BNFO 602: Foundations of bioinformatics II
Spring 2009

Instructor:
Usman Roshan, GITC 3802
Ph: 973-596-2872
Office hours: Thu 3-5:30
Email: usman@cs.njit.edu

Grading: Course project. This will be a programming/research project with three class presentations. The project must be approved by the instructor in advance. The deadline for project approval is Feb 5th. The first presentation is the project proposal (5-10 mins); the second is background and details of the experimental methodology and algorithms involved (45-60 mins); and the last one is the results of the project (30 mins). The project can be an implementation of a newly published algorithm or experimental study of new and existing software.

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	01/22/09	Introduction Basic bio background Bioinformatics problems I Bioinformatics problems II
Proposal presentations	02/05/09
GWAS	02/12/09	GWAS
Population structure identification and phylogeny reconstruction	02/19/09	Population structure identification Phylogeny reconstruction Reading assignment: Principal component analysis (Alpaydin 2004, Chapter 6)
Project paper presentations	02/26/09	Paras: improved PSI-BLAST Raghav: SNP detection
Project paper presentations	03/05/09	Hareesh, Manoj, Aditya, Harish, and Anusha: sequence database with utilities Reading assignment: Introduction to machine learning (Alpaydin 2004, Chapter 1) Reading assignment: Risk and loss functions (Scholkopf and Smola, 2002, Chapter 3)
Project paper presentations	03/12/09	Ankur and Greg: combining multiple gene trees vs. one tree on concatenated sequences Shefali: multiple gene order alignment
Spring break	03/19/09
Project paper presentations	03/26/09	Ozkur: phylogenetic motifs Praveen and Soundarya: gene expression clustering Anurag: transcription factor families
Project paper presentations	04/02/09	Abraham: micro-RNA identification Young-Jae: genome sequencing Anoop: effect of guide-tree on sequence alignment
Project paper presentations	04/09/09	Niraj: PCA for population structure prediction Krisha and Anirudh: finding SNPs associated with disease by text mining Sampath, Vishnu, and Varun: gene set enrichment analysis Aparna: Max-rank statistic for ranking SNPs
Project paper presentations	04/16/09	Wasay, and Hajira: Odds-ratios and chi-square for SNP selection Deepika and Lalitha: Phylogeny of primates Mitul: Contact-based sequence alignment Yiyi: Identification of micro-RNA by SVM and random forests Paras (final presentation): SIB-BLAST vs PSI-BLAST on yeast benchmark Raghav (final presentation): Comparison of SNP detection programs
Final presentations	04/23/09	Anirudh and Krishna Jayanth (final presentation): Text mining for disease associated genes and SNPs Ankur and Greg (final presentation): Combining multiple gene trees vs. one tree on concatenated sequences Shefali (final presentation): Gene order alignment Deepika and Lalitha (final presentation): Primate phylogeny from RNA sequences Wasay (final presentation): SNP selection from GWAS Sampath, Vishnu, and Varun (final presentation) : Gene set enrichment analysis Mitul (final talk): Contact based sequence alignment Abraham (final talk): Micro-RNA identification
Final presentations	04/30/09	Hareesh et. al. (final presentation): Sequence analysis database Soundraya et. al. (final presentation): Gene expression clustering Ozgur (final presentation): Phylogenetic motifs Young-Jae (final presentation): Wasp genome assembly Niraj (final presentation): PCA for population structure Anurag (final talk): Transcription factor families Aparna and Hajira (final presentation): SNP selection from GWAS
Final reports due	05/07/09