A5026321844- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Gene Regulatory Network Analysis
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Epigenetics and DNA Methylation
- Metabolomics and Mass Spectrometry Studies
- Advanced biosensing and bioanalysis techniques
- SARS-CoV-2 and COVID-19 Research
- Genetic diversity and population structure
- Ferroptosis and cancer prognosis
- Bladder and Urothelial Cancer Treatments
- COVID-19 Clinical Research Studies
- Peptidase Inhibition and Analysis
- Nanopore and Nanochannel Transport Studies
- MicroRNA in disease regulation
- Heavy metals in environment
- Adsorption and Cooling Systems
- RNA Research and Splicing
- Microbial Metabolic Engineering and Bioproduction
Sun Yat-sen University
2024-2025
BGI Research
2024-2025
BGI Group (China)
2021-2025
Third Affiliated Hospital of Sun Yat-sen University
2024-2025
Hunan University
2025
Yale University
2023-2024
Guangzhou Medical University
2013-2024
Second Affiliated Hospital of Nanchang University
2020-2024
Xinjiang Institute of Ecology and Geography
2022-2024
University of Chinese Academy of Sciences
2017-2024
Single-cell RNA sequencing (scRNA-seq) is able to give an insight into the gene-gene associations or transcriptional networks among cell populations based on of a large number cells. However, traditional network methods are limited grouped cells instead each single cell, and thus heterogeneity will be erased. We present new method construct cell-specific (CSN) for from scRNA-seq data (i.e. one cell), which transforms 'unstable' gene expression form 'stable' association single-cell basis. In...
Identifying early warning signals of critical transitions during disease progression is a key to achieving diagnosis complex diseases. By exploiting rich information high-throughput data, novel model-free method has been developed detect Its theoretical foundation based on dynamical network biomarker (DNB), which also called as the driver (or leading) because components or molecules in DNB actually drive whole system from one state (e.g. normal state) another state). In this article, we...
Abstract Motivation It is a challenging task to discover personalized driver genes that provide crucial information on disease risk and drug sensitivity for individual patients. However, few methods have been proposed identify the personalized-sample from cancer omics data due lack of samples each individual. To circumvent this problem, here we present novel single-sample controller strategy (SCS) mutation profiles network controllability perspective. Results SCS integrates expression into...
A central theme in learning from image data is to develop appropriate representations for the specific task at hand. Traditional methods used handcrafted local features combined with high-level generate image-level representations. Thus, a practical challenge determine what are tasks. For example, study of gene expression patterns Drosophila melanogaster, texture based on wavelets were particularly effective determining developmental stages situ hybridization (ISH) images. Such...
Abstract The 2019 coronavirus disease (COVID-19) outbreak caused by the SARS-CoV-2 virus is an ongoing global health emergency. However, virus’ pathogenesis remains unclear, and there no cure for disease. We investigated dynamic changes of blood immune response in patients with COVID-19 at different stages using 5’ gene expression, T cell receptor (TCR), B receptors (BCR) V(D)J transcriptome analysis a single-cell resolution. obtained mRNA sequencing (scRNA-seq) data 341,420 peripheral...
The fluorescence method has made great progress in the construction of sensitive sensors but background matrix and photobleaching limit its broad application clinical diagnosis. Here, we propose a digital single virus immunoassay for multiplex detection by using fluorescent magnetic multifunctional nanospheres as both capture carriers signal labels. superparamagnetism strong response ability can realize efficient separation targets without sample pretreatment. Due to their distinguishable...
The world-wide Coronavirus Disease 2019 (COVID-19) pandemic was triggered by the widespread of a new strain coronavirus named as severe acute respiratory syndrome 2 (SARS-CoV-2). Multiple studies on pathogenesis SARS-CoV-2 have been conducted immediately after spread disease. However, molecular virus and related diseases has still not fully revealed. In this study, we attempted to identify transcriptomic signatures candidate diagnostic models for clinical testing or therapeutic targets...
Ferroptosis plays a critical role in LPS-induced acute lung injury and is modulated by endoplasmic reticulum stress (ERS). As typical ER stress-responsive protein, recently mesencephalic astrocyte-derived neurotrophic factor (MANF) has been demonstrated to attenuate (ALI) through repressing macrophage activation. However, whether MANF exerts preventive on ferroptosis excess remains unclear. Here, we first built protein-protein interaction (PPI) network obtain potential interacting proteins...
Innate immunity and metabolites link to the pathogenesis severity of acute pancreatitis (AP). However, liver metabolism its role in immune response AP progression remain elusive. We investigated function AP.Circulating ketone body β-hydroxybutyrate (βOHB) levels were determined clinical cohorts caerulein-induced (CER-AP) mouse models receiving seven (Cer*7) or twelve (Cer*12) injection regimens at hourly intervals. Liver transcriptomics metabolomics compared between CER-AP (Cer*12)....
CycloneSEQ is a novel long-read sequencing platform developed by BGI-Research This protocol follows library construction tailored for the assembly of circular complete genomes from mixed microbial communities. DNA extracted bacterial strains and after resulting libraries can be sequenced on platform. following steps.
Single molecule electrochemistry (SME) has gained much progress in fundamental studies, but it is difficult to use practice due its less reliability. We have solved the reliability of single electrochemical detection by integration digital analysis with efficient signal amplification enzyme-induced metallization (EIM) together high-throughput parallelism microelectrode array (MA), establishing a method (dSMED). Our dSMED been successfully used for alkaline phosphatase (ALP) complex sample...
Integrating different omics profiles is a challenging task, which provides comprehensive way to understand complex diseases in multi-view manner. One key for such an integration extract intrinsic patterns concordance with data structures, so as discover consistent information across various types even noise pollution. Thus, we proposed novel framework called 'pattern fusion analysis' (PFA), performs automated alignment and bias correction, fuse local sample-patterns (e.g. from each type)...
Predicting pre-disease state or tipping point just before irreversible deterioration of health is a difficult task. Edge-network analysis (ENA) with dynamic network biomarker (DNB) theory opens new way to study this problem by exploring rich dynamical and high-dimensional information omics data. Although theoretically ENA has the ability identify during disease progression, it requires multiple samples for such prediction on each individual, which are generally not available in clinical...
Network or edge biomarkers are a reliable form to characterize phenotypes diseases. However, obtaining edges correlations between molecules for an individual requires measurement of multiple samples that individual, which generally unavailable in clinical practice. Thus, it is strongly demanded diagnose disease by network one-sample-for-one-individual context. Here, we developed new computational framework, EdgeBiomarker, integrate and node phenotype each single test sample. By applying the...
Although existing computational models have identified many common driver genes, it remains challenging to identify the personalized genes by using samples of an individual patient. Recently, methods exploiting structure-based control principles complex networks provide new clues for identifying minimum number nodes drive state transition large-scale from initial desired state. However, network cannot be directly applied due unknown dynamics system. Here we proposed model (PNC) employing...
The 2014-16 Ebola virus (EBOV) outbreak in West Africa has attracted widespread concern. Rapid and sensitive detection methods are urgently needed for diagnosis treatment of the disease. Here, we propose a novel method EBOV based on efficient amplification electroluminescent nanospheres (ENs) coupled with immunomagnetic separation. Uniform ENs made by embedding abundant amounts CdSe/ZnS quantum dots (QDs) into copolymer through simple ultrasound. Compared to QDs, can enhance...
Viviparous (live-bearing) vertebrates have evolved repeatedly within otherwise oviparous (egg-laying) clades. Over two-thirds of these changes in vertebrate reproductive parity mode happened squamate reptiles, where the transition has between 98 and 129 times. The from oviparity to viviparity requires numerous physiological, morphological, immunological female tract, including eggshell reduction, delayed oviposition, placental development for supply water nutrition embryo by mother, enhanced...