Genome Biology for Computational and Physical Scientists
BIOL L504 Fall 2014
Course description
BIOL L504 GBPS
Lecture times and locations
Tues, Thur 9:30a-10:45a, Myers Hall (MY) 209
Tentative schedule
HTML version of this schedule
| DAY | DATE | LECTURE | TOPIC | LECTURER |
| Tues | Aug 27 | 0.1 | Orientation Introduction: Scope of class and resources National Center for Biotechnology Information (NCBI), a great starting point for "anything" genomics 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) | Volker Brendel, Chun-Yuan Huang |
| Thur | Aug 29 | 0.2 | Proteins, DNA, and the flow of biological information | Volker Brendel |
| Tues | Sept 3 | 0.3 | Biological Sequence Analysis II (Lecturer: Dr. Andy Baxevanis) | Volker Brendel |
| Thur | Sept 5 | 0.4 | Chun-Yuan Huang | |
| Tues | Sept 10 | 1.1 | Topic I: Gene structure and expression MIT video 1 MIT video 2 MIT video 3 MIT video 4 MIT video 5 MIT video 6 | Volker Brendel |
| Thur | Sept 12 | 1.2 | Volker Brendel | |
| Tues | Sept 17 | 1.3 | The ENCODE project:ENCyclopedia Of DNA Elements Nature ENCODE Explorer A critique ... ... commented on ... and going on | Volker Brendel |
| Thur | Sept 19 | 1.4 | Quiz I | |
| Tues | Sept 24 | 2.1 | Topic II: Genome content and organization Genome Browsers (Lecturer: Dr. Tyra Wolfsberg) | Volker Brendel |
| Thur | Sept 26 | 2.2 | Volker Brendel | |
| Tues | Oct 1 | 2.3 | Student presentations: UCSC Genome Browser Ensembl Genome Browser NCBI MapViewer | Students |
| Thur | Oct 3 | 2.4 | Quiz II | |
| Tues | Oct 8 | 3.1 | Topic III: RNA structure and function non-coding RNA 16S RNA Analysis siRNA small RNA Eterna | Volker Brendel |
| Thur | Oct 10 | 3.2 | Volker Brendel | |
| Tues | Oct 15 | 3.4 | Gene Silencing by Double Stranded RNA Return to the RNAi World: Rethinking Gene Expression and Evolution | Volker Brendel |
| Thur | Oct 17 | 3.4 | Quiz III | |
| Tues | Oct 22 | 4.1 | Topic IV: Protein structure and function Overview - the protein folding problem (lecture by Steven Skiena) | Volker Brendel |
| Thur | Oct 24 | 4.2 | RCSB PDB PDB-101 - a number of wonderful tutorials! SWISS-MODEL - what to do if my protein is not in PDB!? (start here) | Volker Brendel |
| Tues | Oct 29 | DNA Sequencing | James Ford | |
| Thur | Oct 31 | Ecological Genomics | Melissa Pespeni | |
| Tues | Nov 5 | 4.3 | Protein structure: various topics continued | Volker Brendel |
| Thur | Nov 7 | 4.4 | Quiz IV | |
| Tues | Nov 12 | 5.1 | Topic V: Gene Expression Studies NHI-NHGRI Current Topics in Genome Analysis 2012 - Paul Meltzer lecture | Volker Brendel |
| Thur | Nov 14 | 5.2 | iPlant Tuxedo Protocol RNA-Seq 1/2 iPlant Tuxedo Protocol RNA-Seq 2/2 NCBI GEO | Volker Brendel |
| Tues | Nov 19 | 5.3 | Volker Brendel | |
| Thur | Nov 21 | 5.4 | Quiz V | |
| Tues | Nov 26 | THANKSGIVING BREAK | n/a | |
| Thur | Nov 28 | THANKSGIVING BREAK | n/a | |
| Tues | Dec 3 | 6.3 | Topic VI: Molecular Evolution BIS2C FALL2012 Lecture 4 - Parsimony Character Reconstruction and Tree Inference (Lecture by Dr. Jonathan Eisen, UC Davis) BIS2C FALL2012 Lecture 5 - Parsimony Tree Inference (Lecture by Dr. Jonathan Eisen, UC Davis) | Volker Brendel |
| Thur | Dec 5 | 6.4 | Review article | Volker Brendel |
| Tues | Dec 10 | 7.1 | Quiz VI | |
| Thur | Dec 12 | 7.2 | Review | Volker Brendel |
| Tues | Dec 17 | 10:15am - 12:15pm | Final Exam | Students |