Nikleotide!

Research

(in brief…)

  • Currently I am a cancer genomics post-doctoral research fellow at human genetics department, McGill University. Here, I study cancer genomes, more specifically, I study the somatic variations causing cancer, its progression, and evolution. I work on two separate projects. One of them which is a big consortia and several groups from different universities are involved in and is called iCHANGE is evolved around paediatric glioblastoma cancer (kid’s brain cancer). The other one which is more my own project, is on developing a framework to study the evolution of the cancer tumors.
  • I did another post-doctorate at Biodiversity Institute of Ontario (BIO) located at University of Guelph. At BIO, I was responsible of developing new methods for next generation sequencing data analysis (for both 454 Roche platform as well as Illumina MiSeq), along with improving the current methods. I also developed a pipeline for a better, easier, and more straight forward analysis of the NGS data.
  • I did my PhD thesis on the “evolution of genome nucleotide content and structure” at Concordia University, under the supervision of distinguished professor Donal A. Hickey.
    The topic of my dissertation is: “The evolutionary ebb and flow of genomics nucleotide content”. For my research, I analyzed different model organisms’ genomic data: both nuclear and mitochondrial genome of two Plasmodium species; P. falciparum, P. vivax, as well as the mitochondrial genome of P. reichenowi, human, and chimpanzee in order to see the effect of mutation and selection on the evolution of these genomes. I also analyzed the nuclear genome of Honeybee and 12 species of genus Drosophila in my studies. In my project the main interest was to understand the effects of different evolutionary forces (e.g. mutation bias, selection, etc.) on the structure and composition of the genome of mentioned species. Specifically understanding the key players behind the heterogeneity in genome nucleotide content has been the puzzles of my interest. I also studied the various effects this heterogeneity might have on different aspects of a species (such as transition/transversion ratio, protein content, codon usage, etc.). Two papers are to be submitted soon based on the results of my research. Also as a part of my project I had been developing a Java package simulating the interplay between background selection, selective sweep and recombination and their effect on the heterogeneity of the genome composition and structure (I have put this project on hold for the time being).
    WES based CNV detection

  • For the first year of my PhD, I worked on developing an XML based database and search engine for DNA barcode sequences (available at http://www.dnabarcodelinker.com). A paper is being published based on this research in Molecular Ecology Resources Journal in 2010 (at the time I send this email, this search engine and the machines are being moved to Ontario’s Biodiversity Center located in Guelph University).
  • I did my masters in (Bioinformatics/Cell and Molecular Biology) specifically on protein secondary structure. During my masters time I developed a database for secondary structure of proteins using relational database.
  • After my masters time, I had a two years collaboration with computer engineering department at Tehran University working on improving the accuracy of protein secondary structure prediction methods using classifier
    fusion approaches. Our efforts led to a 2% improvement in accuracy comparing the best currently existing methods. The achievements of this research  led to a five publications in Bioinformatics and  Computer science journals.
  • I have a bachelor in Cell and Molecular Biology (specialty in Microbiology).