Hasindu Gamaarachchi

发表

ESWEEK: G: Real-time, Portable and Lightweight Nanopore DNA Sequence Analysis using System-on-Chip

Martin A. Smith, S. Parameswaran, Supervisor, 2020 .

SLOW5: a new �le format enables massive acceleration of nanopore sequencing data analysis

Ira W. Deveson, I. Deveson, Martin A. Smith, 2021 .

DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing

Damayanthi Herath, Hasindu Gamaarachchi, Anjana Senanayake, 2022, bioRxiv.

Efficient real-time selective genome sequencing on resource-constrained devices

S. Parameswaran, Hassaan Saadat, Hasindu Gamaarachchi, 2022, GigaScience.

ApproxTrain: Fast Simulation of Approximate Multipliers for DNN Training and Inference

S. Parameswaran, Haris Javaid, Hassaan Saadat, 2022, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems.

Fast nanopore sequencing data analysis with SLOW5

I. Deveson, Martin A. Smith, S. Parameswaran, 2022, Nature Biotechnology.

Fast nanopore sequencing data analysis with SLOW5

Ira W. Deveson, I. Deveson, Martin A. Smith, 2022, Nature Biotechnology.

SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis

Ira W. Deveson, I. Deveson, Martin A. Smith, 2021, bioRxiv.

GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis

Hasindu Gamaarachchi, Sri Parameswaran, Jared T. Simpson, 2019, BMC Bioinformatics.

Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

F. Luciani, I. Deveson, R. Bull, 2020, Nature Communications.

Cache Friendly Optimisation of de Bruijn Graph Based Local Re-Assembly in Variant Calling

Sri Parameswaran, Hasindu Gamaarachchi, Arash Bayat, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses

I. Deveson, Thanh Nguyen, J. Ferguson, 2021, bioRxiv.

Genopo: a nanopore sequencing analysis toolkit for portable Android devices

Hasindu Gamaarachchi, Hiruna Samarakoon, Ira W. Deveson, 2020, Communications Biology.

Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing

Ira W. Deveson, G. Ravenscroft, N. Laing, 2021, medRxiv.

Accelerated nanopore basecalling with SLOW5 data format

Ira W. Deveson, I. Deveson, Hasindu Gamaarachchi, 2023, bioRxiv.

SWARAM: Portable Energy and Cost Efficient Embedded System for Genomic Processing

Ram Prasad Mohanty, A. Lambert, S. Parameswaran, 2019, ACM Trans. Embed. Comput. Syst..

SWARAM

Ram Prasad Mohanty, Hasindu Gamaarachchi, Andrew Lambert, 2019, ACM Transactions on Embedded Computing Systems.

Seed-and-Vote based In-Memory Accelerator for DNA Read Mapping

Michael Niemier, Sri Parameswaran, Hasindu Gamaarachchi, 2020, 2020 IEEE/ACM International Conference On Computer Aided Design (ICCAD).

Optimization of Plagiarism Detection using Vector Space Model on CUDA Architecture

Hasindu Gamaarachchi, Jiffriya Mohamed Abdul Cader, Roshan G. Ragel, 2022, International Journal of Innovative Computing and Applications.

minimap2-fpga: Integrating hardware-accelerated chaining for efficient end-to-end long-read sequence mapping

S. Parameswaran, Hasindu Gamaarachchi, Hiruna Samarakoon, 2023, bioRxiv.

Methods for De-novo Genome Assembly

M. Wilkins, N. Deshpande, S. Parameswaran, 2020 .

Autonomic trust management in cloud-based and highly dynamic IoT applications

Gyu Myoung Lee, Hasindu Gamaarachchi, Tai-Won Um, 2015, 2015 ITU Kaleidoscope: Trust in the Information Society (K-2015).

Flexible and efficient handling of nanopore sequencing signal data with slow5tools

Ira W. Deveson, I. Deveson, S. Parameswaran, 2022, bioRxiv.

Extensive DNA methylome rearrangement during early lamprey embryogenesis

Ira W. Deveson, R. Klose, I. Deveson, 2023, bioRxiv.

Squigulator: simulation of nanopore sequencing signal data with tunable noise parameters

Ira W. Deveson, I. Deveson, Hasindu Gamaarachchi, 2023, bioRxiv.

RFC1 in an Australasian neurological disease cohort: extending the genetic heterogeneity and implications for diagnostics

B. Weisburd, G. Ravenscroft, N. Laing, 2023, Brain communications.

Invited: Algorithms and Architectures for Accelerating Long Read Sequence Analysis

Hasindu Gamaarachchi, Kisaru Liyanage, Sri Parameswaran, 2023, 2023 60th ACM/IEEE Design Automation Conference (DAC).

F5N: Nanopore Sequence Analysis Toolkit for Android Smartphones

Hasindu Gamaarachchi, Hiruna Samarakoon, Roshan Ragel, 2020, bioRxiv.

Featherweight long read alignment using partitioned reference indexes

Sri Parameswaran, Hasindu Gamaarachchi, Martin A Smith, 2018, Scientific Reports.

A CCG expansion in ABCD3 causes oculopharyngodistal myopathy in individuals of European ancestry

Liam G. Fearnley, B. Weisburd, M. Bahlo, 2023, medRxiv.

The landscape of genomic structural variation in Indigenous Australians

Ira W. Deveson, B. Llamas, O. Siggs, 2023, bioRxiv.

Breaking Speck cryptosystem using correlation power analysis attack

Harsha Ganegoda, Hasindu Gamaarachchi, Roshan Ragel, 2017 .

Streamlining remote nanopore data access with slow5curl

Ira W. Deveson, Hasindu Gamaarachchi, James M. Ferguson, 2023, bioRxiv.

Simulation of nanopore sequencing signal data with tunable parameters

Ira W. Deveson, Hasindu Gamaarachchi, Hiruna Samarakoon, 2024, Genome research.

Leveraging Basecaller’s Move Table to Generate a Lightweight k-mer Model

I. Deveson, Hasindu Gamaarachchi, Hiruna Samarakoon, 2024, bioRxiv.