Publications - Luo Lab

2026

Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data

Nature Communications

[Nat. Comm.]

(Guest editor) International Conference on Genome Informatics ISCB-Asia 2025 Abstract Book

Briefings in Bioinformatics

[Brief. Bioinform.]

2025

Clair-Mosaic: A deep-learning method for long-read mosaic small variant calling

bioRxiv

[bioRxiv]

Guess till correct: Gungnir codec enabling high error-tolerance and low-redundancy DNA storage through substantial computing power

bioRxiv

[bioRxiv]

Optimizing long-term prevention of cardiovascular disease with reinforcement learning

npj Digital Medicine

[npj Digit. Med.] [medRxiv]

Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D

Nature Structural & Molecular Biology

[Nat. Struct. Mol. Biol]

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

PLoS ONE

[PLoS ONE] [SSRN Preprints]

Assessing large-scale genomic language models in predicting personal gene expression: promises and limitations

bioRxiv

[bioRxiv]

ClairS-TO: A deep-learning method for long-read tumor-only somatic small variant calling

Nature Communications

[Nat. Comm.]

Real-time raw signal genomic analysis using fully integrated memristor hardware

Nature Computational Science

[Nat. Comp. Sci.]

Toward owner governance in genomic data privacy with Governome

Cell Reports Methods

[Cell Rep. Methods]

AutoPM3: Enhancing Variant Interpretation via LLM-driven PM3 Evidence Extraction from Scientific Literature

Bioinformatics

[Bioinformatics]

(co-authored) DECODE: Deep learning-based common deconvolution framework for various omics data

ResearchSquare

[ResSq]

(co-authored) cuteFC: regenotyping structural variants through an accurate and efficient force-calling method

Genome Biology

[Genome Biol.]

(co-authored) Observational, causal relationship and shared genetic basis between cholelithiasis and gastroesophageal reflux disease: evidence from a cohort study and comprehensive genetic analysis

GigaScience

[GigaScience]

2024

ShiftCAM: A Time-Domain Content Addressable Memory Utilizing Shifted Hamming Distance for Robust Genome Analysis

ICCAD 2024

[ICCAD 2024]

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

Briefings in Bioinformatics

[Brief. Bioinform.]

EPInformer: A Scalable Deep Learning Framework for Gene Expression Prediction by Integrating Promoter-enhancer Sequences with Multimodal Epigenomic Data

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

Briefings in Bioinformatics

[Brief. Bioinform.]

2023

ClairS: a deep-learning method for long-read somatic small variant calling

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]

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-first authored) Streptococcus oriscaviae sp. nov. Infection Associated with Guinea Pigs

Microbiology Spectrum

[Microbiol. Spectr.]

(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] [Simplified Chinese] [Tracking Website]

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-first authored) High Prevalence and Mechanism Associated With Extended Spectrum Beta-Lactamase-Positive Phenotype in Laribacter hongkongensis

Frontiers in Microbiology

[Front. Microbiol.]

(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-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) MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data

BMC Genomics

[BMC Genomics] [SourceForge]

(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

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Nature Communications

[Nat. Comm.] [GitHub]

(co-first authored) RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature

RECOMB 2019

[Springer]

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]

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-first authored) Serine peptidase inhibitor Kazal type 1 (SPINK1) as novel downstream effector of the cadherin-17/β-catenin axis in hepatocellular carcinoma

Cellular Oncology

[PubMed]

(co-authored) MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs

BMC Bioinformatics

[PubMed]

2016

BASE: a practical de novo assembler for large genomes using long NGS reads

BMC Genomics

[PubMed]

(co-first authored) MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

Methods

[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]

MICA: A fast short-read aligner that takes full advantage of Intel Many Integrated Core Architecture (MIC)

BMC Bioinformatics

[PubMed] [SourceForge] [GitHub]

(co-first authored) De novo assembly of a haplotype-resolved human genome

Nature Biotechnology

[PubMed]

(co-first authored) MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Bioinformatics

[PubMed] [GitHub]

(co-authored) Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

Plant Cell

[PubMed]

2014

BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU

PeerJ

[PubMed] [SourceForge]

(co-first authored) Exome sequencing of tumor cell lines: Optimizing for cancer variants

Cancer Research

[AACR]

(co-first authored) SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads

Bioinformatics

[PubMed] [SourceForge] [GitHub]

(co-authored) 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]

(co-first authored) 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

(co-first authored) 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

(co-first authored) 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]