By Dr Hasindu Malshan Gamaarachchi

Journal articles

Jayasooriya K; Jenner SP; Marasinghe P; Senanayake U; Saadat H; Taubman D; Ragel R; Gamaarachchi H; Deveson IW, 2025, 'A new compression strategy to reduce the size of nanopore sequencing data.', Genome Res, http://dx.doi.org/10.1101/gr.280090.124

Chen Y; Davidson NM; Wan YK; Yao F; Su Y; Gamaarachchi H; Sim A; Patel H; Low HM; Hendra C; Wratten L; Hakkaart C; Sawyer C; Iakovleva V; Lee PL; Xin L; Ng HEV; Loo JM; Ong X; Ng HQA; Wang J; Koh WQC; Poon SYP; Stanojevic D; Tran HD; Lim KHE; Toh SY; Ewels PA; Ng HH; Iyer NG; Thiery A; Chng WJ; Chen L; DasGupta R; Sikic M; Chan YS; Tan BOP; Wan Y; Tam WL; Yu Q; Khor CC; Wüstefeld T; Lezhava A; Pratanwanich PN; Love MI; Goh WSS; Ng SB; Oshlack A; Göke J, 2025, 'A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines', Nature Methods, 22, pp. 801 - 812, http://dx.doi.org/10.1038/s41592-025-02623-4

Samarakoon H; Wan YK; Parameswaran S; Göke J; Gamaarachchi H; Deveson IW, 2025, 'Leveraging basecaller’s move table to generate a lightweight k-mer model for nanopore sequencing analysis', Bioinformatics, 41, http://dx.doi.org/10.1093/bioinformatics/btaf111

Samarasinghe S; Deveson I; Gamaarachchi H, 2025, 'Realfreq: real-time base modification analysis for nanopore sequencing', Bioinformatics, 41, http://dx.doi.org/10.1093/bioinformatics/btaf151

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 GM; Martin A; Manser D; Tchan M; Ng K; Kennerson ML; Deveson IW; Kumar KR, 2025, 'Targeted Long-Read Sequencing as a Single Assay Improves the Diagnosis of Spastic-Ataxia Disorders', Annals of Clinical and Translational Neurology, 12, pp. 832 - 841, http://dx.doi.org/10.1002/acn3.70008

Cortese A; Beecroft SJ; Facchini S; Curro R; Cabrera-Serrano M; Stevanovski I; Chintalaphani SR; Gamaarachchi H; Weisburd B; Folland C; Monahan G; Scriba CK; Dofash L; Johari M; Grosz BR; Ellis M; Fearnley LG; Tankard R; Read J; Merve A; Dominik N; Vegezzi E; Schnekenberg RP; Fernandez-Eulate G; Masingue M; Giovannini D; Delatycki MB; Storey E; Gardner M; Amor DJ; Nicholson G; Vucic S; Henderson RD; Robertson T; Dyke J; Fabian V; Mastaglia F; Davis MR; Kennerson M; Quinlivan R; Hammans S; Tucci A; Bahlo M; McLean CA; Laing NG; Stojkovic T; Houlden H; Hanna MG; Deveson IW; Lockhart PJ; Lamont PJ; Fahey MC; Bugiardini E; Ravenscroft G; Oflazer P; Başak NA; Kayserili H; Yeşil G; Malfatti E; Lilliker JB; Wicklund M; Pitceathly RDS; Brady S; Brais B; Pellerin D; Zuchner S; Danzi MC; Grandis M; Comi GP; Corti SP; Abati E; Toscano A; Manini A; Ghia A; Tassorelli C; Quartesan I; Simone R; Rossor AM; Reilly MM; Carroll L; Straub V; Udd B; Chen Z; Bonne G, 2024, 'A CCG expansion in ABCD3 causes oculopharyngodistal myopathy in individuals of European ancestry', Nature Communications, 15, http://dx.doi.org/10.1038/s41467-024-49950-2

Cortese A; Beecroft SJ; Facchini S; Curro R; Cabrera-Serrano M; Stevanovski I; Chintalaphani SR; Gamaarachchi H; Weisburd B; Folland C; Monahan G; Scriba CK; Dofash L; Johari M; Grosz BR; Ellis M; Fearnley LG; Tankard R; Read J; Merve A; Dominik N; Vegezzi E; Schnekenberg RP; Fernandez-Eulate G; Masingue M; Giovannini D; Delatycki MB; Storey E; Gardner M; Amor DJ; Nicholson G; Vucic S; Henderson RD; Robertson T; Dyke J; Fabian V; Mastaglia F; Davis MR; Kennerson M; Bonne G; Chen Z; Udd B; Straub V; Carroll L; Reilly MM; Rossor AM; Simone R; Quartesan I; Tassorelli C; Ghia A; Manini A; Toscano A; Abati E; Corti SP; Comi GP; Grandis M; Danzi MC; Zuchner S; Pellerin D; Brais B; Brady S; Pitceathly RDS; Wicklund M; Lilleker JB; Malfatti E; Yeşil G; Kayserili H; Başak NA; Oflazer P; Quinlivan R; Hammans S; Tucci A; Bahlo M; McLean CA; Laing NG; Stojkovic T; Houlden H; Hanna MG; Deveson IW; Lockhart PJ; Lamont PJ; Fahey MC; Bugiardini E; Ravenscroft G, 2024, 'Correction to: A CCG expansion in ABCD3 causes oculopharyngodistal myopathy in individuals of European ancestry (Nature Communications, (2024), 15, 1, (6327), 10.1038/s41467-024-49950-2)', Nature Communications, 15, http://dx.doi.org/10.1038/s41467-024-53151-2

Angeloni A; Fissette S; Kaya D; Hammond JM; Gamaarachchi H; Deveson IW; Klose RJ; Li W; Zhang X; Bogdanovic O, 2024, 'Extensive DNA methylome rearrangement during early lamprey embryogenesis', Nature Communications, 15, http://dx.doi.org/10.1038/s41467-024-46085-2

Samarakoon H; Liyanage K; Ferguson JM; Parameswaran S; Gamaarachchi H; Deveson IW, 2024, 'Interactive visualization of nanopore sequencing signal data with Squigualiser', Bioinformatics, 40, http://dx.doi.org/10.1093/bioinformatics/btae501

Gamaarachchi H; Ferguson JM; Samarakoon H; Liyanage K; Deveson IW, 2024, 'Simulation of nanopore sequencing signal data with tunable parameters', Genome Research, 34, pp. 778 - 783, http://dx.doi.org/10.1101/gr.278730.123

Wong B; Ferguson JM; Do JY; Gamaarachchi H; Deveson IW, 2024, 'Streamlining remote nanopore data access with slow5curl', Gigascience, 13, http://dx.doi.org/10.1093/gigascience/giae016

Reis ALM; Rapadas M; Hammond JM; Gamaarachchi H; Stevanovski I; Ayuputeri Kumaheri M; Chintalaphani SR; Dissanayake DSB; Siggs OM; Hewitt AW; Llamas B; Brown A; Baynam G; Mann GJ; McMorran BJ; Easteal S; Hermes A; Jenkins MR; Pearson G; Roe Y; Mohamed J; Murray B; Ormond-Parker L; Kneipp E; Nugent K; Patel HR; Deveson IW, 2023, 'The landscape of genomic structural variation in Indigenous Australians', Nature, 624, pp. 602 - 610, http://dx.doi.org/10.1038/s41586-023-06842-7

Senanayake A; Gamaarachchi H; Herath D; Ragel R, 2023, 'DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing', BMC Bioinformatics, 24, http://dx.doi.org/10.1186/s12859-023-05151-0

Liyanage K; Samarakoon H; Parameswaran S; Gamaarachchi H, 2023, 'Efficient end-to-end long-read sequence mapping using minimap2-fpga integrated with hardware accelerated chaining', Scientific Reports, 13, http://dx.doi.org/10.1038/s41598-023-47354-8

Samarakoon H; Ferguson JM; Jenner SP; Amos TG; Parameswaran S; Gamaarachchi H; Deveson IW, 2023, 'Flexible and efficient handling of nanopore sequencing signal data with slow5tools', Genome Biology, 24, http://dx.doi.org/10.1186/s13059-023-02910-3

Gong J; Saadat H; Gamaarachchi H; Javaid H; Hu XS; Parameswaran S, 2023, 'ApproxTrain: Fast Simulation of Approximate Multipliers for DNN Training and Inference', IEEE Transactions on Computer Aided Design of Integrated Circuits and Systems, 42, pp. 3505 - 3518, http://dx.doi.org/10.1109/TCAD.2023.3253045

Liyanage K; Gamaarachchi H; Ragel R; Parameswaran S, 2023, 'Cross Layer Design Using HW/SW Co-Design and HLS to Accelerate Chaining in Genomic Analysis', IEEE Transactions on Computer Aided Design of Integrated Circuits and Systems, 42, pp. 2924 - 2937, http://dx.doi.org/10.1109/TCAD.2023.3236559

Samarakoon H; Ferguson JM; Gamaarachchi H; Deveson IW, 2023, 'Accelerated nanopore basecalling with SLOW5 data format', Bioinformatics, 39, http://dx.doi.org/10.1093/bioinformatics/btad352

Shih PJ; Saadat H; Parameswaran S; Gamaarachchi H, 2023, 'Efficient real-time selective genome sequencing on resource-constrained devices', Gigascience, 12, http://dx.doi.org/10.1093/gigascience/giad046

Scriba CK; Stevanovski I; Chintalaphani SR; Gamaarachchi H; Ghaoui R; Ghia D; Henderson RD; Jordan N; Winkel A; Lamont PJ; Rodrigues MJ; Roxburgh RH; Weisburd B; Laing NG; Deveson IW; Davis MR; Ravenscroft G, 2023, 'RFC1 in an Australasian neurological disease cohort: Extending the genetic heterogeneity and implications for diagnostics', Brain Communications, 5, http://dx.doi.org/10.1093/braincomms/fcad208

Gamaarachchi H; Samarakoon H; Jenner SP; Ferguson JM; Amos TG; Hammond JM; Saadat H; Smith MA; Parameswaran S; Deveson IW, 2022, 'Fast nanopore sequencing data analysis with SLOW5', Nature Biotechnology, 40, pp. 1026 - 1029, http://dx.doi.org/10.1038/s41587-021-01147-4

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, 2022, 'Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing', Science Advances, 8, http://dx.doi.org/10.1126/sciadv.abm5386

Ferguson JM; Gamaarachchi H; Nguyen T; Gollon A; Tong S; Aquilina-Reid C; Bowen-James R; Deveson IW, 2022, 'InterARTIC: An interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses', Bioinformatics, 38, pp. 1443 - 1446, http://dx.doi.org/10.1093/bioinformatics/btab846

Abdul Cader JM; Abdul Cader AJM; Gamaarachchi H; Ragel RG, 2022, 'Optimisation of plagiarism detection using vector space model on CUDA architecture', International Journal of Innovative Computing and Applications, 13, pp. 232 - 244, http://dx.doi.org/10.1504/ijica.2022.125675

Mohamed Abdul Cader J; G. Ragel R; Gamaarachchi H; Mohamed Abdul Cader AJ, 2022, 'Optimization of Plagiarism Detection using Vector Space Model on CUDA Architecture', International Journal of Innovative Computing and Applications, 13, pp. 1 - 1, http://dx.doi.org/10.1504/ijica.2022.10042480

Gamaarachchi H, 2021, 'Computer Architecture-Aware Optimisation of DNA Analysis Systems', , http://arxiv.org/abs/2101.05012v1

Ferguson J; Gamaarachchi H; Nguyen T; Gollon A; Tong S; Aquilina-Reid C; Bowen-James R; Deveson I, 2021, '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

Gamaarachchi H; Samarakoon H; Jenner S; Ferguson J; Amos T; Hammond J; Saadat H; Smith M; Parameswaran S; Deveson I, 2021, 'SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis', , http://dx.doi.org/10.1101/2021.06.29.450255

Gamaarachchi H; Samarakoon H; Jenner S; Ferguson J; Amos T; Hammond J; Saadat H; Smith M; Parameswaran S; Deveson I, 2021, 'SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis', , http://dx.doi.org/10.21203/rs.3.rs-668517/v1

Bull RA; Adikari TN; Ferguson JM; Hammond JM; Stevanovski I; Beukers AG; Naing Z; Yeang M; Verich A; Gamaarachchi H; Kim KW; Luciani F; Stelzer-Braid S; Eden JS; Rawlinson WD; van Hal SJ; Deveson IW, 2020, 'Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-020-20075-6

Samarakoon H; Punchihewa S; Senanayake A; Hammond JM; Stevanovski I; Ferguson JM; Ragel R; Gamaarachchi H; Deveson IW, 2020, 'Genopo: a nanopore sequencing analysis toolkit for portable Android devices', Communications Biology, 3, http://dx.doi.org/10.1038/s42003-020-01270-z

Gamaarachchi H; Lam CW; Jayatilaka G; Samarakoon H; Simpson JT; Smith MA; Parameswaran S, 2020, 'GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis', BMC Bioinformatics, 21, http://dx.doi.org/10.1186/s12859-020-03697-x

Gamaarachchi H; Bayat A; Gaeta B; Parameswaran S, 2020, 'Cache Friendly Optimisation of de Bruijn Graph Based Local Re-Assembly in Variant Calling', IEEE ACM Transactions on Computational Biology and Bioinformatics, 17, pp. 1125 - 1133, http://dx.doi.org/10.1109/TCBB.2018.2881975

Samarakoon H; Punchihewa S; Senanayake A; Ragel R; Gamaarachchi H, 2020, 'F5N: Nanopore Sequence Analysis Toolkit for Android Smartphones', , http://dx.doi.org/10.1101/2020.03.22.002030

Gamaarachchi H; Parameswaran S; Smith MA, 2019, 'Featherweight long read alignment using partitioned reference indexes', Scientific Reports, 9, pp. 4318, http://dx.doi.org/10.1038/s41598-019-40739-8

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', bioRxiv, http://dx.doi.org/10.1101/756122

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

Gamaarachchi H; Ganegoda H, 2018, 'Power Analysis Based Side Channel Attack', , http://arxiv.org/abs/1801.00932v1

Gamaarachchi H; Ganegoda H; Ragel R, 2017, 'Breaking speck cryptosystem using correlation power analysis attack', Journal of the National Science Foundation of Sri Lanka, 45, pp. 393 - 404, http://dx.doi.org/10.4038/jnsfsr.v45i4.8233

Namal S; Gamaarachchi H; Lee GM; Um T-W, 2016, 'Autonomic Trust Management in Cloud-Based and Highly Dynamic IOT Applications', JOURNAL OF INTERNATIONAL BUSINESS RESEARCH AND MARKETING, 1, pp. 26 - 32, http://dx.doi.org/10.18775/jibrm.1849-8558.2015.15.3004

Conference Papers

Liyanage K; Gamaarachchi H; Saadat H; Li T; Samarakoon H; Parameswaran S, 2024, 'Accelerating Chaining in Genomic Analysis Using RISC- V Custom Instructions', in Proceedings Design Automation and Test in Europe Date

Gong J; Saadat H; Javaid H; Gamaarachchi H; Taubman D; Parameswaran S, 2024, 'SEA: Sign-Separated Accumulation Scheme for Resource-Efficient DNN Accelerators', in Proceedings Design Automation and Test in Europe Date

Gamaarachchi H; Liyanage K; Parameswaran S, 2023, 'Invited: Algorithms and Architectures for Accelerating Long Read Sequence Analysis', in Proceedings Design Automation Conference, http://dx.doi.org/10.1109/DAC56929.2023.10247772

Samarasinghe S; Premathilaka P; Herath W; Gamaarachchi H; Ragel R, 2021, 'Energy Efficient Adaptive Banded Event Alignment using OpenCL on FPGAs', in 2021 10th International Conference on Information and Automation for Sustainability Iciafs 2021, pp. 369 - 374, http://dx.doi.org/10.1109/ICIAfS52090.2021.9606056

Laguna AF; Gamaarachchi H; Yin X; Niemier M; Parameswaran S; Hu XS, 2020, 'Seed-and-Vote based In-Memory Accelerator for DNA Read Mapping', in IEEE ACM International Conference on Computer Aided Design Digest of Technical Papers Iccad, http://dx.doi.org/10.1145/3400302.3415651

Prasad Mohanty R; Gamaarachchi H; Lambert A; Parameswaran S, 2019, 'Swaram: Portable energy and cost efficient embedded system for genomic processing', in ACM Transactions on Embedded Computing Systems, http://dx.doi.org/10.1145/3358211

Gamaarachchi H; Fawsan M; Fasna F; Elkaduwe D, 2017, 'User-friendly interface for GPGPU programming', in Proceedings of the 2017 6th National Conference on Technology and Management Excel in Research and Build the Nation Nctm 2017, pp. 99 - 104, http://dx.doi.org/10.1109/NCTM.2017.7872835

Kumara TN; Gamaarachchi H; Prathap G; Ragel R, 2017, 'Generalized and hybrid fast-ICA implementation using GPU', in 16th International Conference on Advances in ICT for Emerging Regions Icter 2016 Conference Proceedings, pp. 13 - 20, http://dx.doi.org/10.1109/ICTER.2016.7829893

Prematilake M; Wickramasinghe B; Vithanage O; Gamaarachchi H; Ragel R, 2016, 'Accelerating Mutual Information Analysis based Power Analysis Attacks Using GPU', in 2016 IEEE International Conference on Information and Automation for Sustainability Interoperable Sustainable Smart Systems for Next Generation Iciafs 2016, http://dx.doi.org/10.1109/ICIAFS.2016.7946531

Jiffriya M; Jahan MA; Gamaarachchi H; Ragel RG, 2016, 'Accelerating text-based plagiarism detection using GPUs', in 2015 IEEE 10th International Conference on Industrial and Information Systems Iciis 2015 Conference Proceedings, pp. 395 - 400, http://dx.doi.org/10.1109/ICIINFS.2015.7399044

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