October 27
Welcome! What is genomics? and molecular biology review
Daily Dozen
Readings
Notes
Genomics preview/overview
DNA/RNA structure
Transcription, translation
Chromosomes
Gene structure and numbers
New developments
Databases and journals of interest
Historic overview
October 29
Probability and algorithms
Daily Dozen
Readings
Notes
Definitions
Independent variables
Conditional probability
Bernoulli, Binomial, Hypergeometric, Uniform, Geometric, Poisson distributions
Bayes' theorem
Some common and useful algorithms: sort methods, search methods, time/space complexity
How to write pseudocode
November 3
Pairwise alignment
Daily Dozen
Readings
Notes
Dot-matrix
Dynamic programming
Needleman-Wunsch
Smith-Waterman
Global vs. local
November 5
Alignment scoring statistics and scoring matrices
Daily Dozen
Readings
Notes
PAM and BLOSUM
Expectation
Karlin-Altschul statistics
Heuristic pairwise alignment (BLAST, FASTA)
Daily Dozen
Readings
Notes
Basic algorithms
Gapped BLAST, PSI-BLAST
Meaning of BLAST scores
BLAT
November 12
Hidden Markov Models (HMMs)
Daily Dozen
Readings
Notes
Introduction
Forward, Backward, and Forward-Backward algorithms
November 17
Baum-Welch algorithm
GLIMMER
GENSCAN
Multiple alignment I
Daily Dozen
Readings
Notes
Basic principles
ClustalW algorithm
November 24
Multiple alignment II
Daily Dozen
Readings
Notes
MUSCLE algorithm
ProbCons algorithm
November 26
Thanksgiving break
enjoy!
December 1
Computational approaches to real-life data
Taught by Loris Mularoni
Daily Dozen
Readings
Notes
Python
Unix introduction
Common tools: BLAST, Bowtie
Phylogenetic trees
Daily Dozen
Readings
Notes
UPGMA
Neighbor-joining
December 8
Phylogenetic trees
Daily Dozen
Readings
Notes
Parsimony likelihood approach
Comparison of methods
December 10
Applications to microarrays and high-throughput sequencing
Daily Dozen
Readings
Notes
Multiple alignment in shotgun sequencing
Sequencing methods
Handling sequencing data, tools
December 15
Alignment-free sequence comparison and network analysis
Daily Dozen
Readings
Notes
Sequence comparison, complexity
Systems biology concepts
December 17
Features of RNA secondary structure
Sequence covariation and mutual information
miRNA sequencing
December 22
Transposons and other strange sequences
Daily Dozen
Readings
Notes
Finding transposons in sequencing and microarray data: why and how
Repetitive sequence
Complexity/composition variations