The University of Arizona

ECOL 453/553
EVOLUTIONARY & FUNCTIONAL
GENOMICS

 

SYLLABUS

FALL 2009

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Date Lecture Topic Reading Computational Section


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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    
 
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