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Genomes and Genome Evolution



Genomes and Genome Evolution (BIOL 4301/6301) - Syllabus

Spring 2016 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).
    DNA replication tutorial.
    Another DNA replication animation.
    A transcription tutorial.

Unit 2 - Genomes as the Hub of Biology PowerPoint
    The opossum genome paper discussed in class.
    C. elegans dining.  Not the same example as in class but a similar instance.
    The neanderthal genome manuscript discussed in class.
    Reviving the mammoth article.

Unit 3 - Maps, Sequencing, Assembly, etc. PowerPoint
    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.
    Helicos sequencing.
    Ion Torrent sequencing.
    Nanopore sequencing.
    DeBruijn graph examples.
    Debruijn graph generator.

Unit 4 - Transcriptomics Powerpoint
    Northern Blotting.
    Why strand-specific libraries are preferred.
    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 Medicine - PowerPoint

Unit 7 - Selected Genome Projects PowerPoint

Graduate Student Lectures
Jenny Korstian - Phylogenomics
    Saba Nafees - CRISPR
    Amin Ferdous - Disease Identification
    Haley Hale - Polyploid Genomics
    Taylor Soniat - Metagenomics
    Jack Francis - Conservation Genomics
    Michaela Halsey - TE-Thrust
    Carlos De-Niz - Transcriptome Pipeline

In-Class Discussion papers
    January 27 - Acinonyx jubatus, Ray powerpoint
    February 3 - Aegypius monachus
February 10 -Anser cygnoides
February 17 - Apteryx mantelli
February 25 - Aspergillus fumigatus
March 2 - Bombus spp
March 9 - Fasciola hepatica
March 23 -Hordeum vulgare
March 30 - Musca domestica
April 6 - Physcomitrella patens
April 13 - Primula veris
April 20 - Serinus canaria
April 27 - Spirometra erinaceieuropaei
    Ophiophagus hannahUstilago maydis