Optimizing change detection in distributed digital collections: An architectural perspective of change detection. - Lakmal Meegahapola; Roshan Alwis; Eranga Nimalarathna; Vijini Mallawaarachchi; Dulani Meedeniya; Sampath Jayarathna (SNPD, 2017)

Efficient Bioinformatics Computations through GPU Accelerated Web Services. - Vijini Mallawaarachchi; Anuradha Wickramarachchi; Anuradha Welivita; Indika Perera; Dulani Meedeniya (ICACS, 2018)

Random Forest Classifier based Scheduler Optimization for Search Engine Web Crawlers. - Lakmal Meegahapola; Vijini Mallawaarachchi; Roshan Alwis; Eranga Nimalarathna; Dulani Meedeniya; Sampath Jayarathna (ICSCA, 2018)

Enhanced Student Learning in Proteomics - an Interactive Tool Support for Teaching Workflows. - Anuradha Wickramarachchi; Vijini Mallawaarachchi; Dulani Meedeniya; Indika Perera; Anuradha Welivita (TALE, 2018)

Experiential Learning in Bioinformatics - Learner Support for Complex Workflow Modelling and Analysis. - Vijini Mallawaarachchi; Anuradha Wickaramarachchi; Anuradha Weliwita; Indika Perera; Dulani Meedeniya (Int. J. Emerg. Technol. Learn., 2018)

Change Detection and Notification of Webpages: A Survey. - Vijini Mallawaarachchi; Lakmal Meegahapola; Roshan Alwis; Eranga Nimalarathna; Dulani Meedeniya; Sampath Jayarathna (CoRR, 2019)

GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs. - Vijini Mallawaarachchi; Anuradha Wickramarachchi; Yu Lin 001 (WABI, 2020)

GraphBin: refined binning of metagenomic contigs using assembly graphs. - Vijini Mallawaarachchi; Anuradha Wickramarachchi; Yu Lin 001 (Bioinform., 2020)

MetaBCC-LR: metagenomics binning by coverage and composition for long reads. - Anuradha Wickramarachchi; Vijini Mallawaarachchi; Vaibhav Rajan; Yu Lin 001 (Bioinform., 2020)

Phylogenetic Tree Construction Using K-Mer Forest- Based Distance Calculation. - Gihan Gamage; Nadeeshan Gimhana; Indika Perera; Shanaka Bandara; Thilina Pathirana; Anuradha Wickramarachchi; Vijini Mallawaarachchi (Int. J. Online Biomed. Eng., 2020)

Improving metagenomic binning results with overlapped bins using assembly graphs. - Vijini Mallawaarachchi; Anuradha Wickramarachchi; Yu Lin 001 (Algorithms Mol. Biol., 2021)

Change Detection and Notification of Web Pages: A Survey. - Vijini Mallawaarachchi; Lakmal Meegahapola; Roshan Madhushanka; Eranga Heshan; Dulani Meedeniya; Sampath Jayarathna (ACM Comput. Surv., 2021)

RepBin: Constraint-Based Graph Representation Learning for Metagenomic Binning. - Hansheng Xue; Vijini Mallawaarachchi; Yujia Zhang; Vaibhav Rajan; Yu Lin 001 (AAAI, 2022)

MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs. - Vijini Mallawaarachchi; Yu Lin 001 (RECOMB, 2022)

CH-Bin: A convex hull based approach for binning metagenomic contigs. - Sunera Chandrasiri; Thumula Perera; Anjala Dilhara; Indika Perera; Vijini Mallawaarachchi (Comput. Biol. Chem., 2022)

Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs. - Vijini Mallawaarachchi; Yu Lin 001 (J. Comput. Biol., 2022)

Ten simple rules and a template for creating workflows-as-applications. - Michael J. Roach 001; N. Tessa Pierce-Ward; Radoslaw Suchecki; Vijini Mallawaarachchi; Bhavya Nalagampalli Papudeshi; Scott A. Handley; C. Titus Brown; Nathan S. Watson-Haigh; Robert A. Edwards (PLoS Comput. Biol., 2022)

Phables: from fragmented assemblies to high-quality bacteriophage genomes. - Vijini Mallawaarachchi; Michael J. Roach 001; Przemyslaw Decewicz; Bhavya Nalagampalli Papudeshi; Sarah K. Giles; Susanna R. Grigson; George Bouras; Ryan D. Hesse; Laura K. Inglis; Abbey L. K. Hutton; Elizabeth A. Dinsdale; Robert A. Edwards (Bioinform., 2023)

Encoding Unitig-level Assembly Graphs with Heterophilous Constraints for Metagenomic Contigs Binning. - Hansheng Xue; Vijini Mallawaarachchi; Lexing Xie; Vaibhav Rajan (ICLR, 2024)

Solving genomic puzzles: computational methods for metagenomic binning. - Vijini Mallawaarachchi; Anuradha Wickramarachchi; Hansheng Xue; Bhavya Nalagampalli Papudeshi; Susanna R. Grigson; George Bouras; Rosa E. Prahl; Anubhav Kaphle; Andrey Verich; Berenice Talamantes-Becerra; Elizabeth A. Dinsdale; Robert A. Edwards (Briefings Bioinform., 2024)

Dnaapler: A tool to reorient circular microbial genomes. - George Bouras; Susanna R. Grigson; Bhavya Nalagampalli Papudeshi; Vijini Mallawaarachchi; Michael J. Roach 001 (J. Open Source Softw., 2024)

Koverage: Read-coverage analysis for massive (meta)genomics datasets. - Michael J. Roach 001; Bradley J. Hart; Sarah J. Beecroft; Bhavya Nalagampalli Papudeshi; Laura K. Inglis; Susanna R. Grigson; Vijini Mallawaarachchi; George Bouras; Robert A. Edwards (J. Open Source Softw., 2024)

GraphBin-Tk: assembly graph-based metagenomic binning toolkit. - Vijini Mallawaarachchi; Anuradha Wickramarachchi; Robert McArthur; Yapeng Lang; Katherine Caley; Gavin A. Huttley (J. Open Source Softw., 2025)