SB@NL2014 Invited Speakers
The SB@NL2014 symposium programme consists of 7 sessions divided over two days. Each session features 2 invited speakers, followed by 2 selected speakers (selected from the submitted abstract). In total, the symposium boasts seventeen (17!) invited speakers. These are listed below in alphabetical order.
Prof. Judy Armitage, PhD, FRS
Department of Biochemistry, Oxford Centre for Integrative Systems Biology (OCISB), University of Oxford, UK.
Judy Armitage did her BSc and PhD in Microbiology at University College London before being awarded a personal Lister Fellowship to start her own lab. After a brief period with Bob Macnab at Yale, she was awarded a university lectureship in the Biochemistry Department at the University of Oxford, becoming a full professor in 1996. She became Director of the Oxford Centre for Integrative Systems Biology in 2006 and has been Associate Head of Department since 2010. Her research centres on bacterial motility and chemotaxis, and more recently the coordination of chromosome and protein segregation through the cell cycle. She is a Member of EMBO, a Fellow of American Society of Microbiology and a Fellow of the Royal Society. She lives in Oxford with her husband, a neuroscientist, and has two grown up daughters.
Prof. Gary Bader
The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, CA
Gary D. Bader is a computational biology faculty member at the University of Toronto, since 2006. He is in the Department of Molecular Genetics in the Faculty of Medicine and also the Department of Computer Science. Gary runs a research lab of over 20 researchers and primarily works in the area of biological network analysis as applied to the study of a number of diseases, including cancer. Gary studied at Memorial Sloan-Kettering Cancer Center in New York, Mount Sinai Hospital in Toronto and McGill University and has a background in Biochemistry and Computer Science.
Prof. Dr Rudy Balling
Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, LU
Rudi Balling is a developmental biologist and geneticist. He studied human and animal nutrition at the Universities of Bonn and Washington State University, USA and received his PhD in Human Nutrition from the University of Bonn, Germany. After completing research posts at the Samuel Lunenfeld Research Institute in Toronto Canada (1985-1986), the Max Planck Institute of Biophysical Chemistry in Göttingen (1987-1991) and the Max Planck Institute of Immunbiology in Freiburg, Germany (1991-1993), he became Director of the Institute of Mammalian Genetics at the GSF National Research Centre for Environment and Health in Munich. In 2001 he took over the position as Director of the Helmholtz Centre for Infection Research in Braunschweig, Germany. In 2009 he became founding Director of the Luxembourg Centre for Systems Biomedicine, an interdisciplinary centre of the University of Luxembourg dedicated to the analysis of neurodegenerative diseases through computational and system biology oriented approaches.
Prof.em. Dr Roel van Driel
Synthetic Systems Biology and Nuclear Organisation Group (NOG), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), Amsterdam, NL
Research addresses the question how our genome/DNA functions inside its natural environment: the nucleus of the living mammalian cell. Focus on 3D chromatin and chromosome structure in relation to the regulation of gene expression and the dynamics of the in vivo assembly and functioning of regulatory chromatin-associated multi-protein complexes. Strong interest in the future of the life sciences in general and systems biology in particular. This is the basis of several national and European initiatives and is outlined in: Swierstra, T., Vermeulen, N., Braeckman, J. and Van Driel, R. 2013. Rethinking the life sciences. EMBO reports 14, 310-4.
Prof. Dr Chris T.A. Evelo
BiGCaT group, Department of Bioinformatics, Faculty of Health, Medicine and Life Sciences, Maastricht University (UM), Maastricht, NL
Chris Evelo leads an enthusiastic group of researchers at the department of Bioinformatics – BiGCaT at Maastricht University and is a PI in the new Maastricht Centre for Systems Biology (MaCSBio).
His research focuses on bioinformatics for integrative systems biology; aiming at a better interpretation of experimental data through integration in data models that build on structuring existing knowledge.
Integrative approaches are multi-facetted, and Chris is involved in many projects related to capturing and processing experimental data. His focus is on the interoperability approaches underlying such efforts: standards, ontologies, mapping tools and documentation of the origin of the data and methods used (the provenance). Another main aspect is the organisation of existing knowledge. His core project for this is WikiPathways, a resource for community curation of biological pathways that originate from collaboration between Chris’ Maastricht group and Alex Pico’s group at UCSF. He is also a PI in the Open PHACTS project for large-scale semantic web based knowledge structuring of relations between chemicals, gene-products and diseases. While primarily developed for drug discovery and repositioning it is in fact useful in many other fields.
For pathway analysis, and thereby integration of data and knowledge, Chris’ group developed PathVisio, a modular open source research tool, to which different research groups can and do contribute by developing plugins and research applications. His group developed apps to link pathway analysis to network analysis in Cytoscape and to allow network extension with targeted relationships. To do all that data linking effectively his group developed BridgeDb. It is a reusable open source software framework and web service. It is also the basis for the identifier mapping service in the Open PHACTS system.
While all these approaches are in principle generic, Chris’ background in toxicology and pharmacology and his experience in the nutrition field lead to a broad focus on the human interaction with the molecular environment.
Google Scholar: http://scholar.google.com/citations?user=2dm_Du0AAAAJ.
Prof. Dr Lude H. Franke
Department of Genetics, University Medical Centre Groningen (UMCG), Groningen, NL
Lude Franke is associate professor at the Department of Genetics of the University Medical Centre Groningen. His research group concentrates on the development and application of computational algorithms to functional genomics datasets. The goal is to get to a better understanding what the downstream molecular consequences are of genetic risk factors, by using reconstructed gene coregulation networks (Pers et al, Nature Communications 2014), conducting trans-eQTL analysis (Westra et al, Nature Genetics 2013), and re-analysing publicly available RNA-seq data (Westra et al, BioRxiv 2014).
Prof. Dr Jan van der Greef
Microbiology & Systems Biology, Netherlands Organisation for Applied Scientific Research (TNO), Zeist, NL
Jan van der Greef is a principal scientist at TNO, currently focusing on Systems Biology as a way to innovate and scientifically bridge different health care concepts. In addition Jan van der Greef is Professor of Analytical Biosciences at Leiden University within the Leiden/Amsterdam Center for Drug Research (LACDR) and director of the Sino-Dutch Center for preventive and personalized Medicine (SD-PPM), a joint initiative of the CAS, Netherlands Metabolomics Center, Leiden University and TNO. He is co-founder of SU BioMedicine a spin-off company of TNO, based on an innovative scientific concept developed for herbal medicine. He is a co-founder of BG Medicine Inc (founded 2000, NASDAQ BGMD), the first Systems Biology company and developed the concept of Systems Biology for Pharmaceutical industry and Life Sciences. He is also a scientific co-founder of the Leiden university spin-off company Kiadis based on novel high resolution screening platforms for natural products.
His PhD was completed at the University of Amsterdam in the field of mass spectrometry in 1980. He has published over 300 papers in international journals, supervised more than 25 PhD thesis projects and has given opening, plenary and keynote lectures (> 300) at major life sciences, analytical and pharmaceutical based conferences. He is co-inventor of several patents in Life Sciences. He is considered as a pioneer in the field of liquid chromatography coupled to mass spectrometry, the field of metabolomics in the biomedical domain (since 1980) , among the first to develop single cell profiling by mass spectrometry and early pioneer (2000) in the field of Systems Biology in Medicine. He received an award for major contributions in drug analysis by the Belgium Society of Pharmaceutical sciences in 1998. He became doctor honoris causa at Ghent University in 2000 and received an AAPS award as one of the authors of the best analytical paper in 2002. He was chosen as Lilly distinguished lecturer in the area of Analytical Chemistry in 2004 and granted the prestigious Scheele award by the Swedish Academy for Pharmaceutical Sciences in 2005. He also received a honorary professorship from the Chinese Academy of Sciences at the Dalian Institute of Chemical Physics and visiting professorship’s from the Chinese Academy of Engineering at the Jiao Tong university in Shanghai in 2005 and from the Hangzhou Medical university and Westminster university in London in 2010. His research was recognized among the top-ten innovations in China in 2012. In 2012 the research and understanding of Chinese Medicine via systems biology was honoured as one of the top-10 innovations in China.
Dr Peter-Bram ‘t Hoen
Department of Human Genetics, Leiden University Medical Centre (LUMC), Leiden, NL
Peter-Bram ‘t Hoen is Associate Professor in Bioinformatics at Leiden University Medical Centre. Since 2010, he has been responsible for all bioinformatics activities within the department of Human Genetics. He is leading a multidisciplinary team of researchers (molecular biologists and bioinformaticians) working on transcriptomics (RNA-seq) and proteomics data analysis, modeling of transcriptional networks, (cross-species) data integration, analysis of biological networks, and discovery of molecular biomarkers. He is an expert in RNA sequencing and coordinator of the annual BioSB course on ‘Advanced RNA sequencing data analysis’. He is also a member of the management team of BBMRI’s biobank-based integrative omics study (BIOS). His main research interest is the regulation of gene expression and the mechanisms controlling alternative transcription, splicing, polyadenylation, and translation.
Dr Laurens Landeweerd
CSG Centre for Society and the Life Sciences, Radboud University Nijmegen (RUN), Nijmegen, NL
Dr Laurens Landeweerd (philosopher) holds a position as assistant professor at Radboud University Nijmegen’s Institute for Science Innovation and Society and as researcher at Delft University of Technology (section Biotechnology and Society). His research areas include human enhancement, problems of justification in philosophy, ELSA issues in industrial biotechnology and theory of ethics. He has established a position in the area of social, philosophical and ethical issues in biotechnology innovation, more specifically the relation between science and technology, the status of knowledge, the acceptability and justification of specific innovation trajectories (in both medical and industrial biotechnology).
After his original studies of philosophy (Amsterdam) and Culture and Science (Maastricht), Landeweerd worked on the revision of a Dutch history of philosophy (25 Eeuwen (Westerse) Filosofie). Between 2002 and 2008 he wrote his thesis ( Reconstructing the Self (2009)) at the department of Health Ethics and Philosophy (now Health, Ethics and Society) at Maastricht University. He has contributed to (the application and execution of) several national and international projects on the governance of synthetic biology, nanotechnology and reproductive genetics. He is involved in several Dutch projects, specifically for the Netherlands Organisation for Scientific Research (NWO) Responsible Innovation programme and also for the Centre for Society and the Life Sciences (CSG). European projects to which he contributed include the European projects SynthEthics (as applicant and acting coordinator), Synenergene, Value Isobars, EPOCH, BioTethed, ENHANCE and BioTethics.
Prof. Dr Gerard Muijzer
Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics (IBED), Faculty of Science, University of Amsterdam, NL
Gerard Muyzer is Professor in Microbial Systems Ecology at the University of Amsterdam. He started his scientific career in molecular paleontology using antibodies to study the macromolecular remains in fossil shells and dinosaur bones. Inspired by the work of the American scientists Norman Pace and David Stahl, he changed his research interests from dinosaurs to microbes. In 1993 he introduced denaturing gradient gel electrophoresis (DGGE) in microbial ecology as an easy, rapid and cost-effective method to study the structure and dynamics of microbial communities. The method became so popular, that until today its publication is the most cited article (5750 citations) in the prestigious scientific journal Applied and Environmental Microbiology. He has worked at the Max-Planck-Institute for Marine Microbiology in Bremen, Germany, the Royal Netherlands Institute for Sea Research, and Delft University of Technology. In 2012 he received a prestigious ERC Advanced Grant on a project entitled The Paradox of Sulfur Bacteria in Soda Lakes, in which he will try to obtain a comprehensive understanding of the diversity and ecophysiology of sulfur bacteria in soda lakes, their niche differentiation and the molecular mechanisms by which they adapt to the extreme halo-alkaline conditions.
Prof. Dr Gert-Jan B. van Ommen
Department of Human Genetics, Centre for Medical Systems Biology, Leiden University Medical Centre (LUMC), Leiden, NL
Prof. Dr Gert-Jan B. van Ommen, PhD, is the former head (1991-2012) of the Department of Human Genetics of Leiden University Medical Centre (LUMC). He established the Leiden Genome Technology Centre (LGTC), and the Centre for Medical Systems Biology (CMSB). He is Editor-in-Chief of the European Journal of Human Genetics, past president of HUGO (1998-2000) of the European and Dutch Societies of Human Genetics, and treasurer of the Public Population Project in Genomics and Society (P3G). His main aim is to help improving diagnosis, therapy and prevention of rare and common diseases. He is National Coordinator or Ophanet, founding member of the European Biobanking and Biomolecular Research Infrastructure BBMRI, and director of BBMRI-NL (www.bbmri.nl). As the Dutch National Coordinator of BBMRI-ERIC he is advisor in the BBMRI-ERIC Assembly of Members and member of its Management Committee. His department has contributed to the finding of the gene defects and disease mechanisms underlying Duchenne Muscular Dystrophy, Huntington Disease, Polycystic Kidney Disease, Hereditary Neuropathies, Fragile X Syndrome, Rubinstein-Taybi Syndrome, Familial Hemiplegic Migraine and FacioScapulohumeral Muscular Dystrophy. His group was an early developer of molecular diagnostics for genetic disease, performed the first prenatal diagnosis using DNA markers of a disease (DMD) of which the gene was (then) still unknown, developed many gene mapping techniques, generated the first megabase map of a human gene (DMD), and developed several innovative mutation detection techniques. More recently his group pioneered the exon-skipping approach for therapy of Duchenne Muscular Dystrophy. Further exon skip developments are under way for HD, CADASIL, LGMD (dysferlin), and inflammatory and fibrotic diseases. Professor van Ommen has been PhD supervisor of 45 PhD students and (co-)published ca. 600 papers, reviews, book chapters and policy documents, including ca. 500 papers in peer-reviewed journals, with 25.000 citations (av. 41 citations per paper, H-index 77). Of his 64 papers receiving over 100 citations, 45 originate from his own group.
Prof. Nadine Peyriéras
BioEmergences USR, Centre National de la Recherche Scientifique (CNRS), Gif sur Yvette, FR
Nadine Peyriéras is research director at the CNRS (France) and director of the laboratory USR BioEmergences (Gif sur Yvette, France). She was trained as a biochemist (Ecole Normale Supérieure de Cachan, France). She got her PhD from University Paris 6 with a thesis on cell adhesion in preimplantation mouse embryo (1986 Pasteur Institute under the Supervision of François Jacob). She launched in 2005 with Paul Bourgine, at the time director of the Ecole Polytechnique/CNRS laboratory “Research centre in applied epistemology”, a transdisciplinary project for the reconstruction of multi level dynamics in animal morphogenesis, through two European projects of the NEST FP6 programme called “Embryomics” and “BioEmergences”. The BioEmergences laboratory, partner of the infrastructure France BioImaging http://france-bioimaging.org/, which is the French component of EuroBioImaging http://www.eurobioimaging.eu/, develops methodologies to tackle the reconstruction of multilevel dynamics in animal morphogenesis from the multiscale in vivo observation of developing model organisms.
Prof. Dr Tsjalling Swierstra
Department of Phylosophy, Faculty of Arts and Social Sciences, Maastricht University (UM), Maastricht, NL
Prof. Dr Tsjalling Swierstra is head of the Philosophy Department at the University of Maastricht. He studied philosophy and political science (both cum laude), received his PhD in philosophy in Groningen, and worked at the Technical University of Twente until he was appointed full professor in Maastricht. He is member of the Maastricht University Science and Technology Studies (MUSTS) research programme which received the highest scores on all dimensions from an international research assessment in 2005 and 2011. He is director of the centre for Ethics and Politics of Emerging Technologies, member of the Advisory Committee on Health Research, and of the Programme Committee of the ‘Responsible Innovation’ program funded by the Dutch Research Council (NWO). He has published widely on the ethics of new and emerging science and technology (NEST-ethics) and on technomoral change, i.e. the mutual shaping of science and technology and morals.
Prof. Dr Dolf Weijers
Laboratory of Biochemistry, Wageningen University and Research Centre (WUR), Wageningen, NL
Dolf Weijers is personal chair in Biochemistry of Plant Development at Wageningen University. He leads an international team that studies principles of multicellular plant development, using the early Arabidopsis embryo as a model. Central questions are how tissues and their stem cells are specified, and how genetic control ensures organised 3-dimensional growth. Furthermore, he uses the early plant embryo to understand how a generic signalling molecule can trigger different cellular responses. In his research he combines protein biochemistry with genetics, cell biology and computational biology. His research is supported by grants from the European Research Council (ERC) and from NWO (including VIDI). Prior to his current post, he has been associate and assistant professor at Wageningen University, junior group leader and EMBO post-doc at Tübingen University (Germany). He received his PhD degree in Developmental Genetics at Leiden University.
Prof. Dr Hans V. Westerhoff
Synthetic Systems Biology, Swammerdam Institute for Life Sciences (SILS), Faculty of Science, University of Amsterdam, NL
Molecular Cell Physiology, AIMMS, VU University Amsterdam, NL
Manchester Centre for Integrative Systems Biology, University of Manchester, UK
Hans V. Westerhoff and friends discovered how (and which) properties of components of hierarchical biological networks determine the complex control of metabolite concentrations, fluxes, signalling, and gene expression. They measured how regulation of processes of life is distributed between transcription, translation and metabolism and also developed differential network-based drug design. With this they nailed the coffin of single key steps determining biology three times over. More generally, Westerhoff studies how biological functions emerge in the complex interactions between the components of living systems. He has shown how this requires an integration of modelling, theory, and precise experimentation, and an engagement of diverse scientific disciplines from biochemistry and medicine to physics and philosophy. This ‘systems biology’ led him from molecules to constellations of cells such as in mammals and ecosystems. It also convinced him that systems biology is a new science escaping Occam’s razor because of the irreducible complexity and circular causalities of living organisms. He works to help this new science deliver what the life sciences have always promised to accomplish, for instance through empowerment by an infrastructure of systems biology in Europe (ISBE). Westerhoff’s recent interests include nuclear hormone receptor signalling and the determination of human mood and temper, systems pharmacology and immunology, precision biotechnology, dynamic DNA/chromatin structure and function, drug idiosyncrasy, and individualised medicine through genome-wide metabolic maps. Westerhoff’s PhD with Karel van Dam at the University of Amsterdam was succeeded by an Odyssey through Padova, Bethesda, Stellenbosch, and Manchester back to Amsterdam, with various discoveries, a monograph and >400 publications. Amongst these ‘watchmaker models’ of yeast and Trypanosome glycolysis, of prokaryotic ammonia assimilation, and of mammalian glutathione metabolism, that are used as benchmarks in systems biology. Westerhoff is Professor of Systems Biology at the Universities of Manchester and Amsterdam and of Molecular Cell Physiology at the VU University in Amsterdam. He is foreign member of the Italian Academy of Sciences and Fellow of the International Society for Systems Biology.
Dr Katy J. Wolstencroft
Leiden Institute of Advanced Computer Science (LIACS), Faculty of Science, University of Leiden (UL), Leiden, NL
Dr Katy Wolstencroft is Assistant Professor in Bioinformatics at the Leiden Institute of Advanced Computer Science (LIACS). Her work focuses on data and knowledge integration in the life sciences and her interest lies in developing methodologies for exploiting computer science technologies, such as scientific workflows and the semantic web. Before joining LIACS, Wolstencroft was post-doctoral research fellow and bioinformatics team leader for the myGrid Consortium at the University of Manchester. She was a co-investigator in the European SysMO-DB initiative, which developed strategies and software for exchanging and managing systems biology data and models. The SEEK platform, developed in SysMO-DB, has now been adopted by many other European systems biology consortia and is part of the FAIRDom initiative to develop a European-wide resource. Wolstencroft is also an associate partner in the ISBE-ESFRI initiative (Infrastructure for Systems Biology in Europe), where she works on data and metadata management.
Prof. Ioannes Xenarios
Vital-IT, Unil, CIG, Swiss Institute of Bioinformatics (SIB), Lausanne, CH
Ioannis Xenarios is the Director of Vital-IT Group in Lausanne as well as the Swiss-Prot Group in Geneva. He received a PhD 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 modelling. Since August 2010, Ioannis Xenarios is UNIL full Professor ad personam, affiliated with the CIG.