Launching a Bioinformatics

Program at Roosevelt University

Ogan Gurel, MD MPhil

Adjunct Professor
13 January 2005
 Outline
• Setting the stage
• Mission
• Strategy
• Resources
• Plan
 What is bioinformatics?
• What is Bioinformatics? - Research,
development, or application of computational
tools and approaches for expanding the use of
biological, medical, behavioral or health data,
including those to acquire, store, organize,
archive, analyze, or visualize such data.

• What is Computational Biology? - The

development and application of data-analytical
and theoretical methods, mathematical modeling
and computational simulation techniques to the
study of biological, behavioral, and social
systems.
 Information Flows in
Biology
• The Central Dogma
– Genomics
– Proteomics
– Structural Bioinformatics
– Cellular, organism, population and ecosystem
information flows
• The Scientific Method
– Create hypotheses
– Design experiments
– Evaluate data and
– Extend/modify hypotheses
 Major U.S. Bioinformatics
programs
California New Jersey
• Stanford University Biomedical Informatics
• GraduateProgram
Studies in Computational

• UCSD Bioinformatics and Computational Biology, Department of Bioengi

•
New
Keck Graduate Institute, Professional Masters in Applied Biosciences
York
• Columbia University Department of
• UC-Berkeley Program in Genomics and Computational Biology

Connecticut Pennsylvania
• Bioinformatics at Yale • Keck Center for Advanced Training in Computational Biology
• Penn State University Center for Computational Biology

Illinois
• University of Illinois at Urbana-Champaign Texas
– Center for Biophysics and Computational Biology • W.M. Keck Center for Computational Biology at Rice University
– W.M. Keck Center for Bioinformatics

Massachusetts Tennessee
• MIT Whitehead Center for Genome Research
• Biomedical Informatics at Vanderbil
Bioinformatics programs in
Illinois
• Bioinformatics at University of Illinois at C

• University of Illinois at Urbana-

Champaign
– Center for Biophysics and Computational Bio

– W.M. Keck Center for Bioinformatics

• University of Chicago
• Northern Illinois University
 Why Roosevelt?
• Existing industry-oriented successful
Biotechnology program
• Many of the core courses are already
offered
• Relatively little capital required to
establish a research program
• Relatively strong industrial base –
Abbott pharmaceuticals, biotech, hospital
industry
• The university has flexibility to
accommodate this intrinsically
 The Mission for
Bioinformatics at Roosevelt
• Strong core program of
bioinformatics
• Training students for professional
careers in industry
• Establishing a practically-oriented
research program
 A possible model: The
Northeastern Bioinformatics
•
Master’s
http://www.bioinformatics.neu.edu/
program
• About the Program We are experiencing an
unparalleled boom in the already significant
biotechnology and pharmaceutical industries,
particularly in the Boston area. A January 1999 study
by the accounting firm Ernst & Young shows that New
England area has surpassed San Francisco, in the
formation of firms searching for gene-based drugs. It is
estimated that the Massachusetts biotechnology
industry now employs triple the number of employees
that it did in 1991 (25,000 currently and increasing).
Our practice-oriented, professional M.S.
Program in Bioinformatics therefore has a strong
foundation in our geographical region.
• The explosion in genomic information and in the
elucidation of metabolic and signaling pathways of
various cell types has created an unprecedented,
but largely unmet, need for professionals with a
working knowledge of the biological sciences
and computational methods. The shortage, which
is especially severe in the biotechnology and
pharmaceutical industries, has been discussed in the
press and at workshops. We can expect a comparable
demand in hospital and other clinical settings as the
impact of new technologies diffuses into clinical
research and medical practice. The change has been
so rapid that universities have been caught
unprepared: few offer suitable courses, and virtually
none offer a well integrated curriculum that meets the
needs that are sure to grow and evolve as life sciences
become increasingly conceptual and quantitative. This
Northeastern University M.S. Program in
Bioinformatics is designed to address these
needs through interdisciplinary training that
bridges departments, colleges, and universities,
includes industrial internships, and educates
professionals who are prepared for immediate
productivity in industrial or clinical settings.
• Curriculum
Our curriculum has four parts (Fundamental Courses,
Core Courses, Internship, Electives) with a total of 32
points. All courses are available in the late afternoon
or evening to accommodate student who are
employed during the day.
• Fundamental Courses
BIOG300 Graduate Biochemistry (4)
BIOG301 Molecular Cell Biology (4)
MTHG340 Statistics for Bioinformatics (4)
CSG100 Data Structures (4)
• All of these courses are required but students with
strong backgrounds in either the biological sciences or
the computer/information sciences will be exempted
from these courses as appropriate.
• Core Courses
BIOG381 Ethics in Biological Research (2)
CSG102 Database Management (4)
BIOG302 Bioinformatics Methods and Algorithms (5)
SCG100 Concepts in Pharmaceutical Science (2)
BIOG506 Bioinformatics Internship Tutorial (1)
BIOG385 Bioinformatics Seminar (this course taken twice)
(2)
• Electives
At least one four point elective. More electives will be
available to students who have been exempted from
more than two fundamental courses. A wide range of
electives is available including advanced work in
computer science, mathematics and biology.
 Strategy
• Phase Ia Offer bioinformatics as a concentration option
with the existing biotechnology program
– Easy to accomplish
– Further differentiates for and builds competitive advantage with the existing
biotechnology program
• Phase Ib Offer bioinformatics as a certificate program
• Phase Ic In parallel, establish one or two research
programs
– Relatively easy to accomplish
– Builds competitive advantage
– Attracts faculty
• Phase II Offer full professional master’s program in
bioinformatics
• Phase III Offer a medical informatics program
– Meets longer-term anticipated demand in this field
– Coordinate with a hospital/medical school
– More readily tied into biomedical research funding including bioterrorism
 Resources: Present
faculty
• Sathees Chandra (Biology)
• Ogan Gurel (Biology & Mathematics)
• James Kenevan (Computer Science)
• Robert Seiser (Biology)
• Yao Wang (Mathematics)
• Cornelius Watson (Biology)
• Ray Wright (Computer Science)
 Resources: Potential
Advisors
• Phil Bourne, UCSD (structural
bioinformatics) – has agreed to be an
advisor
• Ted Shortliffe, Columbia (medical
informatics) – has expressed
interested in being an advisor
• Wayne Hendrickson (structural biology),
Columbia
• Ilhan Dilber (computational fluid
dynamics), Fluent USA
• Leon Glass (mathematical modelling),
McGill
 Resources: Funding I
• Private
– National
• Keck Foundation
• Burroughs-Welcome Foundation
– Local
• Industry (e.g. Abbott)
• Illinois Biotechnology Industry Organiation
(IBIO)
• Local foundations (McCormick – Tribune,
Pritzker, etc.)
 Resources: Funding II
• Government
– Federal
• NIH Protein Structure Initiative
• NSF Information Technology Research
program
• NIH Biomedical Information Science and
Technology Initiative (BISTI)
http://www.bisti.nih.gov/
– State
• Department of Labor (BiTmap)
• Other state initiatives
Epilogue