A5100431827- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Esophageal Cancer Research and Treatment
- Computational Drug Discovery Methods
- Gastric Cancer Management and Outcomes
- Machine Learning in Bioinformatics
- Esophageal and GI Pathology
- Photosynthetic Processes and Mechanisms
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Plant biochemistry and biosynthesis
- Ferroptosis and cancer prognosis
- Microbial Natural Products and Biosynthesis
- Lung Cancer Diagnosis and Treatment
- Radiomics and Machine Learning in Medical Imaging
- Microbial Metabolic Engineering and Bioproduction
- Metastasis and carcinoma case studies
- Plant Gene Expression Analysis
- Cancer Immunotherapy and Biomarkers
- Advanced Proteomics Techniques and Applications
- Cancer-related molecular mechanisms research
- Pancreatic and Hepatic Oncology Research
- Metabolomics and Mass Spectrometry Studies
- Gene Regulatory Network Analysis
- Phytochemistry and Bioactive Compounds
Hubei Academy of Forestry
2024-2025
Heilongjiang Institute of Technology
2015-2024
Alibaba Group (China)
2024
Jiangxi University of Traditional Chinese Medicine
2023
Anhui Medical University
2012-2023
First Affiliated Hospital of Anhui Medical University
2012-2023
Wuhan University
2022
Renmin Hospital of Wuhan University
2022
Shantou University
2017-2021
Shantou University Medical College
2017-2021
Abstract Esophageal cancer (EC) is a type of aggressive without clinically relevant molecular subtypes, hindering the development effective strategies for treatment. To define subtypes EC, we perform mass spectrometry-based proteomic and phosphoproteomics profiling EC tumors adjacent non-tumor tissues, revealing catalog proteins phosphosites that are dysregulated in ECs. The cohort stratified into two subtypes—S1 S2—based on analysis, with S2 subtype characterized by upregulation...
Abstract Drought is one of the main environmental factors affecting plant survival and growth. Atraphaxis bracteata a common desert mainly utilized in afforestation desertification control. This study analyzed morphological, physiological molecular regulatory characteristics different organs A. under drought stress. The results showed that with intensification stress, height, root length leaf area seedlings decreased, while content osmotic substances antioxidant enzyme activity increased....
Protein-protein interaction (PPI) networks serve as a powerful tool for unraveling protein functions, disease-gene and disease-disease associations. However, direct strategy integrating interaction, function diseases is still absent. Moreover, the interrelated relationships among these three levels are poorly understood. Here we present novel systematic method to integrate function, disease networks. We first identified topological modules in human data using network algorithm (NeTA)...
Accurately predicting the risk of cancer patients is a central challenge for clinical research. For high-dimensional gene expression data, Cox proportional hazard model with least absolute shrinkage and selection operator variable (Lasso-Cox) one most popular feature prediction algorithms. However, Lasso-Cox treats all genes equally, ignoring biological characteristics themselves. This often encounters problem poor prognostic performance on independent datasets.Here, we propose Reweighted...
For high-dimensional expression data, most prognostic models perform feature selection based on individual genes, which usually lead to unstable prognosis, and the identified risk genes are inherently insufficient in revealing complex molecular mechanisms. Since carry out cellular functions by forming protein complexes-basic representatives of functional modules, identifying complexes may greatly improve our understanding disease biology. Coupled with fact that have been shown innate...
Immune checkpoint inhibitor (ICI) therapy has become a powerful clinical strategy for treating melanoma. The relationship between somatic mutations and the benefits of immunotherapy been widely recognized. However, gene-based predictive biomarkers are less stable due to heterogeneity cancer at individual gene level. Recent studies have suggested that accumulation in biological pathways may activate antitumor immune responses. Herein, novel pathway mutation signature (PMS) was constructed...
Abstract High temperature and drought are common environmental stresses that desert plants must withstand to grow reproduce. In order understand the resistance mechanisms of plant Atraphaxis bracteata (A. Los) responding natural high conditions, we combined physiological characteristics, transcriptome, metabolome analysis explore its responses in three different ages CK. The results showed most indicators A. increased with age, except for SOD activity. There were 4 698, 7 594, 8 485...
Signal flow direction is one of the most important features protein-protein interactions in signaling networks. However, almost all outcomes current high-throughout techniques for mapping are usually supposed to be non-directional. Based on pairwise interaction domains, here we defined a novel parameter protein directional score and then used it predict signal between proteins proteome-wide Using 5-fold cross-validation, our approach obtained satisfied performance with accuracy 89.79%,...
Identifying dysregulated pathways from high-throughput experimental data in order to infer underlying biological insights is an important task. Current pathway-identification methods focus on single isolation; however, consideration of crosstalk between could improve our understanding alterations states. We propose a novel method pathway analysis based global influence (PAGI) identify pathways, by considering both within-pathway effects and pathways. constructed gene–gene network the...
Accurately predicting patient risk and identifying survival biomarkers are two important tasks in analysis. For the emerging high-throughput gene expression data, random forest (RSF) is attracting more attention as it not only shows excellent performance on prediction problems with high-dimensional variables, but also capable of variables according to variable importance automatically calculated within algorithm. However, RSF still suffers from some such limited predictive accuracy...
4064 Background: Camrelizumab combined with chemotherapy has a very ideal therapeutic effect and low toxicity in the treatment of solid tumors. camrelizumab plays an important role locally advanced esophageal squamous cell carcinoma. Methods: This study is prospective, multicenter, randomized controlled study. Inclusion criteria were patients aged 18-75 years ECOG score 0-1 who had not received other treatments previously histologically confirmed resectable carcinoma (clinical stages...
For knee osteoarthritis patients, analyzing alignment of lower limbs is essential for therapy, which currently measured from standing long-leg radiographs anteroposterior X-ray (LLR) manually. To address the time wasting, poor reproducibility and inconvenience use caused by existing methods, we present an automated measurement model in portable devices assessing LLRs.
Toward precise survival outcome prediction by inferring associated pathway activities.
To evaluate the efficacy of salvage radiochemotherapy (SRC) in patients with recurrent lymph node after radical surgery esophageal cancer.This study enrolled 58 squamous cell carcinoma who underwent SRC for recurrence from August 2011 to November 2015 at our hospital. Survival rates were calculated by Kaplan-Meier method log-rank test. Multivariate analysis was conducted using Cox model.The overall 1-, 3-, and 5-year survival 94.8%, 53.0%, 29.6%, respectively. The 1- 3-year 68.7% 26.9%,...
Integration of pathway and protein-protein interaction (PPI) data can provide more information that could lead to new biological insights. PPIs are usually represented by a simple binary model, whereas pathways complicated models. We developed series rules for transforming protein interactions from the seven databases, including PID, BioCarta, Reactome, NetPath, INOH, SPIKE KEGG, were transformed based on these rules. These pathway-derived integrated with other five PPI databases HPRD,...
To identify the association between width of gastric conduit and benign anastomotic stricture (BAS) after esophagectomy with end-to-side cervical anastomosis for esophageal cancer.Patients cancer who underwent July 2013 2014 were included in this study. The was used reconstruction all patients performed using a circular stapler. divided into narrow group (3-5 cm) wide (>5 based on width. Univariate multivariate logistic regressions to analyze possible factors (patients' age, gender,...
While gene fusions have been increasingly detected by next-generation sequencing (NGS) technologies based methods in human cancers, these limitations identifying driver fusions. In addition, the existing to identify ignored specificity among different cancers or only considered their local rather than global topology features networks. Here, we proposed a novel network-based method, called RWCFusion, phenotype-specific cancer To evaluate its performance, used leave-one-out cross-validation...
To analyze the prognostic factors and survival rate of lung cancer patients with obstructive sleep apnea (OSA) by nomogram. The nomogram was established a development cohort (n = 90), validation included 38 patients. Factors in were identified Cox hazard analysis. We tested accuracy nomograms discrimination calibration, plotted decision curves to assess benefits nomogram-assisted decisions. There significant difference sex, hypopnea index (AHI), Tumor Node Metastasis (TNM), coronary heart...
Accurate predictions of classification biomarkers and disease status are indispensable for clinical cancer diagnosis research. However, the robustness conventional gene is limited by issues with reproducibility across different measurement platforms cohorts patients. In this study, we collected 4775 samples from 12 datasets, which contained 4636 TCGA 139 GEO samples. A new method was developed to detect miRNA-mediated subpathway activities using directed random walk (miDRW). To calculate...
Background: Blood-based biomarkers specific for breast cancer is urgently demanded to facilitate the screening and reduce cancer-related deaths. This study evaluated potential of methylated septin 9 gene (mSEPT9) as a biomarker cancer. Methods: A total 86 biopsy samples were collected from 59 patients with 27 benign tumor. Two hundred seven plasma 80 cancer, tumor patients, 100 healthy volunteers. mSEPT9 was detected using Epi proColon 2.0 CE test. Additionally, 40 tissue cases analysed by...
Accurately predicting the risk of cancer relapse or death is important for clinical utility.