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SIB - Swiss Institute of Bioinformatics

SWISS BIOINFORMATICS

SIB NEWSLETTER - DECEMBER 2018

IN THIS ISSUE

While birthday years are always special for any institution, 2018 truly was pivotal for SIB, with some key structural changes such as the reshaping of one of SIB’s largest groups, Vital-IT (read below) and the set-up of a co-directorship at the head of the Institute (see last issue).
These changes came on top of SIB’s 20 years anniversary events and projects, which continue to grant Swiss Bioinformatics a great visibility, to reinforce the links within the community and to demonstrate the impact of this discipline and the people mastering it (follow #SIB20years on Twitter).
Also in this last edition of the year: understanding the role of bioinformatics in precision medicine in four videos; deep learning to the rescue of protein structure prediction; the list of our 2019 bioinformatics training courses; and our very best wishes for the festive season with an intriguing protein.

TAKING THE PULSE OF SIB

Best wishes from SIB! An ice-binding protein to celebrate winter… and the start of a New Year

With the festive season approaching and temperatures dropping down, discover what nature has in stock to protect life from cold

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Some strategic thoughts about SIB’s development, continued

Where will SIB be adding value in the years to come? Which are the fields where SIB’s expertise will be needed the most? Following the directions set out in SIB's Roadmap, the series of articles focusing on some themes of interest for the future continues with: increasing the impact of SIB’s bioinformatics resources and shaping the future of its pioneer bioinformatics core facility.

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ISMB/ECCB and [BC]2 – a bioinformatics summer in 2019

Switzerland is hosting two main bioinformatics conferences in 2019: ISMB/ECCB (21-25 July) and [BC]2 (9-12 September). While co-organizing the tutorial programme of ISMB/ECCB, SIB has a full responsibility for the [BC]2 scientific programme. Calls for [BC]2 workshops and tutorial sessions are now opened

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FOCUS ON PERSONALIZED HEALTH

Article in Swiss Medical Informatics on the SVIP project for somatic variant interpretation

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In the latest issue of the Swiss Medical Informatics journal, SIB Group Leaders Valérie Barbié, Patrick Ruch and Daniel Stekhoven offer a clear overview of the SPHN-supported Project, which “will provide a joint knowledge-base for somatic variants found in Swiss hospitals during cancer diagnostic sequencing”...

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Precision medicine and the role of bioinformatics: four short films to understand

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How do hospitals and researchers benefit from bioinformatics to help patients? SIB collaborated with Canal9 TV Channel and the Oncology department of UNIL/CHUV to illustrate the answers to this exact question. Four short films have been produced (with EN, FR, DE and IT subtitles), each explaining different aspects of precision medicine: from the multidisciplinary tumour board and pathology institute to molecular modelling and oncology.

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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.

Zooming into our metabolism with an R package

By which underlying mechanisms is our metabolism regulated? Marco Pagni and colleagues from SIB’s Vital-IT Group and the CHUV propose a new method combining genome scale metabolic networks and transcriptomics to offer a finer understanding of our metabolism’s underlying gene regulations as well as the means to predict them…

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Happy birthday, SWISS-MODEL! 25 years of 3D protein homology modelling

Take a closer look at an SIB Resource dedicated to making protein modelling accessible to life scientists from around the world: on the occasion of its 25th anniversary, we put a few questions to the SWISS-MODEL development team at the Biozentrum (University of Basel) – the Computational Structural Biology Group, led by Torsten Schwede

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Enhanced enzyme annotation in UniProtKB using Rhea

Integrating biological and chemical knowledge for a more complete understanding of biological systems: SIB Group Leader Alan Bridge tells us more about the new link between Rhea, the knowledgebase of biochemical reactions, and UniProt

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RESEARCH AT SIB

Switzerland: a good place to be to study ancient bones

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The genomic history of the Americas’ peopling was recently uncovered from ancient DNA by a team of over 50 researchers, with SIB Group Leader Anna-Sapfo Malaspinas at the University of Lausanne co-leading the bioinformatics analyses. The lead author on the paper, published in the journal Science, José Víctor Moreno-Mayar, has since joined her Group in Lausanne...

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Deep learning: a leap forward for protein structure prediction

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Generations of structural biologists have been restlessly trying to crack the protein-folding nut, with more or less success. Last week, several deep learning methods have led to remarkable advances at the global event for the evaluation of protein structure prediction methods: the 13th CASP experiment. Torsten Schwede and Matteo Dal Peraro, two SIB Group Leaders involved on the organizational and evaluation side of CASP13, tell us more…

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Latest Virtual Seminar: The hills and valleys of evolution

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Joshua L. Payne – SIB Group Leader at the Institute of Integrative Biology of the Department of Environmental Systems Science (ETH Zurich) – begins his fascinating talk on the underlying mechanics of evolution, how these mechanics themselves evolve and the notion of evolutionary landscapes. Landscapes? During the course of the 20th Century, the American population geneticist Sewall Wright was the first to depict evolution as landscapes…

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Decoding the genome of the wheat stem sawfly, a major agricultural pest

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What makes the wheat stem sawfly such a major pest in the grasslands of North America? An international study co-led by Rob Waterhouse’s SIB Group at the University of Lausanne unravels its genome and finds clues on possible mechanisms it employs to...

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PERFECT YOUR BIOINFORMATICS SKILLS WITH SIB TRAINING

2019 SIB bioinformatics courses

The list of SIB Training Courses for 2019 is online. It already includes over 30 scheduled events spanning areas such as NGS and other omics data analysis, single-cell, statistics, programming, machine learning, several SIB Resources, with many more to come. Save the dates in your calendar, subscribe to the courses' mailing-list to be informed when registrations open and share this information with your colleagues who might be interested as well!

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PROTEIN SPOTLIGHT

On mar and motion

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Movement is what sustains life. Organisms need to move to find food, seek shelter and to reproduce. Mobility is also essential inside organisms where cells are continuously dividing and migrating. There is also unceasing movement inside every cell where myriads of molecules are being trafficked, and cellular compartments of all shapes and sizes shifted. What keeps things moving?

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