Hongkai Ji

The paper introduces CLIC scores to quantify confidence in gene-peak associations for single-cell RNA-ATAC integration, improving integration accuracy and biological interpretability.

The paper analyzes DNA methylation stochasticity in AML subtypes, identifying high-entropy subtypes and linking methylation entropy to transcriptional variability and leukemogenesis.

This study shows immune checkpoint inhibitors enhance type 2 immunity and regeneration in ECM-treated wounds by promoting Treg/TH2 plasticity and pro-regenerative macrophages.

The paper evaluates 47 highly variable gene selection methods for scRNA-seq across 19 datasets and finds hybrid methods outperform individual methods, proposing a new approach called mixHVG.

The paper introduces Hi-Plex CUT&Tag, a method to detect co-localization of over 600 CRF pairs, enabling comprehensive analysis of chromatin regulatory interactions in a single experiment.

This study shows that library size in spATAC-seq data is biologically informative and that standard normalization methods can obscure important biological signals.

This study examines how dual checkpoint blockade with Anti-PD-1 and Anti-LAG-3 affects T cell clones in glioblastoma, showing increased clonal expansion and differentiation into effector T cells.

The paper develops a spatial biomarker, DONUTS, to predict treatment response in lung cancer by analyzing the niche surrounding CD8+FoxP3+ T-cells.

The paper investigates DNA methylation changes during pancreatic acinar-ductal metaplasia (ADM) and their persistence without Kras mutation, linking epigenetic memory to signaling pathway alterations and cancer cell plasticity.

This paper introduces a consensus variant-to-function score to prioritize disease-causing variants, showing improved performance in heritability enrichment and fine-mapping.

The paper introduces FUNCODE, a framework to quantify functional conservation between human and mouse regulatory elements using in silico sample matching, identifying 3.3 million conserved element pairs and demonstrating its applications in annotation and cross-species data integration.

Lamian is a statistical framework for analyzing pseudotime differences across multiple scRNA-seq samples, improving generalizability by accounting for sample variability.

DAESC is a statistical method for differential allele-specific expression analysis in scRNA-seq data, identifying genes with context-specific regulatory effects in endoderm differentiation and type 2 diabetes.

The paper shows SMARCC1 does not mediate GLI3 repression of Hedgehog target genes, as it maintains chromatin accessibility at GLI-regulated enhancers independently of GLI3.

The paper examines regional gene expression differences in the retina, optic nerve head, and optic nerve of mice with glaucoma and optic nerve crush using bulk RNA-sequencing.

The paper analyzes DNA methylation entropy in human and mouse datasets, finding associations with sequence features, developmental patterns, and gene expression variability.

The paper identifies novel pathways that enhance oligodendrocyte maturation and myelination through high-throughput screening of 2500 compounds using engineered human stem cell-derived OPCs.

PRECAST integrates spatial transcriptomics data from multiple sources, improving cell and domain detection through probabilistic embedding, clustering, and alignment.

This study shows that Sonic hedgehog (SHH) signaling is critical for maintaining epithelial integrity in the larynx and anterior foregut, with SHH loss causing abnormal epithelial to mesenchymal transition and replacement by Pax-1 expressing cells.

This paper introduces quantitative fate mapping to reconstruct progenitor field dynamics using lineage barcodes and validates it with simulations and experiments.

The paper identifies cis-regulatory elements in dorsal root ganglion neurons that show differential chromatin accessibility and TF binding after nerve injury, linking them to chronic pain.

The paper shows GLI3 repression does not prevent precocious activation of HH target genes or regulate anterior-posterior limb polarity.

TreeCorTreat analyzes and visualizes phenotype-cell type associations in multi-sample single-cell RNA-seq data using a tree-based correlation approach.

The paper identifies neuroprotective compounds for retinitis pigmentosa using cross-species drug screens in zebrafish and mouse models, finding additive effects in some combinations.

The paper identifies transcriptomic and epigenetic changes in rat dorsal root ganglia under two chronic pain models, revealing shared and distinct chromatin accessibility alterations.

This study evaluates 18 scRNA-seq imputation methods using cell line and tissue data, finding significant variability in performance and recommending caution in downstream analyses.

SCATE improves the accuracy of estimating cis-regulatory element activities in single-cell ATAC-seq data by integrating co-activated elements, similar cells, and regulome data.

The paper identifies HH-responsive enhancers that lose acetylation in the absence of Hedgehog signaling and are regulated by GLI repression rather than Polycomb complexes.

The paper identifies sex-related gene expression differences in the dorsal root ganglion of male and female rats after nerve injury using RNA-seq.

This study identifies global decreases in chromatin accessibility in AMD patients, linking epigenetic changes to disease progression and suggesting HDAC11 as a potential therapeutic target.