BNFO 602: Foundations of bioinformatics II
Spring 2012

Instructor:
Usman Roshan, GITC 3802
Ph: 973-596-2872
Office hours: Mon and Wed 1 to 3, Tue 4 to 5:30
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 14th 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:
   

Topic	Date	Lectures
Introduction and GWAS	01/17/12	Basic bio background GWAS Programming and system Perl Basic Unix command sheet Instructions for AFS login
Phylogenetics - distance based methods	01/24/12	Phylogenetics I
Quiz I, Phylogenetics - character based methods	01/31/12	Phylogenetics II
Phylogenetics (ML), Sequence alignment	02/07/12	Phylogenetics (ML) Pairwise sequence alignment Multiple sequence alignment
Quiz II, GWAS	02/14/12	GWAS II
Project Proposals and Bayesian classification	02/21/12	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	02/28/12	GWAS III
Support vector machines (SVMs) and kernels	03/06/12	SVMs and kernels
Spring break	03/13/12
Regularized risk minimization	03/20/12	Regularized risk minimization slides Programming assignment #2 assignment2.pl BMRM training config file BMRM test config file
Dimensionality reduction	03/27/12	Dimensionality reduction slides
Quiz III, Risk prediction with kernels and ranking SNPs	04/03/12	Slides
Project presentations	04/10/12	Palak and Alexander: Gene tree vs species tree Jharna, Hajira, and Harishita: Accuracy and speed of short read mapping programs Bharati: Cancer risk prediction through GWAS
Project presentations	04/17/12	Programming assignment #3 Yumeng and Xiao: multivariate and univariate SNP selection in GWAS Yuanpeng: Population structure identification Vinay and Sridevi: Phylogeny reconstruction on simulated data Lamine: Bayesian vs ML phylogeny reconstruction Karthik and Utsav: Univariate tests for GWAS
Project presentations	04/24/12