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CS5263_4233 Bioinformatics

The document outlines the CS5263/4233 Bioinformatics course, detailing its overview, prerequisites, schedule, instructor information, and grading policy. Key topics include algorithms in bioinformatics, sequence comparison, motif finding, and gene expression analysis. Required and optional textbooks are listed, along with a structured lecture schedule and collaboration policies.

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huangy56
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4 views3 pages

CS5263_4233 Bioinformatics

The document outlines the CS5263/4233 Bioinformatics course, detailing its overview, prerequisites, schedule, instructor information, and grading policy. Key topics include algorithms in bioinformatics, sequence comparison, motif finding, and gene expression analysis. Required and optional textbooks are listed, along with a structured lecture schedule and collaboration policies.

Uploaded by

huangy56
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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3/1/2019 CS5263/4233 Bioinformatics

CS 5263 & CS4233 (Bioinformatics)


News and Announcements

8/21: Welcome to CS4233 & CS5263 (Bioinformatics)! Please take some time to complete a background survey.

Overview | Prerequisite | Time and Location | Instructor | Textbooks and Resources | Policies | Lecture
Schedule and Slides | Assignments

Overview

This course is a survey of algorithms and methods in bioinformatics and computational biology, approached from a
(more or less) computational viewpoint. Topics covered include: fundamental biology, sequence comparison
(dynamic programming), motif finding (combinatorial algorithms, stochastic heuristic search algorithms, suffix
trees), next-generation sequencing (suffix array, Burrows Wheeler transform), gene expression data analysis
(statics, data mining), and gene network/pathway analysis (graph algorithms).

Prerequisite

This course is primarily designed for graduate students and advanced undergraduate students in the Computer
Science department. Fundamental understanding of data structure, algorithms, excellent programming experience
in at least one programming language, as well as some knowledge of probability and statistics are expected. Some
prior exposure to molecular biology is preferred, but not required, as we will introduce basic biological concepts
and terms along the way. Students without background in Algorithms or Statistics should consult the
instructor prior to taking the course.

Time and Location

We meet in room AET 0.214. Lecturers are Tuesday and Thursday, 2:30-3:45 PM.

Instructor and TA

Instructor: Dr. Jianhua Ruan


Office location: NPB 3.318
Office hours: Thursday 9-11am or by appointment
Email: jianhua.ruan 'at' utsa 'dot' edu
Phone: (210) 458-6819

Teaching Assistant: TBD


Office location: TBD
Office hours: TBD
Email: TBD

Textbooks and Resources

Required:

Fundamentals of Bioinformatics and Computational Biology: Methods and Exercises in MATLAB by


Gautam B. Singh

Optional:

Bioinformatics A Computing Perspective by Gopal, Haake, Jones and Tymann (GHJT)


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3/1/2019 CS5263/4233 Bioinformatics

Basics of Bioinformatics - Lecture Notes of the Graduate Summer School on Bioinformatics of China, edited
by Jiang, Zhang and Zhang (JZZ)

Additional Readings and Resources

Grading Policy

10% Attendance and participation


40% Homeworks and in-class exercises
20% Midterm exam / project
30% Final exam / project
Late assignments will not be accepted and a score of zero will be given, unless approved by the instructor.

Collaboration Policy

Assignments

Lecture Schedule and Slides

Part I: Course introduction, biology basics, and intro to MATLAB


Slides
Slides: NGS
Required reading: JZZ Ch 1
MATLAB tutorial
Optional reading:
GHJT Ch2,3
Molecular biology for computer scientists, in Artificial intelligence and molecular biology, Lawrence
Hunter.

Part II: Sequence alignment

Slides: Pairwise sequence alignment


Slides: Multiple sequence alignment
Required reading: GHJT Ch 5.4, 5.7-5.9
Optional reading:
GHJT Ch 5.5-5.6
What is dynamic programming? (if you have no background in dynamic programming)
Linear-space alignment algorithm
Alignment statistics
Statistics and Probability Primer for Computational Biologist

Part III: Motif finding

Slides
Reading:
o Statistics and Probability Primer for Computational Biologist
What are DNA motifs?
How to find motifs?
Additional reading:
Gibbs Sampling
MultiProfiler algorithm
Practical strategies

Part IV: String matching and short-read mapping


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3/1/2019 CS5263/4233 Bioinformatics

Slides set 1
Slides set 2
Additional reading:
Exact string matching
Weeder algorithm
Next-generation DNA sequencing, Shendure and Ji, Nat Biotechnol. 2008.
Sense from sequence reads: methods for alignment and assembly, Flicek & Birney, Nature Methods,
2009
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Langmead
et al, Genome Biology 2009, 10:R25

Part V: Hidden Markov models and gene prediction

Slides
Reading:

Part VI: NGS and genome databases

ChIP seq
Genome Databases

Part VII: Transcriptomic data analysis and data mining

slides
Additional reading material:
1. Review on microarray data normalization 1 , 2
2. Review on microarray data analysis 1 , 2
3. Computation for ChIP-seq and RNA-seq studies download

Part VIII: Biological networks


· slides

Tentative lecture topics

Topics Number of weeks


Introduction to molecular biology 1
Sequence alignment 2
String matching algorithms and applications 2
Motif finding 1
RNA structure prediction 1
Transcriptomic data analysis and data mining 4
Next-generation sequencing 2
Biological networks 1

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