GeneRAIN: multifaceted representation of genes via deep learning of gene expression networks
Genome BiologyPublished: September 22, 2025
10.1186/s13059-025-03749-6
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.
Age‐Related Dynamics and Spectral Characteristics of the TCRβ Repertoire in Healthy Children: Implications for Immune Aging
Aging CellPublished: April 202510.1111/acel.14460Mutations in AMBRA1 aggravate β-thalassemia by impairing autophagy-mediated clearance of free α-globin
BloodPublished: December 18, 202410.1182/blood.2023022688Post-transcriptional regulation supports the homeostatic expression of mature RNA
Briefings in BioinformaticsPublished: November 22, 202410.1093/bib/bbaf027Whole-genome Sequencing Association Analysis of Quantitative Platelet Traits in A Large Cohort of β-thalassemia
Genomics, Proteomics & BioinformaticsPublished: September 27, 202410.1093/gpbjnl/qzae065An atypical form of 60S ribosomal subunit in Diamond-Blackfan anemia linked to RPL17 variants
JCI InsightPublished: September 10, 202410.1172/jci.insight.172475INDELpred: Improving the prediction and interpretation of indel pathogenicity within the clinical genome
HGG AdvancesPublished: July 10, 202410.1016/j.xhgg.2024.100325Genes in Humans and Mice: Insights from Deep learning of 777K Bulk Transcriptomes
Preprint (bioRxiv)Published: April 2, 202410.1101/2024.04.01.587517An efficient large‐scale whole‐genome sequencing analyses practice with an average daily analysis of 100Tbp: ZBOLT
Clinical and Translational DiscoveryPublished: December 202310.1002/ctd2.252Age‐dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging
Aging CellPublished: November 27, 202310.1111/acel.14028DMD-Associated Dilated Cardiomyopathy: Genotypes, Phenotypes, and Phenocopies
Circulation: Genomic and Precision MedicinePublished: October 202310.1161/CIRCGEN.123.004221The STROMICS genome study: deep whole-genome sequencing and analysis of 10K Chinese patients with ischemic stroke reveal complex genetic and phenotypic interplay
Cell DiscoveryPublished: July 21, 202310.1038/s41421-023-00582-8Integrated multi-omics analyses and functional validation reveal TTK as a novel EMT activator for endometrial cancer
Journal of Translational MedicinePublished: February 25, 202310.1186/s12967-023-03998-8CMDB: the comprehensive population genome variation database of China
Nucleic Acids ResearchPublished: January 6, 202310.1093/nar/gkac638A population-based study of precision health assessments using multi-omics network-derived biological functional modules
Cell Reports MedicinePublished: December 202210.1016/j.xcrm.2022.100847VIPPID: a gene-specific single nucleotide variant pathogenicity prediction tool for primary immunodeficiency diseases
Briefings in BioinformaticsPublished: September 20, 202210.1093/bib/bbac176A pilot study of assessing whole genome sequencing in newborn screening in unselected children in China
Clinical and Translational MedicinePublished: June 202210.1002/ctm2.843Rare Variants in Inborn Errors of Immunity Genes Associated With Covid-19 Severity
Frontiers in Cellular and Infection MicrobiologyPublished: May 27, 202210.3389/fcimb.2022.888582Identification of Potential Biomarkers for Pan-Cancer Diagnosis and Prognosis Through the Integration of Large-Scale Transcriptomic Data
Frontiers in PharmacologyPublished: May 23, 202210.3389/fphar.2022.870660T Cell Repertoire Abnormality in Immunodeficiency Patients with DNA Repair and Methylation Defects
Journal of Clinical ImmunologyPublished: February 202210.1007/s10875-021-01178-1Species-Level Analysis of the Human Gut Microbiome Shows Antibiotic Resistance Genes Associated With Colorectal Cancer
Frontiers in MicrobiologyPublished: December 15, 202110.3389/fmicb.2021.765291RNA-seq in DMD urinary stem cells recognized muscle-related transcription signatures and addressed the identification of atypical mutations by whole-genome sequencing
HGG AdvancesPublished: August 24, 202110.1016/j.xhgg.2021.100054Molecular Classification and Interpretation of Amyotrophic Lateral Sclerosis Using Deep Convolution Neural Networks and Shapley Values
GenesPublished: 202110.3390/genes12111754New genetic variants associated with major adverse cardiovascular events in patients with acute coronary syndromes and treated with clopidogrel and aspirin
The Pharmacogenomics JournalPublished: 202110.1038/s41397-021-00245-5Integrated genetic analyses revealed novel human longevity loci and reduced risks of multiple diseases in a cohort study of 15,651 Chinese individuals
Aging CellPublished: March 3, 202110.1111/acel.13323More severe than CVID: Combined immunodeficiency due to a novel NFKB2 mutation
Pediatric Allergy and ImmunologyPublished: December 28, 202010.1111/pai.13441Ethnicity-related DMD Genotype Landscapes in European and Non-European Countries
Neurology: GeneticsPublished: December 24, 202010.1212/nxg.0000000000000536Bi-Allelic Pathogenic Variations in MERTK Including Deletions Are Associated with an Early Onset Progressive Form of Retinitis Pigmentosa
GenesPublished: December 18, 202010.3390/genes11121517Severe Bleeding Diathesis in Siblings with Platelet Dysfunction due to a Novel Nonsense RASGRP2 Mutation
TH OpenPublished: October 1, 202010.1055/s-0040-1718910Developing an Unbiased Multiplex PCR System to Enrich the TRB Repertoire Toward Accurate Detection in Leukemia
Frontiers in ImmunologyPublished: August 6, 202010.3389/fimmu.2020.01631NAXD Deficiency Associated with Perinatal Autoinflammation, Pancytopenia, Dermatitis, Colitis, and Cystic Encephalomalacia
Journal of Pediatric NeurologyPublished: July 20, 202010.1055/s-0040-1713682Janus kinase inhibition in complement component 1 deficiency
Journal of Allergy and Clinical ImmunologyPublished: April 20, 202010.1016/j.jaci.2020.04.002ATPase domain AFG3L2 mutations alter OPA1 processing and cause Optic Neuropathy
Annals of NeurologyPublished: March 26, 202010.1002/ana.25723Clinical Implications of Experimental Analyses of AID Function on Predictive Computational Tools: Challenge of Missense Variants
Clinical GeneticsPublished: March 11, 202010.1111/cge.13737Noncoding RNA transcription alters chromosomal topology to promote isotype-specific class switch recombination
Science ImmunologyPublished: February 14, 202010.1126/sciimmunol.aay5864A Missense Mutation in RAB28 in a Family with Cone-Rod Dystrophy and Postaxial Polydactyly Prevents Localization of RAB28 to the Primary Cilium
Investigative Ophthalmology & Visual SciencePublished: February 1, 202010.1167/iovs.61.2.29Molecular Basis of Allogeneic Pluripotent Stem Cell Treatment of a Patient with Sporadic ALS
OBM GeriatricsPublished: 202010.21926/obm.geriatr.2101164Panoramic Visualization of Circulating MicroRNAs Across Neurodegenerative Diseases in Humans
Molecular NeurobiologyPublished: 201910.1007/s12035-019-1615-1The gut microbiome in atherosclerotic cardiovascular disease
Nature CommunicationsPublished: 201710.1038/s41467-017-00900-1