Seminar in Computer Science (Section 4138):
Fundamental Models and Algorithms in Bioinformatics

CSCI B490 Fall 2013

Course description


Lecture times and locations

Mon, Wed 4:00p-5:15p, Lindley Hall (LH) 008

Tentative schedule (class notes can be viewed with Adobe Acrobat Reader)

HTML version of this schedule

Mon Aug 26 0.1 Orientation
Introduction: Topics in bioinformatics, scope of class, and resources

National Center for Biotechnology Information (NCBI), a great starting point for "anything" bioinformatics

Current Topics in Genome Analysis 2012, a National Human Genome Research Institute lecture series:

The Genomic Landscape (Lecturer: Dr. Andy Green)
Biological Sequence Analysis I (Lecturer: Dr. Andy Baxevanis)
Biological Sequence Analysis II (Lecturer: Dr. Andy Baxevanis)
Volker Brendel
Wed Aug 28 0.2 Thinking about sequences, by example:
Estimating genome (text) size by sampling words (k-mers)
Disk-based k-mer counting on a PC (BMC Bioinformatics 14:160)
(see References for links to other software)
KMC code
Volker Brendel
Mon Sept 2 No class (Labor Day)
Wed Sept 4 0.3 Software development environments for this class and bioinformatics in general

More code for the genome-size estimation project:
GenRGenS: software for generating random genomic sequences and structures (Bioinformatics 22:1534); GenRGenS code
wgsim (read simulator)
Daniel Standage
Mon Sept 9 1.1 Topic I: Simple sequence models
Volker Brendel
Wed Sept 11 1.2 Volker Brendel
Mon Sept 16 1.3 Volker Brendel
Wed Sept 18 1.4 Quiz I
Mon Sept 23 2.1 Topic II: Advanced sequence models
Volker Brendel
Wed Sept 25 2.2 Volker Brendel
Mon Sept 30 2.3 Volker Brendel
Wed Oct 2 2.4 Quiz II
Mon Oct 7 3.1 Topic III: Pairwise sequence alignment
Volker Brendel
Wed Oct 9 3.2 Volker Brendel
Mon Oct 14 3.4 Volker Brendel
Wed Oct 16 3.4 Quiz III
Mon Oct 21 4.1 Topic IV: Sequence analysis with scores
Volker Brendel
Wed Oct 23 4.2 Volker Brendel
Mon Oct 28 4.3 Volker Brendel
Wed Oct 30 4.4 Quiz IV
Mon Nov 4 5.1 Topic V:
Pattern probabilities
Volker Brendel
Wed Nov 6 5.2 Volker Brendel
Mon Nov 11 5.3 Volker Brendel
Wed Nov 13 5.4 Quiz V
Mon Nov 18 6.1 Topic VI:
Applications of Markov models: Introduction
Volker Brendel
Wed Nov 20 6.2 Applications of Markov models: Gennotate

(Review of evaluation basics)
Volker Brendel
Mon Dec 2 6.3 Volker Brendel
Wed Dec 4 6.4 Quiz VI
Mon Dec 9 7.1 Review Volker Brendel
Wed Dec 11 7.2 Review Volker Brendel
Mon Dec 16 10:15am - 12:15pm Final Exam Students