EVE161 – 2019 – microBEnet: the microbiology of the Built Environment network

#	Topic	Reading	Topics	Slides
1	Intro to class How to read a scientific paper	Hug et al. A new view of the Tree of Life Raff. How to Read and Understand a Scientific Paper: A Step-by-Step Guide for Non-Scientist Short PDF version	How to read papers General outline of class	L1
2	DNA Sequencing	Sanger 1977 Review: Heather and Chain 2016 Extra: Mardis 2013. Quick.	How DNA sequencing works and has changed over the years
3	Era I – Cultured Microbes: rRNA, phylogeny and the three domains	Woese & Fox, Fox et al. Review: Baldauf 2003	What is a phylogenetic tree? Features useful for phylogenetic studies of microbes What is ribosomal RNA? Why is ribosomal RNA used for phylogenetic studies?	L3
4	Era I – Cultured Microbes: Phylogenetic Trees	Baldauf 2003	How does phylogenetic inference work What are the different approaches	L4
5	Era I – Cultured Microbes Microbial Diversity	Parfrey et al.	Why use rRNA vs. other genes? Consider issue of more taxa vs. more data Why use multiple phylogenetic methods?	L5
6	Era II – Uncultured Microbes GPA, rRNA sequencing	Lane et al. Stahl et al. Review: Pace 2009	What do you do when you can’t grow an organism in the lab? How to sequence from environmental samples?	L6
7	Era II – Uncultured Microbes PCR, phylogenetic diversity	Weisburg et al. Hugenholtz et al.	Sequencing RNA vs. DNA Why use one vs. other? What is PCR? Diversity of life vs. diversity of cultured life	L7
8	Era II – Uncultured Microbes rRNA ecology	Hughes et al; Lozupone & Knight	How to use sequence to measure diversity Different aspects of diversity (alpha, beta) and different metrics (taxonomic, phylogenetic)	L8
9	Era II – Uncultured Microbes rRNA Case Study	Earth Microbiome Project	Cataloguing biodiversity via sequencing Big data analytics	L9
10	Era III – Genome sequencing	Fleischmann	How random sequencing can be better and cheaper than targeted sequencing Genome assembly and annotation	L10
11	Era III – Genomes Assembly, Structural Annotation	Tatusova et al	How to assemble and structurally annotate a genome	L11
12	Era III – Genomes Functional Annotation	A Genomic Perspective on Protein Families	How to functionally annotate a genome	L12
13	Era III – Genomes Phylogenomics and Comparative Genomics	Tettelin et al. Pangenome paper ”	Comparative genomics	L13
14	Era IV – Metagenomics Large insert	Beja et al. #1 Beja et al. #2	Introduction to metagenomics – large inserts	L14
15	Era IV – Metagenomics Shotgun metagenomics	Venter et al Review: Quince et al	Introduction to metagenomics – shotgun	L15a L15b
16	Era IV – Metagenomic Functional Predictions	Langille et al. PICRUSt	Functional prediction from metagenomic data	L16
17	Era IV – Metagenomic Case Study	Park et al’s ” 8,000 MAGs”	How far can we go with metagenomics? MAGs – the good and the bad	L17
18	Revisiting Class #1	Hug et al.	Back to Day 1 – how much have we learned?	L18
19	Presentations
20	Presentations

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