Mohammad Shabbir Hasan

Ph.D. Student, Computer Science, Virgina Tech



Research Interest

My research interest mostly includes Next Generation Sequencing, Evolutionary Genomics, Bioinformatics, and Computational Biology. Previously I was involved in Software Engineering and Web Application research projects as well.

Currently I am working in the Computational Biology and Bioinformatics Lab at Virginia Tech. I am working with Prof. Liqing Zhang on calling InDels from Next Generation Sequence (NGS) data. Studies showed that Insertion and Deletions(InDels) of base pairs in the DNA sequence of human may cause changes in gene functions which lead to diseases like schizophrenia, autism, mental retardation and cancers. Moreover, indels also change gene expression and can be used as genetic markers in natural populations. Our goal is to develop efficient algorithms to determine the inserted/deleted regions in DNA sequences from NGS data.

During my Masters at The University of Akron, I worked with Prof. Zhong-Hui Duan on Investigating gene-gene relations in microarray data using clustering algorithms. There we developed a new clustering algorithm which combines hierarchical clustering and k-means clustering.

I also worked with Prof. Dongsheng Che to predict Genomic Island in bacterial genomes. I am the developer of EGID - an ensemble algorithm to predict genomic islands in genomic sequences which performs 12.14% better than the prevoius best method.

Previously, during my undergrad studies, I also explored my research activities while working with Prof. K.M. Azharul Hasan of Department of Computer Science and Engineering, Khulna University of Engineering and Technology (KUET) to find out a mechanism for reducing development cost to make an object oriented system more reusable.

You can find more detail about some of the projects here.

Recent Projects

1. UPS-indel: Universal Positioning System for indels.
2. P-Dindel: A p-thread based tool for calling indels from short reads.
3. SPAI: Single Platform for Analyzing Indels.
4. Performance evaluation of indel calling tools using real short-read data.

Past Projects

1. Investigating gene-gene relationships in microarray expression.
2. EGID: An ensemble algorithm for genomic island detection.
3. GIST: Genomic Island Suite of Tools.
4. A Trustworthy Online Based Voting System.
5. A Methodology for Reducing Development Cost to Make an Object Oriented System More Reusable.

Copyright © 2011- Mohammad Shabbir Hasan. All rights reserved.