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References from Multi-omics mapping of PSC genetic risk to a high TWAS-active JAML+ lipid-associated macrophage program: bridging single-cell heterogeneity, spatial fibrotic niches, and machine learning selection. Local targets link to admitted publications; unresolved targets remain external evidence.
XgCPred: cell type classification using XGBoost-CNN integration and exploiting gene expression imaging in single-cell RNAseq data
10.1016/j.compbiomed.2024.109066 · 2024 · External reference
SCENIC: single-cell regulatory network inference and clustering
10.1038/nmeth.4463 · 2017 · External reference
10.1016/j.csbj.2021.06.043 · 2021 · Admitted local publication
Monitoring of blood vessels and tissues by a population of monocytes with patrolling behavior
2007 · External reference
Mast cell and innate immune cell communication in cholestatic liver disease
10.1055/a-2104-9034 · 2023 · External reference
Macrophage migration inhibitory factor: a regulator of innate immunity
10.1038/nri1200 · 2003 · External reference
Management of primary sclerosing cholangitis: Current state-of-the-art
2024 · External reference
10.1371/journal.pone.0302696 · 2024 · Admitted local publication
Knowledge-slanted random forest method for high-dimensional data and small sample size with a feature selection application for gene expression data
10.1186/s13040-024-00388-8 · 2024 · External reference
Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges
10.1016/j.jgg.2023.03.011 · 2023 · External reference
Human CD14dim monocytes patrol and sense nucleic acids and viruses via TLR7 and TLR8 receptors
10.1016/j.immuni.2010.08.012 · 2010 · External reference
Macrophage junctional adhesion molecule-like (JAML) protein promotes NLRP3 inflammasome activation in the development of atherosclerosis
10.1038/s41418-025-01489-5 · 2025 · External reference
Mast cell and macrophage chemokines CXCL1/CXCL2 control the early stage of neutrophil recruitment during tissue inflammation
10.1182/blood-2013-02-486217 · 2013 · External reference
Osteopontin characterizes bile duct-associated macrophages and correlates with liver fibrosis severity in primary sclerosing cholangitis
10.1097/hep.0000000000000557 · 2024 · External reference
TGF-β in Hepatic Stellate Cell Activation and Liver Fibrogenesis-Updated 2019
10.3390/cells8111419 · 2019 · External reference
Immunomodulatory properties of human dental pulp stromal cells: the role of IL-6/JAK/STAT3 pathway and PD-L1
10.3389/fimmu.2026.1713704 · 2026 · External reference
Primary sclerosing cholangitis
2018 · External reference
EASL Clinical Practice Guidelines on sclerosing cholangitis
10.1016/j.jhep.2022.05.011 · 2022 · External reference
Identification of a broadly fibrogenic macrophage subset induced by type 3 inflammation
2023 · External reference
irGSEA: the integration of single-cell rank-based gene set enrichment analysis
10.1093/bib/bbae243 · 2024 · External reference
STLBRF: an improved random forest algorithm based on standardized-threshold for feature screening of gene expression data
10.1093/bfgp/elae048 · 2025 · External reference
Single sample scoring of molecular phenotypes
10.1186/s12859-018-2435-4 · 2018 · External reference
Doublet identification in single-cell sequencing data using scDblFinder
2021 · External reference
Galectin-3-Insights from inflammatory bowel disease and primary sclerosing cholangitis
10.3390/ijms26136101 · 2025 · External reference
Macrophages contribute to the pathogenesis of sclerosing cholangitis in mice
10.1016/j.jhep.2018.05.018 · 2018 · External reference
Complement inhibition alleviates cholestatic liver injury through mediating macrophage infiltration and function in mice
10.3389/fimmu.2021.785287 · 2021 · External reference
Integrative approaches for large-scale transcriptome-wide association studies
2016 · External reference
Identifying potential circulating miRNA biomarkers for the diagnosis and prediction of ovarian cancer using machine-learning approach: application of boruta
10.3389/fdgth.2023.1187578 · 2023 · External reference
Construction of a human cell landscape at single-cell level
10.1038/s41586-020-2157-4 · 2020 · External reference
GSVA: gene set variation analysis for microarray and RNA-Seq data
10.1186/1471-2105-14-7 · 2013 · External reference
Integrated analysis of multimodal single-cell data
10.1016/j.cell.2021.04.048 · 2021 · External reference
JAML promotes the antitumor role of tumor-resident CD8(+) T cells by facilitating their innate-like function in human lung cancer
10.1016/j.canlet.2024.216839 · 2024 · External reference
Unresolved reference
2009 · External reference
Mechanism and regulation of NLRP3 inflammasome activation
10.1016/j.tibs.2016.09.002 · 2016 · External reference
JAML promotes acute kidney injury mainly through a macrophage-dependent mechanism
10.1172/jci.insight.158571 · 2022 · External reference
Central role for cholangiocyte pathobiology in cholestatic liver diseases
2025 · External reference
Inference and analysis of cell-cell communication using CellChat
2021 · External reference
Primary sclerosing cholangitis - a comprehensive review
2017 · External reference
Fast, sensitive and accurate integration of single-cell data with Harmony
10.1038/s41592-019-0619-0 · 2019 · External reference
CCCP induces hepatic stellate cell activation and liver fibrogenesis via mitochondrial and lysosomal dysfunction
10.1016/j.freeradbiomed.2024.10.259 · 2024 · External reference
The molecular signatures database (MSigDB) hallmark gene set collection
10.1016/j.cels.2015.12.004 · 2015 · External reference
Unresolved reference
2023 · External reference
Transcriptome-wide association studies: recent advances in methods, applications and available databases
2023 · External reference
New insights on the role of vascular endothelial growth factor in biliary pathophysiology
10.1016/j.jhepr.2021.100251 · 2021 · External reference
The inflammasome: a molecular platform triggering activation of inflammatory caspases and processing of proIL-beta
10.1016/s1097-2765(02)00599-3 · 2002 · External reference
Expression and upregulation of cathepsin S and other early molecules required for antigen presentation in activated hepatic stellate cells upon IFN-Gamma treatment
10.1016/j.bbamcr.2006.11.005 · 2007 · External reference
Protective and pathogenic functions of macrophage subsets
10.1038/nri3073 · 2011 · External reference
Spatial proteomics and cell-cell crosstalk analysis reveal PD-L1 and IL-6 interaction in human primary sclerosing cholangitis
10.1016/j.jhepr.2026.101903 · 2026 · External reference
scTenifoldKnk: an efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation
10.1016/j.patter.2022.100434 · 2022 · External reference
Resolving the fibrotic niche of human liver cirrhosis at single-cell level
2019 · External reference
The ins and outs of MHC class II-mediated antigen processing and presentation
10.1038/nri3818 · 2015 · External reference
Multiplex transcriptional analysis of paraffin-embedded liver needle biopsy from patients with liver fibrosis
10.1186/1755-1536-5-21 · 2012 · External reference
Primary sclerosing cholangitis, part 1: epidemiology, etiopathogenesis, clinical features, and treatment
2018 · External reference
Regression shrinkage and selection Via the lasso
10.1111/j.2517-6161.1996.tb02080.x · 1996 · External reference
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-Seq
10.1126/science.aad0501 · 2016 · External reference
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
2014 · External reference
Critical roles for CCR2 and MCP-3 in monocyte mobilization from bone marrow and recruitment to inflammatory sites
10.1172/jci29919 · 2007 · External reference
The molecular interaction of CAR and JAML recruits the central cell signal transducer PI3K
10.1126/science.1187996 · 2010 · External reference
Single-cell RNA-Seq reveals new types of human blood dendritic cells, monocytes, and progenitors
10.1126/science.aah4573 · 2017 · External reference
A comparative study of machine learning techniques for cell annotation of scRNA-Seq data
10.3390/a18040232 · 2025 · External reference
Spatial transcriptomics of healthy and fibrotic human liver at single-cell resolution
10.1038/s41467-024-55325-4 · 2025 · External reference
The junctional adhesion molecule JAML is a costimulatory receptor for epithelial gammadelta T cell activation
10.1126/science.1192698 · 2010 · External reference
Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis
2019 · External reference
Identification of conserved and tissue-restricted transcriptional profiles for lipid associated macrophages
10.1038/s42003-025-08387-z · 2025 · External reference
clusterProfiler: an R package for comparing biological themes among gene clusters
10.1089/omi.2011.0118 · 2012 · External reference
A polynomial algorithm for best-subset selection problem
10.1073/pnas.2014241117 · 2020 · External reference
