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Genomes and Genome Evolution



Genomes and Genome Evolution (BIOL 4340/6301) - Grad students, Undergraduates

Spring 2019 Lecture notes, etc. (NOTE: All information on this page is a work in progress and may change at any time)

Unit 1 - Introduction and Biological Concepts PowerPoint
Below are some tutorials and animations to refresh your understanding of basic biological concepts for understanding the material in the course.  This should all be review from previous courses.  
    Model of the interactions between the double helix and the lac repressor.
    Model of a zinc finger/double helix interaction. 
    DNA replication on the leading and lagging strands (click the first link).
    Another DNA replication animation.
Unix introduction

Unit 2 - Maps, Sequencing, Assembly, etc. PowerPoint
    A paper we will be reading for class.
A nice, historically based explanation of recombination based genetic maps.
    Simple and short explanation of Sanger sequencing.
    A more detailed explanation of Sanger sequencing.
    454 pyrosequencing.
    Illumina sequencing.
    PacBio sequencing.
    Nanopore sequencing animations - 1 and 2.
    DeBruijn graph examples.
    Debruijn graph generator.
Assembly exercise
Unicycler assembly
ABYSS bacterial assembly
ABYSS eukaryotic assembly
Canu long-read eukaryotic assembly

Unit 3 - Detecting Variation Powerpoint
Variant calling exercise

Unit 4 - Transcriptomics Powerpoint
    Northern Blotting.
    Why strand-specific libraries are preferred.
    dUTP strand specific library construction
    How Trinity works.
    RNASeq paper dicussed in class.
    On the immortality of television sets...
    Classification of genomic Function

Unit 5 - Transposable Elements PowerPoint
Alu mobilization
    Transposable element annotation paper
    Horizontal transfer in insects and viruses paper
    Horizontal transfer via blood feeding parasites paper
    Transcriptome presentation from Laramie

Unit 6 - Genomic Manipulation - PowerPoint

In-Class Discussion papers
    September 1 - Acinonyx jubatus, Ray powerpoint 
    September 8 - Snake sex chromosomes, Snake powerpoint, Pangolin genome, pangolin powerpoint
    September 15 - Rice genome powerpoint, Rice paper, Lizard powerpoint, Lizard paper
    September 22 -Whale shark powerpoint, whale shark paper, Spider powerpoint, spider paper
    September 29 - Colletotrichum genome powerpoint, Colletotrichum paper, TBD
    October 13- Tardigrade 1, Tardigrade 1 powerpoint, Tardigrade 2, Tardigrade 2 powerpoint
    October 20 - Tardigrade 3, Tardigrade 3 powerpoint, Tardigrade 4, Tardigrade 4 powerepoint
    October 27 -Salamanders powerpoint, Salamanders paper, Hair evolution powerpoint, Hair evolution paper
    November 3 - TBD, TBD
    November 10 - TBD, TBD
    November 17 - Natural killer cells powerpoint, Natural killer cells paper, Phylogenetic conflict powerpoint, Phylogenetic conflict paper
    December 1 - TBD, TBD