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Select Publications

Preprints

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

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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