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    Syllabus

    GEN875:Genomic and Proteomic Analysis

    Fall 2010


    M Sept 6 Labor Day (No Class)

    W Sept 8 Sequencing and Genome Assembly

    Lecture Slides: Download file "Lec1-SequencingAndAssembly2010.ppt"

    Homework Assignment #1 - due next Weds - bring a copy to class

    Download file "HomeworkAssignmentOne.doc"

    Two good reviews of next-generation sequence analysis:

    Schatz et al. 2010. Assembly of large genomes using second-generation sequencing. Genome Research E-pub.

    Download file "Schatz2010_AssemblyReview.pdf"

    Flicek and Birney. 2009. Sense from sequence reads: methods for alignment and assembly. Nature Methods Supplement. S6-S12.

    Download file "FlicekBirney2009_NGSReview.pdf"


    M Sept 13 Sequencing and de novo genome assembly (Assembly and Alignment Lab)

    Papers that describe software we will use in lab:

    Simpson et al. 2009. ABySS, a parallel assembler for short read sequence data

    Download file "Simpson2009_ABySS.pdf"

    Rissman et al. Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics. 2009 Aug 15;25(16):2071-3.

    Download file "Rissman2009_ReorderingContings.pdf"

    The lab exercise can be downloaded here Download file "LabExercise_Assembly.doc" but you must also download the data set and software from one of these sites (the same file is on both servers, and includes a copy of the lab exercise as well): Genetics875_Assembly.zip (mywebspace) or Genetics875_Assembly.zip (genome.wisc.edu)


    Here are the results from ABySS assemblies with different k-mers:

    Download file "ABySS_assembly_stats.doc"

    W Sept 15 Other short-read sequencing applications

    Levin et al. 2010. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nature Methods 7(9):709.

    Download file "Levin2010_RNASeq.pdf"


    M Sept 20 Alignment Types (Short-read mapping Lab)

    Lecture Slides: Download file "Lec-AlignmentAndShortReads2010.ppt"

    Software we'll use in lab: Download file "Langmead2009_Bowtie.pdf"

    The lab exercise can be downloaded here Download file "LabExercise_Mapping.doc" but you must also download additional files from one of two other sites (the same files are on both servers). The lab exercise is not included in the downloads, but the links are provided in the lab exercise.

    (1) Genetics875_lab2_bowtie.zip (609 MB): [genome.wisc.edu] - OR - [GEL]

    (2) Genetics875_lab2_Mauve.zip (11 MB): [genome.wisc.edu] - OR - [GEL]

    (3) you will also need to download and install Mauve again: [Mauve]

    These files take quite while to download, so we will also have them on at least one USB "stick" in the classroom.

    W Sept 22 Local Alignment and BLAST

    Lecture Slides:Download file "Lec-LocalAlignmentAndBLAST2010.ppt"

    Read "The Statistics of Sequence Similarity Scores"available at NCBI.


    M Sept 27 BLAST and Orthology (RBH BLAST Lab)

    Lecture Slides: Download file "Lec-HomologyAndOrthology2010.ppt"

    Chen et al. Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes. PLoS One 2007 4:e383.

    Download file "Chen2007_OrthologyComparison.pdf"

    Lab Exercise: Download file "LabExercise_BLAST and Orthology .doc"

    Data for Lab Exercise: Download file "Genetics875_lab3.zip"

    W Sept 29 Whole Genome Alignment

    Lecture Slides: Download file "Lec-GenomeAllignment2010.ppt"

    Marguilies et al. Analyses of Deep Mammalian Sequence Alignments and Constraint Predictions for 1% of the Human Genome.Genome Res. 2007 17: 760-774

    Download file "Margulies2007_MammalianAlignment.pdf"


    M Oct 4 Multiple alignment and Phylogeny (Phylogeny Lab)

    Lecture Slides: Download file "Lec-Phylogeny2010.ppt"

    Lab Exercise: Download file "LabExercise_Phylogeny .doc"

    Software and data for Lab Exercise: Download file "Genetics875_lab4.zip"

    W Oct 6 Phylogeny and Genomes

    Lecture Slides: Download file "Lecture-TreeOfLife.ppt"

    Puigbo et al. J Biol. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. 2009;8(6):59. Download file "Puigbo2009_TreeOfLife.pdf"


    M Oct 11 Interpro, GO, Functional Enrichment (Functional Enrichment Lab)

    Lecture Slides: Download file "Lec-Functional Annotation and Functional Enrichment2010.ppt"

    Huang et al. 2008 Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research, 2009, Vol. 37, No. 1.

    Download file "Huang2008_EnrichmentTools.pdf"

    Lab Exercise: Download file "FunctionLab.zip"

    W Oct 13 HMMs - Predicting Genes and Function

    Lecture Slides:Download file "Lec-HMMsAndGenePrediction.ppt"

    Eddy. 2004. What is a hidden Markov model? Nature Biotechnology, 2004, Volume 22(10).

    Download file "Eddy2004_HMM.pdf"


    M Oct 18 Metabolic reconstruction and modeling (Lab: Help with class projects)

    Lecture Slides:
    Download file "Lec-MetabolicReconstruction.ppt"

    Oberhardt et al. Applications of genome-scale metabolic reconstructions. Molecular Systems Biology 5; Article number 320

    Download file "Oberhardt2009_MetabolicReconstruction.pdf"

    W Oct 20 Discussion of genome papers

    *************** AUDREY'S SECTION ******************

    Click on links to find reading!


    M Oct 25 Microarrays & Sequencing for gene expression analysis (Intro to R lab)

    W Oct 27 Gene expression data analysis – Part I


    M Nov 1 Gene expression data analysis – Part II (Limma Lab)

    W Nov 3Clustering analysis – Part I


    M Nov 8Clustering analysis – Part II (Clustering Lab)

    W Nov 10Motif analysis – Part I


    M Nov 15 Motif analysis – Part II (MEME Lab)

    W Nov 17ChIP/RIP/Nucleosome-Seq


    M Nov 22 Genotyping and Haplotype mapping (Lab: Help with class projects)

    W Nov 24(Day before Thanksgiving – NO CLASS)


    M Nov 29 Network analysis (Cytoscape Lab)

    W Dec 1 Signaling & Other Networks


    M Dec 6 Proteomics – Part I (Intro to PERL Lab)

    W Dec 8 Proteomics – Part II


    M Dec 13 Project Presentations

    W Dec 15 Project Presentations