By Dr Hasindu Malshan Gamaarachchi

Conference Papers

Gamaarachchi H; Ganegoda H; Ragel R, 2016, 'The A to Z of building a testbed for Power Analysis attacks', in 2015 IEEE 10th International Conference on Industrial and Information Systems Iciis 2015 Conference Proceedings, pp. 501 - 506, http://dx.doi.org/10.1109/ICIINFS.2015.7399063

Namal S; Gamaarachchi H; Lee GM; Um TW, 2016, 'Autonomic trust management in cloud-based and highly dynamic IoT applications', in Proceedings of the 2015 ITU Kaleidoscope Trust in the Information Society K 2015 Academic Conference, http://dx.doi.org/10.1109/Kaleidoscope.2015.7383635

Namal S; Gamaarachchi H; Lee GM; Um T-W, 2015, 'AUTONOMIC TRUST MANAGEMENT IN CLOUD-BASED AND HIGHLY DYNAMIC IOT APPLICATIONS', in 2015 ITU KALEIDOSCOPE: TRUST IN THE INFORMATION SOCIETY (K-2015), IEEE, SPAIN, Univ Autonoma, Barcelona, pp. 83 - 90, presented at ITU Kaleidoscope Academic Conference on Trust in the Information Society, SPAIN, Univ Autonoma, Barcelona, 09 December 2015 - 11 December 2015, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000380568500017&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Gamaarachchi H; Ragel R; Jayasinghe D, 2014, 'Accelerating correlation power analysis using graphics processing units (GPUs)', in 2014 7th International Conference on Information and Automation for Sustainability Sharpening the Future with Sustainable Technology Iciafs 2014, http://dx.doi.org/10.1109/ICIAFS.2014.7069547

Gamaarachchi H; Ragel R; Jayasinghe D, 2014, 'Accelerating correlation power analysis using graphics processing units (GPUs)', in 2014 7th International Conference on Information and Automation for Sustainability: "Sharpening the Future with Sustainable Technology", ICIAfS 2014, http://dx.doi.org/10.1109/ICIAFS.2014.7069547

Preprints

Gamaarachchi H; Stevanovski I; Hammond JM; Reis ALM; Rapadas M; Jayasooriya K; Russell T; Yeow D; Hort Y; Mallett AJ; Stackpoole E; Roman L; Silver LW; Hogg CJ; Streeting L; Bogdanovic O; Rodrigues R; Nascimento L; Cardoso AL; Georges A; Cheng H; Patel HR; Kumar KR; Mallawaarachchi AC; Deveson IW, 2025, Adaptively integrated sequencing and assembly of near-complete genomes, http://dx.doi.org/10.1101/2025.03.31.646505

Samarasinghe S; Deveson I; Gamaarachchi H, 2025, Realfreq: Real-time base modification analysis for nanopore sequencing, http://dx.doi.org/10.1101/2025.01.23.634192

Jayasooriya K; Jenner S; Marasinghe P; Senanayake U; Saadat H; Taubman D; Ragel R; Gamaarachchi H; Deveson I, 2024, A new compression strategy to reduce the size of nanopore sequencing data, http://dx.doi.org/10.1101/2024.10.02.616377

Samarakoon H; Liyanage K; Ferguson J; Parameswaran S; Gamaarachchi H; Deveson I, 2024, Interactive visualisation of raw nanopore signal data with Squigualiser, http://dx.doi.org/10.1101/2024.02.19.581111

Samarakoon H; Wan YK; Parameswaran S; Göke J; Gamaarachchi H; Deveson I, 2024, Leveraging Basecaller’s Move Table to Generate a Lightweight k-mer Model, http://dx.doi.org/10.1101/2024.06.30.601452

Rudaks LI; Stevanovski I; Yeow D; Reis A; Chintalaphani S; Cheong PL; Gamaarachchi H; Worgan L; Ahmad K; Hayes M; Hannaford A; Kim S; Fung V; Halmagyi M; Martin A; Manser D; Tchan M; Ng K; Kennerson M; Deveson I; Kumar KR, 2024, Targeted long-read sequencing as a single assay improves diagnosis of spastic-ataxia disorders, http://dx.doi.org/10.1101/2024.09.04.24312938

Reis ALM; Rapadas M; Hammond JM; Gamaarachchi H; Stevanovski I; Kumaheri MA; Chintalaphani SR; Dissanayake DSB; Siggs OM; Hewitt AW; Llamas B; Brown A; Baynam G; Mann GJ; Hermes A; Patel HR; Deveson IW, 2023, The landscape of genomic structural variation in Indigenous Australians, http://dx.doi.org/10.1101/2023.10.17.562810

Cortese A; Beecroft SJ; Facchini S; Curro R; Cabrera-Serrano M; Stevanovski I; Chintalaphani S; Gamaarachchi H; Weisburd B; Folland C; Monahan G; Scriba CK; Dofash L; Johari M; Grosz BR; Ellis M; Fearnley LG; Tankard R; Read J; Bahlo M; Merve A; Dominik N; Vegezzi E; Schnekenberg RP; Fernandez G; Masingue M; Giovannini D; Delatycki M; Storey E; Gardner M; Amor D; Nicholson G; Vucic S; Henderson RD; Robertson T; Dyke J; Fabian V; Mastaglia F; Davis MR; Kennerson M; England G; Quinlivan R; Hammans S; Tucci A; McLean CA; Laing NG; Stojkovic T; Houlden H; Hanna MG; Deveson I; Lockhart PJ; Lamont PJ; Fahey MC; Bugiardini E; Ravenscroft G, 2023, A CCG expansion inABCD3causes oculopharyngodistal myopathy in individuals of European ancestry, http://dx.doi.org/10.1101/2023.10.09.23296582

Liyanage K; Samarakoon H; Parameswaran S; Gamaarachchi H, 2023, minimap2-fpga: Integrating hardware-accelerated chaining for efficient end-to-end long-read sequence mapping, http://dx.doi.org/10.1101/2023.05.30.542681

Samarakoon H; Ferguson J; Gamaarachchi H; Deveson I, 2023, Accelerated nanopore basecalling with SLOW5 data format, http://dx.doi.org/10.1101/2023.02.06.527365

Angeloni A; Fissette S; Kaya D; Hammond J; Gamaarachchi H; Deveson I; Klose R; Li W; Zhang X; Bogdanovic O, 2023, Extensive DNA methylome rearrangement during early lamprey embryogenesis, http://dx.doi.org/10.1101/2023.05.25.542242

Gamaarachchi H; Ferguson J; Samarakoon H; Liyanage K; Deveson I, 2023, Squigulator: simulation of nanopore sequencing signal data with tunable noise parameters, http://dx.doi.org/10.1101/2023.05.09.539953

Wong B; Ferguson J; Gamaarachchi H; Deveson I, 2023, Streamlining remote nanopore data access withslow5curl, http://dx.doi.org/10.1101/2023.11.28.569128

Shih PJ; Saadat H; Parameswaran S; Gamaarachchi H, 2022, Efficient Real-Time Selective Genome Sequencing on Resource-Constrained Devices, http://arxiv.org/abs/2211.07340v1

Gong J; Saadat H; Gamaarachchi H; Javaid H; Hu XS; Parameswaran S, 2022, ApproxTrain: Fast Simulation of Approximate Multipliers for DNN Training and Inference, http://dx.doi.org/10.48550/arxiv.2209.04161

Senanayake A; Gamaarachchi H; Herath D; Ragel R, 2022, DeepSelectNet: Deep Neural Network Based Selective Sequencing for Oxford Nanopore Sequencing, http://dx.doi.org/10.1101/2022.10.24.513498

Samarakoon H; Ferguson J; Jenner S; Amos T; Parameswaran S; Gamaarachchi H; Deveson I, 2022, Flexible and efficient handling of nanopore sequencing signal data with slow5tools, http://dx.doi.org/10.1101/2022.06.19.496732

Gamaarachchi H, 2021, Computer Architecture-Aware Optimisation of DNA Analysis Systems, http://dx.doi.org/10.48550/arxiv.2101.05012

Stevanovski I; Chintalaphani S; Gamaarachchi H; Ferguson J; Pineda S; Scriba C; Tchan M; Fung V; Ng K; Cortese A; Houlden H; Dobson-Stone C; Fitzpatrick L; Halliday G; Ravenscroft G; Davis M; Laing N; Fellner A; Kennerson M; Kumar K; Deveson I, 2021, Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing, http://dx.doi.org/10.1101/2021.09.27.21263187

Bull R; Adikari T; Ferguson J; Hammond J; Stevanovski I; Beukers A; Naing Z; Yeang M; Verich A; Gamaarachchi H; Kim KW; Luciani F; Stelzer-Braid S; Eden J-S; Rawlinson W; van Hal S; Deveson I, 2020, Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis, http://dx.doi.org/10.1101/2020.08.04.236893

Bayat A; Gamaarachchi H; Deshpande N; Wilkins M; Parameswaran S, 2020, Methods for De-novo Genome Assembly, http://dx.doi.org/10.20944/preprints202006.0324.v1

Gamaarachchi H; Ganegoda H, 2018, Power Analysis Based Side Channel Attack, http://dx.doi.org/10.48550/arxiv.1801.00932

Gamaarachchi H; Ragel R; Jayasinghe D, 2014, Accelerating Correlation Power Analysis Using Graphics Processing Units, http://dx.doi.org/10.48550/arxiv.1412.7682

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