Genomes and Genome Evolution
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.
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.
Nanopore sequencing animations - 1 and 2.
DeBruijn graph examples.
Debruijn graph generator.
ABYSS bacterial assembly
ABYSS eukaryotic assembly
Canu long-read eukaryotic assembly
Unit 3 - Detecting Variation Powerpoint
Variant calling exercise
Unit 4 - Transcriptomics Powerpoint
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
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