Seminar in Computer Science (Section 4138):
Fundamental Models and Algorithms in Bioinformatics
Fundamental Models and Algorithms in Bioinformatics
CSCI B490 Fall 2013
Course description
CSCI B490 FMAB
Lecture times and locations
Mon, Wed 4:00p-5:15p, Lindley Hall (LH) 008
Tentative schedule (click the icon for a 
version)
| DAY | DATE | LECTURE | TOPIC | LECTURER |
| 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 Lecture | 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 Lecture | 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 Lecture | 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 Lecture | 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 | Nov 25 | THANKSGIVING BREAK | n/a | |
| Wed | Nov 27 | THANKSGIVING BREAK | n/a | |
| 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 |