SciLifeLab

SciLifeLab Integrated Structural Biology Platform Symposium
2022-12-12 09:00 - 16:00 (Europe/Stockholm) | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
SciLifeLab Integrated Structural Biology invites you to the ISB annual users meeting to be held in Solna on December 12, 9-16.

The program will contain an overview of infrastructures in Sweden that can support your structural biology project, from gene to final 3D structure. We will also hear examples of projects that were supported by the SciLifeLab infrastructures during 2022, comprising Cryo-EM, Structural Proteomics and NMR.

We welcome you to join in person in the SciLIfeLab building (Tomtebodavägen 23, 171 65 Solna) but also understand if you prefer to join in by zoom. The meeting will be a hybrid meeting.

Registration

Program

Program – December 12

ISB2022_221212Download

Science & SciLifeLab Prize Symposium
2022-12-08 09:30 - 12:30 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
Welcome to the Scientific Symposium presenting the winners of the 2022 Science & SciLifeLab Prize for Young Scientists.

You can still register to join on Zoom and onsite if seats are available. For onsite registration, we can not consider special food requirements after November 30.

registration

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.

The Prize was launched with the vision of recognizing that global economic health depends on a vibrant research community. A vision that will only come true if we encourage our best and brightest to continue in their chosen fields of research.

Considering the difficult economic environment for budding scientists, it is crucial that we provide them with extra encouragement as they begin their scientific careers.

The international Prize is awarded annually to four young scientists for outstanding life science research based on a doctoral degree earned in the previous two years. Each year, a Grand Prize winner is selected from the applicants to receive 30,000 USD in prize money, and the three other category winners are awarded 10,000 USD each for their accomplishments. The grand prize-winning essay will be published in Science, and essays from the three category winners will be published online.

All four winners of the Science & SciLifeLab Prize for Young Scientists are invited to Sweden December 6-11 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.

Program

09:00Breakfast is served outside the Lecture Hall09:30Welcome words:Olli Kallioniemi, SciLifeLab Director Valda Vinson, Science AAAS09:45The winners present their research (15’+5′)Moderators: Alexandra Teleki & Mikael Sellin, SciLifeLab FellowsEndosomes, Receptors and Viruses: Deciphering the Mechanisms of Infection at the Host-Pathogen Interface James Daly, Cell & Molecular Biology Category Prize WinnerUncovering the Degrader of D-type Cyclins Daniele Simoneschi, Molecular Medicine Category Prize WinnerCoffee break How do bacteria cope with a changing world? Stefany Moreno-Gámez, Ecology and Environment Category Prize WinnerThe autobiography of a gut bacterium Florian Schmidt, Proteomics and Systems Biology Approaches, Grand Prize Winner11:35Interview with the WinnersModerators: Alexandra Teleki & Mikael Sellin, SciLifeLab Fellows11:55Keynote lecture: Rediscover Your Why – Don’t Lose Sight of Why You Pursued Scientific InquiryGilda A. Barabino, President of the American Association for the Advancement of Science (Bio below)12:25Closing words:Mia Phillipson, SciLifeLab Co-Director12:30Lunch is served

Booklet

Gilda A. Barabino – Bio

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

Data-driven Epidemiology and biology of infections Research Area Symposium
2022-12-07 13:00 - 2022-12-08 13:00 | Europasalen, Konferenscentrum Wallenberg, Gothenburg, Medicinaregatan 20, Göteborg, 413 90, Sweden
Welcome to a symposia with the new DDLS Fellows and national as well as international researchers within the area of data-driven epidemiology and biology of infections.

We encourage personal participation to network with the new DDLS Fellows and other experts of the field however online participation is possible.

Deadline for registration November 29th

Register here

Program Wednesday, 7 December

12:00 LUNCH will be served

13:00- 13:20 Welcomes and Introductions

Siv Andersson, Head of Basic Research at Knut and Alice Wallenberg Foundation, Uppsala University,

Olli Kallioniemi, Director SciLifeLab and DDLS Director, Karolinska Institutet

Maria Smedh Site Coordinator, SciLifeLab Göteborg

13:20 DDLS in Epidemiology and Biology of Infection

Oliver Billker, DDLS Research Area Lead, Umeå University

13:30 Keynote: Using genomic surveillance data to understand bacterial epidemiology

Nicholas J Croucher, Imperial College London

14:10 DDLS Fellow talk: Predicting the disease threats of the future

Johan Bengtsson-Palme, DDLS Fellow at Chalmers University of Technology

14:50 Keynote (virtual) Data and decisions in an imperfect world

Bill Hanage, Associate Professor, Harvard, School of Public Health

15:30 COFFEE

16:00 DDLS Fellow talk: A global perspective on antimicrobial resistance in animals raised for food

Thomas van Boeckel, ETH Zurich and future DDLS Fellow at Gothenburg University

16:40 Pandemic preparedness – The SciLifeLab perspective

Staffan Svärd, SciLifeLab Scientific Director, Uppsala University

17:10 Discussion and conclusion of the first day

17:30 Snacks and mingle in Restaurant Nordic

18:30 SYMPOSIUM DINNER in Restaurant Nordic

Program Thursday, 8 December

8:30 DDLS Fellow Talk: Strength in numbers: leveraging publicly available (meta)genomic data to gain insight into the epidemiology and virulence potential of bacterial pathogens

Laura Michelle Carroll, Umeå University

9:10 Keynote: Data-driven dynamic disease surveillance and studies for mapping systemic effects of the human gut microbiome

Tove Fall, Uppsala University

9:50 COFFEE

10:20 DDLS Fellow Talk: Intimately microbial: symbioses in OB-GYN,

Luisa Warchavchik Hugerth, DDLS Fellow Uppsala University

11:00 National services for data and bioinformatics within DDLS and SciLifeLab

Sara El-Gebali, SciLifeLab Data Centre,

Björn Nystedt, National Bioinformatics Infrastructure

Short presentations followed by a discussion to determine needs for computational support for infections research in Sweden.

12:00 Discussion: DDLS initiative and Data-Driven Epidemiology and Biology of Infection: where next?

12:30 LUNCH will be served

Cancelled: OligoNova Hub - National resource for development of oligonucleotide therapies
2022-12-06 12:00 - 13:00 | Birgit Thilander Lecture Hall, Medicinaregatan 3, Göteborg
OligoNova Hub – National resource for development of oligonucleotide therapies

Pär Matsson

We will present OligoNova Hub and the capabilities we provide for academic researchers to transform their scientific discoveries into new oligonucleotide therapies.

SciLifeLab is a national infrastructure within life science with a wide range of advanced technology and expertise. The newly started SciLifeLab site in Gothenburg includes units at both the University of Gothenburg and Chalmers University of Technology and has a strong connection to Sahlgrenska University Hospital.

A light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available, please click the zoom-link below to join the event at the appointed time.

Venue

This event has been cancelled.

SciLifeLab Uppsala PhD&Postdoc Online Seminar Series – Cancer Theme
2022-12-06 11:00 - 12:00 | Online event via Zoom
Welcome back to the SciLifeLab Uppsala PhD&Postdoc seminar series!
This seminar will take place on Tuesday December 6 from 11h to 11:50h on Zoom (https://uu-se.zoom.us/j/66489618700)
For this occasion the speakers will be:
1. Xiaonan Zhang, Postdoc at Tobias Sjöblom’s Lab (Cancer Precision Medicine), Dept. of Immunology, Genetics and Pathology, Uppsala University

Title: Exploiting allelic loss in cancer therapy: Identification of NAT2 and CYP2D6 as potential targets

Summary:
Loss of heterozygosity (LOH) is observed in >90% of human cancers and results in the loss of allelic variation in thousands of genes. LOH thus creates genetic differences between tumor and normal cells, particularly at gene loci where the individual is heterozygous for a wildtype and a loss-of-function (LoF) allele. We have sought to identify genes with common LoF polymorphisms where tumor cells that have lost the gene activity can be targeted by low-molecular-weight drugs or other means. We previously reported that recurring LOH at the NAT2 locus at 8p22 in colorectal cancers (CRCs), and the ensuing loss of NAT2 enzyme activity, could be exploited for anticancer therapy. Recently, we discovered a group of ATPase inhibitors that exhibited specific toxicity to CRC cells with high NAT2 activity. In parallel, we investigated the CYP2D6 locus as the CYP2D6 enzyme metabolizes ~25% of clinically used drugs and frequently undergoes LOH in several tumor types. We have established liver cancer cell models and demonstrated that the activity of three anti-cancer compounds, used in clinic or in clinical trials, is dependent on CYP2D6. We anticipate that a subset of CRC and liver cancer patients with LOH events in NAT2 or CYP2D6 will benefit from this research.

2. Kehuan Wang, PhD Student at Carl-Henrik Heldin’s Lab (Cancer), Dept. of Medical Biochemistry and Microbiology, Uppsala University

Title: The Proteasomal, Lysosomal and Autophagosomal Degradation Pathways of PDGFRβ

Summary:

Platelet-derived growth factor (PDGF)-induced signaling via PDGF receptor β (PDGFRβ) leads to activation of downstream signaling pathways which regulate multiple cellular responses, such cell migration, proliferation and survival. Signaling via PDGFRβ is dependent on subcellular location of signaling molecules and hence the internalization of the receptor. It is not clear exactly how PDGFRβ is degraded, both endosomal/lysosomal and proteasomal degradation has been suggested. In this study, we have characterized the proteolytic cleavage of ligand-induced PDGFRβ and found that proteolytic cleavage of PDGFRβ resulted in two fragments. This cleavage is dependent on the internalization of PDGFRβ, which can be blocked by the treatment with bortezomib. Treatment with bortezomib resulted in increased phosphorylation of PDGFRβ and the down-stream signaling molecules PLCγ and STAT3, while phosphorylation of Erk1/2 MAPK was reduced and Akt was unaffected. We also investigated the possibility that PDGFRβ is degraded by selective autophagy in response to starvation or ligand-induced downregulation of receptor from the cell surface. We found that PDGFRβ accumulated in cells treated with bafilomycin A1 upon serum starvation which could be reversed by inhibition of protein synthesis with cycloheximide. Overexpression of LC3A, but not LC3B, promoted the formation of a complex between PDGFRβ and p62. Additionally, PDGFRβ interacted with LC3A and other members of LC3-like family, i.e. GABARAP and GABARAPL1. In conclusion, we speculate that the step-wise proteolytic cleavage of PDGFRβ may have functional consequences for signaling. Macroautophagy may not play a major role in ligand-induced downregulation of PDGFRβ but it could be involved in downregulation of PDGFRβ during starvation via targeting by p62 to non-conventional autophagic or proteasomal pathways that include LC3A and GABARAPs. The functional involvement of these pathways in the control of PDGFRβ levels remains to be further investigated.

SciLifeLab Optical Clearing and Expansion symposium
2022-12-06 09:00 - 18:45 | Eva & Georg Klein, Solnavägen 9, Stockholm, 17165, Sweden
The Advanced Light Microscopy unit at Science for Life laboratory cordially welcomes you to a symposium on developments and applications of clearing and expansion methods from world leading experts.

Registration

Registration form

Program

12:45Whole-body/organ imaging with single-cell resolution by CUBICHiroki Ueda – University Tokyo/Riken BDR, Japan13:15DISCO clearing approaches paired with spatial molecular mappingHarsharan Bhatia, Helmholtz Munich, Germany13:45Volumetric imaging of cleared samplesJacques Paysan – ZEISS14:15Coffee break14:40Expansion Microscopy: Development, Application, and Future DirectionsJinyoung Kang – MIT, USA15:10Pan-ExM-t for molecular ultrastructural visualization of brain tissueOns M’Saad – Yale University, USA15:40Coffee break16:05Cryo-ExM: coupling cryo-fixation with expansion microscopyVirginie Hamel – University of Geneva, Switzerland16:35Visualizing cellular and tissue ultrastructure using TRExHugo Damstra – Utrecht University, The Netherlands17:15-18:45POSTER session with snacks/beverages

Contact

hans.blom@scilifelab.se

Workshop on Advanced Correlative Light and Electron Microscopy (CLEM) methods
2022-12-05 08:00 - 2022-12-08 17:00 | Kemiskt Biologiskt Centrum, Umeå University, Linnaeus väg 6, Umeå, 90736
This 4-day workshop aims to highlight the advanced correlative light and electron microscopy (CLEM) techniques. Participants will learn the latest workflows on how to correlate fluorescence microscopy images with high resolution EM images obtained from state-of-the-art equipment.

Read more

Workshop Content:The workshop includes both theory lectures and practical sessions on In-resin preserved florescence for CLEM, Tokuyasu ultramicrotome sectioning combined with staining techniques on sections, Cryo-CLEM and cryo-FIB milling, as well as opportunities to discuss specific research projects and receive practical advice. Technical challenges and new ideas will be discussed, and the participants are welcome to contribute with their experiences.

Target Audience:This workshop is supported by the Nordic EMBL partnership for Molecular Medicine and welcomes applications from its members and other institutions. Participants are required to have practical experience in both light and electron microscopy. Due to limited number of places, registration is based on a selection process. Selected lectures will be open to a larger range of participants and can be registered for under a ‘lecture only’ registration.Certificate/Credits:A course certificate will be provided to successful participants and a recommendation for 1,5 ECTS.

[Clinical Talks] Recording biology to the genome itself
2022-12-01 17:30 - 18:00 | Online event via Zoom
Jay Shendure

Professor of Genome Sciences at the University of Washington

Jay Shendure is a Investigator of the Howard Hughes Medical Institute, Professor of Genome Sciences at the University of Washington, Director of the Allen Discovery Center for Cell Lineage Tracing, and Scientific Director of the Brotman Baty Institute for Precision Medicine.

His 2005 doctoral thesis with George Church included one of the first successful reductions to practice of next generation DNA sequencing. Dr. Shendure’s research group in Seattle pioneered exome sequencing and its earliest applications to gene discovery for Mendelian disorders and autism; cell-free DNA diagnostics for cancer and reproductive medicine; massively parallel reporter assays, saturation genome editing; whole organism lineage tracing, and massively parallel molecular profiling of single cells.Dr. Shendure is the recipient of the Curt Stern Award from the American Society of Human Genetics (2012), the Richard Lounsbery Award from the National Academy of Sciences (2019) and the Mendel Award from the European Society of Human Genetics (2022) and is an elected member of the American Association for the Advancement of Science (AAAS) and the National Academy of Sciences (NAS). He serves or has previously served as an advisor to the NIH Director, the US Precision Medicine Initiative, the National Human Genome Research Institute, the Chan-Zuckerberg Initiative and the Allen Institutes for Cell Science and Immunology. He received his MD and PhD degrees from Harvard Medical School in 2007.

register to receive zoom link

Moderator: Michael Akhras, Colibri Ventures

Clinical Talks

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

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

Campus Solna Seminar Series: Pontus Höjer and Guido Baselli
2022-12-01 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:

Pontus Höjer

Afshin Ahmadian – alpha 3

Omics exploration with Droplet Barcode Sequencing (DBS).

Guido Baselli

Vicent Pelechano – gamma 5

Identification of novel factors regulating non genetic cell plasticity in Chronic Myeloid Leukemia.

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

FAIRPoints-Introducing Community Guidelines for Sharing Dataset Quality Information
2022-11-30 17:00 - 18:00 | Online event via Zoom
Location: Online via Zoom

See Event in your Time Zone

Speaker: Dr.Ge Peng

Knowledge about the quality of data and associated metadata, software, workflows and computing environment is important to establish the trustworthiness of individual datasets, support informed decisions on their (re)use, and is an essential part of the diverse data and information distribution ecosystem that supports open-source science. However, quality information, being difficult to curate and often context-specific, is currently not readily available for sharing within and across disciplines.

To help address this challenge, and to promote the creation and (re)use of freely and openly shared dataset quality information, members of multiple, international groups collaborating with domain experts have undertaken the development of community guidelines with practical recommendations for the Earth science community. The guidelines follow the guiding principles of being findable, accessible, interoperable, and reusable (FAIR).

The FAIR dataset quality information guidelines are intended to help stakeholders, such as scientific data centers, digital data repositories, and producers, publishers, stewards and managers of data, to achieve the following: i) capture, describe, and represent quality information of their datasets in a manner that is consistent with the FAIR guiding principles; ii) allow for the maximum discovery, trust, sharing, and reuse of their datasets; and iii) enable international access to and integration of dataset quality information.

Bio:

Dr.Ge Peng is currently a Senior principal research scientist from the University of Alabama in Huntsville (UAH), supporting the NASA Interagency Implementation and Advanced Concepts Team (IMPACT) Project. With a Ph.D. in meteorology and a primary research focus on exploring the variability of essential climate variables of Earth atmosphere, ocean, and cryosphere, she has worked with various types of Earth observations and derived data products. She has first-hand experience of the challenges in finding and obtaining data quality information, which led her to find ways to systematically evaluate data quality as well as document and share quality information. Dr. Peng is a strong advocate of promoting scientific data stewardship and open science. She has volunteered for organizations that strive to minimize the barrier to data and information sharing, such as the Earth System Science Data (ESSD) Journal, the World Meteorological Organization (WMO), and the Earth Science Information Partners (ESIP). Dr. Peng is a leading author of several data stewardship assessment models for national and international Earth science organizations and has published a number of peer-reviewed papers on trends and variability of climate data, research data management and stewardship.

FAIRPoints is an event series highlighting pragmatic measures developed by the community towards the implementation of the FAIR (Findable, Accessible, Interoperable, Reusable) data principles, in collaboration with GoFAIR US, SDSC, and SciLifeLab Data Centre.

Register here

Sign up for future events here

Twitter: @FAIR_Points

Biophysical experiments and biomolecular simulations: A perfect match?
2022-11-30 16:00 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Abstract-BRAINSTRUC__lindorff__Download

A special seminar by Professor Kresten Lindorff-Larsen, University of Copenhagen

DDLS Industry PhD Collaboration Dialogue - online
2022-11-30 09:00 - 11:00 | Online event via Zoom
The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) is a national 12-year research program that involves 11 partner organizations, collaborators nationally and internationally, the Swedish life science community, industry, healthcare, and other stakeholders in society at large.

During the program, more than 250 PhD students and 200 postdocs in academia and industry will be recruited to facilitate collaborations across sectors and disciplines. The DDLS academic and industrial PhD students and postdocs will all be enrolled in the DDLS Research School promoting acquisition of high competence and skills. This is to meet the future needs within data-driven life sciences, industrial R&D, health care and society. The DDLS Research School will be launched in 2024.

Now, both well established companies, small and medium-sized enterprises, within the data-driven life science sector as well as academia, are invited to partake in this event and contribute to the future of the program.

Aim

The aim of this event is to:

Inform about the program and KAW donation letter that specifies industrial PhDs and Postdocs.

Inform about the DDLS Research School, timeline and recruiting models for industrial PhDs.

Engage industry in the DDLS Program (e.g., being part of the DDLS review committees and involved in decisions and other types of evaluations regarding the DDLS research school).

Discuss how industry would like to contribute to the the DDLS Research School and the program.

Preliminary Agenda

Welcome

Presentation of the DDLS program

Overview of the DDLS Research School

Recruitment Models for DDLS PhD Program – Academia & Industry

Discussion/Dialogue

Registration

Register as soon as possible but no later than November 28th.

Register here

Contact

Mojgan Seraji (contact information below) or DDLS support team: ddls@scilifelab.se

Mojgan SerajiCollaboration ManagerProject leading, SciLifeLab Code of Conduct, DDLS PhD & Postdoc Programs, DDLS Industry CollaborationMojgan.Seraji@scilifelab.uu.se +46 (0) 73 46 97 306

Ancient DNA symposium
2022-11-29 09:00 - 16:30 | Large auditorium, Swedish Museum of Natural History, Frescativägen 40, Stockholm, Sweden
SciLifeLab Ancient DNA. Photo. Mikael Wallerstedt.

The possibility of studying humans, animals, plants, and other forms of life that lived in the past using DNA analysis is providing new insight into history, often with important implications for understanding our contemporary world. Ancient DNA can support investigation of e.g. prehistoric migrations and interactions, cultural practices, and development of agriculture, as well as research into evolution, ecology, and biodiversity.

This symposium is organized to present the forefront and breadth of ancient DNA analysis and its value in context of other information in order to facilitate cross-disciplinary projects.

The event is organized by the Centre for Palaeogenetics at Stockholm University and Swedish Museum of Natural History, in collaboration with SciLifeLab Ancient DNA unit and the National Genomics Infrastructure.

The symposium is free of charge. Deadline for registration is November 18th for on-site participation.

During the coffee breaks, representatives of SciLifeLab Ancient DNA unit, the National Genomics Infrastructure (NGI), and the National Bioinformatics Infrastructure Sweden (NBIS) are available for project discussions.

If you are unable to join the meeting physically, you can take part in all presentations online. Please register below to receive the link.

Registration

Please register for online participation. Registration for on-site participation is closed.

Program and Abstracts

2022-Ancient-DNA-symposium-program-and-abstracts-1Download

The Centre for Cellular Imaging - A research infrastructure for correlated multimodal imaging
2022-11-28 12:00 - 13:00 | Birgit Thilander Lecture Hall, Medicinaregatan 3, Göteborg
The Centre for Cellular Imaging – A research infrastructure for correlated multimodal imaging

Julia Fernandez-Rodriguez

The CCI specializes in 3D correlative imaging, i.e. the sequential combination of two or more imaging techniques to gain knowledge across multiple scales

SciLifeLab is a national infrastructure within life science with a wide range of advanced technology and expertise. The newly started SciLifeLab site in Gothenburg includes units at both the University of Gothenburg and Chalmers University of Technology and has a strong connection to Sahlgrenska University Hospital.

A light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available, please click the zoom-link below to join the event at the appointed time.

Venue

Assembly Room Birgit Thilander, Medicinaregatan 3

Chemical Biology Seminar
2022-11-24 15:00 - 17:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
“DATA-DRIVEN HALLMARKS OF ACUTE MYELOID LEUKEMIA:

BIOLOGICAL, PROGNOSTIC AND THERAPEUTIC IMPLICATIONS”

Tom Erkers

Assistant professor, Dept. of Oncology-Pathology, Karolinska Institutet

“SYNTHETIC SWITCHES FOR DNA REPAIR –

CONTROLLING ENZYMATIC FUNCTIONS AT WILL”

Maurice Michel

Assistant professor, Dept. of Oncology-Pathology, Karolinska Institutet

Nov. 24 at 3.30 pm

Gamma 2 Lunch Room, SciLifeLab Stockholm

And on Zoom

https://ki-se.zoom.us/j/64941340588

Research seminar - Distributing biotechnology and hardware to advance research and health care
2022-11-24 15:00 - 16:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Research seminar with Keith Pardee
Where: Lunch room in Gamma-building floor 2 at SciLifeLab. If you don’t have an access card, wait in the SciLifeLab LobbyWhen: Thursday 24th November, at 3 pm (The early birds will be served some fika, so be there on time)
Keith PardeeAssociate professor, Leslie Dan Faculty of Pharmacy, University of TorontoCanada Research Chair in Synthetic Biology and Human HealthCo-Director, PRiME, Precision Medicine Initiative, Medicine by Design Investigator
Bio
Prof. Keith Pardee is working at the intersection of synthetic biology and human health. His lab is pioneering the development of in vitro devices to host cell-free synthetic gene networks for broad applications in research and human health. Pardee’s research interests include the development of molecular diagnostic tools for communicable diseases like Zika virus, distributed drug manufacturing, and regenerative medicine.
He is also the co-founder of several companies and initiatives including PRiME: A Precision Medicine Initiative, En Carta Diagnostics, Medicine by Design 2.0, LSK Technologies, and Liberum Biotech.
https://www.pardeelab.org/

Campus Solna Seminar Series: Charlotte Stadler and Linnea Påvenius
2022-11-24 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:

Charlotte Stadler

Spatial Proteomics – alpha 2

New multiplexed imaging services and translational research within the Spatial Proteomics Unit.

Linnea Påvenius

Hjalmar Brismar – gamma 3

Mitochondrial dynamics in primary and transformed cells.

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

SciLifeLab Platform Day - Uppsala site
2022-11-24 09:00 - 17:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
This day will be held to promote and introduce an array of SciLifeLab infrastructure platforms based in Uppsala.
Venue: Trippelrummet, and on ZoomTime: 9:00-17:00

REGISTER HERE

SEE THE PROGRAM HERE

Aquatic Microbiome Research Initiative -All-Hands meeting
2022-11-24 08:00 - 2022-11-25 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
This year’s AMRI All-Hands meeting will feature speakers from EMBL, Centro Nacional de Biotecnología, Umeå University, and the LEAF sustainable lab program.

Read more and register

The evening of the 24th we will welcome all AMRI participants on an excursion to the Baltic Sea Science Centre, followed by a dinner.

**A dinner for postdocs and early career researchers is scheduled for the evening of November 23rd, to be followed by a morning workshop designed for postdocs and early careers on November 24th.

AMRI covers the cost of travel and accommodations for those traveling from outside the Stockholm/Uppsala area.

National support with superresolution light microscopy
2022-11-22 12:00 - 13:00 | Glasburen Seminar Room, Chemical Biological Centre (KBC) Building, Umeå University, Umeå, 901 87, Sweden
In the frame of the “SciLifeLab Site Umeå / KBC Infrastructure Seminar Series”, the seminars will be organised every second Tuesday during autumn 2022, in turn with IceLab Lunch Pitches. The seminars will be held in a hybrid format IRL in Glasburen, KBC, and online via Zoom. Take the chance to get information on facilities, possibilities and services that infrastructure, both SciLifeLab-associated and local, can offer! Learn more about the seminar series and the schedule for autumn 2022 here.

On November 22nd, 12:00-13:00, you are welcome to participate in the seminar

National support with superresolution light microscopy

by Hans Blom, Royal Institute of Technology (KTH), Head of the Advanced Light Microscopy (ALM) Unit, SciLifeLab

More information about the national SciLifeLab facility Integrated Microscopy Technologies.

About Hans Blom

registration

Registration deadline: Monday, November 21st, 10:00.

Online attendance: You can also join the seminar on Zoom, https://umu.zoom.us/j/63138997026

Organisers: SciLifeLab Site Umeå and Chemical Biological Centre (KBC)

Glycoproteomics - How to analyze the importance of protein glycosylation
2022-11-21 12:00 - 13:00 | Birgit Thilander Lecture Hall, Medicinaregatan 3, Göteborg
Glycoproteomics – How to analyze the importance of protein glycosylation

Carina Sihlbom

Changes in the glycosylation of proteins is one of the first signs of a disease, and advanced mass spectrometry is central for the study of such protein structure.

SciLifeLab is a national infrastructure within life science with a wide range of advanced technology and expertise. The newly started SciLifeLab site in Gothenburg includes units at both the University of Gothenburg and Chalmers University of Technology and has a strong connection to Sahlgrenska University Hospital.

A light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available, please click the zoom-link below to join the event at the appointed time.

Venue

Assembly Room Birgit Thilander, Medicinaregatan 3

NBIS/ELIXIR-SE Tools for Reproducible Research - ONLINE
2022-11-21 09:00 - 2022-11-25 15:30 | Online event via Zoom
NBIS / ELIXIR-SE course is 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

Contact information: edu.trr@nbis.se

Apply here

Course webpage

Important dates

Application open: Sep 5, 2022

Application deadline: Oct 21, 2022

Confirmation to accepted participants: Oct 28, 2022

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

Topics covered

Good practices for data analysisVersion control and collaborative code developmentPackage and environment managementWorkflow managementDocumentation and reportingContainerized computational environments

Learning outcomes

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

Organize and structure computational projectsTrack changes and collaborate on code using GitInstall packages and manage software environments using CondaStructure computational steps into workflows with Snakemake and NextflowCreate automated reports and document their analyses with RMarkdown and JupyterPackage and distribute computational environments using Docker and Singularity

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.

Comprehensive genomic profiling in routine cancer care - experiences from Uppsala
2022-11-18 14:00 - 15:00 | Online event via Zoom
This webinar is jointly organized by the Clinical Genomics platform and Genomic Medicine Sweden and will focus on comprehensive genomic profiling of solid tumors in routine cancer care. Clinical, laboratory and bioinformatic aspects will be covered.

Speakers

Johan Botling, Assoc Professor of Pathology, Senior Consultant Histopathologist

Gilbert Lauter, PhD, molecular biologist

Jonas Almlöf, PhD, bioinformatician

When: Friday November 18, at 14.00-15.00

Where: Zoom videoconference. Register to receive Zoom link.

Host: Malin Melin, Head of CG Uppsala

If you have questions about the webinar, you are welcome to contact Eva Berglund (eva.berglund@scilifelab.uu.se) or Malin Melin (malin.melin@scilifelab.uu.se).

registration

Campus Solna Seminar Series: Petra Marttila and Sammy Park
2022-11-17 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:

Petra Marttila

Thomas Helleday – alpha 5

Targeting one-carbon metabolism in cancer – a journey of curiosity and collaboration to uncover a detailed mechanism of action of small-molecule MTHFD1/2 inhibitors.

Sammy Park

Olli Kallioniemi – alpha 4

Pre-clinical assessment of radiopharmaceutical therapy in paediatric high-risk neuroblastoma.

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

BAM Seminar: Grant opportunities for PhDs and Postdocs
2022-11-15 13:00 - 14:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
As part of our “Biology At Most” seminar series we invite speakers from all types of life science career paths. They will share their visions, perspectives and expertise in their field in a informal environment.

Today’s Guests

Representatives of the scholarship offices from Stockholm University, Kungliga Tekniska Högskolan and Karolinska Institutet: Carina Lindblad (SU), Veronica Haegeland (KTH) and Daniela Strodthoff (KI)

These speakers will inform us about the grant opportunities available from our three universities for researchers at the PhD or Postdoc level. As researchers in academia we all rely on grants to carry out our research or to attend workshops and conferences. The seminar will cover topics and discussions that will be helpful for PhD students and Postdocs to further their research interests and consider new avenues to expand into high quality research ideas.

This event is mainly aimed at PhD students and Postdocs, but researchers in all stages of their career are of course welcome to attend.

You can join the meeting in person or via zoom (Meeting ID: 651 4642 5776).

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

DDLS Annual Conference
2022-11-15 12:30 - 2022-11-16 12:30 | Eva & Georg Klein, Solnavägen 9, Stockholm, 17165, Sweden
Welcome to a lunch-to-lunch conference focused on Data-driven Life Science. Listen to the DDLS Fellows and take part in social activities onsite.

The Data-Driven Life Science conference on November 15-16, 2022, is the first in-person conference of the DDLS program. This meeting brings together the community in biomolecular data science and AI, introduces newly appointed DDLS fellows, and provides opportunities for networking across the research community and SciLifeLab infrastructures. We are excited to host two international keynote speakers and welcome the community to join us. We are excited to meet in person at the poster session and other social events.

DDLS Annual Conference Poster session

Lightning talk and Poster session

The lightning talk is 1 minute and will be strictly timed. No slides. Please, indicate in the registration if you like to present a poster with, or without, a 1 min lightning talk.

DDLS Annual Conference Best Poster Award

The DDLS Annual Conference Best Poster Award encourages the submission and exhibition of high-quality posters carried out by young scientists, including Ph.D. students, post-doctoral researchers, etc. The poster should be on a topic related to data-driven life science. The Prize, which is based upon the decision of a Scientific Committee-appointed Jury, consists of a certificate and a travel grant of up to 5 000 SEK. The travel must be booked and ordered through the DDLS Support team and follow regular University travel policy. The trip should be completed before 2023-12-31.

Target group: We welcome all researchers interested in the DDLS program and data-driven life science.

Participants onsite: Venue Eva & Georg Klein, Floor 3 (ground floor), Biomedicum, Stockholm

Participate online: Online participation info, e.g, zoom link will be sent out upon registration

Organizer: SciLifeLab, host of SciLifeLab & Wallenberg National Program for Data-Driven Life Science.

Register here

Onsite: Register before November 9 at 12:00, so we can order coffee and lunch.

Download Flyer

Download Program

Agenda

Tuesday, November 1511:45Drop-in Registration with Coffee and WrapsArea: Social area directly to the right of the entrance. You can leave your coat and bag in the Lecture Hall. We ask the participants to be seated at 12:30.12:30WelcomeTuuli Lappalainen, KTH/SciLifeLabDDLS updatesOlli Kallioniemi, SciLifeLab13:00Keynote: Samuli Ripatti, Institute for Molecular Medicine, University of HelsinkiGenetic variation and risk of common diseases over the life course13:45Coffee break14:15DDLS Fellow Talk: Tom van der Valk, Museum of Natural HistoryEnvironmental DNA in the genomic decade14:35Infrastructures for data-driven life scienceJohan Rung, SciLifeLab Data CentreSciLifeLab Data Centre14:45Ola Spjuth, SciLifeLab Data CentreManaging the life cycle of AI models and apps15:00Matts Karlsson, Linköping UniversityNAIS, Berzelius and the road ahead15:15Poster lightning talks (1 minute per poster)Poster session with snacks and beverage17:30End of Day 1Wednesday, November 1609:00Keynote: Cecilia Clementi, Freie Universität BerlinDesigning molecular models with machine learning and experimental data09:45DDLS Fellow Talk: Johan Bengtsson-Palme, Chalmers University of TechnologyUnderstanding the Evolution of Pathogenicity: Predicting and Preventing the Disease Threats of the Future10:05Announcement of DDLS Annual Conference Best Poster Award10:15Coffee break10:45DDLS Fellow Talk: Tobias Andermann, Uppsala UniversityBig data approaches for assessing biodiversity value and potential11:05DDLS Fellow Talk: Fredrik Edfors, Royal Institute of Technology, KTHHarnessing the promise of next-generation plasma profiling for pan-cancer diagnostics11:25DDLS Fellow Talk: Clemens Wittenbecher, Chalmers University of TechnologyMetabolomics profiling generates candidate biomarkers for precision nutrition approaches11:45Panel discussion: Training in Data Driven Life ScienceChair: Carolina Wählby, Uppsala UniversityPanelists: Leslie Solorzano Vargas, postdoc at KINina Norgren, coordinator for DDLS education and training, Umeå UniversityKrzysztof Jurdzinski, PhD student at KTHDaniel Gedon, PhD student at UU12:30Joint conference lunchProgram updated 2022-11-12

Abstract

Cecilia Clemens
Designing molecular models with machine learning and experimental data. Cecilia Clemens.

The last years have seen an immense increase in high-throughput and high-resolution technologies for experimental observation as well as high-performance techniques to simulate molecular systems at a microscopic level, resulting in vast and ever-increasing amounts of high-dimensional data. However, experiments provide only a partial view of the molecular processes and are limited in their temporal and spatial resolution. On the other hand, simulations are still not able to completely characterize large and/or complex molecular processes over long timescales, thus leaving significant gaps in our ability to study these processes at a physically relevant scale. We present our efforts to bridge these gaps, by combining statistical physics with state-of-the-art machine-learning methods to design optimal coarse models for complex macromolecular systems. We derive simplified molecular models to reproduce the essential information contained both in microscopic simulation and experimental measurements.

Samuli Ripatti
Genetic variation and risk of common diseases over the life course. Samuli Ripatti.

Past 15 years have seen tremendous success in identifying genetic loci associated with common diseases and traits. Much of the current activities focus on strategies for inferring causal variants and genes driving these associations and on the potential translational opportunities arising from the genetic discoveries. I will highlight some of the opportunities, risks and gaps in our knowledge related to both causal inference and genetic prediction and translation. I will provide examples from FinnGen study (www.finngen.fi) consisting of genome wide profiles and longitudinal health registry data for half a million Finns and from a network on biobanks and machine learning/AI -methods developers in INTERVENE Consortium (https://www.interveneproject.eu).

Johan Bengtsson-Palme
Predicting the disease threats of the future. Johan Bengtsson-Palme

Our inability to restrain covid-19 to remain a local disease outbreak highlighted an important vulnerability in our preparedness for new infectious diseases – our inability to predict what the future disease agents might look like. This inability makes it impossible to preemptively monitor for potential future pathogens and makes it harder to quickly adapt existing disease surveillance to novel outbreaks. There is no guarantee that the next major outbreak will be viral – with increasing antibiotic resistance, multidrug-resistant bacteria may very well be the next pandemic. In this talk, I will discuss how we can predict which genes to look for to find future pathogens before they become widespread in clinics or among the general population, both in terms of genes responsible for pathogenicity and in terms of antibiotic resistance genes. I will also outline how surveillance for antimicrobial resistance could be adapted to also include markers for pathogenicity and thus allow us to prevent or constrain disease outbreaks early.

Fredrik Edfors
Harnessing the promise of next-generation plasma profiling for pan-cancer diagnostics. Fredrik Edfors

Cancer is one of our biggest worldwide health problems, causing almost 10 million deaths annually. Despite significant advancements in cancer therapy over the past three decades, diagnosis and treatment still have a great deal of opportunity for improvement.

Here, a total of 12 prevalent cancer types represented by more than 1,400 cancer patients’ plasma profiles of 1,463 proteins were evaluated in trace amounts of blood plasma taken at the time of diagnosis and prior to treatment. A group of proteins linked to each of the examined malignancies was found using ML-based disease prediction models. This precision medicine strategy has the potential to benefit from advances in proteomics and precision and personalized medicine.

Tobias Andermann
Big data approaches for assessing biodiversity value and potential. Tobias Andermann

Our human societies worldwide are having a profound negative impact on the natural world surrounding us, leading to experts declaring the current biodiversity crisis. However, to date it is difficult if not impossible to actually quantify the magnitude of our impact on biodiversity. This is largely due to the overwhelming complexity of biodiversity, which is not easily summarized and reduced into manageable metrics. Yet, solving this task is necessary and is arguably one of the biggest and most urgent contemporary challenges for the biological research community. In this talk I will discuss the utility of environmental DNA (eDNA) sequencing as a tool for gathering comprehensive biodiversity data in the field. I will touch upon the challenges and possibilities regarding the application of eDNA data for this purpose, in particular how these data can be applied to train AI models with the ability to model biodiversity and simulate changes thereof.

Scientific Committee

Tuuli Lappalainen, chair and DDLS Steering group member, Clemens Wittenbecher, DDLS Fellow, Simon Olsson, WASP and Johan Rung, Data Centre.

Organizing Committee

Project leader Erika Erkstam, Operations office, and the DDLS support team Heidi T Persson, Ulrika Wallenquist, Titti Ekegren.

Spatial and Single Cell Biology Webinar
2022-11-14 13:00 - 15:00 | Online event via Zoom
The Spatial and Single Cell Biology Platform at SciLifeLab invites you to a virtual event where you can learn about the service we provide within the field of spatial and single cell omics. Take the opportunity to learn about cutting edge methods including spatial transcriptomics with Visium, in situ sequencing, spatial proteomics using highly multiplexed imaging, spatial metabolomics with MALDI imaging and advanced FISH technologies. The presentations will be given by our experts in there respective methods, working within the platform.

The event is open for anyone to attend, who are interested in including spatial omics in their research projects or with a general interest to learn about the methods.

register here

TEM sample preparation practical course part II
2022-11-14 08:00 - 2022-11-18 17:00 | Kemiskt Biologiskt Centrum, Umeå University, Linnaeus väg 6, Umeå, 90736
TEM sample preparation course – Chemical fixation, high pressure freezing, plastic embedding and staining methods including practice on ultra-microtome sectioning, TEM imaging and an introduction to CLEM (Correlative Light and Electron Microscopy), FIB-SEM (Focused Ion Beam) and electron tomography.

Read more

Pre-requisite criterion: Basic EM course at UCEM or equal previous experiences of EM methods.

Participants will practice EM sample preparation and EM imaging with one sample from their own project. Our lab space limits the number of participants to 8 so we will select participants based on your motivation and how your project aims fits to the course content. Please write a short project description, a motivation for participating and what sample you would like to process during the course.

Please, look at the program and the methods that are covered in this course. Make sure you have time to participate full days and the entire week. Since the fixation and plastic embedding takes time, you should bring one test-sample to Agnieszka on Monday 7 of November, and a new test-sample on the first course day, 14 November.

Preliminary Program:The course preliminary program will be announced here once it is organised.

Location:Lectures at KBC and laboratory demonstrations at UCEM – Level 5, 6 + new EM building (Level 1), Umeå University.

Participants:8 persons. Open to all research students, postdocs and staff.

Instructors:

Sara Henriksson – EM research engineerGayathri Vegesna – EM research engineerAgnieszka Ziolkowska – EM research engineerCamilla Holmlund – EM research engineerLinda Sandblad – EM facility director

Duration:5 days

Breaks/Refreshments:Coffee, cookies and fruit will be served.

Costs:No course fee, but full attendance is required!

Credits:Students that attend all theoretical and practical parts of the course, will receive a certificate for 1,5 hp.

[Clinical Talks] Combining AI and in situ sequencing to explore the tumor micro-environment
2022-11-11 09:00 - 09:30 | Online event via Zoom
Carolina Wählby

Professor in quantitative microscopy, SciLifeLab and Dept. IT, Uppsala University

Carolina Wählby is professor in Quantitative Microscopy at the Dept. of Information Technology, Uppsala University, and Scientific Director of the National SciLifeLab Bioimage Informatics Unit. Her research is focused on developing computational approaches for extracting information from image data with focus on precision medicine and life science. Methods include traditional image analysis as well as AI and deep learning for understanding dynamics of cancer tissue, antibiotics susceptibility and spatial transcriptomics, funded primarily by the ERC TissUUmaps project and the Swedish Foundation for Strategic research. She received the SBI2 President’s innovation award in 2014 for her work on in situ sequencing, and the Thuréus prize in 2015 for development of open tools for image analysis. She is a member of the Royal Society of Sciences at Uppsala and the Royal Swedish Academy of Engineering Sciences. She has a MSc in molecular biotechnology and a PhD in digital image analysis, and carried out postdoc research within genetics and pathology. She was part of the Imaging Platform of the Broad Institute of Harvard and MIT in 2009-2015 and became full professor at Uppsala University in 2014. She is a member of the steering group of a 300M€ effort on Data Driven Life Science, funded by the Knut and Alice Wallenberg Foundation, with the ambitious goal of training the next generation of life scientists. Her heart lies in the intersection between life science and computational image analysis, and she is intrigued by the possibilities of technological developments and convergence of the scientific fields.

register to receive zoom link

Moderator: Päivi Östling, SciLifeLab

Clinical Talks

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

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

Workshop on biomolecular simulations
2022-11-09 08:00 - 17:00 | Inghesalen, Tomtebodavägen 18a,, Solna, 171 65 171 65, Sweden
The main focus of ‘Biomoelcular simulations workshop’ is on molecular dynamics simulations of biomolecular systems. The target audience of this workshop is the researchers working in Sweden on biomolecular simulations. The goal of this workshop is to bring together all the researchers from Sweden interested in biomolecular simulations and to provide an opportunity to junior researchers in the field to present their work. This will be a single day event with some talks by other researchers from abroad and ample opportunities for discussion and interactions among the people in the field.

Confirmed speakers

Simon Olsson, Chalmers, GothenburgMilosz Wieczor, IRB BarcelonaMercedes Alfonso-Prieto, Forschungszentrum Jülich

Program and abstracts are collapsible items – click to expand.

Program
09:30Morning Coffee, MingleInghesalen, Karolinska Institutet09:55Welcome from organizersOrganizing Committee10:00Multiscale simulations to study proton transfer: from enzymes to membrane proteinsMercedes Alfonso-Prieto, Forschungszentrum Jülich, Germany10:40Exploring the selectivity profile of plant UDP dependent glycosyl transferases (UGTs) by computational and experimental studiesJunhao Li, Uppsala University11:00Multi-scale Modeling of Axonal Injury (coupling of finite element analysis with molecular dynamics simulations)Maryam Majdolhosseini, KTH Royal Institute of Technology11:20Coffee Break11:40A Machine-Learned Atomistic Force Field for Nucleic AcidsMiłosz Wieczór, IRB Barcelona12:20Combining evolution and physics with coevolution-powered machine learningDarko Mitrovic, KTH Royal Institute of Technology12:40Lipid-ethanol mixtures for topical drug delivery applications: A molecular dynamics and NMR studyAmanda Quinones Vallin, Stockholm University13:00Lunch14:00Machine learning to reconcile experiment and simulationSimon Olsson, Chalmers University of Technology14:40Effective Molecular Dynamics from Neural-Network Based Structure Prediction ModelsAlexander Jussupow, Stockholm University15:00Opportunities and Challenges in GPCR SBDD: Finding the Sweet SpotsPierre Matricon, Sosei Heptares15:20Wrap up, Thank youOrganizing Committee

Multiscale simulations to study proton transfer: from enzymes to membrane proteins
Mercedes Alfonso-Prieto, Assistant Professor, Forschungszentrum Jülich, Germany

Proton transfer (PT) is one the most common processes in biology. Studying PT at the molecular level is a challenging task, due to the intrinsic complexity of proteins, including their functional dynamics and the presence of several titratable residues. Therefore, combination of experimental and computational techniques is needed to obtain a more comprehensive picture. Recent methodological and software advancements have enabled the efficient application of quantum mechanics/molecular mechanics (QM/MM) simulations to (large) biological systems. This multiscale approach allows treating the region of the protein where PT takes place at the QM level, while including the effect of the rest of the protein and its environment at the MM level. In this talk, I will show some examples of QM/MM simulations applied to PT processes in different systems, from enzymes to membrane proteins. Such hybrid simulations have provided atomistic insights complementary to experiments.

A Machine-Learned Atomistic Force Field for Nucleic Acids
Miłosz Wieczór, Postdoctoral fellow, IRB Barcelona

We present a new paradigm for the parametrization of nonbonded interactions in molecular force fields directly from quantum chemical data. The proposed machine-learned force field (ML-FF) accurately reproduces well-validated quantum chemical interaction energies, as well as allows for the systematic incorporation of experimental data such as measured affinity constants. Contrary to many recently published general ML-FFs, our force field ensures stability in molecular dynamics simulations thanks to a combination of regularization and active learning, and permits gradual upgrades should issues arise in previously untested systems. Meanwhile, a simple embedding scheme allows the parameters learned from minimal methyl-nucleobase systems to be employed in simulations of large biomacromolecules at virtually no computational overhead. We also present several key directions for the future evolution of our force field, both in terms of accuracy and applicability.

Machine learning to reconcile experiment and simulation
Simon Olsson, Assistant Professor, Chalmers University of Technology

Long-time-scale and enhanced sampling molecular dynamics simulations reveal the approximations of classical molecular dynamics force fields disagreeing with experimental data. However, under ideal conditions, experiments and simulations observe the same process — consequently, by optimally balancing experimental and simulation data, we may build models extracting helpful information from both. In this talk, I will overview efforts in this direction and talk about Augmented Markov models, and their recent extension dynamic Augmented Markov models.

Registration
