SciLifeLab

MTLS Alumni Network Speaker Day
2021-12-03 10:00 - 15:00 (Europe/Stockholm) | Widerströmska Huset, Tomtebodavägen 18, Solna, Sweden
The joint master’s programme in Molecular Techniques in Life Science fosters graduates for a professional research career in life science. It has a strong focus on molecular techniques for disease therapies and diagnostic tools, coupled with substantial training in data analysis (bioinformatics and programming). The programme is a collaboration between Karolinska Institutet, KTH and Stockholm University at the Science for Life Laboratory in Stockholm, offering students the unique opportunity to study at all three institutions.

Facts

Date: Friday, December 3rdTime: 10:00-15:00Location: Widerströmska Huset, KI Campus Solna (Next to Scilifelab)

We are looking forward to welcoming alumni from Academia, Industry, and other science fields to this event, where they will share their wisdom and experience with current students.

Agenda:10:00-12:00 Session 112:00-13:00 Lunchbreak and Mingle13:00-15:00 Session 2

We will announce the speaker list closer to the event.

Learn more about the master’s programme here.

Campus Solna Seminar Series: Tojo James and Karl Olofsson
2021-12-02 13:00 - 14:00
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 Presentation of ongoing (unpublished) projects is strongly encouraged.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 13:00-13:50 and following current regulations, they will be broadcast via zoom.

This week

Single-cell transcriptional changes associated with drug response in AMLTojo James (Päivi Östling, alpha 4)

Multicellular tutor diskoids: A 3D cell culture geometry optimised for microscopyKarl Olofsson (Martin Viklund, gamma 3)

Registration

Register to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series, i.e. only one registration is necessary.

SciLifeLab COVID-19 seminars: Ralf Bartenschlager and Kristian Sandberg
2021-12-01 15:15 - 16:45 | Online event via Zoom
Topic: Drug screening and emerging viruses

The last of the five SciLifeLab COVID-19 seminars this autumn starts with Ralf Bartenschlager, Professor, Department of Infectious Diseases, Molecular Virology, Heidelberg University & Virus-associated Carcinogenesis, German Cancer Research Center, Heidelberg, talking about Architecture and biogenesis of ER-derived viral replication organelles.Kristian Sandberg, PhD, Associate Professor., and SciLifeLab Drug Discovery and Development Platform Co-Director at Uppsala University, then continues the seminar with his talk on Establishing a drug discovery platform for corona virus disease at SciLifeLab

Moderator: Marianna Tampere, KI

Registration is mandatory to get the Zoom link for the event

REGISTRATION

BIOS & ABSTRACTS

Uppsala PhD&Postdoc seminars: Weifeng Lin & Liza Löf
2021-11-30 11:00 - 11:50 | Online event via Zoom
Welcome to SciLifeLab Uppsala PhD&Postdoc seminars!We are very happy to host exciting talks by PhD students and Postdocs from a great variety of fields within SciLifeLab.The seminars will take online place every Tuesday from 11:00 to 11:50

For this occasion the seminars will be: Weifeng Lin, PhD student in Globisch labTitle: Unique chemoselective probes for discovery and investigation of metabolites in human samples with enhanced mass spectrometric sensitivityLiza Löf, Postdoc in Landegren Lab (Molecular Tools)Title: Development of methods to characterize the impact on signaling pathways by targeted therapy in chronic myeloid leukemia

Link to seminar

Swedish Microfluidics in Life Science 2021
2021-11-30 10:30 - 2021-12-01 15:00 | Lund University, Lund, Sweden
The Swedish Microfluidics in Life Science meeting gathers researchers in the field of micro- and nanofluidics. The meeting offers an opportunity to present your research, to network with researchers at Swedish universities, institutes and companies , and to listen to invited talks by a panel of well reputed research leaders. Confirmed speakers are Stefan Löfås (Innovido AB), Edith Hammer (Lund University), Christoph Merten (Ecole Polytechnique Fédérale de Lausanne), Anja Boisen (‎Technical University of Denmark) and Madhavi Krishnan (University of Oxford)

Save the date and please help spread this information in your groups and local networks.

Read more

Clinical Talks: The road towards precision medicine in Sweden
2021-11-26 09:00 - 09:30 | Online event via Zoom
On November 26, we will host Karolinska Institutet (KI) Professor Richard Rosenquist Brandell. In addition to his academic research and clinical work, he also co-founded the Genomic Medicine Sweden (GMS) initiative and serves as the Director of GMS. Richard will share his insights on Sweden’s national strategy to implement precision medicine into our healthcare environment and pave the way for the amazing potential the approach has to offer. To benefit from the sustainable advantages of tailored and efficient use of diagnostics and treatment options, Sweden needs to prepare our society for the legal challenges and infrastructures necessary to support and enable this transformation.

Read more about clinical talks

Richard Rosenquist Brandell, MD, PhD, is Professor of Clinical Genetics at Karolinska Institutet, Senior Physician at Karolinska University Hospital and director of Genomic Medicine Sweden, a national infrastructure for implementation of precision medicine. He obtained his MD degree in 1996, and later his PhD in Medicine in 1998, from Umeå University. In 2000 Richard joined Uppsala University Hospital (“Akademiska Sjukhuset”) and in 2007 became a Professor at the Department of Immunology, Genetics and Pathology, Uppsala University. In April 2017, he relocated to the Karolinska University Hospital as a Senior Physician and Professor. Richard’s work focuses on hematological malignancies and utilizing high-throughput sequencing technologies, his team has identified novel prognostic and predictive biomarkers that have significantly improved patient risk-stratification. Dr Rosenquist Brandell is also a member of the Nobel Assembly at Karolinska Institutet.

Genomic Medicine Sweden (GMS) started as a bottom-up initiative within the national Clinical Genomics Platform (previously named the Diagnostics Development platform) at the Swedish Science for Life Laboratory (SciLifeLab). In 2017 and 2018 discussions with funding agencies, decision-makers, healthcare providers, patient organisations, universities, and industry led to the founding of GMS as a national venture. GMS strategic mission is to foster collaboration between healthcare providers, academia, patient organizations and industry and realize precision medicine by effectively utilizing the rapidly advancing sequencing technologies to provide the highest standards of genomic testing in routine clinical care throughout Sweden.

Registration

Campus Solna Seminar Series: Casper Winsnes and Morteza Aslanzadeh
2021-11-25 13:00 - 14:00
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 13:00-13:50 and following current regulations, they will be broadcast via zoom.

This week

Casper Winsnes (Emma Lundberg, alpha 2)

The impact of miRNAs on Variation and Covariation of Proteins in Single CellsMorteza Aslanzadeh (Marc Friedländer, gamma 5)

Registration

Register to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series, i.e. only one registration is necessary.

Uppsala PhD&Postdoc seminars: Gang Pan & Adrian Garcia Concejo
2021-11-23 11:00 - 11:50 | Online event via Zoom
Welcome to SciLifeLab Uppsala PhD&Postdoc seminars!We are very happy to host exciting talks by PhD students and Postdocs from a great variety of fields within SciLifeLab.The seminars will take online place every Tuesday from 11:00 to 11:50

For this occasion the seminars will be: Gang Pan, Researcher in Claes Wadelius´ research groupTitle: Trs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 ExpressionAdrian Garcia Concejo, Postdoc in Dan Larhammar´s research groupTitle: Regulation of memory receptors by protein kinase C

LINK to Seminar:

SciLifeLab AI Seminar Series: A sneak peek into the future of AI-assisted life science
2021-11-23 10:00 - 11:00
SciLifeLab Data Centre hosts a seminar series on the topic of applied AI in life science research. SciLifeLab AI Seminar Series combines scientific highlights from SciLifeLab-affiliated researchers and invited experts on the general topic of AI applications in Life Science.

The seminar will be held physically at SciLifeLab Gamma 7 lunch room in Solna and online via Zoom. Physical participation is recommended since some AI models are not allowed to be shown via streaming and there will be no recording after the seminar according to the live demonstration policy of OpenAI.

Contact: Prof. Ola Spjuth, AI coordinator, SciLifeLab Data Center.

Speaker: Wei OUYANGKTH Royal Institute of Technology and Science for Life Laboratory

Abstract

Have you imagined how AI may one day help you with your research by proposing new ideas, running experiments, analyzing data, and even writing manuscripts? While current AI systems are too weak for those tasks, we are closer than ever before!

In June 2020, OpenAI revealed the most advanced AI model in the world, GPT-3. It is the largest natural language processing model ever created with 175 billion parameters, trained on about 45TB of text data, and it cost $12 million for a single training run that may be utilized and reused for many tasks. Not only are these numbers impressive, its “text in, text out” interface can be used as a general purpose tool for almost any language task with impressively good performance. With the newly released Codex model (a descendant of GPT-3), it can even generate source code in popular programming languages by following instructions in natural languages, e.g., English. GPT-3 not only brings us to a new paradigm of AI-assisted coding, but it also has a great potential to address long-standing challenges in deep learning about generalization and interpretability.

We are excited to share with you what we have learned so far about GPT-3 and its applications in life science. In this talk, we will give you an overview and discuss the promises and pitfalls of GPT-3. You will also see live demos in biomedical applications, such as processing genomic sequences, analyzing microscopy images, and creating user-friendly software with graphical user interfaces (GUIs). Hopefully, this session will serve as inspiration for your own research, serve as a basis for discussion about AI in life science, and convey how these tools may accelerate data-driven life science at SciLifeLab.

Biography

Wei OUYANG is a researcher in Prof. Emma Lundberg’s group at the Science for Life Laboratory and KTH Royal Institute of Technology. He has a diverse background across several different fields including material science, computer science and advanced microscopy imaging. In 2018, Dr. Ouyang obtained his PhD in computational image analysis at Institut Pasteur, Paris where he mainly focuses on applying deep learning for super-resolution microscopy. During this period, he developed a deep learning method called ANNA-PALM which massively accelerates super-resolution localization microscopy by 100x. To address the challenges in the dissemination of AI tools, he developed an open-source computational platform, ImJoy, which makes deep learning tools easier to build and more accessible to the user. He is actively involved in consortiums and community activities for promoting more open, scalable, accessible and reproducible scientific tools. Dr Ouyang has been focusing on AI augmented microscopy imaging and data-driven whole cell modeling. More recently, he is excited about the recent progress in the field of AI and has a knee interest in exploring the next generation of data-driven life science powered by AI, robotics, blockchain and decentralized applications.

Register here

The Svedberg seminar series: Prof. Tuuli Lappalainen
2021-11-22 15:15 - 16:30 | Online event via Zoom
Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden

New York Genome Center, New York, USA

LINK TO SEMINAR

Tuuli Lappalainen is a Professor in Genomics at KTH Royal Institute of Technology, an Associate Faculty Member at the New York Genome Center, and the Director of the National Genomics Infrastructure of SciLifeLab. She is also an Adjunct Professor at the Department of Systems Biology at Columbia University.

Her research focuses on functional genetic variation in human populations and its contribution to traits and diseases. She has pioneered the intergration of large-scale genome and transcriptome sequencing data to understand how genetic variation affects gene expression, providing insight to cellular mechanisms underlying genetic risk for disease.

Functional variation in the human genome: lessons from the transcriptome

Detailed characterization of molecular and cellular effects of genetic variants is essential for understanding biological processes that underlie genetic associations to disease. A particularly scalable approach has been linking genetic variants to effects in the transcriptome that is amenable for scalable measurements in human populations and in experimental settings, including at the single cell level. Our multi-omic analysis in human cohorts in the TOPMed project has identified genetic and environmental effects on molecular variation together with their complex interplay with clinical phenotypes. Furthermore, in this talk I will discuss how CRISPRi silencing of regulatory elements followed by single-cell analysis provides novel insights of mechanisms of genetic associations to complex traits. Altogether, these diverse approaches for integration genome and transcriptome data uncover functional genetic architecture of human traits, and enhances our understanding of both basic biology and precision medicine applications.

Host: Jessica Nordlund, Uppsala University

DDLS Conference: Strategic research areas - postponed!
2021-11-22 08:30 - 17:00
Join us at the first conference within The SciLifeLab and Wallenberg national program for Data-Driven Life Science!

The practice of life science is continuously becoming more data-dependent. The amount and complexity of data is growing exponentially, and more scientific discoveries are enabled when data is openly available to researchers across the world. This is the basis for the SciLifeLab and Wallenberg National Program on Data-Driven Life Science (DDLS).

The program focuses on four strategic areas for data-driven research, all of which are essential for improving the lives of people as well as animals and nature, detecting and treating diseases, protecting biodiversity and creating sustainability:

Cell and molecular biologyEpidemiology and infection biologyEvolution and biodiversityPrecision medicine and diagnostics

The conference will focus on enthusing research within the four research areas and aims to bring together researchers within the field for discussion and sharing the latest within the research areas. The meeting will offer an exciting compilation of keynotes, special lectures within the four fields and opportunities to meet and discuss with prominent researchers.

Anyone with interest in the data-driven research field is welcome to participate. The full-day conference will be virtual (Zoom).

The program with confirmed speakers will be available shortly.

The conference is part of the SciLifeLab and Wallenberg national program for the DDLS program, funded by the Alice and Knut Wallenbergs Foundation.

Introduction to bioinformatics using NGS data - ONLINE
2021-11-22 08:00 - 2021-11-26 17:00
National workshop for PhD students, postdocs, researchers, and other employees within Swedish academia. This workshop is organized by the National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI).

Due to the Covid-19 situation, this workshop will be held online.

If you have questions regarding the workshop, please email: edu.intro-ngs@nbis.se

Important dates

Application opens: August 16, 2021

Application closes: October 10, 2021

Confirmation to accepted students: October 15, 2021

Responsible teachers

Malin Larsson, Martin Dahlö, Roy Francis

Course 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

Course content

This intense one-week workshop provides an introduction to the analysis of next generation sequencing data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures.

After this workshop you should be able to:

Describe the basic principles of next generation sequencing.Use the Linux command line interface to manage simple file processing operations, and organize directory structures.Connect to and work on a remote high performance compute cluster.Apply programs in Linux for analysis of NGS data.Summarise the applications of current NGS technologies, including the weakness and strengths of the approaches and when it is appropriate to use which one of them.Explain common NGS file formats.Interpret quality control of NGS reads.Explain the steps involved in variant calling using whole genome sequencing data.Independently perform a basic variant calling workflow on example data.Explain the steps involved in differential gene expression using RNA seq data.Independently perform differential gene expression analysis on example data.

Entry requirements

A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable. To get the maximum benefit from the workshop we would like you to

Have relevant previous experience in sequencing or analysis.Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing.It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others.

Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance.

Link to application

The application opens on August 16, 2021.

Nurturing wellbeing in academia
2021-11-18 14:15 - 15:45 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
DEI committee continues series of events “Our community, ourselves” dedicated to raising awareness and improving mental health in Academia. The following event “Nurturing wellbeing in academia” is brought to us by Deborah Rupert and Frida Rångtell, well-being coaches from “Dear Academia”. Dear Academia offers interactive seminars and holistic workshops focused on individual mental wellbeing, burnout prevention, peer-to-peer support and creation of healthy environment in academic settings.

More information here: https://deborahrupert.com/dear-academia/

We are each other’s working environment. Nurturing taking care of ourselves and of each other is one key aspect of cultivating a healthy academic work environment – together with active conscious leadership.

At an interactive webinar where we will explore how to create a human friendly work environment covering how to:

Improve your sleep and implement healthy routinesDevelop strategies to manage your stress and grow resilienceBe an ally to cultivate wellbeing at work

Taking care of our mental health is paramount to the individual wellbeing, performance and to a healthy working culture.

join zoom meeting 18 November 14:15

Speakers:

Deborah Rupert, PhD

Wellbeing and career coach, Dear Academia

Déborah Rupert is the founder of Dear Academia and is a wellbeing and career coach. She is certified from the International Coaching Federation and holds a PhD in biological physics from Chalmers Technical University, Sweden. She is dedicated to burnout prevention and supporting researchers with mental clarity and career strategy. She is a career coach for researchers in career transition at Trygghetsstiftelsen and the nordic director of Enkindle Global, focusing on burnout prevention for individual change makers and leaders within organisations.

Frida Rångtell, PhD

Sleep and habits educator, Dear Academia

Frida Rångtell has a PhD in sleep and memory from Uppsala University, Sweden. Today she works as a sleep and habits educator, scientific advisor and runs Slumra of Sweden.

Campus Solna Seminar Series: Haris Babacic and Gustavo Jeuken
2021-11-18 13:00 - 14:00
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 13:00-13:50 and following current regulations, they will be broadcast via zoom.

This week

Plasma proteome alterations in glioblastoma: preliminary resultsHaris Babacic (Janne Lehtiö, alpha 1)

Pathway Activity-based Survival AnalysisGustavo Jeuken (Lukas Käll, gamma 6)

Registration

Register to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series, i.e. only one registration is necessary.

Uppsala PhD&Postdoc seminars: Niki Sarri & Ankit Gupta
2021-11-16 11:00 - 11:50 | Online event via Zoom
Welcome to SciLifeLab Uppsala PhD&Postdoc seminars!We are very happy to host exciting talks by PhD students and Postdocs from a great variety of fields within SciLifeLab.The seminars will take online place every Tuesday from 11:00 to 11:50

For this occasion the seminars will be: Niki Sarri, PhD student in Carl-Henrik Heldin’s research groupTitle: Deubiquitinating enzymes USP4 and USP17 fine-tune the trafficking of PDGFRβ and affect PDGF-BB-induced STAT3 signallingAnkit Gupta, PhD student in Wählby lab, Division of Visual Information and InteractionTitle: SimSearch: A Human-in-the-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images

ELIXIR Tools for Reproducible Research - ONLINE
2021-11-15 09:00 - 2021-11-19 14:30
Elixir / NBIS course open for PhD students, postdocs, group leaders and core facility staff interested in making their computational analysis more reproducible. International applications are welcome, but we will give approximately half of the participant slots to applicants from Swedish universities at minimum, due to the national role NBIS plays in Sweden.

The course is organized by NBIS (ELIXIR-SE).

Responsible teachers: John Sundh, Erik Fasterius, Verena Kutschera

Contact information: edu.trr@nbis.se

Application

Course website

Important dates

Application open: September 1

Application deadline: October 15

Confirmation to accepted participants: October 22

Course 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 2,000 SEK.*Please note that NBIS cannot invoice individuals

Course description

One of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis, e.g. bioinformatics or computational biology, have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete, undocumented and/or unavailable code. This essentially prevents any possibility of attempting to reproduce the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication based on computational analysis should be distributed along with all the raw data and metadata used in the study, all the code and/or computational notebooks needed to produce results from the raw data, and the computational environment or a complete description thereof.

Reproducible research not only leads to proper scientific conduct but also provides other researchers the access to build upon previous work. Most importantly, the person setting up a reproducible research project will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self!

Course content

In this course you will learn how to make your data analyses reproducible. In particular, you will learn:

good practices for data analysishow to use the version control system git to track edits and collaborate on codinghow to use the package and environment manager Condahow to use the workflow managers Snakemake and Nextflowhow to use R Markdown to generate automated reportshow to use Jupyter notebooks to document your ongoing analysishow to use Docker and Singularity to distribute containerized computational environments

Entry requirements

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

familiarity with using the terminal (e.g. be familiar with commands such as ls, cd, touch, mkdir, pwd, wget, man, etc.)a computer with a webcamYou will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the coursesome knowledge in R and/or python is beneficial but not strictly required

Selection criteria

The course can accommodate 20 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.

Meet the BioInnivation Institute
2021-11-15 09:00 - 09:30 | Online event via Zoom
BioInnovation Institute (BII) is an international commercial foundation with a non-profit objective supported by the Novo Nordisk Foundation. BII operates an incubator to accelerate world-class life science innovation that drives the development of new solutions through the creation of life science start-ups for the benefit of people and society. BII offers help to early-stage projects and start-ups in health tech, bio-industrials and therapeutics through their two programs VentureLab and Creation House.

The programmes are open for applications twice a year. The next application deadlines are November 25th 2021 for Creation House and February 24th 2022 for Venture Lab.

Learn more about the call on Monday, November 15, 09:00.

RNA-seq data analysis ONLINE
2021-11-15 08:00 - 2021-11-19 17:00
This workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of online lectures and computer practicals. The workshop will be held online.

Important dates

Application open: August 27, 2021Application deadline: October 15, 2021

Responsible teacher/s

Johan Reimegård, Julie Lorent

Contact information for questions regarding the course

edu.rnaseq@nbis.se

Course fee

This online workshop has no fee. However, if you accept a position and do not participate you will be invoiced* 1300 kr

*Please note that NBIS cannot invoice individuals

Course content

Topics covered will include:

RNA seq introductionRNA seq read mapping programsRNA seq QC analysisDifferential expression analysisGene set enrichment analysis

More details about the course can be found at the previous year’s webpage

The course will follow similar structure and topics.

Entry requirements

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

Basic knowledge in Linux and RSteady and fast internet connection to be able to follow the workshop.Your own laptop with the following specs:At least 6 GB of RAM. Operating system Win10, OS X or LinuxAt 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 practise 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.

Link to application

[Drug Discovery Seminar] PROTAC Degraders: From Fundamental Chemical Biology to Translation and Entrepreneurship
2021-11-12 14:00 - 15:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
SciLifeLab Drug Discovery Seminars, hosted by the DDD platform, is a series of educational lectures about recent developments, technologies, and trends in drug discovery and development that aims to enlighten, and spark a discussion, within the Swedish drug discovery community.

Alessio Ciulli

Professor of Chemical Structural Biology

Centre for Targeted Protein Degradation, School of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee

Abstract

Proteolysis-targeting chimeras (PROTACs) are a new class of chemical tools and drugs that target disease-causing proteins for degradation. They are designed to harness the cell’s natural disposal system (the ubiquitin-proteasome) to specifically remove proteins. A PROTAC is a two-headed (i.e. bifunctional) molecule where one end binds an enzyme (an E3 ubiquitin ligase) and the other binds the target protein, bringing the two proteins into close proximity as a ternary complex. The ligase is then able to label the target protein for ubiquitination and so degradation by the cell’s disposal system. Whereas conventional drugs only inhibit disease proteins by binding and locking up their most important functional parts for the duration of the drug’s action, PROTACs can bind at any positions and rapidly cause the disease protein’s permanent and long-lasting destruction. Due to this revolutionary mode of action, PROTACs can attack targets previously thought ‘undruggable’.

In my lecture, I will outline some key discoveries from my laboratory that have advanced the chemical structural biology of PROTACs, and are providing fundamental insights into our understanding of their molecular recognition, mechanism of action and drug design. I will also offer insights from our efforts to translate this fundamental science into molecular therapeutics to benefit patients, via both partnerships with big pharma and formation of company spin-outs. Finally I will highlight the vision and mission of our recently announced new Centre for Targeted Protein Degradation at Dundee.

Short Bio

Alessio Ciulli holds the Personal Chair of Chemical Structural Biology at the School of Life Sciences, University of Dundee. He is also the Director of the newly announced Dundee’s Centre for Targeted Protein Degradation (CeTPD). Dr Ciulli’s laboratory has made important contributions to selective chemical intervention on protein-protein interactions targets and to the development of proteolysis-targeting chimeric molecules (PROTACs) as a viable strategy for targeted protein degradation. Amongst his most significant discoveries are the fragment-based design of ligands for the E3 ligase von Hippel-Lindau (VHL), and their use to design one of the first VHL-based PROTACs: the BET degrader MZ1. Dr Ciulli’s Lab later illuminated fundamental insights into PROTACs’ mechanism of action, solving the first crystal structure of a PROTAC ternary complex. Dr. Ciulli is the scientific founder of Amphista therapeutics, a company that develops new protein degradation platforms. Before joining Dundee, Dr Ciulli was a group leader at the University of Cambridge, where he previously earned his PhD degree. Amongst his honours are the EFMC Prize for Young Medicinal Chemist in Academia, the RSC Capps Green Zomaya Award in medicinal computational chemistry, and election as Fellow of the Royal Society of Chemistry.

Registration

Open webinar: How can SciLifeLab, MAX IV and ESS contribute to drug discovery and development?
2021-11-12 13:00 - 14:30 | Online event via Zoom
During this seminar the three large-scale research infrastructures – SciLifeLab, MAX IV and ESS – will present their offer to the Life Science industry in form of advanced technologies in the shape of research infrastructure, as well as relevant data support and structures. Together they can provide technologies ranging from genomics, proteomics, genome engineering and drug discovery, to X-ray beamlines and the most powerful neutron source worldwide.

The webinar is a joint venture between Lif and InfraLife, the initiative that serve as a hubconnecting stakeholders, displaying the potential of the advanced technologies, and making these unprecedented tools accessible to be utilized in addressing complex research questions.Who should attend?

Everyone who works within pharma industry and the Life Science-ecosystem in Sweden and iscurious about what services these three major national infrastructures can offer and how to starta research project.

Registration

Preliminary program:

WelcomeFrida Lundmark, Lif

The InfraLife projectElin Jonsson and Josefin Lundgren Gawell, project coordinators InfraLife

SciLifeLab – possibilities in drug discovery & DevelopmentPer Arvidsson, Director Drug Discovery & Development platform, SciLifeLab

Cryo-EM recent development and great possibilities for drug researchMarta Carroni, Platform Director, Cell and Molecular Imaging, SciLifeLab

The MAX IV synchrotron and possibilities for Life ScienceSelma Maric, Industrial Relations, Life Science and Soft Matter, MAX IV

Neutron research possibilities for drug development and the European Spallation Source (ESS)Zoë Fisher, Group Leader for Deuteration and Macromolecular Crystallisation, ESS

Industry examples from X-ray and neutron experimentsEmanuel Larsson, Postdoctoral fellow, Solid Mechanics, Expert Lunarc (Centre for Scientific and Technological Computing), Lund University

Time for questions

Wrap up and future perspectives

Campus Solna Seminar Series: Michael Hawgood and Akshay Sridhar
2021-11-11 13:00 - 14:00
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 13:00-13:50 and following current regulations, they will be broadcast via zoom.

This week

Exploring DNA Replication Using Super Resolution and Expansion MicroscopyMichael Hawgood (Jiri Bartek, alpha 5)

Lipid modulation of membrane protein functionAkshay Sridhar (Lucie Delemotte/Erik Lindahl)

Registration

Register to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series, i.e. only one registration is necessary.

[Drug Discovery Seminar] How protein degradation led to faculty entrepreneurship at Yale: A personal Perspective
2021-11-10 14:00 - 15:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
SciLifeLab Drug Discovery Seminars, hosted by the DDD platform, is a series of educational lectures about recent developments, technologies, and trends in drug discovery and development that aims to enlighten, and spark a discussion, within the Swedish drug discovery community.

Craig Crews

John C. Malone Professor of Molecular, Cellular, and Developmental Biology and Professor of Chemistry, of Pharmacology, and of Management; Executive Dirictor, Yale Center for Molecular Discovery, Yale University

Abstract

Prof. Crews is the 2021 recipient of the Scheele prize from the Swedish Pharmaceutical Society for his seminal work on protein degradation. In this talk Prof. Crews will discuss his efforts to translate research from his lab into new biopharma ventures. To date, these entrepreneurial efforts have resulted in a FDA approved drug (Kyprolis) and a new therapeutic modality (PROTACs). While each of his four companies has been launched based on different science, they have all followed a similar business model and Prof. Crews will discuss efforts at Yale to ’systematize’ faculty entrepreneurism via a core ‘biotech accelerator’ facility.

registration

Biography

Crews is the John C. Malone Professor of Molecular, Cellular and Developmental Biology and holds joint appointments in the departments of Chemistry and Pharmacology at Yale University. He graduated from the U.Virginia with a B.A. in Chemistry and received his Ph.D. from Harvard University in Biochemistry. Dr. Crews has a foothold in both the academic and biotech arenas; on the faculty at Yale since 1995, his laboratory has pioneered the use of small molecules to control intracellular protein levels.

In 2003, he co-founded Proteolix, Inc., whose proteasome inhibitor, Kyprolis™ received FDA approval for the treatment of multiple myeloma. Since Proteolix’s purchase by Onyx Pharmaceuticals in 2009, Dr. Crews has focused on a new drug development technology, which served as the founding intellectual property for his latest New Haven-based biotech venture, Arvinas, Inc.

Currently, Dr. Crews serves on several editorial boards and was Editor of Cell Chemical Biology (2008-2018). In addition, he has received numerous awards and honors, including the 2013 CURE Entrepreneur of the Year Award, 2014 Ehrlich Award for Medicinal Chemistry, 2015 Yale Cancer Center Translational Research Prize, a NIH R35 Outstanding Investigator Award (2015), the AACR Award for Chemistry in Cancer Research (2017), Khorana Prize from the Royal Society of Chemistry (2018), Pierre Fabre Award for Therapeutic Innovation (2018), the Pharmacia-ASPET Award for Experimental Therapeutics (2019), the Heinrich Wieland Prize (2020) and the Scheele Prize (2021). In 2019, he was named an American Cancer Society Professor.

Insights into EMBO’s Fellowship Programme
2021-11-09 15:00 - 16:00 | Online event via Zoom
Kelly Sheehan-Rooney, Head of the Fellowship Programme at EMBO, will give an overview of the eligibility and evaluation criteria of EMBO’s Postdoctoral Fellowships, Scientific Exchange Grants, and the New Venture Fellowships. She will also give some top tips for grant writing, and an insight into her career move from academic research to international research development.

Kelly Sheehan-Rooney is Head of the Fellowship Programme at EMBO. She obtained her PhD in Developmental Biology from the University of Manchester, UK, before carrying out a three-year postdoctoral position at the University of Texas in Austin, USA. Now with 10 years’ experience in international research development, Kelly has worked with thousands of scientists across the world; supporting them in their various careers, building collaborative networks, and fostering a research environment where scientists can achieve their best work.

Researchers in all stages of their career are welcome to attend and could find the talk useful. The fellowships are a great opportunity for early-stage researchers as well as for group leaders to further their research interests and consider new avenues to expand into high quality research ideas.

Meeting Flyer

The curious case of a leak channel that never wants to be open
2021-11-09 10:00 - 11:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Stephan Pless, PhD

Professor of Molecular and Cellular PharmacologyUniversity of Copenhagen, Denmark

The Pless lab is interested in the molecular function and pharmacology of ion channels. These complex membrane proteins regulate cellular excitability by controlling the flux of ions across cell membranes in response to a diverse set of stimuli. Their dysfunction is associated with numerous diseases, resulting in an ever-increasing demand for new drugs targeting these fascinating molecules.

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Annual lecture in structural biology by Jennifer Lippincott-Schwartz
2021-11-08 16:00 - 17:00 | Biomedicum, Solnavägen 9, Solna
Jennifer Lippincott-Schwartz from the Howard Hughes Medical Institute will give the lecture entitled ‘Emerging Imaging Technologies to Study Cell Architecture, Dynamics, and Function’ on November 8, 2021 at 4.00pm in the Biomedicum lecture theatre. Using cutting-edge, superresolution imaging technology to visualize cellular activity at the nano-scale, Lippincott-Schwartz lab has redefined how we look at protein dynamics in the cell.

The annual lecture series is set up in the recognition of the development of electron microscopy and will be delivered by eminent scientists in the field of structural biology and molecular visualisation. The event is open to anyone. A holder of the lectureship will particularly spend time with students and postdocs. Therefore, Jennifer will also give an account of her career path and discuss with students and postdocs at 09.30am in the SciLifeLab Air&Fire auditorium.

About Jennifer Lippincott-Schwartz

Research in Lippincott-Schwartz lab is aimed at developing live cell imaging to elucidate the dynamics inside eukaryotic cells. She pioneered photobleaching and photoactivation techniques which allow investigation of subcellular localization, turnover and trafficking of important cellular proteins related to membrane compartmentalization. Her work on photoactivatable GFP led to the development of one of the first super-resolution imaging technologies, photoactivation localization microscopy. Jennifer then used her methods to assess organelles dynamics and interactions revealing a novel picture of how the peripheral endoplasmic reticulum is structured. In addition, the Golgi apparatus is central to Jennifer’s studies, where her team demonstrated a novel pathway of enzymes recycling important for the organelle’s biogenesis and maintenance. Together, the obtained findings have provided insights into how genetic diseases affect proteins that help shape the endoplasmic reticulum.

In 2016, Lippincott-Schwartz initiated the Neuronal Cell Biology Program at Janelia. She is Fellow of the American Academy of Arts and Sciences Fellow, and also Honorary Fellow of the Royal Microscopical Society.

Background information

The annual lecture in structural biology is named in honour of Fritiof Sjöstrand, who pioneered the electron microscopy in Sweden. In the early 1950’s he developed an advanced microtome for thin sectioning, and by applying it for structural analysis of mitochondria produced a major breakthrough with the determination of the double membrane system. He then engineered a next generation of microtomes using electrical heating of the specimen to advance it toward the knife, and the instrument became known as the ‘‘Sjöstrand Ultramicrotome”. In 1959, Fritiof Sjöstrand moved to UCLA, where his research focused on mitochondrial membranes and retinal synapses. Fritiof Sjöstrand founded and was Editor in Chief of the Journal of Structural Biology for 33 years. Lectures in the previous years were given by Venki Ramakrishnan and Jennifer Doudna.

Contact

Alexey Amunts, amunts@scilifelab.se

The Svedberg seminar series: Ass. Prof. Maria Kasper
2021-11-08 15:15 - 16:30 | Online event via Zoom
Karolinska Institutet, Department of Cell and Molecular Biology, Sweden

LINK TO SEMINAR

Maria Kasper is Associate Professor at the Karolinska Institutet in Stockholm, Department of Cell and Molecular Biology. She received her PhD at the University of Salzburg in genetics, with the majors in human genetics and molecular tumor biology. She came to Sweden in 2007, where she spent a fruitful postdoctoral time in Rune Toftgårds lab, and in 2013 she started her own lab focusing on skin, stem cell biology and single-cell RNA sequencing. In 2016, her lab pioneered the use of single-cell transcriptomics in the organ skin and has overall contributed with important work in skin biology and regenerative medicine. Maria has received a number of national recognitions such as the Framtidens Forskningsledare from SSF, Ragnar Söderberg Fellow in Medicine and the CIMED young investigator award, as well as the prestigious international LEO Foundation Gold Award for outstanding skin research. Since 2020, she also coordinates together with Fiona Watt the Human Cell Atlas bionetwork for the organ skin.

Decoding the molecular anatomy of skin

Skin architecture and its function are determined by a rich variety of epithelial, mesenchymal and immune cells that together orchestrate skin homeostasis, including cyclical hair growth and barrier function. Previously, my lab generated a comprehensive molecular and spatial atlas of epithelial and stromal cells during hair growth and rest. These studies revealed underlying molecular programs during progenitor-cell commitment and lineage differentiation, as well as spatiotemporal fibroblast heterogeneity and potential epithelial-stromal interactions. The importance of cell-type specific signaling during homeostasis, and the unrecognized potential of cell-type restricted signaling-changes were exemplified by our recent discovery of how to induce new hair follicles in adult mouse skin by modulating a single signaling pathway. Building on the molecular knowledge and computational skills gained, our ongoing work uncovers new insights in the molecular orchestration of embryonic hair follicle development, as well as the coordination of adult skin stem cell differentiation by tissue resident immune cells.Host: Gabriella Lindgren, SLU

Career path discussions with Jennifer Lippincott-Schwartz
2021-11-08 09:30 - 10:30 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Jennifer Lippincott-Schwartz from the Howard Hughes Medical Institute will give an account of her career path and discuss with students and postdocs at 09.30 in the SciLifeLab Air&Fire auditorium. Since the number of places is limited, please register below to participate in this session.

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Using cutting-edge, superresolution imaging technology to visualize cellular activity at the nano-scale, Lippincott-Schwartz lab has redefined how we look at protein dynamics in the cell. When describing her mentorship philosophy, Jennifer comments that she encourages her group members to develop their own projects. It is only when a colleague feels that he or she “owns” the project that real dedication, determination, and creativity emerge. In developing projects, she considers it is important to build on the strengths and interests of students and postdocs, rather than focusing exclusively on a group leader’s specific interests at the time.

The annual lecture series is set up in the recognition of the development of electron microscopy and will be delivered by eminent scientists in the field of structural biology and molecular visualisation. The event is open to anyone. The main lecture will take place at 4.00pm in the Biomedicum Lecture Theatre.

Contact

Alexey Amunts, amunts@scilifelab.se

Campus Solna Seminar Series: Eva Gracia Villacampa and Lilit Nersisyan
2021-11-04 13:00 - 14:00
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 13:00-13:50 and following current regulations, they will be broadcast via zoom.

This week

Genome-wide Spatial Expression Profiling in FFPE tissuesEva Gracia Villacampa (Joakim Lundeberg, alpha 3)

RNA degradation analysis reveals ribosome dynamics in complex microbiome samplesLilit Nersisyan (Vicent Pelechano, gamma 5)

Registration

Register to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series, i.e. only one registration is necessary.

SciLifeLab COVID-19 seminars: Lars Juhl Jensen and Sonja Aits
2021-11-03 15:15 - 16:45 | Online event via Zoom
The fourth seminar in this series starts with Lars Juhl Jensen, Professor, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, who will talk about From intraspecies protein networks to host–pathogen networks.

Sonja Aits, Associate senior lecturer at Cell Death, Lysosomes and Artificial Intelligence, Lund University, then continues the seminar with a talk on Text mining for COVID-19 knowledge extraction

Registration is mandatory to get the Zoom link for the event

REGISTRATION

BIOS & ABSTRACTS

BioImage Informatics Call4Help Webinar: CellPose
2021-11-02 09:00 - 10:00
For our next Call4Help session we are organizing a tool-presentation seminar about CellPose, a generalist algorithm for cell and nuclei segmentation. CellPose is a deep learning-based segmentation method trained on a wide range of image types. It can be applied to both 2D and 3D images.

During this seminar we will explore different ways to run CellPose, including demos powered by the ImJoy server which aim to make it easier for users to analyse large datasets in computing clusters. The webinar will be given by Gisele Miranda (BIIF) and Wei Ouyang (KTH, developer of ImJoy) and will take place on November 2nd, 09:00-10:00. There will be time for questions and discussion, so we hope this event to be very interactive. Please register here.

registration

Important links

https://github.com/MouseLand/cellposehttps://imjoy.io/
