MMCB 716: Applied
Bioinformatics
Spring 2005 course
Instructors: S. DasSarma and O.C.
Stine
(dassarma@umbi.umd.edu; ostin001@umaryland.edu)
Teaching assistant: Beenish
Bhatia (beenish1@umbc.edu)
Class meetings: Tuesday-Thursday
Course description:
The
explosive growth of information derived from genome projects has revolutionized
biology. As a result, a solid foundation in computational biology and
bioinformatics is now essential for practitioners of biological and biomedical
research. This course emphasizes both theory and usage of fundamental
computer-based approaches to data mining, interpretation and integration of
information concerning genes and their function. Using a problem-based
learning approach, students will acquire facility in using computer-based tools
to analyze the structure and function of nucleic acid and protein sequences.
This
three-credit course is intended for advanced students in the biological
sciences. Due to the nature of the subject, completion of all assigned
problems and final project is critical to achieving the learning objectives.
The course will utilize a fully networked classroom in the HSL with each
student at his or her own workstation; access to a networked computer outside
of class is also highly desirable. Familiarity with fundamentals of
genetics, biochemistry, cell and molecular biology will be assumed. A
background in statistics or mathematical analysis is also helpful.
Topics
to be covered include: history of genomics and bioinfomatics,
basic computer commands, GCG/EMBOSS packages, genome sequencing and assembly,
gene and promoter prediction with HMM, BLAST and related search tools,
annotation and recursive analysis using Perl scripts, phylogenetic
analysis, local databases, large databases, including NCBI and TIGR, microarray development and usage, proteomics, protein
structure, rational drug design, and medical bioinformatics.
Prerequisites: Advanced
undergraduate or graduate-level courses in genetics, biochemistry, and
molecular biology. Experience with
computational analysis of DNA sequences is helpful but not essential.
Textbook: None
required. Relevant readings will be
posted on the course web site. A
bibliography of bioinformatics texts is listed below.
Web site: http://www.umaryland.edu/graduate_mcb/mmcb716/index.html
Class
attendance: Class attendance and participation are required, and
will be recorded and factored into grading.
Homework exercises and
project: Homework exercises will be assigned in class. Students will be expected to do the exercises
in a timely manner and hand in during class.
A final project of the students’ choosing is required. Results of exercises, and other analysis, may
be used for the project during the course of the semester. The project results must be presented in the
form of a paper for a bioinformatics journal and an oral report to the class. Examples of papers from former students will
be provided.
Grading: Grading
will be based on three factors: Class
attendance and participation (20 %), satisfactory performance on weekly
exercises (30 %), and oral and written reports on projects (50 %).
Textbooks:
Bioinformatics: Sequence and Genome Analysis
David W. Mount
Cold Spring
Harbor Laboratory Press; 2001 (first edition); 2004 (second edition).
Bioinformatics: A Practical Guide to the
Analysis of Genes and Proteins
Edited by: Andreas D. Baxevanis, B.F. Francis Ouellette
Wiley-Interscience 1st edition: 1998; 2nd
edition: 2001; 3rd edition: 2005
Bioinformatics
and functional genomics
Jonathan Pevsner
Wiley & Sons; 2003
Introduction
to Bioinformatics: A Theoretical and
Practical Approach
Edited
by: Stephen A. Krawetz and David Womble
Humana
Press; 2003
A
Primer of Genome Science
Greg
Gibson and Spencer V Muse
Sinauer
Associates; 2002
Introduction
to Bioinformatics
Teresa
K. Attwood & David J. Parry-Smith
Prentice
Hall; 1999
Bioinformatics, Biocomputing
and Perl
Michael
Moorehouse and Paul Barry
Wiley
& Sons; 2004
Of
URFS and ORFS: A Primer on How to
Analyze Derived Amino Acid Sequences
Russell
F. Doolittle
University
Science Books; 1986