GraphBin: Refined Binning of Metagenomic Contigs using Assembly Graphs
Vijini Mallawaarachchi, Anuradha Wickramarachchi, and Yu LinBioinformatics, 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 LinThe 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 LinThe 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 LinThe 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 LinThe Workshop on Algorithms in Bioinformatics (WABI 2020).
Kmer2SNP: reference-free SNP calling from raw reads based on matching
Yanbo Li, Hardip Patel, and Yu LinInternational 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 LinThe 19th Asia Pacific Bioinformatics Conference (APBC 2021).
GraphPlas: Refined Classification of Plasmid Sequences using Assembly Graphs
Anuradha Wickramarachchi and Yu LinThe 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 LinThe 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 LinAlgorithms for Molecular Biology.
RepBin: Constraint-based Graph Representation Learning for Metagenomic Binning
Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan, and Yu Lin36th AAAI Conference on Artificial Intelligence (AAAI 2022).
MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
Vijini Mallawaarachchi and Yu LinThe 26th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2022).
Metagenomics Binning of Long Reads Using Read-Overlap Graphs
Anuradha Wickramarachchi and Yu LinThe 19th Annual Satellite Conference of RECOMB on Comparative Genomics (RECOMB-CG 2022).
Graph Coloring via Neural Networks for Haplotype Assembly and Viral Quasispecies Reconstruction
Hansheng Xue, vaibhav Rajan, and Yu LinThirty-sixth Conference on Neural Information Processing Systems (NeurIPS 2022).
Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs
Vijini Mallawaarachchi and Yu LinJournal of Computational Biology.
Binning long reads in metagenomics datasets using composition and coverage information