Science Council

genome genter science council

genome genter science council
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Michael Baudis
University of Zurich

oncogenomics, genomic data management

The focus of my research at the University of Zurich is the analysis of structural variations in cancer genomes by computational genomics...

Prof. Michael Baudis

At the core of my research as Professor of Bioinformatics at the University of Zurich is the analysis of variations in cancer genomes by computational genomics and bioinformatics. The work of the group centers around our continuously expanding collections of cancer genome variants with a focus on structural genome abnormalities and especially copy number variations (CNV). Individual projects deal with the development of computational methods for cancer genome data analysis, genomic aberration analysis in specific tumor entities, and the large scale exploration of mutation patterns in cancers.

An important aspect of my group's work is the curation of public cancer genome datasets. Our Progenetix project currently contains data of more than 100'000 genomic profiling experiments using chromosomal, array, and sequencing-based genome screening techniques, as well as structured metadata and tools to enable data access and visualization.

Since 2014 I have been a member of the Global Alliance for Genomics and Health (GA4GH)and have served there in various leadership roles in groups working on the development of data standards and technologies for genomic data annotation and exchange. Since December 2018, i am co-chair of the GA4GH "Discovery" workstream where I represent Beacon, an ELIXIR supported project to develop & promote a federated data protocol supporting an "Internet of Genomics".

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Murielle Bochud
University of Lausanne

epidemiology, preventive medicine

Murielle Bochud is professor of public health and epidemiology at the Faculty of Biology and Medicine of the University of Lausanne...

Muriel Bochud, MD PhD

Murielle Bochud is professor of public health and epidemiology at the Faculty of Biology and Medicine of the University of Lausanne and head of the department of epidemiology and health systems at Unisanté (Center for Primary Care and Public Health), Lausanne. She has a Swiss federal diploma of Medicine from Geneva University (1994), an MD from Lausanne University (2002) and a PhD in genetic epidemiology from Case Western Reserve University (2007). Her research focuses on the epidemiology of cardiometabolic, renal and nutritional phenotypes, including their genetic determinants. With her group, she is interested in exploring phenotypic and molecular traits with a population-based perspective aiming at public health relevance.

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Olivier Delaneau
University of Lausanne

systems and population genetics

Our group is interested in the regulatory machinery controlling gene expression...

Olivier Delaneau, PhD

Our group is interested in the regulatory machinery controlling gene expression. We investigate it by analyzing population scale multi-omics data sets (e.g. genomics, transcriptomics, epigenomics, proteomics) in which we use genetic variations as natural perturbations of the systems in order to unravel the various interactions between molecular features (e.g. genes, regulatory elements, proteins). One leitmotiv in our research is the development of innovative computational methods to efficiently process and analyse large scale genomic data sets.

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Bart Deplancke
EPFL

genome regulation, systems biology

In 2007, he established his lab at the EPFL School of Life Sciences where he is now a tenured Full Professor and Vice-Dean of Innovation...

Prof. Bart Deplancke

Bart Deplancke graduated as a Biochemical Engineer at Ghent University (Belgium, 1998) after which he pursued doctoral studies in Immunobiology at the University of Illinois (USA) and postdoctoral work in regulatory genomics at the Harvard and UMass Medical Schools. In 2007, he established his lab at the EPFL School of Life Sciences where he is now a tenured Full Professor and Vice-Dean of Innovation and is developing new experimental and computational approaches to study the biology of the genome. In 2013, he became a Swiss Institute of Bioinformatics Group Leader and in 2017 a National Research Council member of the Swiss National Science Foundation.

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Laurent Excoffier
University of Bern

computational biology

I am interested in the development of computational methods to understand evolutionary processes at the population and species level...

Laurent Excoffier, PhD

I am interested in the development of computational methods to understand evolutionary processes at the population and species level, for instance to study how past climatic and environmental changes have influenced the pattern of genetic diversity of a given species, or to detect evidence of local adaptations from genomic information.

I have been recently studying the effect of complex demography on the molecular genetic diversity of a species, for instance such as after a spatial expansion in a heterogeneous environment. I am therefore investigating how various aspects of a species genetic diversity are influenced by historical and spatial constraints, and how these effects contrast with those of selection. We are thus aiming at designing better tests of selective neutrality, taking into account the potentially complex demographic history of a species.

With Stephan Peischl, we have been recently investigating the effect of spatial range expansion on non-neutral (functional) diversity, evidencing the buildup of a mutation load due to inefficient purifying selection on wave fronts. We are testing these theoretical predictions by studying the genomic diversity of populations having gone through recent range expansions like humans and bacteria. 

I am also involved in the development of statistical methods, which rely on massive computer simulations, to reconstruct the past demography of a species from its genetic diversity, and to test among various alternative evolutionary scenarios. I have recently switched focus from Approximate Bayesian Computations (ABC) methods to composite-likelihood methods based on the Site Frequency Spectrum (SFS)  to make inference from genomic data. I have specifically developed the fastsimcoal2 software package to both simulate genomic data and perform demographic inference. These developments are mainly applied to the reconstruction of past human history, using current and ancient genomic data, but it could be applied to any other species.

I am finally still devoting quite some time to the maintenance and extension of various computer programs listed here, including the popular program Arlequin for the analysis of population genetics data.

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Jacques Fellay
University of Lausanne

genomic medicine, human/population genetics

Jacques Fellay is a medical doctor and researcher, with expertise in genomics and infectious diseases...

Jacques Fellay, MD PhD

Jacques Fellay is a medical doctor and researcher, with expertise in genomics and infectious diseases and strong interest in personalized health. He is the founding director of the Precision Medicine Unit of the Lausanne University Hospital (CHUV) and leads a genomics laboratory at the EPFL School of Life Sciences.

The aim of his research is to decipher the genetic basis of inter-individual differences in immunity and responses to infections.
His group explores the role of human genetic variation in the host-pathogen battle, in the hope of shedding new light on basic biological mechanisms, and of paving the way toward more personalized approaches to health.

He received multiple awards, including the National Latsis Prize in 2011 for his work on the genetic control of HIV and hepatitis C virus infections.

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Zoltán Kutalik
University of Lausanne

genetics of complex traits, statistical genetics

Associate professor at the University of Lausanne. In parallel, he is an honorary senior lecturer at the University of Exeter...

Dr Zoltán Kutalik

Zoltán Kutalik, PhD is a statistical geneticist, associate professor at the University of Lausanne. In parallel, he is an honorary senior lecturer at the University of Exeter. His main research interest lies in developing statistical methods integrating various omics data in order to better understand the genetic architecture of complex human diseases. He is a council member of the Swiss Institute of Bioinformatics (SIB), scientific program committee member of the European Society of Human Genetics and evaluation committee member of the Swiss National Science Foundation (SNSF).

Zoltan is an editorial board member of Human Molecular Genetics, EJHG, and Frontiers in Genetics. He received the Early Career Bioinformatician Award of the SIB, the Investigator-in-training award of the Faculty of Biology and Medicine, and shared the Leenaards Prize in 2013. Zoltan published over 180 peer-reviewed articles (>30,000 citations, h-index of 74) in international scientific journals, including Nature, Nature Biotechnology, Nature Genetics, and Nature Communications. His research has been financed by the SNSF, the SIB, the SystemsX.ch, and the Leenaards Foundation.

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Tosso Leeb
University of Bern

veterinary genetics and rare diseases

He is currently a professor of veterinary genetics and animal breeding at the University of Bern...

Prof. Tosso Leeb

Tosso Leeb studied chemistry and has a PhD in biochemistry from the University of Munich. He has been studying inherited traits and diseases in domestic animals for more than 20 years and discovered many spontaneous large animal models for human rare diseases. He is currently a professor of veterinary genetics and animal breeding at the University of Bern. He is also the founding director of the Next Generation Sequencing Platform at the University of Bern.

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Anna-Sapfo Malaspinas
University of Lausanne

evolutionary population genomics

Anna-Sapfo Malaspinas is an assistant professor in the Department of Computational Biology...

Dr Anna-Sapfo Malaspinas

Anna-Sapfo Malaspinas is an assistant professor in the Department of Computational Biology at the University of Lausanne, Switzerland. She studied biology and physics as an undergraduate at the University of Geneva, Switzerland. She then did her PhD in population genetics and computational biology at the University of California, Berkeley, (USA) under the supervision of Montgomery Slatkin. Before returning to Switzerland as an assistant professor at the University of Bern, Anna-Sapfo did a postdoc at the University of Copenhagen with Eske Willerslev. Her current research focuses on theoretical population genetics, with a particular emphasis on the analysis of ancient DNA. Her lab combines the development of computational tools with large-scale data analysis, such as high-throughput genome sequencing, to better understand how humans colonized the world and adapted to the new environments they encountered.

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Gunnar Rätsch
ETH

computational genomics, machine learning, medical Informatics

My group’s research at ETH lies at the interface between methods research in machine learning, sequence analysis...

Gunnar Rätsch, PhD

My group’s research at ETH lies at the interface between methods research in machine learning, sequence analysis, and relevant application areas in biology & medicine. In interdisciplinary collaborations, my group has significantly contributed to understanding several RNA-dependent processes, including RNA splicing and translation. The current research focus includes large-scale Machine Learning, cancer transcriptomics, developing clinical decision support systems, and developing methods and resources for international data sharing of genomic and clinical data.

I lead the Biomedical Informatics group at the Institute of Machine Learning at ETH Zurich since May 2016. Before, I was an Associate Professor at Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College in New York City, where I held adjunct positions until 2019. My background is computer science and physics, and I obtained a Ph.D. degree in Machine Learning in 2001 at the National Institute for Data Analysis in Berlin, Germany.

 

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Alexandre Reymond
University of Lausanne

genome structure and expression

He moved to the Center for Integrative Genomics in October 2004 and became its Director in 2015...

Prof. Alexandre Reymond

Alexandre Reymond carried out his thesis in the laboratory of Dr. Viesturs Simanis at the Swiss Institute for Experimental Cancer Research (ISREC) and received his Ph.D. from the University of Lausanne in 1993. After completion of his postdoctoral training with Dr Roger Brent in the Department of Molecular Biology, Massachusetts General Hospital and in the Department of Genetics, Harvard Medical School in Boston, he moved to the Telethon Institute of Genetics and Medicine (TIGEM) in Milan in 1998 to lead a research group. He joined in 2000 the Department of Genetic Medicine and Development, University of Geneva Medical School. He moved to the Center for Integrative Genomics in October 2004 and became its Director in 2015. He is the President of the European Society of Human Genetics.

His laboratory has assessed the functional impact of genome structural changes, such as CNVs and balance rearrangements. His team demonstrated that expression levels of genes within CNVs tend to correlate with copy number changes, and that structural changes influence the expression of genes in their vicinity - an effect that may extends over the entire length of the affected chromosome. They provided initial evidence that CNVs shape tissue transcriptomes on a global scale and thus represent a substantial source for within-species phenotypic variation. His laboratory participated in disentangling the natural history of the 16p11.2 rearrangements, i.e. their evolution, associated phenotypes and identification of major driver genes.

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Mark Robinson
University of Zurich

statistical bioinformatics, genome-scale data analysis

Mark Robinson has been an Associate Professor since 2017 after joining Department of Molecular Life Sciences of the University of Zurich...

Prof. Mark Robinson

Mark Robinson has been an Associate Professor since 2017 after joining Department of Molecular Life Sciences of the University of Zurich (UZH) in 2011.  He studied Applied Mathematics (BSc, Uni. Guelph) and Statistics (MSc, Uni. British Columbia), and did a PhD in statistical bioinformatics at the University of Melbourne. He has predoctoral experience at the Banting and Best Department of Medical Research (Uni. Toronto) and postdoctoral experience in Cancer Epigenomics at the Garvan Institute in Sydney. The Robinson group at UZH develops statistical methods for interpreting high-throughput sequencing and other omics technologies in the context of genome sequencing, gene expression and regulation and analysis of epigenomes, with a current focus on the analysis of single-cell datasets. As one of UZH's appointed Open Science Delegates, he is a staunch supporter of open and reproducible science in its various forms (open data, open code, preprints, etc.).

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Didier Trono
EPFL

epigenetics, regulatory genomics

Didier Trono has had a long-standing interest for interactions between viruses and their hosts...

Didier Trono, MD PhD

After obtaining an M.D. from the University of Geneva and completing a clinical training in pathology, internal medicine and infectious diseases in Geneva and at Massachusetts General Hospital in Boston, Didier Trono embarked in a scientific career at the Whitehead Institute for Biomedical Research of MIT. In 1990, he joined the faculty of the Salk Institute for Biological Studies to launch a center for AIDS research. He moved back to Europe seven years later, before taking the reins of the newly created EPFL School of Life Sciences, which he directed from 2004 to 2012.

Didier Trono has had a long-standing interest for interactions between viruses and their hosts. This led him to study the biology of pathogens such as human immunodeficiency virus and hepatitis B virus, and to develop virus-based delivery systems for human gene therapy. Over the last ten years, his research shifted towards the field of epigenetics, to explore the impact of retroelements and their controlling mechanisms on the development and physiology of higher organisms, including humans.

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Daniel Wegman
Daniel Wegmann
University of Fribourg

evolutionary and computational genomics

We develop statistical and computational methods to answer biological questions from big data...

Daniel Wegmann, PhD

We develop statistical and computational methods to answer biological questions from big data, from genomic sequence data to images. Our work is motivated by both the wealth of biological data currently being generated, as well as by the observation that dedicated models are often required to answer long-standing questions in biology.

We work closely with our collaborators from many areas of biology and interact equally closely with research groups in statistics and computer science to push our approaches beyond the state-of-the-art in the field.

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Evgeny Zdobnov
University of Geneva

comparative genomics, metagenomics

We carry out research in the field of comparative genomics and molecular evolution...

Evgeny Zdobnov, PhD

Our group carries out research in the field of comparative genomics and molecular evolution, focusing on multiple genome analysis to elucidate and quantify evolutionary processes that shape the repertoires of functional genomic elements.

The research studies the functions of such elements on the basis of sequence variability among different species and within populations, and addresses questions concerning the robustness and evolvability of molecular systems.

Comparative genomics strives to understand “Nature’s experimentation”, which results in genomic sequence variability, by analysing the rapidly accumulating amounts of sequencing data to assess selection pressures on functional elements as well as to generate and to test hypotheses of the origin and evolution of biological complexity. In this framework, we employ multiple-genome analyses to elucidate and quantify evolutionary processes that shape the repertoires of protein-coding genes, non-coding RNAs (ncRNAs, e.g. microRNAs), and Conserved Non-Coding sequences (CNCs), as well as to investigate their putative functions.

With a particular focus on medical and evolutionary questions, the group collaborates extensively with experimental and clinical laboratories and participates in international consortia, such as the VectorBase project for research on invertebrate vectors of human pathogens.

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news & events

news & events
21.09.2023

Genomic medicine gets closer to the clinic

The Health 2030 Genome Center (Genome Center) has obtained a major accreditation extension for human genome sequencing…

12.04.2023

Meet the Genome Center at the European Society of Human Genetics!

The annual meeting of the European Society of  Human Genetics (ESHG)  brings together scientists and health care…

Image: Copyright Julien Gregorio/HUG
07.07.2022

Hunt for the genome of SARS-CoV-2 variants goes on in Switzerland

The Swiss National SARS-CoV-2 Genomic Surveillance Program introduced in May 2021 by the Federal Office of Public…

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