BNFO 601: Foundations of Bioinformatics I
Fall 2009

Instructor: Usman Roshan
Office: GITC 3802
Ph: 973-596-2872
Office hours: Monday 4-6pm and Friday 2-4pm
Email: usman@cs.njit.edu

Recommended Textbooks:

• An Introduction to Bioinformatics Algorithms by Pavel Pevzner
• Biological Sequence Analysis by Durbin et. al.
• Introduction to Bioinformatics by Arthur M. Lesk
• Beginning Perl for Bioinformatics by James Tisdall
• Introduction to Machine Learning by Ethem Alpaydin

Grading: 25% two mid-terms and 50% final exam

Course Overview: We will cover Perl programming, sequence alignment, and hidden Markov models (HMM). We will implement a pairwise sequence alignment program using dynamic programming and the Viterbi algorithm for HMM sequence alignment. We will also cover genome-wide association studies.

Course plan:

Topic	Date	Remarks
Pairwise sequence alignment	08/31/09	Slides Perl slides Basic Unix command sheet Instructions for AFS login
Perl basics	09/14/09
Pairwise sequence alignment in Perl; Subroutines and returning arrays and hashes	09/21/09	Slides Affine gaps Affine gaps (more notes)
Affine gaps, scoring matrices, local alignment and BLAST, alignment accuracy	09/28/09	Nature BLOSUM paper NAR MUSCLE paper BAliBASE 3.0 reference alignments Local alignment and BLAST Profile alignment
BLAST exercise	10/05/09
Hidden Markov models (HMMs)	10/12/09	Slides HMM notes from Ron Shamir's course
HMMs	10/19/09
HMMs	10/26/09
SNPs, population structure, and PCA	11/02/09	SNPs and population structure dentification PCA for population structure identification PCA correlated SNPs The International HapMap Project Additional alignment notes (I) (II)
PCA and k-means	11/09/09	K-means clustering
K-means clustering in Perl	11/16/09	PCA projection for HapMap Japanese Chinese dataset (all eigens) PCA projection for HapMap Japanese Chinese dataset (2 eigens)( PCA projection for Rosenberg's East Asian dataset (all eigens)( PCA projection for Rosenberg's East Asian dataset (4 eigens)( PCA projection for Rosenberg's Middle Eastern dataset (all eigens)( PCA projection for Rosenberg's Middle Eastern dataset (4 eigens)(
Mid-term solution and spherical k-means	11/30/09	Genome-wide association studies Extra credit assignment
Final exam	12/07/09	Second extra credit assignment