A5100614504- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- MicroRNA in disease regulation
- Single-cell and spatial transcriptomics
- Retinal Development and Disorders
- Circular RNAs in diseases
- Cancer Genomics and Diagnostics
- Remote Sensing and LiDAR Applications
- Genomics and Chromatin Dynamics
- interferon and immune responses
- Gene expression and cancer classification
- Neuroinflammation and Neurodegeneration Mechanisms
- Forest ecology and management
- Genetic Syndromes and Imprinting
- Gut microbiota and health
- Genomics and Phylogenetic Studies
- RNA regulation and disease
- Reproductive Physiology in Livestock
- Endoplasmic Reticulum Stress and Disease
- Neuroendocrine regulation and behavior
- Reproductive System and Pregnancy
- Geology and Paleoclimatology Research
University of California, Irvine
2021-2025
Baylor College of Medicine
2015-2024
Chinese Academy of Sciences
2019-2024
Yuhuangding Hospital
2021-2024
Qingdao University
2021-2024
Union Hospital
2019-2024
Institute of Zoology
2020-2024
Huazhong University of Science and Technology
2019-2024
BGI Genomics
2024
Qilu University of Technology
2024
Abstract When identifying differentially expressed genes between two conditions using human population RNA-seq samples, we found a phenomenon by permutation analysis: popular bioinformatics methods, DESeq2 and edgeR, have unexpectedly high false discovery rates. Expanding the analysis to limma-voom, NOISeq, dearseq, Wilcoxon rank-sum test, that FDR control is often failed except for test. Particularly, actual FDRs of edgeR sometimes exceed 20% when target 5%. Based on these results,...
This study investigated the application of a therapeutic tumor cell–derived microparticle-based nanodelivery platform in malignant pleural effusion.
Rod and cone photoreceptors are light-sensing cells in the human retina. Rods dominant peripheral retina, whereas cones enriched macula, which is responsible for central vision visual acuity. Macular degenerations affect most currently incurable. Here we report generation, transcriptome profiling, functional validation of cone-rich retinal organoids differentiated from hESCs using an improved differentiation system. Induced by extracellular matrix, aggregates formed single-lumen cysts...
RNA-seq was used to generate an extensive map of the Drosophila melanogaster transcriptome by broad sampling 10 developmental stages. In total, 142.2 million uniquely mapped 64-100-bp paired-end reads were generated on Illumina GA II yielding 356× sequencing coverage. More than 95% FlyBase genes and 90% splicing junctions observed. Modifications 30% gene models made extension untranslated regions, inclusion novel exons, identification events. A total 319 transcripts identified, representing...
Inherited retinal degenerations are a common cause of untreatable blindness worldwide, with retinitis pigmentosa and cone dystrophy affecting approximately 1 in 3500 10,000 individuals, respectively. A major limitation to the development effective therapies is lack availability animal models that fully replicate human condition. Particularly for disorders, rodent, canine, feline no true macula have substantive limitations. By contrast, cone-rich nonhuman primate (NHP) closely mirrors retina....
DNA methylation is thought to be an important determinant of human phenotypic variation, but its inherent cell type specificity has impeded progress on this question. At exceptional genomic regions, interindividual variation in occurs systemically. Like genetic variants, systemic epigenetic variants are stable, can influence phenotype, and assessed any easily biopsiable sample. We describe unbiased screen for regions at which not tissue-specific. For each 10 donors from the NIH...
Abstract The ability to detect, respond and adapt mitochondrial stress ensures the development survival of organisms. Caenorhabditis elegans responds by activating unfolded protein response (UPR mt ) buffer folding environment, rewire metabolic state, promote innate immunity lifespan extension. Here we show that HDA-1, C. ortholog mammalian histone deacetylase (HDAC) is required for stress-mediated activation UPR . HDA-1 interacts coordinates with genome organizer DVE-1 induce transcription...
Abstract Background Genetic variants can modulate phenotypic outcomes via epigenetic intermediates, for example at methylation quantitative trait loci (mQTL). We present the first large-scale assessment of mQTL human genomic regions selected interindividual variation in CpG methylation, which we call correlated systemic (CoRSIVs). These be assayed blood DNA and do not reflect cellular composition. Results use target-capture bisulfite sequencing to assess 4086 CoRSIVs multiple tissues from...
The ability to determine the gene expression pattern in low quantities of cells or single is important for resolving a variety problems many biological disciplines. A robust description signature cell requires determination full-length sequence expressed mRNAs cell, yet existing methods have either 3′ biased variable transcript representation. Here, we report our protocols amplification and high-throughput sequencing very small amounts RNA using procedures semirandom primed PCR phi29 DNA...
Haploinsufficiency of EFTUD2 (Elongation Factor Tu GTP Binding Domain Containing 2) is linked to human mandibulofacial dysostosis, Guion-Almeida type (MFDGA), but the underlying cellular and molecular mechanisms remain be addressed. We report here isolation, cloning functional analysis mutated eftud2 (snu114) in a novel neuronal mutant fn10a zebrafish. This displayed abnormal brain development with evident apoptosis while other organs appeared less affected. Positional revealed nonsense...
We report the emerging role of microRNA (miRNA) deregulation associated with activation an oncogene SOX4 (a member SRY-related HMG-box) in esophageal carcinoma. Paired cancer and adjacent non-tumor tissues were obtained from 42 patients who underwent primary surgical resection for cancer. Experiments such as real-time PCR, western blot analysis, luciferase-reporter assay, cell proliferation colony formation assays, vitro migration invasion a wound-healing assay performed to determine effects...
The present study is to investigate the role of microRNA-21 (miR-21) in nasopharyngeal carcinoma (NPC) and mechanisms regulation PTEN by miR-21. Fifty-four tissue samples were collected from 42 patients with NPC 12 healthy controls. Human cell lines CNE-1, CNE-2, TWO3 C666-1 used for assays. To expression miR-21, RT-PCR was employed. RT-PCR, Western blotting, immunohistochemistry measure STAT3 mRNA protein. test effect miR-21 on growth apoptosis cells vitro, transfection CNE1 CNE2 flow...
Rationale: Polycomb repressive complex 2 is a major epigenetic repressor that deposits methylation on histone H3 lysine 27 (H3K27me) and controls differentiation function of many cells, including cardiac myocytes. EZH1 EZH2 are alternative catalytic subunits with partial functional redundancy. The relative roles in heart development regeneration unknown. Objective: We compared the versus neonatal regeneration. Methods Results: Heart was normal Ezh1 −/− ( Ezh 1 knockout) Ezh2 f/f ::cTNT −Cre...
Forest inventory holds an essential role in forest management and research, but the existing field methods are highly time-consuming labor-intensive. Here, we developed a simultaneous localization mapping-based backpack light detection ranging (LiDAR) system with dual orthogonal laser scanners open-source Python package called Forest3D for efficient accurate applications. Two key variables, tree height diameter at breast (DBH), were extracted six study sites different species compositions....
We perform a single-cell RNA sequencing analysis to investigate the phenotypic and functional heterogeneity of adult mouse prostate stromal cells. Our identifies three major cell populations representing smooth muscle cells two types fibroblast enriched by Sca-1 CD90. The Sca-1+CD90+ are in direct contact with epithelial express growth factors genes associated motility, developmental process, androgen biosynthesis. This suggests that they may regulate survival growth. Sca-1+CD90-/low...
Abstract Background Precision agriculture is an emerging research field that relies on monitoring and managing variability in phenotypic traits. An important trait biomass, a comprehensive indicator can reflect crop yields. However, non-destructive biomass estimation at fine levels unknown challenging due to the lack of accurate high-throughput data algorithms. Results In this study, we evaluated capability terrestrial light detection ranging (lidar) estimating maize plot, individual plant,...