By Dr Hasindu Malshan Gamaarachchi

Conference Papers

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

Shih PJ; Saadat H; Parameswaran S; Gamaarachchi H, 2022, Efficient Real-Time Selective Genome Sequencing on Resource-Constrained Devices, http://dx.doi.org/10.48550/arxiv.2211.07340

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

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

Gamaarachchi H; Lam CW; Jayatilaka G; Samarakoon H; Simpson J; Smith M; Parameswaran S, 2019, GPU Accelerated Adaptive Banded Event Alignment for Rapid Comparative Nanopore Signal Analysis, http://dx.doi.org/10.1101/756122

Gamaarachchi H; Parameswaran S; Smith M, 2018, Featherweight long read alignment using partitioned reference indexes, http://dx.doi.org/10.1101/386847

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

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; group OS; 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, A CCG expansion in ABCD3 causes oculopharyngodistal myopathy in individuals of European ancestry, http://dx.doi.org/10.1101/2023.10.09.23296582

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

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

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

Samarasinghe S; Deveson I; Gamaarachchi H, Base modification analysis in long read sequencing data using Minimod, http://dx.doi.org/10.1101/2025.07.16.665072

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

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

Angeloni A; Hammond JM; Peters TJ; Reis ALM; Kemp L; Amos T; Gamaarachchi H; Humphries S; Wilmott LA; Pal S; Masamsetti VP; Weatherstone M; Ip KCK; Pazaky K; Steel A; Lyons R; Walters ED; Liu N; Tam P; Polo JM; Waters P; Clark SJ; Richards LJ; Smith AD; Lee H; Deveson IW; Griffith OW; Skvortsova K, DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage, http://dx.doi.org/10.1101/2025.11.09.686659

Skvortsova K; Angeloni A; Hammond J; Peters T; Reis ALM; Kemp L; Amos T; Gamaarachchi H; Humphries S; Wilmott L; Pal S; Masamsetti VP; Weatherstone M; Ip KCK; Pazaky K; Steel A; Lyons R; Walters E; Liu N; Tam P; Polo J; Waters P; Clark S; Richards L; Smith A; Lee H; Deveson I; Griffith O, DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage, http://dx.doi.org/10.21203/rs.3.rs-8110586/v1

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

Samarakoon H; Punchihewa S; Senanayake A; Ragel R; Gamaarachchi H, F5N : Nanopore Sequence Analysis Toolkit for Android Smartphones, http://dx.doi.org/10.1101/2020.03.22.002030

Samarakoon H; Ferguson JM; Jenner SP; Amos TG; Parameswaran S; Gamaarachchi H; Deveson IW, Flexible and efficient handling of nanopore sequencing signal data with slow5tools, http://dx.doi.org/10.1101/2022.06.19.496732

González-Rajal Á; D’Araujo TY; Ovchinnikov V; Alcalá JLG-J; Wang T; Lausen B; Brethouwer T; Angeloni A; Ross SE; Burgos-Ruiz AM; Álvarez-Presas M; Mota-Gómez I; Acemel RD; Harris RJ; Loi-Luu P; Jimenez GE; Daners A; Ferguson JM; Hammond JM; Gamaarachchi H; Degnan BM; Degnan SM; Mackay JP; Undheim EAB; Ruiz-Trillo I; Clark SJ; Tena JJ; Lupiáñez DG; Church SH; Dunn CW; Marletaz F; Deveson IW; Cummins SF; Neely GG; de Mendoza A; Bogdanovic O, Integrative genomics of the siphonophore Physalia utriculus reveals the regulatory logic of colonial division of labour and the molecular basis of venom activity, http://dx.doi.org/10.64898/2026.08.01.742136

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

Ferguson JM; Gamaarachchi H; Nguyen T; Gollon A; Tong S; Aquilina-Reid C; Bowen-James R; Deveson IW, InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses, http://dx.doi.org/10.1101/2021.04.21.440861

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

Bayat A; Gamaarachchi H; Deshpande NP; Wilkins MR; Parameswaran S, Methods for De-Novo Genome Assembly, http://dx.doi.org/10.20944/preprints202006.0324.v1

Liyanage K; Samarakoon H; Parameswaran S; Gamaarachchi H, 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

Wong B; Singh G; Javaid H; Denolf K; Liyanage K; Samarakoon H; Deveson IW; Gamarachchi H, Open-source, Hardware-Independent GPU Acceleration for Scalable Nanopore Basecalling with Slorado and Openfish, http://dx.doi.org/10.64898/2026.03.25.714356

Shih PJ; Sanghani Z; Guarracino A; Gamaarachchi H; Batten C, Panomap: Unbiased Nanopore Signal Mapping with Pangenome Variation Graphs, http://dx.doi.org/10.64898/2026.07.10.737796

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

Gamaarachchi H; Samarakoon H; Jenner S; Ferguson J; Amos T; Hammond J; Saadat H; Smith M; Parameswaran S; Deveson I, SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis, http://dx.doi.org/10.21203/rs.3.rs-668517/v1

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

Wong B; Ferguson JM; Gamaarachchi H; Deveson IW, Streamlining remote nanopore data access with slow5curl, http://dx.doi.org/10.1101/2023.11.28.569128

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

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

Gamaarachchi H; Jenner S; Samarakoon H; Ferguson JM; Deveson IW, The enduring advantages of the SLOW5 file format for raw nanopore sequencing data, http://dx.doi.org/10.1101/2025.06.30.662478

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; Genomics CFI; Patel HR; Deveson IW, The landscape of genomic structural variation in Indigenous Australians, http://dx.doi.org/10.1101/2023.10.17.562810

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