ECOL 453/553 |
SYLLABUS FALL 2009 |
||||
| Home | |||||
| Course Info | Syllabus | Reading | Exercises | Contact Info | |
| Click on highlighted topics for a .pdf copy of the lecture slides. | |||||
| Date | Lecture Topic | Reading | Computational Section |
|
|||
| 8/25 | Introduction to genome structure and organization - Nachman | GM chapter 1, pp 107-113; Brown chapters 1-2 | Introduction to Computational Lab |
| 8/27 | Mutational processes & sequence evolution - Nachman | GM pp 146-152; Brown chapters 13-14 | Working with Data in Excel - Merchant |
| 9/1 | Population processes and genomic change - Nachman | Graur & Li chapter 2 | Survey of Online Tools and Resources for Genomic Data Analysis - Degnan |
| 9/3 | Mutation and drift; neutral theory - Nachman | Biswas & Akey (2006) Trends in Genetics 22(8): 437-446 | Genomic Data Management and Computational Strategies - Merchant |
| 9/8 | Detecting selection in genomes - Nachman | Nachman (2006) | Introduction to Unix and the HPC - Miller |
| 9/10 | Genetic and physical mapping - Nachman | GM pp 133-177; Brown chapter 14 | |
| 9/15 | Recombination, linkage disequilibrium, and association studies - Nachman | GM pp 4-10; Brown chapter 5 | Command line tools for Genomic Data Analysis - Degnan |
| 9/17 | Forward and reverse genetics - Nachman | GM pp 294-317; Brown chapter 7 | |
| 9/22 | Midterm exam #1 - KEY | Review Questions | Introduction to Perl: strings, numbers, arrays - Miller (Beginning Perl, ch 1,2) |
| 9/24 | Intro computational genomics: problems, algorithms & complexity - Sanderson | Pardi & Goldman (2005) PLoS Genetics 1: 672-675 | |
| 9/29 | Sequence alignment - Sanderson | Eddy (2004) Nature Biotechnology 22(7): 909-910, Blanchette et al. (2004) Genome Research 14: 2412-2423 | Perl arrays and hashes, control flow - Miller (Beginning Perl, ch 3,4) |
| 10/1 | Database homology search - Sanderson | Altschul et al. (1997) Nucleic Acids Research 25(17): 3389-3402 | |
| 10/6 | Probability, markov models and HMMs - Sanderson | Reading and writing files, wrapping applications in Perl - Miller (Beginning Perl, ch 6) | |
| 10/8 | Phylogenetic trees - Sanderson | ||
| 10/13 | Phylogenomics - Sanderson | Perl Functions - Miller | |
| 10/15 | Paleogenomics I - Sanderson | Perl Review | |
| 10/20 | Paleogeomics II - Sanderson | Perl regular expressions - Miller (Beginning Perl, ch 5) | |
| 10/22 | Midterm exam #2 - KEY | Review Questions | |
| 10/27 | Sequencing genomes - Moran | GM, pp 13-21, 63-73, 79-89, 92-95; Venter et al. (2001) Science 291: ONLY pp.1304-1316; IHGSC (2001) Nature 409: ONLY pp. 860-874 | Perl regular expressions - Miller |
| 10/29 | Annotating genomes - Moran | GM, pp.95-107; Clamp et al. (2007) PNAS 104:19428 | Perl Subroutines, Modules, and Objects - Miller (Beginning Perl, ch 8,10) |
| 11/3 | Interrogating transcriptomes - Moran | GM, pp.191-227 (skim), 231-255 | |
| 11/5 | Bacterial genomes - Moran | GM, pp.48-55; Sorek et al. (2007) Science |
BioPerl - Miller |
| 11/10 | Inferring gene functions - Moran | GM, pp.113-119,122, 124-128, 331-333 | Introduction to Databases - Merchant |
| 11/12 | Metagenomics - Moran | TBA | |
| 11/17 | Midterm exam #3 | Perl and databases - Miller (Beginning Perl, ch 13) | |
| 11/19 | Grad student presentations | ||
| 11/24 | Grad student presentations | Perl Review - Miller | |
| 11/26 | THANKSGIVING - NO CLASS | Thanksgiving | |
| 12/1 | Plant genomes and their functional analysis - Tax | Workflows - Merchant | |
| 12/3 | Genome organization and implications for phenotypic variation - Bosco | Scientific computing languages - Merchant | |
| 12/8 | Comparative genomics of basal eukaryotes - Hackett | TBA | |
| 12/17 | FINAL EXAM - Thursday December 17, 2:00-4:00 pm | ||
| Course Info | Syllabus | Reading | Exercises | Contact Info | |