BNFO 602: Foundations of bioinformatics II
Spring 2011

Instructor:
Usman Roshan, GITC 3802
Ph: 973-596-2872
Office hours: Tue and Thu 12 to 2
Email: usman@cs.njit.edu

Course overview: We will cover sequence alignment, genome-wide association studies, phylogenetics, phylogenetic motifs, classification, logistic regression, support vector machines, and recent papers in the field of bioinformatics.

Grading:

• Several short quizzes spread through the semester and completed before presentation of course projects. Quizzes are worth 50% and project 50%.
• Course project: This will be a programming/research project. The project can be an implementation of a newly published algorithm or experimental study of new and existing software. You are free to select on your own or from this list. Select a project by February 15th, which is the final deadeline, and make sure to have it approved by me.

Recommended texts:

• Introduction to Bioinformatics Algorithms by Neil C. Jones and Pavel A. Pevzner
• Introduction to Bioinformatics by Arthur Lesk
• Biological Sequence Analysis by Durbin et. al.
• Algorithms on strings, trees, and sequences: computer science and computational biology by Dan Gusfield

Bioinformatics journals:

• Bioinformatics (Oxford press)
• BMC Bioinformatics (Biomed central; open access)
• PLoS Computational Biology (ISCB official journal; open access)
• More journals here

Bioinformatics conferences:

• Intelligent Systems for Molecular Biology (ISMB)
• Research in Computational Biology (RECOMB)
• Computational Systems Bioinformatics (CSB)
• Workshop on Algorithms in Bioinformatics (WABI)
• International Conference on Bioinformatics and Bioengineering (BIBE)

Course plan:
   

Topic	Date	Lectures
Introduction	01/18/11	Basic bio background Alignment Alignment notes I Alignment notes II Perl Basic Unix command sheet Instructions for AFS login
Class cancelled and will be rescheduled	01/25/11
Genome-wide association studies (GWAS) I	02/01/11	GWAS Risk prediction papers
Quiz, GWAS II, classification algorithms, and phylogenetics	02/08/11	GWAS II Phylogenetics
Project proposals, quiz, classification, and phylogenetics	02/15/11	GWAS II Phylogenetics
Proposals, Risk predictions, and maximum parsimony	02/22/11	GWAS III Phylogenetics II Model trees for students with projects in phylognetics African Eve tree from Maddison et. al. Systematic Zoology, 41:111-124, 1992 Chloroplast rbcL gene tree from Rice et. al., Systematic Biology, 1997
Phylogeny reconstruction - maximum parsimony and maximum likelihood	03/01/11
Bayesian classification	03/08/11	GWAS III
Spring break	03/15/11
Support vector machines (SVMs)	03/22/10	SVMs and disease risk prediction Slides by Martin Law, Michigan State University
Kernels and ranking SNPs with SVMs	03/29/11	Slides
Multiple sequence alignment, phylogenetic motif, and aligning reads to genomes	04/05/11	Mutiple sequence alignment Phylogenetic motifs BFAST: An Alignment Tool for Large Scale Genome Resequencing
Project presentations	04/12/11	Project presentations: Prediction of "Crohn's disease" disease risk Comparison of neighbor joining and UPGMA on simulated data
Project presentations	04/19/11	Project presentations MUGSY vs PECAN genome alignment Maximum likelihood vs neighbor joining tree reconstruction on simulated data
Project presentations	04/26/11	Project presentations SVM classification of sequence alignments Prediction of arthritis disease risk Weighbor vs FASTTREE tree reconstruction on simulated data Genome alignment ( Slides by Mark Craven) 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
Final quiz and submission of final project	05/10/11	Project presentations HMM vs Needleman-Wunschi sequence alignment Prediction of disease risk - seven WTCCC datasets