Dr Hasindu Gamaarachchi

Genomics Computing Research Scientist

Dr Hasindu Gamaarachchi

Hasindu Gamaarachchi completed his bachelor’s degree with first-class honours for Computer Engineering from the University of Peradeniya, Sri Lanka in 2015, where he received the award for best performance in Engineering. He has served as a lecturer at the Department of Computer Engineering and a re

Biography

Hasindu Gamaarachchi completed his bachelor’s degree with first-class honours for Computer Engineering from the University of Peradeniya, Sri Lanka in 2015, where he received the award for best performance in Engineering. 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. Hasindu completed his PhD in Computer Science and Engineering at UNSW Sydney under the supervision of Professor Sri Parameswaran, Dr Aleksandar Ignjatovic and Dr Martin A. Smith, in 2020. Hasindu has also been a visiting researcher at Garvan Institute of Medical Research during his PhD. 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.

Currently, Hasindu is working as a Genomics Computing Systems Engineer in the Genomic Technologies Group. His work is primarily focused on design, development, optimisation and maintenance of bioinformatics software for real-time third-generation sequencing data analysis and prototyping novel domain-specific computer systems for efficient genomics data analysis.

Hasindu Gamaarachchi completed his bachelor’s degree with first-class honours for Computer Engineering from the University of Peradeniya, Sri Lanka in 2015, where he received the award for best performance in Engineering. 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. Hasindu completed his PhD in Computer Science and Engineering at UNSW Sydney under the supervision of Professor Sri Parameswaran, Dr Aleksandar Ignjatovic and Dr Martin A. Smith, in 2020. Hasindu has also been a visiting researcher at Garvan Institute of Medical Research during his PhD. 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.

Currently, Hasindu is working as a Genomics Computing Systems Engineer in the Genomic Technologies Group. His work is primarily focused on design, development, optimisation and maintenance of bioinformatics software for real-time third-generation sequencing data analysis and prototyping novel domain-specific computer systems for efficient genomics data analysis.

Awards and Honours

2021 / Outstanding PhD Thesis award by Australian Bioinformatics And Computational Biology Society (ABACBS)
2021 / Dean's Award for Outstanding PhD Theses awarded by UNSW Sydney
2020 / Grand finalist (third place winner) in the Association for Computing Machinery Student Research Competition (ACM SRC) [https://src.acm.org/grand-finalists/2020]
2019 / First place in the Association for Computing Machinery Special Interest Group on Embedded Systems Student Research Competition (ACM SIGBED SRC) at Embedded Systems Week Conference [https://sigbed.org/2019/10/28/sigbed_src/]
2019 / Best poster award in Australasian Genomic Technologies Association (AGTA) Conference
2016 / C.A. Hewavitharana Prize awarded by University of Peradeniya for best performance in Engineering
2016 / Industrial and Financial Systems (IFS) Gold Medal awarded by University of Peradeniya for best
performance in Computer Engineering
2016 / Best presenter award in Present Around The World 2016 organised by Institution of Engineering and Technology-Young Professionals Section (IET-YPS) Sri Lanka
2016 / Best technical paper award in Annual Technical Conference of Institution of Engineering and Technology-Young Professionals Section (IET-YPS) Sri Lanka

Education

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

Selected Publications

  • Hasindu Gamaarachchi, Hiruna Samarakoon, Sasha Jenner, James Ferguson, Timothy Amos, Jillian Hammond, Hassaan Saadat, Martin Smith, Sri Parameswaran, and Ira Deveson. “Fast nanopore sequencing data analysis with SLOW5”. In: Nature Biotechnology (2022)
  • Igor Stevanovski, Sanjog Chintalaphani, Hasindu Gamaarachchi, James Ferguson, ... & Ira Deveson. “Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing”. In: Science Advances (2022)
  • James M Ferguson*, Hasindu Gamaarachchi*, Thanh Nguyen, Alyne Gollon, Stephanie Tong, Chiara Aquilina-Reid, Rachel Bowen-James, and Ira W Deveson. “InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses”. In: Bioinformatics (2021) *joint first author
  • Rowena A Bull, Thiruni Adikari, Jillian M Hammond, Igor Stevanovski, James M Ferguson, Alicia G Beukers, Zin Naing, Malinna Yeang, Andrey Verich, Hasindu Gamaarachchi, Ki Wook Kim, Fabio Luciani, Sacha Stelzer-Braid, John-Sebastian Eden, William D. Rawlinson, Sebastiaan J. van Hal, and Ira W. Deveson. “Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis”. In: Nature Communications 11.1 (2020)
  • Hiruna Samarakoon, Sanoj Punchihewa, Anjana Senanayake, Jillian M Hammond, Igor Stevanovski, James M Ferguson, Roshan Ragel, Hasindu Gamaarachchi#, and Ira W Deveson#. “Genopo: a nanopore sequencing analysis toolkit for portable Android devices”. Communications Biology 3.1 (2020) #joint senior author
  • Hasindu Gamaarachchi, Chun Wai Lam, Gihan Jayatilaka, Hiruna Samarakoon, Jared T Simpson, Martin A Smith, and Sri Parameswaran. “GPU Accelerated Adaptive Banded Event Alignment for Rapid Comparative Nanopore Signal Analysis”, BMC bioinformatics 21.1 (2020)
  • Hasindu Gamaarachchi, Sri Parameswaran, and Martin A Smith. “Featherweight long read alignment using partitioned reference indexes”. In: Scientific reports 9.1 (2019)
  • Ram Prasad Mohanty, Hasindu Gamaarachchi, Andrew Lambert, and Sri Parameswaran. “SWARAM: Portable Energy and Cost Efficient Embedded System for Genomic Processing”. In: ACM Transactions on Embedded Computing Systems (2019)
  • Hasindu Gamaarachchi, Arash Bayat, Bruno Gaeta, and Sri Parameswaran. “Cache Friendly Optimisation of de Bruijn Graph based Local Re-assembly in Variant Calling”. In: IEEE/ACM transactions on computational biology and bioinformatics (2018).