BNFO 602: Foundations of bioinformatics II
Spring 2013

Instructor:
Usman Roshan, GITC 3802
Ph: 973-596-2872
Office hours: Wed and Fri 1 to 2:30 and by appointment
Email: usman@cs.njit.edu

Course overview: We will cover sequence alignment, genome alignment, genome-wide association studies, phylogenetics, 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 12th 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
• Introduction to Machine Learning by Ethem Alpaydin

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:
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Topic	Date	Lectures
Introduction and GWAS	01/22/13	Basic bio background GWAS (pdf) Programming and system Perl Basic Unix command sheet Instructions for AFS login
Phylogenetics	01/29/13	Phylogenetics I Phylogenetics II
Quiz 1, phylogenetics (ML), and sequence alignment	02/05/13	Phylogenetics (ML) Pairwise sequence alignment Multiple sequence alignment
Quiz 2, GWAS II	02/12/13	GWAS II
Quiz 3 and project proposals	02/19/13
Project proposals, basic classification, and logistic regression	02/26/13	Model trees for students with projects in phylogenetics African Eve tree from Maddison et. al. Systematic Zoology, 41:111-124, 1992 Chloroplast rbcL gene tree from Rice et. al., Systematic Biology, 1997
Bayesian classification	03/05/13	GWAS III
Kernel nearest means	03/12/13	Kernel nearest means classifier
Spring break	03/19/13
Kernel nearest means, support vector machines	03/26/13	SVMs and kernels Programming assignment #1 Nearest neighbor to be completed as part of above assignment
Risk prediction with kernels, ranking SNPs, regularized risk minimization	04/02/13	Slides A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets Regularized risk minimization slides Programming assignment #2 assignment2.pl BMRM training config file BMRM test config file
Dimensionality reduction	04/09/13	Risk prediction experimental results Dimensionality reduction slides
Project presentations	04/16/13	(1) Molly, (2) Junfie and Megnan, and (3) Akhila and Renuka
Project presentations	04/23/13	(1) Chao, (2) Ellen, (3) Amiel
Project presentations	04/30/13	(1) Indrajit, (2) Ron, (3) Likhita and Sri-Keerthi, (4) Paul