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Vijini Mallawaarachchi

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2020 – today

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2024
[j13]
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  - journals/bib/MallawaarachchiWXPGBPKV24
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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:
Solving genomic puzzles: computational methods for metagenomic binning. Briefings Bioinform. 25(5) (2024)
[j12]
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George Bouras, Susanna R. Grigson, Bhavya Nalagampalli Papudeshi, Vijini Mallawaarachchi, Michael J. Roach:
Dnaapler: A tool to reorient circular microbial genomes. J. Open Source Softw. 9(94): 5968 (2024)
[j11]
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Michael J. Roach, Bradley J. Hart, Sarah J. Beecroft, Bhavya Nalagampalli Papudeshi, Laura K. Inglis, Susanna R. Grigson, Vijini Mallawaarachchi, George Bouras, Robert A. Edwards:
Koverage: Read-coverage analysis for massive (meta)genomics datasets. J. Open Source Softw. 9(96): 6235 (2024)
[c8]
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Hansheng Xue, Vijini Mallawaarachchi, Lexing Xie, Vaibhav Rajan:
Encoding Unitig-level Assembly Graphs with Heterophilous Constraints for Metagenomic Contigs Binning. ICLR 2024
2023
[j10]
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  - journals/bioinformatics/MallawaarachchiRDPGGBHIH23
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Vijini Mallawaarachchi, Michael J. Roach, 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:
Phables: from fragmented assemblies to high-quality bacteriophage genomes. Bioinform. 39(10) (2023)
2022
[j9]
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Sunera Chandrasiri, Thumula Perera, Anjala Dilhara, Indika Perera, Vijini Mallawaarachchi:
CH-Bin: A convex hull based approach for binning metagenomic contigs. Comput. Biol. Chem. 100: 107734 (2022)
[j8]
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Vijini Mallawaarachchi, Yu Lin:
Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs. J. Comput. Biol. 29(12): 1357-1376 (2022)
[j7]
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Michael J. Roach, N. Tessa Pierce-Ward, Radoslaw Suchecki, Vijini Mallawaarachchi, Bhavya Nalagampalli Papudeshi, Scott A. Handley, C. Titus Brown, Nathan S. Watson-Haigh, Robert A. Edwards:
Ten simple rules and a template for creating workflows-as-applications. PLoS Comput. Biol. 18(12): 1010705 (2022)
[c7]
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  - conf/aaai/XueMZR022
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Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan, Yu Lin:
RepBin: Constraint-Based Graph Representation Learning for Metagenomic Binning. AAAI 2022: 4637-4645
[c6]
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Vijini Mallawaarachchi, Yu Lin:
MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs. RECOMB 2022: 70-85
2021
[j6]
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  - journals/almob/Mallawaarachchi21
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Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin:
Improving metagenomic binning results with overlapped bins using assembly graphs. Algorithms Mol. Biol. 16(1): 3 (2021)
[j5]
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  - journals/csur/Mallawaarachchi20
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Vijini Mallawaarachchi, Lakmal Meegahapola, Roshan Madhushanka, Eranga Heshan, Dulani Meedeniya, Sampath Jayarathna:
Change Detection and Notification of Web Pages: A Survey. ACM Comput. Surv. 53(1): 15:1-15:35 (2021)
[i2]
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  - journals/corr/abs-2112-11696
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Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan, Yu Lin:
RepBin: Constraint-based Graph Representation Learning for Metagenomic Binning. CoRR abs/2112.11696 (2021)
2020
[j4]
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  - journals/bioinformatics/Mallawaarachchi20
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Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin:
GraphBin: refined binning of metagenomic contigs using assembly graphs. Bioinform. 36(11): 3307-3313 (2020)
[j3]
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  - journals/bioinformatics/Wickramarachchi20
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Anuradha Wickramarachchi, Vijini Mallawaarachchi, Vaibhav Rajan, Yu Lin:
MetaBCC-LR: metagenomics binning by coverage and composition for long reads. Bioinform. 36(Supplement-1): i3-i11 (2020)
[j2]
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  - journals/ijoe/GamageGPBPWM20
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Gihan Gamage, Nadeeshan Gimhana, Indika Perera, Shanaka Bandara, Thilina Pathirana, Anuradha Wickramarachchi, Vijini Mallawaarachchi:
Phylogenetic Tree Construction Using K-Mer Forest- Based Distance Calculation. Int. J. Online Biomed. Eng. 16(7): 4-20 (2020)
[c5]
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  - conf/wabi/Mallawaarachchi20
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Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin:
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs. WABI 2020: 8:1-8:21

2010 – 2019

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2019
[i1]
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  - journals/corr/abs-1901-02660
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Vijini Mallawaarachchi, Lakmal Meegahapola, Roshan Alwis, Eranga Nimalarathna, Dulani Meedeniya, Sampath Jayarathna:
Change Detection and Notification of Webpages: A Survey. CoRR abs/1901.02660 (2019)
2018
[j1]
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  - journals/ijet/Mallawaarachchi18
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Vijini Mallawaarachchi, Anuradha Wickaramarachchi, Anuradha Weliwita, Indika Perera, Dulani Meedeniya:
Experiential Learning in Bioinformatics - Learner Support for Complex Workflow Modelling and Analysis. Int. J. Emerg. Technol. Learn. 13(12): 19-34 (2018)
[c4]
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Vijini Mallawaarachchi, Anuradha Wickramarachchi, Anuradha Welivita, Indika Perera, Dulani Meedeniya:
Efficient Bioinformatics Computations through GPU Accelerated Web Services. ICACS 2018: 94-98
[c3]
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  - conf/icsca/MeegahapolaMANM18
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Lakmal Meegahapola, Vijini Mallawaarachchi, Roshan Alwis, Eranga Nimalarathna, Dulani Meedeniya, Sampath Jayarathna:
Random Forest Classifier based Scheduler Optimization for Search Engine Web Crawlers. ICSCA 2018: 285-289
[c2]
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  - conf/tale/Wickramarachchi18
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Anuradha Wickramarachchi, Vijini Mallawaarachchi, Dulani Meedeniya, Indika Perera, Anuradha Welivita:
Enhanced Student Learning in Proteomics - an Interactive Tool Support for Teaching Workflows. TALE 2018: 228-235
2017
[c1]
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  - conf/snpd/MeegahapolaANMM17
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Lakmal Meegahapola, Roshan Alwis, Eranga Nimalarathna, Vijini Mallawaarachchi, Dulani Meedeniya, Sampath Jayarathna:
Optimizing change detection in distributed digital collections: An architectural perspective of change detection. SNPD 2017: 277-282

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