By Dr Hasindu Malshan Gamaarachchi

Journal articles

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

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

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