Cytoscape WikiCytoscape Symposium 2007: Speaker details, abstracts and presentations
November 8 the Cytoscape Public Symposium was held. We've tried to gather all the presentations and tutorials that were given during the retreat and these are available through the links below. Due to sensitivity of content some of them could not be made available, in that case only the abstract is available
Leroy Hood: Biological networks and disease
Position/Title/Institute
President, Institute for Systems Biology
Talk Link
N.A.
Talk Abstract
I will discuss a systems approach to disease using as an example prion infection in mice. I will show how the dynamics of protein networks derived from the dynamic analyses of brain transcriptomes superimposed on protein/protein networks from the literature and integrated together with various types of phenotypic data actually explain much of the known dynamics of the disease. I will also show how this disease-perturbed network view of disease leads to a new approach to blood diagnostics that promises to transform early disease diagnosis and following responses to therapies. I will also show how this approach is driving the development of new measurement technologies employing microfluidics and nanotechnology. These systems approaches together with the new measurement technologies are driving the emergence of a new medicine that will be predictive, personalized, preventive and participatory (P4). I will also discuss the long-term implications of P4 medicine for world health.
Biography / Awards
Dr. Hood's research has focused on the study of molecular immunology, biotechnology, and genomics. His professional career began at Caltech where he and his colleagues pioneered four instruments - the DNA gene sequencer and synthesizer, and the protein synthesizer and sequencer - which comprise the technological foundation for contemporary molecular biology. In particular, the DNA sequencer has revolutionized genomics by allowing the rapid automated sequencing of DNA, which played a crucial role in contributing to the successful mapping of the human genome during the 1990s. In 1992, Dr. Hood moved to the University of Washington as founder and Chairman of the cross-disciplinary Department of Molecular Biotechnology. In 2000, he co-founded the Institute for Systems Biology in Seattle, Washington to pioneer systems approaches to biology and medicine. Most recently, Dr. Hood's lifelong contributions to biotechnology have earned him the prestigious 2004 Biotechnology Heritage Award, and for his pioneering efforts in molecular diagnostics the 2003 Association for Molecular Pathology (AMP) Award for Excellence in Molecular Diagnostics. In 2006 he received the Heinz Award in Technology, the Economy and Employment for his extraordinary breakthroughs in biomedical science at the genetic level. In 2007 he was elected to the Inventors Hall of Fame (for the automated DNA sequencer). He has published more than 600 peer-reviewed papers, received 14 patents, and has co-authored textbooks in biochemistry, immunology, molecular biology, and genetics and is just finishing a text book on systems biology. In addition, he coauthored with Dan Keveles a popular book on the human genome project-The Code of Codes. Dr. Hood is a member of the National Academy of Sciences, the American Philosophical Society, the American Academy of Arts and Sciences, the Institute of Medicine and the National Academy of Engineering. Indeed, Dr. Hood is one of 7 (of more than 6000) scientists elected to all three academies (NAS, NAE and IOM). Dr. Hood has also played a role in founding more than 14 biotechnology companies, including Amgen, Applied Biosystems, Systemix, Darwin and Rosetta. He is currently pioneering systems medicine and the systems approach to disease. Awards:
- 2005 Heinz Award for Technology,for the Economy and Employment Development and commercialization of high throughput biology (automated protein and DNA sequencing).
- 2003 Lemelson-MIT Prize for Invention and Innovation of an Automated DNA sequencer that made the Human Genome Project possible.
- 2002 Kyoto Prize for the Development of advanced biological instrumentation.
Andrew Hopkins: Network Pharmacology - chemical opportunities for systems biology
Position/Title/Institute
SULSA Professor of Translational Biology and Chair of Chemical Informatics, University of Dundee</p></td>
Talk Link
N.A.
Talk Abstract
In recent years, it has been appreciated that many effective drugs, in therapeutic areas as diverse as oncology, psychiatry and anti-infectives, act on multiple-gene products rather than single targets. Furthermore, the advent of chemogenomics and wide ligand profiling has provided evidence that many drugs act on multiple targets: what is known as polypharmacology. This is in contrast to the predominant paradigm in drug discovery for the past two decades in which the concept of designing exquisitely selective ligands, to avoid unwanted side effects. Polypharmacology has traditionally been viewed by drug designers as an undesirable property that needs removed or reduced to produce 'clean' drugs act on single targets. However, a growing body of post-genomic biology is revealing is a far more complex picture of drug action. The combination of gene-deletion observations of phenotypic robustness and network biology theory indicate that in several instances exquisitely selective compounds may exhibit a lower than desired efficacy for the treatment of disease. Thus compounds which selectively act on two or more targets of interest could increase the confidence-in-rationale or the range of efficacy. Traditionally medicinal chemists have approached the design of ligands with multiple activities with trepidation, fearing complex structure-activity relationships or conjugated ligands with high molecular weights. Here we discuss how combining chemogenomics with network biology may enable a new 'network pharmacology' approach to drug discovery to help rationally identify compounds that act on the level of the biological network rather than a single targets, with the hope of developing more effective medicines for complex disease.
Biography / Awards
Andrew L. Hopkins is the SULSA Research Professor of Translational Biology and Chair of Chemical Informatics in the College of Life Sciences at the University of Dundee. Before taking up his appointment at Dundee, Prof. Hopkins was spent nine years in the pharmaceutical industry, his most recent position as Associate Research Fellow and Head of Chemical Genomics at the Sandwich site of Pfizer Global Research and Development. Prof. Hopkins won a British Steel scholarship to attend the University of Manchester from where he graduated with first class honours in 1993 with a First Class B.Sc.(Hons) in Chemistry. Following a brief spell in the steel industry he won a Wellcome studentship to attend the University of Oxford, working with Professor David I. Stuart FRS. He received his D.Phil. in Structural Biology from the University of Oxford in 1998. During his doctorate research Prof. Hopkins designed a new class of anti-HIV agents which where developed to drug candidates by Glaxo-Wellcome. Following his interest in drug discovery he then joined Pfizer directly after graduating from Oxford in 1998. Over the years established various new functions for the company, including, Target Analysis in 1999, Indications Discovery in 2001 and Knowledge Discovery in 2004 and won several company awards for his efforts. Prof. Hopkins's research involves integrating chemical and biological knowledge to identify new targets or other new opportunities for medicines. His work has involved the design and construction of informatics systems, including a hypothesis-generation system based on text-mining and ontologies and a large-scale chemogenomics integrated knowledge-base. As leader of the Indications Discovery group in he championed the initiation of several new clinical proof-of-concept studies for maraviroc, from ideas that were derived from data-mining. Prof. Hopkins is the author of over 30 scientific publications and holds 7 patents covering a diverse range of inventions, including compound design, protein engineering, new indications and informatics systems. Five of Prof Hopkins's papers have over 100 citations and 2 of which have been classified as 'hot papers' by the Thomas ISI Science Citation Index. Currently Prof. Hopkins consults for the Organization of Economic Co-operation and Development and the World Health Organization Special Programme for Training and Research in Tropical Diseases and is a member of the International Federation of Pharmaceutical Manufacturers & Associations (IFPMA) Taskforce on Partnerships. In 2007 Professor Hopkins was made a Fellow of the Royal Society of Chemistry and won the Corwin Hansch Award.