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SIB - Swiss Institute of Bioinformatics

SWISS BIOINFORMATICS

SIB NEWSLETTER - OCTOBER 2020

IN THIS ISSUE

In 1993, SIB’s ExPASy started off as the very first life science website. Today it is a fully-fledged bioinformatics discovery tool, supporting research and connecting to the 160+ bioinformatics databases and software tools developed by SIB Groups. We are very happy to announce its last major release, which we invite you to explore.

In this new edition, you will also discover the diversity of SIB partnerships, from quality control organizations to hospitals and the private sector, supporting external quality assessments, open data as well as cancer diagnostics. Also, not to be missed: the open call for the SIB bioinformatics awards!

Enjoy the read!

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.

Discover the new Expasy.org, the Swiss Bioinformatics Resource Portal

Exploring the 160 databases and software tools developed by SIB Groups has never been this easy. Created in 1993, Expasy, the SIB bioinformatics resource portal, is now available as a new release, after a major overhaul. It includes tools that support a wide range of life science and clinical research domains. Add Expasy to your bookmarks to ensure you keep your favorite bioinformatics tools at your fingertips.

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in silico talks series: #11: An improved view of influenza evolution with CoalRe

“Accounting for reassortment events reduces bias in influenza inference”. In this in silico talk, SIB’s Ugnė Stolz from Tanja Stadler’s Group at ETH Zurich introduces CoalRe, a framework enabling to take into account reassortment when inferring virus evolution and infection pathways. In a recent paper published in PNAS, the team showed that this framework permits better estimates of effective population size and evolutionary rates.

Read the full story and watch the talk
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SIB resources supporting SARS-CoV-2 research: the list keeps growing

Created early April, the page listing all data services, training and analysis tools developed by SIB Groups and targeting COVID-19 is regularly updated.

Access the list
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ENYO Pharma SA and SIB make human protein interaction data publicly available

Understanding how proteins interact with each other offers key insights into a range of physiological and pathological processes. New knowledge on this topic is now available: the SIB CALIPHO Group and ENYO Pharma SA have worked hand-in-hand in a transnational public-private partnership (PPP) to make human protein interaction data publicly available and FAIR, through the SIB Resource neXtProt.

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TAKING THE PULSE OF SIB

SIB Awards 2021: call for entries now open!

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Are you a bioinformatician with a remarkable early career or a graduate student who published an remarkable paper? SIB is supporting excellence at the national and international levels through the SIB Bioinformatics Awards. The Early Career Bioinformatician, Best Swiss Graduate Paper Awards and Resource Innovation Awards are now open for applications: follow the latest news and announcements related to the SIB Awards on our website and on Twitter (#SIBawards).

Website

SIB signs the manifesto for EU COVID-19 research

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Last July the Commission launched the manifesto to maximise the accessibility of research results in the fight against COVID-19. By endorsing it SIB commits for instance to make the generated results public and accessible without delay and following the FAIR principles, and where possible, to grant for a limited time non-exclusive royalty free licences on the intellectual property resulting from EU-funded research.

More commitments

Discover the latest pictures of our Group Leaders

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Artists, sailors, cyclists… Discover the surprising side of SIB’s Group Leaders through the eye of Geneva photographer Nicolas Righetti. Here are the new Group Leaders captured in his lens over the past year: Valentina Boeva (Computational Epigenetics of Cancer); Enkelejda Miho (Laboratory of Artificial Intelligence in Health); Christian Panse (Proteome Informatics); Berend Snijder (Functional Precision Medicine Group); Patrick Pedrioli and Bernd Wollscheid (Clinical Proteotype Analysis Center).

RESEARCH AT SIB

Understanding pollinators: genomic characterisation of bumblebee biodiversity

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A changing planet threatens many species, including bumblebees - globally important pollinators in natural ecosystems and in agricultural food production. To better understand the genetic variations and adaptations underlying their diverse ecology and behaviour, an international team co-led by SIB researchers at the University of Lausanne sequenced the genomes of 17 bumblebee species. This first genus-wide genomic characterisation of bumblebees opens up new possibilities to protect their biodiversity.

Discover the article

HEALTH AND CLINICAL APPLICATIONS

SIB becomes a partner of QCMD for quality assessment programmes

SIB is a new bioinformatics partner of the QCMD (Quality Control for Molecular Diagnostics) organization. The partnership aims to enhance bioinformatics solutions for international molecular external quality assessments. It will initially focus on the development of new computational tools to support nucleic acid sequence data analysis in the context of viral metagenomics and drug resistance.

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Addex and SIB receive Innosuisse grant to repurpose potent dopamine antagonist

Addex Therapeutics and SIB have been awarded a CHF600K Innosuisse grant to apply computational approaches developed by SIB to identify new therapeutic indications for ADX10061, a potent and selective dopamine D1 receptor antagonist. Dopamine is a major neurotransmitter in the central nervous system and D1 receptors are believed to play an important role in the control of diverse aspects of brain function, including cognition, motivation, motricity, sleep, and memory.

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New development in the cancer diagnostics platform used at the HUG

In its latest version, the cancer diagnostics platform developed jointly by the Geneva University Hospitals (HUG) and SIB offers key additional molecular insights. In addition to guiding the interpretation of sequencing data from patients, the new OncoBench® now enables clinicians to reliably analyse variations in the number of copies of particular genes – information that is linked with several cancer therapies.

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Bringing AI to image analytics in cancer diagnosis

SIB, Lunaphore and the Geneva University Hospitals (HUG) are collaborating to enable precision cancer medicine. As part of an Innosuisse project, they aim to develop an integrative solution for the phenotypic analysis of tumors powered by automated multiplex staining, image analysis and machine learning.

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PERFECT YOUR BIOINFORMATICS SKILLS

CAS in Personalized Molecular Oncology: apply to participate

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Are you a professional involved/interested in the field of personalized molecular oncology? This course will provide you with a comprehensive and integrative view of the field, including methodologies used to generate, analyze and interpret patients’ molecular profiles, while touching upon the associated technical, regulatory and ethical challenges. The CAS is co-organized by SIB with the University Hospital Basel and Lausanne university hospital.

Information & registration

SIB courses available in streaming and 2021 programme

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There is still time to register for courses on Parallelisation with OpenMP, Protein Bioinformatics: Sequence-Structure-Function, and others! Courses of the first semester of 2021 are now online: NGS, RNA-seq, and single-cell data analysis, machine learning, statistics, programming... Save the date for your favorite courses, subscribe to the mailing list, share this information with your colleagues, and check out the courses made available online.

Upcoming courses

BIOINFORMATICS FOR ALL

Outreach resources to understand the biology of the coronavirus

A new workshop for classrooms, and associated resources for the public, offer the opportunity to discover the SARS-CoV-2 coronavirus, in particular its genome and proteins. These materials result from a partnership between SIB and the Culture and Scientific Outreach Department of the University of Lausanne (SCMS).

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Latest Protein Spotlight: A wasp's sting

Nature has always inspired humans. We extract scents from flowers to make perfume, and use pigments from minerals to reproduce colours. We copy the streamlined bodies of birds to build planes, and mimic the toughness of spider silk to design textiles. As our knowledge accumulates, and technology evolves, we have even reached a point where we are able to tamper with the very basics of Nature to twist it to our advantage. Take antimicrobial peptides...

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