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🧬 Bioinformatics and Computational Biology 🧬


The following list of work has been undertaken during the period of 2018-August to present as a part of PhD candidature at Australian National University.


LRBinner: Binning Long Reads in Metagenomics Datasets

Anuradha Wickramarachchi, Yu Lin (21st International Workshop on Algorithms in Bioinformatics (WABI 2021)) DOI: 10.4230/LIPIcs.WABI.2021.11

PlasLR Enables Adaptation of Plasmid Prediction for Error-Prone Long Reads (preprint available)

Anuradha Wickramarachchi, Vijini Mallawaarachchi, Lianrong Pu, Yu Lin (14th Great Lakes Bioinformatics (GLBIO) conference) DOI: 10.1101/2021.06.14.448306

GraphPlas: Refined Classification of Plasmid Sequences using Assembly Graphs

Anuradha Wickramarachchi, Yu Lin (EEE/ACM Transactions on Computational Biology and Bioinformatics 2021) DOI: 10.1109/TCBB.2021.3082915

MetaBCC-LR: Metagenomics Binning by Coverage and Composition for Long Reads

Anuradha Wickramarachchi, Vijini Mallawaarachchi, Vaibhav Rajan, Yu Lin (ISMB 2020) DOI: 10.1093/bioinformatics/btaa441

GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs

Vijini G Mallawaarachchi, Anuradha S Wickramarachchi, Yu Lin (20th International Workshop on Algorithms in Bioinformatics; WABI 2020) DOI: 10.4230/LIPIcs.WABI.2020.8

GraphBin: refined binning of metagenomic contigs using assembly graphs

Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin (Bioinformatics 2020) DOI: 10.1093/bioinformatics/btaa180

Experiential Learning in Bioinformatics-Learner Support for Complex Workflow Modelling and Analysis

Vijini Mallawaarachchi, Anuradha Wickaramarachchi, Anuradha Weliwita, Indika Perera, Dulani Meedeniya (International Journal of Emerging Technologies in Learning Vol 13, No 12 (2018)) DOI: 10.3991/ijet.v13i12.8608


💻 Software Engineering 💻


The following list of work has been undertaken during the period of 2017-August to 2018-August as a part of BSc undergraduate course (honours year project) at University of Moratuwa.


Managing Complex Workflows in Bioinformatics: An Interactive Toolkit with GPU Acceleration

Anuradha Welivita, Indika Perera, Dulani Meedeniya, Anuradha Wickramarachchi, Vijini Mallawaarachchi (IEEE Transactions on Nanobioscience 2018) DOI: 10.1109/TNB.2018.2837122

Use of Nomadic Computing Devices for Storage Synchronization

Anuradha Wickramarachchi, Dulaj Atapattu, Pamoda Wimalasiri, Ravidu Mallawa Arachchi, Gihan Dias (International Conference on Information Networking (ICOIN), 2018) DOI: 10.1109/ICOIN.2018.8343204


👩🏻‍💻 Student Supervision at University of Motaruwa (FYPs) 🧑🏻‍💻


The following list of work has been undertaken during the period of 2018-August to present as an external supervisor for students in honours year BSc in Computer Science and Engineering. The respective work is individual efforts of students and my contribution has been guiding them, providing resources and support in designing experiments/writing/modelling.


MetaG: A Comprehensive Visualization Tool to Explore Metagenomes

Kalana Wijegunarathna, Uditha Maduranga, Sadeep Weerasinghe, Indika Perera, Anuradha Wickramarachchi (2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)) DOI: 10.1109/BIBM49941.2020.9313166

Resource Aware Task Clustering for Scientific Workflow Execution in High Performance Computing Environments

Ayesh Weerasinghe, Kalana Wijethunga, Randika Jayasekara, Indika Perera, Anuradha Wickramarachchi 2020 IEEE 22nd International Conference on High Performance Computing and Communications; IEEE 18th International Conference on Smart City; IEEE 6th International Conference on Data Science and Systems (HPCC/SmartCity/DSS) DOI: 10.1109/HPCC-SmartCity-DSS50907.2020.00032

SwarmForm: A Distributed Workflow Management System with Task Clustering

Ayesh Weerasinghe, Kalana Wijethunga, Randika Jayasekara, Indika Perera, Anuradha Wickramarachchi (2020 20th International Conference on Advances in ICT for Emerging Regions (ICTer)) DOI: 10.1109/ICTer51097.2020.9325496

Dimensionality Reduction for Cluster Identification in Metagenomics Using Autoencoders

Uditha Maduranga, Kalana Wijegunarathna, Sadeep Weerasinghe, Indika Perera, Anuradha Wickramarachchi (2020 20th International Conference on Advances in ICT for Emerging Regions (ICTer)) DOI: 10.1109/ICTer51097.2020.9325447

Phylogenetic Tree Construction Using K-Mer Forest-Based Distance Calculation

Gihan Gamage, Nadeeshan Gimhana, Indika Perera, Shanaka Bandara, Thilina Pathirana, Anuradha Wickramarachchi, Vijini Mallawaarachchi URL: learntechlib

Genetic Distance Calculation based on Locality Sensitive Hashing

Thilina Pathirana, Shanaka Bandara, Gihan Gamage, Gimhana Silva, Anuradha Wickramaarachchi, Indika Perera DOI: biorxiv

Alignment-free Whole Genome Comparison Using k-mer Forests

G Gamage, N Gimhana, A Wickramarachchi, V Mallawaarachchi, I Perera (2019 19th International Conference on Advances in ICT for Emerging Regions (ICTer)) DOI: 10.1109/ICTer48817.2019.9023714

An Adapter Architecture for Heterogeneous Data Processing in Bioinformatics Pipelines

Damitha Lenadora, Anuradha Wickramarachchi, Dulani Meedeniya, Vijini Mallawaarachchi, Indika Perera (2019 Moratuwa Engineering Research Conference (MERCon)) DOI: 10.1109/MERCon.2019.8818781

A Realtime Monitoring Platform for Workflow Subroutines

D Rathnayake, A Wickramarachchi, V Mallawaarachchi, D Meedeniya, I Perera (2018 18th International Conference on Advances in ICT for Emerging Regions (ICTer)) DOI: 10.1109/ICTER.2018.8615557