Professional Summary
I am a Senior Research Scientist and veterinary pathologist at CSIRO’s Australian Centre for Disease Preparedness (ACDP), with a distinctive dual expertise in veterinary anatomic pathology and genomics/bioinformatics — a combination that is rare both nationally and internationally. I bring over a decade of experience spanning diagnostic pathology, infectious disease research, comparative genomics, and high-containment laboratory operations.
At CSIRO, I lead research at the interface of pathology and pathogen biology, investigating the genesis, pathogenesis and host responses to emerging infectious diseases in wildlife and domestic species, with particular depth in avian influenza, Japanese encephalitis virus, lyssaviruses, and SARS-CoV-2. My work integrates whole-genome and transcriptomic analysis with classical pathological investigation to deliver insights that neither discipline could achieve alone.
I am actively progressing toward board certification as a Diplomate of the American College of Veterinary Pathologists (ACVP), having passed Phase I of the ACVP Board Examination. I have performed over 1,000 post-mortem examinations across domestic and wild species, and I am trained and certified to operate in Physical Containment Level 3 (PC3) facilities.
Beyond the bench, I serve as a member of the ACDP Academic Board, supervise two PhD students and multiple Honours and undergraduate research students, and have secured over $520,000 in competitive grant funding as lead or co-lead investigator, with additional internal grants and a pending external application in environmental biosecurity. I have contributed to national capacity development in the Northern Territory and to Indo-Pacific infectious disease surveillance partnerships through James Cook University.
My research has attracted international recognition, including the ESWI Young Scientist Award, the Sri Lankan Presidential Award for Scientific Publication, and nomination for the CSIRO Health & Biosecurity Research Excellence Award. My work on black swan susceptibility to avian influenza received national media coverage (ABC Science) and was published in Genome Biology.
Key Research Capabilities
| Domain | Expertise |
|---|---|
| Veterinary Pathology | Anatomic pathology, diagnostic histopathology, gross and microscopic lesion interpretation, special staining, 1,000+ post-mortems (domestic and wildlife), ACVP Phase I passed |
| Genomics & Bioinformatics | De novo genome assembly, transcriptomics (RNA-seq), metagenomics, variant calling, long-read sequencing (PacBio, Oxford Nanopore) |
| Virology & Immunopathology | Avian influenza (HPAI/LPAI), Japanese encephalitis virus, SARS-CoV-2, lyssavirus; cell culture, viral infection models, molecular and immunopathology |
| High-Containment Operations | PC3 facility trained and certified (ACDP); biosafety and approved arrangement certified |
| Computational Skills | Python, R, Unix/Linux, Snakemake workflow manager, HPC job management (Slurm, PBSpro) |
| Environmental Biosecurity | eDNA-based surveillance, environmental genomics, next-generation surveillance technologies |
| Research Leadership | $520K+ in grants (lead/co-lead), 2 PhD students, Honours & undergrad supervision, ACDP Academic Board member |
| Engagement & Impact | Cross-institutional collaborations (JCU, Deakin, UQ, international), NT capacity development, Indo-Pacific disease surveillance, media engagement, 6+ invited talks |
Education
PhD (Pathobiology and Genomics) — University of
Queensland, Australia (2021)
Thesis: “Swan genomics and transcriptomics give insights into the
pathogenesis of highly pathogenic avian influenza in Australian Black
swans”
Supported by UQ Postgraduate Scholarship and CSIRO Top-Up Scholarship
(Australian Animal Health Laboratory)
Master of Philosophy (MPhil) — Veterinary Anatomic
Pathology — University of Peradeniya, Sri Lanka (2017)
Specialisation: Wildlife diseases
Thesis: “Pathological Conditions in Indian Flying Fox (Pteropus
medius) found dead in Peradeniya, Sri Lanka”
Joint student, MSc Veterinary Anatomic Pathology, Western College of
Veterinary Medicine, University of Saskatchewan, Canada (one full
semester of intensive pathology training, 2014)
Supported by International Development Research Centre Scholarship
Bachelor of Veterinary Science (Honours, Second Upper Division) — University of Peradeniya, Sri Lanka (2011)
Professional Credentials
- ACVP Board Examination — Phase I passed (progressing toward Diplomate ACVP)
- Sri Lanka Veterinary Council — Registered Practitioner, Reg. No. 1745
- PC3 Facility Certification — Australian Centre for Disease Preparedness, CSIRO
- Approved Arrangement and Biosafety Awareness — Department of Agriculture and Water Resources, Australian Government (2019)
Employment History
Senior Research Scientist — Pathology and Pathogen Biology Team
Australian Centre for Disease Preparedness (ACDP), CSIRO,
Geelong
February 2023 – Present
Leading research in pathology and pathogen biology with a focus on emerging infectious diseases in avian and wildlife species. Integrating comparative genomics, transcriptomics, and anatomic pathology to understand host susceptibility and pathogenesis. Key activities include:
- Principal investigator on multiple internally funded projects; co-lead on externally funded programs
- Member of the ACDP Academic Board
- Supervising 2 PhD students, Honours students, and undergraduate research students
- Contributing to Northern Territory capacity development
- Submitted grant application for an environmental biosecurity project
- Progressing toward ACVP board certification (Phase I passed)
CSIRO Early Career Research Fellow (Postdoctoral Researcher) — Emerging Infectious Diseases
Australian Centre for Disease Preparedness (ACDP), CSIRO,
Geelong
November 2021 – February 2023
Investigated the genesis and pathogenesis of viral diseases in avian species using genomics, transcriptomics, bioinformatics, virology, and immunopathology approaches.
- Led genomic characterisation of Australian black swan susceptibility to HPAI, published in Genome Biology
- Established Oxford Nanopore Technology sequencing capability at ACDP
- Initiated eDNA-based surveillance project (Environomics Future Science Platform)
- Commenced student supervision (Deakin University, James Cook University)
PhD Candidature — Pathobiology and Genomics
University of Queensland / Australian Animal Health
Laboratory, CSIRO
2018 – 2021
Assembled the first black swan reference genome and conducted comparative genomic and transcriptomic analyses to elucidate the molecular basis of HPAI susceptibility in Australian waterfowl. Trained in PC3 operations, cell culture, viral infection models, and HPC-based bioinformatics.
Research Assistant / Veterinary Pathologist
Department of Veterinary Pathobiology, University of
Peradeniya, Sri Lanka
October 2013 – March 2017
Conducted routine diagnostic and research veterinary pathology across domestic and wild animal species. Performed over 1,000 post-mortem examinations. Prepared histological samples, interpreted gross and microscopic pathological lesions, and authored diagnostic reports. Contributed to multiple wildlife disease research publications.
Lecturer (Contract) — Veterinary Pathology
Department of Veterinary Pathobiology, University of
Peradeniya, Sri Lanka
November 2012 – September 2013
Delivered practical teaching in gross and microscopic pathology to 2nd-year BVSc students. Supervised student projects, conducted post-mortem diagnosis of rabies, and taught histopathology laboratory methods.
Veterinary Internships
- Colombo Municipal Council, Colombo, Sri Lanka — February–May 2012
- Department of Animal Production and Health, Sri Lanka — November 2011–February 2012
Institutional Service & Governance
- Member, ACDP Academic Board — Australian Centre for Disease Preparedness, CSIRO (February 2025 – present)
- Co-organiser, ACDP Student Wellbeing Check-in
Program — February 2025 – present
Designed and coordinate a structured program of regular check-in sessions between research students and supervisors, providing a confidential and supportive forum to monitor wellbeing, identify support needs, and facilitate open communication across the ACDP research community. Lead evaluation of session outcomes and student feedback to inform continuous improvement of the program. - ACDP Academic Board — Website Administrator —
February 2025 – present
Responsible for administering and maintaining the ACDP Academic Board website, ensuring content currency, accessibility, and alignment with the Board’s research governance and communications objectives.
Research Grants & Funding
Total competitive funding as lead or co-lead: $605,000+
| # | Grant Title | Role | Funder | Period | Amount |
|---|---|---|---|---|---|
| 1 | Improving capacity for emerging infectious diseases research and surveillance in the Indo-Pacific | Co-lead | James Cook University & CSIRO | 2023–2025 | $300,000 |
| 2 | Artificial Intelligence for Mission Postgraduate Program | Co-lead | CSIRO | 2022–2026 | $155,000 |
| 3 | Environmental DNA based next generation surveillance technology | Project Lead | CSIRO Environomics Future Science Platform | 2022–2023 | $35,000 |
| 4 | High-performance desktop computer and Oxford Nanopore Technology sequencing platform (P2 Solo) | Project Lead | CSIRO CAPEX | 2021 | $30,000 |
| 5 | Spatial transcriptomics capability development at ACDP: Lumpy skin disease pathogenesis investigation | Project Lead | IADZ | 2024–present | $30,000 |
| 6 | Spatial transcriptomics to uncover the mechanisms of pathology of highly pathogenic avian influenza in commercial layers | Project Lead | IADZ | 2024–present | $25,000 |
| 7 | Deakin University collaboration for JEV surveillance in Victorian waterbirds | Project Lead | VicHealth | Ongoing | $30,000 |
Submitted:
| # | Grant Title | Role | Funder | Amount |
|---|---|---|---|---|
| 1 | AI4AI: A Robust AI-Driven Platform for Streamlining IHC-Based Avian Influenza Surveillance and Response | Project Lead | DAFF | $300,000 |
Higher Degree Research Supervision
PhD Students (Current)
| # | Student Name | University | Project Title | Role | Period |
|---|---|---|---|---|---|
| 1 | R. P. | James Cook University | Bat flies as vectors for infectious agent transmission | Co-supervisor | 2023–2027 |
| 2 | G. M. | University of Queensland | Long COVID and the nasal transcriptome | Co-supervisor | 2023–2026 |
Honours Students
| # | Student Name | University | Project Title | Role | Year |
|---|---|---|---|---|---|
| 1 | N. B. | Deakin University | Machine learning for peptide prediction | Principal Supervisor | 2024 |
| 2 | A. D. | Deakin University | JEV surveillance in Australian wild birds | Co-supervisor | 2024 |
Undergraduate & Short-term Supervision
- Supervision of veterinary undergraduate students (James Cook University) — TV3002 course (mock research project)
- Supervision of Deakin University and James Cook University students/internees (up to 3 months) at ACDP, Geelong
Publications in Peer-Reviewed Journals
For a complete and current list of publications, see Google Scholar or ORCID.
2025
Ahmed, K. A., Karawita, A. C., Klein, M. J., Mincarelli, L. F., Secondini, B., Satta, G., … Hardy, C. M. (2025). Complete mitochondrial genomes of Culicoides brevitarsis and Culicoides imicola biting midge vectors of Bluetongue Virus. Mitochondrial DNA Part B, 10(1): 67–71. https://doi.org/10.1080/23802359.2024.2447750
Gofton, A. W., Short, M., Michie, M., Gallaway, D., Smith, I., Blasdell, K., Karawita, A. C., Klein, M. J., Herbert, C. A., Barker, S. C. (2025). Exploring Borrelia in Australia: Isolation, genomic characterisation, and host and vector associations. Ticks and Tick-borne Diseases, 16(4): 102505.
McNamara, B. J., Cornish, J., Blasdell, K. R., Athan, E., Clarke, N. E., Pe, T., Hussain, M. A., Muleme, M., Tay, E. L., Dunn, M., Boyd, V., Karawita, A. C., O’Brien, D. P. (2025). Mycobacterium ulcerans in possum feces before emergence in humans, Australia. Emerging Infectious Diseases, 31(3): 569.
2024
- Sinclair, J. E., Vedelago, C., Ryan, F. J., Carney, M., Redd, M. A., Lynn, M. A., Grubor-Bauk, B., Cao, Y., Henders, A. K., Chew, K. Y., Gilroy, D., Greaves, K., Labzin, L., Ziser, L., Ronacher, K., Wallace, L. M., Zhang, Y., Macauslane, K., Ellis, D. J., Rao, S., Burr, L., Bain, A., Karawita, A. C., Schulz, B. L., Li, J., Lynn, D. J., Palpant, N., Wuethrich, A., Trau, M., Short, K. R. (2024). Post-acute sequelae of SARS-CoV-2 cardiovascular symptoms are associated with trace-level cytokines that affect cardiomyocyte function. Nature Microbiology, 9(12): 3135–3147.
Preprints:
- McNamara, B. J., Cornish, J., Blasdell, K. R., Athan, E., Clarke, N. E., Pe, T., Hussain, M. A., Muleme, M., Tay, E. L., Dunn, M., Boyd, V., Karawita, A. C., O’Brien, D. P. (2024). Possum faeces, the ‘canary in the coalmine’ heralding the emergence of Buruli ulcer in an Australian urban centre. medRxiv. (Subsequently published as McNamara et al., 2025, Emerging Infectious Diseases)
2015–2023 (published)
Karawita, A. C., Cheng, Y., Chew, K. Y., Challagulla, A., Kraus, R., Mueller, R. C., et al. (2023). The Swan Genome and Transcriptome, It Is Not All Black And White. Genome Biology, 1(24). https://doi.org/10.1186/s13059-022-02838-0
Zhu, Y., Chew, K. Y., Wu, M., Karawita, A. C., McCallum, G., et al. (2022). Ancestral SARS-CoV-2, but not Omicron, replicates less efficiently in primary pediatric nasal epithelial cells. PLOS Biology, 20(8): e3001728. https://doi.org/10.1371/journal.pbio.3001728
Lu, J., Yang, Z., Karawita, A. C., Bunte, M., Chew, K. Y., Pegg, C., Mackay, I., Whiley, D., Short, K. R. (2021). Limited evidence for the role of environmental factors in the unusual peak of influenza in Brisbane during the 2018–2019 Australian summer. Science of The Total Environment, 776, 145967. https://doi.org/10.1016/j.scitotenv.2021.145967
Hulme, K. D., Karawita, A. C., Pegg, C., Bunte, M. J. M., Bielefeldt-Ohmann, H., Bloxham, C. J., Van den Hoecke, S., Setoh, Y. X., Vrancken, B., Spronken, M., Steele, L. E., Verzele, N. A. J., Upton, K. R., Khromykh, A. A., Chew, K. Y., Sukkar, M., Phipps, S., Short, K. R. (2021). A paucigranulocytic asthma host environment promotes the emergence of virulent influenza viral variants. eLife, 10:e61803. https://doi.org/10.7554/eLife.61803
Karawita, A. C., Tong, M. Z. W., Short, K. R. (2019). A delicate balancing act: immunity and immunopathology in human H7N9 influenza virus infections. Current Opinion in Infectious Diseases.
Une, Y., Yamazaki, M., Morimoto, M., Kametani, F., Parker, D., Karawita, A., Scott, S. J., Yamazaki, M., Kametani, S., Parker, K. (2018). Cerebral amyloid angiopathy and comparative analysis of amyloid-β protein in birds. bioRxiv, p.486340.
Karawita, A. C., Himsworth, C. G., Rajapakse, R. P. V. J., Bollinger, T. K., Gunawardena, P. de S. (2016). Toxocara pteropodis in Indian flying fox Pteropus medius in Sri Lanka. Journal of Wildlife Diseases, 53(2): 414–416. http://dx.doi.org/10.7589/2016-07-170
Gunawardena, P. de S., Marston, D. A., Wise, E. L., Karawita, A. C., Breed, A. C., McElhinney, L. M., Johnson, N., Banyard, A. C., Fooks, A. R. (2016). Lyssavirus in Indian Flying foxes, Sri Lanka. Emerging Infectious Diseases, 22(8): 1456–1459.
Karawita, A. C., Perera, B. V. P., Perera, G. I. S., de Silva, M. D. S., Jayaweera, W. R., Himsworth, C. G., Bollinger, T. K., Gunawardena, G. S. P. de S. (2016). Calodium hepaticum in Jungle Cats (Felis chaus) in Sri Lanka. Journal of Wildlife Diseases.
Karawita, A. C., Rajapakse, R. C., Amarasiri, P. G. I. D., Ramanayake, R. M. T. M., Jayaweera, W. R., Bollinger, T. K., Gunawardena, G. S. P. De S. (2015). Cecocolic Intussusception in an Asian Elephant (Elephas maximus) in Sri Lanka Associated with Chronic Hepato-Intestinal Schistosomiasis: First Case Report. International Journal of Applied Sciences and Biotechnology, 3(4), 744–746.
Conference Presentations & Published Abstracts
Oral Presentations
- Karawita, A. C., Cheng, Y., Tong, M., Mueller, R., Bielefeldt-Ohmann, H., Chew, K., Bruxner, T., Kraus, R., Challagulla, A., Lowther, S., McAuley, A., Smith, J., Kuo, R., Baker, M., Burt, D., Short, K. (2020). Comparative genomics and transcriptomics help unravel why Australian Black Swans are uniquely susceptible to highly pathogenic avian influenza (HPAI). European Scientific Working Group in Influenza (ESWI) 7th Conference, Spain.
Poster Presentations & Published Abstracts
Karawita, A. C., Blasdell, K., Blanch-Lazaro, B., Challagulla, A., Selleck, P., McGinness, H., McLelland, J., Su, J., Suen, W., Wong, F., Wille, M., Horwood, P., Klaassen, M., Short, K., Hickson, R. (2023). Assembly and analysis of the native Australian ibis genomes to understand the species’ competency for infectious diseases. International Congress of Genetics and Genomics, Melbourne.
Karawita, A. C., Cheng, Y., Bielefeldt-Ohmann, H., Burt, D., Short, K. (2018). Highly Pathogenic Avian Influenza in Australian Black Swans (Cygnus atratus). Australian Ornithological Society Conference.
Karawita, A. C., Jagatheesan, M., Koizumi, N., Gamage, C. D., Bollinger, T. K., Gunawardena, P. de S. (2016). Infectious Agents in Indian Flying Fox (Pteropus medius) in Sri Lanka. 4th International One Health Congress & 6th Biennial Congress of the International Association for Ecology and Health, Melbourne.
Perera, B. V. P., Karawita, A. C., Jinadasa, H. R. N., Rajapakse, R. P. V. J., Bollinger, T. K., Gunawardena, G. S. P. de S. (2016). Zoonotic Pathogens in Free Ranging Wild Mammals in Sri Lanka. One Health Eco Health 2016, Melbourne.
Jagatheesan, M., Karawita, A. C., Muthusinghe, D. S., Lokugalappatti, L. G. S., Bollinger, T. K., Gunawardena, P. De S., Koizumi, N., Gamage, C. D. (2016). Presence of Pathogenic Leptospira sp. in Indian Flying foxes in Sri Lanka. 4th Annual Sessions of The Sri Lanka Society for Microbiology, Kandy.
Perera, B. V. P., Karawita, A. C., Gunawardena, G. S. P. De S., Rajapakse, R. P. V. J. (2015). Presence of zoonotic pathogens in free ranging wild cats in Sri Lanka. Symposium on Wild Cats of South Asia: Past and Present, Sri Lanka.
Amarasiri, P. G. I. D., Ramanayake, R. M. T. M., Karawita, A. C., Perera, K. U. E., Jayaweera, W. R., Gunawardena, G. S. P. de S. (2015). Bovine Tuberculosis: A Histopathological Study Of The Lung Lesions. Peradeniya University International Research Sessions, Sri Lanka.
Ramanayake, R. M. T. M., Amarasiri, P. G. I. D., Karawita, A. C., Jayaweera, W. R., Obayashi, Y., Hiko, T., Gunawardena, G. S. P. de S. (2015). Changes in the demographic pattern of animal rabies in the Central province of Sri Lanka. Conference on Sri Lanka Japan Collaborative Research.
Ramanayake, R. M. T. M., Amarasiri, P. G. I. D., Karawita, A. C., Jayaweera, W. R., Obayashi, Y., Hiko, T., Gunawardena, G. S. P. de S. (2015). Sensitivity and Specificity of the Negri Body Test using Sellers’ Stain in the Diagnosis of Rabies in Dogs. Conference on Sri Lanka Japan Collaborative Research.
Karawita, A. C., Ariyarathna, H. M. H. S., Fernando, W. D. D., Nizananthan, K., Amarasinghe, A. A. A. W. K., de Silva, L. N. A., Rajapakse, R. P. V. J., Jayaweera, W. R., Gunawardena, G. S. P. De S. (2013). Arterial thromboembolism caused by Strongylus vulgaris larvae migration in a thoroughbred horse — a case report. Scientific Sessions — Sri Lanka Veterinary Association. (Poster)
Karawita, A. C., Ariyarathna, H. M. H. S., Jayaweera, W. R., Obayashi, Y., Umemura, T., Tamashiro, H., Gunawardena, G. S. P. De S. (2013). Presence of Rabies and its Distribution among Animals in the Central Province in Sri Lanka. Conference on Sri Lanka Japan Collaborative Research.
Ariyarathna, H. M. H. S., Karawita, A. C., Jayaweera, W. R., Gunawardena, G. S. P. De S. (2012). A Retrospective Study on Necropsy Findings in dogs with renal disease. Peradeniya University Research Sessions.
Ariyarathna, H. M. H. S., Mallawa, M. R. C. K., Bandara, T. P. M. S. D., Jayaweera, W. R., Karawita, A. C., Bandara, A. M. R., Silva, I. D., Arulkanthan, A., Gunawardena, G. S. P. De S. (2013). Canine Urinalysis with Dipsticks Designed for Humans: Uses and Limitations. Scientific Sessions — Sri Lanka Veterinary Association.
Abeygunawardena, H. E., Silva, I. D., De Silva, D. D. N., Dangolla, A., Weerasinghe, J. U., Hewapathirana, I. S., Bandara, A. M. R., Gunasekara, W. U. S., Karawita, A. C. (2010). An embolectomy in the left external iliac artery in a paraplegic dog. Peradeniya University Research Sessions, Vol. 15, 193–195.
Invited Talks
- Invited speaker — Wildlife research symposium for University of Melbourne final year Veterinary students, 26 October 2023
- Invited speaker — International Plant and Animal Genome Conference / PAG 30, San Diego, USA, 13–18 January 2023
- Invited speaker — 2nd Sino-Australia Symposium, James Cook University, July 2022
- Invited speaker — “Molecular Horizons”, University of Wollongong, 30 June 2022
- Invited speaker — 3rd Ecosystem Change and Population Health (ECAPH) Virtual Symposium, QUT, June 2022
- Invited speaker — STEM student visit, Western Heights College, 9 November 2022
- Invited speaker — ANZCVS Science Week, Gold Coast, 24 July 2026 — “Molecular meets morphology! An introduction to ISH and spatial transcriptomics”
Awards & Recognition
- CSIRO Health & Biosecurity “Research Excellence Award” — Nominated (2023) for The Swan Genome and Transcriptome, It Is Not All Black And White (Genome Biology)
- European Scientific Working Group on Influenza (ESWI) Young Scientist Award — October 2020
- Presidential Award for Scientific Publications — National Research Council of Sri Lanka, November 2018, for “Lyssavirus in Indian Flying Foxes in Sri Lanka” (Emerging Infectious Diseases)
- Sri Lankan President’s Award for Scientific Publication — November 2018
- University of Queensland Postgraduate Scholarship — Living stipend and tuition fee, 2018–2022
- CSIRO Top-Up Scholarship — Australian Animal Health Laboratory, 2018–2022
- Taronga Conservation Society Australia Scholarship — Wildlife Health and Pathology Short Course, February 2019
- International Development Research Centre (IDRC) Scholarship — MPhil Research, 2013–2017
Applied Impact & Capacity Development
- Northern Territory ISH Capacity Development — Co-lead consultant for Developing In Situ Hybridisation Capability for Pathogen Detection in the Northern Territory. Designed and currently validating approximately 8 novel RNAscope probes targeting viral agents of biosecurity significance. Delivered practical, hands-on RNAscope workflow and probe design training to NT personnel. Project ongoing.
- Indo-Pacific emerging infectious disease surveillance — Co-lead, James Cook University & CSIRO collaborative project (2023–2025, $300,000) building research and surveillance capacity across the Indo-Pacific region
- Environmental biosecurity — Submitted competitive grant for next-generation environmental biosecurity surveillance (see Submitted Grants)
Media Coverage
- “Bird flu could wipe out Australian black swans; gene study reveals” — ABC Science, 23 January 2023
- “Are bin chickens spreading Japanese encephalitis?” — Science in Public, 19 July 2023
Technical Skills
| Category | Detail |
|---|---|
| Pathology | Gross and microscopic pathological examination; diagnostic histopathology; H&E and special staining; sample trimming, processing, embedding; post-mortem examination (domestic and wild species); rabies diagnosis |
| Genomics | De novo genome assembly; transcriptomics (RNA-seq); metagenomics; long-read sequencing (PacBio HiFi, Oxford Nanopore); QIIME2 microbiome analysis |
| Virology | Cell culture; viral infection models; molecular and immunopathology; influenza, JEV, SARS-CoV-2, lyssavirus |
| Programming | Python, R, Unix/Linux shell scripting |
| Workflow & HPC | Snakemake; Galaxy; Slurm; PBSpro; high-performance computing cluster management |
| Biosafety | PC3 facility operations (ACDP); Approved Arrangement and Biosafety Awareness certified |
| General | MS Office (Word, Excel, PowerPoint) |
Professional Training (Selected)
| Year | Training | Provider |
|---|---|---|
| 2022 | QIIME2 microbiome analysis | AustralianBioComms |
| 2020 | Variant Calling and De Novo Genome Assembly with PacBio HiFi Reads (webinar) | PacBio |
| 2019 | Genome Assembly Using Galaxy Workshop | QFAB / University of Queensland |
| 2019 | Assembly of long-read sequencing (2-day workshop) | QFAB Australia |
| 2019 | Approved Arrangement and Biosafety Awareness Certificate | Dept. of Agriculture and Water Resources, Australian Government |
| 2019 | Physical Containment Facility 3 (PC3) Training | AAHL / CSIRO, Geelong |
| 2019 | Wildlife Health and Pathology Short Course | Taronga Zoo, Sydney |
| 2018 | High-Performance Computing (HPC) Training | Research Computing Centre, University of Queensland |
| 2018 | Software Carpentry (Unix, Python, R) | University of Southern Queensland |
| 2016 | PC3 Induction — Biosciences Laboratory | Dept. of Agriculture and Fisheries, Queensland |
| 2014 | Intensive training in veterinary pathology (1 semester) | University of Saskatchewan, Canada — Dr C. G. Himsworth (Dipl. ACVP), Dr H. Philibert, Dr T. K. Bollinger |
| 2013 | Introduction to Laboratory Animal Science | Sri Lanka Association for Laboratory Animal Science |
Training & Workshops Delivered (as Resource Person)
- “Wildlife Health & Management Training Program for Wildlife Officers” — Elephant Transit Home, Uda-walawe, Sri Lanka, August 2014
- “Workshop on Collection of Brain Samples from Animals for Diagnosis of Rabies” — Dept. of Animal Production & Health / Dept. of Wildlife Conservation / University of Peradeniya / Sri Lanka Wildlife Health Centre, December 2013
- “Disease Surveillance in Wildlife: Procedures for Collection, Storage and Transport of Laboratory Samples” — Dept. of Animal Production & Health / Dept. of Wildlife Conservation / University of Peradeniya / Sri Lanka Wildlife Health Centre, February 2013