A5100701314- Single-cell and spatial transcriptomics
- Corneal Surgery and Treatments
- Corneal surgery and disorders
- Genomics and Phylogenetic Studies
- Retinal Development and Disorders
- RNA modifications and cancer
- Intraocular Surgery and Lenses
- RNA and protein synthesis mechanisms
- Ocular Surface and Contact Lens
- Ophthalmology and Visual Impairment Studies
- interferon and immune responses
- Chromosomal and Genetic Variations
- Molecular Biology Techniques and Applications
- Geological and Geochemical Analysis
- Genomic variations and chromosomal abnormalities
- Neuroinflammation and Neurodegeneration Mechanisms
- Global Maternal and Child Health
- Glaucoma and retinal disorders
- Retinal Diseases and Treatments
- Geochemistry and Geologic Mapping
- Recommender Systems and Techniques
- earthquake and tectonic studies
- Urban Green Space and Health
- High-pressure geophysics and materials
- Developmental Biology and Gene Regulation
Shandong University
2014-2025
Sun Yat-sen University
2013-2024
Chinese Academy of Medical Sciences & Peking Union Medical College
2020-2024
Hunan University of Science and Technology
2019-2024
Chengdu University
2024
Ministry of Agriculture and Rural Affairs
2024
Chinese Academy of Sciences
2009-2022
Guangzhou Regenerative Medicine and Health Guangdong Laboratory
2020-2022
Clemson University
2022
BGI Group (China)
2022
Long nanopore reads are advantageous in de novo genome assembly. However, usually have broad error distribution and high-error-rate subsequences. Existing correction tools cannot correct efficiently effectively. Most methods trim subsequences during correction, which reduces both the length of contiguity final Here, we develop an assembly tool designed to overcome complex errors reads. We propose adaptive read selection two-step progressive method quickly high accuracy. introduce a two-stage...
The COVID-19 pandemic has led to worldwide school closures, with millions of children confined online learning at home. As a result, may be susceptible anxiety and digital eye strain, highlighting need for population interventions.The objective our study was investigate whether behavior change intervention aimed promoting physical activity could reduce children's strain while undergoing prolonged homeschooling during the pandemic.In this cluster randomized controlled trial, homeschooled...
Although long-read single-cell RNA isoform sequencing (scISO-Seq) can reveal alternative splicing in individual cells, it suffers from a low read throughput. Here, we introduce HIT-scISOseq, method that removes most artifact cDNAs and concatenates multiple for PacBio circular consensus (CCS) to achieve high-throughput high-accuracy sequencing. HIT-scISOseq yield >10 million long-reads single Sequel II SMRT Cell 8M. We also report the development of scISA-Tools demultiplex concatenated reads...
Abstract A complete characterization of genetic variation is a fundamental goal human genome research. Long-read sequencing has improved the sensitivity structural variant discovery. Here, we conduct long-read sequencing-based analysis for 405 unrelated Chinese individuals, with 68 phenotypic and clinical measurements. We discover landscape 132,312 nonredundant variants, which 45.2% are novel. The identified variants high-quality, an estimated false discovery rate 3.2%. concatenated length...
Abstract Adult stem cell identity, plasticity, and homeostasis are precisely orchestrated by lineage-restricted epigenetic transcriptional regulatory networks. Here, integrating super-enhancer chromatin accessibility landscapes, we delineate core transcription circuitries (CRCs) of limbal stem/progenitor cells (LSCs) find that RUNX1 SMAD3 required for maintenance corneal epithelial identity homeostasis. or depletion inhibits PAX6 induces LSCs to differentiate into epidermal-like cells....
Retinal ganglion cells (RGCs) are the brain's gateway to visual world. They can be classified into different types on basis of their electrophysiological, transcriptomic, or morphological characteristics. Here, we characterize morphological, and functional features 472 high-quality RGCs using Patch sequencing (Patch-seq), providing annotation many transcriptomic-defined cell a previously established RGC atlas. We show convergence modalities in defining identity reveal degree correspondence...
Abstract Uveitis is a severe autoimmune disease, and common cause of blindness; however, its individual cellular dynamics pathogenic mechanism remain poorly understood. Herein, by performing single-cell RNA sequencing (scRNA-seq) on experimental uveitis (EAU), we identify disease-associated alterations in cell composition transcriptional regulation as the disease progressed, well disease-related molecule, PIM1. Inhibiting PIM1 reduces Th17 proportion increases Treg proportion, likely due to...
Vaccinia virus infection causes a host shutoff that is marked by global inhibition of protein synthesis. Though the may facilitate reallocation cellular resources for viral replication and evasion antiviral immune responses, it poses challenge continuous synthesis proteins are important replication. It is, however, unclear whether how certain be selectively synthesized during vaccinia virus-induced shutoff. Using simultaneous RNA sequencing ribosome profiling, two techniques quantifying...
Abstract Although long Nanopore reads are advantageous in de novo genome assembly, applying genomic studies is still hindered by their complex errors. Here, we developed NECAT, an error correction and assembly tool designed to overcome errors reads. We proposed adaptive read selection two-step progressive method quickly correct high accuracy. introduced a two-stage assembler utilize the full length of NECAT achieves superior performance both requires only 7,225 CPU hours assemble 35X...
<h3>Importance</h3> Allergic conjunctivitis (AC) is one of the most common allergic diseases and especially problematic in children adolescents. The course AC generally prolonged often recurs. Understanding health-related quality life (QOL) both with their parents would be useful. <h3>Objective</h3> To evaluate association between QOL parents. <h3>Design, Setting, Participants</h3> A prospective case-control study was conducted at Zhongshan Ophthalmic Center, a single tertiary referral...
Nonreference sequences (NRSs) are DNA present in global populations but absent the current human reference genome. However, extent and functional significance of NRSs genomes remains unclear. Here, we de novo assembled 539 from five genetically divergent using long-read sequencing technology, resulting identification 5.1 million NRSs. These were merged into 45284 unique NRSs, with 29.7% being novel discoveries. Among these 38.7% common across populations, 35.6% population specific. The use a...
Abstract The insights into how genome topology couples with epigenetic states to govern the function and identity of corneal epithelium are poorly understood. Here, we generate a high-resolution Hi-C interaction map human limbal stem/progenitor cells (LSCs) show that chromatin multi-hierarchical organisation is coupled gene expression. By integrating Hi-C, epigenome transcriptome data, characterize comprehensive 3D epigenomic landscapes LSCs. We find super-silencers mediate repression...
Virus-like particles (VLP) are a promising tool for intracellular gene delivery, yet their potential in ocular therapy remains underexplored. In this study, we bridged knowledge gap by demonstrating the successful generation and application of vesicular stomatitis virus glycoprotein (VSVG)-pseudotyped mouse PEG10 (MmPEG10)-VLP intraocular mRNA delivery. Our findings revealed that PEG10-VLP can efficiently deliver GFP to adult retinal pigment epithelial cell line-19 (ARPE-19) cells, leading...
Coronavirus disease 2019 (COVID-19), driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a global pandemic in March 2020. Pathogenic T cells and inflammatory monocytes are regarded as the central drivers of cytokine storm associated with severity COVID-19. In this study, we explored characteristic peripheral cellular profiles patients COVID-19 both convalescent phases single-cell mass cytometry (CyTOF). Using combination algorithm-guided data analyses,...
Abstract Accumulated oxidative damage may lead to irreversible retinal pigmented epithelium (RPE) cell death, which is considered be the primary cause of dry age-related macular degeneration (AMD), leading blindness in elderly. However, an effective therapy for this disease lacking. Here, we described a robust high-content screening procedure with library 814 protective compounds and found that D609 strongly protected RPE cells from sodium iodate (SI)-induced death prolonged their healthy...
Abstract The differences in transcription start sites (TSS) and end (TES) among gene isoforms can affect the stability, localization, translation efficiency of mRNA. Gene allow a single diverse functions across different cell types, isoform dynamics over time. However, methods to efficiently identify quantify RNA genome-wide cells are still lacking. Here, we introduce Cap And Tail sequencing (scRCAT-seq), method demarcate boundaries based on short-read sequencing, with higher lower cost than...