Duwage Dahampriya Baladeva Deshan Perera
Stanford University - Postdoctoral scholar at Fraser Lab
Email: deshan@stanford.edu
GPA: 3.967/4.00
Thesis: High-performance computing solutions for the study of within-host evolution
Areas of interest: Within host evolution, Pathogen and Cancer genomics
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)
August 2025 - Present
Department of Biology, School of Humanities and Sciences, Stanford University, USA.
September 2019 - August 2025
Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Canada.
Bioinformatics (2023, 2025)
BMC Genomics (2025)
December 2017 - August 2019
Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Sri Lanka.
December 2016 - February 2017
Industrial Technology Institute, Sri Lanka.
Perera, D., Li, E., Gordon, P.M.K., van der Meer, F., Lynch, T., Gill, J., Church, L.D., de Koning, A.P.J., Huber, C.D., van Marle, G.‡, Platt, A.‡ and Long, Q.‡ (2024).
Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.
Nature Communications (IF = 14.7)
https://doi.org/10.1038/s41467-025-60988-8
(‡ = Joint corresponding authors)
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)
https://doi.org/10.1371/journal.pgen.1011074
(* = Joint first author)
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
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-variants into transcript ome-wide association analyses.
Nucleic Acids Research (IF = 16.6)
https://doi.org/10.1093/nar/gkae1035
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)
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.
Perera, D., Li, E., Huber, C., van Marle, G., Platt, A., Long, Q. (July 12th, 2024)
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)
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.
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.
Perera, D., Long, Q. (June 21st 2024)
Oral presentation
CATE & Apollo: Accelerating evolutionary testing and within-host viral simulation through a novel GPU-powered scalable framework.
Gordon Dixon Awardee, Biochemistry and Molecular Biology Advances, University of Calgary, Kananaskis.
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)
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.
Perera, D., Peiris, L.D.C. (23rd November, 2018)
Oral presentation
23rd International Forestry and Environment Symposium, University of Sri Jayewardenepura, Colombo, Sri Lanka.
Awarded the certificate in recognition of the best research paper during the technical session.
2025, 2026, 2027 Stanford Data Science Postdoctoral Fellowship, Stanford University, USA.
2025, 2026 Stanford Center for Computational, Evolutionary, and Human Genomics Postdoctoral Fellowship, Stanford University, USA.
2025 MDBC Nominee for Chancellor's Graduate Medal and Governor General's Gold Medal, University of Calgary, Canada.
2024 Graduate Faculty Council Scholarship (Doctoral), University of Calgary, Canada.
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.
Prof. Quan Long (Ph.D. supervisor)
Professor of Bioinformatics,
Cumming School of Medicine,
University of Calgary,
Canada.
Prof. L.D.C Peiris (Undergraduate supervisor)
Professor in Zoology,
Department of Zoology,
University of Sri Jayewardenepura,
Sri Lanka.