Candidate, Doctor of Philosophy, Specialization in Bioinformatics

Cumming School of Medicine, University of Calgary, Canada.

GPA: 3.967/4.00

Areas of interest: Within host evolution, Pathogen genomics

Bachelor of Science, First Class (Special) in Biology

Faculty of Applied Sciences, University of Sri Jayewardepura, Sri Lanka.

GPA: 3.72/4.00

SLQF Level: 6

Thesis: In-silico analysis and molecular cloning of Cystatin C from Oplegnathus fasciatus (Temminck and Schlegel, 1844)

Professional qualifications

Research Associate 

(September 2019 - Present)

Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Canada.

Reviewer 

Bioinformatics (2023)

Demonstrator

(Dcemeber 2017 - August 2019)

Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Sri Lanka.

Research Scientist

(December 2016 - February 2017)

Industrial Technology Institute, Sri Lanka.

Published journal articles

FIRST author publications

Wang, D.*, Perera, D.*, He, J.*, Cao, C., Kossinna, P., Li, Q., Zhang, W., Guo, X., Platt, A., Wu, J. and Zhang, Q. (2023).

cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions.

PLoS genetics (IF = 5.917).

(* = Joint first author)

https://doi.org/10.1371/journal.pgen.1011074

Perera, D., Reisenhofer, E., Hussein, S., Higgins, E., Huber, C.D. and Long, Q. (2023).

CATE: A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data.

Methods in Ecology and Evolution (IF = 7.781)

https://doi.org/10.1111/2041-210X.14168

Perera, D., Perks, B., Potemkin, M., Gordon, P., Gill, J., Long, Q. ‡, van Marle, G. ‡ (2021).

Reconstructing SARS-CoV-2 infection dynamics through the phylogenetic inference of unsampled sources of infection.

PLOS One. (IF = 3.24)

https://doi.org/10.1371/journal.pone.0261422

(‡ = Joint corresponding authors)

Perera, D.‡, Perera, K. M. L., Peiris, L.D.C.‡ (2021).

A novel in silico benchmarked pipeline capable of complete protein analysis: a possible tool for potential drug discovery.

Biology, 10(11), 1113. (IF = 5.079)

https://doi.org/10.3390/biology10111113

(‡ = Joint corresponding author)

Dissanayake, D. M. I. H.*, Perera, D. D. B. D.*, Keerthirathna, L. R., Heendeniya, S., Anderson, R. J., Williams, D. E., & Peiris, L. D. C. (2020).

Antimicrobial activity of Plumbago indica and ligand screening of plumbagin against methicillin-resistant Staphylococcus aureus.

Journal of Biomolecular Structure and Dynamics. (IF = 4.150) https://doi.org/10.1080/07391102.2020.1846622

(* = Joint first author)

Mak, L.*, Perera, D.*, Lang, R., Kossinna, P., He, J., Gill, M. J., Long, Q. ‡, & van Marle, G. ‡ (2020).

Evaluation of a phylogenetic pipeline to examine transmission networks in a Canadian HIV cohort.

Microorganisms, 8(2), 196. (IF = 4.926)

https://doi.org/10.3390/microorganisms8020196

(* = Joint first author)

(‡ = Joint corresponding authors)

CO-author publications

Li, Q., Perera, D., Cao, C., He, J., Chen, X., Azeem, F., Howe, A., Au, B., Yan, J., & Long, Q. (2023).

Interaction-integrated linear mixed model reveals 3D-genetic basis underlying Autism.

Genomics (IF  = 4.31)

https://doi.org/10.1016/j.ygeno.2023.110575

Abeywardhana, S., Bandaranyake, U., Perera, D., Premathilaka, M., Peiris, L.D.C. (2022).

In silico study of SARS-CoV-2 Spike protein RBD and human ACE-2 affinity dynamics across variants and Omicron sub-variants.

Journal of Medical Virology (IF = 20.693)

https://doi.org/10.1002/jmv.28406

Cao, C., He, J., Mak, L., Perera, D., Kwok, D., Wang, J., Li, M., Mourier, T., Gavriliuc, S., Greenberg, M., Morrissy, A. S., Sycuro, L. K., Yang, G., Jeffares, D. C., & Long, Q. (2021). Reconstruction of microbial haplotypes by integration of statistical and physical linkage in scaffolding.

Molecular Biology and Evolution. (IF = 11.062)

https://doi.org/10.1093/molbev/msab037

In progress journal manuscripts

He, J., Perera, D., Wen, W., Ping, J., Li, Q., Chen, Z., Shu, X., Long, J., Cai, Q., Shu, X.O., Zheng, W., Long, Q., Guo, X. (2024).

Enhancing Disease Risk Gene Discovery by Integrating Transcription Factor-Linked Trans-located Variants into Transcriptome-Wide Association Analyses.

medRxiv, pp.2023-10.

Under revision at Genome Biology (IF=13.583)

https://doi.org/10.1101/2023.10.10.23295443

Li, Q., Perera, D., Chen, Z., Wen, W., Wang, D., Yan, J., Shu, X.O., Zheng, W., Guo, X. and Long, Q., (2024).

Tissue-specific transfer-learning enables re-tasking of a general comprehensive model to a specific domain.

bioRxiv, pp.2023-09.

https://doi.org/10.1101/2023.09.11.557208

Presentations

International conferences

Perera, D., Li, E., Huber, C., van Marle, G., Platt, A., Long, Q. (July 12th, 2024)

Oral presentation

Apollo: A comprehensive GPU-powered Within-host Viral simulator with tissue and cellular hierarchies for studying viral evolutionary and infection dynamics.

32nd conference on Intelligent Systems for Molecular Biology (ISMB), Montreal, Quebec.

Perera, D., Reisenhofer, E., Hussein, S., Higgins, E., Huber, D. C., Long, Q. (February 12th, 2024)

Oral presentation

CATE: An accelerated and scalable solution for large-scale genomic data processing through GPU and CPU-based parallelization.

Statistical Aspects of Trustworthy Machine Learning, Banff International Research Station (BIRS) for Mathematical Innovation and Discovery, Banff Center, Calgary, Alberta.

Perera, D., Reisenhofer, E., Hussein, S., Higgins, E., Huber, D. C., Long, Q. (May 9th, 2023)

Poster presentation

CATE: An accelerated and scalable solution for large-scale genomic data processing through GPU and CPU-based parallelization.

The Biology of Genomes 2023, Cold Springs Harbor Laboratory, New York, USA.

Provincial conferences

Perera, D., Hubber, C., Long, Q. (May 25th, 2022)

Oral and Poster presentation

CATE: CUDA Accelerated Testing of Evolution, A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data.

The 2nd Annual BioNet Conference 2022, University of Calgary, Alberta.

Perera, D., Long, Q., and van Marle, G. (September 20th, 2019).

Oral and Poster presentation

Validation of a phylogenetic pipeline to examine transmission networks in a Canadian HIV cohort.
The 1st Annual BioNet Conference 2019, University of Lethbridge, Alberta.

Institutional conferences

Perera, D., Long, Q. (May 8th, 2024)

Oral presentation

CATE & Apollo: Harnessing GPU powered large scale parallel processing technologies for evolutionary testing and simulation at scale.

Biostatistics Research Day, University of Calgary Biostatistics Centre, Calgary, Alberta.

Perera, D., Reisenhofer, E., Hussein, S., Higgins, E., Huber, D. C., Long, Q. (November 23rd, 2023)

Oral & Poster presentation

CATE: An accelerated and scalable solution for large-scale genomic data processing through GPU and CPU based parallelization.

2023 ACHRI Research Retreat, Banff Center, Calgary, Alberta.

Awards and scholarships

2024 Gordon H. Dixon Award for the most meritorious doctoral student in the year 2023 at 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, 2024 Biochemistry and Molecular Biology First Author Award, University of Calgary, Canada.

References