SIB Profile 2022 - Data scientists for life

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SIB Profile 2022

Data scientists for life

INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY SWITZERLAND ON THE INTERNATIONAL MAP


COVER IMAGE

Screening water for pollutants This artwork visualizes machine learning-based clustering of organic micro-pollutants (OMP) for potential detection in drinking water using mass spectrometry. The image is derived from the work conducted by SIB Group Leader Christian Panse (FGCZ ETH Zurich | University of Zurich) and Andrea Mizzi Brunner (TNO, Netherlands). DOI: 10.3390/MOLECULES25184189



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Forewords

M

uch of a country’s economy and social development relies on its infrastructure. The key is to make such infrastructure agile and adaptable to new needs and challenges. These are exactly the types of solution developed by SIB for the life sciences. Scalable, secure and reliable, they ensure the best long-term value is achieved for every franc invested. The recipe? A deep understanding of the underlying data, combined with technical mastery. With user adhesion at their heart, these solutions are set out in a collaborative fashion, their implementation supported by capacity building and well-thought through regulatory frameworks. The result: tangible impacts for society: preparing the country for epide­mics, supporting the development of precision medicine and enabling reproducible science. And benefitting from such resources reinforces Switzerland’s attractiveness for talents and innovation. •

Felix Gutzwiller President of the Foundation Council

“Few countries benefit from such a coordinated vision of the value of biodata.”

W

hile Switzerland may be a small country, it has a strong voice in the global life science field. The activities of SIB and of its members have largely contributed to this: be it for data sharing, data management or data analysis, the institute has brought the expertise and contributions of Swiss bioinformatics to the world for over 20 years. Such knowledge exchange is particularly important for biological and biomedical data, whose value only reveals itself through expert processing. By determining which data have the highest value, finding innovative ways to make them usable, or how to safeguard them in the long-term: SIB is active in so many ways to make public investments in research as efficient as possible. Few countries benefit from such a coordinated vision of the value of biodata, which contributes to anchoring the country among leaders for tackling Big Data challenges. •

Jérôme Wojcik Chairman of the Board of Directors


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SIB Profile 2022

A

fter two intense years punctuated by viral waves, one thing is certain: the solutions developed to support research and public health decisions in this context are here to last, and ready for the next epidemic. This year, SIB is also entering a new era: on 1 April, it welcomed Christophe Dessimoz, Group Leader since 2016, as new Joint Executive Director. Under his and Ron Appel’s leadership, and with the support of our highly committed employees and members, our institute will continue to strengthen its key position in the life science landscape. SIB’s position, at the forefront of national and international infrastructure solutions, including biological data science expertise and policy support, results from a combination of factors. Three, in particular, contribute to making our institute unique. First, the way it is organized: collaborative by design, with one third of its 200 employees embedded in research labs, and a network of 600+ affiliated members across Switzerland. This organizational structure makes SIB an independent partner of choice for decentralized, multidisciplinary, nationwide projects. Second, the complementarity of its competence centres. By bringing together experts in biocuration, computa­ tional biology, clinical bioinformatics, personalized health informatics and bioinformatics training, knowledge transfer is accelerated, and best practices are rolled out in record time across the multidisciplinary life science ecosystem. Finally, a deep commitment from our staff and members to scientific excellence and to making a clear impact on science and society. This is visible through the enthusiasm for our conferences and the diversity and quality of science produced, as well as through

“This organizational structure makes SIB an independent partner of choice for decentralized, multidisciplinary, nationwide projects.” the energy invested in ad hoc initiatives and committees, such as the Remarkable Outputs, Award Committee or Diversity working group. The result is a highly dynamic environment that we are proud to represent. The SIB adventure is thus a deeply human one, and we thank the Federal government for making it possible, through the State Secretariat for Education, Research and Innovation SERI. •

Christine Durinx Joint Executive Director until 31 March 2022

Ron Appel Joint Executive Director

Christophe Dessimoz succeeded Christine Durinx on 1 April 2022: meet him on p. 11


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SIB Profile 2022

Table of contents 06

Data scientists for life

08

Bioinformatics: a definition

10

SIB in brief

14

Supporting our partners’ needs

18

A network of scientific expertise

26

Organization and governance

32

Infrastructure solutions for research and society

34

A national platform to track SARS-CoV-2 variants and boost research

36

Software tools and databases to sustain worldwide life science research

38

Connecting researchers to biomedical data to foster personalized health

40

A vision for the future of data-driven life science research in Switzerland

42

Switzerland on the international map

44

A key player for sensitive data processing

46

Among global leaders to sustain biological knowledge

51

Index of SIB Group and Team Leaders

55

Acknowledgements

5


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Collaborative by design

Fostering scientific excellence


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SIB Profile 2022

Data scientists for life This is who we are: multi­ disciplinary experts safeguarding data and making them speak to solve biological questions. Find out how we work and some of the scientific highlights of the year, by our members and teams.

Answering biological questions


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

Bioinformatics: a definition Thanks to computer-based approaches, researchers can improve their understanding of complex systems. Life scientists and clinicians have always tried to assemble data and evidence to find the right answers to fundamental questions. Nowadays, there is no shortage of data. But a different kind of problem has emerged. New technologies are producing data at an unprecedented speed. Indeed, so much data – and of such variety – that they can no longer be interpreted by the human mind alone. Enter bioinformatics.

Bioinformatics encompasses: DATABASES for storing, retrieving and

organizing information to maximize the value of biological data; SOFTWARE TOOLS for modelling, visualizing, interpreting and comparing biological data; ANALYSIS of complex biological datasets or systems using novel statistical approaches or machine learning techniques; RESEARCH in a wide variety of biolog-

Bioinformatics is the application of computer technology to the understanding and effective use of biological and biomedical data. It is the discipline that stores, analyses and interprets the Big Data generated by life-science experiments, or collected in a clinical context. This multidisciplinary field is driven by experts from a variety of backgrounds: biologists, computer scientists, mathematicians, statisticians and physicists.

COMPUTING AND STORAGE to process and safeguard large amounts of data.

DNA, RNA or proteins

Imaging data

ical fields and leading to applications in diverse areas, from agriculture to precision medicine;

What sort of data are we talking about? Bioinformatics deals with a broad spectrum of complex data types. Expression data, such as the level of expression of a gene in a sample

Text And more...


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SIB Profile 2022

BRINGING BIOINFORMATICS TO SOCIETY

From precision medicine to drug design and DNA testing: bioinformatics is increasingly tied to health and societal issues. SIB informs the public about the discipline and its applications through public outreach activities. In 2021, the website lightofevolution.org was launched, to show real-life implications of evolutionary biology: what does the evolution of coronaviruses tell us about the pandemic? Or, what do we, humans, have in common with bananas? This SNSF-Agora funded project was developed by SIB Employees and Members and awarded the 2021 Optimus Agora prize. It was also selected as a Remarkable Output for the year, read p. 24.

In 2022, meet the team at a booth “The chimp, the banana and us”: MYSTÈRES DE L’UNIL University of Lausanne 19-22 May

The University’s open days around the theme “Life paths” wp.unil.ch/mysteres/

NUIT DE LA SCIENCE Geneva, 9-10 July

In 2021,

1,000 participants took part in over

50

activities and events, including: Workshops on the coronavirus ’Hunting SARS-CoV-2, its variants and its origin’ TecDays organized by the Swiss Academy of Engineering Sciences SATW for students aged 15-20

Featured in the story ‘Banana split’ on lightofevolution.org, the website OhMyGenes.org offers insights into tantalizing questions such as what humans have in common with bananas: try it for yourself and generate memes to share on social media!

Diabetes and Obesity Open Day of the University of Geneva

Two days and nights around the theme “And yet” tinyurl.com/5n8f4tfs More activities and news on Facebook, our dedicated outreach channel in French and English goo.gl/4c6xCZ


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

SIB in brief Since its creation more than 20 years ago, SIB has become one of the leading biological and biomedical data science organizations in Europe, through infrastructure solutions, services and community engagement.

85 807 190 25 160 groups

Infrastructure

Community

members, including

SIB provides the national and international life-science community with a state-of-the-art bioinformatics infrastruc­ ture, including resources, expertise, collaborative support and services. DATABASES, SOFTWARE AND NATIONAL PLATFORMS

We create and maintain a large portfolio of leading Open Science databases and software tools, diagnostic tools, secure national online platforms and IT networks, enabling researchers and clinicians to leverage knowledge about life and foster innovations (SEE P. 33).

employees

institutional partners across Switzerland

databases and software tools developed by our members and accessible via the Expasy web portal

3,700 peer-reviewed articles published since SIB’s creation in 1998

COMPETENCE CENTRES

We offer in-depth expertise and services in bioinformatics, from computational analyses of all kinds of biological data to software development and data management (SEE P. 16).

As of 1 January 2022

SIB brings together worldclass researchers based in Switzerland and delivers training in bioinformatics. SCIENTIFIC COLLABORATION

Through knowledge exchange networks, participation in international initiatives such as ELIXIR Europe or the Global Biodata Coalition (GBC), collaborative projects and events, we strengthen cooperation on shared issues among bioinformatics groups from Swiss schools of higher education and research institutes, and with the global community. TRAINING IN BIOINFORMATICS

To ensure that life scientists and clinicians make the best of the data, we provide them with a large portfolio of courses and workshops. We also foster exchanges and training among bioinformatics and computational biology PhD students.


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SIB Profile 2022

WELCOMING A BRILLIANT SCIENTIST AS NEW JOINT EXECUTIVE DIRECTOR

SHORT BIO Master’s in Biology in 2003 at ETH Zurich PhD in Computer Science in 2009 at ETH Zurich Postdoc at the European Bioinformatics Institute, Cambridge (UK) from 2011 to 2013 Faculty member at University College London from 2013 to 2022 SNSF professor at the University of Lausanne since 2015 and Associate Professor since 2021 SIB Group Leader since 2016

Christophe Dessimoz succeeds Christine Durinx as SIB’s Joint Executive Director, alongside Ron Appel. He took office on 1 April 2022. An insider of Swiss bio­infor­ matics, deeply committed to the data science community… Christophe Dessimoz is an inter­ nationally recognized scientist who is intimately familiar with the Swiss life science ecosystem. Based at the University of Lausanne as Associate Professor, he has always been deeply committed to the life of the institute as an SIB Group Leader and as an elected member of the SIB Board of Directors since 2018. His enthusiasm for bridging the gap between wet lab and computer-based approaches led him to chair the Life Science Switzerland (LS2) Bioinformatics Intersection from its inception to January 2022.

…with an international aura in comparative genomics and Big Data analysis Christophe leads a highly collaborative and interdisciplinary research group. His team develops the OMA database, which relates genomes across the tree of life, and has been part of SIB’s resource portfolio since 2012. Among several distinctions, he was awarded the Overton Prize by the International Society for Computational Biology (ISCB) in 2019. Not only passionate about conducting research, but also about communicating its relevance to society, Christophe also engages in scientific outreach projects: in 2021, the project “In the Light of Evolution” to demystify evolutionary biology, codeveloped with other SIB Members, received the Optimus Agora Prize of the SNSF (SEE P. 9).

Bidding farewell to a pioneer in biodata infrastructure During her eight years at SIB, Christine Durinx helped to shape the development of the institute, internally and externally, and to affirm its leading position in life science, at national and international level. In particular, her activities in international science policy, including at ELIXIR and in setting up the Global Biodata Coalition, have reinforced SIB’s capacity to ensure the long-term sustainability of life science infrastructure. Since 1 April, Christine has been Managing Director at VIB, the Flemish Institute for Biotechnology, a non-profit research institute with more than 1,800 scientists.


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

Hospitals and clinics

Research institutes

Private sector

Life sciences and health actors

Converting biological questions into answers

Hospitals Research Hospitals Hospitals Research Research Private clinics clinics institutes and clinics andand institutes institutes sector

Private Private sector sector

Hospitals and clinics

Research institutes

Private sector

with various applications Tailoring treatment to cancer patients Basic research Environmental Basic research Basic research Medicine Environmental Agriculture Basic research Medicine Medicine Environmental AgricultureAgriculture sciences sciences sciences

Identifying micro-pollutants

Tailoring Tailoring treatment treatment to cancer to cancer patients patients

Medicine

Environmental sciences

Preventing diabetes

Agricultur


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SIB Profile 2022

Massive amount of data of various types: genetics, text, biochemical, imaging, etc.

SIB Swiss Institute of Bioinformatics

Training incl. latest bioinformatics techniques and resources

Tracking COVID-19

Collaborative support and services

Biodata infrastructure

incl. data management and analysis, software engineering and expert biocuration

incl. national platforms, secure computing networks and Open Science software tools & databases

Dedicated multidisciplinary experts


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

Supporting our partners’ needs Discover our competences and meet our experts.

SECURE SERVICES FOR SENSITIVE DATA

Dedicated, secure IT environment to process sensitive human data Our encrypted information technology infrastructure complies with all current data protection regulations (incl. GDPR) and IT security standards. Our partners can therefore process and host both sensitive data – such as genomic information or health records – and non-sensitive data – with complete confidence. We use modern virtualization technologies such as OpenStack to protect our computing environments.

The national BioMedIT network, set up by SIB and operational at all three nodes in Basel (managed by the University of Basel), Lausanne (managed by the University of Lausanne with the collaboration of SIB) and Zurich (managed by ETH Zurich), allows researchers to approach national collaborative projects involving human health data with trust and ease. Discover the infographic p. 38.

EXPERT BIOCURATION TRAINING

Generating high-quality, up-to-date annotations Our biocuration experts excel in the art of generating knowledge from a growing body of publications. We pro­vide expert biocuration on various data types including proteomics, lipidomics and transcriptomics. This includes help with setting up expert-­ annotated resources for a wide range of applications, such as understanding protein function, facilitating clinical interpretation of cancer variants or enabling biomarker discovery.

Boosting bioinformatics skills Our comprehensive – and constantly evolving – course portfolio provides hands-on experience of the most up-to-date bioinformatics techniques and resources, including clinical applications for researchers or healthcare professionals. We offer about 100 course-days per year. Find the full list of courses at sib.swiss/training

BIOSTATISTICS AND BIOINFORMATICS ANALYSIS

Making biological data speak Our specific areas of expertise include: biomarker identification; de novo assembly of sequencing data; genome comparative data analysis; targeted, exome and whole genome sequencing analysis; metagenomic data analysis; omics analysis; data integration; gene prediction and annotation and machine learning.

Who takes part in SIB courses? 36% PhD candidates 30% Postdoctoral researchers 12% Senior scientists / Principal investigators 10% Research assistants / Technicians 9% Other scientists 3% Master’s students


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SIB Profile 2022

Our approach: collaborative, independent and reliable From one-off services to longterm collaborations, we turn our in-depth expertise into integrated solutions, in line with your goals and regulatory requirements, to make your projects a reality.

SOFTWARE ENGINEERING AND TAILORING

DATA MANAGEMENT

Developing engaging and customized tools

Organizing data for long-term reuse

Our software engineers and User eXperience specialists contribute to some of the world-leading databases and tools for life sciences, as well as tailored applications for personalized medicine in hospitals or industry settings. They assist our partners in creating user-friendly software – or adapting existing products to meet specific needs – based on the most up-to-date web technologies.

We assist our partners by defining and implementing their Data Management Plans (DMP) for research proposals; reaching data interoperability targets, from local to international scales, within academic or regulated environments and ensuring the long-term management and storage of biological data.


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

MEET OUR TEAMS

Our competence centres, comprising and headed by SIB Employees, harness their complementary expertise to collaborate with external partners and other SIB Groups on a daily basis.

Clinical Bioinformatics

Personalized Health Informatics

Swiss-Prot Knowledgebases

Valérie Barbié

Katrin Crameri

Alan Bridge

“We support health professionals from hospitals and the pharma industry to make the most of an exponential ow of data, in order to enhance diagnostics and to foster optimal patient care and well-being. We do this through dedicated tools and methods, benchmarking and practice harmonization.” EXAMPLES

Diagnostic applications (cancer, genetic diseases, etc.) for the medical and pharmaceutical domain. Collaborative platforms to enable data sharing for research or clinical purposes. TAGS personalized medicine; oncology;

infectious disease; human genetics; interoperability; outreach; training

“We are convinced that in order to ensure high-quality care and patient safety in the long term, healthcare and research must go hand-in hand. In the context of the Swiss Personalized Health Network, we are thus making health-related data in Switzerland available to research in a lasting way. This is done through their FAIRification* and the creation of the national secure IT infrastructure BioMedIT.” EXAMPLE

BioMedIT, the national infrastructure for the secure handling of health data, which can be jointly used by Swiss universities, research institutions and hospitals. TAGS information security; interoperability;

personalized medicine; training

“As a competence centre for biocuration and knowledge management we develop, annotate and maintain internationally renowned knowledge resources such as UniProtKB/ Swiss-Prot. Our resources provide an essential framework for biological data science.” EXAMPLES

Some of our flagship resources include: UniProtKB/Swiss-Prot, ENZYME, Rhea, SwissLipids, HAMAP, PROSITE and ViralZone. TAGS database curation; proteins and proteomes;

systems biology; biochemistry; ontology; lipidomics; metabolomics; proteomics; semantic web


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SIB Profile 2022

Training

Vital-IT – Computational biology Mark Ibberson

Patricia Palagi

Synergies between our teams Gathering these complementary competences under a single roof facilitates knowledge sharing and innovation. It allows us to act as domain experts from fundamental research support to research and development, all the way to clinical applications. Some examples of synergies: VITAL-IT & PHI

“Thanks to the unique pool of leading experts making up SIB’s scientific network, we are able to provide a rich nationwide training offer across the spectrum of bioinformatics techniques, methods and tools, and thus support the fast-evolving needs of researchers.”

“As both computational biologists and software developers, we understand data and how to manage them, as well as the underlying biological questions. Our focus is on finding innovative approaches to data analysis, such as overcoming constraints related to sensitive data.”

KEY FIGURES 2021

EXAMPLE

60

courses offered to the community by groups from across Switzerland and bioinformatics domains

71 1,700 experts and trainers

participants

Setting up a federated data analysis system across several countries to enable access to large patient cohorts while addressing legal, ethical and FAIR principles*.

Aligning expertise between Vital-IT and Personalized Health Informatics on the sharing of sensitive data needed as part of the Swiss Personalized Health Network (SPHN) SWISS-PROT & CLINICAL BIOINFORMATICS

Swiss-Prot biocurators working with Clinical Bioinformatics experts as part of the Swiss Variant Interpretation Platform (SEE P. 49) TRAINING & VITAL-IT

Joining forces and expertise to organize a course on multivariate analysis for -omics data integration CLINICAL BIOINFORMATICS & VITAL-IT

TAGS structural biology; systems biology;

machine learning; data management; mass spectrometry; next-generation sequencing; data mining; genome reconstruction; software engineering; personalized medicine

*FAIR : a set of guiding principles to improve the Findability, Accessibility, Interoperability, and Reuse of digital assets

Supporting an independent provider of External Quality Assessment programmes for molecular diagnostics through a collaboration between Clinical Bioinformatics and Vital-IT


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

A network of scientific expertise Bioinformatics is an interdisciplinary field, where the encounter between genetics, physiology, chemistry and physics leads to many fields of activities and applications.

Genes and genomes

Proteins and proteomes

Evolution and phylogeny

Life’s instruction manual

More than meets the eye

Splitting ends

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54

A genome is the sum of genetic material of an organism, including all of its genes. It is composed of DNA and contains all the information needed to create and maintain an organism, as well as the instructions on how this information should be expressed.

Bioinformatics develops tools to read genomes, store, analyse and interpret the resulting data.

Number of groups per domain (only the groups that gave these themes as their main activities are listed)

Key resources on Expasy.ch (160 tools and databases developed)

7

74

A proteome is the sum of proteins expressed by a cell, a tissue or an organism, at a given time. Proteins are the products of genes, and are involved in nearly every task carried out within an organism – from carrying oxygen to fighting off pathogens. Bioinformatics develops tools to understand the role of proteins.

Our competence centres (see previous page) collaborate with affiliated groups across all domains of activities.

17

28

Changes that occur in genomes tell life scientists how an organism has evolved over time. Comparisons made between genomes from different species or populations tell them how they are related to one another – this is the field of phylogenetics. Bioinformatics develops tools to compare the genomes of organisms, as well as computational methods to reconstruct their past and build their ‘family’ trees.


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SIB Profile 2022

…AGRICULTURE 9 GROUPS

Structural biology

Systems biology

The third dimension

Never alone

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16

Macromolecules such as DNA and proteins have specific 3D structures that are dictated by their sequence. A protein’s function is defined by its 3D structure, which in turn defines the way it interacts with other molecules. Bioinformatics develops software to create 3D models of proteins to study their interactions with other molecules, such as drugs.

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36

Life occurs and is sustained by a mesh of interactions within and between cells, tissues, organisms and their environment. Understanding how these complex systems function allows scientists to predict what happens if one of the components changes or the conditions are altered. Bioinformatics methods help to predict metabolic pathways.

from predicting the spread of bird flu outbreaks and understanding the lifecycle of agricultural pests, to improving crop productivity.

…BASIC RESEARCH 47 GROUPS

from unravelling the evolutionary processes that have shaped today’s biodiversity, to solving the equation behind a lizard’s scale colour pattern.

…ENVIRONMENTAL SCIENCES 8 GROUPS

Machine learning and text mining

Core facilities The means to an end

Rise of the machines

6

4

Machine learning (ML) techniques allow computers to learn from data without explicit instructions, and to draw inferences from data patterns. Text mining algorithms, often based on ML, are designed to recognize patterns within text, such as biomedical terms. Bioinformatics is supported by and feeds into ML algorithms, with diverse applications including drug design, biomarker discovery and text mining to facilitate literature triage.

from understanding how organisms adapt to climate change, to how microbial communities can be used to break down pollutants in oil spills.

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The quantity of data generated by the life sciences has grown exponentially over the years, and needs to be stored and processed. Researchers also need support in making sense of their data. Core facilities centralize research resources, and provide tools, technologies, services and expert consultation to this end. Bioinformatics core facilities are located in the major Swiss academic institutions.

…MEDICINE AND HEALTH 48 GROUPS

from designing optimized proteins in cancer immunotherapy, to creating biomedical decision-support tools.


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

COLLABORATIVE BY DESIGN

Through partnerships with major Swiss schools of higher education and renowned Swiss research institutes, we enable fruitful collaborations and ambitious projects.

BASEL 184 MEMBERS 15 GROUPS

Figures as of 1 January 2022

807 185

SIB Members, incl. 190 employees (SEE P.  30), across 25 partner institutions

BERN 39 MEMBERS 4 GROUPS

YVERDON

students taking part in the SIB PhD Training Network

4 MEMBERS 1 GROUP

FRIBOURG 16 MEMBERS 4 GROUPS

LAUSANNE 251 MEMBERS 26 GROUPS

GENEVA 121 MEMBERS 8 GROUPS

FRIBOURG

GENEVA

LAUSANNE

YVERDON

BERN

BASEL


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SIB Profile 2022

VILLIGEN 1 MEMBER 1 GROUP

ST GALLEN 3 MEMBERS 1 GROUP

ZURICH 150 MEMBERS 18 GROUPS

WÄDENSWIL 15 MEMBERS 2 GROUPS

“Being able to rely on a dedicated organization like SIB is a strong asset for our data-driven projects. Its independence and established position in the ecosystem acts as a booster for collaborations among stakeholders. Our work together led, for example, to the first ever nationwide project in medical genetics, bringing together all Swiss academic centres in the discipline*.”

DAVOS 5 MEMBERS 1 GROUP

Anita Rauch Director, Institute of Medical Genetics University of Zurich * Anita Rauch is main Principal Investigator of the SPHN Infrastructure Development project SwissGenVar

An ideal partner for projects spanning multiple institutions

BELLINZONA 10 MEMBERS 2 GROUPS

Collaborative by design and with every partner institution being represented on its Foundation Council, SIB is also independent: this positioning makes the institute an ideal coordinating party for multicentric projects and large-scale national infrastructure solutions such as BioMedIT (SEE P. 38), the Swiss SARS-CoV-2 Data Hub (SEE P. 34) and the SwissBioData ecosystem (SEE P. 40).

LUGANO 8 MEMBERS 2 GROUPS VILLIGEN

DAVOS

ZURICH

WÄDENSWIL

LUGANO

BELLINZONA

ST GALLEN


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

SCIENCE THROUGHOUT THE YEAR…

Making the achievements of our community visible to the global scientific community and the public through science news, press releases and talks: a selection.

134,072 6,063 9,513 visitors to the SIB website

followers on Twitter

followers on LinkedIn

A unified language to depict metabolic models Representing metabolites, and the biochemical reactions they engage in, in a way that is understandable to both humans and computers is a massive database challenge. MetaNetX/MNXref offers a solution to this end and powers many applications, from metabolic models to bioengineering. GROUP INVOLVED

Vital-IT, led by Mark Ibberson

WATCH THE IN SILICO TALK ABOUT THE PAPER

Inferring human genomes at a fraction of the current cost promises to boost biomedical research

A shortcut to the genetics of molecular circadian rhythm

For less than $1, GLIMPSE is able to statistically infer a complete human genome from a very small amount of data. This method thus offers game-changing possibilities for genetic association studies and biomedical research, and a wider inclusion of underrepresented populations.

Do you usually wake up feeling rested but not hungry? It may be the sign of a particularly large meal the evening before, or reflect the difference in circadian rhythm between your gut and brain. The methodological shortcut presented here could save researchers precious time when studying such tissuespecific patterns, while further opening up the field of large-scale genomic research.

GROUP INVOLVED

GROUP INVOLVED

Systems and Population Genetics, led by Olivier Delaneau

Laboratory of Systems Biology and Genetics, led by Bart Deplancke

Published in Nature Genetics DOI: 10.1038/s41588-020-00756-0

Published in Sciences Advances DOI: 10.1126/sciadv.abc3781 WATCH THE IN SILICO TALK ABOUT THE PAPER


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SIB Profile 2022

The eventful settlement history of South Pacific islands

Improved interpretation of gene expression data from single cells

When genetics makes ancient civilizations speak

An international research team has reconstructed the human settlement history of the South Pacific, by sequencing a large number of genomes from this region. The results challenge current knowledge about the first settlement of the Vanuatu archipelago and Polynesia.

Single-cell technologies examining gene expression at the level of individual cells in a given population (e.g. a tumour) have revolutionized the way human diseases are studied. This work and talk present a method and tool to obtain reliable cell state definitions and systematic comparisons across studies. GROUP INVOLVED

The study of ancient civilizations is not only the preserve of historians and archaeologists. Genetics is a precious aid to understand how human beings colonized different regions of the planet and adapted to new environments. Based on the analysis of ancient DNA, this study sheds light on the settlement and cultural transition of Greece during the Bronze Age.

Cancer Systems Immunology, led by Santiago Carmona

GROUP INVOLVED

GROUP INVOLVED

Computational and Molecular Population Genetics, led by Laurent Excoffier Published in Nature DOI: s41586-021-03236-5

Published in Nature Communications DOI: 10.1038/s41467-021-23324-4 WATCH THE IN SILICO TALK ABOUT THE PAPER

Evolutionary Genomics, led by Anna-Sapfo Malaspinas Published in Cell DOI: 10.1016/j.cell.2021.03.039

Find all news of 2021 at sib.swiss/about-sib/news/10037-news2021 – and register to our newsletter to keep up-to-date along the year


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

SIB REMARKABLE OUTPUTS 2021

Discover the 10 best achievements and work produced by our scientists over the last year.

CoV-Spectrum — In-depth analysis of new SARS-CoV-2 variants cov-spectrum.org GROUP INVOLVED

Computational Evolution, led by Tanja Stadler, Zurich & Basel WHAT THE COMMITTEE SAID ABOUT THE WORK

“CoV-Spectrum responds to urgent needs to track known and identify new variants of concern. It highlights the importance of data sharing and is remarkable in how it scales with the volumes of data.”

APSiC — A robust statistical framework for discovery of novel cancer genes

Staying abreast of the latest advances and bright ideas emerging in a field as diverse as bioinformatics is challenging. To provide the global bioinformatics community with a shortlist of work produced during the year by SIB Scientists that is particularly deserving of attention, the SIB Award Committee has launched the Remarkable Outputs initiative. These outputs can include peer-reviewed publications, preprints, resources, software tools, databases, videos, tutorials, outreach programmes, science advocacy, etc.

480 publications by SIB Groups in 2021

BUSCO — Assessing genomic data quality and beyond busco.ezlab.org GROUP INVOLVED

Computational Evolutionary Genomics, led by Evgeny Zdobnov and Evgenia Kriventseva, Geneva WHAT THE COMMITTEE SAID ABOUT THE WORK

“2021 showcased the maturation of this widely used software with a step change in usability, speed, taxonomic breadth and variety of applications in genomics, metagenomics, phylogenomics and beyond.”

Inferring positive selection on enhancers reveals a regulatory basis for the developmental hourglass model

DOI: 10.1093/nar/gkab627

DOI: 10.1101/gr.275212.121

GROUPS INVOLVED

GROUP INVOLVED

Oncogenomics, led by Charlotte Ng, Bern and Computational Biology, led by Niko Beerenwinkel, Basel

Evolutionary Bioinformatics, led by Marc Robinson-Rechavi and Frédéric Bastian, Lausanne

WHAT THE COMMITTEE SAID ABOUT THE WORK

WHAT THE COMMITTEE SAID ABOUT THE WORK

“This new algorithm enables the identification of new cancer-related genes even with data from few samples, showcasing on the APSiC portal its application to a real-world oncology dataset.”

“This work elegantly shows the utility of a novel method to detect positive selection in non-coding DNA regions, and applying it to better understand the hourglass pattern of animal evolution.”

19A

20A


A

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SIB Profile 2022

Multidisciplinary approaches to trace the archaeal origins of gamete fusion

Public engagement with science through — In the Light of Evolution

DOI: 10.1101/2021.10.13.464100

LHC-MR — A powerful method for estimating causal effects of risk factors on complex human traits

GROUP INVOLVED

DOI: 10.1038/s41467-021-26970-w

GROUPS INVOLVED

Computational Evolutionary Biology and Genomics, led by Christophe Dessimoz, Lausanne WHAT THE COMMITTEE SAID ABOUT THE WORK

“This discovery, using homology searches, solving the protein structure, and performing functional assays, is a major contribution to understanding the evolution of sexual reproduction.”

GROUP INVOLVED

Statistical Genetics, led by Zoltán Kutalik, Lausanne WHAT THE COMMITTEE SAID ABOUT THE WORK

“This outstanding work substantially extends a widely applied statistical method, enabling estimation of bi-directional causal effects, direct heritabilities, and confounder effects.”

Swiss-Prot, led by Alan Bridge, Geneva, Laboratory of Computational Evolutionary Biology, led by Christophe Dessimoz, Lausanne, and Training, led by Patricia Palagi, Lausanne WHAT THE COMMITTEE SAID ABOUT THE WORK

“This innovative outreach project for engaging the public on the topic of species evolution is very well conceived and executed. It is didactic and fun, with already a significant impact in classrooms.”

Nextclade — Clade assignment, mutation calling and quality control for viral genomes

Mass spectra-based machine learning to predict antimicrobial resistance DOI: 10.1038/S41591-021-01619-9

SwissDrugDesign in 2021 — A freely accessible web-based in silico drug design environment

clades.nextstrain.org

GROUP INVOLVED

molecular-modelling.ch/swiss-drug-design.html

GROUP INVOLVED

Microbial Evolution, led by Richard Neher, Basel WHAT THE COMMITTEE SAID ABOUT THE WORK

Machine Learning and Computational Biology Lab, led by Karsten Borgwardt, Basel, Zurich WHAT THE COMMITTEE SAID ABOUT THE WORK

“Exploiting a unique and content-rich “Nextclade has demonstrated its data source, this ML-based approach 21G (Lambda) 20D impact in an impressive way during to deliver robust predictions represents 20F the pandemic, with user-friendly tools an important new tool for accelerating for informative analysis of sequencing 20I (Alpha) and improving resistance testing in 20B data from SARS-CoV-2 and seasonal 20J (Gamma)the clinic.” influenza viruses.” 21E (Theta) 21K (Omicron) 21M (Omicron) 21L (Omicron)

20G 19B

lightofevolution.org

20H(Beta)

20C

21C (Epsilon) 20E

21F (Iota)

GROUP INVOLVED

Molecular Modelling led by Olivier Michielin and Vincent Zoete, Lausanne WHAT THE COMMITTEE SAID ABOUT THE WORK

“The ecosystem of original, reliable, and user-friendly tools in the SwissDrugDesign suite is truly impressive, exemplified by the recent rebuilding of the SwissBioisostere and SwissSimilarity portals.”


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

Organization and governance Even across a modestly sized country like Switzerland, federating an interdisciplinary science such as bioinformatics requires a unique organizational structure. GOVERNING BODIES

The Foundation Council Each of SIB’s partner institutions is represented on the Council. President Prof. Felix Gutzwiller Former Senator

Mr Thomas Baenninger Chief Financial Officer, Ludwig Institute for Cancer Research

Founding Members Prof. Ron Appel SIB Executive Director

Prof. Claudia Bagni Vice-Dean for Research and Innovation, Faculty of Biology and Medicine, University of Lausanne

Prof. Amos Bairoch Group Leader, SIB and University of Geneva Dr Philipp Bucher Affiliate Group Leader, SIB Prof. Denis Hochstrasser Former Vice-Rector, University of Geneva Prof. C. Victor Jongeneel Carl R. Woese Institute for Genomic Biology, University of Illinois, USA Prof. Manuel Peitsch Chief Scientific Officer Research at Philip Morris International Ex officio Members Prof. Hugues Abriel Vice-rector for Research, University of Bern Prof. Cezmi A. Akdis Director, Swiss Institute of Allergy and Asthma Research (SIAF)

Prof. Edouard Bugnion EPFL Prof. Carlo Catapano Director, IOR Institute of Oncology Research Prof. Alex Dommann Head of Department “Materials meet Life”, Swiss Federal Laboratories for Materials Science and Technology (Empa) Prof. Estelle Doudet Vice Rector “Research”, University of Lausanne Prof. Boas Erez Rector, Università della Svizzera Italiana Prof. Katharina Fromm Vice-Rector, University of Fribourg Prof. Cem Gabay Dean, Faculty of Medicine, University of Geneva Prof. Brigitte Galliot Vice-Rector, University of Geneva

Prof. Antoine Geissbühler Vice-Rector, University of Geneva Head of eHealth and Telemedicine Division, Geneva University Hospitals (HUG) Prof. Detlef Günther Vice-President Research and Corporate Relations, ETH Zurich Dr Corinne Jud Head of the Competence Division Method Development and Analytics, Agroscope Prof. Jérôme Lacour Dean, Faculty of Science, University of Geneva Dr Vincent Peiris Dean, School of Business and Engineering Vaud (HEIG-VD), HES-SO Prof. Jean-Marc Piveteau President, Zurich University of Applied Sciences (ZHAW) Prof. Giambattista Ravano Director of Research and Development and Knowledge, University of Applied Sciences and Arts of Southern Switzerland (SUPSI) Prof. Alexandre Reymond Director, Centre for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne

Prof. Davide Robbiani Director Institute for Research in Biomedicine (IRB) Prof. Patrick Ruch Head of Research, School of Business Administration (HEG-Geneva), HES-SO Prof. Gebhard Schertler Head of Biology and Chemistry Division PSI – Paul Scherrer Institute Prof. Falko Schlottig Director, FHNW School of Life Sciences Prof. Dirk Schübeler Co-Director, Friedrich Miescher Institute for Biomedical Research (FMI) Prof. Torsten Schwede Vice President of Research and Talent Promotion, University of Basel Prof. Elisabeth Stark Vice-President Research, University of Zurich Prof. Juerg Utzinger Director, Swiss Tropical and Public Health Institute Co-opted Member Prof. Alfonso Valencia ICREA Professor Life Sciences Department Director Barcelona Supercomputing Centre, Spain

The Board of Directors (BoD)

The Scientific Advisory Board (SAB)

The BoD consists of two Group Leaders elected jointly by the Council of Group Leaders and the BoD, two external members elected by the Foundation Council on the recommendation of the BoD, and the SIB Executive Directors. Members of the BoD are appointed for a renewable five-year period.

The SAB is made up of at least five members, who are internationally renowned scientists from the institute’s fields of activity.

Dr Jérôme Wojcik (Chairman) Industrial Data Scientist & Entrepreneur Prof. Ron Appel and Prof. Christophe Dessimoz (as of 1 April 2022) Joint SIB Executive Directors

PD Dr Katja Bärenfaller Group Leader, SIB and Swiss Institute of Allergy and Asthma Research (SIAF) Ms Martine Brunschwig Graf Former National Councillor Prof. Robert Waterhouse Group Leader, SIB and University of Lausanne

Council of Group Leaders The Council consists of the Group Leaders and the SIB Executive Directors.

Prof. Alfonso Valencia (Chairman) ICREA Professor Life Sciences Department Director Barcelona Supercomputing Centre, Spain

Prof. Alexey I. Nesvizhskii Department of Pathology and Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, USA

Prof. Søren Brunak Founder of the Centre for Biological Sequence Analysis, Technical University of Denmark, Denmark

Prof. Christine Orengo Department of Structural and Molecular Biology, University College London, UK

Prof. Melissa Haendel Director of the Ontology Development Group, Oregon Health & Science University, Portland, USA

Prof. Ron Shamir Computational Genomics Group at the Blavatnik School of Computer Science, Tel Aviv University, Israel

Prof. Claudine Médigue Head of the Laboratory of Bioinformatics Analyses for Genomics and Metabolism (LABGeM), Génoscope & CNRS, Evry, France


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SIB Profile 2022

As a non-profit foundation and with 25 partner institutions (SEE P.  20), SIB’s governance structure ensures both scientific independence and efficient internal functioning.

Foundation Council

Highest authority in the institute, with supervisory powers. Its responsibilities include changes to SIB’s statutes, nomination of Group Leaders, and approval of the annual budget and financial report.

Scientific Advisory Board Board of Directors Acts as a consultative body, providing recommendations to the Board of Directors and the Council of Group Leaders. Its main tasks consist in monitoring service and infrastructure activities, such as the SIB Resources. (SEE P.  36)

Define and implement the institute’s strategic goals as well as ensuring the organization’s representation at the national and international level. Support functions include finance & grant services, legal & technology transfer, human resources, information technology, cyber security, resource usability & support, and communication & scientific events.

Two external members from the political and industrial sectors

One Executive Director

Management and support teams

Takes the decisions necessary to achieve the aims of the institute, such as defining the scientific strategy and internal procedures, and allocating federal funds to service and infrastructure activities.

Two Group Leaders

Council of Group Leaders

Discusses all matters relating to SIB Groups as a whole, and proposes new Group Leaders for nomination.

SIB Internal Groups

SIB Affiliated Groups

Staffed and headed by SIB Employees, these competence centres focus on SIB’s core missions.

Academic groups from partner institutions across Switzerland. They include groups maintaining and developing an SIB-supported infrastructure, such as an SIB Resource (SEE P.  36) or a core facility and can thus include SIB Employees as well.

(SEE P.  16)


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

FINANCES

SERI’s contribution represents 41% of our institute’s 2021 budget, excluding the specific BioMedIT/SPHN funding. CHF 10.8 million were raised in addition to fulfil SIB’s mission.

Funds received for 2021 Swiss government – SERI

11.6 million

41%

Swiss government – BioMedIT/SPHN 1

6.3 million

22%

European funds

2.3 million

8%

National Institutes of Health (NIH)

2.3 million

8%

Swiss universities

2.1 million

7%

Swiss National Science Foundation (SNSF) / Innosuisse

1.5 million

5%

Private sector / Foreign universities

1.2 million

4%

Other 2

1 million

Swiss hospitals

0.4 million

4% 1%

28.7 million

SIB is funded primarily by the Swiss government, but also by a range of sources, including hospitals, universities, health institutes and private companies, in Switzerland and abroad. This diversity highlights the breadth of services the institute offers to the global scientific community in the framework of its mission to provide life science infrastructure.


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SIB Profile 2022

81%

An integrated model: out of 190 employees 5 (162 FTEs)...

of SIB’s financial resources are allocated to the payment of salaries, reflecting the expertise underlying our computer-based activities

Allocation of the funds received in 2021 by SIB for its core mission, showing how our competences and projects enable to leverage SERI’s support.

83% Infrastructure for life science 23.9 million Supporting the life science and health community with national platforms and networks, open science databases, expertise in analysis, software development and biocuration

4% Community and education 1.1 million Supporting and organizing computational biology events and fostering training across bioinformatics

13% Management and support functions 3 3.7 million Providing support to SIB Groups with innovative IT and security solutions, specialized legal advice or communication actions

INFRASTRUCTURE

The SIB Resources: anchoring open science infrastructure in research SIB Resources are developed and maintained in academic research groups by a mix of collaborators including SIB Employees, funded by SERI 4. This integrated model allows SIB databases and software tools to be anchored in an academic environment close to users. This ensures that they remain at the cutting edge of technology by evolving in conjunction with science. MANAGEMENT AND SUPPORT FUNCTIONS

Data protection: cutting-edge expertise for health data sharing The implementation of the SPHN initiative raises significant challenges in terms of data protection law, such as the reuse of data at the end of projects funded by the new National Data Streams call. Within this framework, the SIB Legal & Techno­logy Transfer Office provides compliance and legal solutions to all projects as an expert team available for the community.

137

are in internal groups or part of the management and support functions (117 FTEs)

102 have a PhD degree

53

are embedded in university research groups (45 FTEs) mainly working on SIB Resources

64 MSc degree

6 BSc degree

1 SIB received CHF 1.7 million of government funds for the SPHN Data Coordination Centre. In addition, SIB received CHF 4.6 million in 2021 for BioMedIT (SEE P. 38), out of which CHF 1.4 million were used for BioMedIT projects and computational nodes. 2 Loss of income insurances, etc. 3 SIB’s Management and support teams are funded by the Swiss government as well as through the provision of internal services. 4 With the exception of UniProtKB/Swiss-Prot, which is composed exclusively of SIB Employees 5 As of 1 January 2022


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

PEOPLE AND CULTURE

SIB Employees share a common passion: making a positive impact on society through biological and biomedical data science.

SIB has 190 employees of 29 different nationalities *

* As of 1 January 2022

Fostering Equality, Diversity and Inclusion (EDI) THROUGH POLICIES...

An inclusive parental leave policy was rolled out in 2021 by the People & Culture department to cater for different family situations, beyond the current Swiss legislation. …AND AWARENESS-RAISING EVENTS

A screening of the movie ‘Picture a Scientist’, sponsored by SIB, was followed by an informal discussion organized by the Diversity working group to exchange views and experiences around EDI-related issues in the workplace.

A flexible and supportive environment With most employees already able to partially work from home before the pandemic, the successive transitions to full home-office over the past two years were smooth. And with 42% working part-time, SIB strives to provide a good work-life balance for its employees. Since October 2021, they also benefit from free and confidential occupational health services to address work-related conditions.


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SIB Profile 2022

Geneva 73 employees 7 groups

Lausanne 87 employees 9 groups including Management and support

Basel 25 employees 5 groups

Zurich 5 employees 2 groups

Laith Abu-Nawwas Data manager at SIB

“I joined SIB in October 2021, during the COVID pandemic and with all colleagues working remotely. A strange period to join a new environment! However, the onboarding from my direct colleagues and the People and Culture team was exceptional and made me feel most welcome.” READ THE FULL INTERVIEW

Access to a rich training catalogue Some of the soft- and hard-skills courses followed by employees in 2021, organized by SIB or through LinkedIn Learning:

Artificial Intelligence

Project Git Leadership management Unconscious

Python

biais

Docker

There are 93 women (49%) and 97 men (51%) working at SIB

44

The median age at SIB is 44 years old, with a balanced age pyramid favouring knowledge exchange by bringing early career scientists together with senior experts

8

The median length of service is 8 years, with 43% of employees having been at SIB for over 10 years


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National preparedness for epidemics

Long-term support for international research

Improved healthcare


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SIB Profile 2022

Infrastructure solutions for research and society Bridges, roads and the internet enable a country to develop its wealth and knowledge for the benefit of its people. Similarly, the life sciences infrastructure solutions developed by SIB provide researchers and clinicians with the necessary resources to advance their projects with direct benefits for health and society. From secure national online platforms and IT networks to leading Open Science databases and software and diagnostic tools: discover some 2021 highlights.

Making Switzerland ready for the digital age


A national to track SARS-C and boost

All genetic sequences of are centralized in the Swis co-led by SIB. The secure pl vision of the circulation authorities and feeds in to boost researc

Switzerland is in the top 5 of contributing countries for SARS-CoV-2 sequences

Beyond COVID-19, application to any pathogen This national genomic surveillance platform, acting as the Swiss SARS-CoV-2 Data Hub, was initially launched under the name ‘Swiss Pathogen Surveillance Platform’ (SPSP) and has the potential to welcome any pathogen sequences of public health interest (e.g. flu, legio­ ne­l­losis or antibiotic resistant bacteria). SPSP.ch is a collaborative platform following the Onehealth approach, i.e. multidisciplinary and aiming, among other things, to optimize human health outcomes. It is co-managed by SIB in collaboration with the University Hospitals of Basel, Lausanne and Geneva, as well as the Universities of Bern and Zurich.

From a nose swab to the FOPH’s dashboard

1

About 5% of all positive PCRs detected in diagnostic laboratories get sequenced by one of the 15 sequencing laboratories across Switzerland, coordinated by the Center of Reference for Emerging Viral Infections - Crive (HUG) and the Federal Office of Public Health (FOPH)

2

About 2-3,000 sequences were generated per week in 2021, converging on the central platform (over 100,000 since the beginning of the pandemic) and stored on SIB’s secure infrastructure for sensitive biodata, BioMedIT (SEE P. 38)

3

Sequences are harmonized and annotated, and variants or new mutations are identified

4

A detailed tailormade standardized report is sent 3 times a week to the FOPH, leading to huge time savings and increased granularity in the analysis


“The possibility of using SPSP in the long term to link the genomic data of emerging bacteria or viruses in Switzerland with epidemiological data has promise for ensuring the exemplary responsiveness of the country in the field of public health.”

DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

f the virus in Switzerland ss SARS-CoV-2 Data Hub, latform offers a nationwide of variants to the health nternational databases ch on the virus.

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l platform CoV-2 variants t research

Mirjam Mäusezahl, Co-director of the epidemiology section at the FOPH

A fast-track for international research on the virus The platform sends anonymized sequences in bulk to the Open Science European COVID-19 data portal and GISAID.

SIB Profile 2022

The wealth of data generated feeds databases and software tools used by researchers from around the globe to infer virus evolution, study its biology, identify vulnerabilities to drugs and develop vaccines (see next page).

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Software tools to sustain w life science

Tracking the virus around the globe

The study of biologica in diseases, biodiversit Open Science software such as the SIB Resou discover how knowledge and s SARS-C

Through the analysis and sharing of massive amounts of genetic sequences, the evolutionary history of the virus can be unfolded to track it ‘live’, all around the world. Analysis of over half of all sequences generated in Switzerland, from clinical and wastewater samples V-PIPE Enabling real-time tracking of the evolution of the virus and helping public health laboratories understand how cases are connected to each other NEXTSTRAIN

Revealing how it enters our cells

Unravelling its impacts on our bodies Understanding the biological mechanisms of the virus’s entry and interaction with our organism enables the development of treatments and vaccines. Deep insights into the 3D structure and function of viral and host proteins helps pinpoint potential entry-points and binding sites, such as ACE2 UNIPROTKB/SWISS-PROT, NEXTPROT, STRING, SWISS-MODEL

Identifying potential and sometimes intermediate hosts for the virus as well as putative transmission chains, by comparing the receptor ACE2 across multiple species SWISSORTHOLOGY

To grasp the complexities of infection severity or organs affected, zooming in at the molecular level is needed. Understanding the regulatory response to infection by comparing pre- and post-infection gene expression profiles; how diverse the virus’s targets are, especially in long COVID, by revealing the expression of target genes in various organs; how the circadian clock affects the virus’s pathogenicity… ASAP, SWISSREGULON, BGEE, EPD

MORE RESOURCES BY SIB GROUPS SUPPORTING SARS-COV-2 RESEARCH

Gaining insights into the metabolic dysfunctions induced by the virus, or those which put patients at greater risk of developing a severe form of the disease SWISSLIPIDS, RHEA


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al processes involved ty or evolution relies on e tools and databases, urces. As an example, w they provide strategies to fight CoV-2.

The SIB Resources ASAP Automated single-cell analysis portal BGEE Gene expression expertise CELLOSAURUS Cell lines knowledge resource

STRING Proteinprotein interaction networks and functional enrichment analysis SWISSDRUGDESIGN Widening access to computer-aided drug design

EPD Eukaryotic promoter database

SWISSLIPIDS Knowledge resource for lipids

GLYCO@EXPASY Zooming in on webbased glycoinformatics resources

SWISS-MODEL Protein structure homology-modelling

NEXTPROT Human protein knowledgebase NEXTSTRAIN Real-time tracking of pathogen evolution RHEA Knowledgebase of biochemical reactions

SWISSORTHOLOGY One-stop shop for orthologs SWISSREGULON PORTAL Tools and data for regulatory genomics UNIPROTKB/ SWISS-PROT Protein knowledgebase V-PIPE Viral genomics pipeline

The SIB Resources are used by

DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

and databases worldwide e research

2.5 million scientists every month

Supporting vaccine development

Designing drugs Sugar molecules are coating the SARS-CoV-2 spike protein. These molecules or glycans can interfere with the action of vaccines.

GLYCO@EXPASY

Drug discovery relies both on computer and in vitro techniques before they are rolled out to clinical trials. Discovering, selecting and optimizing promising chemical compounds in silico, to target specific proteins such as enzymes or receptors of the virus SWISSDRUGDESIGN

Pointing to the cell lines that can be used to grow the virus and thus to test the in vitro effect of potential drugs CELLOSAURUS

SIB Profile 2022

Making the sugar coating motif of the spike protein easily accessible helps researchers along the 3D modelling process to optimize vaccine efficiency

Aligned with Open Science principles and interconnected Openly accessible and sharing the same ontologies and standards, the SIB Resources are interconnected data sources. They can be combined to ask complex questions to which no single resource has the answer.

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Connecting researc data to foster per

Personalized health aims to optim and treatment based on individua to sensitive datasets from patient institutions. Today, researchers b structure to move the field forward:

The BioMedIT network serves

over 60 national and international health-related projects* *Including over 20 funded by SPHN / Personalized Health and Related Technologies (PHRT)

A single entry point to assess the availability of consented datasets

In 2017, the fed government la Swiss Personal Network (SPHN to accelerate re this area. SIB is of this initiativ with the Swiss of Medical Scie

Since 2021, researchers have been able to assess if, where and how many patients present the condition of interest for an envisaged study over all five university hospitals in Switzerland at once – a key feasibility step for large-scale biomedical projects. This milestone results from a nationwide coordination among clinical partners, piloted by SIB’s Personalized Health Informatics Group.

More about the initiative: sphn

g idin rov ons P ti ta Da stitu I N In ATA D

BioMedIT Network

ETH Zurich

RE

EXPLORE THE BIOMEDIT WEBSITE

University of Lausanne & SIB

SU

Res e

LT

arc

SO UT

her

s

University of Basel

S in h

T o p b L L a th th fo se


n.ch

Switzerland has its secure nfrastructure to analyse health data

Ultimately improving healthcare for patients and citizens Among the health-related research projects currently running on BioMedIT, we can focus on on two SPHN projects and an international project co-led by SIB. Their goals are to: Recognize a bacterial sepsis earlier and predict its course more precisely for an individual patient using machine learning and combining omics and clinical data: the Personalized Swiss Sepsis Study co-led by SIB Group Leader Karsten Borgwardt Infer the clinical relevance of genetic variants detected in sequenced tumours, a global challenge in oncology: the Swiss Variant Interpretation Platform for Oncology (SVIP-O) (SEE P. 49) Understand what drives the resistance of some patients to immunotherapies by bringing together molecular profiling data and cellular spatial data: IMMUcan, a European Innovative Medicines Initiative co-led by SIB’s Vital-IT Group. DOI: 10.18609/ioi.2021.038

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The BioMedIT network led by SIB builds on three scientific IT competence platforms: sciCOREmed in Basel, managed by the University of Basel, SENSA in Lausanne, managed by the University of Lausanne with the collaboration of SIB, and Leonhard Med in Zurich, managed by he ETH Zurich. Authorized users access he network and the data made available or their research through a dedicated ecure portal.

Data fragmentation and diversity, a lack of common standards and metadata hinder efforts to combine data from different sources. The SPHN Data Coordination Centre (DCC) at SIB is coordinating solutions among the many contributing Swiss institutions to ensure datasets follow FAIR (findable, accessible, interoperable and reusable) principles. In 2021, for instance, the national framework for the semantic interoperability of research data was implemented by all Swiss university hospitals. An ecosystem around Semantic Web Technologies has been established to manage and link data for research purposes.

SIB Profile 2022

deral aunched the lized Health N) initiative esearch in s at the heart ve, together Academy ences.

A common language for a lasting Swiss infrastructure

DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

mize diagnostics, disease prevention al characteristics. It relies on access ts, which are scattered across Swiss benefit from a national secure infra­ the BioMedIT network, set up by SIB.

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chers to biomedical rsonalized health


A vision for the fut life science resear

Imagine a national dece which data, methods, softwa be shared and reused… The SwissBioData ecosystem capacity to convert resea and inno Reusing data and transform them into assets Only a very small part of the data produced today is used for new discoveries. The rest is discarded, or forgotten: microscopic images that would enable scientists to answer questions beyond those that led to their collection; genetic sequences that could hide information about rare diseases and tests that would avoid someone else the trouble of redoing them.

Every day, in Swiss biology labs,

How lif

Dive deeper and into fundamental q organisms o

Reproducible science

Enable more transparent, evidence-based and beneficial science

dozens of terabytes of data are produced.

Scaling up SIB’s expertise to all of Switzerland through partnerships This vision developed over the last three years with 16 other institutions has been submitted to SERI’s Roadmap for Research Infrastructure 2023. SIB is also lending its expertise to other research infrastructure in this framework, such as MIMO, in the domain of microbiology, or SwissMetNet in the area of metabolic phenotyping.

Together with

16 Swiss institutions, 44 platforms, core facilities and research groups

SBDe is fully with the Fede Digital Switze Strategy and commissione National Ope Data Strategy all seven guid formulated t TWO MOVIES TO GO FURTHER:

FROM OPEN DATA TO OPEN KNOWLEDGE (SIB, 2019)


fe works

d more efficiently questions about cells, or ecosystems

d

AI-powered innovations

Allow the mining of ever-more clean, high-quality data

The vision: make Switzerland fit for the digital age The SwissBioData ecosystem aims to support life science researchers from all Swiss schools of higher education and research institutes, from data generation all the way to their analysis and sharing for reuse. For instance, it would harmonize the computing environment across multiple institutions for dataintensive projects, such as those that are AI-driven. It would also foster the longterm availability of datasets of different types produced in Swiss labs – all this by building on the existing outstanding expertise and resources.

DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

entralized laboratory in are tools and workflows can … for the greater good. m would boost Switzerland’s arch data into knowledge ovation.

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ture of data-driven rch in Switzerland

How would it work? Three main principles: #COORDINATION to select and implement formats, standards and cloud services #CURATION to identify the most valuable data, annotate them using appropriate standards and facilitate their reuse by non-specialists and AI #TECHNOLOGIES

aligned eral Council’s erland the SERIed Swiss en Research y, and fulfilling ding principles therein.

SIB Profile 2022

to facilitate sharing, searching and integrating data across distributed databases

FORGOTTEN DATA: THE LEFTOVERS OF SCIENCE (SIMONE RAFFAELLO PENGUE AND LORENZO PENGUE, 2021)

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nd rla e tz wi oice s S ve g v ue Gi tron l iss a a s glob g nd in ectin cal a data aff logi ical bio med bio ence sci


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SIB Profile 2022

Switzerland on the international map SIB represents Switzerland in numerous international cutting-edge research initiatives. From innovative data management solutions to fight diabetes or obesity at the European scale, to co-piloting international SARS-CoV-2 data sharing efforts, here are some examples of activities and involvements.

ain d’s int rlan ess l a M itze ven ona Sw racti rnati att inte for ents tal


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

As part of pan-European

A key player for sensitive data processing

F

Some of the projects where SIB acts as Data Coordination Centre

Diabetes

RHAPSODY

From cancer to obesity, European public-private projects rely on SIB’s expertise for the management and analysis of sensitive data from dozens of countries.

or years, the institute has been acting as a Data Coordination Centre – in other words, it orchestrates data management for several large Innovative Medicines Initiative (IMI) projects over many European countries. Our teams are experts in providing researchers and clinicians with safe and efficient access to large numbers of datasets from clinical studies: this enables them to detect signals in the data that would otherwise be hard to find, and that could be more efficiently actionable in practice and thus benefit patients.

public-private projects

improving diabetes prevention and treatment

Hypo-RESOLVE The IMI projects where SIB acts as Data Coordination Centre span across

18 162 16 countries and include

public institutions and

pharmaceutical companies

“As co-leads of the Data analysis and integration work package in HIPPOCRATES, we will be supporting all other actors in the project from data harmonization and vocabulary standardization to implementing FAIR principles, and will contribute to the data analysis efforts.” Vassilios Ioannidis Lead Computational Biologist, Vital-IT

better solutions to alleviate the burden and consequences of hypoglycaemia

BEAt-DKD towards personalized treatments of diabetic kidney disease

CARDIATEAM preventing diabetic cardiomyopathy

Cancer

IMMUcan

Clinical Database server

understanding how the immune system and tumours interact and the impact of therapeutic interventions (SEE P. 39)

Obesity

SOPHIA improving obesity treatment

Arthritis

HIPPOCRATES

(new in 2021)

improving psoriatic arthritis diagnostics and treatment


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SIB Profile 2022

Clinical Database server

Clinical Database server

“Federated analysis is increasingly used in a variety of setups to achieve greater health value. What is unique with our approach is that it enables mining a diversity of datasets, from multiomics to clinical, spanning several countries. Further more, thanks to opensource technologies, no part of the code we develop or use is private.” Mark Ibberson Director of Vital-IT, SIB

Central server

Clinical Database server

SIB’s Vital-IT Group has set up an innovative and scalable federated analysis system to safely leverage sensitive health data. The patient data never leaves the server on which it is hosted, whilst enabling analysis to be performed remotely on each server. This way, researchers and clinicians can obtain results without any sensitive patient data being disclosed.

‘Share without sharing’: SIB’s expertise in a growing international movement How can health data be protected but still exploited? In cross-border consortia such as the IMIs, legal or ethical constraints often prevent the centralized storing of individual patient-­level data, or the transferring of data between participating centres in a research project. Federated analysis is a way to protect the patient’s data while enabling their use for research. Vital-IT Director Mark Ibberson presented SIB’s expertise as a panelist in an event that brought together over 100 international participants in Basel, representing PMEs, startups, pharmaceutical companies, hospitals and universities. The workshop, co-organized by SIB (Leila Alexander and Torsten Schwede), in collaboration with SPHN, Eucor and the University of Basel, was dedicated to health data, distributed computing, privacy and trust, and tackled the challenges of this quickly growing field.

Clinic Datab serve

Combining data management with analytical expertise to offer new insights into type 2 diabetes in Rhapsody Thanks to a unique dataset from living donors and innovative multi-omics analysis, an international research team led by investigators at the Paul-Langerhans-Institute Dresden, SIB and the Max-Planck-Institute of Biochemistry has shed light on the molecular processes driving pancreatic islet beta cells dysfunction and uncovered potential biomarkers to monitor the disease.

Clinic Datab serve

DOI: 10.1038/s42255-021-00420-9 MORE ABOUT THE FEDERATED ANALYSIS


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

Among global leaders to sustain biological knowledge SIB is the voice of Switzerland in global issues affecting biological and biomedical data science. A panorama.

Education and capacity building at the service of global pandemic preparedness SIB’s Training group is co-leading capacity-building efforts to tackle the data challenges that can hinder an effective pandemic response as part of the ELIXIR BY-COVID project, which brings together 53 partners from across 19 countries in Europe.

S

scientific advances are made possible thanks to the seamless exchange of knowledge derived from data – within, but also across countries, which raises several challenges. Switzerland, with its unique model of national organization for data science in biology and biomedicine, is very well placed on the global scene in this respect. Through capacity building, conferences, knowledgebases, thought leadership and durable partnerships, SIB conveys the expertise of the Swiss bioinformatics community applied to biodiversity, oncology, epidemiology and many other topics.

Joining forces on responsible sharing of genomic data for the benefit of human health Several SIB Members contributed to a 2021 special issue of the journal Cell Genomic, summing up the purpose and advances of the Global Alliance for Genomics and Health (GA4GH), of which SIB is a member. This is a worldwide initiative to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data.

Influential contributions to the scientific debate amidst the COVID crisis Among the numerous research articles produced in the face of the pandemic, SIB Members also contributed as thought leaders through letters and opinion pieces in prestigious journals such as: Nature, with SIB scientists co-leading a global group of researchers calling for better integration of viral genetics, bioinformatics and public health to enable an efficient pandemic response (Christophe Dessimoz and Emma Hodcroft). DOI: 10.1038/d41586-021-00525-x Science, with two SIB scientists among the three Europe-based authors on the letter regarding the origins of SARS-CoV-2 (Richard Neher and Erik van Nimwegen). DOI: 10.1126/science.abj0016


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SIB Profile 2022

Accelerating research and the international reputation of Swiss expertise, by providing essential databases and software tools to the international life science community

Supporting the setup of the Global Biodata Coalition SIB is a strategic partner in the reflection on the sustainability of research infrastructure crucial to the life sciences: it contributed to the setup of the coalition and is still actively involved now that the first call for such resources has been launched.

Developing internationally recognized databases and tools Among the ca. 20 SIB Resources used by more than 2.5 million scientists each month, UniProt, STRING – and in 2021, Rhea and Cellosaurus – have been awarded the European label of excellence "ELIXIR Core Data Resource" (SEE P. 36).

Co-steering European efforts to foster open sharing of SARS-CoV-2 genomic data SIB’s Clinical Bioinformatics group is co-leading an international initiative to facilitate open sharing of viral genomic sequences in other countries, to improve COVID-19 research efficiency, variant surveillance and general pandemic preparedness. Through SIB, Switzerland is thus sharing its experience in setting up and using a national viral genomics platform (Swiss SARS-CoV-2 Data Hub, SEE P. 34). The initiative involves about 20 countries across Europe, as well as South Africa, as part of the ELIXIRCONVERGE project.


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DATA SCIENTISTS FOR LIFE - INFRASTRUCTURE SOLUTIONS FOR RESEARCH AND SOCIETY - SWITZERLAND ON THE INTERNATIONAL MAP

A European initiative to support species conservation through genomics Increasing knowledge of the genetic characteristics of species, including endangered ones, can help explain how they respond to environmental change. Five SIB groups are participating in a pilot project to sequence the genomes of selected species in Europe, as members of the Swiss node of the European Reference Genome Atlas (ERGA) initiative, a growing consortium of more than 500 researchers from 48 countries.


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SIB Profile 2022

Making Switzerland an international hub for bioinformatics excellence SIB organizes what has become a key computational biology event, and has singled out outstanding work, careers and resources through the Bioinformatics Awards since 2008: The 15th edition of the [BC]2 Basel Computational Conference organized by SIB attracted 530 participants in September 2021, with half of the countries represented located outside Europe. – Heba Sailem received the Early Career Bioinformatician Award; – Stephanie L. Hyland, Martin Faltys, Matthias Hüser, Xinrui Lyu and Thomas Gumbsch jointly received the Swiss Bioinformatics Graduate Paper Award; – The Bioinformatics Resource Innovation Award went to Nextflow.io.

International efforts to interpret genetic variants in cancer Inferring the clinical relevance of variants detected in sequenced tumours is a global challenge in oncology. The Swiss Variant Interpretation Platform SVIP-O has been developed by SIB* to offer such answers to clinicians in a centralized and harmonized way. A key component of the platform is its biocuration interface, which allows experts at the Swiss-Prot Group to annotate observed variants with the best possible evidence from the literature regarding their clinical significance for diagnosis, prognosis and optimal therapeutic response; annotations which are then submitted to a clinical expert panel for validation. This approach is regularly discussed within the international clinical genomic community (e.g. Variant Interpretation for Cancer Consortium) to align efforts. *Co-principal investigators: Nexus (Daniel Stekhoven, ETH Zurich); Clinical Bioinformatics (Valérie Barbié); Text Mining (Patrick Ruch, HES-SO), in collaboration with: Swiss-Prot, SIS (ETH Zurich) and Core-IT

“Coordinated action is particularly crucial in the domain of personalized oncology. It is truly inspiring to be involved in international variant interpretation efforts, and to leverage decades of protein annotation knowhow at SIB to provide clinicians with tools that can facilitate their work and eventually may improve patients’ care.” Anne Estreicher Senior biocurator, Swiss-Prot


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SIB Profile 2022

INDEX OF SIB GROUP AND TEAM LEADERS As of 1 January 2022

NAME

FIELDS OF ACTIVITY

LOCATION

Ahrens Christian

Proteins and proteomes

Agroscope

Anisimova Maria

Evolution and phylogeny

Zurich University of Applied Sciences (ZHAW)

Arguello Roman

Evolution and phylogeny

University of Lausanne

Baerenfaller Katja

Proteins and proteomes

SIAF – University of Zurich

Bairoch Amos

Proteins and proteomes

University of Geneva

Bank Claudia NEW

Evolution and phylogeny

University of Bern

Barbié Valérie

Competence centres

SIB

Bastian Frédéric

Evolution and phylogeny

University of Lausanne

Baudis Michael

Genes and genomes

University of Zurich

Beerenwinkel Niko

Evolution and phylogeny

ETH Zurich, D-BSSE

Bergmann Sven

Genes and genomes

University of Lausanne

Bitbol Anne-Florence

Evolution and phylogeny

EPFL

Boeva Valentina

Systems biology

ETH Zurich

Borgwardt Karsten

Text mining and machine learning

ETH Zurich

Bridge Alan

Competence centres

SIB

Bruggmann Rémy

Core facilities

University of Bern

Buljan Marija

Systems biology

Empa

Carmona Santiago

Systems biology

University of Lausanne

Cascione Luciano

Core facilities

Institute of Oncology Research

A B

C

Cavalli Andrea

Structural biology

Università della Svizzera italiana

Chopard Bastien

Systems biology

University of Geneva

Ciriello Giovanni

Systems biology

University of Lausanne

Correia Bruno

Structural biology

EPFL

Crameri Katrin

Competence centres

SIB


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NAME

FIELDS OF ACTIVITY

LOCATION

Dal Peraro Matteo

Structural biology

EPFL

Delaneau Olivier

Genes and genomes

University of Lausanne

Delorenzi Mauro

Core facilities

University of Lausanne

Deupi Xavier

D

Structural biology

Paul Scherrer Institute (PSI)

Deplancke Bart

Genes and genomes

EPFL

Dessimoz Christophe

Evolution and phylogeny

University of Lausanne

Evolution and phylogeny

University of Bern

Falquet Laurent

Genes and genomes

University of Fribourg

Fellay Jacques

Genes and genomes

EPFL

Gfeller David

Proteins and proteomes

University of Lausanne

Gonnet Gaston

Evolution and phylogeny

ETH Zurich

Goudet Jérôme

Evolution and phylogeny

University of Lausanne

Core facilities

University of Lausanne

Ibberson Mark

Competence centres

SIB

Iber Dagmar

Systems biology

ETH Zurich, D-BSSE

Ivanek Robert

Systems biology

University of Basel & University Hospital Basel

NEW

E

Excoffier Laurent

F

G

Gottardo Raphael

NEW

I

K

Kahraman Abdullah

Core facilities

University Hospital Zurich

Kriventseva Evgenia

Genes and genomes

University of Geneva

Kutalik Zoltán

Genes and genomes

University of Lausanne


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SIB Profile 2022

NAME

FIELDS OF ACTIVITY

LOCATION

Lane Lydie

Proteins and proteomes

University of Geneva

Lisacek Frédérique

Proteins and proteomes

University of Geneva

Malaspinas Anna-Sapfo

Genes and genomes

University of Lausanne

Mazza Christian

Systems biology

University of Fribourg

Michielin Olivier

Structural biology

University of Lausanne

Miho Enkelejda

Systems biology

FHNW University of Applied Sciences and Arts Northwestern Switzerland

Milinkovitch Michel

Systems biology

University of Geneva

Mitri Sara

Evolution and phylogeny

University of Lausanne

Neher Richard

Evolution and phylogeny

University of Basel

Ng Charlotte

Systems biology

University of Bern

Palagi Patricia

Competence centres

SIB

Panse Christian

Core facilities

ETH Zurich

Payne Joshua

Evolution and phylogeny

ETH Zurich

Pedrioli Patrick

Proteins and proteomes

ETH Zurich

Peña-Reyes Carlos-Andrés

Text mining and machine learning

HEIG-VD

Pivkin Igor

Systems biology

Università della Svizzera italiana

L

M

N

NEW

P

R

Rätsch Gunnar

Text mining and machine learning

ETH Zurich

Rehrauer Hubert

Core facilities

ETH Zurich, University of Zurich

Riedi Marcel

Core facilities

University of Zurich

Rinaldi Fabio

Text mining and machine learning

SUPSI

Rinn Bernd

Core facilities

ETH Zurich, D-BSSE

Robinson Mark

Genes and genomes

University of Zurich

Robinson-Rechavi Marc

Evolution and phylogeny

University of Lausanne

Ruch Patrick

Text mining and machine learning

HES-SO - Geneva School of Business Administration (HEG)


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NAME

FIELDS OF ACTIVITY

LOCATION

Schütz Frédéric

Core facilities

University of Lausanne

Schwede Torsten

Structural biology, Core facilities

University of Basel

Core facilities

University of Basel

S

Sengstag Thierry Silvestro Daniele

Evolution and phylogeny

University of Fribourg

Snijder Berend

Systems biology

ETH Zurich

Stadler Michael

Genes and genomes

Friedrich Miescher Institute for Biomedical Research

Stadler Tanja

Evolution and phylogeny

ETH Zurich, D-BSSE

Stekhoven Daniel

Core facilities

ETH Zurich

Stelling Jürg

Systems biology

ETH Zurich, D-BSSE

Sunagawa Shinichi

Genes and genomes

ETH Zurich

van Nimwegen Erik

Genes and genomes

University of Basel

Vogt Julia

Text mining and machine learning

ETH Zurich

von Mering Christian

Proteins and proteomes

University of Zurich

Wagner Andreas

Evolution and phylogeny

University of Zurich

Waterhouse Robert

Genes and genomes

University of Lausanne

Wegmann Daniel

Evolution and phylogeny

University of Fribourg

Wollscheid Bernd

Proteins and proteomes

ETH Zurich

Zavolan Mihaela

Systems biology

University of Basel

Zdobnov Evgeny

Genes and genomes

University of Geneva

Zoete Vincent

Structural biology

University of Lausanne

NEW

V

W Z


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SIB Profile 2022

ACKNOWLEDGEMENTS

IMPRESSUM

We gratefully acknowledge the following funders, sponsors and partners for their financial support and encouragement in helping us fulfil our mission in 2021.

© 2022 – SIB Swiss Institute of Bioinformatics

The Swiss government and in particular: The State Secretariat for Education, Research and Innovation SERI The Swiss National Science Foundation (SNSF)

ILLUSTRATION BY

Davide Bonazzi / Salzmanart davidebonazzi.com DESIGN AND LAYOUT BY

Bogsch & Bacco, bogsch-bacco.ch IMAGE CREDITS (from top to bottom and from left to right)

P. 2 P. 3 P.4

Innosuisse Our institutional partners The European Commission The National Institutes of Health (NIH) The Research for Life Foundation

P. 8

swissuniversities Bangartner Foundation

We also thank all industrial, public health and academic partners who trust SIB’s expertise – and all employees and members who contributed to this edition of the SIB Profile.

P. 9 P. 11 P. 15 P. 16 P. 17 P. 22 P. 23

P. 25 P. 34 P. 36 P. 38 P. 40 P. 45 P. 46 P. 48

P. 49

Nicolas Righetti, lundi13.ch Nicolas Righetti, lundi13.ch Universal Images Group North America LLC / Alamy Stock Photo Steve Gschmeissner/Science Photo Library Davide Bonazzi Sudowoodo / Shutterstock Swiss-PO 2020 Images / Alamy Stock Photo Franziska Gruhl - SIB. All rights reserved Franziska Gruhl - SIB. All rights reserved Sutthaburawonk / iStock Fabio Rinaldi - SIB. All rights reserved DR Nicolas Righetti, lundi13.ch Nicolas Righetti, lundi13.ch Nicolas Righetti, lundi13.ch Nicolas Righetti, lundi13.ch 2013 Roblan / Shutterstock Universal Images Group North America LLC / Alamy Stock Photo Steve Gschmeissner / Science Photo Library Wikimedia CC-BY-NC-ND 4.0 International license Nextstrain.org, CC BY 4.0 Davide Bonazzi Davide Bonazzi Davide Bonazzi Davide Bonazzi Nicolas Righetti, lundi13.ch Sudowoodo / Shutterstock Frank Hecker / Alamy Stock Photo 2019 khlungcenter / Shutterstock Ernie Janes / Alamy Stock Photo Swiss-PO




SIB Swiss Institute of Bioinformatics T. +41 21 692 40 50 www.sib.swiss


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