A5060457543- Genetic Associations and Epidemiology
- Machine Learning in Bioinformatics
- Epigenetics and DNA Methylation
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Fractal and DNA sequence analysis
- Gene Regulatory Network Analysis
- RNA modifications and cancer
- Eosinophilic Disorders and Syndromes
- Myeloproliferative Neoplasms: Diagnosis and Treatment
- Lymphoma Diagnosis and Treatment
- Nutrition, Genetics, and Disease
- Genomics and Phylogenetic Studies
- Mathematical Analysis and Transform Methods
- Ferroptosis and cancer prognosis
- Image and Signal Denoising Methods
- Adipose Tissue and Metabolism
- RNA and protein synthesis mechanisms
- Liver Disease Diagnosis and Treatment
- Cancer-related gene regulation
- Breast Cancer Treatment Studies
- Genetic Mapping and Diversity in Plants and Animals
- Immune Cell Function and Interaction
- Blind Source Separation Techniques
- Microbial Metabolic Engineering and Bioproduction
Dalian Maritime University
2014-2025
Harvard University Press
2014-2023
Harvard University
2013-2022
Tianjin Medical University Cancer Institute and Hospital
2022
Beth Israel Deaconess Medical Center
2014
Lung Institute
2014
Imperial College London
2014
In individuals with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the severity of illness ranges from asymptomatic to fatal.1Wu Z, McGoogan JM. Characteristics and important lessons disease 2019 (COVID-19) outbreak in China: summary a report 72314 cases Chinese Center for Disease Control Prevention [published online ahead print February 24, 2020]. JAMA. https://doi.org/10.1001/jama.2020.2648.Google Scholar The Centers currently list asthma as risk factor...
Abstract Differences in methylation across tissues are critical to cell differentiation and key understanding the role of epigenetics complex diseases. In this investigation, we found that locus-specific differences between highly consistent individuals. We developed a novel statistical model predict target tissue based on surrogate tissue. The method was evaluated publicly available data two studies using latest IlluminaBeadChips: childhood asthma study with measured both peripheral blood...
We aimed to examine the associations of obesity-related traits (body mass index [BMI], central obesity) and their genetic predisposition with risk developing severe COVID-19 in a population-based data.We analyzed data from 489,769 adults enrolled UK Biobank-a cohort study. The exposures interest are BMI categories obesity (e.g., larger waist circumference). Using genome-wide genotyping data, we also computed polygenic scores (PRSs) that represent an individual's overall for each trait....
Gene regulatory networks (GRNs) capture the interactions between genes, resulting from fundamental biological process of transcription and translation. In some cases, topology GRNs is not known, has to be inferred gene expression data. Most existing reconstruction algorithms are either applied time-series data or steady-state Although include more information about system dynamics, imply stability underlying networks.In this article, we propose a method for inferring jointly. We make use...
Background Lung function is a heritable complex phenotype with obesity being one of its important risk factors. However, knowledge their shared genetic basis limited. Most genome-wide association studies (GWASs) for lung have been based on European populations, limiting the generalisability across populations. Large-scale GWASs in other populations are lacking. Methods We included 100 285 subjects from China Kadoorie Biobank (CKB). To identify novel loci function, single-trait GWAS analyses...
Abstract Marginal zone lymphoma (MZL) is the third most common subtype of B-cell non-Hodgkin lymphoma. Here we perform a two-stage GWAS 1,281 MZL cases and 7,127 controls European ancestry identify two independent loci near BTNL2 (rs9461741, P =3.95 × 10 −15 ) HLA-B (rs2922994, =2.43 −9 in HLA region significantly associated with risk. This first evidence that genetic variation major histocompatibility complex influences susceptibility.
Objectives: Lung adenocarcinoma (LUAD) accounts for a majority of cancer-related deaths worldwide annually. The identification prognostic biomarkers and prediction prognosis LUAD patients is necessary. Materials Methods: In this study, RNA-Seq data clinical from the Cancer Genome Atlas (TCGA) were divided into TCGA cohort I (n = 338) II 168). was used model construction, Gene Expression Omnibus (GSE72094 cohort, n 393; GSE11969 149) utilized validation. First, survival-related seed genes...
Survival analysis using gene expression profiles plays a crucial role in the interpretation of clinical research and assessment disease therapy programs. Several prediction models have been developed to explore relationship between patients' covariates survival. However, high-dimensional genomic features limit performance survival model. Thus, an accurate reliable model is necessary for data.In this study, we proposed improved based on XGBoost framework called XGBLC, which used Lasso-Cox...
Background Both genetic and lifestyle factors contribute to the risk of type 2 diabetes, but extent which there is a synergistic effect unclear. The aim this study was examine joint associations diet quality with incident diabetes. Methods findings We analyzed data from 35,759 men women in United States participating Nurses’ Health Study (NHS) I (1986 2016) II (1991 2017) Professionals Follow-up (HPFS; 1986 available who did not have cardiovascular disease, or cancer at baseline. Genetic...
Genome-wide association studies have identified multiple genetic variants associated with risk of esophageal squamous-cell carcinoma (ESCC) in Chinese populations. We examined whether these factors, along non-genetic can contribute to ESCC prediction. 25 single nucleotide polymorphisms (SNPs) and 4 factors (sex, age, smoking drinking) 9805 cases 10 493 controls from Weighted score (wGRS) was calculated logistic regression used analyze the between wGRS risk. area under curve (AUC) using...
ABSTRACT Uncovering additional causal clinical traits and exposure variables is important when studying osteoporosis mechanisms for the prevention of osteoporosis. Until recently, relationship between anthropometric measurements had not been fully revealed. In present study, we utilized several state-of-the-art Mendelian randomization (MR) methods to investigate whether height, body mass index (BMI), waist-to-hip ratio (WHR), hip circumference (HC), waist (WC) are causally associated with...
Abstract The potential role of DNA methylation from paracancerous tissues in cancer diagnosis has not been explored until now. In this study, we built classification models using well-known machine learning based on profiles tissues. We evaluated our methods nine datasets collected Cancer Genome Atlas (TCGA) and utilized fivefold cross-validation to assess the performance models. Additionally, performed gene ontology (GO) enrichment analysis basis significant CpG sites selected by feature...
DNA methylation is known to be responsive prenatal exposures, which may a part of the mechanism linking early developmental exposures future chronic diseases. Many studies use blood measure methylation, yet we know that tissue specific. Placenta central fetal growth and development, but it rarely feasible collect this in large epidemiological studies; on other hand, cord samples are more accessible. In study, based paired both placenta tissues from 169 individuals, investigated concordance...
Gene regulatory network can help to analyze and understand the underlying mechanism interaction among genes, it plays a central role in morphogenesis of complex diseases such as cancer. DNA sequencing technology has efficiently produced large amount data for constructing gene networks. However, measured expression usually contain uncertain noise, inference model under non-Gaussian noise is challenging issue which needs be addressed. In this study, joint algorithm integrating genetic...
Most kidney cancers are renal clear cell carcinoma (KIRC) that is a main cause of cancer-related deaths. Polygenic risk score (PRS) weighted linear combination phenotypic related alleles on the genome can be used to assess KIRC risk. However, standalone SNP data as input PRS model may not provide satisfactory result. Therefore, Transcriptional scores (TRS) based multi-omics and machine learning models were proposed KIRC. First, we collected four types (DNA methylation, miRNA, mRNA lncRNA)...
ABSTRACT The case‐only test has been proposed as a more powerful approach to detect gene–environment (G × E) interactions. This assumes that the genetic and environmental factors are independent. Although it is well known Type I error rate will increase if this assumption violated, less widely appreciated G E correlation can also lead power loss. We illustrate phenomenon by comparing performance of other approaches interactions in genome‐wide association study (GWAS) esophageal squamous‐cell...
Our database tool, called Real-Time Engine for Expression Quantitative Trait Loci Analyses (RTeQTL), can efficiently provide eQTL association results that are not available in existing databases browsers. These functions include (i) single SNP (single-nucleotide polymorphism) and (ii) two-SNP conditional effects on gene expression regardless of the magnitude P -values. The is based lymphoblastoid cell lines from >900 samples with global genome-wide genotyped imputed data. detailed result any...
<abstract> <sec><title>Background</title><p>Polygenic risk score (PRS) can evaluate the individual-level genetic of breast cancer. However, standalone single nucleotide polymorphisms (SNP) data used for PRS may not provide satisfactory prediction accuracy. Additionally, current models based on linear regression have insufficient power to leverage non-linear effects from thousands associated SNPs. Here, we proposed a transcriptional (TRS) multiple omics estimate...
With the enormous amount of biological data that is available in public domain, signal processing plays an important role genomic and proteomic processing. Digital filters have been applied to predict genes proteins, but need be redesigned when periodic behavior or characteristic frequency changed. In this paper, we propose a novel approach based on adaptive filtering theory which can identify proteins unified framework. At first, review popular Voss representation maps alphabetic DNA...