Vijini Mallawaarachchi

Publications

Selected journal and conference publications.

Selected Journal Publications

  1. agtools: a software framework to manipulate assembly graphs Bioinformatics Advances, 6(1), 2026 Authors: Vijini Mallawaarachchi, George Bouras, Ryan R Wick, Susanna R Grigson, Bhavya Papudeshi and Robert A Edwards
  2. GraphBin-Tk: assembly graph-based metagenomic binning toolkit Journal of Open Source Software, 10(109), 2025 Authors: Vijini Mallawaarachchi, Anuradha Wickramarachchi, Robert McArthur, Yapeng Lang, Katherine Caley and Gavin Huttley
  3. Solving genomic puzzles: computational methods for metagenomic binning Briefings in Bioinformatics, 25(5), 2024 Authors: Vijini Mallawaarachchi, Anuradha Wickramarachchi, Hansheng Xue, Bhavya Papudeshi, Susanna R Grigson, George Bouras, Rosa E Prahl, Anubhav Kaphle, Andrey Verich, Berenice Talamantes-Becerra, Elizabeth A Dinsdale and Robert A Edwards
  4. Contigs directed gene annotation for accurate protein sequence database construction in metaproteomics Microbiome, 12(1), 2024 Authors: Enhui Wu, Vijini Mallawaarachchi, Jinzhi Zhao, Yi Yang, Hebin Liu, Xiaoqing Wang, Chengpin Shen, Yu Lin and Liang Qiao
  5. Phables: from fragmented assemblies to high-quality bacteriophage genomes Bioinformatics, 39(10), 2023 Authors: Vijini Mallawaarachchi, Michael J Roach, Przemyslaw Decewicz, Bhavya Papudeshi, Sarah K Giles, Susanna R Grigson, George Bouras, Ryan D Hesse, Laura K Inglis, Abbey L K Hutton, Elizabeth A Dinsdale and Robert A Edwards
  6. Accurate binning of metagenomic contigs using composition, coverage, and assembly graphs Journal of Computational Biology, 29(12), 2022 Authors: Vijini Mallawaarachchi and Yu Lin
  7. CH-Bin: A convex hull based approach for binning metagenomic contigs Computational Biology and Chemistry, 100, 2022 Accepted for presentation at the 20th Asia Pacific Bioinformatics Conference (APBC 2022), Malaysia Authors: Sunera Chandrasiri, Thumula Perera, Anjala Dilhara, Indika Perera and Vijini Mallawaarachchi
  8. Improving metagenomic binning results with overlapped bins using assembly graphs Algorithms for Molecular Biology, 16(1), 2021 Authors: Vijini Mallawaarachchi, Anuradha Wickramarachchi and Yu Lin
  9. GraphBin: refined binning of metagenomic contigs using assembly graphs Bioinformatics, 36(11), 2020 Authors: Vijini Mallawaarachchi, Anuradha Wickramarachchi and Yu Lin
  10. Change Detection and Notification of Web Pages: A Survey ACM Computing Surveys, 53(1), 2020 Authors: Vijini Mallawaarachchi, Lakmal Meegahapola, Roshan Madhushanka, Eranga Heshan, Dulani Meedeniya and Sampath Jayarathna
  11. Experiential Learning in Bioinformatics - Learner Support for Complex Workflow Modelling and Analysis International Journal of Emerging Technologies in Learning (iJET), 13(12), 2018 Authors: Vijini Mallawaarachchi, Anuradha Wickramarachchi, Anuradha Welivita, Indika Perera and Dulani Meedeniya
  12. Managing Complex Workflows in Bioinformatics - An Interactive Toolkit with GPU Acceleration IEEE Transactions on NanoBioscience, 17(3), 2018 Authors: Anuradha Welivita, Indika Perera, Dulani Meedeniya, Anuradha Wickramarachchi and Vijini Mallawaarachchi

Selected Conference Publications

  1. Encoding unitig-level assembly graphs with heterophilous constraints for metagenomic contigs binning 12th International Conference on Learning Representations (ICLR 2024), Vienna, Austria, May 2024 Authors: Hansheng Xue, Vijini Mallawaarachchi, Lexing Xie and Vaibhav Rajan
  2. MetaCoAG: binning metagenomic contigs via composition, coverage and assembly graphs 26th International Conference on Research in Computational Molecular Biology (RECOMB 2022), San Diego, USA, May 2022 Authors: Vijini Mallawaarachchi and Yu Lin
  3. RepBin: Constraint-based graph representation learning for metagenomic binning Thirty-Seventh AAAI Conference on Artificial Intelligence (AAAI 2022), Virtual Conference, Feb 2022 Authors: Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan and Yu Lin
  4. GraphBin2: refined and overlapped binning of metagenomic contigs using assembly graphs 20th International Workshop on Algorithms in Bioinformatics (WABI 2020), Pisa, Italy (Virtual Conference), September 2020 Authors: Vijini Mallawaarachchi, Anuradha Wickramarachchi and Yu Lin
  5. MetaBCC-LR: Metagenomics Binning by Coverage and Composition for Long Reads 28th Conference on Intelligent Systems for Molecular Biology ISMB'20 (Virtual Conference), July 2020 Authors: Anuradha Wickramarachchi, Vijini Mallawaarachchi, Vaibhav Rajan and Yu Lin
  6. Enhanced Student Learning in Proteomics - An Interactive Tool Support for Teaching Workflows IEEE International Conference on Teaching, Assessment and Learning for Engineering (TALE) 2018, Wollongong, Australia, December 2018 Authors: Anuradha Wickramarachchi, Vijini Mallawaarachchi, Anuradha Welivita, Indika Perera and Dulani Meedeniya
  7. Efficient Scheduling for Scalable Bioinformatics Analysis Platform with Microservices 18th IEEE International Conference of Advances in ICT for Emerging Regions (ICTer) 2018, Colombo, Sri Lanka, September 2018 Authors: Sanduni Prasadi, Vijini Mallawaarachchi, Anuradha Wickramarachchi, Indika Perera and Dulani Meedeniya
  8. Efficient Bioinformatics Computations through GPU Accelerated Web Services 2018 2nd International Conference on Algorithms, Computing and Systems, Beijing, China, July 2018 Authors: Vijini Mallawaarachchi, Anuradha Wickramarachchi, Anuradha Welivita, Indika Perera and Dulani Meedeniya
  9. Random Forest Classifier based Scheduler Optimization for Search Engine Web Crawlers 7th International Conference on Software and Computer Applications (ICSCA) 2018, Kuantan, Malaysia, February 2018 Awards: Won the excellent oral presentation certificate of the Computer Science and Information Communication session Authors: Lakmal Meegahapola, Vijini Mallawaarachchi, Roshan Alwis, Eranga Nimalarathna, Dulani Meedeniya and Sampath Jayarathna
  10. Adaptive Technique for Web Page Change Detection using Multi-threaded Crawlers 7th IEEE International Conference on Innovative Computing Technology (INTECH) 2017, London, United Kingdom, August 2017 Authors: Lakmal Meegahapola, Roshan Alwis, Eranga Nimalarathna, Vijini Mallawaarachchi, Dulani Meedeniya and Sampath Jayarathna