CH391L

Lectures & Handouts

April 5, 2011 - Classification

• The best open software for do-it-yourself data mining: Weka
• Mahalanobis
• SVD of gene expression 1, 2
• European men, their genomes, and their geography

Mar 31, 2011 - Clustering & Classification

• AML vs ALL
• Diffuse large B cell lymphoma redux

Mar 29, 2011 - Clustering 2

• Fuzzy k-means
• SOM gene expression
  • & links to various applications of SOMs: 1, 2, 3, 4, and a picture of Teuvo himself

An assortment of datasets for Problem Set 4, due Apr. 12, 2011

• Yeast protein sequences
• Yeast protein phylogenetic profiles
• Yeast mRNA expression profiles
• For simplicity, here are the summary files (edited slightly, showing total read counts, counts of reads where F3 and F5 map to the same organism, counts of F3 and counts of F5 reads) of all of the searches on the 5 environmental samples:
  • V3BC21
  • V3BC22
  • V3BC23
  • V3BC24
  • V3BC25
  • & A link to the raw data

Mar 24, 2011 - Clustering

• News of the day: multiple myeloma cancer genomes
• Phylogenetic profiles
• Review of phylogenetic profiles
• Example phylo profiles from Neurospora
• B cell lymphomas
• Primer on clustering
• K-means example (.ppt)

Mar 22, 2011 - Gene expression

• Gene expression by ESTs
• Gene expression by SAGE
• Affy microarrays 1
• Affy microarrays 2
• cDNA microarrays
• Clustering by gene expression
• Cell cycle data
• Clustering

Mar 8, 2011 - Assembling genomes + next-gen sequencing

• NextGen sequencing general review
• NextGen sequencing analysis review
• Mapping primer

• We're running a bit behind on our next-gen sequencing datasets, which were intended for Problem Set 3. I'll plan to add these data to Problem Set 4. Instead, for Problem Set 3, I'll give credit for turning in one (full) paragraph laying out your planned work for your final course project. The deadline will be extended to March 10. (Turn them in by email. Remember, no class on the 10th.)
• Here are a few examples of final projects from previous years: 1, 2, 3, 4, 5

Mar 3, 2011 - Assembling genomes

• Due March 8 by email - One paragraph describing your plans for a final project
• Fly - the genome
• Fly - the genome assembly
• GigAssembler

Mar 1, 2011 - Assembling genomes

• Next-gen sequencing news from the latest Science
• Prenatal screening by sequencing
• The H. influenzae genome paper
• BACs, YACs, and cosmids, oh my!

Feb 24, 2011 - Gene finding

• The GENSCAN paper
• Evaluating gene annotations: GASP, EGASP, & nGASP
• HW2.1
• T segment histogram

Feb 22, 2011 - HMMs and gene finding

• Fly cell Markov chains

Feb 17, 2011 - HMMs

• HMM primer
• Problem Set 2, due Feb. 24, 2011
• State sequences
• Soluble sequences
• Transmembrane sequences

Feb 15, 2011 - Profiles

• A commentary on computational challenges arising from DNA sequencing
• The remarkable growth of Genbank, and similarly, UniProt

Feb 10, 2011 - BLAST

• The original BLAST paper
• Teaching BLAST
• The protein homology graph paper. Just for fun, here's a link to a stylized version we exhibited in the engaging Design and the Elastic Mind show at New York's Museum of Modern Art.

Feb 8, 2011 - Sequence Alignment III

• A few examples of proteins with internally repetitive sequences: 1, 2, 3
• Repeats in the human genome, tallied here

Feb 3, 2011 - Sequence Alignment II

• An example of dynamic programming using Excel, created by Michael Hoffman (a former CH391L student; you can read more about Michael here)
• Dynamic programming primer

Jan 27, 2011 - Sequence Alignment I

• Taejoon's presentation file
• BLOSUM primer
• The original BLOSUM paper (hot off the presses from 1992!)

Jan 25, 2011 - Perl primer

• Problem Set 1, due Feb. 8, 2011
• E. coli genome
• T. volcanium genome (to a student who asked me about 'a strange character' in this file, I checked this file and found no strange 'character' in this file. -- Taejoon)
• 3 mystery genes (for Problem 5): Mgene1, Mgene2, Mgene3