Home/Syllabus

Schedule/Notes

Readings

Topics

Labs

Readings (and videos)

• Week 1
  
  • Chapter 1 (The Nucleic Acid World)
    
  • Chapter 2 (Protein Structure)
    
  • [Primer] Molecular biology primer
    
  • [Opinion] The real cost of sequencing: higher than you think! (2011)
    
  • [Paper] Biology: The big challenges of big data (2013)
    
• Week 2
  
  • Chapter 1: Where in the Genome Does DNA Replication Begin? (the first video)
• Week 3
  
  • [Paper] Compressive genomics (2012)
• Week 4
  
  • [Paper] Fast and sensitive protein alignment using DIAMOND (2015)
• Week 5
  
  • Chapter 7 (Revealing Evolutionary History)
  • Chapter 8 (Building Phylogenetic Trees)
  • [Paper] Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote (2013)
• Week 6
  
  • [Blog] Not so fast, FastTree (the Darling lab)
  • [Web-site] Next-Gen Sequencing 2014 Update
  • [Paper] A first look at the Oxford Nanopore MinION sequencer
  • [Web-site] Your genes can now be sequenced using your USB port
• Week 7
  
  • [Video] Richard Resnick: Welcome to the genomic revolution
  • [Primer] How to apply de Bruijn graphs to genome assembly
  • [Paper] Why We Should Not Use the Affordable Care Act to Encourage Widespread Whole Genome Sequencing
  • [Paper] Next-generation sequencing in the clinic: are we ready?
  • [Paper] Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm (NAR 2014)
• Week 8
  
  • [Paper] Basic statistical analysis in genetic case-control studies
• Week 9
  
  • [Paper] Extracting patterns of database and software usage from the bioinformatics literature
• Week 10
  
  • [Paper] Human symptoms–disease network [2014]
• Week 11
  
  • [Paper] Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs
  • [Paper] Origins and Mechanisms of miRNAs and siRNAs
• Week 12
  
  • [Paper] Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
• Week 13
  
  • [Paper] Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters
  • [Paper] Crystal structure of the CRISPR RNA–guided surveillance complex from Escherichia coli
• Week 14
  
• Week 15
  
  • [Paper] Global analysis of protein structural changes in complex proteomes