22 August 2008
University of Western Cape
Stanford University, University of Western Cape, and University of Cape Town host the Stanford-South Africa Biomedical Training programme: Training the next generation of leaders in health research bioinformatics in South Africa.
This free workshop brings together the world’s most respected biomedical informatics scientists to guide South Africans training in this cutting edge field. It provides an opportunity to discover just how bioinformatics is shaping research in health across the globe, from Vietnam to San Diego.
Please accept this invitation to find out more about opportunities in training with the programme and about leading edge research in biomedical informatics and bioinformatics, to meet with faculty that include two former presidents of the International Society for Computational Biology.
If you are considering a career in bioinformatics, have an interest in how informatics impacts on disease, or are keen to meet with world leaders in this exciting field, this is your opportunity.
Invited Speakers
Philip E. Bourne, PhD is a Professor in the Department of Pharmacology and Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California San Diego, Associate Director of the Protein Data Bank and an Adjunct Professor at the Burnham Institute. He is a Past President of the International Society for Computational Biology. He is an elected fellow of the American Medical Informatics Association. He is the Founding Editor-in-Chief of the open access journal PLoS Computational Biology and on the Editorial Board of IEEE Trends in Computational Biology and Bioinformatics and a long standing member of the National Science Foundation, National Institutes of Health and Genome Canada panels responsible for reviewing proposals relating to computational biology. He is a past member of the US National Committee for Crystallography, past chairman of the International Union of Crystallography Computing Commission IUCrCC and past chairman of the American Crystallography Association (ACA) Computing Committee. Recent awards include the Flinders University Convocation Medal for Outstanding Achievement 2004 and the Sun Microsystems Convergence Award 2002. Bourne's professional interests focus on relevant biological and educational outcomes derived from computation and scholarly communication. This implies algorithms, text mining, machine learning, metalanguages, biological databases, and visualization applied to problems in evolution, cell signaling, apoptosis, systems biology and scientific dissemination. He has published over 200 papers and 4 books, one of which sold over 150,000 copies. He has co-founded 4 companies: ViSoft Inc., Protein Vision Inc., a company distributing independent films for free and most recently SciVee. Bourne is committed to furthering the free dissemination of science through new models of publishing and better integration and subsequent dissemination of data and results which as far as possible should be freely available to all.
Lucila Ohno-Machado, MD, PhD, is Associate Professor of Radiology and Health Sciences and Technology, Harvard Medical School, Brigham and Women’s Hospital. Recent developments in functional genomics suggest that it may be possible to do even more precise diagnoses if gene expression is taken into account. Since the new methodology is heavily dependent on computation, Dr. Ohno-Machado research interest focuses on computer models that will help plan treatment for diseases using the patient’s medical history and diagnosis. She also has several ongoing research projects in medical informatics that uses algorithms to construct diagnostic and prognostic models of diseases. Additionally, she is working on designing a computer program that can automate the process of selecting patients for clinical trials.Recent developments in functional genomics suggest that it may be possible to do even more precise diagnoses if gene expression is taken into account. Since the new methodology is heavily dependent on computation, Dr. Ohno-Machado research interest focuses on computer models that will help plan treatment for diseases using the patient’s medical history and diagnosis. She also has several ongoing research projects in medical informatics that uses algorithms to construct diagnostic and prognostic models of diseases. Additionally, she is working on designing a computer program that can automate the process of selecting patients for clinical trials. Dr. Ohno-Machado's honors and awards include the Martin Epstein Award, the American Medical Informatics Association 1994 Award for Outstanding Contributions to Research, Department of Radiology, BWH, 2000. She was elected a member of the American College of Medical Informatics in 2002.
Chuong Huynh, PhD, is a government consultant in infectious diseases especially in the Southeast Asia. He was formerly the head of international training for the U.S. National Center for Biotechnology Information (NCBI).
SSABMI Faculty
Russ Biagio Altman, MD, PhD, is professor of bioengineering, genetics, & medicine (and of computer science by courtesy) and chairman of the Bioengineering Department at Stanford University. His primary research interests are in the application of computing technology to basic molecular biological problems of relevance to medicine. He is currently developing techniques for collaborative scientific computation over the Internet, including novel user interfaces to biological data, particularly for pharmacogenomics (e.g. http://www.pharmgkb.org/). Other work focuses on the analysis of functional microenvironments within macromolecules and the application of algorithms for determining the structure, dynamics and function of biological macromolecules (e.g. http://simbios.stanford.edu/). Dr. Altman holds an M.D. from Stanford Medical School, a Ph.D. in medical information sciences from Stanford, and an A.B. from Harvard College. He has been the recipient of the U.S. Presidential Early Career Award for Scientists and Engineers, a National Science Foundation CAREER Award. He is a fellow of the American College of Physicians and the American College of Medical Informatics. He is a past-president and founding board member of the International Society for Computational Biology, an organizer of the annual Pacific Symposium on Biocomputing. He leads one of seven NIH-supported National Centers for Biomedical Computation, focusing on physics-based simulation of biological structures (http://simbios.stanford.edu/). He won the Stanford Medical School graduate teaching award in 2000.
Win Hide, PhD
Cathal Seioghe, PhD
Vladimir Bajic, PhD
Seminar Program
Program: Stanford-South Africa Biomedical Informatics Research Symposium
22 August 2008
08:15 – 08:45
Registration & Coffee
08:45 – 09:00
Welcome and overview of SSABMI
Russ Altman
Session 1: Biomedical informatics research presentations from external program advisors (Chairperson: Russ Altman)
09:00 – 09:40
Personalized Risk Assessment: Are we there yet?
Lucila Ohno-Machado
09:40 – 10:20
Determining drug side effects and drug repositioning
Phil Bourne
10:20 – 11:00
Perspective on Bioinformatics Education, Training, Outreach in Developing Countries: Africa
Chuong Huynh
11:00 – 11:30
Coffee
Session 2: Research presentations from local and international SSABMI faculty
(Chairperson: Betty Cheng)
11:30 – 12:00
New methods for identifying pharmacogenes
Russ Altman
12:00 – 12:30
Can distant time-change of gene expression be predicted?
Vladimir B Bajic
12:30 – 13:00
Deciphering Regulatory networks in cancer stem cells
Win Hide
13:00 – 13:30
Genome-wide survey of allele-specific mRNA splicing in human
Cathal Seoighe
13:30 – 14:30 Lunch
Session 3: Research presentations from SSABMI students and visiting fellows (Chairperson: Win Hide)
14:30 – 15:00
Inferring positive selection when dN < dS
Konrad Scheffler
15:00 – 15:20
Simplified ontologies allowing comparison of mammalian developmental gene expression
Adéle Kruger
15:20 – 15:40
HIV-1 sequence evolution patterns and adaptation to human host's immune response
Nobubelo Ngandu
15:40 – 16:00
Gene Regulatory Networks in Mycobacterium tuberculosis Under Hypoxic Conditions
Cameron MacPherson
16:00 – 16:20
Coffee
16:20 – 16:40
Identification of Bacterial Pathogenic Gene Classes Subject to Diversifying Selection
Sumir Panji
16:40 – 17:00
Rapid statistical classification on the Medline database of biomedical literature
Graham Poulter
18:00 – 20:00
Cocktail party and poster session
Hosted by the SA National Bioinformatics Institute, www.sanbi.ac.za
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© 2005 Stanford University
Please send us your questions and/or comments.
updated August 18, 2008
This work supported by the NIH/Fogarty International Center under grant D43 TW00699
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