BNFO 602: Foundations of bioinformatics II
Spring 2010

Instructor:
Usman Roshan, GITC 3802
Ph: 973-596-2872
Office hours: Tue 4-5 and Fri 4-5
Email: usman@cs.njit.edu

Grading:

• Five short quizzes spread through the semester and completed before presentation of course projects.
• 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 mid February 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	01/22/10	Basic bio background Alignment Alignment notes I Alignment notes II
Alignment	01/29/10	Alignment
Genome-wide association studies (GWAS) I	02/05/10	GWAS
GWAS II	02/12/10	GWAS II
Phylogenetics	02/19/10	Phylogenetics
Class cancelled due to storm	02/26/10
Project proposal presentations	03/05/10
Phylogenetics	03/12/10	Phylogenetics II
Spring break	03/19/10
Phylogenetic motifs and classification	03/26/10	Phylogenetic motifs Classification
Good Friday	04/02/10
Support vector machines, expected accuracy alignment, and project work	04/09/10	Support vector machines and disease risk prediction
Short read alignment	04/16/10	Project presentation: (BFAST) Rohini, Mohit, and Joanne
Expected accuracy alignment	04/23/10	Expected accuracy alignment Project presentations: Madhu, Jay, and Swanith
Project presentations	04/25/10	Expected accuracy alignment Project presentations: Maria, Seif, Arpit and Krupa, and Sujith and Hafeejullah
Risk prediction	05/04/10	Papers on risk and phenotype prediction: Support vector machine vs logistic regression on type 1 diabetes Pathways for risk prediction<\li> Risk prediction on WTCCC data Predicting Unobserved Phenotypes for Complex Traits from Whole-Genome SNP Data Interpretation of Genetic Association Studies: Markers with Replicated Highly Significant Odds Ratios May Be Poor Classifiers Evaluation of risk prediction updates from commercial genome-wide scans Beyond odds ratios Genotype Score in Addition to Common Risk Factors for Prediction of Type 2 Diabetes Multi-SNP pharmacogenomic classifier is superior to single-SNP models for predicting drug outcome in complex diseases Prediction of individual genetic risk to disease from genome-wide association studies Prediction of Coronary Heart Disease Risk using a Genetic Risk Score: The Atherosclerosis Risk in Communities Study Gauging the Performance of SNPs, Biomarkers, and Clinical Factors for Predicting Risk of Breast Cancer Polygenes, Risk Prediction, and Targeted Prevention of Breast Cancer Genetic risk prediction: are we there yet? Genome-based prediction of common diseases: advances and prospects
Project presentations	05/07/10	Project presentations: Meera, Susan, Yanzhao, Drew, Sai Teja, Devarshi, Pragya and Paritra, Raghavendra, and Naga
Final project deadline (no exceptions under any condition)	05/14/10