BIO 5376/4375 (Fall 2005)

Applied Bioinformatics
A graduate-level course that presents a practical approach to quantitative and statistical analysis of biological sequence and
structural information. Classroom lectures are accompanied by practical demonstrations and laboratory exercises. Topics may
include, but are not limited to, genomic information content, data searches and sequence alignment, mutations and distance-
based phylogenetic analysis, genomics and gene recognition, polymorphisms and forensic applications, nucleic-acid and protein
array analysis, structure prediction of biological macromolecules.

PREREQUISITES Two semesters calculus and one semester introductory statistics or BIOL 5V00-6A/6M
and MATH 5V00-6A/6M
TIMES AND LOCATION TR 11:00 - 12:15 PM
FO 3.616 (lecture) and TBA (lab)
INSTRUCTOR Stephen Levene
FN 3.114
Phone: X2503, Email: sdlevene@utdallas.edu
OFFICE HOURS TR 2-3 PM and by appointment
REQUIRED TEXTS Bioinformatics and Functional Genomics by
Jonathan Pevsner
Wiley-Liss, Hoboken, NJ; 2003
ISBN 0471210048
ADDITIONAL READINGS Other assigned or recommended readings, including journal articles, as appropriate.
OTHER REQUIREMENTS All students registered for this class are required to have computer and internet access.
Student computer accounts can be obtained through UTD’s Information Resources
department at no cost.
GRADING In-class quizzes (50%); two 75-min exams (25% each). Ungraded homework
assignments (and answers) will be distributed as a study aid. No makeup quizzes or
exams will be given except in case of a serious emergency (documentation required).
ACADEMIC DISHONESTY POLICY Students are required to abide by UT-Dallas policies concerning academic integrity (for
details, see http://www.utdallas.edu/student/slife/scholastic.html). Failure to comply with
these terms will be subject to appropriate disciplinary action.
REGRADING POLICY If you wish to submit an examination or quiz question for regrading, my policy is that the
entire exam or quiz then becomes eligible for regrading. If there are erroneous answers
that I missed previously, regrading may cause your exam or quiz score to decrease
instead of increase.
STUDENTS WITH DISABILITIES If you have a disability that requires accommodation, you must notify the instructor and
file a request through Disability Services (SU 1.610, x2098) on or before the first day of
class. By doing so, you can be assured of full cooperation in making appropriate
arrangements.
Week Date Topic Date Topic Assigned
Readings
1 8/18 Overview and Ch. 1
Introduction
2 8/23 Sequences and strings 8/25 Accessing biological Ch. 2,3
databases
3 8/30 Pairwise alignment, 9/1 Quiz, BLAST searches Chs. 3,4
dynamic programming (Dr. Bu)
(Dr. Bu)
4 9/6 Advanced BLAST 9/8 Lab: BLAST searching Chs. 4,5
methods (Dr. Pace)
5 9/13 The protein-folding 9/15 Quiz, Simulation of Chs. 8,9
problem biological
macromolecules
6 9/20 Protein-structure 9/22 Lab: Protein-structure Ch. 9
prediction visualization tools
7 9/27 Protein-structure 9/29 Exam No. 1 (covers all TBA
prediction (cont’d) material up to 9/22)
8 10/4 Molecular phylogeny 10/6 Molecular phylogeny Ch. 10
and trees and trees (cont’d)
9 10/11 Multiple alignment 10/13 Quiz, Multiple alignment Ch. 11
(cont’d)
10 10/18 Genomic analysis 10/20 Lab: Genome Chs. 12,14,15
databases
11 10/25 SNPs, forensic 10/27 Quiz, Genetic disorders Chs. 16, 17
applications
12 11/1 Protein and nucleic-acid 11/3 Protein and nucleic-acid Ch. 18
arrays arrays (cont’d)
13 11/8 Using Matlab’s 11/10 Quiz, Lab: Microarray Ch. 7
Bioinformatics Toolbox analysis
14 11/15 Using Matlab’s 11/17 Using Matlab’s TBA
Bioinformatics Toolbox Bioinformatics Toolbox
15 11/22 Exam No. 2