Deshan Perera
About Me
My name is Deshan Perera. I am currently a Ph.D. (specialization in Bioinformatics) Candidate in the Department of Biochemistry and Molecular Biology, Cumming School of Medicine at the University of Calgary, Canada. My main research focus is on within-host evolution and pathogen genomics. My areas of expertise lie in understanding evolutionary dynamics within organisms and developing high-performance computational solutions to analyze these problems.
My academic journey began with the completion of a Bachelor of Science (B.Sc. Hons) degree with a specialization in Biology from the Faculty of Applied Sciences at the University of Sri Jayewardenepura, Sri Lanka where I graduated with a First Class. During these four years, I trained in mainly wet lab sciences and explored the genetic and physiological factors of organisms. My undergraduate thesis explored the molecular cloning of the Cystatin C (CST3) protein from Oplegnathus fasciatus as well as an in-detail in-silico study of its protein-protein interactions and viability as a cysteine protease inhibitor via protein docking and gene-gene interaction mapping. I was supervised by Prof. Dinithi Peiris.
After the successful completion of my undergraduate studies, I shifted from wet-lab biology to dry-lab Bioinformatics for my Ph.D. My supervisor is Prof. Quan Long (Long Lab) and we investigate evolutionary dynamics experienced by organisms with focuses on pathogen genomics and neutrality.
Academic Publications
Google Scholar, ResearchGate, Semantic Scholar, Web of Science, ORCiD
Research Interests
My current goal is to explore the development of computational tools for solving genetic problems. Ideally, I design and develop accelerated and scalable software solutions. A major drawback the expanding genetic data faces is the inability to process these vast repositories. Therefore, I wish to develop software solutions that are not only capable of rapid processing times via the use of parallel processing technologies such as the GPU, CPU, and SSD but also make these software resource efficient so that they can be scaled to adapt to the dataset being processed and the hardware resources at hand.
Expertise
My areas of expertise are from both dry lab (Ph.D. (Bioinformatics)) and wet lab (B.Sc. (Hons) Biology) sciences.
Dry Lab
Statistical population genetics
Evolution and selection
Genomic analysis such as:
Sequence Alignment,
Phylogenetics (BEAST, MEGA),
Variant Calling (GATK best practices).
Protein modeling and docking
C/C++ CUDA based low level programming solutions
Large scale parallel processing program designs (GPU, CPU, and SSD solutions)
JAVA, R, Python, and TensorFlow solutions
Wet Lab
Molecular cloning
DNA extraction
Recombinant DNA techniques
PCR (Polymerase Chain Reaction), Gel electrophoresis
Professional work experiences
Research Associate at the Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Canada.
Reviewer for article in Bioinformatics (2023)
Demonstrator at the Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Sri Lanka.
Research Scientist at the Industrial Technology Institute, Sri Lanka.
Affiliations
Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Canada.
Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Sri Lanka.
Scholarships and Awards
2024 Gordon H. Dixon Award for meritorious doctoral student in the Department of Biochemistry & Molecular Biology, University of Calgary, Canada.
2021, 2022 & 2023 Alberta Innovates Graduate Student Scholarship.
2021, 2024 Eyes High International Scholarship, University of Calgary, Canada.
2020, 2021, and 2024 Biochemistry and Molecular Biology First Author Award, University of Calgary, Canada.