A5016835023- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Metabolomics and Mass Spectrometry Studies
- Single-cell and spatial transcriptomics
- HIV Research and Treatment
- Air Quality and Health Impacts
- Gene Regulatory Network Analysis
- Diet and metabolism studies
- Analytical Chemistry and Chromatography
- Cancer-related molecular mechanisms research
- Carcinogens and Genotoxicity Assessment
- Immune Cell Function and Interaction
- Molecular Biology Techniques and Applications
- Air Quality Monitoring and Forecasting
- Immunotherapy and Immune Responses
- Monoclonal and Polyclonal Antibodies Research
- RNA modifications and cancer
- Liver Disease Diagnosis and Treatment
- Advanced Chemical Sensor Technologies
- Genomics, phytochemicals, and oxidative stress
- Microbial Metabolic Engineering and Bioproduction
- Health, Environment, Cognitive Aging
- Computational Drug Discovery Methods
- Cancer, Hypoxia, and Metabolism
- Toxic Organic Pollutants Impact
Chinese University of Hong Kong, Shenzhen
2019-2025
Inner Mongolia Medical University
2021-2025
Shenzhen Research Institute of Big Data
2021-2025
Peking University
2023-2025
Peking University Cancer Hospital
2023-2025
Emory University
2015-2024
China University of Geosciences (Beijing)
2023-2024
State Key Laboratory For Conservation and Utilization of Subtropical Agro-Bioresources
2024
Guangxi University
2024
University of Southern California
2023
With modern technologies such as microarray, deep sequencing, and liquid chromatography-mass spectrometry (LC-MS), it is possible to measure the expression levels of thousands genes/proteins simultaneously unravel important biological processes. A very first step towards elucidating hidden patterns understanding massive data application clustering techniques. Nonlinear relations, which were mostly unutilized in contrast linear correlations, are prevalent high-throughput data. In many cases,...
Abstract Objective To identify a panel of protein and messenger RNA (mRNA) biomarkers in human whole saliva (WS) that may be used the detection primary Sjögren's syndrome (SS). Methods Mass spectrometry expression microarray profiling were to candidate mRNA SS WS samples. Validation discovered was also demonstrated using real‐time quantitative polymerase chain reaction immunoblotting techniques. Results Sixteen proteins found down‐regulated 25 up‐regulated patients compared with matched...
Abstract Motivation: Liquid chromatography-mass spectrometry (LC/MS) profiling is a promising approach for the quantification of metabolites from complex biological samples. Significant challenges exist in analysis LC/MS data, including noise reduction, feature identification/ quantification, alignment and computation efficiency. Result: Here we present set algorithms processing high-resolution data. The major technical improvements include adaptive tolerance level searching rather than hard...
Abstract Background The head and neck/oral squamous cell carcinoma (HNOSCC) is a diverse group of cancers, which develop from many different anatomic sites are associated with risk factors genetic characteristics. oral tongue (OTSCC) one the most common types HNOSCC. It significantly more aggressive than other forms HNOSCC, in terms local invasion spread. In this study, we aim to identify specific transcriptomic signatures that OTSCC. Results Genome-wide profiles were obtained for 53 primary...
Detection of low abundance metabolites is important for de novo mapping metabolic pathways related to diet, microbiome or environmental exposures. Multiple algorithms are available extract m/z features from liquid chromatography-mass spectral data in a conservative manner, which tends preclude detection chemicals and found small subsets samples. The present study provides software enhance such feature detection, quality assessment, annotation.xMSanalyzer set utilities automated processing...
Atmospheric particulate matter with diameter <2.5 um (PM2.5) was collected at Peking University (PKU) in Beijing, China before, during, and after the 2008 Olympics analyzed for black carbon (BC), organic (OC), lower molecular weight (MW < 300) MW302 Polycyclic Aromatic Hydrocarbons (PAHs), nitrated PAHs (NPAHs) oxygenated (OPAHs). In addition, direct indirect acting mutagenicity of PM2.5 potential DNA damage to human lung cells were also measured. Significant reductions BC (45%), OC (31%),...
Ebola virus (EBOV) remains a public health threat. We performed longitudinal study of B cell responses to EBOV in four survivors the 2014 West African outbreak. Infection induced lasting EBOV-specific immunoglobulin G (IgG) antibodies, but their subclass composition changed over time, with IgG1 persisting, IgG3 rapidly declining, and IgG4 appearing late. Striking changes occurred repertoire, massive recruitment naive cells that subsequently underwent hypermutation. characterized large panel...
We have previously shown that human mRNAs are present in saliva and can be used as biomarkers of oral cancer. In this study, we analyzed the integrity, sources, stability salivary RNA.We measured integrity RNA with reverse transcription followed by PCR (RT-PCR) or RT-quantitative (RT-qPCR). To study entry sites into cavity, RT-PCR analysis from 3 major glands, gingival crevice fluid, desquamated epithelial cells. beta-actin mRNA RT-qPCR incubated at room temperature for different periods...
In predictive model development, gene expression data is associated with the unique challenge that number of samples (n) much smaller than amount features (p). This "n ≪ p" property has prevented classification from deep learning techniques, which have been proved powerful under > scenarios in other application fields, such as image classification. Further, sparsity effective unknown correlation structures profiles brings more challenges for tasks. To tackle these problems, we propose a...
Abstract Background Histone deacetylase (HDAC) inhibitors are currently undergoing clinical evaluation as anti-cancer agents. Dietary constituents share certain properties of HDAC inhibitor drugs, including the ability to induce global histone acetylation, turn-on epigenetically-silenced genes, and trigger cell cycle arrest, apoptosis, or differentiation in cancer cells. One such example is sulforaphane (SFN), an isothiocyanate derived from glucosinolate precursor glucoraphanin, which...
Sulforaphane (SFN), an isothiocyanate derived from crucifers, has numerous health benefits. SFN bioavailability dietary sources is a critical determinant of its efficacy in humans. A key factor absorption the release glucosinolate precursor, glucoraphanin, by myrosinase. Dietary supplements are used clinical trials to deliver consistent doses, but myrosinase often inactivated available supplements. We evaluated myrosinase-treated broccoli sprout extract (BSE) and first report effects twice...
Histone deacetylases (HDACs) and acetyltransferases have important roles in the regulation of protein acetylation, chromatin dynamics DNA damage response. Here, we show human colon cancer cells that dietary isothiocyanates (ITCs) inhibit HDAC activity increase turnover with potency proportional to alkyl chain length, i.e., AITC < sulforaphane (SFN) 6-SFN 9-SFN. Molecular docking studies provided insights into interactions ITC metabolites HDAC3, implicating allosteric site between HDAC3 its...
Gene expression data represents a unique challenge in predictive model building, because of the small number samples (n) compared with huge amount features (p). This 'n≪p' property has hampered application deep learning techniques for disease outcome classification. Sparse by incorporating external gene network information could be potential solution to this issue. Still, problem is very challenging (i) there are tens thousands and only hundreds training samples, (ii) scale-free structure...
The heterogeneous reactions of ambient particulate matter (PM)-bound polycyclic aromatic hydrocarbons (PAHs) and nitro-PAHs (NPAHs) with NO3/N2O5, OH radicals, O3 were studied in a laboratory photochemical chamber. Ambient PM2.5 PM10 samples collected from Beijing, China, Riverside, California, exposed under simulated atmospheric long-range transport conditions for NO3 radicals. Changes the masses 23 PAHs 20 NPAHs, as well direct indirect-acting mutagenicity PM (determined using Salmonella...
Significance HIV infection is associated with elevated inflammation and aberrant cellular immune activation. Indeed, the activation status of an HIV-infected individual often more predictive disease trajectory than viral load. Here, we highlight importance replicative fitness transmitted variant in driving early inflammatory state, characterized by T-cell dysfunction. This impact on homeostasis independent protective host response genes Highly replicating variants were also significantly...
Mechanisms underlying the effects of traffic-related air pollution on people with asthma remain largely unknown, despite abundance observational and controlled studies reporting associations between traffic sources exacerbation hospitalizations.To identify molecular pathways perturbed following exposures, we analyzed data as part Atlanta Commuters Exposure (ACE-2) study, a crossover panel commuters without asthma.We measured 27 pollutants conducted high-resolution metabolomics profiling...
We propose a statistical framework, named genoCN, to simultaneously dissect copy number states and genotypes using high-density SNP (single nucleotide polymorphism) arrays. There are at least two types of genomic DNA differences: variations (CNVs) aberrations (CNAs). While CNVs naturally occurring inheritable, CNAs acquired somatic alterations most often observed in tumor tissues only. tend be short more sparsely located the genome compared with CNAs. GenoCN consists components, genoCNV...
Initial studies of 88 transmission pairs in the Zambia Emory HIV Research Project cohort demonstrated that number transmitted HLA-B associated polymorphisms Gag, but not Nef, was negatively correlated to set point viral load (VL) newly infected partners. These results suggested accumulation CTL escape mutations Gag might attenuate replication and provide a clinical benefit during early stages infection. Using novel approach, we have cloned gag sequences isolated from earliest seroconversion...
Feature detection is a critical step in the preprocessing of liquid chromatography-mass spectrometry (LC-MS) metabolomics data. Currently, predominant approach to detect features using noise filters and peak shape models based on data at hand alone. Databases known metabolites historical contain information that could help boost sensitivity feature detection, especially for low-concentration metabolites. However, utilizing such targeted may cause large number false positives because high...