Our lab
Chen Jinmiao Lab
Single-Cell Multi/Spatial-Omics and Precision Immunology
Bioinformatics Institute (BII), A*STAR · Duke-NUS Medical School
About
The Chen Jinmiao Lab is a multidisciplinary computational biology research laboratory spanning the Bioinformatics Institute (BII) at the Agency for Science, Technology and Research (A*STAR) and Duke-NUS Medical School in Singapore.
To advance biomedical discovery and precision medicine through innovative artificial intelligence, computational biology, and integrative single-cell and spatial omics research.
Principal Investigator
Associate Professor Jinmiao Chen
- Senior Principal Investigator, A*STAR Bioinformatics Institute
- Associate Professor, Duke-NUS Medical School
- Associate Professor, NUS Yong Loo Lin School of Medicine
Associate Professor Jinmiao Chen is a computational biologist specializing in artificial intelligence, single-cell and spatial omics, and precision immunology.
Team
A*STAR Bioinformatics Institute
- Xu HangResearch Scientist
- Raman SethiResearch Officer
- Rom UddamvathanakResearch Officer
- Laura SamPhD Student
Duke-NUS Medical School
- Samueh ChuahResearch Scientist
- Xiao MengResearch Scientist
- Xu HuaResearch Scientist
- Yan JunPhD Student
- Yu LingPhD Student
- Ren LiangruiResearch Scientist
- KaijiePhD Student
- Chen YiruPhD Student
Alumni
- Yahui LongResearch Scientist, A*STAR BII
- Li MengweiResearch Scientist, A*STAR BII
- Zhong ChengweiResearch Officer, A*STAR BII
Research
Artificial Intelligence for Single-Cell Omics
Computational and deep-learning approaches to study cellular diversity and biological processes using single-cell omics data.
Spatial Transcriptomics and Spatial Multi-Omics
Methods to understand the spatial organization of cells and tissues by integrating gene expression with spatial and complementary molecular information.
Large-Scale Single-Cell Data Integration
Computational resources and analytical tools for integrating publicly available single-cell datasets.
AI for Drug Discovery and Cellular Perturbations
Computational approaches for modeling biological responses to drug treatment and genetic perturbations.
Precision Immunology and Virtual Immunity
Computational biology and AI to characterize immune-cell states and investigate immune-system complexity.
Software
Publications
- 2026Mosaic integration of spatial multi-omics with SpaMosaicNature Genetics
- 2026SMART: spatial multi-omic aggregation using graph neural networks and metric learningNature Communications
- 2025Spatial dynamics of brain development and neuroinflammationNature
- 2025Septal LYVE1+ macrophages control adipocyte stem cell adipogenic potentialScience
- 2025Single-nucleus transcriptomics reveals a distinct microglial state and increased MSR1-mediated phagocytosis as common features across dementia subtypesGenome Medicine
- 2025Microglial mechanisms drive amyloid-β clearance in immunized patients with Alzheimer's diseaseNature Medicine
Browse all 124 publications
- 2026Uni-TINT: Unifying T and Innate Lymphoid Cell Taxonomy with a high resolution, pan-disease and pan-tissue single-cell transcriptomic atlasPreprint
- 2026SpatioTemporal Omics Consortium: a global effort for biological discovery across species, space and timeNat Methods
- 2026Direct contact between iPSC-derived macrophages and hepatocytes drives reciprocal acquisition of Kupffer cell identity and hepatocyte maturationElife · cited by 1
- 2026AI-guided prediction of ncRNA biochemical features for therapeutic targetingTrends Pharmacol Sci
- 2026Mosaic integration of spatial multi-omics with SpaMosaicNat Genet · cited by 11
- 2026SMART: spatial multi-omic aggregation using graph neural networks and metric learningNature Communications
- 2026Spatial cartography of human thymus enables the geopositioning of lineage transcription factors in rare mimetic thymic epithelial cellsNat Commun · cited by 3
- 2026scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignmentGenome Res · cited by 1
- 2026FAST: Scalable Factor Analysis for Spatial Dimension Reduction of Multi-section Spatial TranscriptomicsGenomics Proteomics Bioinformatics
- 2026Irf7 Deficiency Confers Protection Against Influenza Infection, Independent of irf3Int J Biol Sci · cited by 2
- 2025A Population-Scale Single-Cell Atlas of the Human Heart Reveals Cellular Remodeling and Cell–Cell Communication in Aging and Cardiac DiseasePreprint
- 2025Spatial dynamics of brain development and neuroinflammationNature · cited by 48
- 2025ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic IntegrationGenomics Proteomics Bioinformatics
- 2025Septal LYVE1+ macrophages control adipocyte stem cell adipogenic potentialScience · cited by 31
- 2025Single-nucleus transcriptomics reveals a distinct microglial state and increased MSR1-mediated phagocytosis as common features across dementia subtypesGenome Medicine
- 2025StereoMM: a graph fusion model for integrating spatial transcriptomic data and pathological imagesBrief Bioinform · cited by 6
- 2025Microglial mechanisms drive amyloid-β clearance in immunized patients with Alzheimer's diseaseNat Med · cited by 151
- 2025Rediscovering publicly available single-cell data with the DISCO platformNucleic Acids Res · cited by 23
- 2024Differential contributions of fetal mononuclear phagocytes to Zika virus neuroinvasion versus neuroprotection during congenital infectionCell · cited by 11
- 2024Interpretable spatially aware dimension reduction of spatial transcriptomics with STAMPNat Methods · cited by 46
- 2024ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientistsNat Commun · cited by 22
- 2024Deciphering spatial domains from spatial multi-omics with SpatialGlueNat Methods · cited by 180
- 2024Single-cell and spatial atlas of steatotic liver disease-related hepatocellular carcinomaPreprint · cited by 1
- 2024Relative deficiency in interferon-γ-secreting CD4+ T cells is strongly associated with poorer COVID-19 vaccination responses in older adultsAging Cell · cited by 5
- 2024Deterministic reprogramming of neutrophils within tumorsScience · cited by 389
- 2024Unsupervised spatially embedded deep representation of spatial transcriptomicsGenome Med · cited by 325
- 2023Late inflammatory monocytes define circulatory immune dysregulation observed in skin microbiome-stratified atopic dermatitisJ Dermatol Sci · cited by 1
- 2023iPS-cell-derived microglia promote brain organoid maturation via cholesterol transferNature · cited by 211
- 2023Analyzing COVID-19 Vaccine Responses in Transplant RecipientsImmunohorizons · cited by 1
- 2024Singapore's diverse immunology landscape: interconnected research networks enabling blue sky ideas through to translationImmunol Cell Biol
- 2023scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularizationBioinformatics · cited by 10
- 2023FAST: a fast and scalable factor analysis for spatially aware dimension reduction of multi-section spatial transcriptomics dataPreprint · cited by 2
- 2023The axis of complement C1 and nucleolus in antinuclear autoimmunityFront Immunol · cited by 5
- 2023Patterns of Oncogene Coexpression at Single-Cell Resolution Influence Survival in LymphomaCancer Discov · cited by 7
- 2023Integrated analysis of spatial multi-omics with SpatialGluePreprint · cited by 4
- 2023Establishing a human bone marrow single cell reference atlas to study ageing and diseasesFront Immunol · cited by 20
- 2023Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphSTNat Commun · cited by 537
- 2023Dampened Inflammation and Improved Survival After CXCL5 Administration in Murine Lupus via Myeloid and Neutrophil PathwaysArthritis Rheumatol · cited by 15
- 2023Conditional Knockout of Hypoxia-Inducible Factor 1-Alpha in Tumor-Infiltrating Neutrophils Protects against Pancreatic Ductal AdenocarcinomaInt J Mol Sci · cited by 18
- 2022Intraperitoneally Delivered Umbilical Cord Lining Mesenchymal Stromal Cells Improve Survival and Kidney Function in Murine Lupus via Myeloid Pathway TargetingInt J Mol Sci · cited by 5
- 2023CD8+ T Cells Trigger Auricular Dermatitis and Blepharitis in Mice after Zika Virus Infection in the Absence of CD4+ T CellsJ Invest Dermatol · cited by 4
- 2022Notch-dependent cooperativity between myeloid lineages promotes Langerhans cell histiocytosis pathologySci Immunol · cited by 18
- 2022Editorial: The role of omics characteristics in the diagnosis, treatment, and prognosis of autoimmune diseasesFront Immunol
- 2022DeepST: A versatile graph contrastive learning framework for spatially informed clustering, integration, and deconvolution of spatial transcriptomicsPreprint · cited by 2
- 2022Dual ontogeny of disease-associated microglia and disease inflammatory macrophages in aging and neurodegenerationImmunity · cited by 373
- 2023Uncertainty-aware dynamic integration for multi-omics classification of tumorsJ Cancer Res Clin Oncol · cited by 3
- 2022Reviving human γδT cells from apoptosis induced by IL-12/18 via p-JNK inhibitionJ Leukoc Biol · cited by 6
- 2022FastIntegration: a fast and high-capacity version of Seurat Integration for large-scale integration of single-cell dataPreprint
- 2022FastIntegration: a versatile R package for accessing and integrating large-scale single-cell RNA-seq dataPreprint · cited by 2
- 2022Annexin-A1 deficiency attenuates stress-induced tumor growth via fatty acid metabolism in mice: an Integrated multiple omics analysis on the stress- microbiome-metabolite-epigenetic-oncology (SMMEO) axisTheranostics · cited by 13
- 2022Uncoupling immune trajectories of response and adverse events from anti-PD-1 immunotherapy in hepatocellular carcinomaJ Hepatol · cited by 105
- 2022Pre-training graph neural networks for link prediction in biomedical networksBioinformatics · cited by 43
- 2022DISCO: a database of Deeply Integrated human Single-Cell Omics dataNucleic Acids Res · cited by 186
- 2021A subset of Kupffer cells regulates metabolism through the expression of CD36Immunity · cited by 213
- 2021Cross-tissue single-cell landscape of human monocytes and macrophages in health and diseaseImmunity · cited by 614
- 2021Non-terminally exhausted tumor-resident memory HBV-specific T cell responses correlate with relapse-free survival in hepatocellular carcinomaImmunity · cited by 121
- 2021Resident macrophages restrain pathological adipose tissue remodeling and protect vascular integrity in obese miceEMBO Rep · cited by 47
- 2021Targeting Glycolysis in Macrophages Confers Protection Against Pancreatic Ductal AdenocarcinomaInt J Mol Sci · cited by 36
- 2021CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct functioniScience · cited by 18
- 2021Iqgap3-Ras axis drives stem cell proliferation in the stomach corpus during homoeostasis and repairGut · cited by 53
- 2020Proliferative and quiescent human gastric cancer stem-like cells are associated with differential chemoresistance and patient mortalityPreprint
- 2020Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil ProgenitorImmunity · cited by 263
- 2020The Extended Polydimensional Immunome Characterization (EPIC) web-based reference and discovery tool for cytometry dataNat Biotechnol · cited by 41
- 2020Immunological history governs human stem cell memory CD4 heterogeneity via the Wnt signaling pathwayNat Commun · cited by 40
- 2020A benchmark of batch-effect correction methods for single-cell RNA sequencing dataGenome Biol · cited by 878
- 2020IL-13-driven alterations in hepatic cholesterol handling contributes to hypercholesterolemia in a rat model of minimal change diseaseClin Sci (Lond) · cited by 14
- 2020T-cell phenotyping uncovers systemic features of atopic dermatitis and psoriasisJ Allergy Clin Immunol · cited by 17
- 2019Large-Scale HLA Tetramer Tracking of T Cells during Dengue Infection Reveals Broad Acute Activation and Differentiation into Two Memory Cell FatesImmunity · cited by 44
- 2019Fate Mapping via Ms4a3-Expression History Traces Monocyte-Derived CellsCell · cited by 675
- 2019Single-Cell Analysis of Human Mononuclear Phagocytes Reveals Subset-Defining Markers and Identifies Circulating Inflammatory Dendritic CellsImmunity · cited by 465
- 2019A Novel, Five-Marker Alternative to CD16-CD14 Gating to Identify the Three Human Monocyte SubsetsFront Immunol · cited by 96
- 2019RIG-I Activation by a Designer Short RNA Ligand Protects Human Immune Cells against Dengue Virus Infection without Causing CytotoxicityJ Virol · cited by 15
- 2019Plasmacytoid dendritic cells develop from Ly6D+ lymphoid progenitors distinct from the myeloid lineageNat Immunol · cited by 219
- 2019Metformin Alters Human Host Responses to Mycobacterium tuberculosis in Healthy SubjectsJ Infect Dis · cited by 93
- 2019A Subset of Type I Conventional Dendritic Cells Controls Cutaneous Bacterial Infections through VEGFα-Mediated Recruitment of NeutrophilsImmunity · cited by 59
- 2019Studies on B Cells in the Fruit-Eating Black Flying Fox (Pteropus alecto)Front Immunol · cited by 26
- 2019Two distinct interstitial macrophage populations coexist across tissues in specific subtissular nichesScience · cited by 1,013
- 2019Comparison Between UMAP and t-SNE for Multiplex-Immunofluorescence Derived Single-Cell Data from Tissue SectionsPreprint
- 2019Prognostic value of CD8 + PD-1+ immune infiltrates and PDCD1 gene expression in triple negative breast cancerJ Immunother Cancer · cited by 87
- 2019Multifactorial heterogeneity of virus-specific T cells and association with the progression of human chronic hepatitis B infectionSci Immunol · cited by 81
- 2019Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarctionNat Immunol · cited by 809
- 2019Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State ChangesImmunity · cited by 1,979
- 2018A Single-Cell Sequencing Guide for ImmunologistsFront Immunol · cited by 158
- 2018Influenza A Virus Facilitates Its Infectivity by Activating p53 to Inhibit the Expression of Interferon-Induced Transmembrane ProteinsFront Immunol · cited by 28
- 2018Hemogenic Endothelial Fate Mapping Reveals Dual Developmental Origin of Mast CellsImmunity · cited by 276
- 2018Developmental Analysis of Bone Marrow Neutrophils Reveals Populations Specialized in Expansion, Trafficking, and Effector FunctionsImmunity · cited by 646
- 2018Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific MannerCell · cited by 659
- 2018Constructing cell lineages from single-cell transcriptomesMol Aspects Med · cited by 23
- 2017cycleX: multi-dimensional pseudotime reveals cell cycle and differentiation relationship of dendritic cell progenitorsPreprint · cited by 1
- 2017IgG1 memory B cells keep the memory of IgE responsesNat Commun · cited by 156
- 2017Induced-Pluripotent-Stem-Cell-Derived Primitive Macrophages Provide a Platform for Modeling Tissue-Resident Macrophage Differentiation and FunctionImmunity · cited by 301
- 2017Intrahepatic CD206+ macrophages contribute to inflammation in advanced viral-related liver diseaseJ Hepatol · cited by 65
- 2017Mapping the human DC lineage through the integration of high-dimensional techniquesScience · cited by 486
- 2017Host sirtuin 1 regulates mycobacterial immunopathogenesis and represents a therapeutic target against tuberculosisSci Immunol · cited by 115
- 2017Establishing High Dimensional Immune Signatures from Peripheral Blood via Mass Cytometry in a Discovery Cohort of Stage IV Melanoma PatientsJ Immunol · cited by 29
- 2016CXCR4 identifies transitional bone marrow premonocytes that replenish the mature monocyte pool for peripheral responsesJ Exp Med · cited by 125
- 2016Novel role of Vav1-Rac1 pathway in actin cytoskeleton regulation in interleukin-13-induced minimal change-like nephropathyClin Sci (Lond) · cited by 10
- 2016Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis PipelinePLoS Comput Biol · cited by 305
- 2016Unsupervised High-Dimensional Analysis Aligns Dendritic Cells across Tissues and SpeciesImmunity · cited by 719
- 2016Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during developmentNat Commun · cited by 61
- 2016flowAI: automatic and interactive anomaly discerning tools for flow cytometry dataBioinformatics · cited by 252
- 2017Interaction between tumour-infiltrating B cells and T cells controls the progression of hepatocellular carcinomaGut · cited by 397
- 2016Purification, Visualization, and Molecular Signature of Neural Stem CellsStem Cells Dev · cited by 8
- 2015CD103(+) Dendritic Cells Control Th17 Cell Function in the LungCell Rep · cited by 82
- 2015MicroRNA expression profiling of human blood monocyte subsets highlights functional differencesImmunology · cited by 29
- 2015Mapping the Diversity of Follicular Helper T Cells in Human Blood and Tonsils Using High-Dimensional Mass Cytometry AnalysisCell Rep · cited by 104
- 2015Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrowNat Immunol · cited by 461
- 2015C-Myb(+) erythro-myeloid progenitor-derived fetal monocytes give rise to adult tissue-resident macrophagesImmunity · cited by 987
- 2015Human monocytes undergo functional re-programming during sepsis mediated by hypoxia-inducible factor-1αImmunity · cited by 365
- 2015The transcriptional stress response of Candida albicans to weak organic acidsG3 (Bethesda) · cited by 47
- 2015Bimodal Influence of Vitamin D in Host Response to Systemic Candida Infection-Vitamin D Dose MattersJ Infect Dis · cited by 23
- 2014Calcium and calcineurin-NFAT signaling regulate granulocyte-monocyte progenitor cell cycle via Flt3-LStem Cells · cited by 21
- 2014Metformin as adjunct antituberculosis therapySci Transl Med · cited by 415
- 2014Molecular profiling reveals a tumor-promoting phenotype of monocytes and macrophages in human cancer progressionImmunity · cited by 250
- 2014High-dimensional analysis of the murine myeloid cell systemNat Immunol · cited by 298
- 2014Mapping of HPV transcripts in four human cervical lesions using RNAseq suggests quantitative rearrangements during carcinogenic progressionVirology · cited by 45
- 2012Single-cell mRNA profiling identifies progenitor subclasses in neurospheresStem Cells Dev · cited by 13
- 2012Calcineurin/NFAT signalling inhibits myeloid haematopoiesisEMBO Mol Med · cited by 31
- 2011Loss of macrophage migration inhibitory factor impairs the growth properties of human HeLa cervical cancer cellsCell Prolif · cited by 14
- 2012Chemokine-driven lymphocyte infiltration: an early intratumoural event determining long-term survival in resectable hepatocellular carcinomaGut · cited by 282
- 2011miRNA studies in in vitro and in vivo activated hepatic stellate cellsWorld J Gastroenterol · cited by 39
- 2011Persistent arthralgia induced by Chikungunya virus infection is associated with interleukin-6 and granulocyte macrophage colony-stimulating factorJ Infect Dis · cited by 325
- 2009Segmented-memory recurrent neural networksIEEE Trans Neural Netw · cited by 5
- 2007Cascaded bidirectional recurrent neural networks for protein secondary structure predictionIEEE/ACM Trans Comput Biol Bioinform · cited by 11