BigData 2018: Difference between revisions
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==Case studies from Qiu Lab== | ==Case studies from Qiu Lab== | ||
* Between-sepcies genome comparisons: Comparative genomics of worldwide Lyme disease pathogens: [http://borreliabase.org/ BorreliaBase] [[File:Lp54-gain-loss.png| | * Between-sepcies genome comparisons: Comparative genomics of worldwide Lyme disease pathogens: [http://borreliabase.org/ BorreliaBase] [[File:Lp54-gain-loss.png|100px|Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)]] | ||
* Within-population genome comparison: Genomic epidemiology of Group B Streptococcus | * Within-population genome comparison: Genomic epidemiology of Group B Streptococcus | ||
* Within-host genome evolution: Evolution of multi-drug antibiotic-resistance Pseudomonas in cancer patients | * Within-host genome evolution: Evolution of multi-drug antibiotic-resistance Pseudomonas in cancer patients | ||
[[File:Igv mdpa.png| | [[File:Igv mdpa.png|100px|Developmnt of drug resistance mutation in Pseudomonas in a single cancer patient: top (April) vs. bottom (July)]] | ||
==Reference== | ==Reference== | ||
Revision as of 04:28, 21 June 2018
What is evolutionary genomics?
Genomes differ among individuals and species. Evolutionary genomics studies genome variability and genome changes using evolutionary principles. Typical applications include identification of human genome variations associated with diseases and identification of pathogen virulence genes.
Genome changes are studied at two distinct levels: (1) within-species/within-population variations (e.g., human genetic variation), and (2) between-species divergence (e.g., human-mouse comparisons).
The key for analyzing genome variations within species is "population-thinking", the idea that there is no one individual genome that is standard, normal, or disease-free.
The key for comparing genomes across species is "tree-thinking", the idea that evolution happens by diversification (like a branching tree), not by climbing a ladder. There is no such thing as "advanced" or "primitive" species. All living species have the exact same evolutionary distances/time of divergence since the origin of life.
Case studies from Qiu Lab
- Between-sepcies genome comparisons: Comparative genomics of worldwide Lyme disease pathogens: BorreliaBase
- Within-population genome comparison: Genomic epidemiology of Group B Streptococcus
- Within-host genome evolution: Evolution of multi-drug antibiotic-resistance Pseudomonas in cancer patients
Reference
- Graur, 2016, Molecular and Genome Evolution, First Edition, Sinauer Associates, Inc. ISBN: 978-1-60535-469-9. Publisher's Website
- Baum & Smith, 2013. Tree Thinking: an Introduction to Phylogenetic Biology, Roberts & Company Publishers, Inc.
Learning Goals
- Be able to compare evolutionary relationships using phylogenetic trees
- Be able to use command-line tools for batch-processing of genome files
- Be able to perform genome-wide association analysis on the R platform
Quizzes & Assignments
- "Tree Thinking Quizzes"
- FASTA manipulations with
bioseq