EVE 161: DNA sequence based studies of microbial diversity

EVE 161: Microbial Phylogenomics: DNA sequence based studies of microbial diversity.


 

2016 Class – Instructors Jonathan Eisen and Holly Ganz

### Topic Reading Slides
1 Introduction to microbial diversity and the four eras of sequencing Eisen 2007 Slides
2 Sequencing revolution and other omics. Mardis 2013
Mardis 2008
3 Era I: Woese and the Tree of Life Woese 1977
Fox 1977
Slides
4 Era I: Background on Phylogeny Slides
5 Era I: Modern View of the Tree of Life Parfrey 2010
Williams 2012
Slides
6 Era II: Culture Independent rRNA Studies Lane 1985
Stahl 1985
Slides
7 Era II: rRNA PCR and Major Groups Hugenholtz
Pace
Slides
8 Era II: rRNA ecology. Hughes 2001
Lozupone 2005
9 Era II: rRNA Skittles exercise
10 Era II: Case Study: Built Environment Metaanalysis Adams et al Slides
11 Era III: Genome Sequencing Fraser 2000
Loman 2012
Slides
12 Era III: Genome Sequencing Fraser 2000
Loman 2012
Slides
13 Era III: Genome Annotation Koonin & Wolf; Yandell and Ence Slides
14 Era IV: Metagenomics Beja, Beja Slides
15 Era IV: Shotgun metagenomics Venter et al. Slides
16 Era IV: Shotgun metagenomics part 2 Venter et al. Slides
17 Era IV: Genomes from uncultured Brown et al. Slides
18 Era IV: Genomes from uncultured Brown et al. Slides

 


2014 Class

Course taught by Jonathan Eisen at UC Davis. Winter 2014.  Teaching Assistant: Dr. Holly Ganz. Video slideshows from lecture are being posted to Youtube (though these did not record any of the writing on the board, which was much of the class many days).

# Topic Reading Blog and Notes Slides Video
1 Introduction to microbial diversity and the four eras of sequencing. Eisen 2007 L1Blog Slides Vid
2 Sequencing revolution and other omics. Mardis 2013
Mardis 2008
L2Blog Slides Vid
3 I: The tree of life: historical studies Woese 1977
Fox 1977
L3, Blog Slides Vid
4 I: The tree of life: modern studies Parfrey 2010
Williams 2012
L4, Blog Slides Vid
5 II: GPA, rRNA from environment, PCR Lane 1985
Stahl 1985
Weisburg 1991
L5 Slides Vid
6 II: rRNA PCR: Major lineages Hugenholtz 1998
Pace 2009
L6 Slides Vid
7 II: rRNA PCR: Workflows http://qiime.org/ L7 Slides Vid
8 II: rRNA PCR: Ecology, OTUs, alpha and beta diversity Hughes 2001
Lozupone 2005
L8 Slides Vid
9 II: rRNA PCR-Case Study – Built Environment Song 2013 L9 Slides Vid
10 III: Genomes: History Fleischmann 1995 L10 Slides Vid
11 III: Genomes: Sequencing and assembling Fraser 2000
Loman 2012
L11 Slides Vid
12 Guest Lecture by Holly Ganz L12 Slides
13 III: Genomes: Evolution and LGT Evolution Chapter 7
Wu 2009
L13 Slides Vid
14 Era IV: Metagenomics History and Large Inserts Beja 2000
Beja 2001
L14 Slides
15 Era IV: Shotgun Metagenomics Venter 2004
Tyson 2004
L15 Slides
16 Era IV: Metagenomic Diversity Wu 2006
Wu 2008
L16 Slides
17 Era IV: Metagenomic Functions Tringe 2005
Delong 2006
L17 Slides
18 Era IV: Metagenomic Case Study HMP Qin 2010
HMP 2012
Turnbaugh 2009
L18 Slides

 

 

 

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