SciLifeLab

SciLifeLab Bioinformatics Platform NBIS celebrates 15 years
2023-11-24 10:00 - 16:00 (Europe/Stockholm) | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
NBIS celebrates 15 years and organises an Anniversary Symposium on Friday 24 November at 10:00 – 16:00 with mingle afterwards in Uppsala, SciLifeLab Trippelrummet.On the agenda so far:KeynotesPresentation of Human Protein Atlas (HPA) by Mathias UhlénPresentation of Bigpicture by Jeroen van der LaakUser presentations2–3 user presentations (users of the national bioinformatics infrastructure NBIS)NBIS presentationsPresentation of NBIS 15 years and ELIXIR 10 years by Bengt PerssonPresentation of WABI 10 years by Björn NystedtHuman data — 1+MG och GDI (Anna Hagwall/Johan Viklund)Presentation of our Training activities by Jessica LindvallPresentation of computational support by Jonas SöderbergData management – enable FAIR data for Swedish research (Niclas Jareborg)Mingle afterwards with drinks and finger food.Preliminary programme and link to registration available

Read more

[The Svedberg seminar] - Brain-wide hierarchical and multiplexed encoding of behaviour in C. elegans
2023-11-27 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Manuel Zimmer

Professor Department of Neuroscience and Developmental Biology, The University of Vienna

Bio

Manuel Zimmer studied biochemistry at the Free University of Berlin and performed his undergraduate thesis in 1998 on neuromuscular synapse formation with Steve Burden at the Skirball Institute of Biomolecular Medicine, New York University Medical School, New York. Afterward, he moved back to Germany to perform his Ph.D. work with Rüdiger Klein at the European Molecular Biology Laboratory in Heidelberg and the Max Planck Institute of Neurobiology in Munich, until 2003. Here, he focused on the molecular mechanisms that wire up the nervous system during development. From 2004 to 2010, he performed his postdoctoral studies with Cori Bargmann at the University of California, San Francisco, and Rockefeller University, New York. Here, he developed lab-on-a-chip and calcium-imaging techniques to investigate the chemosensory mechanisms by which animals sense oxygen in the environment. Since 2010, he has lived in Austria, where he works as an independent group leader at the Research Institute of Molecular Pathology in Vienna. Dr. Zimmer’s current research is focused on how neuronal network dynamics in the brain of C. elegans arise from sleep to wakefulness to engage in processing the sensory world and to produce competent behaviors, like foraging and navigation.

Brain-wide hierarchical and multiplexed encoding of behaviour in C. elegans

Large-scale neuronal recordings in the brains of different species have revealed brain-wide, highly coordinated patterns of neuronal activity associated with the animals’ ongoing behaviours. It is not known why behaviour is represented in the brain on such a global scale. In the nematode C. elegans, the activity of such neuronal populations recorded from immobilised animals was suggested to correlate with brain-wide motor commands orchestrating a major action sequence. Direct confirmation of this conclusion in freely crawling animals has been lacking. I will present unpublished data from a new imaging pipeline to record brain-wide activity at single cell resolution in freely crawling animals performing a variety of motor behaviours.Extending our previous findings, we observe population-wide neural activity in the form of a structured low-dimensional manifold from which the major motor programmes, arranged as an action sequence, can be decoded. However, the brain-wide activity appears to be much richer than just encoding the identity of the main actions: while all behaviourally relevant neuronal activity patterns we detect in our recordings are modulated by the global population modes, many individual neurons show multiplexed activity, i.e. they carry additional residual signals. These can represent a variety of behaviourally relevant information, such as graded movement metrics, the animal’s undulatory gate, or even re-afferent sensation of movement-triggered external signals.In summary, we discover a brain-wide hierarchical organisation of behaviour in which information about the current slow time-scale behavioural state is broadcast across the brain via a low-dimensional population mode, providing a context for the encoding of fine-tuned fast movement patterns and even sensory perception. We propose this as an organising principle that may apply to animals with larger brains.

https://neurodevbio.univie.ac.at/zimmer-research/

Host: Klas Kullander, UU

Science visualisation workshop
2023-11-28 09:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
How to effectively communicate your research through visualisations

This workshop consists of lectures and short practical exercises on how to create scientific visualisations that clearly communicate your message. We will draw from Graphic Design knowledge on layout, typography and colour, define the steps in the design process of a visualisation that you can directly apply, discuss common visual formats used in science communication (eg posters, graphical abstracts), compare software options for creating your visualisations, and learn about concepts from cognitive psychology and visual perception that explain what makes a visualisation effective.

Register your interest to participate before November 1.

Registration

The content will be adjusted to the interest of the participants. Everyone within the SciLifeLab Community is invited to attend, priority will be given to PhD students and postdocs.

Correlated Array Tomography Workshop
2023-11-29 08:00 - 2023-12-01 17:00 | Centre for Cellular Imaging, Medicinaregatan 7A, Göteborg
Array Tomography workflow: Fixation of the specimen and embedding in a suitable matrix; Serial sectioning of the specimen, and collection of the sections to create a ribbon; Staining of the sections; Sections are identified and imaged at low resolution to find ROIs, which are later imaged at high-resolution to create a 3D view of the specimen.

The Centre for Cellular Imaging, which is the national SciLifeLab facility for Correlative Array Tomography in Sweden, has the great pleasure to welcome you to the first Cellular 3D volume – Correlative Array Tomography (CAT) Workshop! The workshop will take place from November 29th to December 1st. The lectures will take place at the Wallenberg Centre, located at Medicinareberget, above the Sahlgrenska Hospital in Gothenburg. The hands-on sessions will take place in the Centre for Cellular Imaging, Core Facilities, at Medicinareberget.

It is a great pleasure to welcome you to first Cellular 3D volume – Correlative Array Tomography (CAT) Workshop 2023 – Centre for Cellular Imaging the National SciLifeLab Facility in Correlative Array Tomography in Sweden

Many biological functions depend critically upon fine details of tissue molecular architecture that have resisted exploration by existing imaging techniques. Array tomography encompasses light and electron microscopy modalities that offer unparalleled opportunities to explore three-dimensional cellular architectures of large samples in extremely fine structural and molecular detail, including neural circuits, organs (e.g. brain, pancreas, kidney, heart), small model organisms and subcellular organelle networks. Based on methods for constructing and repeatedly staining and imaging ordered arrays of ultrathin resin-embedded serial sections on glass slides, silicon wafers or tapes, array tomography allows for quantitative, high-resolution, large-field volumetric imaging of large numbers of antigens, fluorescent proteins, and ultrastructure in individual tissue specimens. This will contribute further to the understanding of the complex 3D architecture of tissues in their natural context, which is crucial for gaining understanding of the structure function correlation in biological systems, and especially to resolve questions not possible to dissect with conventional scanning or transmission electron microscopy techniques.

The CAT 2023 Workshop is designed to bring experts, researchers and industry together interested in Cellular 3D volume – Correlative Array Tomography to introduce this new technology, stimulate knowledge exchange and the formation of collaborations. No matter where you are in your career, participating at this Workshop will allow you to stay abreast of this new imaging technology, learn new sample preparation and image analysis methods, and most importantly, network with colleagues and make new connections.

The program will offer an attractive combination of lectures and hands-on demonstrations from electron and light microscopy to image analysis. It will also provide excellent opportunities for discussions and informal gatherings. The sessions will cover the following topics within cellular 3D volume-array tomography research: Volume electron/light microscopy-array tomography; Sample preparation for Array Tomography; Image processing and analysis for Array Tomography; Correlative array tomography; Multibeam scanning electron microscopy. Take the opportunity to challenge your brain and create a new network!

Julia Fernandez-Rodriguez

Chair of the Cellular 3D volume – Correlative Array Tomography Workshop

read more

registration

CLEM example: Correlative light and electron microscopy to identify cells of interest in skin equivalent. The image represents only a small example of the CAT dataset.

SciLifeLab FAIR storage - how to apply for storage resources
2023-11-30 10:00 - 11:30
SAVE THE DATE

In order to support data-driven life science research, SciLifeLab offers storage resources for data sharing in accordance with the FAIR principles for projects that advance scientific knowledge and discovery within the field of Swedish data-driven life science. SciLifeLab Data Centre is responsible for allocating these resources and for the application process. The applications to use FAIRstorage is now open through the Swedish User and Project Repository (SUPR) Portal (call open Nov 16 -Dec 31). Following the recent launch of FAIRstorage, this is an event where the FAIRstorage applications process, along with Research Data Management resources needed for the application, will be presented. The target group for this call is researchers, research groups, and organisations.

Adhering to Open Science and FAIR principles the applicants will be required to submit a Data Management Plan (DMP) already at the time of application and should be actively maintained, as DMP is a living document, during the project. Awarded applicants are also expected to openly publish data output from the project. SciLifeLab Data Centre and NBIS are offering a support event where the FAIRstorage applications process, along with Research Data Management resources needed for the application, will be presented.

When: Nov 30, 10-11.30 AM

Where: Virtual event on Zoom

Register: before Nov 30, at 9 AM

10.00-10.20 Introduction to FAIRstorage and an overview of processes for applying for FAIRstorage using SUPR, Jonas Svensson, IT manager, and Elisabeth Sundström, Project leader, SciLifeLab Data Centre

10.20-10.50 Data Stewardship Wizard-a DMP tool- as a resource for your SUPR application, Wolmar Nyberg Åkerström, Data steward, NBIS

10.50-11.00 SciLifeLab Data Repository- publishing your data- as a resource for your SUPR application, Angela Fuentes Pardo, Data steward, SciLifeLab Data Centre

11.00-11.30 Q & A

Register

This is an event in the SciLifeLab Data Centre and NBIS SciLifeLab Data Management seminar series.

Learn more about FAIRstorage and the call here: https://data.scilifelab.se/services/fairstorage/

Mail: FAIRstorage@scilifelab.se Contact the SciLifeLab Data Centre and NBIS joint Data Management support team data-management@scilifelab.se

Campus Solna Seminar Series: Carmen Navarro & Elisabeth Söderberg
2023-11-30 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:

Carmen Navarro

Simon Elsässer – alpha 4

The role of Polycomb Repressive Complex 2 in early human development

Elisabeth Söderberg

Per-olof Syren – gamma 5

A safer and more sustainable by design perspective in biocatalytic amide-bond coupling of in-silico controlled chemical space

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

SciLifeLab workshop on dynamical microscopy
2023-12-04 08:00 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to a SciLifeLab workshop on dynamical microscopy covering modalities AIRY, lattice lightsheet and FCS/DP, including quality control and image analysis.

Agenda

12:00 Introduction – Hans Blom, ALM/SciLifeLab

12:05 AIRY scan imaging – Eric Murén ZEISS & Hjalmar Brismar, ALM/SciLifeLab

12:35 Quality Control – Chris Lagerholm, Turku Bioimaging Center

13:05 Lattice light-sheet imaging – Steven Edwards, ALM/SciLifeLab & Jan Schlegel Karolinska Institutet

13:35 Coffee break

13:50 Dynamical analysis with FCS – Stefan Wennmalm, ALM/SciLifeLab

14:15 Multiplexed dynamical analysis with DP – Maria Trulsson ZEISS

14:40 Advanced image analysis support – Molly McQuilken, ZEISS arivis

15:20 – 16:20 3x Demo sessions (project discussions)

Fast AIRY scan microscopy & FCS/DP; Lattice light-sheet imaging; Image analysis support

Registration: hans.blom@scilifelab.se

Snakemake “bring-your-own-code” (BYOC) workshop - Cancelled
2023-12-04 09:00 - 2023-12-06 17:00 | Online event via Zoom
National course open for PhD students, postdocs, researchers and other employees in all Swedish universities, in need of skills to write Snakemake workflows for reproducible and scalable bioinformatics data analyses. CANCELLED!

Important dates and information

Application opens: 2023-09-11

Application closes: 2023-10-29

Confirmation to accepted students: 2023-11-06

Course Leader and teachers: Verena Kutschera (CL), Marcel Martin, John Sundh. In case you have any workshop-specific questions, please contact: edu.byoc-snakemake@nbis.se

Application

Course Website

Course fee

This online training event has no fee. However, if you confirm your participation but do not do so (no-show) you will be invoiced 2,000 SEK*.*Please note that NBIS cannot invoice individuals

Course content

As data analysis projects grow and change over time, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake can be used to set up, perform and monitor defined sequences of computational tasks (“workflows”), thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well suited for bioinformatics workflows.

The NBIS Tools for reproducible research course is held twice a year and provides an introduction into Snakemake and a tutorial to learn how to use Snakemake.

This Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as bash, R or python into a Snakemake workflow, or B) apply more advanced techniques to their existing Snakemake workflows.

Learning Outcomes

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

Be able to create Snakemake workflows for bioinformatics data analysis

Demonstrate knowledge of the structure and syntax of different types of Snakemake workflows

Demonstrate knowledge of advanced features of the Snakemake workflow language

Entry requirements

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

Previous participation in the NBIS Tools for reproducible research course. The workshop is also open for participants who can demonstrate experience in writing Snakemake workflows and with at least basic Unix/bash knowledge (e.g. being familiar with commands such as ls, cd, touch, mkdir, pwd, wget, man, etc.).

Your own bioinformatics analysis scripts in any programming language that you would like to convert into Snakemake OR your own Snakemake workflow that you would like to improve.

A computer with a webcam running Linux or Mac OS (if you run Windows and are accepted as a participant, additional setup will be required).

Due to limited space the course can accommodate a maximum of 12 participants. If we receive more applications, participants will be selected based on selection criteria, including (but not limited to) correct entry requirements, motivation to attend the course, as well as gender and geographical balance.

[The Svedberg seminar] - Intersecting population genetics, stem cell biology, and cellular genomics to study complex human disease
2023-12-04 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Joseph Powell

Professor Garvan Institute of Medical Research, Sydney Australia

Bio

Professor Powell is the Director of Translational Genomics at the Garvan Institute and Director of the UNSW Cellular Genomics Futures Institute. He received his PhD from the University of Edinburgh. Subsequently, he undertook postdoctoral training with Professor Peter Visscher’s FAA FRS and started his lab in 2016. In 2018, he was recruited as the inaugural Director of the Garvan-Weizmann Centre for Cellular Genomics and developed a multidisciplinary program in translational genomics research.

Abstract: Genetic variants can contribute to disease in many ways. In complex diseases, hundreds to thousands of variants independently contribute to disease risk, and an accumulation of risk alleles – often combined with specific environmental exposures –is required to develop the disease phenotype. The overwhelming evidence showing enrichment of disease-associated variants in regulatory regions suggests that regulation of gene expression is likely a dominant mediator for disease risk. Expression quantitative trait loci (eQTL) analysis links disease risk-SNPs to downstream expression effects. An essential next step is defining the cellular contexts in which disease risk-SNPs affect gene expression levels. This will help better understand the molecular and cellular mechanisms by which disease risk is conferred and inform therapeutic strategies. This talk will cover a body of work on how single-cell sequencing technology can be scaled to enable the type of population genetics studies required to address these biological questions. I will present recent research on how we have resolved how genetic variation acts at the level of individual cells in immune cell and stem cell systems and outline the next steps in translating these findings into clinical impact.

Host: Weronica Ek, UU

DDLS Biomarker Discovery: from theory to real world examples
2023-12-06 08:00 - 2023-12-08 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
National workshop open for PhD students, postdocs, researchers and other employees in all Swedish universities, in need of understanding biomarker research and methods.

Workshop location: SciLifeLab, Tomtebodavägen 23A, Solna

Venue: Air&Fire (G2690) and Milky Way (A2631)

Important dates and information

Application opens: 2023-10-01

Application closes: 2023-10-30

Confirmation to accepted students: 2023-11-15

Course Leaders and teachers: Animesh Acharjee, Clemens Wittenbecher, Markus Mayrhofer, Mun-Gwan Hong, Paul Pyl, Prasoon Agarwal

please contact edu.biomarkers@nbis.se for course-specific questions

Application

Workshop fee

A course fee* of 2000 SEK will be invoiced to accepted participants. The fee includes lunch and coffee.

*Please note that NBIS cannot invoice individuals

Workshop content

The main purpose of this workshop is to provide a good overview of biomarkers and biomarker studies. This workshop will explore recent research, showcasing diverse biomarker applications within clinical trials. Methods employed to identify biomarkers through various omics datasets will be reviewed. Participants will engage in discussion on biomarker studies and data analysis exercises that encompass approaches like machine learning methods and other integrative omics strategies used in biomarker discovery.

Topics covered will include:

Biomarker study design for “context of use”

Types of biomarkers, diagnostic, prognostic, and wellness

Biomarkers are in use for various diseases such as cancer, cardiovascular diseases

Biomarker discovery from various omics data including proteome, microbiome

Biomarker and multi-omics data integration

Machine learning methods, lasso logistic regression and random forest, to identify biomarkers

Performance indicators, e.g. sensitivity and specificity

Internal/external validation

Entry requirements

The following is a list of skills required to be able to follow the workshop and complete the exercises:

Ability to bring your own laptop with R installed for the practical exercises

Basic Programming/scripting experience in R

or took an R course NBIS prepared.

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

Some basic knowledge of biostatistics

Previous experience in biomarker-related studies

Due to limited space, the course can accommodate a maximum of 20 participants. If we receive more applications, participants will be selected based on selection criteria, including (but not limited to) correct entry requirements, motivation to attend the course, as well as gender and geographical balance.

Integrated Structural Biology users meeting
2023-12-06 09:00 - 16:00 | Wangari, Widerströmska building,, Tomtebodavägen 18, Solna, Sweden
We invite Structural Biologists in Sweden to participate in 2023 Integrated Structural Biology Users meeting, held in Solna on Dec 6, 9-16, see program below.

Please register before November 30

registration

All PhD students and post docs within areas such as Cryo-EM, Structural Proteomics, NMR, protein production and other relevant areas are welcome and encouraged to send an abstract and be provided a time slot for a flash talk. If traveling to Solna is needed, we will pay for travel and one hotel night (December 5). If more applicants than time slots, we will distribute nationally and from different areas.

Program

ISB-User-MeetingDownload

Introducing Molecular Pixelation - Spatial proteomics of single cells by Next Generation Sequencing
2023-12-06 10:00 - 13:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
We are pleased to invite you to our Spatial Proteomics Seminar organized together with SNP&SEQ Technology Platform/National Genomics Infrastructure (NGI). We will take you beyond the use of flow cytometry and focal microscopy into the intriguing and dynamic world of the cell-surface proteome of single cells through next-generation sequencing.

Following the seminar, we will serve sandwiches and refreshments.

Date: Wednesday, December 6, 2023Time: 10:00 to 13:00 CETLocation: SciLifeLab Uppsala (Navet)Uppsala Biomedicinska CentrumHusargatan 3, entrance C11,752 37 Uppsala

Molecular Pixelation

By simultaneously analyzing changes in the dynamic protein architecture of cellmembranes across 1000s of single cells, a new chapter has unfolded. This allows us toassess how subtle alterations in the spatial orchestration of proteins impact the immunesystem, disease outcomes, and responses to treatment.

Agenda

10:00 – 10:05 WelcomeAnnaLotta Schiller, Pixelgen10:05 – 10:35 Introducing Molecular PixelationSimon Fredriksson, Pixelgen10:35 – 10:55 Mapping individual drug responses using Molecular PixelationJessica Nordlund, SciLifeLab, NGI, UU10:55 – 11:05 Sequencing single cells at the SciLifeLab National Genomics InfrastructureHenrik Gezelius, SciLifeLab, NGI, UU11:05 – 11:35 Panel discussion including Q&ASimon, Jessica & Henrik11:35 – 13.00 Sandwiches & Cake

The seminar will be accessible in both in-person and virtual formats

Reserve Your Spot

To secure your place for the lunch seminar, register on the link below, specifying your attendance and lunch preferences. All participants must register including the speakers as well as both in person and virtual attendees

Register here

Joined DanioReadout, Local SciLifeLab Service Facility and CIV Zebrafish Core Facility information meeting
2023-12-06 14:00 - 16:30 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
Zebrafish model focused afternoon with useful information on newly opened, cutting-edge Uppsala University Zebrafish Core Facility (CIV) and DanioReadout Service Facility (Local SciLifeLab Facility), dedicated for researchers interested in zebrafish model and its applications

Host: Aristidis Moustakas (SciLifeLab Scientific Director, Uppsala University)

Organizer: Beata Filipek-Gorniok (DanioReadout Operational Director)

Contact: danioreadout@uu.se

Program

14:00WelcomeAristidis Moustakas, SciLifeLab-Uppsala Scientific Director14:15OpeningKaska Koltowska, DanioReadout Scientific Director, and Joakim Holmdal,CIV Director14:30Zebrafish Core FacilityTiffany Klingström, zebrafish facility manager14:40Inspirational talk15:10Coffee Break15:30DanioReadout service facilityBeata Filipek-Gorniok and Amin Allalou15:50How do I utilize zebrafish model in my project?short presentations by zebrafish researchers16:30Wrap up

Registration

Deadline 2023-11-30

More about DanioReadout services

Campus Solna Seminar Series: Cenk Gurdap
2023-12-07 12:00 - 13:00 | Milkyway SciLifeLab Solna, Tomtebodavägen 23, Solna
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

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

This week:

Cenk Gurdap

Erdinc Sezgin – gamma 3

Spectral biophysical cytometry with smart probes: high-throughput and multi-parametric cell phenotyping

We have only one talk this week in order to have enough time to go to the Nobel Prize lectures in physiology or medicine at Aula Medica, Nobels väg 6, Karolinska institutet, Campus Solna

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

Multi Omics Data Integration - A translational perspective
2023-12-07 13:15 - 14:00 | Online event via Zoom
The forefront of deriving valuable insights into cellular functions involves the analysis of multi-omics data along with clinical information. The integration of multi-omics data, which encompasses information from diverse biomolecular layers, holds promise for systematically and comprehensively understanding complex biology. Integrated approaches involve combining individual omics data either sequentially or simultaneously, offering a means to explore the intricate interplay of molecules. This method proves valuable in assessing the flow of information across omics levels, thereby bridging the gap from genotype to phenotype. Integrative approaches, through their holistic examination of biological phenomena, have the potential to enhance prognostic and predictive accuracy for disease phenotypes. Consequently, they stand to contribute significantly to improved treatment and prevention strategies. In this talk I will show multiple approaches to integrate diverse data types and how we can use them in a translational medicine.

join zoom meeting

Animesh Acharjee, PhDAssistant Professor, Institute of Cancer and Genomic Sciences, University of Birmingham, United Kingdom

Biography

Dr. Acharjee’s research interests encompass integrative data analytics, predictive biomarker discovery, bioinformatics methods for diagnostics, and network biology. His multidisciplinary approach reflects his commitment to bridging the gap between computational methodologies and biological insights. Throughout his illustrious career, Dr. Acharjee has been recognized with numerous fellowships, including those from the British Council, the Dutch Government, and Newton fellowships. These accolades underscore his dedication to advancing scientific knowledge and his contributions to the fields of bioinformatics, data analytics, and biostatistics. Dr. Acharjee’s journey continues to be marked by a relentless pursuit of excellence in research and a commitment to unraveling the intricacies of metabolicdiseases through innovative methodologies.

[The Svedberg seminar] - Engineered Salmonella for drug delivery to solid tumors
2023-12-08 15:15 - 16:15 | BMC Room C4:301, Husargatan 3, entrance C1, Uppsala, Sweden
Neil Forbes

Professor of Chemical EngineeringUniversity of Massachusetts, USA

Bio

Neil Forbes is a Professor of Chemical Engineering at the University of Massachusetts, Amherst. He is an adjunct member of the Molecular and Cell Biology Program and a member of the Institute for Applied Life Sciences. He received a BS in Chemical Engineering from Case Western Reserve University, received a PhD in Chemical Engineering from the University of California at Berkeley (with Harvey Blanch and Douglas Clark), and was a postdoctoral fellow (with Rakesh Jain) in Radiation Oncology at Harvard Medical School / Massachusetts General Hospital.

Engineered Salmonella for drug delivery to solid tumors

Abstract: Engineered bacteria have the potential to overcome the limitations that cause cancer therapies to fail. We have created intracellular delivering Salmonella that accumulate in tumors over healthy tissue and deposit deliver therapeutic payloads directly into the cytoplasm of cancer cells. Bacterial delivery of constitutively active caspase-3 blocks the growth of hepatocellular carcinoma and lung metastases, and increases survival in mice. Salmonella delivery of an exogenous antigen, such as from a childhood vaccine, marks cancer cells as foreign, and triggers a cytotoxic, antigen-specific CD8 T cell responses. In mice, intracellular antigen delivery clears established pancreatic tumors, increases survival, and prevents tumor re-implantation by establishing new immunity to intrinsic tumor antigens. This tunable platform could deliver an array of protein drugs to target many hard-to-treat intracellular pathways. As an off-the-shelf therapy, these bacteria are not dependent on intrinsic tumor characteristics and would be effective for a broad range of cancer patients.

Host: Mia Phillipson mia.phillipson@mcb.uu.se, UU

Re-Imaging and Re-Imagining Science
2023-12-11 11:30 - 14:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
As part of the 10th anniversary celebration of the Science & SciLifeLab Prize for young researchers, we have got the honour to host a lunch seminar with Shirley Malcom who is senior advisor and director of SEA Change at the American Association for the Advancement of Science (AAAS). For more than 40 years at AAAS she has worked to improve the quality and increase access to education and careers in STEMM for all.

For the SciLifeLab audience, Shirley will not only give an inspiring lecture. She will also take part of a panel discussion and attend an open discussion/networking session.

Do not miss out on this opportunity!

Questions to be discussed;

How we can look critically at what is being done and not being done regarding inclusion?

How do we support excellence and what do we want research to look like?

What kind of engagement do we want?

How do we bring assets into science and take advantage of people’s differences?

Register

Program

11.30Lunch is served11.55Welcome, Ylva Engström, president SciLifeLab board12.00Re-Imaging and Re-Imagining Science, Shirley Malcom AAAS12.30Panel discussion with Shirley Malcom, DEI-committe, Public Engagement, Code of Conduct and Coaching in Science Initiativechair: Erdinc Sezgin13.05Concluding remarks, Per Ljungdahl, director Campus Solna SciLifeLab13.15Coffee, Exhibition and Open Discussion in Gamma 2 lunchroom

Read more

Shirley Malcom biography

SEA Change

Coaching in Science Initiative

SciLifeLab Code of Conduct

Science & SciLifeLab Prize Symposium 2023
2023-12-12 09:00 - 13:30 | Beijersalen, Kungl. Vetenskapakademien, Lilla Frescativägen 4A, Stockholm, Sweden
Welcome to the Scientific Symposium presenting the winners of the 2023 Science & SciLifeLab Prize for Young Scientists.

N.b. This page concerns the Science & SciLifeLab Prize Symposium 2023. To learn about the 2024 event – please click the button below.

Read about the science & SciLifeLab Prize symposium 2024

Science, the American Association for the Advancement of Science (AAAS), and SciLifeLab joined forces in 2013, creating the Science & SciLifeLab Prize for Young Scientists to recognize excellence amongst young researchers from around the world. A global Prize aimed at rewarding scientists at an early stage of their careers, this year celebrating its 10th anniversary.

The Science & SciLifeLab Prize for Young Scientists is an international prize, awarded annually to four young scientists for outstanding life science research based on a doctoral degree earned in the previous two years.The grand prize-winning essay will be published in Science, and essays from the three category winners will be published in online issue.

All four winners of the Science & SciLifeLab Prize for Young Scientists are invited to Sweden December 9-14 to participate in a unique week filled with events in honor of science. They will have the opportunity to meet with leading scientists in their field of research and create life-long connections to support their careers.

The four winners 2023 are

Zuzanna Kozicka

Molecular Medicine, Grand Prize WinnerEssay: Gluing the pieces together: Illuminating the path to degrading troublesome proteins

Rachel Kratofil

Cell and Molecular BiologyEssay: Working up an appetite to promote repair: Immune-derived hunger hormones restore tissue post-infection

Yodai Takei

Genomics, Proteomics, and Systems Biology ApproachesEssay: Imaging nuclear architecture in single cells: Multiplexed imaging technologies uncover precise 3D maps of single nuclei

Jessica Kendall-Bar

Ecology and EnvironmentEssay: Lessons from sleep in the deep: Records of seal sleep at sea reveal extreme sleep duration flexibility

For the 10th anniversary of Science and SciLifeLab Prize, we have invited 2014 year’s category winner Chelsea Wood to give a keynote lecture with the title; Is the world wormier than it used to be? Answers from a new subdiscipline: the historical ecology of parasitism.

Program

Program flyer_Prize_A4_01 (2)Download

Chelsea Wood – Bio

Read more About the Prize

Please contact events@scilifelab.se if you have any questions.

Stronger together; Making space on Team Science for Diverse Career Paths
2023-12-13 13:30 - 15:30 | IVA Conference center, Grev Turegatan 16, Stockholm
Science & SciLifeLab Webinar

By harnessing different types of expertise and offering several diverse career paths in research, the definition of what it means to be a life scientist can be broadened and inclusive of a wide array of skill-sets. In this panel discussion, broadcasted live by Science, the panel will explore how life scientists can foster a future that maximizes the potential of each researcher and the field overall.

In this discussion, participants will

Learn about how career paths can be diversified and how diverse backgrounds bring value to research excellence, innovation, and problem-solving.

Gain insights into why team science is key for multidisciplinary research and collaboration.

Hear how universities and other employers can support individuals pursuing non-traditional career paths in science and build inclusive research communities.

Take part in shaping the future of research incentives and other drivers of open science.

Program

13.30 Coffee and mingle at IVA conference center

14.15 Everyone seated in the Wallenberg lecture hall

14.30 Panel discussion

15.15 Q&A from the audience

Panel

Annika Jenmalm Jensen, Infrastructure director at SciLifeLab

Chelsea Wood, Associate professor University of Washington and Science & SciLifeLab Prize Winner 2014

David Seekell, Head of Sustainable Investing at Atle and Science & SciLifeLab Prize Winner 2016

Erik Lindahl, professor Stockholm University

Moderator

Sacha Vignieri, Deputy Editor for Research at AAAS/Science magazine

Registration

Molecular Design of the Kidney Filtration Barrier
2023-12-13 15:30 - 16:30 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Prof. Thomas Benzing, University Hospital ofCologne, Germany

Prof. Thomas Benzing will in this talk describe how his group has over the past years made novel discoveries regarding the molecular mechanisms of kidney filtration. Many of these findings are the result of a collaboration with researchers at SciLifeLab/KTH.

Most welcome!

CSI Seminar: ‘Moving our Mental Roadblocks’
2023-12-15 14:00 - 14:30 | Hybrid event in Gamma 2 lunchroom and zoom, Tomtebodavägen 23 B, Solna, 17165, Sweden
We are excited to host a new Coaching in Science Initiative (CSI) Seminar titled: ‘Moving our Mental Roadblocks’

In this CSI seminar, we will raise awareness about mental obstacles and barriers that keep us from the change we want. We will explore Why sustainable change has yet to happen for us, How we can change that, and What tools we can use to make it happen!

This seminar will be helpful for when we want to make changes in our life, and yet they don’t happen, e.g., New Year’s resolutions we keep promising ourselves. Starting on that thing, which we have procrastinated for quite some time. Beginning on a project task early instead of at the last minute. Forming healthy new habits, such as flossing our teeth or a 30 min walk every day. When we mean to plan rest into our schedule to reduce the stress in our lives, but – it just does not happen.

With our Moving Mental Roadblocks Model, we will explore why the change we want has yet to happen, and introduce our mental tool, the Emotion-Thought-Action (ETA) ladder, which can be used to enact sustainable change effectively.

Date: 15/12/2023Time: 14:00 – 14:30Zoom link: https://kth-se.zoom.us/j/69311596145On-site location: Gamma 2 lunch room

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

To help facilitate discussion and reflection, consider the follow starter questions:

Awareness: where do we experience mental roadblocks in our lives?Analysis: how well do I currently handle mental roadblocks?Alternative: how can we relate to mental roadblocks, in ourselves and others?Action: how will knowledge of mental roadblocks change my decisions going forward?

Please forward this to friends and colleagues!

Yours sincerely,The CSI Team

Activity-regulated organization of neuronal protein at the molecular scale
2023-12-15 14:00 - 16:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Mini symposium on “Activity-regulated organization of neuronal protein at the molecular scale”

For attendees without SciLifeLab access, we will meet you at the reception of SciLifeLab at 1.50 pm.

Program

2.00 – 3.00 PM

Molecular function of Arc in brain plasticity: from hub protein to retroviral-like capsid

Clive Bramham, University of Bergen, Norway

3.00 – 4.00 PM

Deciphering the spatiotemporal and mechanical regulation of adhesive and cytoskeletal structures at the nanoscale

Grégory Giannone, CNRS, University of Bordeaux, UMR5297, Interdisciplinary Institute for Neuroscience, France

Event_Bramham-and-Giannone_locationDownload

[The Svedberg seminar] - Describing tissue pathogenesis with spatial technologies
2023-12-18 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Sanja Vickovic

Wallenberg Academy Fellow and SciLifeLab FellowDepartment of Immunology, Genetics and Pathology at Uppsala University

Bio

Dr. Vickovic is currently a Wallenberg Academy Fellow and SciLifeLab Fellow at the Department of Immunology, Genetics and Pathology at Uppsala University. Dr. Vickovic received her PhD in Gene Technology from the Royal Institute of Technology in Stockholm. Following her graduate work, Dr. Vickovic joined the Broad Institute of MIT and Harvard, Columbia University and the New York Genome Center before continuing in her current role as Assistant Professor at Uppsala University. Dr. Vickovic has extensively worked on pioneering novel spatially resolved transcriptomics and genomics methods that enable massively parallel in situ profiling of intact tissue samples.

Describing tissue pathogenesis with spatial technologies

Abstract: Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. In recent years, we developed high-definition spatial transcriptomics and multi-omics technologies, which captures RNA, protein information or microbiota from histological tissue sections on spatially barcoded arrays. Today, I will present how these different technologies were developed and are applied in different biological settings.

Host: Ulf Landegren ulf.landegren@igp.uu.se, UU

Calls for new project support in chemical biology and drug discovery
2024-01-12 11:00 - 12:00 | Online event via Zoom
The chemical biology unit (CBCS) and the Drug discovery and development (DDD) platform at SciLifeLab have calls out for projects – see https://anubis.scilifelab.se

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

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

Some users and projects are at the intersection between chemical biology and drug discovery. We believe this webinar will help you to find out were your project fits in best.

sign up here

Program:

1. Presentation of CBCS offerings2. Presentation of the DDDp offerings3. Q&A

Organizer: the Chemical Biology Consortium Sweden and the Drug Discovery & Development platform

DDLS Data Science Node information
2024-01-12 13:00 - 14:00
Welcome to a brief update on the status of the Data Science Node (DSN) for Cell and Molecular Biology (CMB) and information about a community survey that will open after this meeting. Data Science Node management, Sverker Holmgren and Thomas Svensson will describe the survey and answer questions. The event is open to everyone. Please register to get the Zoom link in your mailbox. You can pre-send input or questions regarding the DSN in CMB to Sverker and Thomas in the registration form.

Registration

Survey

Link to Survey

Read more about DDLS Data Science Nodes

Genomics, Imaging and AI - three technologies which are changing biological research and clinical practice
2024-01-15 15:00 - 16:00 | Eva & Georg Klein lecture hall, Biomedicum, Karolinska Institutet, Solnavägen 9, Solna, Solnavägen 9, Solna
Prof. Ewan Birney is Deputy Director General of EMBL and Joint Director of EMBL-EBI. Prof. Birney will come to Stockholm to give a talk on Jan 15 from 15:00 to 16:00 at Biomedicum, KI Campus Solna. Come and listen to an exciting talk about the next steps in medical research!

Jan 15 at 15:00 – 16:00

Eva & Georg Klein Conference hall, Biomedicum, Solnavägen 9

Welcome!

Prof. Ewan Birney flyer Jan 15Download flyer

Opening of the Lightsheet 7 at the Centre for Cellular Imaging
2024-01-18 09:00 - 15:00 | Birgit Thilander Lecture Hall, Medicinaregatan 3, Göteborg
The Centre for Cellular Imaging is pleased to announce the purchase and installation of the Lightsheet 7 fluorescence microscopemicroscope.

Light sheet fluorescence microscopy (LSFM) uses a thin sheet of light to excite only fluorophores within the focal volume. It is ideal for fast and gentle imaging of whole living model organisms, tissues, and cells as they develop – over extended periods of time. Furthermore, the Lightsheet 7 is designed to handle large optically cleared specimens with subcellular resolution. Dedicated optics, sample chambers, and holders allow adaption to the refractive index of the chosen clearing method.

The Lightsheet 7 is now installed at the Centre for Cellular Imaging and to celebrate this we will host an “Opening Day” with seminars and demos, where you can learn about this technology and other types of equipment available at the CCI.Please join us on January 18th to explore what is possible with this new instrumentation!

Registration deadline: January 11th

registration

Campus Solna Seminar Series: Samu Himanen & Donal Barrett
2024-01-18 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:

Samu Himanen

Anniina Vihervaara – alpha 3

Tracking Pol II modifications and nascent trascription by Pol I-III complexes at single-nucleotide resolution

Donal Barrett

Vicent Pelechano – gamma 5

Rapid electronic quantification of clinical pathogens using novel DNA nanoballs

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

AICell Lab -- Building AI Systems for Human Cell Modeling and Simulation
2024-01-19 10:00 - 11:00 | Online event via Zoom
NBIS, Scilifelab’s Bioinformatics platform, arranges an open AI and IO Seminar Series aimed at knowledge-sharing about Artificial Intelligence and Integrative Omics (AI & IO) analysis and applications in the Life Science community. The seminar series is open to everyone. The seminar is run over Zoom on the third Friday of the month during academic terms, typically between 10 and 11 am, with ca. 45 min long presentation and 15 min discussion.

For further info, please see this website.

AICell Lab — Building AI Systems for Human Cell Modeling and Simulation

Wei Ouyang, DDLS fellow, Royal Institute of Technology, KTH

The AICell Lab is a newly founded group by the Data-Driven Life Science fellows program at the department of applied physics at KTH. The lab is dedicated to building artificial intelligence (AI) systems for cell and molecular biology, with the ultimate goal of modeling the human cell and building human cell simulators using powerful AI models. The lab’s approach to this grand challenge involves not only innovations in data analysis and modeling, but also in data generation, specifically the creation of an automated imaging farm equipped with multiple microscopes, robotic arms, liquid handling robots, and automatic incubators. The lab’s AI software infrastructure enables real-time augmentation of microscopy views, generating artificial labels and annotations, and optimizing experimental conditions to capture rare events in live cells. The long-term goal of the AICell Lab is to create large-scale whole human cell models trained on existing multi-omics datasets and new data generated by the imaging farm, which have the potential to revolutionize in-silico cell experimentation and drug discovery while contributing to a holistic and systematic understanding of the human cell.

Click here to join zoom conference

Webinar: SiMSen-seq, new tool for ultrasensitive detection of circulating tumor DNA in childhood malignancies
2024-01-19 13:00 - 14:00 | Online event via Zoom
Next up on the Clinical Genomics Webinar Series:

Clinical Genomics Gothenburg has organised an exciting new webinar to be held on Friday 19th January 2024 at 13:00 on Zoom (click here to join).

In the seminar: “SiMSen-seq: A new tool for ultrasensitive detection of circulating tumor DNA in childhood malignancies”, focuses on ultrasensitive sequencing, Martin Dalin, sheds light on a clinical application of SiMSen-seq.

If you have questions, please contact the host Marcela Davila (marcela.davila@gu.se) or CG vicePCO Esther González-Padilla (esther.gonzalez-padilla@scilifelab.se).

Everyone is welcome so feel free to spread the details with anyone who might be interested.

Martin Dalin is a professor at Sahlgrenska Center for Cancer Research, Wallenberg Centre for Molecular and Translational Medicine, the Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg
