Ms Vijini Mallawaarachchi

I am currently pursuing my PhD studies at the School of Computing, at the Australian National University. My research work is focused on algorithms and computational models related to metagenomics binning. Metagenomics involves the study of various genetic material obtained from the genomes found in microbial communities. A microbial community such as lake water or forest soil can contain a large number of organisms. We need to identify the species present in order to investigate the taxonomic structure of a given metagenomic sample. Firstly, reads are assembled into longer contigs which are then binned into groups of contigs that belong to different taxonomic groups present in the metagenomic sample. Various reference-free contig-binning methods have been proposed previously that make use of composition and covergae information of the contigs. However, the majority of these tools fail to recover short contigs.

As metagenomic contigs are derived from assembling the reads, they are output from the underlying assembly graph which holds valuable connectivity information between contigs that can be used for binning. My research work aims to develop improved contig-binning tools that can recover short contigs and bin the contigs accurately with the help of assembly graphs.

My supervisors are Dr. Yu Lin. Prof. Weifa Liang and Prof. Gavin Huttley.

  • Genomics
  • Metagenomics
  • Algorithms
  • Data Science
  • Machine Learning

Improving metagenomic binning results with overlapped bins using assembly graphs
May 2021
BMC Algorithms for Molecular Biology
Authors: Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin

GraphBin2: Refined and overlapped binning of metagenomic contigs using assembly graphs
Sep 2020
20th International Workshop on Algorithms in Bioinformatics (WABI 2020), Pisa, Italy (Virtual Conference)
Authors: Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin

MetaBCC-LR: Metagenomics Binning by Coverage and Composition for Long Reads
Jul 2020 
28th Conference on Intelligent Systems for Molecular Biology ISMB’20 (Virtual Conference) 
Authors: Anuradha Wickramarachchi, Vijini Mallawaarachchi, Yu Lin

GraphBin: Refined binning of metagenomic contigs using assembly graphs 
Mar 2020 
Bioinformatics, Volume 36, Issue 11, June 2020, Pages 3307–3313
Authors: Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin

Change Detection and Notification of Web Pages: A Survey 
Feb 2020 
ACM Computing Surveys (CSUR) Vol. 53 No. 1 Article No. 15 
Authors: Vijini Mallawaarachchi, Lakmal Meegahapola, Roshan Madhushanka, Eranga Heshan, Dulani Meedeniya, Sampath Jayarathna

Experiential Learning in Bioinformatics – Learner Support for Complex Workflow Modelling and Analysis
Dec 2018
International Journal of Emerging Technologies in Learning (iJET) 13(12):19-34
Authors: Vijini Mallawaarachchi, Anuradha Wickramarachchi, Anuradha Welivita, Indika Perera, Dulani Meedeniya

ANU PhD Scholarship (International)
The Australian National University, Australia
2018

ANU HDR Merit Scholarship
The Australian National University, Australia
2018

Excellent Oral Presentation award
Computer Science and Information Communication session at the 7th ACM International Conference on Software and Computer Applications (ICSCA) 2018, Kuantan, Malaysia
2018

ACM-W Scholarship
Association for Computing Machinery (ACM)
2018

Dean’s List in semesters 1 to 8 (Undergraduate)
University of Moratuwa, Sri Lanka
2014 - 2018

Education

Bachelor of Science in Computer Science and Engineering (Honours) - 1st Class
University of Moratuwa, Sri Lanka (https://uom.lk/)
2014 - 2018

Work Experience

Tutor (Casual Sessional Academic)
School of Computing, The Australian National University, Australia
2019 - Present

Junior Consultant
Department of Computer Science and Engineering, University of Moratuwa, Sri Lanka
Jan 2018 - Jul 2018

Visiting Instructor
Department of Computer Science and Engineering, University of Moratuwa, Sri Lanka
Feb 2017 - Dec 2017

Intern Software Engineer
Sysco Labs, Sri Lanka (https://syscolabs.lk/)
Jul 2016 - Dec 2016

Updated:  10 August 2021/Responsible Officer:  Dean, CECS/Page Contact:  CECS Marketing