Computational Biology Short Courses, Aug. 2004, University of Michigan

Jeffrey R. de Wet jrdewet at
Mon Jul 12 16:37:01 EST 2004

University of Michigan, Ann Arbor
Short Course in Computational Molecular Biology

Cancer Bioinformatics August 4-6, 2004
Proteome Informatics August 5-7, 2004
Bioinformatics August 18-20, 2004

Objectives: Challenging intensive courses covering material from our
regular graduate courses on computational biology in a format that is
accessible to working scientists. Participants will become familiar with
the theory and practice of molecular sequence analysis, proteomics, and
processing and analyzing cancer biology data. The aim is to provide an
appreciation for how and why different analytic approaches are used,
their capabilities and their limitations. We emphasize the use of public
domain software tools rather than focusing on a specific commercial
package. Participants should be familiar with basic molecular biology
and mathematics at the level of college calculus, but programming skills
or higher-level computer science experience is not required. The courses
are targeted to students at the level of a first or second year doctoral
candidate and professional scientist in molecular biology or

Each 3-day course consists of 6 hours of daily lectures: 3 hrs. in the
morning and 3 hrs. in the afternoon.

Cancer Bioinformatics:
Cancer bioinformatics, biostatistics and data modeling, web tools and
data mining
Model organisms and cancer networks, cancer systems biology, integrative
cancer biology
Biomarkers, tissue microarrays, analysis of microarrary data, cancer

Proteome Informatics:
Protein isolation and separation methods, proteome concepts
Mass spectrometry, peptide mass fingerprinting, protein expression
profiling, data analysis
Database structures, database searching and search algorithms, de novo
sequence analysis

Statistics, model based data analysis, HMMs, mathematical methods of
gene mapping and gene finding
Protein models, threading, dynamic programming optimal and suboptimal
RNA alignment and folding
Information measures, Karlin-Altschul statistics, Sum statistics, gapped
BLAST, database searching
Multiple sequence alignment, generalized dynamic programming, phylogeny
and molecular evolution

Supplemental applied scripting and programming sessions will be offered
at some of the courses. Please see the web site for updated information.
All participants are encouraged to bring a laptop computer
(Windows/Intel) for use in the programming sessions. A CD-ROM containing
course lecture notes, problem sets, programming exercises, public domain
software and reference material will be distributed.

Instructors are from the faculty the University of Michigan
Bioinformatics Program. (David States, Philip Andrews, Arul Chinnaiyan,
Debashish Gosh, Gil Omenn, and David Lubman) joined by Warren Gish
(Washington University),  David Tabb (Oak Ridge National Laboratory),
Curt Wilkerson (Michigan State University), Brett Phinney (Michigan
State University), Michael Zuker (Rensselaer Polytechnic Institute) ,
Michael Becich (University of Pittsburgh), Mark Rubin (Brigham and
Women's) Muneesh Tewari (Dana-Farber Cancer Institute). Graduate
students from the program will fill in as teaching assistants.

For additional information see:

Early application is advised, as the number of participants for these
courses has to be restricted.


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