MEFE: microbiome signature identification based on elastic feature extraction. Frontiers of Computer Science 2026
Coordinated Meta-Storms enables comparison of million-level microbiomes. Bioinformatics 2025
Microbial dysbiosis and its diagnostic potential in androgenetic alopecia: insights from multi-kingdom sequencing and machine learning. mSystems 2025
MT-Tracker: A Phylogeny-Aware Algorithm for Quantifying Microbiome Transitions Across Scales and Habitats. Mathematics 2025
TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data. BMC Bioinformatics 2025
Apply a deep learning hybrid model optimized by an improved chimp optimization algorithm in pm2. 5 prediction. Machine Learning with Applications 2025
ACP-TransLSTM: A Novel Deep Learning Framework for Anticancer Peptide Prediction Using Multi-source Feature Integration. ICIC 2025
Accurate assembly of full-length consensus for viral quasispecies. BMC Bioinformatics 2025
VirDiG: a de novo transcriptome assembler for coronavirus. Bioinformatics Advances 2025
Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses. BMC Genomics 2024
TF-BAPred: A Universal Bioactive Peptide Predictor Integrating Multiple Feature Representations. Mathematics 2024
PM-profiler: a high-resolution and fast tool for taxonomy annotation of amplicon-based microbiome. Microbiology Spectrum 2024
A deep learning framework for predicting disease-gene associations with functional modules and graph augmentation. BMC Bioinformatics 2024
ACMGA: a reference-free multiple-genome alignment pipeline for plant species. BMC Genomics 2024
PM-CNN: microbiome status recognition and disease detection model based on phylogeny and multi-path neural network. Bioinformatics Advances 2024
Host Variable-Embedding Augment Microbiome-Based Simultaneous Detection of Multiple Disease by Deep Learning. Advanced Intelligent Systems 2023
Discovering Microbe-disease Associations with Weighted Graph Convolution Networks and Taxonomy Common Tree. Current Bioinformatics 2023
Gut microbiome predicts selenium supplementation efficiency across different Chinese adult cohorts using hybrid modeling and feature refining. Frontiers in Microbiology 2023
Comprehensive Assessment of 16S rRNA Gene Amplicon Sequencing for Microbiome Profiling across Multiple Habitats. Microbiology Spectrum 2023
Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes. Bioinformatics 2023
Parallel-Meta Suite: Interactive and rapid microbiome data analysis on multiple platforms. iMeta 2022
Comprehensive understanding to the public health risk of environmental microbes via a microbiome-based index. Journal of genetics and genomics 2022
Search-based health status detection and disease classification using species-level profiles of metagenomes. Medicine in Microecology 2022
mzMD: visualization-oriented MS data storage and retrieval. Bioinformatics 2022
MultiTrans: An Algorithm for Path Extraction Through Mixed Integer Linear Programming for Transcriptome Assembly. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2022
Elucidating the Beta-Diversity of the Microbiome: from Global Alignment to Local Alignment. mSystems 2021
A Scale-Free, Fully Connected Global Transition Network Underlies Known Microbiome Diversity. mSystems 2021
Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level. mSystems 2021
Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function. BMC Genomics 2021
Hierarchical Meta-Storms enables comprehensive and rapid comparison of microbiome functional profiles on a large scale using hierarchical dissimilarity metrics and parallel computing. Bioinformatics Advances 2021
Towards multi-label classification: Next step of machine learning for microbiome research. Computational and Structural Biotechnology Journal 2021
A novel model-checking approach for dose-response relationships. Statistical Methods in Medical Research 2021
Sorting a Permutation by Best Short Swaps. Algorithmica 2021
mzMD: A New Storage and Retrieval System for Mass Spectrometry Data. Intelligent Computing Theories and Application - 17th International Conference 2021
Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level. Bioinformatics, 2020
Multiple-Disease Detection and Classification across Cohorts via Microbiome Search. mSystems 2020
Method development for cross-study microbiome data mining: Challenges and opportunities. Computational and Structural Biotechnology Journal 2020
Hybrid link prediction via model averaging. Physica A: Statistical Mechanics and its Applications 2020
IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2020
"Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy". mBio 2019
DTA-SiST: de novo transcriptome assembly by using simplified suffix trees. BMC Bioinformatics 2019
Identifying and Predicting Novelty in Microbiome Studies. mBio 2018
The Longest Common Exemplar Subsequence Problem. IEEE International Conference on Bioinformatics and Biomedicine 2018
Can a permutation be sorted by best short swaps? Annual Symposium on Combinatorial Pattern Matching 2018