BNFO 601: Foundations of Bioinformatics I
Fall 2011

Instructor: Usman Roshan
Office: GITC 3802
Ph: 973-596-2872
Office hours: T 3-5pm and Fri 12-2pm
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 exams, 35% final exam, 15% three projects

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	Notes
Pairwise sequence alignment and scoring matrices	09/12/11	Slides Nature BLOSUM paper Pairwise alignment notes (Roshan '05)
Perl basics and pairwise sequence alignment in Perl	09/19/11	Perl slides Basic Unix command sheet Instructions for AFS login
Optimal sequence alignment in Perl and alignment accuracy	09/26/11	How to compute the alignment accuracy Alignment notes from Ron Shamir's course at Univ. of Tel Aviv Global alignment
Affine gaps and parameter selection by cross-validation	10/03/11	Parameter selection by cross-validation PREFAB pairwise alignments Train datasets Test datasets Simple substitution score matrix BLOSUM 62 matrix Alignment notes from Ron Shamir's course at Univ. of Tel Aviv Affine gaps Programming assignment Affine gap alignment
Local alignment, BLAST, and review for exam	10/10/11	Local alignment and BLAST Alignment accuracy script
First exam	10/17/11
Exam solution and cross-validation	10/24/11
Profile alignment, multiple sequence alignment, and BLAST exercise	10/31/11	Train and test data for assignment Random Alexander (test) Bharati (test) Christophe (test) Erode (test) Hajira (test) Jharna (test) Karthik (test) Lamine (test) Louis (test) Lydia (test) Meghana (test) Palak (test) Pavan (test) Rana (test) Sadhana (test) Senthamarai (test) Sinan (test) Sridevi (test) Srividya (test) Surekha (test) Utsav (test) Vinay (test) Xiajon (test) Xiao (test) Yumeng (test) Yuneet (test) Yuanpeng (test) Hands-on bioinformatics exercise Profile alignment Multiple and local alignment notes (Roshan '05) Comparison of multiple alignment programs
Short read alignment and hidden Markov models	11/07/11	Short read alignment: Slides Papers on short read alignment: BFAST: An Alignment Tool for Large Scale Genome Resequencing Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads Fine-scale structural variation of the human genome Mapping and sequencing of structural variation from eight human genomes Detecting structural variations in the human genome using next generation sequencing How to map billions of short reads onto genomes hidden Markov models: HMM slides HMM notes by Ron Shamir
Hidden Markov models	11/14/11	Split function in Perl and using BLOSUM matrix for alignment Programming assignment 3 Chromosome 22 Reads of divergence .01 Reads of divergence .05 Reads of divergence .1 Reads of divergence .15 Reads of divergence .2 Reads of divergence .25 HMM slides HMM notes by Ron Shamir What is the expected maximization algorithm
Sequence alignment HMM	11/21/11	HMM slides
Exam 2	11/28/11
Exam 2 solution and HMMs	12/05/12	Programming assignment #2 (redo)
Review and GWAS	12/12/11
Final exam	12/19/11	GITC 2315C 6-8:30