Week Name Description
File Syllabus
File Calendar
URL Bioinformatics Programming Using Python
URL Final Project Groups
22 January - 28 January File M01 Handout 00: Overview
File M01 Notes: Descriptive statistics
File M01 Presentation: Introduction
File M01 Handout 01: Probability
File Reading: Arumugam Nature 2011
File Problems 00: Pre-test
File Problems 01: Quantitative methods
File W01 Notes: Inference and machine learning
29 January - 4 February File M02 Notes: Introduction to Python (abbreviated)
File M02 Notes: Introduction to Python
File M02 Notes: Python primitives
File M02 Handout 02: Installing Python
File M02 Handout 03: Submitting Python problems
Page Reading: Bioinformatics Programming
File Reading: Dudley PLoS CB 2009
File Problems 02: Introduction to Python
File W02 Notes: Python primitives (abbreviated)
File W02 Notes: References
File Lab1 note
5 February - 11 February File M03 Notes: Functions and I/O (abbreviated)
File M03 Notes: Functions
Page Reading: Bioinformatics Programming
File Reading: Cock Bioinformatics 2009
File Problems 03: I/O and Regular Expressions
File W03 Notes: Modules and I/O (abbreviated)
File W03 Handout 04: I/O
Page Reading: Regular Expressions
File Lab 2 note
File Lab 2 examples
12 February - 18 February File M04 Notes: Regular Expressions
Page Reading: Bioinformatics Programming
File Reading: Jensen Nature 2006
File Problems 04: Regular Expressions, Downloads, and Data Stores
File W04 Notes: Network resources and data stores
File e.coli.pos
File e.coli.genome
Folder Lab 3
19 February - 25 February Page Reading: Testing, arguments, and command line tools
File Reading: Noble PLoS CB 2009
File Problems 05: Reproducible research
File Problems 05: Reproducible research (data)
File W05 Notes: Computational project management and tools
Folder Lab 4
26 February - 3 March File M06: Genomes and sequence alignment
File M06 Presentation: Genomic data resources
Page Reading: Bioinformatics and Functional Genomics
File Reading: Sela PNAS 2008
File W06 Notes: High-throughput sequencing
File W06 Presentation: High-throughput sequencing
File W06 Presentation: 454 sequencing
File W06 Presentation: Illumina sequencing
Page Reading: Bioinformatics and Functional Genomics
File Problems 06: Genomes and Sequencing
File Problems 06: Genomes and Sequencing (data)
4 March - 10 March File M07 Presentation: Sequence analysis
Page Reading: Bioinformatics and Functional Genomics
File Reading: Venter Science 2004
File W07 Presentation: Metagenomics
File Problems 07: Metagenomics
File Problems 07: Metagenomics (data)
File Problems 07: Solution
18 March - 24 March URL M08: Comparative Genomics
Page Reading: Bioinformatics and Functional Genomics
File Reading: Hughes 2000 Cell
File Problems 08: Comparative Genomics and Microarrays
File Problems 08: Comparative Genomics and Microarrays (data)
File W08: Microarrays Data (Aedin)
File W08: Microarrays Analysis (Aedin)
25 March - 31 March File M09 Presentation: Transcriptional Regulation
Page Reading: Regulation and Epigenetics
File Reading: ENCODE PLoS Biology 2011
File W09 Presentation: Epigenetics
File Problems 09: Regulation and Epigenetics
1 April - 7 April File M11 Presentation: Genetic Interactions
Page Reading: Genetic and Disease Interactions
File Reading: Costanzo Science 2010
File Problems X: Review
File W11: Epidemiology
File NGS Video
File Sampson 2011
8 April - 14 April File M11 Presentation: Proteins
Page Reading: Proteins and PPIs
File Reading: Mohan PLoS CB 2009
File W11 Presentation: Network Integration
File Problems 10: Network Integration
15 April - 21 April File Group 6: Liu Nature 2010
File Group 7: Chen Cell 2012
File Group 4: Novembre 2008 Nature
File Group 3: Taylor 2009 Nat Biotech
22 April - 28 April File Monday: Group 5: 2010 Nature
File Monday: Group 2: Gaudet 2010 PLoS Genet
File Monday: Group 8: DeLong 2006 Science
File Wednesday: Group 1: Looft 2012 PNAS
File Wednesday: Group 9: Subhajyoti and Michor 2011 Nat Str Mol Bio