ECOL 453/553 |
SYLLABUS FALL 2008 |
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| Course Info | Syllabus | Reading | Exercises | Contact Info | |
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| Date | Lecture Topic | Reading | Computational Section - Tentative Topic |
MN=Michael Nachman,
HO=Howard Ochman, MS=Michael Sanderson, TW=Travis Wheeler, PD=Patrick
Degnan |
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| 8/26 | Introduction to genome structure and organization MN | GM 105-110; Brown (2002) Genomes 2 chapters 1-2 | Introduction to course HO |
| 8/28 | Introduction to computational genomics MS | Blanchette et al. (2004) Genome Research 14: 2412-2423; Pardi & Goldman (2005) PLoS Genetics 1: 672-675. | Working with data in Microsoft Excel TW |
| 9/2 | Introduction to probability, stochastic processes and statistical inference MS | Genomics tools/resources (e.g. annotation on the web) PD | |
| 9/4 | Mutational processes and sequence evolution MN | GM 147-153; Brown chapters 13-14 | |
| 9/9 | Population processes and genomics change MN | Introduction to Unix: Amadeus and the HPC TW | |
| 9/11 | Detecting selection within genomes MN | ||
| 9/16 | Recombination and linkage disequilibrium in eukaryotic genomes MN | Genomic tools/resources (command line tools) PD | |
| 9/18 | Genetic and physical mapping MN | ||
| 9/23 | Forward and reverse genetics MN | Intro to Perl: strings, numbers, arrays TW | |
| 9/25 | Sequencing strategies and new sequencing technologies HO | GM 13-22, 65-73, 78-86; Venter et al. (2001) Science 291: only pages 1304-1321; IHGSC (2001) Nature 409: only pages 860-874, 896-901 | |
| 9/30 | Sequence assembly and annotation genomes HO | GM 87-93, 96-99 | Perl: arrays & hashes cont, control flow TW |
| 10/2 | Database search (BLAST), computational complexity MS | ||
| 10/7 | Sequence Alignment MS | Perl: reading and writing files, wrapping applications TW | |
| 10/9 | Phylogenetic trees (introduction) MS | ||
| 10/14 | Phylogenetic trees in a genomic context MS | Perl: regular expressions TW | |
| 10/16 | MIDTERM EXAM (in class) | ||
| 10/21 | Interrogating transcriptomes HO | GM 93-96, 195-263 | Perl: regular expressions TW |
| 10/23 | Proteomics HO | GM 266-300 | |
| 10/28 | Funtional genomics and systems biology HO | GM 110-115, 118-119, 122-126, 343-348 | Perl: Subroutines, Modules, and Objects TW |
| 10/30 | Sequence polymorphisms in genomes and SNP databases MN | ||
| 11/4 | Association mapping and applications of genomics to medicine MN | Perl: Modules and Objects cont: BioPerl, parsing BLAST TW | |
| 11/6 | Comparative genomics of bacteria HO | GM 47-55; Rocha (2008) Ann. Rev. Genet. 42 |
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| 11/11 | VETERANS DAY - NO CLASS | Databases: MySQL TW | |
| 11/13 | Community genomics and metagenomics HO | Raes et al. (2007) Current Opinion Microbiol. 10: 490; McHardy & Rigoutsos (2007) Current Opinion Microbiol. 10: 498; Venter et al. (2004) Science 304: 66; Tringe et al. (2005) Science 308: 554 | |
| 11/18 | Comparative genomics of Drosophila | Databases, cont. TW | |
| 11/20 | Comparative genomics of plants MS | ||
| 11/25 | To be announced | Perl: Interacting with databases TW | |
| 11/27 | THANKSGIVING - NO CLASS | Thanksgiving | |
| 12/2 | Hidden markov models (HMMs) MS | Introduction to Java? TW | |
| 12/4 | Evolutionary/phylogenetic discovery of functional elements MS | ||
| 12/9 | Paleogenomics: reconstructing ancient genomes MS | Overflow from previous weeks | |
| 12/16 | FINAL EXAM during scheduled exam period | ||
| Course Info | Syllabus | Reading | Exercises | Contact Info | |