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SIB - Swiss Institute of Bioinformatics

SWISS BIOINFORMATICS

SIB NEWSLETTER - OCTOBER 2019

IN THIS ISSUE

A method to estimate the causal effects of genes on human traits, an approach to reconstruct tumor evolution and a tool to infer the fate of single-cells based on their RNA: these were the themes of the talks given by the respective laureates of the SIB Bioinformatics Awards 2019 – one of the high times of our [BC]2 Basel Computational Biology Conference held in September. You can now watch these talks online!

Also learn about: the nationwide expert groups dedicated to harmonizing health data in the context of the Swiss Personalized Health Network; a symposium to celebrate 10 years of research on human proteins; a standalone version of the SIB orthology Resource OMA; asexuality and genomic invaders; and upcoming SIB Courses.

Enjoy your reading!

TAKING THE PULSE OF SIB

Big data and medical epidemiology on the [BC]2 conference programme

In September, over 300 attendees gathered in Basel to discuss advances and challenges in the field of molecular Big Data and its applications to medicine and health. Among the themes of the conference, the use of pathogen sequencing – and associated bioinformatics tools – to fight infectious diseases, highlighted by an article in the daily newspaper Le Temps.

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“Our expertise is a Swiss speciality”

SIB Director Christine Durinx was interviewed by L’AGEFI, a Swiss daily newspaper focused on economics, finance and politics. From the topic of long-term funding for bioinformatics resources, to SIB’s recent developments on the personalized health front and its activities for the public...

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Save the date for the next public events around bioinformatics

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FOCUS ON PERSONALIZED HEALTH

Bringing Swiss health data to biomedical research: an interoperability journey

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Making health data from patients both accessible and useful to biomedical researchers is the goal of the Swiss Personalized Health Network initiative (SPHN). And to move from fragmented heterogeneous data to a harmonized pool of quality health information, a range of common standards and processes must be developed and adopted. Nationwide expert groups – coordinated by the SIB Personalized Health Informatics Group (PHI) – have been created to this end…

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First Swiss-wide ring trial led by SIB to harmonize viral metagenomics practices in the clinic

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Discover the lessons from this first nationwide quality-control test, which aimed to benchmark current metagenomic workflows used at Swiss clinical virology laboratories, and contribute to the definition of common best practices for their use in routine. The study was led by Thomas Junier (SIB & ETH Zurich), Michael Huber (University of Zurich) and Aitana Lebrand (SIB Clinical Bioinformatics) and published in Genes.

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DIGITAL ID2020 Conference – Digitalization and Infectious Diseases, 20-21 January, Basel

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This edition of the conference (“Digitalization and Infectious Diseases: Improving patient outcome in the age of big data”) aims to enhance your insights of digitalization, machine learning and personalized health in infectious diseases. Join key opinion leaders in these fields, including several SIB Members as part of the scientific committee: IT, Machine Learning and big data, clinical microbiology, infectious diseases, biomedical research, law and ethics...

More information and registration

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.

OMA standalone: resolving difficult phylogenies of non-model species by customizing your ortholog search

Accurately identifying orthologs among species is key to solving their evolutionary relationships but even more challenging for species not closely related to model species, and for which prior information is scarce. A tool, derived from the SIB Resource OMA developed by the team of SIB Group Leader Christophe Dessimoz (UNIL), allows scientists to analyze their own custom genomes or transcriptomes in combination with publicly available data

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RESEARCH AT SIB

Join us to celebrate the 10th anniversary of the CALIPHO Group!

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SIB’ CALIPHO Group, led by Amos Bairoch and Lydie Lane, develops the SIB Resource neXtProt as well as the Cellosaurus knowledgebase on cell lines. To celebrate 10 years of human proteins’ research, a symposium awaits you on 22 October at the University of Geneva. It will feature speakers Prof. Ruedi Aebersold, (ETH Zurich), Dr. Christine Brun (Inserm-Aix-Marseille Université) and Dr. Simon Forbes (Wellcome Sanger Institute)…

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in silico talks series: #3, 4 and 5 – Special SIB Bioinformatics Awards edition!

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The genetics of complex traits, single-cell mutations, RNA velocity: discover the talks given by the three laureates of the 10th edition of the SIB Bioinformatics Awards – Eleonora Porcu (Early Career Bioinformatician Award), Jochen Singer (Best Swiss Bioinformatics Graduate Paper Award) and Sten Linnarsson for the resource Velocyto (Bioinformatics Resource Innovation Award). They are part of a special edition of our in silico talks’ series.

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How asexual reproduction is purging genomes of their parasitic invaders

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Over 40% of our genome is made of transposable elements. With all their jumping and copy/pasting, these ‘genomic parasites’ may contribute to the genetic diversity of organisms to some extent – but often they disrupt gene functions. What is driving their multiplication, or keeping them in check? SIB’s Kamil Jaroň (University of Lausanne) and colleagues show that asexually reproducing yeast is better at controlling the spread of these sequences by…

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PERFECT YOUR BIOINFORMATICS SKILLS WITH SIB TRAINING

Upcoming SIB Training courses

Save the date for your favorite courses among the following topics: introduction to RNA-seq, single-cell RNA-seq (new), drug design, statistics, Advanced R Shiny (new), Git for reproducible research (new), best practices in programming… While we compose the 2020 course programme, subscribe to the mailing list to be notified when it will be online, and when registrations for courses open. Don’t hesitate to share this information with your colleagues!

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PROTEIN SPOTLIGHT

Latest Protein Spotlight: A sense of direction

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Survival depends on cues, mobility and a medium to evolve in. Cues - such as scents, sounds or colours for example - will attract organisms towards food, mating grounds and an environment in which they feel protected and are happy to stay. Thanks to them, organisms usually head off in a direction they expect will be to their advantage, using the means of locomotion they have, to cross all sorts of media…

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