Fast Skyline Community Search in Multi-Valued Networks by Dongxiao Yu, Lifang Zhang, Qi Luo, Xiuzhen Cheng, Jiguo Yu, Zhipeng Cai

“…Community search has been extensively studied in large networks, such as Protein-Protein Interaction (PPI) networks, citation graphs, and collaboration networks. …”
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Expression Profiling of Proliferation and Apoptotic Markers along the Adenoma-Carcinoma Sequence in Familial Adenomatous Polyposis Patients by Jayson Wang, Nabil El-Masry, Ian Talbot, Ian Tomlinson, Malcolm R. Alison, Mona El-Bahrawy

“…Familial adenomatous polyposis (FAP) patients have a germline mutation in the adenomatous polyposis coli (APC) gene. The APC protein interacts with beta-catenin, resulting in the activation of the Wnt signalling pathway. …”
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CENPN contributes to pancreatic carcinoma progression through the MDM2-mediated p53 signaling pathway by Ming Xu, Jie Tang, Qiong Sun, Jing Meng, Guoyu Chen, Yunli Chang, Yao Yao, Jieru Ji, Hao Luo, Lingling Chen, Minxue Lu, Weiwei Shi

“…Material and methods The construction of a protein-protein interaction (PPI) network was based on overlapping differentially expressed genes (DEGs) identified in the GSE16515, GSE32676, and GSE125158 datasets. …”
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The anti-cancerous mechanism of licochalcone A on human hepatoma cell HepG2 based on the miRNA omics by Jun Wang, Xiuxiu Zhang, Zhijing Ni, Elnur Elam, Kiran Thakur, Kexin Li, Chuyan Wang, Jianguo Zhang, Zhaojun Wei

“…FoxO signaling pathway was the hub pathway for the targets. A protein-protein interaction network was structured on the STRING platform to discover the hub genes. …”
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Mechanism of Cordyceps Cicadae in Treating Diabetic Nephropathy Based on Network Pharmacology and Molecular Docking Analysis by Yi Qian, Xin Sun, Xin Wang, Xin Yang, Mengyao Fan, Jiao Zhong, Zejun Pei, Junping Guo

“…The network of active components and targets was drawn by Cytoscape 3.6.0, the protein-protein interaction (PPI) was analyzed by the STRING database, and the DAVID database was used for the enrichment analysis of intersection targets. …”
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The Identification of Key Genes and Pathways in Glioma by Bioinformatics Analysis by Mingfa Liu, Zhennan Xu, Zepeng Du, Bingli Wu, Tao Jin, Ke Xu, Liyan Xu, Enmin Li, Haixiong Xu

“…Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were applied for the enriched pathways. A protein-protein interaction (PPI) network was constructed to find the hub genes. …”
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Personalized prediction of anticancer potential of non-oncology drugs through learning from genome derived molecular pathways by Xiaobao Dong, Huanhuan Liu, Ting Tong, Liuxing Wu, Jianhua Wang, Tianyi You, Yongjian Wei, Xianfu Yi, Hongxi Yang, Jie Hu, Haitao Wang, Xiaoyan Wang, Mulin Jun Li

“…Utilizing protein–protein interaction networks, CHANCE harmonizes multilevel mutation annotations and integrates pharmacological information across different drugs into a single model. …”
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Proteome differences of dental stem cells between permanent and deciduous teeth by data-independent acquisition proteomics by Zhang Suping, Liu Yuqing, Dong Jin, Jiao Min, Gu Yongchun, Chen Liling, Yuan Na, Wang Jianrong, Yang Dezhao, Meng Fanwen

“…Subsequent Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, along with protein–protein interaction network construction, revealed significant metabolic differences and key regulatory nodes. …”
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Genome-Wide Identification and Analysis of the Cytochrome B5 Protein Family in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis) by Han Zheng, Xin Li, Lin Shi, Ying Jing, Qingqing Song, Yanan Chen, Lilong He, Fengde Wang, Jianwei Gao, Yuping Bi

“…Phylogenetic analysis of the CB5 protein sequences from six species showed that the BrCB5s conduct a close evolutionary process with the CB5s of Arabidopsis thaliana and far from those of Oryza sativa. Protein interaction analysis showed that 40 interaction patterns were predicted including two Sucrose Transporter 4 subfamily proteins (SUT 4) and Fatty Acid Hydroxylase 2 protein (FAH 2) can interact with most members of BrCB5s. …”
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Lysosome and Cytoskeleton Pathways Are Robustly Enriched in the Blood of Septic Patients: A Meta-Analysis of Transcriptomic Data by Jie Ma, Chuanxi Chen, Andreas S. Barth, Chris Cheadle, Xiangdong Guan, Li Gao

“…Overall, our study revealed distinct mRNA activation profiles and protein-protein interaction networks in blood of human sepsis. Conclusions. …”
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Integrated Bioinformatic Analysis Identifies Networks and Promising Biomarkers for Hepatitis B Virus-Related Hepatocellular Carcinoma by Yun Ji, Yue Yin, Weizhen Zhang

“…Subsequently, the analysis of function and pathway enrichment as well as the protein-protein interaction network (PPI) was performed. The ten hub genes screened out from the PPI network were further subjected to expression profile and survival analysis. …”
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Potential and mechanisms of indigenous Indonesian medicinal plants in treating sexual dysfunction: A systematic review and pharmacological network overview by Sukardiman, Roihatul Mutiah, Rosita Handayani

“…Network topology was explored with Cytoscape 3.10, and the construction of Protein-Protein Interaction Networks was realized using STRING version 12.0. …”
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Identification of mitophagy-related biomarkers and immune infiltration in polycystic ovarian syndrome by bioinformatic study by Hongjuan Ye, Xicheng Wang, Zhiying He

“…The potential biomarkers of mitophagy-related and immune infiltration in PCOS were screened by protein-protein interaction network using different algorithms, and the area under the curve was calculated to analyze their diagnostic value. …”
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Mesenchymal Stem Cells May Alleviate the Intervertebral Disc Degeneration by Reducing the Oxidative Stress in Nucleus Pulposus Cells by Yongzhao Zhao, Qian Xiang, Yunzhong Cheng, Jialiang Lin, Shuai Jiang, Weishi Li

“…A series of bioinformatic methods were used to calculate the oxidative stress score and autophagy score, identify the OSRDEGs, conduct the function enrichment analysis and protein-protein interaction (PPI) analysis, build the relevant competing endogenous RNA (ceRNA) regulatory networks, and explore the potential association between oxidative stress and autophagy in degenerative NPCs cocultured with MSCs. …”
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Comprehensive Bioinformatics Method to Explore Immune-Related Genes in the Pathogenesis of Myocardial Infarction by Xin Zhang, Yiren Yao, Ying Ding, Wenting Yan, Yang Gu, Xiwen Zhang, Xiaojin Xu

“…We performed differential gene expression analysis, GO/KEGG enrichment analysis, protein-protein interaction (PPI) network analysis, weighted gene co-expression network analysis (WGCNA), gene set enrichment analysis, and immune infiltration studies to identify core immune-related genes associated with MI. …”
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Metastatic melanoma: An integrated analysis to identify critical regulators associated with prognosis, pathogenesis and targeted therapies. by Zeinab Chaharlashkar, Yousof Saeedi Honar, Meghdad Abdollahpour-Alitappeh, Sepideh Parvizpour, Abolfazl Barzegar, Effat Alizadeh

“…After exploration of DEGs of NS and metastatic-melanoma, identification of relevant transcription factors (TFs) and kinases, the Gene Ontology (GO), and pathways analyses of DEGs were performed. Protein-protein interaction (PPI) networks were evaluated by the STRING and Cytoscape. …”
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Differential proteome analysis of pea roots at the early stages of symbiosis with nodule bacteria by I. V. Leppyanen, A. N. Kirienko, A. A. Lobov, E. A. Dolgikh

“…Further experiments are expected to show whether the beta-subunit of the G protein interacts with the receptors to Nod factors, and how this affects the further signaling. …”
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Identification of KIFC1 as an independent prognostic marker in renal clear cell carcinoma correlates with tumor proliferation and immune infiltration by Bin Du, Jia Wang, Jinping Zheng, Jing Huo, Pu Wang

“…By proteomics, we analyzed proteins interacting with KIFC1; spliceosome proteins had the most significant enrichment, indicating the new directions for KIFC1 investigation. …”
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Integrated Approach for Biomarker Discovery and Mechanistic Insights into the Co-Pathogenesis of Type 2 Diabetes Mellitus and Non-Hodgkin Lymphoma by Zhu Y, Liu J, Wang B

“…Subsequently, a protein-protein interaction network was constructed based on the common differentially expressed genes (DEGs) between T2DM and NHL to explore regulatory interactions. …”
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Computer modeling of the peculiarities in the interaction of IL-1 with its receptors in schizophrenia by N. Yu. Chasovskikh, A. A. Bobrysheva, E. E. Chizhik

“…Protein modeling was conducted using the SWISS-MODEL server, and protein interaction modeling was performed using PRISM. …”
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