Developing various computational techniques for the detection and characterization of mobile genetic element insertions in breast cancer using next-generation sequencing (NGS) data.

Analysis of repeat elements, genome assembly, gene annotation and analysis of transcriptomic data in conifers.

Carrying out statistical analysis of cancer mutations found in the p53 gene in humans to ensure reproducibility of data generated in wet-lab. Carry out detailed analysis using the R statistical language to gain new insights into p53 mutations.

My project constitutes study of Chromatic acclimation (CA) in a newly discovered cyanobacteria isolated from Heron Island, Australia. Chromatic acclimation is a phenomenon in which a cyanobacteria can change the expression of light harvesting proteins according to the light its exposed to so as to harvest enough light for photosynthesis. One critical problem that lay in studying this phenomenon in this new organism was the genome of this cyanobacteria was not known. Therefore sequencing the genome and annotating it was a prerequisite before doing any structural studies. However, since this cyanobacteria was obtained directly from nature it had strong interactions with other bacterial species which prevented us from obtaining axenic cultures (pure cyanobacteria cell cultures) for sequencing. Therefore, the unaxenic cultures were sequenced using an Illumina Sequencer. The raw data was assembled using the de-novo assembler Abyss. The cyanobacterial scaffolds were separated from those of other bacteria by constructing a BLAST algorithm using Python which had a positive hit to a gene belonging to a closely related cyanobacteria. These selected scaffolds were further analyzed by tetranucleotide frequency and GC analysis to yield only the cyanobacterial scaffolds. The annotation of the genome was done using the "NCBI prokaryotic annotation pipeline" and also by comparing the gene sequence homology with other known genes. Following the genome annotation, I have determined the protein structure of two of the light harvesting proteins, phycoerythrin and phycocyanin to a resolution of 2 Angstroms using X-ray crystallography.