BNFO 602: Foundations of bioinformatics II
Spring 2014

Instructor:
Usman Roshan, GITC 3802
Ph: 973-596-2872
Office hours: Tue and Fri 4 to 5:30 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 13th 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
Introduction and GWAS	01/23/14	Basic bio background Projects Programming and system Perl Basic Unix command sheet Instructions for AFS login
Phylogenetics	01/30/14	Phylogenetics I
Quiz 1, phylogenetics (MP and ML), and sequence alignment	02/06/14	Whole genome prokaryotic phylogeny Phylogenetics II Phylogenetics (ML) Pairwise sequence alignment Multiple sequence alignment GWAS
NJIT closed due to snow	02/13/14
Phylogenetics and alignment	02/20/14
Quiz 2 and project proposals	02/27/14	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
Basic classification	03/06/14	Linear algebra and probability background Bayesian learning
Quiz 3 and logistic regression	03/13/14	Logistic regression Programming assignment #1 Nearest neighbor to be completed as part of above assignment Balanced error
Spring break	03/20/14
Support vector machines	03/27/14	Support vector machines Perl script for balanced error
Kernel methods and regularized risk minimization	04/03/14	Kernel nearest means SVM light software (SVMlight code) Perl script to obtain top k SNPs Perl script to convert to SVM light format Logistic regression program Logistic regression source code (uses GNU Scientific Library) How to run the logistic regression program Predict labels with logistic regression Regularized risk minimization bmrm.pl BMRM training config file BMRM test config file
Dimensionality reduction, feature selection, and clustering	04/10/14	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 Dimensionality reduction Dimensionality reduction II Clustering
Project presentations	04/17/14	Nihir, Abdulrahman and Weiting
Project presentations	04/24/14	Nidhi and Manan, Das, Lydia, Raj
Project presentations	05/01/14	Nandini, Osman, Hasan and Ranganathan, Ana and Srivika