A5081090509- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Genomics and Chromatin Dynamics
- Cancer Genomics and Diagnostics
- Epigenetics and DNA Methylation
- Alzheimer's disease research and treatments
- Renal Diseases and Glomerulopathies
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Genomics and Phylogenetic Studies
- Pluripotent Stem Cells Research
- Endoplasmic Reticulum Stress and Disease
- Genomics and Rare Diseases
- Pancreatic function and diabetes
- Single-cell and spatial transcriptomics
- Circadian rhythm and melatonin
- Histone Deacetylase Inhibitors Research
- Liver Disease Diagnosis and Treatment
- RNA modifications and cancer
- Renal and related cancers
- Acute Myeloid Leukemia Research
- Mitochondrial Function and Pathology
- GDF15 and Related Biomarkers
- Advanced Fluorescence Microscopy Techniques
- Genetics, Aging, and Longevity in Model Organisms
Shanghai University of Traditional Chinese Medicine
2018-2023
Toronto Public Health
2021
GlaxoSmithKline (China)
2016-2019
Calgary Laboratory Services
2017
Shanghai Institutes for Biological Sciences
2007-2014
Chinese Academy of Sciences
2014
Max Planck Society
2014
Shanghai Medical College of Fudan University
1994
Abstract Aims Adverse cardiovascular events have day/night patterns with peaks in the morning, potentially related to endogenous circadian clock control of platelet activation. Circadian nuclear receptor Rev-erbα is an essential and negative component clock. To date, expression profile biological function platelets never been reported. Methods results Here, we report presence functions human mouse platelets. Both showed a rhythm that positively correlated aggregation. Global knockout...
Abstract Single-cell RNA sequencing provides exciting opportunities to unbiasedly study hematopoiesis. However, our understanding of leukemogenesis was limited due the high individual differences. Integrated analyses hematopoiesis and potentially new insights. Here we analyzed ~200,000 single-cell transcriptomes bone marrow mononuclear cells (BMMCs) its subsets from 23 clinical samples. We constructed a comprehensive cell atlas as hematopoietic reference. developed counterpart composite...
Germline mutations of CIDEB, a lipid droplets (LDs)-associated protein, confer protection against various liver diseases in humans. It remains to be determined whether liver-specific inhibition CIDEB will bring clinical benefits. We aim establish pharmacological proof concept by testing GalNAc-conjugated Cideb surrogate siRNAs respective animal models obesity and MASH develop siRNA drug candidates for investigations. Surrogate targeting mouse were designed evaluated via panel assays....
Neural stem cells and progenitor (NPCs) are increasingly appreciated to hold great promise for regenerative medicine treat CNS injuries neurodegenerative diseases. However, evidence effective stimulation of neuronal production from endogenous or transplanted NPCs neuron replacement with small molecules remains limited. To identify novel chemical entities/targets neurogenesis, we had established a NPC phenotypic screen assay validated it using known small-molecule neurogenesis inducers....
Background: Transcriptional dysregulation is one of the most important features cancer genesis and progression. Applying gene expression information to predict development cancers useful for diagnosis. However, previous studies mainly focused on relationship between a single cancer. Prognostic prediction using combined models remains limited. Materials methods: Gene profiles were downloaded from The Cancer Genome Atlas data sets randomly divided into training test sets. A six-gene signature...
Abstract Recently, increasing studies are indicating a close association between dysregulated enhancers and neurodegenerative diseases, such as Alzheimer’s disease (AD). However, their contributions were poorly defined for lacking direct links to genes. To bridge this gap, we presented the Hi-C datasets of 4 AD patients, dementia-free aged 3 young subjects, including 30 billion reads. As applications, utilized them link risk SNPs epigenetic marks target Combining with data, observed more...
Aging, as a complex biological process, is accompanied by the accumulation of functional loses at different levels, which makes age to be biggest risk factor many neurological diseases. Even following decades investigation, process aging still far from being fully understood, especially systematic level. In this study, we identified related genes in brain collecting ones with sustained and consistent gene expression or DNA methylation changes process. Functional analysis Gene Ontology these...
Background: The pathogenesis of Alzheimer's disease is associated with dysregulation at different levels from transcriptome to cellular functioning. Such complexity necessitates investigations etiology be carried out considering multiple aspects the and use independent strategies. established works more emphasized on structural organization gene regulatory network while neglecting internal regulation changes. Methods: Applying a strategy popularly used co-expression analysis, this study...
Drug-induced nephrotoxicity is a leading cause of acute kidney injury (AKI). A major obstacle in predicting AKI the lack comprehensive experimental model that mimics stable and physiologically relevant functions accurately reflects changes drug induces. Organoids derived from human-induced pluripotent stem cells (iPSCs) are promising models because their reproducibility similarity to vivo conditions. In this study, Esculentoside A, triterpene saponin with highest concentration isolated root...
Photosynthesis is one of the most important biological processes on earth. So far, though molecular mechanisms underlying photosynthesis well understood, however, regulatory networks are poorly studied. Given current interest in improving photosynthetic efficiency for greater crop yield, elucidating detailed controlling construction and maintenance machinery not only scientifically significant but also holding great potential agricultural application. In this study, we first identified...
Plasmacytoid dendritic cells (pDC) are an essential immune microenvironment component. They have been reported for crucial roles in linking the adaptive and systems. However, prognostic role of pDC breast cancer (BRCA) was controversial. In this work, we collected large sample cohorts did a comprehensive investigation to reveal relationship between BRCA by multiomics data analysis. Elevated levels were correlated with prolonged survival outcomes patients. The distinct mutation landscape...
Abstract PacBio sequencing is a powerful approach to study DNA or RNA sequences in longer scope. It especially useful exploring the complex structural variants generated by random integration multiple rearrangement of endogenous exogenous sequences. Here, we present tool, TSD, for variant discovery using targeted data. allows researchers identify and visualize genomic structures unlimited splitting, alignment assembly long reads. Application data derived from an HBV integrated human cell...
Observed co-expression of a group genes is frequently attributed to co-regulation by shared transcription factors. This assumption has led the hypothesis that promoters co-expressed should share common regulatory motifs, which forms basis for numerous computational tools search these motifs. While explored yeast, validity underlying not been assessed systematically in mammals. demonstrates need systematic and quantitative evaluation what degree over-represented motifs We identified 33...
Abstract Motivation: It is commonplace to predict targets of transcription factors (TFs) by sequence matching with their binding motifs. However, this ignores the particular condition cells. Gene expression data can provide condition-specific information, as is, e.g. exploited in Motif Enrichment Analysis. Results: Here, we introduce a novel tool named target prediction (CSTP) for TFs from measured either microarray or RNA-seq. Based on philosophy guilt association, CSTP infers regulators...
Background: Guizhi has the pharmacological activity of anti-inflammatory. However, effect mechanism against nephrotic syndrome (NS) remains unclear. A network approach with experimental verification in vitro and vivo was performed to investigate potential mechanisms treat NS. Methods: Active compounds targets Guizhi, as well related NS were obtained from public databases. The intersecting through Venny 2.1.0. key signaling pathways determined by protein-protein interaction (PPI), genes...
Nephrotic syndrome (NS) is a common glomerular disease caused by variety of causes and the second most kidney disease. Guizhi key drug Wulingsan in treatment NS. However, action mechanism remains unclear. In this study, network pharmacology molecular docking were used to explore underlying treating NS.The active components targets screened Traditional Chinese Medicine Systems Pharmacology Database Analysis Platform (TCMSP), Hitpick, SEA, Swiss Target Prediction database. The related NS...
Drug target discovery is an essential step to reveal the mechanism of action (MoA) underlying drug therapeutic effects and/or side effects. Most approaches are usually labor-intensive while unable identify tissue-specific interacting targets, especially targets with weaker binding affinity. In this work, we proposed integrated pipeline, FL-DTD, predict novel compounds in a manner. This method was built based on hypothesis that cells under status homeostasis would take responses perturbation...
Abstract Genetically modified organisms are widely used in lifescience research, agriculture and commercial products. However, most cases, the genetic modification host genome is often less well characterized with respect to integration location, copy number gene expression. The application of next generation sequencing technologies has enabled characterization transgene events but still limited by lack computational tools. We present a one-stop R tool, transgeneR, as general tool for...
Cells derived by cellular engineering, i.e. differentiation of induced pluripotent stem cells and direct lineage reprogramming, carry a tremendous potential for medical applications in particular regenerative therapies. These approaches consist the definition lineage-specific experimental protocols that, manipulation limited number biological cues-niche mimicking factors, (in)activation transcription to name few-enforce final expression cell-specific (marker) molecules. To date, given...
The causal mechanism of Alzheimer's disease is extremely complex. Achieving great statistical power in association studies usually requires a large number samples. In this work, we illustrated different strategy to identify AD risk genes by clustering patients into modules based on their single-patient differential expression signatures. evaluation suggested that our method could enrich with similar clinical manifestations. Applying cohort only 310 patients, identified 174 loci at strict...