Class activities will be recorded here.

This page has the entire plan for the semester. For weeks in the future, consider it a plan subject to change. For weeks in the past consider it a record of what we have done. As for the current week, keep a watch for updates and changes.

Week 1 : August 19 - August 25
Week 2 : August 26 - September 1
Week 3 : September 2 - September 8
Week 4 : September 9 - September 15
Week 5 : September 16 - September 22
Week 6 : September 23 - September 29
  • Tuesday Project Proposal Presentations
    Project update: Project proposals due.
    Thursday Project Proposal Presentations Continued
Week 7 : September 30 - October 6
  • Tuesday Paper presentation: Marcelo: Short read fragment assembly of bacterial genomes
    Thursday Paper presentation: Manuel: Hapsember: an assembler for highly polymorphic genomes
    Presentation Grading
Week 8 : October 7 - October 13
  • Tuesday Paper presentation: Rene: LOCAS a low coverage assembly tool for resequencing projects.
    Thursday Paper presentation: Mark O.: Quake: quality-aware detection and correction of sequencing errors
Week 9 : October 14 - October 20
  • Tuesday Paper presentation: Waruna: SPAdes: a new genome assembly algorithm and its application to single-cell sequencing.
    Thursday Paper presentation: Satya: SEQuel: improving the accuracy of genome assemblies.
Week 10 : October 21 - October 27
  • Tuesday Paper presentation: Dave: Detection and characterization of novel sequence insertions using next generation sequencing.
    Thursday Paper presentation: Rich: Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing
Week 11 : October 28 - November 3
  • Tuesday Paper presentation: Jesse: The Genome Analysis Toolkit: a mapReduced framework for analyzing next-generation DNA sequencing data.
    Thursday Paper presentation: Zhisheng: De novo transcriptome assembly with ABySS.
Week 12 : November 4 - November 10
  • Tuesday Paper presentation: Indika: HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-seq data.
    Thursday Paper presentation: Majdi: Optimally discriminative subnetwork markers predict response to chemotherapy.
Week 13 : November 11 - November 17
  • Tuesday Paper presentation: Jorge: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoforms switching during cell differentiation.
    Thursday Paper presentation: Jennifer: Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.
Week 14 : November 18 - November 24
  • Tuesday Fall Recess: No Class
    Thursday Fall Recess: No Class
Week 15 : November 25 - December 1
Week 16 : December 2 - December 8
  • Tuesday Project Presentations
    Thursday Class Cancelled: Projects Due December 6th at noon.
    Project update: final projects due.