Week Name Description
File Syllabus
File Calendar
URL Bioinformatics Programming Using Python
URL Final Project Groups
27 January - 2 February File M01 Handout 00: Overview
File M01 Notes: Descriptive statistics
File M01 Presentation: Introduction
File M01 Handout 01: Probability
File Reading: Arumugam Nature 2011
URL Reading: Understanding ANOVA Visually
File Problems 00: Pre-test
File Problems 01: Quantitative methods
File W01 Notes: Inference and hypothesis testing
3 February - 9 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
10 February - 16 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
17 February - 23 February File W04 Notes: Regular Expressions
Page Reading: Bioinformatics Programming
File Reading: Jensen Nature 2006
File Problems 04: Regular Expressions and Data Stores
File e.coli.pos
File e.coli.genome
Folder Lab 3
24 February - 2 March File M05 Notes: Data handling and command environments
File Reading: Noble PLoS CB 2009
File Problems 05: Reproducible research
File Problems 05: Reproducible research (data)
File W05 Notes: Computational experiments
Page Reading: Testing, arguments, and command line tools
3 March - 9 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)
File Problems 06: Genomes and Sequencing (MacOS samtools)
File Problems 06: Genomes and Sequencing (32-bit MacOS samtools)
10 March - 16 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: Metagenomics (32-bit MacOS mothur)
24 March - 30 March File M08: Microarray Data
Page Reading: Bioinformatics and Functional Genomics
File Reading: Hughes 2000 Cell
File W08: Microarray Analysis
File Problems 08: Microarrays
File Problems 08: Microarrays (data)
31 March - 6 April File M09 Presentation: Epigenetics (Shirley Liu)
File M09 Presentation: Epigenetics
Page Reading: Regulation and Epigenetics
File Reading: ENCODE PLoS Biology 2011
URL W09: Comparative Genomics
File Problems 09: Comparative Genomics
File Problems 09: Comparative Genomics (data)
7 April - 13 April File M10 Presentation: Transcriptional Regulation
File M10 Notes: Journal club and final projects
File Reading: Costanzo Science 2010
File M11 Presentation: Genetic Interactions
Page Reading: Genetic and Disease Interactions
File Problems 09: Transcriptional Regulation
14 April - 20 April File M11 Presentation: Biological Network Analysis
File Reading: Mohan PLoS CB 2009
Page Reading: Proteins and PPIs
File W11 Presentation: Proteins and PPIs
File Problems 10: Biological Network Analysis
21 April - 27 April File Monday: Group1 Cell 2009
File Monday: Group2 Science 2011
File Wednesday: Group3 Nature Genetics 2013
File Wednesday: Group4 Nature Biotech 2010
28 April - 4 May File Monday: Group 5 Intratumor NEJM
URL Wednesday: Group 6 GemSIM, BMC
File Wednesday: Group 7 Enterotypes, Nature