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.
Ion Torrent sequencing.
DeBruijn graph examples.
Debruijn graph generator.
Unit 4 - Transcriptomics Powerpoint
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
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 hannah, Ustilago maydis