Dr Hasindu Gamaarachchi
Conjoint Lecturer

Dr Hasindu Gamaarachchi

  • 2020 / PhD in Computer Science and Engineering / UNSW Sydney / Australia
  • 2015 / BSc Engineering (Hons.) in Computer Engineering / University of Peradeniya / Sri Lanka
 

 

Engineering
Computer Science and Engineering

Hasindu Gamaarachchi focuses on the design, development and optimisation of bioinformatics software and hardware for real-time nanopore sequencing data analysis; and, prototyping novel domain-specific computer systems for efficient genomics data analysis. He has around ten years of experience in embedded computing systems, computer architecture, general-purpose computing with the use of a Graphics Processing Unit (GPU), high-performance computing and low-level system programming, which he leverages for the architecture-aware design of efficient computational systems for bioinformatics. Examples of his recent work include: a novel domain-specific file format for efficient nanopore data processing (Gammaarachchi, Nature Biotechnology 2022); GPU-accelerated adaptive banded event alignment algorithm which is a core component in nanopore data analysis (Gammaarachchi, BMC Bioinformatics 2019); memory optimisation of nanopore sequence alignment using partitioned indexes (Gammaarachchi, Scientific Reports 2020); and, optimisation of de Bruijn graphs using cache-friendly data structures in next-generation variant calling (Gammaarachchi, IEEE/ACM transactions on computational biology and bioinformatics / IEEE, 2018). 

Currently, Hasindu is working as a Genomics Computing Research Scientist in the Genomic Technologies Group at Garvan Institute of Medical Research.  He is also a conjoint lecturer at School of Computer Science and Engineering, UNSW Sydney. Hasindu completed his PhD in Computer Science and Engineering at UNSW Sydney in 2020. His PhD research has won multiple awards including third place in the Association for Computing Machinery Student Research Competition (ACM SRC) 2020, globally amongst the shortlisted competitors from over 20 major ACM conferences. He has served as a lecturer at the Department of Computer Engineering and a resource person at NVIDIA research centre at the University of Peradeniya. He completed his bachelor’s degree with first-class honours in Computer Engineering from the University of Peradeniya, Sri Lanka in 2015, where he received the award for best performance in Engineering.

Location
Building K17
  • Journal articles | 2022
    Cader JMA; Cader AJMA; Gamaarachchi H; Ragel RG, 2022, 'Optimisation of plagiarism detection using vector space model on CUDA architecture', International Journal of Innovative Computing and Applications, vol. 13, pp. 232 - 232, http://dx.doi.org/10.1504/ijica.2022.125675
    Journal articles | 2022
    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, vol. 38, pp. 1443 - 1446, http://dx.doi.org/10.1093/bioinformatics/btab846
    Journal articles | 2022
    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, vol. 40, pp. 1026 - 1029, http://dx.doi.org/10.1038/s41587-021-01147-4
    Journal articles | 2022
    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, vol. 13, pp. 1 - 1, http://dx.doi.org/10.1504/ijica.2022.10042480
    Journal articles | 2022
    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, vol. 8, pp. eabm5386, http://dx.doi.org/10.1126/sciadv.abm5386
    Journal articles | 2021
    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
    Journal articles | 2021
    Gamaarachchi H, 2021, 'Computer Architecture-Aware Optimisation of DNA Analysis Systems', , http://arxiv.org/abs/2101.05012v1
    Journal articles | 2021
    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
    Journal articles | 2021
    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
    Journal articles | 2020
    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, vol. 11, pp. 6272, http://dx.doi.org/10.1038/s41467-020-20075-6
    Journal articles | 2020
    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, vol. 17, pp. 1125 - 1133, http://dx.doi.org/10.1109/TCBB.2018.2881975
    Journal articles | 2020
    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, vol. 21, pp. 343, http://dx.doi.org/10.1186/s12859-020-03697-x
    Journal articles | 2020
    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, vol. 3, http://dx.doi.org/10.1038/s42003-020-01270-z
    Journal articles | 2020
    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
    Journal articles | 2019
    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
    Journal articles | 2019
    Gamaarachchi H; Parameswaran S; Smith MA, 2019, 'Featherweight long read alignment using partitioned reference indexes', Scientific Reports, vol. 9, http://dx.doi.org/10.1038/s41598-019-40739-8
    Journal articles | 2018
    Gamaarachchi H; Ganegoda H, 2018, 'Power Analysis Based Side Channel Attack', , http://arxiv.org/abs/1801.00932v1
    Journal articles | 2018
    Gamaarachchi H; Parameswaran S; Smith M, 2018, 'Featherweight long read alignment using partitioned reference indexes', BIORXIV, http://dx.doi.org/10.1101/386847
    Journal articles | 2017
    Gamaarachchi H; Ganegoda H; Ragel R, 2017, 'Breaking speck cryptosystem using correlation power analysis attack', Journal of the National Science Foundation of Sri Lanka, vol. 45, pp. 393 - 404, http://dx.doi.org/10.4038/jnsfsr.v45i4.8233
    Journal articles | 2016
    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, vol. 1, pp. 26 - 32, http://dx.doi.org/10.18775/jibrm.1849-8558.2015.15.3004
  • Preprints | 2022
    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
    Preprints | 2022
    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
    Preprints | 2022
    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
    Preprints | 2021
    Gamaarachchi H, 2021, Computer Architecture-Aware Optimisation of DNA Analysis Systems, http://dx.doi.org/10.48550/arxiv.2101.05012
    Conference Papers | 2021
    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), IEEE, presented at 2021 10th International Conference on Information and Automation for Sustainability (ICIAfS), 11 August 2021 - 13 August 2021, http://dx.doi.org/10.1109/iciafs52090.2021.9606056
    Preprints | 2021
    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
    Preprints | 2020
    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
    Preprints | 2020
    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, 2020, Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis, http://dx.doi.org/10.1101/2020.08.04.236893
    Conference Papers | 2020
    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
    Conference Papers | 2019
    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
    Preprints | 2018
    Gamaarachchi H; Ganegoda H, 2018, Power Analysis Based Side Channel Attack, http://dx.doi.org/10.48550/arxiv.1801.00932
    Conference Papers | 2017
    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 & MANAGEMENT (NCTM) - EXCEL IN RESEARCH AND BUILD THE NATION, IEEE, SRI LANKA, Sri Lanka Inst Informat Technol, pp. 99 - 104, presented at 6th National Conference on Technology and Management (NCTM), SRI LANKA, Sri Lanka Inst Informat Technol, 27 January 2017, http://dx.doi.org/10.1109/nctm.2017.7872835
    Conference Papers | 2017
    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
    Conference Papers | 2016
    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
    Conference Papers | 2016
    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
    Conference Papers | 2016
    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
    Conference Papers | 2015
    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
    Conference Papers | 2015
    Namal S; Gamaarachchi H; MyoungLee G; 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, presented at 2015 ITU Kaleidoscope: Trust in the Information Society (K-2015), 09 December 2015 - 11 December 2015, http://dx.doi.org/10.1109/kaleidoscope.2015.7383635
    Conference Papers | 2014
    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
    Conference Papers | 2014
    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 | 2014
    Gamaarachchi H; Ragel R; Jayasinghe D, 2014, Accelerating Correlation Power Analysis Using Graphics Processing Units, http://dx.doi.org/10.48550/arxiv.1412.7682