Amos Bairoch

Professor of Bioinformatics and chairman of the Department of Structural Biology and Bioinformatics at the Faculty of Medicine of the University of Geneva, Amos Bairoch is group leader of the CALIPHO group which he co-directs with Dr Lydie Lane. In 1986 he founded the Swiss- Prot protein knowledgebase and was director of the Swiss-Prot group of the SIB from April 1998 to July 2009. He was also responsible for the development of the PC/Gene sequence analysis software package, as well as the PROSITE and ENZYME databases. Prof. Bairoch is also co- responsible for the development of ExPASy (www.expasy.org), the world’s first web site dedicated to protein sciences. He is one of the co- founders of the SIB as well as scientific co-founder of two biotechnology companies in Geneva: GeneBio and GeneProt. In the framework of the SIB and University of Geneva CALIPHO group, he directs his efforts toward the advance in our knowledge of human proteins through the combined use of bioinformatics and experimental methodologies. 
See also: CALIPHO

Niko Beerenwinkel

Philipp Bucher

Senior scientist and bioinformatics group leader at the Swiss Institute for Experimental Cancer Research (ISREC), Philipp Bucher is responsible for the development of the Eukaryotic Promoter Database (EPD). He works on the development of the so-called generalized profile method for the detection of weakly conserved motifs in protein and DNA sequences and is responsible for the profile section of PROSITE. He is also responsible for the development of new databases (translated EST sequences TrEST, translated genome sequences TrGen, cSNPs of human chromosome 21), as well as for services and software (ProfileScan server HITS, simulation server for immune response, PFTOOLS, ESTScan).   See also: Computational Cancer genomics

Bastien Chopard

Bastien Chopard is Professor at the Department of Computer Science of the University of Geneva. The group has two main research activities. The first is the study of complex systems through the development of new numerical methods to model and simulate phenomena in natural science, economics, social systems and bio-medical scenarios. Cellular automata, Lattice Boltzmann and multi-agent techniques are the central tools used to address these questions. Parallel programs and algorithms are developed to implement the simulations on PC clusters in order to discover, explain or reproduce new phenomena. The second domain of research activity is bioinformatics, which is undertaken in collaboration with the Swiss Institute of Bioinformatics. New classification methods and algorithmic techniques are developed to analyse signal sequences in proteins and to build large phylogenetic trees.   See also: Scientific and Parallel Computing Group

Mauro Delorenzi

Mauro Delorenzi studied molecular biology and statistics in Zurich and, after a few years working as a teacher, specialized in bioinformatics in Melbourne. Since 2002 in Lausanne, he is currently a group leader in the Department of teaching and research of the University Hospital of the Canton Vaud (CHUV), and the head of the Bioinformatics Core Facility (BCF) at the Swiss Institute of Bioinformatics. The BCF is a research and service whose core competence resides in the interface between biomedical sciences, statistics and computation, particularly in the application of high-throughput genomics technologies, such as gene-expression microarrays, to problems of clinical importance, such as the discovery and development of biomarkers for cancer diagnosis, prognosis and personal treatment optimization. The BCF offers consulting, teaching and training, data analysis support and research collaborations for both academic and industrial partners.
See also: Bioinformatics Core Facility Group

Laurent Excoffier

Laurent Excoffier is Professor of Population Genetics at the Institute of Ecology and Evolution of the University of Bern. His group investigates the effect of past demography, historical events, and selection on the molecular diversity of different species, including humans. He is using intensive computer simulations to infer demographic and selection parameters of various evolutionary scenarios under an Approximate Bayesian Computation (ABC) framework. He is also interested in developing new methods to detect genes under selection, taking into account uncertainties about population histories. He is finally involved in the development of several computer software (Arlequin, SimCoal2, Splatche) to simulate and analyse molecular genetic diversity.
See also: Computational Population Genetics

Gaston Gonnet

Gaston Gonnet is Professor at the Institute of Computational Science of the Swiss Federal Institute of Technology in Zurich (ETHZ). His group research topics cover a broad area in biocomputations. For the Orthologous Matrix Project the group is building a large dataset of orthologous proteins from many different organisms. This data allows the scientists to build highly accurate phylogenetic trees. In collaboration with ETH biochemistry the group also analyzes the effect of codon bias and codon reusage on the speed of translatation in yeast.
See also: Computational Biochemistry Research Group

Dagmar Iber

Henrik Kaessmann

Henrik Kaessmann is Associate Professor at the Center for Integrative Genomics of the University of Lausanne. His group is interested in the functional evolution of mammalian genomes. Using a combination of evolutionary bioinformatics and experimental work, his group has carried out a range of projects related to the evolution of genomes from primates (e.g., the origin of new genes) and other mammals (e.g., the origin and evolution of mammalian sex chromosomes). Current work of the group focuses on the evolution of mammalian tissue transcriptomes.
See also: Functional Evolutionary Genomics Group (FEG)

Frédérique Lisacek

Her group develops proteomics software and databases, in particular the renowned Melanie 2-D gel electrophoresis analysis software and the SWISS-2DPAGE database. Further development of tools is currently underway for the identification and characterisation of proteins using mass spectrometry. The group is co-responsible for ExPASy, the world's first Web site dedicated to protein molecular biology.
See also: Proteome Informatics Group (PIG)

Christian Mazza

Christian Mazza is professor at the Department of Mathematics of the University
of Fribourg. The group main current research is focusing on stochastic dynamics of interest in systems biology and in ecology, like auxin transport in plants and its relations with plant patterning, Gillespie algorithms for simulating the evolution of gene networks, stochastic evolutions in random environments, or the statistical modelling of foodwebs. These studies are performed in close collaboration with biologists, and use techniques from applied probability, statistics and statistical mechanics. We also develop simulations tools for bioinformatical applications using MatLab and the statistical package R.
See also: Biomathematics and Computational Biology

Christian von Mering

Associate Professor at the University of Zurich, Christian von Mering is responsible for the protein interaction database STRING (Search Tool for the Retrieval of Interacting Proteins). Apart from maintaining and developing STRING, he also uses this resource for a number of scientific applications, ranging from Environmental Genomics to Systems Biology. He was trained as a Developmental Biologist, before switching to Computational Biology to begin his Post-Doc years with Peer Bork at the European Molecular Biology Laboratory in Heidelberg, Germany. His main interests are Evolution and various new High-throughput Techniques in Molecular Biology. His group is part of the University Research Priority Program "Systems Biology" at the University of Zurich.  See also: Bioinformatics Systems Biology

Olivier Michielin

Olivier Michielin is an Assistant Professor at the University of Lausanne, associated with the Ludwig Institute for Cancer Research (LICR). He leads the Molecular Modeling group involved in the development and application of techniques such as homology modelling, molecular dynamics, free energy simulations and drug design. He is particularly interested in the T cell receptor-peptide-MHC complex and in the design of optimised peptidic vaccines for cancer immunotherapy.  See also: Molecular Modelling Group

Bernard Moret

Bernard Moret is Professor at the Swiss Federal Institute of Technology, Lausanne (EPFL). The main research interests of his group are algorithm design and algorithm engineering, particularly as they apply to computational biology and bioinformatics. The group is also working on problems which include modelling and computing with genome rearrangements, detection and reconstruction of hybridization and lateral gene transfer events, large-scale phylogenetic reconstruction from sequence data and from whole-genome data, and related issues.
See also: Laboratory for Computational Biology and Bioinformatics

Félix Naef

Felix Naef studied theoretical physics at the ETHZ and obtained his PhD from the EPFL in 2000. He then received postdoctoral training at the Center for Studies in Physics and Biology at the Rockefeller University (NYC) under the guidance of Prof. Magnasco. His research focuses on the modeling and interpretation of high-throughput functional data and the study of biomolecular oscillators. He joined ISREC as an associate scientist in the NCCR Molecular Oncology program in early 2004 and was nominated assistant Professor at EPFL in 2005.  See also: Computational Systems Biology Group

Erik van Nimwegen

Erik van Nimwegen is Professor at the Biozentrum of the University of Basel and leads the Systems Biology group at the Division of Bioinformatics. His research interests revolve around uncovering the design principles of cellular regulatory systems. Current research in his group proceeds along two main threads. The first concerns the development of new algorithms, based on probability theory, for unraveling the regulatory circuitry of cells from large scale biological data sets. The goal of these algorithms is the automated genome-wide annotation of regulatory signals in intergenic regions. The second line of research concerns the evolution of whole genomes. This includes comparative statistical analysis of whole genomes and mathematical modeling of genome evolution. See also: Genome Systems Biology

Bernd Rinn

Bernd Rinn is Director of the Center for Information Sciences and Databases (C-ISD), at the ETH Zurich in Basel. The group's field of expertise includes creating and supporting novel solutions for data-intensive research projects, integrating and federating existing building blocks into custom solutions for researchers, and porting existing solutions to new platforms and environments. C-ISD has established a robust platform for developing high-quality software based on open source de-facto standards, including a common development environment, version control, continuous integration, issue tracking, a common coding style and commonly followed engineering practices in design, building, testing, profiling and documentation. For building native software, a virtual build farm for the relevant computer platforms has been established. See also: CISD, ETH Zurich

Jacques Rougemont

Jacques Rougemont is head of the Bioinformatics and Biostatistics Core Facility of the EPFL School of Life Sciences since 2007 and does research on statistical analysis of large-scale genomic data. He studied physics and mathematics at the University of Geneva and obtained his PhD in 1999, followed by postdoctoral training in numerical analysis and stochastic processes at the Mathematics Department, Heriot-Watt University in Edinburgh. He then worked on microarray data analysis at the TAGC laboratory at INSERM, Marseille, before joining the SIB's Vital-IT group as a computer analyst in 2004.
See also: Bioinformatics and Biostatistics Core Facility

Marc Robinson-Rechavi

Marc Robinson-Rechavi is Assistant Professor at the Department of Ecology and Evolution in the University of Lausanne Biology and Medical School. His group main interest is in the evolution of animal genomes in the context of organismal function and development. They have special interests in the early evolution of chordates and of fishes. The group is developing a bioinformatic framework for the study of gene expression evolution, by integrating homology concepts into existing anatomical and developmental ontologies. A database of vertebrate gene expression is in development to implement this ontology.
See also: Evolutionary Bioinformatics

Nicolas Salamin

Nicolas Salamin is group leader at the Department of Ecology and Evolution in the University of Lausanne. His group focuses its research activities on theoretical and applied aspects of phylogenetic reconstructions. A particular interest is in testing and developping new approaches to build very large phylogenetic trees. They are also developping new approaches to estimate the mode and tempo of evolution from phylogenetic trees using Markov chain Monte Carlo approaches. Finally, they are investigating micro- and macro- evolutionary patterns and processes within the grass plant family.
See also: Computational Phylogenetics

Ivo Sbalzarini

Ivo Sbalzarini is an Assistant Professor at the Institute of Computational Science of ETH Zurich. The research of his group is concerned with developing and simulating spatio-temporal models of biological systems on the basis of first principles from physics. Within this broad topic, the work specifically focuses on elucidating the spatial organization of biological systems and the functional role of shape and geometry. All projects are done in close collaboration with groups in biochemistry, evolutionary genetics, systems biology, applied mathematics, and computer science. The computational methods that are developed and applied in our group cover three areas: numerical simulation methods for complex systems, image processing, and parameter identification and model sensitivity analysis. See also: Computational Biophysics Lab

Torsten Schwede

Torsten Schwede is Professor at the University of Basel and responsible for the Structural Bioinformatics group at the Biozentrum. His group is developing and operating SWISS-MODEL, a server for automated protein structure homology modeling. Current main research activities are the development of homology modeling techniques, the integration of the SWISS-MODEL Repository with functional databases such as InterPro, and the structure based analysis of human disease related sequence variations.
See also: Protein Structure Bioinformatics Group

Michael Stadler

Michael Stadler is heading the Computational Biology group at the Friedrich Miescher Institute (FMI) in Basel. Initially trained as a biologist in Bern, he studied bioinformatics in Geneva, Lausanne and at the MIT in Cambridge, USA. In 2006 he joined the FMI and established the Computational Biology group of the institute. The group provides teaching and bioinformatics infrastructure to the FMI, closely collaborates with experimental biologists and focuses on the computational analysis of genome wide datasets. Using statistical approaches, the group aims to better understand how the different layers of epigenetic, transcriptional and post-transcriptional regulation interact and contribute to the control of gene expression.
See also: FMI Computational Biology Group

Jörg Stelling

Jörg Stelling is Assistant Professor for bioinformatics at the Institute of Computational Science of the Swiss Federal Institute of Technology in Zurich (ETH Zurich). The group research focuses on the development of concepts and tools for network inference, for system modeling and analysis, and for experimental design at larger scales from a bioinformatics and systems theory point of view. All projects involve close collaborations with experimental biologists and computer / systems scientists. In terms of the biological systems studied, the group aims at elucidating design principles of the integration of cellular regulation across metabolism, signal transduction and gene regulation. Current and planned projects cover three areas: Structural network analysis, Systems dynamics of cellular regulation and Synthetic biology.
See also: Computational Systems Biology

Andreas Wagner

Andreas Wagner is Professor in the Institute of Biochemistry at the University of Zurich. He received his Ph.D. in 1995 at Yale University. After fellowships at the Institute for Advanced Study in Berlin and the Santa Fe Institute, he served as a faculty member at the University of New Mexico until 2006. The group’s primary research interest concerns the evolution and evolvability of biological systems on all levels of biological organization, from genes and genomes, to biological networks, and whole organisms. The group’s computational work includes bioinformatic tool development to integrate data from a variety of sources, including comparative whole-genome sequence data, microarray expression data, and high throughput protein interaction data, in order to resolve evolutionary questions. See also: Evolutionary Systems Biology

Ioannis Xenarios

Ioannis Xenarios is a Professor in computational biology at the University of Lausanne. He is serving as the Director of Swiss-Prot and Vital-IT. He received a Ph.D in immunology at the Ludwig Institute of Cancer Research and the Institute of Biochemistry. He worked on the development of the Database of Interacting Proteins (DIP) under the supervision of Prof. David Eisenberg at the University of California Los Angeles. He then became the head of Translational Bioinformatics at Serono (now Merck Serono) where his group developed computational methodologies in the area of proteomics, microarray and genetics. He is one of the Principal investigators of the ENFIN  project aiming at providing methods in dynamical systems modeling.
See also: Vital-IT Group, Swiss-Prot 

Mihaela Zavolan

Mihaela Zavolan is Professor in the Bioinformatics Division of the Biozentrum Basel. She leads a group whose focus is the computational study of the regulatory networks leading to tissue-specific expression of protein forms. The current projects in her lab are aimed at development of computational tools for the discovery of transcription regulatory modules, of splice regulatory signals, and of small regulatory RNAs.
See also: RNA Regulatory Networks Group

Evgeny M. Zdobnov

Evgeny M. Zdobnov is working in the field of comparative genomics and molecular evolution. His group is focusing on multiple analysis of animal genomes to elucidate and quantify evolutionary processes shaping repertoires of genes encoding proteins and ncRNAs (e.g. microRNAs), and conserved non-genic sequences (CNS), as well as to interrogate their function and interacting partners on the basis of sequence variability among different species and within populations.
See also: Computational Evolutionary Genomics