Publications

GraphBin: Refined Binning of Metagenomic Contigs using Assembly Graphs

Vijini Mallawaarachchi, Anuradha Wickramarachchi, and Yu Lin

Bioinformatics, btaa180, https://doi.org/10.1093/bioinformatics/btaa180.
DCHap: A divide-and-conquer haplotype phasing algorithm for third-generation sequencing data

Yanbo Li, and Yu Lin

The 18th Asia Pacific Bioinformatics Conference (APBC 2020).
MetaBCC-LR: Metagenomics Binning by Coverageand Composition for Long Reads

Anuradha Wickramarachchi, Vijini Mallawaarachchi, Vaibhav Rajan, and Yu Lin

The 28th Conference on Intelligent Systems for Molecular Biology (ISMB 2020).
Modeling Dynamic Heterogeneous Network for Link Prediction using Hierarchical Attention with Temporal RNN

Hansheng Xue, Luwei Yang, Wen Jiang, Yi Wei, Yi Hu, and Yu Lin

The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD 2020).
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs

Vijini Mallawaarachchi, Anuradha Wickramarachchi, and Yu Lin

The Workshop on Algorithms in Bioinformatics (WABI 2020).
Kmer2SNP: reference-free SNP calling from raw reads based on matching

Yanbo Li, Hardip Patel, and Yu Lin

International Conference on Bioinformatics and Biomedicine (BIBM 2020).
MultiTrans: a novel algorithm for transcriptome assembly through mixed integer linear programming

Jin Zhao, Haodi Feng, Daming Zhu, and Yu Lin

The 19th Asia Pacific Bioinformatics Conference (APBC 2021).
GraphPlas: Refined Classification of Plasmid Sequences using Assembly Graphs

Anuradha Wickramarachchi and Yu Lin

The 19th Asia Pacific Bioinformatics Conference (APBC 2021).
Multiplex Bipartite Network Embedding using Dual Hypergraph Convolutional Networks

Hansheng Xue, Luwei Yang, Vaibhav Rajan, Wen Jiang, Yi Wei, and Yu Lin

The 30th International World Wide Web Conference (The Web Conf 2021).
Improving metagenomic binning results with overlapped bins using assembly graphs

Vijini Mallawaarachchi, Anuradha Wickramarachchi, and Yu Lin

Algorithms for Molecular Biology.
RepBin: Constraint-based Graph Representation Learning for Metagenomic Binning

Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan, and Yu Lin

36th AAAI Conference on Artificial Intelligence (AAAI 2022).
MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

Vijini Mallawaarachchi and Yu Lin

The 26th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2022).