Bioinformatics Training at Stanford

Russ B. Altman altman at
Wed Sep 8 11:30:04 EST 1993

September, 1993

                Graduate Training in Biomedical Informatics
                  Stanford University School of Medicine

Since 1981, Stanford's Medical Information Science (MIS) program has
provided training in the application of information technologies to
problems in biomedicine.  Although the early emphasis of this program was
on problems in clinical informatics, the area of bioinformatics (the study
of the application of computational technologies to problems in biology,
with an emphasis on molecular biology) has become an important component of
the field and Stanford's program has enthusiastically embraced this area of
research and training.  The Stanford program offers training at the
master's, Ph.D., and post-doctoral levels. This announcement highlights
information that is particularly relevant to bioinformatics. We encourage
interested applicants to contact one of the participating faculty for
further information.

A. Core faculty in bioinformatics.  

Medicine, and by courtesy, COMPUTER SCIENCE)

Dr. Altman's research interests are in the application of computing
technologies to basic molecular biological problems.  He is
particularly interested in the analysis of protein and nucleic acid
structure, and previous work has involved the development of
probabilistic algorithms for the determination of macromolecular structure
from sparse and uncertain experimental data.  These algorithms have
been shown to have some advantages over other methods of structure
determination including the ability to calculate not only a macromolecular
conformation, but also an explicit estimate of the uncertainty in the
position of each atom.  Current efforts are aimed at 1)  using similar
algorithms to determine macromolecular structure/function relationships
 empirical and theoretical constraints, 2) using sequence analysis
strategies for identifying subsequences with high information content for
three-dimensional modelling and 3) developing improved methods for
combining multiple sources of uncertain structural data to produce a robust
structural model, and 4) applying these technologies to elucidate the
structure/function of important biological molecules.  Specific
macromolecular structures of current interest included the trp-repressor
protein/DNA complex, transfer RNA, Ribonuclease P, and related systems.


Dr. Walker's primary research interests are statistical methods, such
as classification trees and neural networks, and their application in
DNA and protein sequence analysis. Aspects of this research include
methods for identifying motifs in sequences and methodology for
estimating probability and for evaluating the accuracy of sequence
classifiers. Other research interests include biostatistics, knowledge
acquisition from databases, computer vision, and rational drug design.
He is currently working on statistical problems related to the Human
Genome Project.


Co-operating faculty in other departments are available to serve as
research advisors to students in bioinformatics. These faculty include
Douglas Brutlag (Biochemistry, interested in pattern recognition and
sequence classification in biological sequence databases), Michael
Levitt (Cell Biology, interested in protein structure, molecular
dynamics), Samuel Karlin (Mathematics, interested in sequence
analysis), Stanley Cohen (Genetics, interested computers in molecular
genetics and drug monitoring), Richard Olshen (Biostatistics,
interested in tree-structured statistical methods for biomedical data
analysis), and numerous other affiliated faculty with interests in
techniques or algorithms relevant to computational biology.

B.  Students in bioinformatics.  Several trainees are already actively
involved in this field and came to Stanford in part because of their
bioinformatics interest. Current student research in bioinformatics
addresses protein structure prediction, modeling of biological processes,
belief nets for protein and DNA sequence analysis, and statistical
methods for analysis of Fluorescence Activated Cell-Sorter (FACS)
data. Many of the research programs of other students share important
methodological problems with the field of bioinformatics.  Thus we see
medical informatics as a broad discipline that involves fundamental
methodologies of applicability in both biological and clinical

C.  NLM Training Program.  Students interested in bioinformatics are
eligible for the National Library of Medicine's predoctoral and
postdoctoral positions, under the rules outlined in the information sheet
available from the program administrator at the address below.

D.  Post-doctoral trainees.  Individuals with PhD's in a biological science
or computer/engineering science may apply for post-doctoral experience in
biomedical informatics.  Depending on the background and experience of the
applicant, a masters degree in MIS may be a useful addition.  However, in
some cases we will accept post-doctoral trainees for 1-2 years without
requiring that the trainee be a formal degree candidate.  Degree candidacy
is not mandatory for a post-doc to be eligible for NLM funding.  We welcome
applications for post-doctoral training in bioinformatics, following the
same application procedures and deadlines as for all other candidates to
the MIS program.

E. Applications  

Applications for admissions to the Stanford training program are due
by January 1, with decisions announced no later than April 15th.
Trainees generally start in mid-September at the beginning of a new
academic year.

For more information, please contact us by email or by telephone at (415)
723-6979,  (fax: (415) 725-7944).

Dr.  Russ B. Altman              or    Dr. Michael Walker
altman at              walker at
Assistant Professor of Medicine        Senior Research Scientist
Section on Medical Informatics         Section on Medical Informatics
For application materials, a curriculum description, or other
questions send inquiries to the program's administrator:

        Ms. Darlene Vian
        Section on Medical Informatics
        MSOB X-215, Stanford University School of Medicine
        300 Pasteur Drive
        Stanford, CA  94305-5479
        (415) 725-3388;  Fax:  (415) 725-7944
        vian at

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