Jiang X. Qian

Isolation and Characterization of Extracellular Vesicles from Mouse Retina Tissue

This paper provides a standardized protocol for isolating and characterizing extracellular vesicles from mouse retinal tissue, improving the study of in vivo EV biology.

Gut-derived metabolic reprogramming drives immune aging and tissue degeneration

This study identifies a diet-induced metabolic-immune axis linking gut microbiome changes to systemic immune aging and retinal degeneration in mice and AMD patients.

Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment

The paper identifies mitochondrial dysfunction in a glaucoma model using single-cell analysis and shows that vitamin B3 treatment protects against IOP elevation.

Single-Cell Characterization of Anterior Segment Development: Cell Types, Pathways, and Signals Driving Formation of the Trabecular Meshwork and Schlemm's Canal

The paper uses single-cell transcriptomics to characterize anterior segment development, identifying cell types, pathways, and signaling networks in trabecular meshwork and Schlemm's canal formation.

Cigarette smoke and biological age induce degenerative heterogeneity in retinalpigment epithelium

This study shows cigarette smoke and aging induce degenerative heterogeneity in RPE cells through distinct epigenetic changes, with young RPE showing compensatory responses not seen in aged RPE.

Attenuated adenosine mediated immune-dampening increases natural killer cell activity in early age-related macular degeneration

The paper investigates immune alterations in early AMD, finding elevated NK cell activity and reduced adenosine, suggesting immune imbalance drives disease progression.

MetaLigand: A database for predicting non-peptide ligand mediated cell-cell communication

MetaLigand predicts non-peptide ligand-receptor interactions using transcriptomic data, revealing unique NPL profiles in retinal cell types associated with age-related macular degeneration.

Transcriptomic profiling of Schlemm's canal cells reveals a lymphatic-biased identity and three major cell states

The paper performs transcriptomic analyses of Schlemm's canal endothelial cells to reveal their lymphatic identity, three major cell states, and interactions with trabecular meshwork cells.

The Drosophila histone methyl-transferase SET1 coordinates multiple signaling pathways in regulating male germline stem cell maintenance and differentiation

This study shows that the Drosophila SET1 histone methyltransferase regulates male germline stem cell maintenance and differentiation by coordinating JAK-STAT and BMP signaling pathways.

Intercellular communication atlas reveals Oprm1 as a neuroprotective factor for retinal ganglion cells

The paper constructs an intercellular communication atlas of the retina, identifying Oprm1 as a neuroprotective factor that enhances RGC survival through ligand-receptor interactions.

Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina.

The paper compares gene regulatory networks in zebrafish retinal regeneration and development after different neuronal subtype losses, finding both similarities and differences.

Histone methyltransferase Ezh2 coordinates mammalian axon regeneration via epigenetic regulation of key regenerative pathways

This study shows Ezh2 promotes axon regeneration in the PNS and CNS by epigenetically regulating genes involved in regeneration and inhibitory signaling.

Molecular regulation of retinal regeneration is context specific

The paper identifies 18 genes regulating retinal ganglion cell regeneration in zebrafish using a combination of genetic models and single-cell omics.

Transcriptomic comparison of two selective retinal cell ablation paradigms in zebrafish reveals shared and cell-specific regenerative responses

The paper compares transcriptomic responses in zebrafish following rod photoreceptor or bipolar cell loss, identifying cell-specific and shared regenerative gene programs and immune-related regulators.

Targeting pioneer transcription factor Ascl1 to promote optic nerve regeneration

This study shows that overexpressing Ascl1 promotes optic nerve regeneration and retinal ganglion cell survival in mice by activating Sox11.

scRNA-sequencing reveals subtype-specific transcriptomic perturbations in DRG neurons of Pirt-EGFPf mice in neuropathic pain condition

The paper uses scRNA-seq to identify subtype-specific transcriptomic changes in DRG neurons of Pirt-EGFPf mice under neuropathic pain conditions.

Transretinal migration of astrocytes and brain/spinal cord-like cells arising from transplanted human retinal organoids.

This study transplants human retinal organoids into mice and identifies two classes of graft-derived cells with distinct migration and maturation behaviors.

Multi-omic Analysis of Developing Human Retina and Organoids Reveals Cell-Specific Cis-Regulatory Elements and Mechanisms of Non-Coding Genetic Disease Risk.

The paper identifies cell-class-specific cis-regulatory elements in human retina and organoids, showing their correlation and function in development and disease.

LRLoop: Feedback loops as a design principle of cell-cell communication

LRLoop identifies bidirectional ligand-receptor feedback loops in cell-cell communication, reducing false positives and revealing new interactions in retinal development.

IReNA: integrated regulatory network analysis of single-cell transcriptomes

IReNA integrates scRNA-seq and scATAC-seq data to infer regulatory networks, outperforming existing methods in identifying known regulators.

Gene regulatory networks controlling temporal patterning, neurogenesis and cell fate specification in the mammalian retina.

This study identifies gene regulatory networks controlling retinal development by integrating single-cell RNA and ATAC-seq data from mouse and human retinas, revealing transcription factors that regulate temporal patterning and cell fate.

Human retinal organoids release extracellular vesicles that regulate gene expression in target human retinal progenitors

This study identifies EVs from human retinal organoids and shows they regulate gene expression in retinal progenitors through miRNA cargo.

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.

Control of neurogenic competence in mammalian hypothalamic tanycytes.

This study identifies NFI factors as repressors of tanycyte-derived neurogenesis and shows their disruption promotes proliferation and neurogenesis in the hypothalamus.

An All-to-All Approach to the Identification of Sequence-Specific Readers for Epigenetic DNA Modifications on Cytosine

The paper withdraws its manuscript due to the need for further experimental validation of its conclusions.

Cross-species transcriptomic and epigenomic analysis reveals key regulators of injury response and neuronal regeneration in vertebrate retinas.

This study identifies gene regulatory networks controlling proliferative and neurogenic competence in retinal Muller glia.

Knocking out non-muscle myosin II in retinal ganglion cells promotes long-distance optic nerve regeneration

This study shows that knocking out myosin IIA/B in retinal ganglion cells promotes optic nerve regeneration, with synergistic effects when combined with Lin28 overexpression.

EAGLE: an algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interaction

EAGLE predicts tissue/cell type-specific enhancer-gene interactions using six genomic features, outperforming existing methods and identifying millions of interactions in human and mouse genomes.

OmicsX: a web server for integrated OMICS analysis

OmicsX is a web server that integrates and compares multi-omics datasets, offering analysis tools and visualization to identify biological insights.

PanoView: An iterative clustering for single-cell RNA sequencing data

PanoView is an iterative clustering method for scRNA-seq data that outperforms existing methods in detecting major and rare cell types without parameter tuning.