By Dr Hasindu Malshan Gamaarachchi

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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