Yuhua Yao

Dr. Yuhua Yao


Research Focus & Metrics

Academic Career Length

4Years (2023-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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18 January 2022 in Briefings in Bioinformatics
Verified
Journal Article
Closed access
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YMYajie Meng
Yajie Meng
CLChangcheng Lu
Changcheng Lu
MJMin Jin
Min Jin
JXJunlin Xu
Junlin Xu
XZXIANGXIANG ZENG
XIANGXIANG ZENG
JYJialiang Yang
Jialiang Yang
Drug repositioning is an efficient and promising strategy for traditional drug discovery and development. Many research efforts are focused on utilizing deep-learning approaches based on a heterogeneous network for modeling complex drug–disease associations. Similar to traditional latent factor models, which directly factorize drug–disease associations, they assume the neighbors are independent of each other in the network and thus tend to be ineffective to capture localized information. In this study, we propose a novel neighborhood and neighborhood interaction-based neural collaborative filtering approach (called DRWBNCF) to infer novel potential drugs for diseases. Specifically, we first construct three networks, including the known drug–disease association network, the drug–drug similarity and disease–disease similarity networks (using the nearest neighbors). To take the advantage of localized information in the three networks, we then design an integration component by proposing a new weighted bilinear graph convolution operation to integrate the information of the known drug–disease association, the drug’s and disease’s neighborhood and neighborhood interactions into a unified representation. Lastly, we introduce a prediction component, which utilizes the multi-layer perceptron optimized by the α-balanced focal loss function and graph regularization to model the complex drug–disease associations. Benchmarking comparisons on three datasets verified the effectiveness of DRWBNCF for drug repositioning. Importantly, the unknown drug–disease associations predicted by DRWBNCF were validated against clinical trials and three authoritative databases and we listed several new DRWBNCF-predicted potential drugs for breast cancer (e.g. valrubicin and teniposide) and small cell lung cancer (e.g. valrubicin and cytarabine).

29 January 2021 in Frontiers in Immunology
Verified
Journal Article
Open access
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XTXianfang Tang
Xianfang Tang
LCLijun Cai
Lijun Cai
YMYajie Meng
Yajie Meng
JXJunlin Xu
Junlin Xu
CLChangcheng Lu
Changcheng Lu
JYJialiang Yang
Jialiang Yang
A novel coronavirus, named COVID-19, has become one of the most prevalent and severe infectious diseases in human history. Currently, there are only very few vaccines and therapeutic drugs against COVID-19, and their efficacies are yet to be tested. Drug repurposing aims to explore new applications of approved drugs, which can significantly reduce time and cost compared with de novo drug discovery. In this study, we built a virus-drug dataset, which included 34 viruses, 210 drugs, and 437 confirmed related virus-drug pairs from existing literature. Besides, we developed an Indicator Regularized non-negative Matrix Factorization (IRNMF) method, which introduced the indicator matrix and Karush-Kuhn-Tucker condition into the non-negative matrix factorization algorithm. According to the 5-fold cross-validation on the virus-drug dataset, the performance of IRNMF was better than other methods, and its Area Under receiver operating characteristic Curve (AUC) value was 0.8127. Additionally, we analyzed the case on COVID-19 infection, and our results suggested that the IRNMF algorithm could prioritize unknown virus-drug associations.

1 October 2018 in Medicine
Verified
Journal Article
Open access
JLJunjie Lang
Junjie Lang
YYYingshui Yao
Yingshui Yao
Recent studies have revealed a high rate of nonsuicidal self-injury (NSSI) behavior in Chinese students, but quantitative syntheses of pooled prevalence are sparse. There have been several NSSI prevalence meta-analyses in other populations. However, given the existence of cultural diversity, racial difference, educational system difference and so on, these results may not be ideal for Chinese populations. Furthermore, the above-mentioned meta-analyses did not include Chinese database which may have led to unintentional bias. Thus, we conducted this meta-analysis to estimate the prevalence of NSSI in Chinese middle-school students. The databases searched included PubMed, Embase, Web of Science, CBM (Chinese database), Chinese National Knowledge Infrastructure (CNKI), Wanfang Data (Chinese database) and the Weipu database (Chinese database). The search terms included: self-injury/self-harm/self-abuse/nonsuicidal self-injury/deliberate self-harm, adolescen∗/youth/teen/students, and China/Chinese. All relevant articles published between January 2000 to November 2017, in either Chinese or English, were included. Two investigators were engaged in this process, and any disagreements were settled by a third investigator. A random effects model was then used to calculate the pooled prevalence. A total of 420 studies with 160,348 participants were retrieved. The pooled prevalence was 22.37% (95% CI: 18.84%–25.70%). Substantial heterogeneity in prevalence estimates was revealed. Subgroup analyses showed that the pooled estimate of prevalence of life time NSSI was 14.5% (95%CI: 0.06%–22.7%), and 6–24 months NSSI was23.3% (95%CI: 20.5%–26.1%). The prevalence for males was 20.6% (95% CI: 16.1%–25.0%), and for females was 21.9% (95% CI: 17.6%–26.2%). The prevalence of NSSI in Chinese middle-school students is relatively high. More attention should be paid to the current situation.

1 September 2020 in Molecular Therapy Nucleic Acids
Verified
Journal Article
Open access
CLChuanying Liu
Chuanying Liu
DWDong Wei
Dong Wei
JXJu Xiang
Ju Xiang
FRFuquan Ren
Fuquan Ren
LHLi Huang
Li Huang
JYJialiang Yang
Jialiang Yang
In this study, we proposed an ensemble learning method, simultaneously integrating a low-rank matrix completion model and a ridge regression model to predict anticancer drug response on cancer cell lines. The model was applied to two benchmark datasets, including the Cancer Cell Line Encyclopedia (CCLE) and the Genomics of Drug Sensitivity in Cancer (GDSC). As previous studies suggest, the dual-layer integrated cell line-drug network model was one of the best models by far and outperformed most state-of-the-art models. Thus, we performed a head-to-head comparison between the dual-layer integrated cell line-drug network model and our model by a 10-fold crossvalidation study. For the CCLE dataset, our model has a higher Pearson correlation coefficient between predicted and observed drug responses than that of the dual-layer integrated cell line-drug network model in 18 out of 23 drugs. For the GDSC dataset, our model is better in 26 out of 28 drugs in the phosphatidylinositol 3-kinase (PI3K) pathway and 26 out of 30 drugs in the extracellular signal-regulated kinase (ERK) signaling pathway, respectively. Based on the prediction results, we carried out two types of case studies, which further verified the effectiveness of the proposed model on the drug-response prediction. In addition, our model is more biologically interpretable than the compared method, since it explicitly outputs the genes involved in the prediction, which are enriched in functions, like transcription, Src homology 2/3 (SH2/3) domain, cell cycle, ATP binding, and zinc finger.

25 May 2018 in Child and Adolescent Psychiatry and Mental Health
Verified
Journal Article
Open access
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YSYao-Jun Shao
Yao-Jun Shao
TZTong Zheng
Tong Zheng
YWYan-Qiu Wang
Yan-Qiu Wang
LLLing Liu
Ling Liu
YCYan Chen
Yan Chen
YYYingshui Yao
Yingshui Yao
With the development of economy and technology, the Internet is becoming more and more popular. Internet addiction has gradually become a serious issue in public health worldwide. The number of Internet users in China has reached 731 million, with an estimated 24 million adolescents determined as having Internet addiction. In this meta-analysis, we attempted to estimate the prevalence of Internet addiction among College Students in the People’s Republic of China in order to improve the mental health level of college students and provide evidence for the prevention of Internet addiction. Eligible articles about the prevalence of Internet addiction among college students in China published between 2006 and 2017 were retrieved from online Chinese periodicals, the full-text databases of Wan Fang, VIP, and the Chinese National Knowledge Infrastructure, as well as PubMed. Stata 11.0 was used to perform the analyses. A total of 26 papers were included in the analyses. The overall sample size was 38,245, with 4573 diagnosed with Internet addiction. The pooled detection rate of Internet addiction was 11% (95% confidence interval [CI] 9–13%) among college students in China. The detection rate was higher in male students (16%) than female students (8%). The Internet addiction detection rate was 11% (95% CI 8–14%) in southern areas, 11% (95% CI 7–14%) in northern areas, 13% (95% CI 8–18%) in eastern areas and 9% (95% CI 8–11%) in the mid-western areas. According to different scales, the Internet addiction detection rate was 11% (95% CI 8–15%) using the Young scale and 9% (95% CI 6–11%) using the Chen scale respectively. Cumulative meta analysis showed that the detection rate had a slight upward trend and gradually stabilized in the last 3 years. The pooled Internet addiction detection rate of Chinese college students in out study was 11%, which is higher than in some other countries and strongly demonstrates a worrisome situation. Effective measures should be taken to prevent further Internet addiction and improve the current situation.

22 November 2023 in Briefings in Bioinformatics
Verified
Journal Article
Open access
PDF file
YMYajie Meng
Yajie Meng
YWYi Wang
Yi Wang
JXJunlin Xu
Junlin Xu
CLChangcheng Lu
Changcheng Lu
XTXianfang Tang
Xianfang Tang
JYJialiang Yang
Jialiang Yang
Drug repositioning, the strategy of redirecting existing drugs to new therapeutic purposes, is pivotal in accelerating drug discovery. While many studies have engaged in modeling complex drug–disease associations, they often overlook the relevance between different node embeddings. Consequently, we propose a novel weighted local information augmented graph neural network model, termed DRAGNN, for drug repositioning. Specifically, DRAGNN firstly incorporates a graph attention mechanism to dynamically allocate attention coefficients to drug and disease heterogeneous nodes, enhancing the effectiveness of target node information collection. To prevent excessive embedding of information in a limited vector space, we omit self-node information aggregation, thereby emphasizing valuable heterogeneous and homogeneous information. Additionally, average pooling in neighbor information aggregation is introduced to enhance local information while maintaining simplicity. A multi-layer perceptron is then employed to generate the final association predictions. The model’s effectiveness for drug repositioning is supported by a 10-times 10-fold cross-validation on three benchmark datasets. Further validation is provided through analysis of the predicted associations using multiple authoritative data sources, molecular docking experiments and drug–disease network analysis, laying a solid foundation for future drug discovery.