Last updated in March 2023

"keep it simple, stupid"

Hiruna Samarakoon

hiruna@unsw.edu.au
Uninversity of New South Wales, Sydeny 2032, Australia
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Contents:

Education

School of Computer Science and Engineering, University of New South Wales - Sydney, Australia : May 2021 - Present

Garvan Institute of Medical Research - Sydney, Australia : May 2021 - Present

Faculty of Engineering, University of Peradeniya - Peradeniya, Sri Lanka : Nov 2015 - Aug 2020

Trinity College - Kandy, Sri Lanka : 2006 - 2014

Academic publications

  1. Samarakoon, H., Ferguson, J.M., Gamaarachchi, H. and Deveson, I.W., 2023. Accelerated nanopore basecalling with SLOW5 data format. bioRxiv, pp.2023-02.

  2. Samarakoon, H., Ferguson, J.M., Jenner, S.P., Amos, T.G., Parameswaran, S., Gamaarachchi, H. and Deveson, I.W., 2022. Flexible and efficient handling of nanopore sequencing signal data with slow5tools. bioRxiv, pp.2022-06 .

  3. Gamaarachchi, H., Samarakoon, H., Jenner, S.P., Ferguson, J.M., Amos, T.G., Hammond, J.M., Saadat, H., Smith, M.A., Parameswaran, S. and Deveson, I.W., 2022. Fast nanopore sequencing data analysis with SLOW5. Nature biotechnology, pp.1-4.

  4. Nilanthi, R.M.R., Samarakoon, H., Jayawardana, N., Hathurusinghe, B., Wijesundara, S. and Bandaranayake, P.C.G., 2022. Strobilanthes glandulata (Acanthaceae), a new species from Sri Lanka based on morphological and molecular evidence. Phytotaxa, 573(1), pp.1-14.

  5. Nilanthi, R.M.R., Samarakoon, H., Jayawardana, N., Wijesundara, S. and Bandaranayake, P.C.G., 2021. Strobilanthes medahinnensis (Acanthaceae) a new species, based on morphological and molecular data, from the Peak Wilderness Nature Reserve, Sri Lanka. Phytotaxa, 514(1), pp.26-38.

  6. Samarakoon, H., Punchihewa, S., Senanayake, A., Hammond, J.M., Stevanovski, I., Ferguson, J.M., Ragel, R., Gamaarachchi, H. and Deveson, I.W., 2020. Genopo: a nanopore sequencing analysis toolkit for portable Android devices. Communications biology, 3(1), pp.1-5.

  7. Gamaarachchi, H., Lam, C.W., Jayatilaka, G., Samarakoon, H., Simpson, J.T., Smith, M.A. and Parameswaran, S., 2020. GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis. BMC bioinformatics, 21(1), pp.1-13.

Awards and Recognition

Work experience

Agricultural Biotechnology Center, University of Peradeniya

20face Enschede, the Netherlands - a company providing privacy proof biometrics

Undergraduate final year research project

The project had three objectives.

  1. Designing a smartphone application for analyzing nanopore DNA sequencing data
  2. Aggregate the computing power of smartphones using a server-client setup for real-time DNA analysis in parallel to DNA sequencing
  3. Algorithmic enhancement in DNA methylation profiling pipeline to limit data storage requirements and introduce complete real-time DNA methylation profiling using smartphones.

Projects

The following are some of the projects I have worked on during my undergraduate studies. Please visit https://github.com/hiruna72 for more information.

Other Interests and Activities

Learning is a never-ending journey. I have taken some online courses in this pandemic situation.

I've started a new habit of writing to share knowledge with a wide audience.

I find myself as an enthusiastic sportsman. I play football regularly. I have won university colors for Hockey in three consecutive years - 2016/17/18. I was lucky enough to be the vice-captain of the college Hockey team (2006-2010).