling, and networking.

This event is open to anyone interested in the topic and is free of charge.

Registration closed If you are interested in participating, please send an email to events@scilifelab.se.

Poster session, Flash Talk & Best Poster Award

Registration opens at 08:45. Please hang your poster on the poster boards upon arrival and in time before the Conference starts at 09:30. Pins are available. There are two poster sessions. Please remove your poster from the poster board after the second session or at 17:00. Any remaining posters after 17:15 will be discarded. The Scientific Committee´s Poster jury will nominate the Science Summit 2023 Best Poster and award the winner a 5 000 SEK Travel Grant. You must stay for the prize ceremony at the end of the conference.

SciLifeLab Science Summit 2023 Poster ListDownload

Four (4) submitted poster abstracts will be selected for Flash Talks à 5 minutes on stage.

The selected Flash Talks speakers are

Cynthia Perez Estrada. Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

Patrik Rödin Mörch. The Role of Population History in Shaping the Mutational Load of Structural Variants Relative to SNPs, in Distinct Island versus Continental Lagopus Lineages

Andreas Wallberg. New insights into the evolutionary history and adaptive potential of World Ocean krill using comparative population transcriptomics

Qiaoling Deng. Genetic parallelism and adaptation to brackish water bodies in sprat (Sprattus sprattus) and Atlantic herring (Clupea harengus)

Important dates

Sept 1. Registration deadline for posters! Poster submission closes, and the selection of Flash Talks will be made.

Sept 4. Poster submission approval email.

Sept 11. Invitation email to selected Flash talk speakers.

Sept 11 at 12:00. Registration for the SciLifeLab Science Summit closes

Sept 11. Poster Abstracts published as a PDF on the website

Free bus transportation

We offer free bus transportation from Uppsala (BMC Campus) at 08:00 to Aula Magna, (SU Campus Frescati) in the morning and back after the Conference at 17:00 and after the mingle at 18:30. Reserve your seat when filling in the registration form.

Satellite Symposium:Computational Methods in Evolution and Biodiversity

On September 21, the Data-Driven Life Science Expert group invites you to a full-day satellite symposium and workshop, “Computational Methods in Evolution and Biodiversity“

Read more

Speakers

Leif Andersson, Uppsala University, SWE

Richard Durbin, Wellcome Sanger Institute, UK

Tom Gilbert, University of Copenhagen, DK

Elinor Karlsson, University of Massachusetts Medical School & Broad Institute, USA

Karin Norén, Stockholm University, SWE

Karin Rengefors, Lund University, SWE

Tanja Slotte, Stockholm University, SWE

Tom van der Valk, Swedish Museum of Natural History, SWE

Please, see the abstracts below the Program

Program

Program Science Summit 2023Download

08:00Bus from BMC Uppsala to Aula Magna08:45Registration and coffee, hanging posters09:30Welcome WordsYlva Engström, Chair of the SciLifeLab BoardIntroduction to the ConferenceKerstin Lindblad-Toh, Chair of the Scientific CommitteeSession I: Moderator Kerstin Lindblad-Toh09:45Investigating mammalian evolution and human disease through comparative genomics in hundreds of speciesElinor Karlsson, UMass Chan Medical School and Broad Institute, USA10:15A Million-Year-Old Journey: Exploring Mammoth Speciation and Adaptive Evolution through timeTom van der Valk, Swedish Museum of Natural History10:40Coffee break and Poster session ISession II: Moderator Leif Andersson11:20Insights from high quality genome sequencing across the tree of lifeRichard Durbin, University of Cambridge, UK11:55Conservation genomics of the Scandinavian Arctic foxKarin Norén, Stockholm University12:20Lunch break and mingle, exhibitionsSession III: Moderator Love Dalén13:40Domestication hologenomics – what are we missing without taking this approach?Tom Gilbert, University of Copenhagen, DK14:15Sequencing the supergene that governs Darwin’s different forms of flowersTanja Slotte, Stockholm University14:40Flash Talks from Junior researchers (selected from submitted abstracts) 5-minute talk/researcher15:05Coffee break and Poster session IISession IV: Moderator Matthew Webster15:45The remarkable population structure of Atlantic and Baltic herring – selection, selection, selectionLeif Andersson, Uppsala University16:20Why cyanobacterial blooms produce toxins – unravelling the underlying genetic diversity in the microcystin gene clusterKarin Rengefors, Lund University16:45Best Poster Award ceremonyClosing words17:00End of ConferenceMeet the speakers and mingle; snacks and free beveragesBus to Uppsala departs at 17:00 and at 18:30

Speaker abstracts

Science Summit speaker abstracts 2023Download

Abstract Leif Andersson – The remarkable population structure of Atlantic and Baltic herring – selection, selection, selection
Initial genetic studies with a handful of neutral markers revealed no genetic differentiation among populations of Atlantic herring, not even between Atlantic and Baltic herring classified as distinct subspecies by Linnaeus. Whole genome sequencing has totally changed the picture. Atlantic herring can now be divided into many subpopulations (ecotypes). It is an adaptive radiation with incomplete reproductive isolation between ecotypes. We find strong genetic differentiation at loci under selection but minute genetic differentiation at neutral loci. The explanation for this is the huge population sizes minimizing drift, high fecundity allowing effective selection, a homing behavior but with gene flow. Herring is a broadcast spawner and it is probably no strong selection for prezygotic reproductive isolation. Ecological adaptation in Atlantic herring is related to a diversity of environmental conditions including salinity, temperature and light conditions as well as behavioral traits such as timing of reproduction and migration. Recently we used SNP-chip analysis to explore the population structure of Baltic herring in the Bothnian Sea. This analysis revealed two major subgroups: spring- and autumn-spawning Baltic herring. However, a third genetically distinct population was present among the spring-spawners. This ecotype had a three-fold larger body size than other populations spawning in the same area at the same time implying a marked difference in feeding behavior. This illustrates the adaptive differentiation occurring in the herring. The results have important implications for fishery management of the herring in the Baltic Sea and elsewhere.

Dr. Leif Andersson is a specialist in genetics and genome biology. He and his group have made ground-breaking studies on the relationship between genetic and phenotypic variation. He has been working on comparative genomics using domestic animals as models for phenotypic evolution. This has resulted in discoveries of genotype-phenotype relationships such as mutations affecting pigmentation, gaits in horses, comb morphology in chickens and muscle growth in pigs. He has also studied the genetic basis for domestication of rabbits, chickens and pigs. The research program has been expanded to natural populations as exemplified by studies of the evolution of Darwin’s finches and their beaks, a supergene controlling male mating strategies in the ruff and genetic basis of ecological adaptation in Atlantic herring. Leif Andersson is professor in Functional Genomics at Uppsala University and in Animal Genomics at Texas A&M University. He was awarded the Wolf prize in Agriculture 2014.

Abstract Richard Durbin – Insights from high quality genome sequencing across the tree of life
I will discuss progress in scaling up the generation of high quality reference genome sequences, and some of the insights that we have obtained from them. Using high accuracy PacBio CCS reads and paired end Illumina Hi-C data we are now obtaining essentially complete, high contiguity chromosomal assemblies at an increasing rate and decreasing cost, with more than a thousand assemblies completed within the Tree of Life programme at the Wellcome Sanger Institute. Because in most cases even heterochromatic repeat DNA is well assembled, we have been able to characterise turnover of centromere-associated repeates which are some of the most rapidly evolving seqence in the genome, observing repeated transitions in plants between satellite tandem repeats and transposon cluster patterns. Furthermore, by selection of very high confidence bases from the individual CCS sequencing reads, we are able to identify signatures of somatic mutations across a very wide range of species, suggesting previously unobserved mutational processes.

Richard Durbin works in computational genomics. He has been leader or co-leader of multiple large collaborative projects, including the 1000 Genomes Project, and more recently has worked on genome assembly and contributed to the Vertebrate Genomes Project and the Earth Biogenome Project. He has also introduced multiple bioinformatic methods and data structures, including bwa for read mapping and the BAM format for genomic data, and worked on evolutionary genomics in non-model vertebrate systems, and understanding human history from ancient and modern DNA data. Richard is a Fellow of the Royal Society of London (2004), a Member of EMBO (2009) and a Foreign Member of the American Academy of Arts and Sciences (2019).

Abstract Tom Gilbert – Domestication hologenomics – what are we missing without taking this approach?
Analyses that compare the genomes of contemporary domestic animals and plants with those of their wild relatives have provided a wealth of insights into not only when and where our ancestors started the process, but also what specific genetic variants are key to modern phenotypes. Furthermore, once coupled to palaeogenomic data, such datasets can also even reveal the order in which such variants arose, shedding further insights into the process itself. However while there is no doubt that we have learnt much about domestication in general, and indeed for most domestic species we can clearly document the genetic basis of why the end product differs from the start, I argue that there may be certain processes that were involved that have been largely overlooked, in particular related to the so-called hologenome.

Tom Gilbert is Professor of Palaeogenomics at the University of Copenhagen, Professor II at NTNU University Museum, and Director of the DNRF Center for Evolutionary Hologenomics. He holds a PhD in the study of ancient DNA from the University of Oxford, and has been active in both trying to develop methods to both expand the potential of ancient DNA to our understanding of the past, as well as more recently leading research aimed at revisiting our understanding of ecological and evolutionary processes using hologenomic techniques – ie the integrative approach of combining host genomes with those of their microbiome.

Abstract Elinor Karlsson – Investigating mammalian evolution and human disease through comparative genomics in hundreds of species
A major challenge in genomics is discerning which bases among billions alter organismal phenotypes and affect health and disease risk. The Zoonomia project compared 240 different placental mammal species to detect which individual bases in the genome are exceptionally conserved (constrained) and likely to be functionally important. Eighty percent of the most constrained bases are outside protein-coding exons, and half have no functional annotations in the ENCODE project. By pairing Zoonomia’s genomic resources with phenotype annotations, we find genomic elements associated with phenotypes that differ between species, including olfaction, hibernation, brain size, and vocal learning. Comparative genomics is advancing human health today by identifying functionally important in both coding and noncoding regions. Exploring the genomic basis of phenotype diversity that has emerged across 100 millions of years of placental mammal evolution is a powerful tool for discovering the next generation of biotechnological advances.

Elinor Karlsson, PhD, is associate professor in Bioinformatics and Integrative Biology at the UMass Chan Medical School, and director of Vertebrate Genomics at the Broad Institute of MIT and Harvard. Her research combines new technology, community science and genomics to investigate diseases and discover the origins of exceptional mammalian traits. Dr. Karlsson’s research includes the Zoonomia project, an international effort to compare the genomes of over 240 mammals (from the African Yellow-spotted Rock Hyrax to the Woodland Dormouse), to identify segments of DNA that are important for survival and health. Dr. Karlsson has a special interest in dog and wolf genetics, and her international Darwin’s Ark project invites all dog owners to enroll their dogs in an open data research project exploring the genetic basis of behavior, as well as diseases such as cancer.

Elinor received her B.A. in biochemistry/cell biology and her B.F.A. (Bachelor of Fine Arts) from Rice University, and earned her Ph.D. in bioinformatics from Boston University. She was a postdoctoral fellow with Pardis Sabeti at Harvard University before starting her research group at UMass Chan in 2014.

Abstract Karin Norén – Conservation genomics of the Scandinavian Arctic fox
Over the past decade, whole genome sequencing has generated important insights about key processes in conservation genetics, e.g. inbreeding depression, genomic erosion and genetic rescue in small and threatened populations. The Scandinavian Arctic fox (Vulpes lagopus) was on the verge of extinction in the late 1990s. In response to efficient conservation actions, the population has increased, but studies have documented that the bottleneck, geographic fragmentation and long-term low population size resulted inbreeding depression and loss of genetic variation. To explore the dynamics of inbreeding, accumulation of deleterious genetic variation and genetic rescue, we assembled a draft reference genome and resequencing data of >80 complete Arctic fox genomes. We found alternating levels of genomic inbreeding and a short-term genetic rescue effect, operating over different time scales. An immigration event resulted in an increased mutational load where immigrant offspring displayed higher proportion of loss of function mutations compared to native individuals. Further, we established a link between deleterious genetic variation and individual fitness. The results from these studies play a fundamental role for making informed decisions in conservation of this particular population, but also make important contributions for conservation of other small and threatened populations and species.

Karin Norén is a researcher and docent in animal ecology at Department of Zoology, Stockholm University. She received a PhD from Stockholm University in 2011. Thereafter, she spent three years as a post-doctoral researcher at University of California, Davis. She is currently a PI in the Swedish Arctic Fox Project and her research is focused on conservation genomics, especially in carnivores, and genetic processes in fluctuating populations in northern ecosystems.

Abstract Karin Rengefors – Why cyanobacterial blooms produce toxins – unravelling the underlying genetic diversity in the microcystin gene cluster
Cyanobacterial blooms are a global threat to freshwater ecosystems since they produce cyanotoxins that are poisonous to humans, wildlife, and livestock. Microcystin is the most common and toxic among the cyanotoxins and induces liver failure and tumor promotion in mammals. However, its function in cyanobacteria is still contested. In Microcystis spp., the most common microcystin-producing genus, microcystin-producing and non microcystin-producing strains co-exist within populations. Moreover the proportions of the strain types vary in time and space. Microcystin is biosynthesized by the constitutively expressed mcy gene cluster consisting of ten modular genes (mcyA-J). Previous studies have suggested that non-producers lack the entire cluster. In the field, toxigenic strains are quantified using quantitative PCR targeting one of the genes in the microcystin gene cluster (usually mcyB or E). However, the number of gene copies are not always correlated with microcystin in the water. To better understand the underlying genotypes of microcystin producers and non-producers we sequenced the genomes of strains of Microcystis isolated from a single bloom. At the same time, the strains were phenotyped to determine microcystin variants. Unexpectedly, non microcystin-producing strains displayed a range of genotypes yet with a common pattern of mostly lacking mcyF, G, and J. Other genes in the cluster were either present or had partial hits against our custom-made microcystin gene database. We suggest that non microcystin-producing Microcystis are genotypically and phenotypically diverse and that genotype composition varies among populations. I will also discuss potential causes of mcy gene-loss and the way forward to unravel the function of microcystin.

Dr. Karin Rengefors is a professor of limnology at the Biology Department of Lund University, and her research interest is on phytoplankton ecology and evolution, with focus on freshwater harmful algal blooms. Currently her research group focuses on understanding the population dynamics and genetic diversity of toxin-producing cyanobacteria. Another research topic is investigating the processes underlying population differentiation and speciation in phytoplankton. Dr. Rengefors also has a strong interest in doctoral education and took the lead in developing and running GENECO, the Graduate Research School in Genomic Ecology at Lund university 2008-2013. For this work she was awarded the Lund University Pedagogical prize in 2012. She has also been a co-director of the internationally renowned Workshop on Genomics in Cesky Krumlow. Dr. Rengefors did her BSc as well as her PhD at Uppsala University, followed by two years postdoc at the Woods Hole Oceanographic Institution, USA. In 2001, she landed an Assistant Professorship at Lund University, and in 2005 a University Lecturer position. She was promoted full professor in 2008, thus becoming the first female professor in limnology in Sweden.

Abstract Tanja Slotte – Sequencing the supergene that governs Darwin’s different forms of flowers
Supergenes are genomic regions containing sets of tightly linked genes that control multi-trait phenotypic polymorphisms. Although supergenes are responsible for a wide variety of balanced polymorphisms in nature, our understanding of the origins and evolution of supergenes remains incomplete. We aim to fully characterize and study evolutionary processes at one of the first described supergenes, the S-locus that governs a floral polymorphism called distyly. We are doing so in Linum, wild flaxseed species, a system where Darwin himself described this floral polymorphism, but where its genetic basis remained unknown. To generate a genomic framework for the study of distyly, we assembled high-quality genomes of a diverse set of Linum species. We then identified the distyly supergene and showed that it harbors indel variation and not inversions, which is typical for many other supergenes. Our results have important implications for the evolution and breakdown of distyly supergenes, and shed light on the genetic architecture and evolution of the classic supergene that governs Darwin’s “different forms of flowers”.

Tanja Slotte is a professor in the Department of Ecology, Environment and Plant Sciences at Stockholm University. Her group works on the evolution of supergenes and plant mating systems primarily using evolutionary genomic analyses. A population geneticist by training, she received her PhD from Uppsala University, followed by a postdoc at the University of Toronto, Canada before starting her own group at Uppsala University. In 2014 she moved to Stockholm University to take up a SciLifeLab Fellow position and since 2022 she is Professor in Ecological Genomics at Stockholm University.

Abstract Tom van der Valk – A Million-Year-Old Journey: Exploring Mammoth Speciation and Adaptive Evolution through time
In this presentation, I will share our efforts over the past years in recovering genome-wide data from woolly mammoths and discuss how the genomic insights have advanced our understanding of evolutionary processes such as speciation and long-term adaptive evolution. Our research involved sequencing specimens from the Early and Middle Pleistocene subepochs, including some of the last surviving woolly mammoths. This work led to the identification of a previously unknown mammoth lineage, evidence of hybridization between different mammoth species, and the finding that most protein-coding changes linked to cold adaptation in woolly mammoths were already present one million years ago. I will show that the woolly mammoths had acquired a diverse array of positively selected genes associated with among others hair and skin development and fat storage at the time of its origin. Our research also identified genes that underwent recent positive selection, including those related to skeletal morphology, body size, and a gene potentially responsible for the small ear size observed in Late Quaternary woolly mammoths. Overall, our findings highlight the potential of palaeogenomics in enriching our understanding of speciation and long-term adaptive evolution.

Tom completed his doctoral studies at Uppsala University, Sweden, with his thesis “Genomics of population decline,” which investigated the genomic consequences of rapid population declines in endangered mammals. He then worked as Postdoctoral Researcher at the Centre for Palaeogenetics in Stockholm, focusing on the computational analysis of ancient and historical genomes of multiple extinct and endangered species. He then served as a Bioinformatician at the National Bioinformatics Infrastructure Sweden, working on a large-scale conifer genome project. As of 2022, Tom is a Data-Driven-Life-Science fellow at the Centre for Palaeogenetics, where his research group focusses on the development of computational methods to analyze complex samples, with a priority on identifying the presence of species from minute amounts of DNA.

Science-Summit-Poster-abstracts-2023Download

Scientific Committee

Kerstin Lindblad-Toh (chair), Leif Andersson, Matt Webster, Love Dalén.

Operations office project leader: Erika Bergqvist Erkstam. Team: Maria Bäckström, David Gotthold, Isolde Palombo and Hampus Persson.

SciLifeLab Science Summit – Proposal for topic 2024

The SciLifeLab Science Summit is a one-day symposium, each year with a new topic. The Science Summit aims to create awareness about SciLifeLab research and researchers, promote collaborations within life science in Sweden, and be a day for the SciLifeLab community to meet and interact.

To SciLifeLab Group Leaders, Platform Directors and Head of Units,

Is your research the theme for SciLifeLab Science Summit in 2024? Send in your proposal now and take part as the scientific committee!

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Computational Methods in Evolution and Biodiversity
2023-09-21 09:00 - 17:00 | Vivi Täckholmsalen (Q-salen), NPQ-huset, Stockholm University, Svante Arrhenius väg 20, Stockholm, Sweden
This symposium and workshop will showcase the latest computational methods for analysing big data in evolution and biodiversity and provide an opportunity for participants to gain hands-on experience in these methods. Two keynote speakers will discuss a) new advances in using image recognition to analyse biodiversity and b) population genomics approaches to understand the effects of climate adaptation on genetic diversity. In addition, there will be three parallel computer workshops focused on the application of computational and machine learning methods to genome variation and biodiversity data. Participants should bring their own computers to join these workshops. This symposium is organised by the DDLS Evolution and Biodiversity expert group in conjunction with the SciLifeLab summit on Genomics of Biodiversity and Evolution.

Post-symposium material from the Workshops

We have the workshop leaders’ permission to share links to the material for the workshops in the DDLS symposium Computational Methods in Evolution and Biodiversity. Feel free to do tutorials from the other workshops than the one you attended.

Tobias Andermann’s workshop (slides, tutorial, and data): https://github.com/tandermann/ai_workshop

Per Unneberg’s workshop: https://percyfal.github.io/workshop-biodiversity-summit/lab/index.html

Marcin Kierczak’s workshop: https://github.com/mkierczak/autoencoders_workshop

Program

09:00Welcome and introduction09:10Challenges in Fine-Grained Image Analysis. Keynote speaker: Serge Belongie, Pioneer Center for AI, Denmark09:50Computational methods give insight into paradigms and paradoxes in landscape genomics. Keynote speaker: Katie E. Lotterhos Northeastern University, USA10:30CoffeeIntroduction to Workshop x 311:00Looking at population structure from a machine learning perspective, Marcin Kierczak11:25Neural Networks for biodiversity research: challenges and opportunities, Tobias Andermann11:50Inference of ancestral recombination graphs for population genomics, Per Unneberg12:15Lunch13:30Workshop x 3; parallel sessions:Room P232, P224, P216. (Guidance on site)From PCA to Generative Deep Learning Models for better understanding population structure, Marcin KierczakBuilding your own customized neural network model (bring your own data if you want), Tobias AndermannIntroduction to whole genome tree sequence inference with tsinfer, Per Unneberg17:00End of DayVenue: Vivi Täckholmsalen (Q-salen), NPQ-huset, Svante Arrhenius väg 20, Stockholm University

Abstract Serge Belongie, Pioneer Center for AI, Denmark
Challenges in Fine-Grained Image Analysis

Fine-grained image analysis (FGIA) is a longstanding and fundamental problem in computer vision and pattern recognition, and underpins a diverse set of real-world applications. The task of FGIA is concerned with visual objects from subordinate categories, e.g., species of birds or models of cars. The small inter-class and large intra-class variation inherent to fine-grained image analysis makes it a challenging problem. Capitalizing on advances in deep learning, in recent years we have witnessed remarkable progress in deep learning powered FGIA. In this talk we review representative examples in the context of recognition, retrieval, and generation/synthesis. In addition, we also review other key issues of FGIA, such as publicly available benchmark datasets, related domain-specific applications, and connections with other modalities including text and audio. We conclude by highlighting several research directions and open problems.

Abstract Katie E. Lotterhos, Northeastern University, USA
Computational methods give insight into paradigms and paradoxes in landscape genomics

Predicting organisms’ vulnerabilities to rapid and multivariate climate change is a major scientific challenge. A hurdle to addressing this challenge arises from evolution in multivariate environments. This talk will highlight how adaptation in multivariate environments can lead to unexpected patterns at the alleles under selection, which has implications for the inference of the genetic basis of adaptation and for predicting vulnerability to environmental change.

Workshop

From PCA to Generative Deep Learning Models for better understanding population structure, Marcin Kierczak

The workshop will focus on looking at different ways of modelling and visualising population structure based on genomic kinship. Starting from more traditional approaches like PCs or MDS as a benchmark, we will build more complex deep learning-based models and discuss when such approach can be beneficial. Finally, we will see how deep learning can potentially be used to augment original input data with some artificially-generated individuals with desired pre-defined kinship relations. Throughout this workshop, we will be using Python and keras interface to Tensorflow.

Building your own customized neural network model (bring your own data if you want), Tobias Andermann

In this workshop we will cover some computational and data processing tools that will come in handy when working with neural network models. The workshop is focused on implementing your own custom-built neural network model for a chosen task. The provided examples will be from the field of biodiversity research, but you can apply the tools we cover during the workshop to problems in other research fields. In general this is an easy to follow and hands-on introduction to using neural network models. The workshop requires very basic familiarity with Python, as the model will be implemented using the Python tensorflow library.

Introduction to whole genome tree sequence inference with tsinfer, Per Unneberg

In this workshop, we will introduce tree sequence (a.k.a. ARG) inference using the tsinfer library. We will build tree sequences from input variation data and look at some applications and analyses using the resulting tree sequences. As the exercises will be performed in jupyter notebooks in Python, basic familiarity with Python is required.

Scientific Committee

Fredrik Ronquist, NRM

Tanja Slotte, SU

Matthew Webster, UU

Data-driven Evolution and biodiversity

The DDLS subject area concerns research that takes advantage of the massive data streams offered by techniques such as high-throughput sequencing of genomes and biomes, continuous recording of video and audio in the wild, high-throughput imaging of biological specimens, and large-scale remote monitoring of organisms or habitats. This research subject area aims to lead the development or application of novel methods relying on machine learning, artificial intelligence, or other computational techniques to analyze these data and take advantage of such methods in addressing major scientific questions in evolution and biodiversity.

The research area Expert Group arranges symposia and workshops and welcomes interested to join the activities. More information about the research area Evolution and Biodiversity here.

Campus Solna Seminar Series: Irene Stevens & Charlotta Heningson
2023-09-21 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 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

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

This week:

Irene Stevens

Vicente Pelechano – gamma 5

The co-translational degradome provides a readout of Fluconazole response in Candida albicans

Charlotta Heningson

Iskra Pollak Dorocic – gamma 5

The effect of SSRIs on the spatio-molecular organization of the serotonin system

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

Metabolomics for the masses
2023-09-21 12:00 - 13:00 | Birgit Thilander Lecture Hall, Medicinaregatan 3, Göteborg
Metabolites reflect the interaction between the gene cascade and surrounding exposures and are therefore essential components in all living organisms. Metabolites can be used to identify biomarkers of both health conditions and environmental exposures. The SciLifeLab Metabolomics platform offers a range of services, which will be presented during this talk, for researchers interested in metabolomics.

The presenter, Otto Savolainen, is head of the Swedish Metabolomics Centre (SMC), which offers small molecule, lipid and metabolomics analysis in biological tissues and fluids using mass spectrometry methods, in Gothenburg. The SciLifeLab site in Gothenburg includes units at both the University of Gothenburg and Chalmers University of Technology and has a strong connection to Sahlgrenska University Hospital. The SMC unit in Gothenburg is part of the Chalmers Mass Spectrometry Infrastructure (CMSI).

A light lunch will be offered for those attending onsite.

registration

Deadline for registration is 19/9.

Dissecting peripheral protein-membrane interfaces
2023-09-25 10:00 - 11:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Speaker: Nathalie Reuter, Department of Chemistry and Computational Biology Unit, University of Bergen

Host: Arne Elofsson

Abstract

Peripheral membrane proteins (PMPs) are soluble proteins that bind transiently to the surface of cell membranes. Peripheral membrane proteins include a wide variety of proteins including membrane-targeting domains such as C1, C2, FYVE, PH, PX, ENTH and GLA, enzymes involved in lipid metabolism such as phospholipases, membrane remodeling. machines such as BAR domains or ESCRTIII, and lipid-transfer proteins to name a few. Having the ability to exist in both a soluble and a membrane-bound form their membrane-binding region is constrained to retain a fine balance of polar and hydrophobic character, which makes it difficult to distinguish it from the rest of their surface. As a result peripheral membrane-binding sites are notoriously difficult to predict.

We collected and curated a dataset containing 2500 structures and compared their membrane-binding sites to the rest of their solvent-accessible surfaces, in order to reveal features of PMPs’membrane-binding sites. We find that, among positively charged amino acids, lysines are significantly more present than arginines. Protruding hydrophobes are a landmark of the interfacial binding sites of ca. 2/3 of peripheral membrane binding proteins, indicating that a majority of PMPs takes advantage of the hydrophobic effect while a non-negligeable minority (1/3) most likely relies on electrostatics interactions or other mechanisms. The IBS of peripheral membrane proteins contain significantly more glycines than the rest of their surface. Furthermore the analysis of 9 superfamilies revealed amino acid distribution patterns in agreement with their known functions and membrane-binding mechanisms.

These findings and the collected dataset will be useful for the development of prediction models for membrane-binding sites of PMPs.

[The Svedberg seminar] - Targeting Non-Coding RNAs Using Synthetic Small Molecules: Original Targets for Innovative Therapies
2023-09-25 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Dr Maria Duca

CNRS Research Director, Université Côte d’Azur, FranceWebsite: icn.univ-cotedazur.fr/tna

Host: Duc Duy Vo duc.duy.vo@kemi.uu.se, UU

Bio

Dr. Maria Duca is head of Targeting of Nucleic Acids research group in the Institute of Chemistry of Nice (Université Côte d’Azur – CNRS). After undergraduate studies in Pharmacy and Medicinal Chemistry (Faculty of Pharmacy, University of Bologna, Italy), she obtained her PhD in Molecular Biochemistry under the supervision of Dr. Paola B. Arimondo (National Natural History Museum, Paris, France) working on topoisomerase II inhibitors. A 2-year post-doctoral training in Sydney Hecht’s lab (Department of Chemistry, University of Virginia, USA) allowed her to pursue the study of nucleic acids working on targeted protein mutagenesis. After CNRS recruitment as a Research Scientist in 2008 and promotion to Director of Research in 2022, her research activities focus on the targeting of non-coding RNAs using synthetic small molecules toward innovative therapeutic approaches for anticancer, antiviral and antimicrobial applications. She has been awarded the Michel Delalande award from the Académie de Pharmacie as well as national and international grants including H2020 grants. She is Associate Editor for RSC Medicinal Chemistry journal, chair of the Chemical Biology Initiative of EFMC as well as vice-president of the French medicinal chemistry society.

Targeting Non-Coding RNAs Using Synthetic Small Molecules: Original Targets for Innovative Therapies

RNA is one of the most intriguing and promising biological targets for the discovery of innovative drugs in a large number of pathologies and various biologically relevant RNAs that could serve as drug targets have already been identified.1 Among the most important ones, it is worth to mention prokaryotic ribosomal RNA which is the target of a number of currently employed antibiotics, viral RNAs such as TAR, RRE and DIS RNA of HIV-1 or oncogenic microRNAs that are tightly involved in the development and progression of various cancers.2 However, difficulties in the rational design of strong and specific small-molecule ligands renders this kind of molecules relatively rare.

In this presentation, the structure-based design of new RNA ligands targeting oncogenic RNAs will be illustrated together with the identification of new compounds bearing a promising biological activity.3 Also, it will be shown how the active binders can be employed as chemical tools for a better understanding of the formed interactions toward the design of optimized compounds.4 Finally, the use of RNA binders for the validation of new antibacterial targets against resistant bacterial strains will be described to highlight the potential of the small-molecule approach in RNA targeting.

References

[1] J. Childs-Disney, X. Yang, Q. Gibaut, Y. Tong, R. Batey, M. Disney, Nat. Rev. Drug. Discov. 2022, 21, 736.

[2] J. Falese, A. Donlic, A. Hargrove, Chem. Soc. Rev. 2021 50, 2224.

[3] D. D. Vo, C. Becquart, T. Tran, A. Di Giorgio, F. Darfeuille, C. Staedel, M. Duca, Org. Biomol. Chem. 2018 16, 6262; C. Staedel, T. Tran, J. Giraud, F. Darfeuille, A. Di Giorgio, N. Tourasse, F. Salin, P. Uriac, M. Duca, Sci. Rep. 2018 8, 1667.

[4] Maucort, C., Vo, D.D., Aouad, S., Charrat, C., Azoulay, S., Di Giorgio, A., Duca, M. ACS Med. Chem. Lett. 2021 12, 899; Tran, T.P.A., Poulet, S., Pernak, M., Rayar, A., Azoulay, S., Di Giorgio A., Duca, M. RSC Med. Chem. 2022 13, 311; Scheheoleva I., Fernandez-Remacha, D., Estrada-Tejedor, R., Duca, M., Michelet, V. Chem. Eur. J. 2023 doi.org/10.1002/chem.202300825

Basic Course in Scanning and Transmission Electron Microscopy for Life Sciences
2023-09-26 08:00 - 2023-09-28 17:00 | KBC Building Umeå, Linneaus Väg 6, Umeå
This course covers lectures and practical demonstrations in SEM and TEM techniques, specifically for life science applications. The contents include principles of electron microscopy, specimen preparation, cryo-electron microscopy and correlative light-electron microscopy. For electron microscopy in physical science applications, there will be a similar-content basic course in early 2024.

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Application deadline: The registration closes on September 15 2023.

Location: Lectures at 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.

FAIRPoints 'Ask Me Anything' webinar on Equitable and transparent access to information
2023-09-26 14:00 - 15:30 | Online event via Zoom
Welcome to join SciLifeLab Data Centre for this virtual FAIRPoints ‘Ask Me Anything’ event. The theme of this session is “FAIRPoints ‘Ask Me Anything’ on Equitable and transparent access to information“. A discussion about the role of infrastructure for open and equitable access of information, how this reflects in design decisions and how open and FAIR relate to or mean to the rest of the world.

Speakers: Sharif Islam; DiSSCo (Distributed System of Scientific Collections), and Karl Meyer; GÉANT. The event is moderated by Emma Wilson.

When: Sept 26th 14.00-15.30 CEST virtual event.

This event is hosted by SciLifeLab Data Centre in collaboration with FAIRPoints, RDA, EOSC and FDO.

Register

For more information or inquiries please contact: Sara El-Gebali, SciLifeLab Data Centre, Project leader, Metadata and curation, sara.elgebali@scilifelab.uu.se or fairpoints@protonmail.com

Learn more about FAIRPoints, an event series highlighting pragmatic measures developed by the community towards the implementation of the FAIR (Findable, Accessible, Interoperable, Reusable) data principles here.

Blending Chemistry and Biology to Enable Systems Pharmacology
2023-09-27 10:00 - 11:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Patrick Aloy, Prof., Institute for Research in Biomedicine (IRB Barcelona)

Organizers

CBCS-KI and PhenoTarget Research Community Program

Join the seminar on Zoomhttps://ki-se.zoom.us/j/64473979770

Abstract

Big Data analytical techniques and AI have the potential to transform drug discovery, as they are reshaping other areas of science and technology, but we need to blend biology and chemistry in a format that is amenable for modern machine learning. In this talk, I will present the Chemical Checker (CC), a resource that provides processed, harmonized and integrated bioactivity data on small molecules. The CC divides data into five levels of increasing complexity, ranging from the chemical properties of compounds to their clinical outcomes. In between, it considers targets, off-targets, perturbed biological networks and several cell-based assays such as gene expression, growth inhibition and morphological profiles. I will also present the Bioteque, a resource of unprecedented size and scope that contains pre-calculated biomedical embeddings around 11 biological entities (e.g. genes, cells, tissues, disease, etc), derived from a gigantic knowledge graph, so that each entity can be described considering different contexts (e.g. interactions, expression, etc). With small molecule and biological bioactivity descriptors in hand, we now face a new scenario for chemical and biological entities where they both are translated into a common numerical format. In this computational framework, complex connections between entities can be unveiled by means of simple arithmetic operations. Indeed, we demonstrate and experimentally validate that these descriptors can be used to reverse and mimic biological signatures of disease models and genetic perturbations in vitro and in vivo, options that are otherwise impossible using chemical information alone.ReferencesDuran-Frigola et al. Extending the small molecule similarity principle to all levels of biology with the Chemical Checker. 2020. Nat Biotechnol. 38: 1087-1096.

Bertoni et al. Bioactivity descriptors for uncharacterized chemical compounds. 2021. Nat Commun. 12: 3932.

Pauls et al. Identification and drug-induced reversion of molecular signatures of Alzheimer’s disease onset and progression in AppNL-G-F, AppNL-F, and 3xTg-AD mouse models. 2021. Genome Med. 13:168.

Fernández-Torras et al. Connecting chemistry and biology through molecular descriptors. 2022. Curr Opin Chem Biol, 66: 102090.

Fernández-Torras et al. Integrating and formatting biomedical data in the Bioteque, a comprehensive repository of pre-calculated knowledge graph embeddings. 2022. Nat Commun. 13: 5304.

Computational and chemical approaches to drug repurposing
2023-09-27 13:00 - 16:00 | Samuelssonsalen, Tomtebodavägen 6, Solna, Sweden
Welcome to Xuexin Li’s doctoral thesis defense 1 September at 09.00 in Samuelssonsalen, Tomtebodavägen 6, Solna

Title

“Computational and chemical approaches to drug repurposing”

Author

Xuexin Li, Department of Medical Biochemistry and Biophysics, Karolinska Institutet

Principal Supervisor

Prof. Oscar Fernandez-Capetillo, Department of Medical Biochemistry and Biophysics, Karolinska Institutet

Co-supervisor

Dr. Daniela Hühn, Department of Medical Biochemistry and Biophysics, Karolinska Institutet

Opponent

Dr. Brinton Seashore-Ludlow, Department of Oncology-Pathology, Karolinska Institutet

Examination Board

Prof. Per Svenningsson, Department of Clinical Neuroscience, Karolinska Institutet

Prof. Ernest Arenas, Department of Medical Biochemistry and Biophysics, Karolinska Institutet

Prof. Patrick Aloy, Structural Systems Biology lab, Institut de Recerca Biomèdica de Barcelona

SciLifeLab Day Lund
2023-09-28 08:00 - 17:00 | Forum Medicum, Fernströmsalen, Sölvegatan 19, Lund, Sweden
SciLifeLab has launched four new sites across Sweden in 2022. The sites, located in Gothenburg, Linköping, Lund, and Umeå, will be crucial in promoting scientific research and research infrastructure nationally, while also strengthening the collaboration between all Swedish universities.

The expansion of SciLifeLab’s network will provide researchers across Sweden with state-of-the-art research infrastructure and technology, enabling them to perform cutting-edge research in areas such as genomics, proteomics, and bioinformatics. This will not only help to advance scientific knowledge but also contribute to the development of innovative solutions to pressing societal challenges.

The launch of the national sites, in addition to existing ones in Stockholm and Uppsala, will also contribute to the development of a stronger research environment, crucial for attracting talented researchers and investment to the country, further cementing Sweden’s position as a leader in scientific research.

Throughout this year, each site arrange a whole day program to highlight the national and local perspectives of SciLifeLab.

Conference proceedings

SciLifeLab-Day-Lund-Booklet-finalDownload

Program

SciLifeLab-Day-in-Lund-ProgrammeDownload

Contact

lund@scilifelab.se

Esther González-PadillaLund UniversitySite Coordinator SciLifeLab Lundesther.gonzalez-padilla@scilifelab.se (+46) 76-517 38 35

Venue

SciLifeLab Days on the national sites

Gothenburg, April 17

Umeå, September 11

Lund, September 28

Linköping, October 10
