A differentor-based adaptive ontology-matching approach. - Peigang Xu; Yadong Wang 001; Bo Liu 023 (J. Inf. Sci., 2012)

PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM Approach. - Xiao Zhu; Henry C. M. Leung; Francis Y. L. Chin; Siu-Ming Yiu; Guangri Quan; Bo Liu 023; Yadong Wang 001 (BCB, 2013)

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads. - Xiao Zhu; Henry C. M. Leung; Rongjie Wang; Francis Y. L. Chin; Siu-Ming Yiu; Guangri Quan; Yajie Li; Rui Zhang; Qinghua Jiang; Bo Liu 023; Yucui Dong; Guohui Zhou; et al. (BMC Bioinform., 2015)

deBGA: read alignment with de Bruijn graph-based seed and extension. - Bo Liu 023; Hongzhe Guo; Michael Brudno; Yadong Wang 001 (Bioinform., 2016)

rHAT: fast alignment of noisy long reads with regional hashing. - Bo Liu 023; Dengfeng Guan; Mingxiang Teng; Yadong Wang 001 (Bioinform., 2016)

deBWT: parallel construction of Burrows-Wheeler Transform for large collection of genomes with de Bruijn-branch encoding. - Bo Liu 023; Dixian Zhu; Yadong Wang 001 (Bioinform., 2016)

LAMSA: fast split read alignment with long approximate matches. - Bo Liu 023; Yan Gao 031; Yadong Wang 001 (Bioinform., 2017)

rMFilter: acceleration of long read-based structure variation calling by chimeric read filtering. - Bo Liu 023; Tao Jiang 021; Siu-Ming Yiu; Junyi Li; Yadong Wang 001 (Bioinform., 2017)

Accurate annotation of metagenomic data without species-level references. - Haobin Yao; Tak Wah Lam; H. F. Ting; Siu-Ming Yiu; Yadong Wang 001; Bo Liu 023 (Int. J. Data Min. Bioinform., 2017)

rCANID: read Clustering and Assembly-based Novel Insertion Detection tool. - Yilei Fu; Tao Jiang 021; Bo Liu 023; Yadong Wang 001 (BIBM, 2018)

deSPI: efficient classification of metagenomics reads with lightweight de Bruijn graph-based reference indexing. - Dengfeng Guan; Bo Liu 023; Yadong Wang 001 (BIBM, 2018)

Fast variation-aware read alignment with deBGA-VARA. - Hongzhe Guo; Bo Liu 023; Dengfeng Guan; Yilei Fu; Yadong Wang 001 (BIBM, 2018)

SALT: a fast, memory-efficient and SNP-aware short read alignment tool. - Wei Quan; Bo Liu 023; Yadong Wang 001 (BIBM, 2019)

A Bidirectional Fuzzy Index and Approximate Search Algorithm for Next Generation Sequencing. - Wei Quan; Guangri Quan; Bo Liu 023; Yadong Wang 001 (BIBM, 2019)

Prediction of Human LncRNAs Based on Integrated Information Entropy Features. - Junyi Li; Huinian Li; Li Zhang; Qingzhe Xu; Yuan Ping; Xiaozhu Jing; Wei Jiang 023; Bo Liu 023; Yadong Wang 001 (ICIC (2), 2019)

TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain. - Yan Gao 031; Bo Liu 023; Yadong Wang 001; Yi Xing (Bioinform., 2019)

rMETL: sensitive mobile element insertion detection with long read realignment. - Tao Jiang 021; Bo Liu 023; Junyi Li; Yadong Wang 001 (Bioinform., 2019)

Integrated entropy-based approach for analyzing exons and introns in DNA sequences. - Junyi Li; Li Zhang; Huinian Li; Yuan Ping; Qingzhe Xu; Rongjie Wang; Renjie Tan; Zhen Wang; Bo Liu 023; Yadong Wang 001 (BMC Bioinform., 2019)

Fast read alignment with incorporation of known genomic variants. - Hongzhe Guo; Bo Liu 023; Dengfeng Guan; Yilei Fu; Yadong Wang 001 (BMC Medical Informatics Decis. Mak., 2019)

Assessment of Machine Learning Methods for Classification in Single Cell ATAC-seq. - Zhe Cui; Bo Liu 023; Liran Juan; Tianyi Zang; Tao Jiang 021; Yadong Wang 001 (BIBM, 2020)

GONET: A Deep Network to Annotate Proteins via Recurrent Convolution Networks. - Junyi Li; Lixin Wang; Xiaoshuai Zhang; Bo Liu 023; Yadong Wang 001 (BIBM, 2020)

Prognostic prediction of carcinoma by a differential-regulatory-network-embedded deep neural network. - Junyi Li; Yuan Ping; Hong Li; Huinian Li; Ying Liu; Bo Liu 023; Yadong Wang 001 (Comput. Biol. Chem., 2020)

ScSSC: Semi-supervised Single Cell Clustering Based on 2D Embedding. - Naile Shi; Yulin Wu 001; Linlin Du; Bo Liu 023; Yadong Wang 001; Junyi Li (ICIC (3), 2021)

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band. - Yan Gao 031; Yongzhuang Liu; Yanmei Ma; Bo Liu 023; Yadong Wang 001; Yi Xing (Bioinform., 2021)

Erratum to: abPOA: an SIMD-based C library for fast partial order alignment using adaptive band. - Yan Gao 031; Yongzhuang Liu; Yanmei Ma; Bo Liu 023; Yadong Wang 001; Yi Xing (Bioinform., 2021)

SKSV: ultrafast structural variation detection from circular consensus sequencing reads. - Yadong Liu; Tao Jiang 021; Junhao Su; Bo Liu 023; Tianyi Zang; Yadong Wang 001 (Bioinform., 2021)

Factor graph-aggregated heterogeneous network embedding for disease-gene association prediction. - Ming He; Chen Huang; Bo Liu 023; Yadong Wang 001; Junyi Li (BMC Bioinform., 2021)

IIMLP: integrated information-entropy-based method for LncRNA prediction. - Junyi Li; Huinian Li; Xiao Ye; Li Zhang; Qingzhe Xu; Yuan Ping; Xiaozhu Jing; Wei Jiang 023; Qing Liao 001; Bo Liu 023; Yadong Wang 001 (BMC Bioinform., 2021)

Fast and SNP-aware short read alignment with SALT. - Wei Quan; Bo Liu 023; Yadong Wang 001 (BMC Bioinform., 2021)

ScGSLC: An unsupervised graph similarity learning framework for single-cell RNA-seq data clustering. - Junyi Li; Wei Jiang 023; Henry Han; Jing Liu; Bo Liu 023; Yadong Wang 001 (Comput. Biol. Chem., 2021)

deGSM: Memory Scalable Construction Of Large Scale de Bruijn Graph. - Hongzhe Guo; Yilei Fu; Yan Gao 031; Junyi Li; Yadong Wang 001; Bo Liu 023 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

OTUCD: Unsupervised GCN based metagenomics non-overlapping community detection. - Zhongqing Zhang; Qiqi Jiao; Yang Zhang; Bo Liu 023; Yadong Wang 001; Junyi Li (Comput. Biol. Chem., 2022)

Deepgmd: A Graph-Neural-Network-Based Method to Detect Gene Regulator Module. - Xiao Ye; Yulin Wu 001; Jiangsheng Pi; Hong Li; Bo Liu 023; Yadong Wang 001; Junyi Li (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

ScCCL: Single-Cell Data Clustering Based on Self-Supervised Contrastive Learning. - Linlin Du; Rui Han; Bo Liu 023; Yadong Wang 001; Junyi Li (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

PSPGO: Cross-Species Heterogeneous Network Propagation for Protein Function Prediction. - Kaitao Wu; Lexiang Wang; Bo Liu 023; Yang Liu 039; Yadong Wang 001; Junyi Li (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Prot2GO: Predicting GO Annotations From Protein Sequences and Interactions. - Xiaoshuai Zhang; Lixin Wang; Hucheng Liu; Xiaofeng Zhang; Bo Liu 023; Yadong Wang 001; Junyi Li (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

HNetGO: protein function prediction via heterogeneous network transformer. - Xiaoshuai Zhang; Huannan Guo; Fan Zhang; Xuan Wang; Kaitao Wu; Shizheng Qiu; Bo Liu 023; Yadong Wang 001; Yang Hu 008; Junyi Li (Briefings Bioinform., 2023)

Struct2GO: protein function prediction based on graph pooling algorithm and AlphaFold2 structure information. - Peishun Jiao; Beibei Wang; Xuan Wang; Bo Liu 023; Yadong Wang 001; Junyi Li (Bioinform., 2023)

miniSNV: accurate and fast single nucleotide variant calling from nanopore sequencing data. - Miao Cui; Yadong Liu; Xian Yu; Hongzhe Guo; Tao Jiang 021; Yadong Wang 001; Bo Liu 023 (Briefings Bioinform., 2024)

Kled: an ultra-fast and sensitive structural variant detection tool for long-read sequencing data. - Zhendong Zhang; Tao Jiang 021; Gaoyang Li; Shuqi Cao; Yadong Liu; Bo Liu 023; Yadong Wang 001 (Briefings Bioinform., 2024)