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SIB - Swiss Institute of Bioinformatics

SWISS BIOINFORMATICS

SIB NEWSLETTER - APRIL 2021

IN THIS ISSUE

What if we could leverage and learn from the vast amount of data generated in clinical routine, or data from healthy people to improve our understanding of diseases and health? 

If you are you an SME, startup, pharma, biotech company – or an academic researcher - developing solutions for preventive medicine, don’t miss the call to submit an abstract and the chance to take part in the ELIXIR Innovation and SME Forum which will take place on 13 September at the [BC]2 Basel Computational Biology Conference 2021! (see call below)

This edition of Swiss Bioinformatics will also bring you: the latest on the SARS CoV-2 data sharing on the Swiss side with the setup of a national data hub, interviews with the developers of leading resources for gene expression and viral genomics, and the 10 achievements of the past year by SIB Scientists which you should really check out before going to bed.

ESSENTIAL RESOURCES FOR THE LIFE SCIENCES

Part of SIB’s mission is to provide and maintain databases and software tools,
which are of fundamental importance to the wider life-science community.

From v1 to v14: the gene expression database Bgee under the spotlight

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The SIB Resource Bgee provides an intuitive answer to the question “where is a gene expressed?” and supports research in cancer and agriculture as well as evolutionary biology. On the occasion of the latest release of this database of gene expression patterns across multiple animal species, co-Group Leaders Marc Robinson-Rechavi and Frédéric Bastian tell us about its evolution over the years and its newest features.

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The viral genomics pipeline V-pipe under the spotlight

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From SARS-CoV-2 monitoring to HIV antiviral drug resistance detection, the SIB Resource V-pipe orchestrates software packages to detect the genomic diversity of a virus population in a sample or individual. The pipeline is a key companion for researchers conducting large-scale epidemiological surveillance as well as patient-focused clinical applications. The team led by Niko Beerenwinkel shares insights on V-pipe’s recent applications and developments.

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TAKING THE PULSE OF SIB

Discover the SIB Remarkable Outputs 2020

Staying abreast of the latest advances and bright ideas emerging in a field as diverse as bioinformatics is challenging. The SIB Remarkable Outputs are selected to provide the global bioinformatics community with a shortlist of achievements of the year by SIB Scientists that are particularly deserving attention. Discover the shortlist of 2020, from standardized images of cells, to deep learning applied to protein function mapping.

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Submit your abstract to [BC]2 2021, 13-15 September

The next edition of the Basel Computational Biology Conference “Harnessing biological data: from molecular processes to human health”, one of the major computational biology events in Europe, is inviting submissions. Share the results of your team’s latest work with the international computational community! Abstracts can be submitted in either of three presentation categories:  oral presentation, poster and poster pitch or poster only. The call will close on 16 May 2021.

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Share your ideas for preventive medicine at the the ELIXIR Innovation and SME Forum at [BC]2

“Building the learning ecosystem of health: from data tracking to preventive medicine” : do you provide support in translating data into preventive guidelines and healthcare measures? Then submit your abstract to participate in the forum, which will discuss new solutions to connect the different components of the learning ecosystem of health and preventive medicine.  The call will close on 16 April 2021.

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HEALTH AND CLINICAL APPLICATIONS

Accelerating global COVID-19 research with a Swiss SARS-CoV-2 Data Hub

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Open sharing of SARS-CoV-2 sequencing data would allow fast, representative and large-scale research on the virus. Initially developed to track the emergence and spread of any pathogens in Switzerland, the Swiss Pathogen Surveillance Platform (SPSP) co-led by SIB is now acting as a Swiss SARS-CoV-2 Data Hub, i.e. a user-friendly platform to collect viral genome sequences produced from Swiss samples and submit them to open data repositories.

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How to track pandemic variants faster

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In a Nature comment piece, an international group of specialists in viral and genetic analysis, led by SIB’s Emma Hodcroft and Christophe Dessimoz, alongside Nick Goldman (EMBL-EBI), lay out the ‘bioinformatics bottlenecks’ that are hindering response to the SARS-CoV-2 pandemic, and propose ways to ‘clear the road’ for better tools and approaches. Here are the key take home messages and perspective from the Swiss angle.

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PERFECT YOUR BIOINFORMATICS SKILLS

SIB courses available in streaming and next months’ programme

Are you starting a project on a topic outside your area of expertise? Do you or your colleagues need a refresher course? Do you need to bring a new hire up to speed? If you answered yes to any of the above or simply want to perfect your skills, SIB courses are for you! Discover our courses on NGS, RNA-seq, single-cell, machine learning and many more.  Subscribe to the upcoming courses mailing list and watch our  online courses. Also, ask us about the courses we can deliver in your company!

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BIOINFORMATICS FOR ALL

Latest Protein Spotlight: Wrong place

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When you reach a certain age, one question arises on a painfully regular basis. It begins with a "Where are my...?" or a "Where is my..." Reading glasses are a constant. Frequently, they are not where they ought to be. Having relocated them, you may well remark that they are not where you put them. But they are. The thing is, in a moment of distraction, you left them where you would not normally…

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