Publications

Discover selected research publications contributed to by our expert bioinformaticians in genomics, computational biology, and life sciences, including work completed through Pepkio and collaborations elsewhere.

2026

  1. Deep learning of 777 K bulk transcriptomes reveals human–mouse gene conservation beyond DNA sequence similarity

    Journal
    Communications Biology
    Published:
    DOI
    10.1038/s42003-026-10189-w
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  2. Harnessing Artificial Intelligence for Genomic Variant Prediction: Advances, Challenges, and Future Directions

    Journal
    GigaScience
    Published:
    DOI
    10.1093/gigascience/giag004
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2025

  1. GeneRAIN: multifaceted representation of genes via deep learning of gene expression networks

    Journal
    Genome Biology
    Published:
    DOI
    10.1186/s13059-025-03749-6
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  2. Age‐Related Dynamics and Spectral Characteristics of the TCRβ Repertoire in Healthy Children: Implications for Immune Aging

    Journal
    Aging Cell
    Published:
    DOI
    10.1111/acel.14460
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2024

  1. Mutations in AMBRA1 aggravate β-thalassemia by impairing autophagy-mediated clearance of free α-globin

    Journal
    Blood
    Published:
    DOI
    10.1182/blood.2023022688
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  2. Post-transcriptional regulation supports the homeostatic expression of mature RNA

    Journal
    Briefings in Bioinformatics
    Published:
    DOI
    10.1093/bib/bbaf027
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  3. Whole-genome Sequencing Association Analysis of Quantitative Platelet Traits in A Large Cohort of β-thalassemia

    Journal
    Genomics, Proteomics & Bioinformatics
    Published:
    DOI
    10.1093/gpbjnl/qzae065
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  4. An atypical form of 60S ribosomal subunit in Diamond-Blackfan anemia linked to RPL17 variants

    Journal
    JCI Insight
    Published:
    DOI
    10.1172/jci.insight.172475
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  5. INDELpred: Improving the prediction and interpretation of indel pathogenicity within the clinical genome

    Journal
    HGG Advances
    Published:
    DOI
    10.1016/j.xhgg.2024.100325
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  6. Genes in Humans and Mice: Insights from Deep learning of 777K Bulk Transcriptomes

    Journal
    Preprint (bioRxiv)
    Published:
    DOI
    10.1101/2024.04.01.587517
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2023

  1. An efficient large‐scale whole‐genome sequencing analyses practice with an average daily analysis of 100Tbp: ZBOLT

    Journal
    Clinical and Translational Discovery
    Published:
    DOI
    10.1002/ctd2.252
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  2. Age‐dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging

    Journal
    Aging Cell
    Published:
    DOI
    10.1111/acel.14028
    View PaperSearch Scholar

  3. DMD-Associated Dilated Cardiomyopathy: Genotypes, Phenotypes, and Phenocopies

    Journal
    Circulation: Genomic and Precision Medicine
    Published:
    DOI
    10.1161/CIRCGEN.123.004221
    View PaperSearch Scholar

  4. The STROMICS genome study: deep whole-genome sequencing and analysis of 10K Chinese patients with ischemic stroke reveal complex genetic and phenotypic interplay

    Journal
    Cell Discovery
    Published:
    DOI
    10.1038/s41421-023-00582-8
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  5. Integrated multi-omics analyses and functional validation reveal TTK as a novel EMT activator for endometrial cancer

    Journal
    Journal of Translational Medicine
    Published:
    DOI
    10.1186/s12967-023-03998-8
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  6. CMDB: the comprehensive population genome variation database of China

    Journal
    Nucleic Acids Research
    Published:
    DOI
    10.1093/nar/gkac638
    View PaperSearch Scholar

2022

  1. A population-based study of precision health assessments using multi-omics network-derived biological functional modules

    Journal
    Cell Reports Medicine
    Published:
    DOI
    10.1016/j.xcrm.2022.100847
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  2. VIPPID: a gene-specific single nucleotide variant pathogenicity prediction tool for primary immunodeficiency diseases

    Journal
    Briefings in Bioinformatics
    Published:
    DOI
    10.1093/bib/bbac176
    View PaperSearch Scholar

  3. A pilot study of assessing whole genome sequencing in newborn screening in unselected children in China

    Journal
    Clinical and Translational Medicine
    Published:
    DOI
    10.1002/ctm2.843
    View PaperSearch Scholar

  4. Rare Variants in Inborn Errors of Immunity Genes Associated With Covid-19 Severity

    Journal
    Frontiers in Cellular and Infection Microbiology
    Published:
    DOI
    10.3389/fcimb.2022.888582
    View PaperSearch Scholar

  5. Identification of Potential Biomarkers for Pan-Cancer Diagnosis and Prognosis Through the Integration of Large-Scale Transcriptomic Data

    Journal
    Frontiers in Pharmacology
    Published:
    DOI
    10.3389/fphar.2022.870660
    View PaperSearch Scholar

  6. T Cell Repertoire Abnormality in Immunodeficiency Patients with DNA Repair and Methylation Defects

    Journal
    Journal of Clinical Immunology
    Published:
    DOI
    10.1007/s10875-021-01178-1
    View PaperSearch Scholar

2021

  1. Species-Level Analysis of the Human Gut Microbiome Shows Antibiotic Resistance Genes Associated With Colorectal Cancer

    Journal
    Frontiers in Microbiology
    Published:
    DOI
    10.3389/fmicb.2021.765291
    View PaperSearch Scholar

  2. RNA-seq in DMD urinary stem cells recognized muscle-related transcription signatures and addressed the identification of atypical mutations by whole-genome sequencing

    Journal
    HGG Advances
    Published:
    DOI
    10.1016/j.xhgg.2021.100054
    View PaperSearch Scholar

  3. Molecular Classification and Interpretation of Amyotrophic Lateral Sclerosis Using Deep Convolution Neural Networks and Shapley Values

    Journal
    Genes
    Published:
    DOI
    10.3390/genes12111754
    View PaperSearch Scholar

  4. New genetic variants associated with major adverse cardiovascular events in patients with acute coronary syndromes and treated with clopidogrel and aspirin

    Journal
    The Pharmacogenomics Journal
    Published:
    DOI
    10.1038/s41397-021-00245-5
    View PaperSearch Scholar

  5. Integrated genetic analyses revealed novel human longevity loci and reduced risks of multiple diseases in a cohort study of 15,651 Chinese individuals

    Journal
    Aging Cell
    Published:
    DOI
    10.1111/acel.13323
    View PaperSearch Scholar

2020

  1. More severe than CVID: Combined immunodeficiency due to a novel NFKB2 mutation

    Journal
    Pediatric Allergy and Immunology
    Published:
    DOI
    10.1111/pai.13441
    View PaperSearch Scholar

  2. Ethnicity-related DMD Genotype Landscapes in European and Non-European Countries

    Journal
    Neurology: Genetics
    Published:
    DOI
    10.1212/nxg.0000000000000536
    View PaperSearch Scholar

  3. Bi-Allelic Pathogenic Variations in MERTK Including Deletions Are Associated with an Early Onset Progressive Form of Retinitis Pigmentosa

    Journal
    Genes
    Published:
    DOI
    10.3390/genes11121517
    View PaperSearch Scholar

  4. Severe Bleeding Diathesis in Siblings with Platelet Dysfunction due to a Novel Nonsense RASGRP2 Mutation

    Journal
    TH Open
    Published:
    DOI
    10.1055/s-0040-1718910
    View PaperSearch Scholar

  5. Developing an Unbiased Multiplex PCR System to Enrich the TRB Repertoire Toward Accurate Detection in Leukemia

    Journal
    Frontiers in Immunology
    Published:
    DOI
    10.3389/fimmu.2020.01631
    View PaperSearch Scholar

  6. NAXD Deficiency Associated with Perinatal Autoinflammation, Pancytopenia, Dermatitis, Colitis, and Cystic Encephalomalacia

    Journal
    Journal of Pediatric Neurology
    Published:
    DOI
    10.1055/s-0040-1713682
    View PaperSearch Scholar

  7. Janus kinase inhibition in complement component 1 deficiency

    Journal
    Journal of Allergy and Clinical Immunology
    Published:
    DOI
    10.1016/j.jaci.2020.04.002
    View PaperSearch Scholar

  8. ATPase domain AFG3L2 mutations alter OPA1 processing and cause Optic Neuropathy

    Journal
    Annals of Neurology
    Published:
    DOI
    10.1002/ana.25723
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  9. Clinical Implications of Experimental Analyses of AID Function on Predictive Computational Tools: Challenge of Missense Variants

    Journal
    Clinical Genetics
    Published:
    DOI
    10.1111/cge.13737
    View PaperSearch Scholar

  10. Noncoding RNA transcription alters chromosomal topology to promote isotype-specific class switch recombination

    Journal
    Science Immunology
    Published:
    DOI
    10.1126/sciimmunol.aay5864
    View PaperSearch Scholar

  11. A Missense Mutation in RAB28 in a Family with Cone-Rod Dystrophy and Postaxial Polydactyly Prevents Localization of RAB28 to the Primary Cilium

    Journal
    Investigative Ophthalmology & Visual Science
    Published:
    DOI
    10.1167/iovs.61.2.29
    View PaperSearch Scholar

  12. Molecular Basis of Allogeneic Pluripotent Stem Cell Treatment of a Patient with Sporadic ALS

    Journal
    OBM Geriatrics
    Published:
    DOI
    10.21926/obm.geriatr.2101164
    View PaperSearch Scholar

2019

  1. Panoramic Visualization of Circulating MicroRNAs Across Neurodegenerative Diseases in Humans

    Journal
    Molecular Neurobiology
    Published:
    DOI
    10.1007/s12035-019-1615-1
    View PaperSearch Scholar

2017

  1. The gut microbiome in atherosclerotic cardiovascular disease

    Journal
    Nature Communications
    Published:
    DOI
    10.1038/s41467-017-00900-1
    View PaperSearch Scholar

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