Learning resources for bacterial genomics

This section is very much under development, but will eventually be home to lots of resources for learning about bacterial genomics…including primers for people getting started in biology, bioinformatics or sequencing…as well as specific resources in bacterial genomics, phylogenetics, molecular evolution and related topics.

Getting started

Primers in biology for computer scientists, bioinformatics for life scientists, and next gen sequencing for everybody

Bacterial genomics

• See this post of mine about bacterial populations and bacterial communities, and some of my work in this area

• Population structure, species concepts, horizontal transfer, homologous recombination
  • The pan-genome
  • Species concept
• Microevolution, subtyping, phylogeography
  • Towards the use of genomics to study microevolutionary change in bacteria
• Bacterial communities and metagenomics
  • Metagenomics primer

Methods

• Phylogenetics
  • Phylogeny for the faint of heart (Sandra Baldauf, 2003, Trends in Genetics)
  • Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods (Aris-Brosou & Xia, 2008, Int J Plant Genomics)
  • Phylogenetics course @ Berkeley
  • Article on phylogenomics (Philippe et al, 2011, PLoS Biology). Includes an explanation of phylogenomics, and glossary of terms relating to phylogenetics & phylogenomics.
  • 2011 Bodega workshop – Phylogenetics wiki. Lecture slides and tutorials from a workshop in March 2011. Covers software packages like MrBayes, RAxML, R, BEAST, BayesTraits and topics including model selection, divergence dating, discrete & continuous character evolution, diversification rates.
  • PLoS Currents – Tree of Life
  • Phyloseminar.Org – online seminars in phylogenetics!
    
    

Useful sources of information

• Databases: NCBI, EBI
• Forums: SEQanswers, BioStar
• Talks: SlideShare – Jon Eisen
• Bioinformatics (journal) – Next gen sequencing virtual issue
• Briefings in Bioinformatics (journal) – Second generation sequencing issue (Sep 2010)
• PLoS:
  • Ten Simple Rules – series of articles with tips for grad students, getting published, presenting
  • Genomics of Emerging Infectious Disease (PLoS Collections)
• NCBI Bookshelfof online books, e.g.:
  • Comparative Genomics: Sequence – Evolution – Function
  • Medical Microbiology
  • Genomes (note, published in 2002 i.e. pre-NGS and many of the more recent genomes, but still a good source for the basics)
  • Intro to genetic analysis (not browsable)