Final Lecture: Further
opportunities in
bioinformatics and
computational biology
Had to go to
a conference
in Salt Lake
City on June
4.
Russ B. Altman
BMI 214
CS 274
Copyright Russ B. Altman
Copyright Russ B. Altman
Bioinformatics in the world
• Many open academic/industrial positions
for people who work in biology/medicine &
information technology.
Human
Genome
• Major role in scientific landmarks of 2000:
human genome draft & ribosomal
structure
• ISCB (www.iscb.org) with ~1500 members
• ISMB conference growing like Genbank
Copyright Russ B. Altman
Copyright Russ B. Altman
Yeast
expression
Copyright Russ B. Altman
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Bioinformatics studies the flow of
information in biomedicine
Information flow from genotype to phenotype
Jump into
Bioinformatics
?
DNA
Protein Function
Organism
Population
DN
Microarrays
Pharm/genomics
Analyzing Structure
Whole Genome analysis
Computing Structure
Information flow from hypothesis to data
Hypothesis
Experiment
Data
Conflict
Hypothesis
Structuring experimental Comparing 3D models
data for computability. to published Data
Copyright Russ B. Altman
Copyright Russ B. Altman
Current hot areas
Long term challenges
• Microarray analysis (clustering, classification,
combination)
1. Computational model of physiology.
Can we give a medication to a computer before
we give it to a human?
• Data integration
2. Design of new compounds for medical and
industrial use.
Can we design a protein or nucleic acid to have
a specified function?
• Natural Language Processing
• Simulation of metabolic/genetic networks
• Assigning function to genes
• High throughput data collection and analysis
Copyright Russ B. Altman
Copyright Russ B. Altman
Long term challenges
3. Engineering new biological pathways.
Can we devise methods for designing and
implementing new metabolic capabilities for
treating disease?
4. Data mining for new knowledge.
Can we ask computer programs to examine data (in
the context of our models) and create new
knowledge?
http://www.iscb.org/
Copyright Russ B. Altman
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Copyright Russ B. Altman
Journals
Books
BIOINFORMATICS
http://smi-web.stanford.edu/PSBbooks.html
J. Computational Biology
Briefings in Bioinformatics
BIOLOGY JOURNALS:
Nucleic Acids Research (esp “DB issue”)
Genome Research (esp genomics)
Journal of Molecular Biology (esp proteins)
RNA (esp RNA)
smatterings of other journals…SCIENCE ;)
Copyright Russ B. Altman
Copyright Russ B. Altman
Conferences
Intelligent Systems for Molecular Biology
(Edmonton, August 2002 & Brisbane,
Australia, 2003)
http://www.ismb02.org/
http://www.ismb03.org/
Pacific Symposiumon Biocomputing (Kauai,
January 2003)
http://psb.stanford.edu/
RECOMB 2003 (Berlin, 2003)
http://www.ctw-congress.de/recomb/default.html
Copyright Russ B. Altman
Copyright Russ B. Altman
Copyright Russ B. Altman
Copyright Russ B. Altman
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Biocomputation at Stanford
BioX Program (jump started by $90M from
Jim Clark) features biocomputation (10/45
faculty)
http://bits.stanford.edu/
Center for Biomedical Computation:
–50+ faculty from all areas of biocomputation
–Training grant with slots for PhD students
–128 Node SGI Origin 3000 series
supercomputer
–NIH grant for Planning Center of Excellence
–Other fund raising under way
Copyright Russ B. Altman
Copyright Russ B. Altman
Biomedical informatics exists
within a larger context
1.
2.
3.
4.
5.
6.
Structural and Functional Genomics
Biomechanical Simulation
Computer assisted interventions/robotics
Image acquisition and analysis
Networked and computer assisted education
Informatics, data modeling & statistics
Physical Systems vs. Knowledge Systems
Copyright Russ B. Altman
Copyright Russ B. Altman
• Mike Liang
[email protected]
Next
BCatS:
October
26, 2002
• Yueyi Irene Liu
[email protected]
• Michelle Green
[email protected]
• Serkan Apaydin
[email protected]
• Madhup Gulati
[email protected]
• Devshruti Pahuja
[email protected]
Copyright Russ B. Altman
Copyright Russ B. Altman
Page 4
Curriculum (Biomedical
Informatics Training Program)
Bioinformatics + Clinical informatics
= Biomedical Informatics
1. Core biomedical informatics
Clinical informatics: the study of information
flow in support of patient care.
2. CS courses (databases, algorithms & data
structures, machine learning, programming
languages)
Bioinformatics: the study of information flow
in the context of basic biology/physiology.
3. Statistics/probability
At Stanford, they coexist under one
administrative structure within the
Department of Medicine = Biomedical
Informatics. (MS, PhD, maybe online MS,
co-terms also possible)
4. Biology courses
5. Ethical, legal, social implications
Copyright Russ B. Altman
Copyright Russ B. Altman
This is a pretty short course
Other faculty in Bioinformatics
(see http://www.smi.stanford.edu/people/altman/bioinformatics.html
Some others…
David Botstein (Yeast Genome DB, microarrays)
Mike Cherry (GO, Yeast Genome DB, microrrrays)
Seb Doniach (Protein structure/folding)
Leo Guibas (Computational geometry)
Sam Karlin (statistical analysis of seq/struct)
Teri Klein (pharmacogenomics, molecular modeling)
Daphne Koller (probabilistic relational models)
Jean-Claude Latombe (drug docking)
Harley McAdams (Genetic networks, microarrays)
Vijay Pande (Protein folding)
Bob Shafer (HIV sequence/structure correlations)
Arend Sidow (Evolutionary trees)
Serafim Batzoglou CS 262
Doug Brutlag’s Biochemistry 231
Michael Levitt’s Structural Biology 228
I am thinking of a project course, in which
students can do an independent project in
teams? Send me email if you are interested (1)
in taking a bioinformatics project course, and (2)
what quarters (including summer) you could
take it.
Copyright Russ B. Altman
Copyright Russ B. Altman
Bio/Statisticians
Others
Trevor Hastie
Susan Holmes
Richard Olshen
Art Owen
Rob Tibshirani
Pat Brown (Microarrays)
Parvati Dev (Education, SUMMIT)
Larry Fagan (Clinical informatics)
Marcus Feldman (Population biology)
Pehr Harbury (Protein design)
Stuart Kim (developmental biology--ma)
Mark Musen (Ontologies in biomedicine)
Neil Risch (Population Genetics)
Gio Wiederhold (Databases in biomedicine)
Almost anybody with biological data…
Copyright Russ B. Altman
Copyright Russ B. Altman
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Getting into this area
Problems with bioinformatics
Know how to program
--prototyping language
--hard core language
• Need to feel comfortable in an
interdiscipline.
• Sometimes, need to depend on other
people’s primary data.
Know the biology or be willing to learn
Take this course… ;)
• Need to be sure you do sound method
development.
Find a “transition experience” in which you
can use your current talents to get the job,
but then get involved in new things to
extend your knowledge/experience.
• Need to be addressing important biological
problems.
Copyright Russ B. Altman
Copyright Russ B. Altman
Thanks.
Good luck on the final.
Good luck in your other courses.
Thanks for your attention.
[email protected]
Copyright Russ B. Altman
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