EVE 161: Microbial Phylogenomics: DNA sequence based studies of microbial diversity.
2018 Class – Instructors Jonathan Eisen and Cassie Ettinger
| ### | Topic | Reading | Slides |
|---|---|---|---|
| 1 | Introduction to course, and reading scientific papers | Raff, Hug et al. |
Slides |
| 2 | Evolution of DNA Sequencing | Sanger et al Heather & Chain |
Slides |
| 3 | Era I: Woese and the Tree of Life | Woese & Fox, Fox et al. |
Slides |
| 4 | Era I: Phylogeny | Baldauf | Slides |
| 5 | Era I: Phylogeny | Baldauf | |
| 6 | Era I: Tree of Life Example Paper | Parfrey et al. | Slides |
| 7 | Era II: rRNA from environment | Lane et al., Stahl et al. |
Slides |
| 8 | Era II: rRNA Gene PCR | Weisburg et al. Hugenholtz et al. | Slides |
| 9 | Era II: rRNA Ecology | Hughes et al; Lozupone & Knight |
Slides |
| 10 | Era II: rRNA Ecology Case Study | Earth Microbiome Project | Slides |
| 11 | Era III – Genome sequencing | Fleischmann et al. | Slides |
| 12 | Era III – Genomes Assembly, Structural Annotation | Tatusova et al | Slides |
| 13 | Era III – Genomes Functional Annotation | A Genomic Perspective on Protein Families | |
| 14 | Era III – Genomes Phylogenomics and Comparative Genomics | Tettelin et al. “Pangenome paper ” | Slides |
| 15 | Era IV – Metagenomics Large insert | Beja et al. #1
Beja et al. #2 |
Slides |
| 16 | Era IV – Metagenomics Shotgun metagenomics | Venter et al
Review: Quince et al |
Slides |
| 17 | Era IV – Metagenomic Functional Predictions | Langille et al. PICRUSt | Slides |
| 18 | Era IV – Metagenomic Case Study | Park et al’s ” 8,000 MAGs” | Slides |
| 19 | Hug et al. again | Hug et al. | Slides |
| 20 | Hug et al. again | Hug et al. |
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 | L1, Blog | Slides | Vid |
| 2 | Sequencing revolution and other omics. | Mardis 2013 Mardis 2008 |
L2, Blog | 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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