Hongkai Ji

Quantifying Cross-Modal Association Confidence for Single-Cell RNA-ATAC Integration

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

DNA methylation stochasticity is linked to transcriptional variability and identifies convergent epigenetic disruption across genetically-defined subtypes of AML

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

Immune checkpoint inhibitors amplify type 2 immune mediated repair bypro-regenerative scaffolds

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.

A systematic evaluation of highly variable gene selection methods for single-cell RNA-sequencing

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.

Global Mapping of Combinatorial Chromatin Regulatory Events Using Hi-Plex CUT&Tag

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.

Library Size in Spatial ATAC-seq: Technical Confounder or Biology?

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

Dual checkpoint blockade of glioblastoma with Anti-PD-1 and Anti-LAG-3 promotes expansion of tumor-reactive T cell clones along a unique pathway of differentiation

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.

Novel Predictive Spatial Biomarker in Non-Small Cell Lung Carcinoma: The Diversity of Niches Unlocking Treatment Sensitivity (DONUTS)

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

DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation

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.

A consensus variant-to-function score to functionally prioritize variants for disease

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

Quantifying Functional Conservation of Human and Mouse Regulatory Elements via FUNCODE

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.

A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples

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

Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects

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.

BAF chromatin complexes do not mediate GLI transcriptional repression of Hedgehog target genes

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.

Regional Gene Expression in the Retina, Optic Nerve Head, and Optic Nerve of Mice with Experimental Glaucoma and Optic Nerve Crush

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.

DNA methylation entropy is associated with DNA sequence featuresand developmental epigenetic divergence

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

High-Throughput Screening for Myelination Promoting Compounds Using Human Stem Cell-derived Oligodendrocyte Progenitor Cells Identifies Novel Targets

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.

Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST

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

Hedgehog regulation of epithelial cell state and morphogenesis in the larynx

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.

Quantitative fate mapping: Reconstructing progenitor field dynamics via retrospective lineage barcoding

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

Identification of regulatory elements in primary sensory neurons involved in neuropathic pain

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.

GLI transcriptional repression is inert prior to Hedgehog pathway activation

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

Tree-based Correlation Screen and Visualization for Exploring Phenotype-Cell Type Association in Multiple Sample Single-Cell RNA-Sequencing Experiments

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

Large-scale Phenotypic Drug Screen Identifies Neuroprotectants in Zebrafish and Mouse Models of Retinitis Pigmentosa

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

Dynamics of global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain

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

A Systematic Evaluation of Single-cell RNA-sequencing Imputation Methods

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.

Single-cell ATAC-seq Signal Extraction and Enhancement with SCATE

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.

GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling

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.

Sex differences in gene regulation in the dorsal root ganglion after nerve injury

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

A widespread decrease of chromatin accessibility in age-related macular degeneration

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.