2024:

• Optimizing long-term prevention of cardiovascular disease with reinforcement learning
  medRxiv.  [medRxiv]
• Unraveling the Genetic Susceptibility of Irritable Bowel Syndrome: integrative genome-wide analyses in 845,492 individuals: a diagnostic study
  International Journal of Surgery.  [Int. J. Surg.]
• Repun: an accurate small variant representation unification method for multiple sequencing platforms
  Briefing in Bioinformatics.  [Brief. Bioinform.]
• Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data
  bioRxiv.  [bioRxiv]
• AutoPM3: Enhancing Variant Interpretation via LLM-driven PM3 Evidence Extraction from Scientific Literature
  bioRxiv.  [bioRxiv]
• EPInformer: A Scalable Deep Learning Framework for Gene Expression Prediction by Integrating Promoter-enhancer Sequences with Multimodal Epigenomic Data
  bioRxiv.  [bioRxiv]
• Towards a new standard in genomic data privacy: a realization of owner-governance
  bioRxiv.  [bioRxiv]
• CellContrast: Reconstructing Spatial Relationships in Single-Cell RNA Sequencing Data via Deep Contrastive Learning
  Patterns.  [Patterns]
• Development and validation of a tool to stratify the treatment effect of low-dose aspirin in patients with cardiovascular disease: VISTA (Vascular Intervention Stratification Tool for Aspirin)
  medRxiv.  [medRxiv]
• Protein Domain-Specific Genotype-Phenotype Correlation Study of Neurofibromatosis Type 1
  SSRN Preprints.  [SSRN Preprints]
• Development and validation of risk prediction model for recurrent cardiovascular events among Chinese: the Personalized CARdiovascular DIsease risk Assessment for Chinese model
  European Heart Journal - Digital Health.  [Eur. Heart J. Digit. Health] [medRxiv]
• ClusterV-Web: A User-Friendly Tool for Profiling HIV Quasispecies and Generating Drug Resistance Reports from Nanopore Long-Read Data
  Bioinformatics Advances.  [Bioinform. Adv.]
• Investigating shared genetic architecture between inflammatory bowel diseases and primary biliary cholangitis
  JHEP Reports.  [JHEP Rep.]
• MirtronStructDB: A Comprehensive Database of Mirtrons with Predicted Secondary Structures
  F1000 Research.  [F1000 Res.]
• (co-authored) ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences
  Microbiome.  [Microbiome]
• (co-authored) Adverse clinical outcomes and immunosuppressive microenvironment of RHO-GTPase activation pattern in hepatocellular carcinoma
  Journal of Translational Medicine.  [J. Transl. Med.]
• (co-authored) Assessing the reproducibility, stability, and biological interpretability of multimodal computed tomography image features for prognosis in advanced non-small cell lung cancer
  iRadiology.  [iRadiology]
• (co-authored) PET/CT deep learning prognosis for treatment decision support in esophageal squamous cell carcinoma
  Insights into imaging.  [Insights Imaging]
• (co-authored) Sleep patterns, genetic susceptibility, and digestive diseases: A large-scale longitudinal cohort study
  International Journal of Surgery.  [Int. Surg. J.]
• (co-authored) SARS-CoV-2 variants divergently infect and damage cardiomyocytes in vitro and in vivo
  Cell & Bioscience.  [Cell Biosci]
• (co-authored) Unveiling promising drug targets for autism spectrum disorder: insights from genetics, transcriptomics, and proteomics
  Briefing in Bioinformatics.  [Brief. Bioinform.]

2023:

• ClairS: a deep-learning method for long-read somatic small variant calling
  bioRxiv.  [bioRxiv]
• Primary Prevention Cardiovascular Disease Risk Prediction Model for Contemporary Chinese (1°P-CARDIAC): Model Derivation and Validation Using a Hybrid Statistical and Machine-Learning Approach
  SSRN Preprints.  [SSRN Preprints]
• High-resolution diploid 3D genome reconstruction using Pore-C data
  bioRxiv.  [bioRxiv]
• Large-scale Dataset and Effective Model for Variant-Disease Associations Extraction
  ACM-BCB 2023.  [ACM-BCB 2023]
• Exploring Pair-Aware Triangular Attention for Biomedical Relation Extraction
  ACM-BCB 2023.  [ACM-BCB 2023]
• Long-Read Sequencing with Hierarchical Clustering for Antiretroviral Resistance Profiling of Mixed Human Immunodeficiency Virus Quasispecies
  Clinical Chemistry.  [Clin. Chem] [GitHub]
• Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP
  BMC Bioinformatics.  [BMC Bioinform.] [GitHub]
• Ultra-low coverage genome-wide association study - insights into gestational age using 17,844 embryo samples with preimplantation genetic testing
  Genome Medicine.  [Genome Med.] [medRxiv]
• Evaluation of Mycobacterium Tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling
  Scientific reports.  [Sci. Rep.] [GitHub]
• Integrated modeling framework reveals co-regulation of transcription factors, miRNAs and lncRNAs on cardiac developmental dynamics
  Stem Cell Research & Therapy.  [Stem Cell Res. Ther]
• (co-authored) The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
  Cell.  [Cell]

2022:

• HKG: An open genetic variant database of 205 Hong Kong Cantonese exomes
  NAR Genomics and Bioinformatics.  [NARGB] [HKG database]
• ECNano: A Cost-Effective Workflow for Target Enrichment Sequencing and Accurate Variant Calling on 4,800 Clinically Significant Genes Using a Single MinION Flowcell
  BMC Medical Genomics.  [BMC Medical Genom] [GitHub]
• SENSV: Detecting Structural Variations with Precise Breakpoints using Low-Depth WGS Data from a Single Oxford Nanopore MinION Flowcell
  Scientific Reports.  [Sci. Rep] [GitHub]
• Streptococcus oriscaviae sp. nov. Infection Associated with Guinea Pigs
  Microbiology Spectrum.  [Microbiol. Spectr.]
• Symphonizing pileup and full-alignment for deep learning-based long-read variant calling
  Nature Computational Science.  [NatComputSci] [GitHub]
• Clair3-Trio: high-performance Nanopore long-read variant calling in family trios with Trio-to-Trio deep neural networks
  Briefings in Bioinformatics  [Brief. Bioinform.] [GitHub]
• Assembly-free discovery of human novel sequences using long reads
  DNA Research.  [DNA Res.]
• Duet: SNP-Assisted Structural Variant Calling and Phasing Using Oxford Nanopore Sequencing
  BMC Bioinformatics.  [BMC Bioinform.] [GitHub]
• (co-authored) Generalized radiograph representation learning via cross-supervision between images and free-text radiology reports
  Nature Machine Intelligence.  [Nat. Mach. Intell.] [PDF] [GitHub]
• (co-authored) Same-Cell Co-Occurrence of RAS Hotspot and BRAF V600E Mutations in Treatment-Naive Colorectal Cancer
  JCO Precision Oncology.  [JCO Precis. Oncol.]
• (co-authored) Temporal Control of the WNT Signaling Pathway During Cardiac Differentiation Impacts Upon the Maturation State of Human Pluripotent Stem Cell Derived Cardiomyocytes
  Frontiers in Molecular Biosciences.  [Front Mol Biosci.]
• (co-authored) A self-blinking DNA probe for live-cell superresolution 3D imaging of hierarchical chromatin structures
  bioRxiv.  [bioRxiv]

2021:

• Building a Chinese pan-genome of 486 individuals
  Communications Biology.  [Commun. Biol.]
• The applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era
  The Innovation.  [The Innovation]
• SARS‐CoV‐2 biology and variants: anticipation of viral evolution and what needs to be done
  Environmental Microbiology.  [Environ. Microbiol.] [Traditional Chinese Translation] [Simplified Chinese Translation] 
  [SARS-CoV-2 Cytosine Attenuation Tracking]
• High Prevalence and Mechanism Associated With Extended Spectrum Beta-Lactamase-Positive Phenotype in Laribacter hongkongensis
  Frontiers in Microbiology.  [Front. Microbiol.]
• BioNumQA-BERT: Answering Biomedical Questions Using Numerical Facts with a Deep Language Representation Model
  ACM-BCB 2021.  [PDF] [Conference]
• RENET2: High-Performance Full-text Gene-Disease Relation Extraction with Iterative Training Data Expansion
  NAR Genomics and Bioinformatics.  [NARGB] [GitHub]
• DNA methylation affects pre-mRNA transcriptional initiation and processing in Arabidopsis
  bioRxiv.  [bioRxiv]
• (co-authored) Drug Repurposing for the Treatment of COVID-19: A Knowledge Graph Approach
  Advanced Therapeutics.  [Adv. Ther.]
• (co-authored) Distinct disease severity between children and older adults with COVID-19: Impacts of ACE2 expression, distribution, and lung progenitor cells
  Clinical Infectious Disease.  [CID]
• (co-authored) Clinical analysis and pluripotent stem cells-based model reveal possible impacts of ACE2 and lung progenitor cells on infacts vulnerable to COVID-19
  Theranostics.  [Theranostics]

2020:

• Exploring the limit of using a deep neural network on pileup data for germline variant calling
  Nature Machine Intelligence.  [Nat. Mach. Intell.] [PDF] [GitHub]
• CONNET: Accurate Diploid Genome Consensus in de novo Assembly of Nanopore Sequencing Data via Deep Learning
  iScience.  [iScience] [GitHub]
• Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants
  International Journal of Computational Biology and Drug Design.  [IJCBDD] [PDF] [GitHub]
• MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data
  BMC Genomics  [BMC Genomics] [SourceForge]
• MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read Metagenomics
  IEEE BIBM 2020.  [PDF] [Conference]
• ChromSeg: Two-Stage Framework for Overlapping Chromosome Segmentation and Reconstruction
  IEEE BIBM 2020.  [PDF] [Conference]
• Tracking cytosine depletion in SARS-CoV-2
  bioRxiv.  [bioRxiv] [Website]
• (co-authored) High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method
  Microbiome.  [Microbiome]
• (co-authored) Identification of Cooperative Gene Regulation Among Transcription Factors, LncRNAs, and MicroRNAs in Diabetic Nephropathy Progression
  Frontiers in Genetics.  [Front. Genet.]
• (co-authored) Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long reads
  ACM-BCB 2020.  [PDF] [Conference]
• (co-authored) MC-Explorer: Analyzing and Visualizing Motif-Cliques on Large Networks
  ICDE 2020.  [PDF] [Demo]

2019:

• RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature
  RECOMB 2019.  [Springer]
• Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
  Nature Communications.  [Nat. Comm.] [GitHub]

2018:

• Restricted Boltzmann Machine and its Potential to Better Predict Cancer Survival
  Biomed J Sci & Tech Res.  [PDF]
• (co-authored) Transcriptome Analysis of Acute Phase Liver Graft Injury in Liver Transplantation
  Biomedicines.  [PubMed]
• (co-authored) AC-DIAMOND v1: Accelerating large-scale DNA-protein alignment
  Bioinformatics.  [PubMed] [GitHub]
• (co-authored) MegaPath: Low-Similarity Pathogen Detection from Metagenomic NGS Data (Extended Abstract)
  ICCABS 2018.  [IEEE]

2017:

• First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans)
  G3: Genes, Genomes, Genetics.  [PubMed]
• Serine peptidase inhibitor Kazal type 1 (SPINK1) as novel downstream effector of the cadherin-17/β-catenin axis in hepatocellular carcinoma
  Cellular Oncology.  [PubMed]
• LRSim: a Linked Reads Simulator generating insights for better genome partitioning
  Computational and Structural Biotechnology Journal.  [PubMed] [GitHub]
• 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
  GigaScience.  [PubMed] [GitHub]
• (co-authored) MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs
  BMC Bioinformatics.  [PubMed]

2016:

• MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
  Methods.  [PubMed]
• BASE: a practical de novo assembler for large genomes using long NGS reads
  BMC Genomics.  [PubMed]
• (co-authored) AC-DIAMOND: Accelerating Protein Alignment via Better SIMD Parallelization and Space-Efficient Indexing
  IWBBIO.  [Springer]

2015:

• database.bio: a web application for interpreting human variations
  Bioinformatics.  [PubMed]
• De novo assembly of a haplotype-resolved human genome
  Nature Biotechnology.  [PubMed]
• MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
  Bioinformatics.  [PubMed] [GitHub]
• MICA: A fast short-read aligner that takes full advantage of Intel Many Integrated Core Architecture (MIC)
  BMC Bioinformtics.  [PubMed] [SourceForge] [GitHub]
• (co-authored) Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber
  Plant Cell.  [PubMed]

2014:

• SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads
  Bioinformatics.  [PubMed] [SourceForge] [GitHub]
• BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU
  PeerJ.  [PubMed] [SourceForge]
• Exome sequencing of tumor cell lines: Optimizing for cancer variants
  Cancer Research.  [AACR]
• GPU-Accelerated BWT Construction for Large Collection of Short Reads
  ArXiv.  [PDF]

2013:

• SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner
  PLoS ONE.  [PubMed] [GitHub]

2012:

• SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
  GigaScience.  [PubMed] [SourceForge] [GitHub]
• COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
  Bioinformatics.  [PubMed] [SourceForge]
• The oyster genome reveals stress adaptation and complexity of shell formation
  Nature.  [PubMed]
• (co-authored) Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression
  BMC Genomics.  [PubMed]
• (co-authored) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
  GigaScience.  [PubMed]
• (co-authored) An integrated map of genetic variation from 1,092 human genome
  Nature.  [PubMed]

2011:

• Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly
  Nature Biotechnology.  [PubMed]
• (co-authored) Mapping copy number variation by population-scale genome sequencing
  Nature.  [PubMed]
• (co-authored) Assemblathon 1: A competitive assessment of de novo short read assembly methods
  Genome Research.  [PubMed]

2010:

• Building the sequence map of the human pan-genome
  Nature Biotechnology.  [PubMed]
• (co-authored) Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude
  Science.  [PubMed]
• (co-authored) The DNA Methylome of Human Peripheral Blood Mononuclear Cells
  PLoS Biology.  [PubMed]
• (co-authored) International network of cancer genome projects
  Nature.  [PubMed]
• (co-authored) A map of human genome variation from population scale sequencing
  Nature.  [PubMed]