SciLifeLab

Campus Solna Seminar Series: Jian Wu and Marcel Tarbier
2023-03-09 12:00 - 13:00 (Europe/Stockholm) | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 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 Presentation of ongoing (unpublished) projects is strongly encouraged.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:

Jian Wu

Stefania Giacomello – alpha 3

Visualization and analysis of spatial transcriptomics data: a geometric approach

Marcel Tarbier

Vicent Pelechano – gamma 5

Imputing cell features from molecular profiling: what we can learn from treating single cells as individuals

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

[Clinical Talks] The PONCH study
2023-03-10 09:00 - 09:30 | Online event via Zoom
The PONCH Study of the influence of diet, obesity and gestational diabetes (GDM) on maternal and child metabolic health

Ulrika Andersson Hall

University of Gothenburg

Ulrika is currently an associate professor and project manager of the Pregnancy Obesity Nutrition and Child Health (PONCH) study headed by professor Agneta Holmäng at the Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg. Ulrika has an MSc in Molecular Biotechnology from Uppsala University and a PhD in Biochemistry from Oxford University. In 2015, after post-doctoral positions at the Medical Research Center of Imperial College, London, and at the Department of Food and Nutrition and Sport Science, University of Gothenburg, she joined the PONCH group. She now runs the PONCH study focusing on maternal and child metabolic health during and after pregnancy, but has also added other branches to the study, particularly with focus on the transition from gestational diabetes to type-2-diabetes.

The PONCH study:

PONCH started in 2009 and is an ongoing prospective, longitudinal study investigating the influence of diet, obesity and gestational diabetes (GDM) on maternal and child metabolic health. The specific aims of PONCH are to better understand how body composition, insulin resistance and energy metabolism change during and after pregnancy in women of normal body weight, with obesity or with GDM, and how this affects the body composition and health of their children. Another important aim is to evaluate insulin resistance after GDM in order to better be able to predict the development of type-2-diabetes in these women. Here, we also investigate the effect of life-style factors in the transition from GDM to type-2-diabetes. Our hope is that the research will influence future clinical care of women with GDM.

register to receive zoom link

Moderator: Päivi Östling, SciLifeLab

Clinical Talks

Clinical Talks is back for more! With a brand new and shiny Season 6. After successfully completing 5 seasons with > 70 enthusiastic Clinical Talkers to our record, we have barely scratched the surface of all the amazing work our clinical, academic and industry Life Science community has to offer. More about the upcoming events is available here.

These events are co-organized by Karolinska Institutet Innovations AB and SciLifeLab, and brought to you by Colibri Ventures.

RNA-seq data analysis
2023-03-13 08:00 - 2023-03-16 17:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
This workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of lectures and computer practicals.

Important dates

Application open: December 15, 2022

Application deadline: February 12, 2023

Responsible teacher/s

Johan Reimegård, Julie Lorent, Nima Rafati

Contact information for questions regarding the course

edu.rnaseq@nbis.se

Course fee

A course fee* of 1800 SEK will be invoiced to accepted participants. This includes lunches, coffee, snacks, and one course dinner. *Please note that NBIS cannot invoice individuals

Course content

Topics covered will include:

RNAseq quality control analysis

Mapping of short reads

Quantification of gene expression

Exploratory data analysis

Differential gene expression

Gene set enrichment analysis

More details about the course can be found at:

The previous year website

The course will follow similar structure and topics. NOTE: In March 2023, the course will be a 4-day-course on-site in Uppsala.

Entry requirements

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

Basic knowledge in Linux and R

Your own laptop with the following specs:

At least 6 GB of RAM.

Operating system Win10, OS X or Linux

At least 30 GB of free storage

Desirable:

Experience working with NGS data analysis or completed the NBIS workshop “Introduction to Bioinformatics using NGS data”

Experience working in R or completed the NBIS course “R Programming Foundations for Life Scientists”

Due to our best practice to have a high teacher to student ratio we have set the number of participants to a maximum of 20 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.

Application

Electro- and Photoredox Chemistry – with a Practical touch
2023-03-14 08:30 - 11:30 | Gamma 7 Lunchroom, Tomtebodavägen 23A, Solna, 17121
At these two seminars you will hear about the two techniques of electrosynthesis and photoredoxchemistry, used more and more today by organic chemists. We will get some background information to the techniques and examples from how it is used in Helena’s and Markus’ labs. After the seminars we hope that you better understand when the techniques are best used and that you also get practical examples on how to get started.

We hope to discuss what can be future developments in field.

At the venue we will bring examples of equipment that can be used.

We meet up in the entrance at Gamma 2 for coffee and walk up together (be there in time, so we can let you in). To reserve a sandwich please register before March 7th to ylva.gravenfors@scilifelab.se

We look forward to seeing you there!

Presenter

Dr Helena Lundberg, Ass. Professor at KTH

hellundb@kth.se

Dr Markus Kärkäs, Assoc. Professor at KTH

karkas@kth.se

Speakers‘ biographies

Helena is Assistant Professor in organic chemistry since 2021 and has been a principal investigator at KTH Royal Institute of Technology since early 2019. Helena’s research interests are centered around catalysis and reductive electrosynthesis.

Markus is Associate Professor in organic chemistry and a principal investigator at KTH Royal Institute of Technology since August 2018. His research interests include photoredox catalysis, organic electrosynthesis, and artificial photosynthesis.

The Drug Discovery and Development Platform

Hit2Lead – Read more

Mass Spectrometry Day
2023-03-15 09:00 - 17:00 | Carl Kempe-salen, KBC Building, Umeå University, Umeå, Sweden
Six leading companies in the field of modern mass spectrometry will present their latest news about analytical applications and technologies. The spectrum of topics will cover metabolomics, proteomics and give special attention to targeted applications. Both mass spectrometry in combination with separation by liquid chromatography and by gas chromatography will be covered.

The event is collaboration between industry and academia. It is organized by the Swedish Mass Spectrometry Society in collaboration with the Swedish Metabolomics Center, the Mass Spectrometry Network Umeå and six leading companies in the field. It will offer a unique opportunity to learn about the latest innovations from Agilent Technologies, Bruker, Sciex, Shimadzu, Thermo Fisher Scientific AB and Waters. In addition, Hamilton will participate with a presentation table with information about their products but without an oral presentation.

The event is on-site at the Chemistry Biology Center of Umeå University (KBC Umeå) and will provide a unique opportunity to attend the presentations of the application experts of the companies and meet company representatives for discussion of analytical applications and instrumental technology. There will also be an opportunity to attend the presentation in Zoom. However, to meet the representatives of the companies attending the event on site is required.

Attending the Mass Spectrometry Day is free of charge, but registration is required for both attending on site and in Zoom. To register for the event please visit the homepage of the Swedish Chemical Society by March 9th at the latest.

Read more

Campus Solna Seminar Series: Philip Yuk Kwong Yung and Anna Karlsson
2023-03-16 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:

Philip Yuk Kwong Yung

Simon Elsässer – alpha 4

Synthetic biology approach to resolve chromatin dynamics in stem cells

Anna Karlsson

Paul Hudson – gamma 5

Exploring protein regulation through thermal proteome profiling in plants and cyanobacteria

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

Chemical Biology Seminar Series with Krister Wennerberg
2023-03-16 16:00 - 16:30 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to two seminars with Krister Wennerberg in the Chemical Biology Seminar Series. Join us either in the Gamma 2 lunchroom or on Zoom

“Exploring cancer cell drug resistance mechanisms and how to overcome them”

Krister Wennerberg, Prof.

BRIC – Biotech Research & Innovation Centre, University of Copenhagen

Join on Zoom

NBIS workshop in Neural Nets and Deep Learning
2023-03-20 09:00 - 2023-03-24 17:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
National course open for PhD students, postdocs, researchers and other employees in need of Neural networks and Deep Learning skills within all Swedish universities.

Important dates

Application opens: 2022-10-25

Application closes: 2023-02-10

Confirmation to accepted students: 2023-02-17

Responsible teachers: Claudio Mirabello, Christophe Avenel

If you do not receive information according to the above dates please contact: edu.neural-nets-deep-learning@nbis.se

Course webpage

Application

Course fee

A course fee* of 2200 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks.

*Please note that NBIS cannot invoice individuals

Course content

This course will give an introduction to the concept of Neural Networks (NN) and Deep Learning.

Topics covered will include:

NN building blocks, including concepts such as neurons, activation functions, loss functions, gradient descent and back-propagation

Convolutional Neural Networks

Recursive Neural Networks

Autoencoders

Best practices when designing NNs

Learning outcomes

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

Distinguish the concepts of “Artificial Intelligence”, “Machine Learning”, “Neural Networks”, “Deep Learning”

Distinguish between different types of learning (e.g. supervised, unsupervised, reinforcement) and recognise which applies to their own problem

Distinguish between linear and non-linear approaches and recognise which is best suited for application to their own problem

Describe what a feed-forward neural network (FFNN) is, along with its components (neurons, layers, weights, bias, activation functions, cost functions)

Explain how training of a FFNN works from a mathematical point of view (gradient descent, learning rate, backpropagation)

Execute with pen and paper a few steps of training of a very simple FFNN model

Tell the difference between a shallow and a deep network

Explain broadly how different NN architectures are wired and how they work

Implement and apply the most appropriate architecture to a given problem/dataset

Analyze training curves and prediction outputs to evaluate if the training has been successful

Debug possible issues with the training and suggest changes to fix them

Explain the difference between training, validation and testing

Define what overfitting is from a mathematical point of view, and what issues it causes

Identify what constitutes good practices of dataset design and how to avoid introducing information leakage or other biases when building their own datasets

Entry requirements

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

Familiarity with Unix/Linux

Ability to bring your own laptop with Python and Jupyter Notebooks installed for the practical exercises

Programming/scripting experience in Python (e.g. having attended the NBIS workshop in basic Python or equivalent)

Basic experience of statistics and mathematics (e.g. having attended the NBIS workshop Introduction to Biostatistics and Machine Learning or equivalent)

Desirable:

You have experience of working with Jupyter Notebooks

You have a necessity to work with large datasets (e.g. thousands of samples)

Due to limited space the course can accommodate a 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 course as well as gender and geographical balance.

Kinase Drug Discovery - Strategies for Success
2023-03-20 11:00 - 17:00 | Inghesalen, Tomtebodavägen 18a,, Solna, 171 65 171 65, Sweden
A half day dedicated to kinases in drug discovery organized by SciLifeLab DDD in collaboration with AstraZeneca.

Kinases continue to attract much attention in drug discovery. Since the first compounds were launched in 2001 the learning curve of how to tackle different challenges has been steep. At the symposium we hope to give a broad overview where the field stands today and the different approaches one can take in drug discovery when interacting with kinases.

In the late afternoon we will dive deeper into the details of data generation and data interpretation to learn and discuss different techniques that can be applied to increase the chance for success.

The meeting is believed to be valuable for researchers in the area of drug discovery like medicinal chemists, structural biologists, pharmacologists, protein scientists, toxicologists etc.

This is a hybrid event. Registration for the conference on site is binding and last day for on site participation is March 14th.

Read more

Register

Program

[The Svedberg seminar] - Protein engineering for functional hybrids and biomaterials: applications in biomedicine and technology
2023-03-20 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Prof. Aitziber Cortajarena

Research Professor Scientific DirectorCenter for Cooperative Research in Biomaterials (CIC biomaGUNE) Spain

Bio

Prof. Aitziber Cortajarena earned her Ph.D. in Biochemistry from the Universidad del País Vasco in 2002. Then, she worked on protein design in the group of Dr. Lynne Regan at Yale University, USA, as a Postdoctoral Fellow and Associate Research Scientist. She joined IMDEA Nanociencia in 2010 and started her independent research in nanobiotechnology. In 2016, she joined CIC biomaGUNE as Ikerbasque Research Professor. Currently, she leads the Biomolecular Nanotechnology group and is Scientific Director at CIC biomaGUNE.

Her research focuses on protein engineering toward the generation of functional nanostructures and bioinspired materials for applications in nanobiotechnology and nanomedicine.

Protein engineering for functional hybrids and biomaterials: applications in biomedicine and technology

Proteins are the most versatile biological building blocks, composed of smaller units called amino acids, which offer a rich chemisty. The diverse 3D structures of proteins translate into a wide range of functionalities, making them ideal candidates for use as building blocks in tailored nanofabrication and the creation of novel protein-based functional composites and biomaterials.

In our group, we aim to leverage the potential of engineered proteins as building blocks for the generation of functional nanostructures and bioinspired materials for a wide range of applications in technology and biomedicine. Our goal is to create versatile platforms based on simple protein building blocks, which can be used to fabricate a variety of protein-based functional composites and biomaterials.

To demonstrate the potential of these engineered protein-based systems, several examples will be shown, including their use in catalysis, bioelectronics, biosensing, and for the treatment and diagnosis of diseases.

Host: Antonietta Parracino antonietta.parracino@kemi.uu.se, UU

HPC2N as an alternative
2023-03-21 12:00 - 13:00 | Glasburen Seminar Room, Chemical Biological Centre (KBC) Building, Umeå University, Umeå, 901 87, Sweden
In the frame of the“SciLifeLab Site Umeå / KBC Infrastructure Seminar Series”, the seminars will be organised every second Tuesday during spring 2023. The seminars will be held in a hybrid format IRL in Glasburen, KBC, and online via Zoom. Take the chance to get information on facilities, possibilities and services that infrastructure, both SciLifeLab-associated and local, can offer! Learn more about the seminar series and Schedule for Spring 2023 here.

On March 21st, 12:00-13:00, SciLifeLab Site Umeå / KBC Infrastructure Seminar Series presents:

Are your simulations saturating your PC or do you need more computing power?: HPC2N as an alternativePedro Ojeda May, Senior research engineer at High Performance Computing Centre North

Sign up (latest by Monday, 20 March, 10 a.m.) for on-site attendance to reserve your free lunch sandwich:

Registration

Abstract

The High Performance Computing Center North (HPC2N) is a local/regional resource for researchers at HPC2N’s partners (IRF, LTU, Mittuniversitetet, SLU and UmU). Our Director of HPC2N is Professor Paolo Bientinesi from the Computing Science Department.

We offer different types of hardware for computing and visualization, including standard CPUs and Graphical Processing Units (GPU)s. Most common packages for Scientific Research are installed on our cluster, for instance, GROMACS, VASP, MATLAB, and R/Rstudio, among others.

To get started with our system, we offer different types of training courses, including introductory courses and more specialized courses in topics such as Molecular Dynamics, QM/MM, Git, R, Machine Learning, MPI, Julia, and OpenMP (Recorded courses: https://www.youtube.com/@HPC2N). We provide general support through a ticket system and more advanced support for specific questions from researchers on-demand.

UROSCAN & UROSCANSEQ
2023-03-22 13:00 - 14:00 | Online event via Zoom
Fredrik Liedberg (Urologist at Skåne University Hospital in Malmö) will present insights from UROSCAN & UROSCANSEQ: a large-scale multicentre effort towards translation of molecular bladder cancer subtypes into clinical practice – from biobank to RNA-sequencing in real time. Join us to learn about clinical implementation of bladder cancer subtypes.

The event has been organized by Clinical Genomics Lund in collaboration with Genomic Medicine Sweden, and will be hosted by Markus Heidenblad, Head of Unit of Clinical Genomics Lund.

This webinar will be held on WEDNESDAY 22nd of March at 13-14.

registration

Towards a better understanding of vaccine-induced protection in the elderly and frail
2023-03-23 10:00 - 11:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Speaker: Mattias Forsell, Associate Professor, Umeå University

Abstract: The impact of age on the induction of protective immunity has been a neglected area of research. However, the recent pandemic has highlighted the vulnerability of the elderly to severe or fatal outcomes after virus infections. This vulnerability is not limited to SARS-CoV-2 but also applies to other common respiratory infections, such as Influenza type A and RSV. To improve our understanding of age-related immune responses, we have implemented a longitudinal strategy to monitor the immunity, infections, and fatalities of individuals living in nursing homes in five different Swedish healthcare regions. This vulnerable population comprises the oldest and most frail individuals in Sweden, with a median age of 86 years and one or several comorbidities. The study began in September 2021, and we have performed repeated capillary blood sampling of more than 3,000 individuals. We will present vaccine-specific antibody responses after sequential COVID-19 mRNA boosts. By combining immunology data with national registry-based data, we will demonstrate the impact of vaccination on SARS-CoV-2-related deaths during a time period characterized by waves of neutralization-resistant Omicron variants BA.1, BA.2, and BA.5. We will discuss the use of such data for the implementation of strategies to identify the frailest individuals of an already vulnerable population and its impact on future vaccine strategies.

Short bio: Mattias Forsell is an Associate Professor of Immunology and a Senior Lecturer in Biomedical Laboratory Sciences at Umeå University. His laboratory is focused on cellular and molecular studies of B cell responses, with the aim of understanding basic processes for protective immunity and how they can be utilized for the development of antibody-based therapeutics and improved vaccine strategies. His research accomplishments include the development of a potential treatment for fatal hantavirus infection, a detailed molecular understanding of B cell responses to heterologous vaccination, and the implementation of a sampling strategy to provide equal access to high-quality serology for inhabitants in Västerbotten. Dr. Forsell completed his graduate studies at MTC, Karolinska Institutet, and the Vaccine Research Center at the National Institutes of Health in the USA. He received a PhD in Medicine and continued as a postdoc at NIH before returning to KI. In 2015, he was recruited to Umeå University, where he established his current research group. In 2020, he received a Consolidator Grant from the Swedish Research Council and is now coordinating KAW-funded SciLife efforts in Vaccine Research and Pandemic Preparedness. His laboratory is also a node for a NIH-funded Center of Excellence in Translational Medicine for the discovery and development of antiviral antibodies.

Campus Solna Seminar Series: Nona Struyf and Miriam Yagüe-Capilla
2023-03-23 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:

Nona Struyf

Olli Kallioniemi – alpha 4

Functional Precision Medicine in Hematopoietic Cancers

Miriam Yagüe-Capilla

Sean Rudd – alpha 5

Targeting nucleotide metabolism to improve nucleoside-based therapeutics in cancer

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

Data-driven life science and the RDA: Leveraging global data communities in regional initiatives and cross-border infrastructures
2023-03-24 09:00 - 13:00 | Lindholmen Conference Center, Lindholmspiren 5, Göteborg, 417 56, Sweden
This workshop will showcase how to leverage the Research Data Alliance (RDA) to support life science research today and what role the RDA and international data infrastructures can play in the transition to an increasingly data-driven research practice. It is organised by ELIXIR, NBIS and the Science for Life Laboratory (SciLifeLab) and includes speakers on life science data & interoperability, stakeholder engagement, and liaison strategies with the RDA.

The workshop aims to promote and refine strategies for liaising with global communities and in particular the RDA to develop and adopt solutions for data-driven life science research. The intended audience is research communities, regional research infrastructures and cross-border infrastructure collaborations. However, registration is open to everyone who is involved in furthering shared principles and standards for life science research data. To accommodate a dynamic and diverse group of participants, the workshop is hosted as a hybrid event, accepting participants on-site in Gothenburg, Sweden or online via Zoom.

The event schedule is organised into two parts where invited speakers will present their experiences leading into discussions focused on finding effective liaison strategies and forming new collaborations across communities and infrastructures. Part 1 focuses on showcasing examples of how to leverage activities and outputs of the RDA to converge on shared principles and practices. Part 2 focuses on networking to outline and refine some elements of realistic and effective liaison strategies that could be implemented across the organisations, initiatives and communities that the participants represent.

Registration is free for both on-site and virtual attendance. The number of spaces for on-site attendance is limited by the size of the room and some spaces will be reserved for speakers to promote wide representation across communities and infrastructures.

Contact: wolmar.n.akerstrom@uu.se

Registration

Part 1: Showcase on leveraging the RDA for life science data

09:00–11:00 CET | Presentations by invited speakers

Life science data communities and infrastructures

Regional resources with national and cross-border data sharing initiatives

Leveraging and promoting RDA outputs and activities

Panel discussion

Part 2: Liaison strategies across communities & infrastructure

11:00–12:00 CET | Guided discussions among participants

Work towards realistic and effective liaison strategies

Potential collaborations and steps going forward

12:00–13:00 CET | Networking lunch for on-site participants

Regional Mass Spectrometry Imaging Spring Workshop
2023-03-27 09:00 - 2023-03-29 17:00 | Uppsala Konsert & Kongress, Vaksala torg 1, Uppsala, 75331, Sweden
The scientific program will aim to reflect cutting edge innovations and current developments in mass spectrometry imaging (MSI), alongside new applications in various areas. The goal for this workshop is to promote and educate academic, industry and government scientists on the latest applications and innovations in MSI applied to biomedical, biological and data science research areas.

A three-day scientific agenda with oral presentations, workshop discussions, and poster presentations covering the latest developments and applications of MSI by leading and upcoming scientists from academic, government, and industry labs

Website, program & Registration

Important dates

February 10, 2023 Deadline for regular fee and abstracts submission

Organizers & Contacts for questions

Per Andrén, Spatial Mass Spectrometry, SciLifeLab, per.andren@farmbio.uu.se

Jeanette Jansson, Apotekarsocieteten, jeanette.jansson@lakemedelsakademin.se

Global Harmonization for Exposomics: Opportunities and Challenges; Campus Solna Seminar Series.
2023-03-27 10:00 - 11:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Professor Gary W Miller, Columbia University

Dr. Miller serves as Vice Dean for Research Strategy and Innovation and Professor of Environmental Health Sciences in the Mailman School of Public Health, and Professor of Molecular Pharmacology and Therapeutics in the Vagelos College of Physicians and Surgeons at Columbia University in New York. He completed his PhD in Pharmacology and Toxicology at the University of Georgia and postdoctoral training in Molecular Neuroscience at Emory University and Duke University. His laboratory studies the role of environmental factors in neurodegenerative diseases, including Parkinson’s disease and Alzheimer’s disease. Dr. Miller founded the first exposome center in the U.S. and wrote the first book on the topic. He has helped develop highresolution mass spectrometry methods to provide an omic-scale analysis of the human exposome. He is a member of the National Institutes of Health All of Us Research Program Advisory Panel and the National Institute of Environmental Health Sciences Advisory Council. Dr. Miller is the founding editor of the new journal Exposome, published by Oxford University Press.

[The Svedberg seminar] - The Underlying Cause of Human Autoimmune Disease
2023-03-27 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
DAVID A. HAFLER, MD, FANA

William S. and Lois Styles Professor of Neurology and ImmunobiologyChair, Department of Neurology, Yale School of MedicineNeurologist-in-Chief, Yale New Haven HospitalFounding Associate Member, Broad Institute of MIT and Harvard

Bio

David A. Hafler, M.D. is the William S. and Lois Stiles Edgerly Professor and Chairman Department ofNeurology and Professor of Immunobiology, Yale School of Medicine, and is the Neurologist-in-Chiefof the Yale-New Haven Hospital. He has made seminal discoveries in the pathogenesis of multiplesclerosis and autoimmune diseases including identification of human autoreactive T cells andthe mechanisms that underlie their dysregulation with the discovery of human regulatory T cells.He led the discovery of genetic variants causing. He was awarded the Dystel Prize for MS researchand the 2023 AAI Steinman Award for Human Immunology Research. He is an Honorary Member ofthe Scandinavian Society for Immunology and has been elected to membership in the AmericanSociety of Clinical Investigation, The Association of American Physicians, and the National Academy of Medicine.

The Underlying Cause of Human Autoimmune Disease

Multiple sclerosis (MS) is a prototypic, genetically mediated autoimmune disease induced by environmental factors where genetic perturbation of cis-regulatory elements leads to immune dysregulation and generation of myelin reactive T cells secreting inflammatory cytokines. We have identified 233 common allelic variants associated with MS risk where approximately 60% of candidate causal variants map to enhancers and super-enhancers marked by chromatin features in T and B cells. We found that CD4+Foxp3+ Tregs are defective in MS and by performing transcriptomic and epigenomic profiling discovered that upregulation of a primate-specific short PRDM1 isoform (PRDM1-S) induces SGK1 independent from evolutionally conserved long PRDM1, leading to destabilization of Foxp3 and Treg dysfunction. This aberrant PRDM1-S/SGK1 axis is shared among other autoimmune diseases and it is of interest that SGK-1 is induced by high salt, an environmental risk factor in MS. Finally, as suggested by genetic mapping, B cells play a critical role in the disease and B cell depletion is highly effective in treating early disease.

Host: Katarina Lundblad katarina.lundblad@neuro.uu.se, UU

Towards the routine data collection from pico-gram crystals
2023-03-28 12:00 - 13:00 | Glasburen Seminar Room, Chemical Biological Centre (KBC) Building, Umeå University, Umeå, 901 87, Sweden
In the frame of the “SciLifeLab Site Umeå / KBC Infrastructure Seminar Series”, the seminars will be organised every second Tuesday during spring 2023. The seminars will be held in a hybrid format IRL in Glasburen, KBC, and online via Zoom. Learn more about the seminar series and Schedule for Spring 2023 here. On March 28th, 12:00-13:00, SciLifeLab Site Umeå / KBC Infrastructure Seminar Series presents:

Towards the routine data collection from pico-gram crystals using MicroED

Johan UngeMicroED core manager and collaborator with the Gonen lab at UCLA, Los Angeles.

Sign up (latest by Monday, 27 March, 10 a.m.) for on-site attendance to reserve your free lunch sandwich:

registration

or follow online via Zoom: https://umu.zoom.us/j/63138997026 (registration is not required).

Abstract: Although electron crystallography has been known almost a century, the current success for organic and biological samples started only a decade ago. The theoretical complications from effects such as for instance dynamical scattering can be largely overcome using continuous rotation as in MicroED or cRED. Today an exponentially growing number of structures are deposited to PDB and CSD from MicroED data collections. The technique has several advantages and is a sample saving addition to the structural biology toolbox. The ability to collect a full data set from crystals 100 nm thick has allowed the structure determination of several proteins from nano sized crystals as well as small molecules directly from powder. The ability to see electrostatic potential as well as hydrogen atoms is useful for many functional studies. Recent experiences, advantages and complications as well as newest developments towards an automatic, accessible and efficient crystal structure determination is presented.

Regulation of protein disaggregation in primates
2023-03-28 13:00 - 14:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Cells have evolved multitiered protein quality control systems to help maintain protein homeostasis, but under acute or chronic proteotoxic stresses, these systems overload and result in accumulation of toxic protein aggregates. Decreased cellular capacity in aggregate clearance could trigger cell dysfunction and death leading to disease and ageing. Human cells possess an Hsp70-based disaggregase system to resolve a wide range of protein aggregates. It is not clear how these disaggregases are assembled and regulated in mammals. We report the identification of a dedicated pathway for rapidly assembling protein disaggregases during stress recovery after protein damage and outlines how aggregate clearance is orchestrated in primate cells.

Exhibition in Navet at BMC
2023-03-29 09:00 - 2023-03-30 15:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
On March 29-30, between 09.00-15.00, you have the opportunity to visit an exhibition in Navet at BMC. This is a chance to receive information and updates from 20 of the leading life science companies in Sweden.

Companies present on Wednesday, March 29

Companies present on Thursday, March 30

Corning Life Sciences

Meso Scale Discovery (MSD®) is a leader in high performance, multiplex-enabled biomarker assays for cytokines, toxicology, neurodegeneration and metabolic disease research, used by leading biopharmaceutical and academic researchers.

Nordic Biolabs is a distributing company representing around 50 different brands in Sweden, like Promega, Biosearch Technologies, Cytiva and many more. We have our head office and warehouse in Täby, Stockholm.

Discover RAMCON at the event! We specialize in a wide range from pipettes, fermentation, automation, HPLC systems and cell solutions to material characterization. Join us and learn more! www.ramcon.eu

Rarity Bioscience was founded in 2021 to further develop the ultrasensitive multiplex superRCA assay technology – enabling full potential of liquid biopsies and radically improving cancer diagnostics.

Saveen & Werner is a supplier of laboratory consumables, reagents, chemicals and instruments in the Nordics, serving customers in Sweden, Finland, Denmark and Norway with local staff and subsidiaries.

Science Imaging Scandinavia AB distributes selected Life Science Products mainly in Scandinavia and Finland. Our goal is to offer comprehensive solutions to the image related problems faced by today’s research communities.

STEMCELL Technologies provides high-quality cell culture media, cell separation technologies, instruments, and educational resources to scientists around the world. Learn more at www.stemcell.com

Takara Bio can offer you solutions within our wide-ranging product portfolios: NGS, Stem cell, Gene editing, Genetic screening, Cloning, Cell biology & cell culture, PCR, qPCR & RT, Transfection, Transduction and many more

Techtum Lab AB delivers smarter reagents, consumables and instruments for customers in research and diagnostics. Wide knowledge in diagnostic microbiology, qPCR/PCR, digital PCR, NGS, extraction, liquid handling robots and biobanking equipment.

Bio-Works supplies the biopharmaceutical and biotech industry with WorkBeadsTM chromatography resins and GoBio™ prepacked columns for the purification of a wide range of biomolecules such as proteins, peptides, oligonucleotides and mAbs.

Hamilton Robotics’ automated liquid handler workstations provide consistent results for assays, ranging from low-throughput pipetting protocols to high-throughput systems with integrated sample storage.

Integrated DNA Technologies (IDT) are experts in oligo synthesis and supports NGS, DNA amplification, genotyping, genome editing, expression profiling, synthetic biology, and functional genomics.

LabLife NordicPlease join us to discuss your research activities. Our innovative products will add to your success! Single cell sequencing, NGS, gene function, proteomics, cell assays and more!

Mettler Toledo (Rainin)delivers pipettes, tips and other pipette management products that reflect our passion for exceptional quality and innovative design. They are built to deliver years of accurate, reliable and ergonomic operation.

Navinci is a Swedish biotech company that specializes in developing innovative solutions for the study of protein interactions based on our proprietary proximity ligation technology – Bringing Precision to Spatial Proteomics.

Nordic BioSite is recognized as a leader in supplying products for biomedical research and diagnostics throughout the Nordics. With more than 5 million products, our portfolio represents top-quality manufacturers and suppliers.

Promega mainly focus on two application areas which are genomics and bioluminescence. Promega has served scientist in all over the world since 1978 making us pioneers within the life science industry. How can we help you?

QIAGEN delivers Sample to Insight solutions for molecular testing and offers products and services that enable our customers to gain valuable insights from any biological sample – from basic research to clinical healthcare.

Thermo Fisher Scientific supplies innovative solutions for the world’s leading academic institutions. We provide a broad range of products and services, including laboratory equipment, analytical instruments, and reagents.

Campus Solna Seminar Series: Richard Tjörnhammar and David Hueting
2023-03-30 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:

Richard Tjörnhammar

Linn Fagerberg – alpha 6

Clustering, Enrichments and Visualisation of Complex Data for Increased Knowledge Quality

David Hueting

Per-olof Syren – gamma 5

Design, structure and plasma binding of ancestral β-CoV scaffold antigens

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

[Clinical Talks] Genetic Testing for a Global Community
2023-03-31 09:00 - 09:30 | Online event via Zoom
Samuel Myllykangas

Biography

Samuel Myllykangas, adjunct Professor at the Institute of Biomedicine, University of Helsinki, and co-founder of Blueprint Genetics. Samuel started his career by designing an entirely new method of sequencing the DNA (Oligonucleotide-Selective Sequencing) while working on his post-doctorate in the Stanford University. This method, published in Nature, sparked an idea of his own genetics company where he could apply his invention in the diagnostics of rare disease patients. Since then, Samuel has built an extensive experience in developing genomics technologies, bioinformatics tools and genetic testing solutions for rare diseases. Samuel runs Specialty Genetics at Quest Diagnostics and is the Managing Director of Blueprint Genetics. He is responsible for the overall success of the business, leading the development and execution of strategy and delivering on financial and operational targets.

Blueprint Genetics

Blueprint Genetics is a genetic testing company focused on inherited diseases. With a patient-first mindset, we deliver high-quality genetic testing to the global clinical community across 14 medical specialties. By combining a state-of-the-art laboratory process, the latest sequencing technology, AI empowered data-crunching tools and techniques, world-class professionals, and a holistic customer experience approach, we are bringing genetic knowledge to mainstream healthcare. Blueprint supports clinicians and their patients with comprehensive and high-quality tools and resources for diagnosis of genetic conditions. In doing so, we provide possibilities for targeted treatment and individualized care for patients.

register to receive zoom link

Moderator: Päivi Östling, SciLifeLab

Clinical Talks

Clinical Talks is back for more! With a brand new and shiny Season 6. After successfully completing 5 seasons with > 70 enthusiastic Clinical Talkers to our record, we have barely scratched the surface of all the amazing work our clinical, academic and industry Life Science community has to offer. More about the upcoming events is available here.

These events are co-organized by Karolinska Institutet Innovations AB and SciLifeLab, together with Colibri Ventures.

Digital image analysis for scientific applications
2023-04-04 08:00 - 2023-05-09 17:00 | Uppsala University, Uppsala, Sweden
Language of instruction: EnglishCourse period: 2023-04-11– 2023-05-09Course structure: The course will be hybrid on site and via zoom to facilitate remote participation. For computer exercises we encourage on-site participation for best possible support, but will do our best to also support those participating remotely.

RECOMMENDED PREREQUISITES

The target group is PhD students from all subjects where digital image analysis (IA) is used as a research tool. No previous experience in IA is required from the course participants, but an interest in its potential as a tool in their own research is important. The course can be followed with a basic knowledge of mathematics (corresponding to upper‐ secondary level entry requirements) and basic computer skills.

LEARNING OUTCOMES

explain fundamental notions of IA, such as digitization, image enhancement, segmentation, and feature extraction and classification;

critically evaluate several different methods for image segmentation, compression, distance computation, frequency analysis, etc.

use software to apply and evaluate algorithms for solving image analysis problems;

analyze and plan the steps necessary to solve a realistic image analysis problem;

give examples of applications in research and industry where image analysis is used.

LEARNING OUTCOMES FOR DOCTORAL DEGREE

The course participants will practice their ability to perform scientific analyses, find and test appropriate IA methods, and present and discuss their scientific results.

COURSE CONTENTS

The focus of the course is on reaching a broad understanding of IA and a basic understanding of the theory and algorithms behind the IA methods. The course starts with basic IA methods and computer exercises, including IA research methodology and IA research ethics. Modern techniques based on Artificial Intelligence will also be discussed in relation to the classical approaches.

INSTRUCTION

The pedagogical approach will combine traditional lectures, examples of real life applications and hands-on exercises. We also use a flipped classroom approach based on our pre-recorded course material which enables participants to prepare for discussions and exercises.

ASSESSMENT

The examination will be divided into two parts:

completed four computer exercises, which enable the course participants to both get familiar with the interfaces of common software and to solve realistic image processing problems,

a written exam

Completed exercises and passing written exam gives 5hp.

COURSE EXAMINER

Carolina Wählby, carolina.wahlby@it.uu.se together with other seniors involved in the BioImage Informatics Unit of SciLifeLab (https://www.scilifelab.se/units/bioimage-informatics/), the Image analysis node of the National Microscopy Infrastructure (http://www.nmisweden.se/), and the Centre for Image Analysis (https://www.cb.uu.se/) hosted at the Dept. of Information Technology.

DEPARTMENT WITH MAIN RESPONSIBILITY

Dept. of Information Technology

CONTACT PERSON/S

Carolina Wählby, carolina.wahlby@it.uu.se

APPLICATION

Submit the application for admission to: carolina.wahlby@it.uu.seSubmit the application not later than: March 25, 2023

Campus Solna Seminar Series: Kaja Harton and Inci Aksoylu
2023-04-06 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 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:

Kaja Harton

Magda Bienko – alpha 4

Mapping DNA in mitotic chromosomes

Inci Aksoylu

Ola Larsson – gamma 5

Translatome analysis of Tuberous Sclerosis Complex 1 patient-derived isogenic neural progenitor cells reveal rapamycin-dependent and independent alterations

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

Campus Solna Seminar Series: Sara Mravinacova and Humam Siga
2023-04-13 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:

Sara Mravinacova

Peter Nilsson – alpha 2

CSF synaptic protein pairs efficiently separate Alzheimer’s disease affected from unaffected individuals through adjustments for individual differences

Humam Siga

Afshin Ahmadian – alpha 3

Analysis of colorectal cancer, whole genome linked-reads data acquired by droplet barcode sequencing (DBS) technology

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

SciLifeLab Day Gothenburg
2023-04-17 09:00 - 17:00 | Conference Centre Wallenberg, Medicinaregatan 20A, Gothenburg, 413 90, Sweden
This event is a kick-off for the national SciLIfeLab site in Gothenburg. Learn more about the services and capabilities that are offered from SciLifeLab, both nationally and locally, and how you can participate in the activities!

The Gothenburg Site of SciLifeLab is happy to welcome the research community in Gothenburg and beyond to this kick-off. Meet with the established site, researchers, local and national infrastructures; interact with the SciLifeLab capabilities, Precision Medicine, Pandemic Laboratory Preparedness and Planetary Biology; learn about the Data Centre services and the Data Driven Life Science program and much more.

Read more

sign up here

Contact

gothenburg@scilifelab.se

Maria SmedhSciLifeLab GothenburgSite Coordinatormaria.smedh@gu.se 0766-229712

SciLifeLab Days on the other sites

Gothenburg, April 17

Umeå, September 11

Lund, September 28

Linköping, October 10

Workshop on Data Visualization in R - Lund
2023-04-17 09:00 - 2023-04-19 17:00 | Retina D227, Biologihuset, Sölvegatan 35, Lund, 223 62
A national course open for PhD students (prioritized), postdocs, researchers and other employees within Swedish universities who are interested in learning to produce publication quality plots using different packages in R.

Responsible teachers: Lokeshwaran Manoharan, Markus Ringner, Juliana Assis

Contact information: edu.plotting.r@nbis.se

Application

Course website

Important dates

Application open: February 23, 2023

Application deadline: March 31, 2023

Confirmation to accepted participants: April 3, 2023

Course fee

The fee for this on-site workshop is 2000 SEK to be paid by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced.

Note that travel and accommodation is not included in the fee and must be arranged by the participants.

Course description

This course aims to help researchers to visualize their data in different ways using R. This course will teach how to produce publication grade figures using R. A part of this course is also about making interactive plots that the researchers can view and share in a web-server to make interactive visualizations of their data.

Course content

In this course you will learn how to visualize your data in R.

In particular, you will learn how to:

format the data necessary for ggplot

make bar-charts, box-plots and others using ggplot

make PCA plots in ggplot

use R packages for heatmaps

plot data on maps using R (optional)

plot and handle phylogenetic trees in R (optional)

make interactive plots in R using Rshiny

host a Rshiny app in one of the available servers

Learning outcomes

By the end of the course the participant will be able to:

handle data in R for visualizations

apply the grammar efficiently in ggplot to obtain the desired plot

combine different data and/or different plots that are of publication-grade

write your own simple Rshiny app

deploy Rshiny apps in public servers.

Entry requirements

Required for being able to follow the course and to complete the plotting exercises:

familiarity with using R and Rstudio

a computer with R and Rstudio installed

installation of necessary R packages prior to the start of the course

Selection criteria

The course can accommodate 25 participants. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry.

Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

KI SciLifeLab Symposium
2023-04-18 08:00 - 17:00 | Nobel Forum, Nobels väg 1, Solna, Sweden
We welcome all KI researchers based at or affiliated with SciLifeLab to the second annual symposium which includes workshops, discussions and great opportunities to mingle!

Date: 18 april, 2023

Time: 09:00 – 17:00

Place: Nobel Forum, KI Campus Solna,Nobels väg 1, S-171 65 Solna Hitta på Google Maps

Registration deadline: 6 April, 2023

Contact: Science Officer, Adina Feldman (adina.feldman@ki.se)

registration

EIRENE Sweden Symposium on the Exposome
2023-04-18 09:00 - 12:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
This half-day symposium at SciLifeLab is hosted by Stockholm University and the National Facility for Exposomics at SciLifeLab, with the goal to increase scientific dialogue on the exposome, and to share perspectives on development of European infrastructure to support large scale exposomics.

Presentations will feature prominent figures in the exposomics field, including keynote lectures from leadership and international collaborators of EIRENE (Environmental Exposure Assessment Research Infrastructure), which is the first EU infrastructure (ESFRI Roadmap 2021) dedicated to human exposome research.

Zoom Link for Remote Participants: https://stockholmuniversity.zoom.us/j/63852683962

Time Speaker, Affiliation Title Session 1, Chaired by Jonathan Martin, Stockholm University 9:00-9:10 Åke Bergman, Örebro University Introductory Remarks, EIRENE Sweden 9:10-9:40 Jana Klánová, Masaryk University EIRENE: What is needed to fill a gap in the ESFRI landscape? 9:40-10:00 Roxana Merino Martinez, Karolinska InstitutetHEAP: Human Exposome Assessment Platform 10:00-10:30 Robert Barouki, Université de Paris Exposome and Toxicology 10:30-10:50 Coffee Break, Sponsored by ThermoFisher Scientific Session 2: Chaired by Craig Wheelock, Karolinska Institutet10:50-11:10 Tuulia Hyötyläinen, Örebro University Sex-specific effects of environmental exposure as contributor to initiation and progression to non-alcoholic fatty liver disease 11:10-11:40 Roel Vermeulen, Utrecht University Observations from The EXPANSE and EXPSOME-NL project 11:40-12:00 Jonathan Martin, Stockholm University Chemical exposomics in people and the environment End of Programme (lunch for those interested)
