BNFO 602: Foundations of bioinformatics II
Spring 2015

Instructor:
Usman Roshan, GITC 3802
Ph: 973-596-2872
Office hours: Tue and Thu 2:30 to 5 and by appointment
Email: usman@cs.njit.edu

Course overview: We will cover genome-wide association studies, phylogenetics, basic sequence alignment, short read mapping, and machine learning algorithms.

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 23rd and make sure to have it approved by your professor.

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
Snow day	01/26/15
Snow day	02/02/15
Introduction and GWAS	02/09/15	Basic bio background Projects Programming and system Perl Basic Unix command sheet Instructions for AFS login
Phylogenetics and quiz 1	02/16/15	Phylogenetics I Phylogenetics II Phylogenetics (ML)
Sequence alignment and GWAS	02/23/15	Pairwise sequence alignment Multiple sequence alignment GWAS
Basic classification and quiz 2	03/02/15	Linear algebra and probability background Bayesian learning 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
Quiz 3 and project proposals	03/09/15	Logistic regression Balanced error Software Logistic regression program Logistic regression source code (uses GNU Scientific Library) How to run the logistic regression program Predict labels with logistic regression Projects Dima: genome alignment Shijie, Sruti, and Kevin: case control prediction from GWAS data Edward and Ittehad: short read alignment Siddharth: univariate SNP ranking Pratyusha: phylogenetics
Quiz 4 and logistic regression	03/23/15	Data Training (labels) Validation (labels)
Support vector machines	03/30/15	Support vector machines Perl script for balanced error SVM light software (SVMlight code) Perl script to obtain top k SNPs Perl script to convert to SVM light format Risk prediction results
Feature selection	04/08/15	Feature selection A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets Feature selection with SVMs and F-score Ranking genomic causal variants with chi-square and SVM
Kernel methods and regularized risk minimization	04/13/15	Kernel nearest means Programming assignment 1 Nearest means in Perl (to be completed for assignment) Regularized risk minimization bmrm.pl BMRM training config file BMRM test config file
Dimensionality reduction	04/20/15	Dimensionality reduction Dimensionality reduction II
Quiz 5 and clustering	04/27/15	Clustering
Quiz 6 and project presentations	05/04/15	Pratyusha, Shijie, Sruti, and Kevin
Project presentations	05/06/15	Siddharth, Dima, Edward, and Ittehad