Seminar in Computer Science (Section 31119):
Fundamental Models and Algorithms in Bioinformatics
Fundamental Models and Algorithms in Bioinformatics
CSCI B490 Fall 2015
Course description
CSCI B490 FMAB
Lecture times and locations
Mon, Wed 1:00p-2:15p, Lindley Hall (LH) 008
Tentative schedule (click the icon for a 
version)
| DAY | DATE | LECTURE | TOPIC | LECTURER |
| Mon | Aug 24 | 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 26 | 0.2 | Mapping biological question onto computational problems Resources: Wikipedia - DNA Howard Hughes Medical Institute BioInteractive Sample BioInteractive Video Where to find sequences: NCBI Nucleotide RCSB Protein Data Bank | Volker Brendel |
| Mon | Aug 31 | 1.1 | Topic I: Parsing genome feature annotation records for simple bioinformatics tasks Class notes Generic Feature Format (GFF3) Biopython | Daniel Standage |
| Wed | Sept 2 | 1.2 | Computer Lab (assignment details) | Daniel Standage |
| Mon | Sept 7 | No class (Labor Day) | ||
| Wed | Sept 9 | 1.3 | Quiz I | |
| Mon | Sept 14 | 2.1 | Topic II: Simple sequence models Lecture | Volker Brendel |
| Wed | Sept 16 | 2.2 | Computer Lab | |
| Mon | Sept 21 | 2.3 | Evaluation | Volker Brendel |
| Wed | Sept 23 | 2.4 | Quiz II | |
| Mon | Sept 28 | 3.1 | Topic III: Advanced sequence models Lecture | Volker Brendel |
| Wed | Sept 30 | 3.2 | Computer Lab | |
| Mon | Oct 5 | 3.3 | Evaluation | Volker Brendel |
| Wed | Oct 7 | 3.4 | Quiz III | |
| Mon | Oct 12 | 4.1 | Topic IV: Pairwise sequence alignment Lecture | Volker Brendel |
| Wed | Oct 14 | 4.2 | Computer Lab | |
| Mon | Oct 19 | 4.3 | Evaluation | Volker Brendel |
| Wed | Oct 21 | 4.4 | Quiz IV | |
| Mon | Oct 26 | 5.1 | Topic V: Hidden Markov Models Lecture | Volker Brendel |
| Wed | Oct 28 | 5.2 | Computer Lab | |
| Mon | Nov 2 | 5.3 | Evaluation | Volker Brendel |
| Wed | Nov 4 | 5.4 | Quiz V | |
| Mon | Nov 9 | 6.1 | Topic VI: Sequence analysis with scores Lecture | Volker Brendel |
| Wed | Nov 11 | 6.2 | Computer Lab | |
| Mon | Nov 16 | 6.3 | Evaluation | Volker Brendel |
| Wed | Nov 18 | 6.4 | Quiz VI | |
| Mon | Nov 23 | THANKSGIVING BREAK | n/a | |
| Wed | Nov 25 | THANKSGIVING BREAK | n/a | |
| Mon | Nov 30 | 7.1 | Applications I | Volker Brendel |
| Wed | Dec 2 | 7.2 | Applications II NCBI BLAST The Statistics of Similarity Scores Guide 1 Guide 2 Align Webinar 1 Webinar 2 | |
| Mon | Dec 7 | 8.1 | Review | Volker Brendel |
| Wed | Dec 9 | 8.2 | Review | Volker Brendel |
| Fri | Dec 18 | 12:30pm - 2:30pm | Final Exam | Students |