Systematic analysis of co-expression network and gene expression profile of differentially expressed lncRNA-mRNA one week after spinal cord injury by Yi Kang, Yijie Song, Zhongju Shi, Qiang Li, Yigang Lv, Mengfan Hou, Cui Ding, Jing Xie, Yongfu Lou, Chi Zhang, Huan Jian, Xueying Li, Hengxing Zhou, Shiqing Feng

“…Moreover, we constructed protein–protein interaction (PPI) networks, the STRING database, and identified the 10 high degree core nodes. …”
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Chemical Biology of G-quadruplex and i-motif DNA: use of topologically constrained DNA by Dejeu, Jérôme, Defrancq, Eric

“…., affine and specific) G4- and i-DNA-interacting ligands, (ii) identify proteins interacting with those structures and determine their cellular relevance and (iii) select specific antibodies for G4 and i-DNA. …”
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Dinuclear Copper(I) Thiodiacetate Complex-Mediated Expeditious Synthesis of the Chlorine-Containing Cyclen-Cored 36-Glucose-Coated Glycodendrimer by Anand K. Agrahari, Sunil Kumar, Anindra Sharma, Vinod K. Tiwari

“…High-sugar-tethered glycodendrimers are a remarkable tool in glycobiology for the investigation of carbohydrate-protein interaction using its multivalency property. An enthralling double-stage convergent synthetic approach was selected to build a novel class of chlorine-containing glucose-coated dendrimers using an efficient click catalyst ‘dinuclear copper(I) thiodiacetate complex.’ …”
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The Influence of Three Statistical Variables on Self-Similarity in Complex Networks by Mingli Lei, Lirong Liu, Daijun Wei

“…Moreover, two real networks are used for numerical simulation, including a USAir network and the yeast protein interaction (YPI) network. The effects of the three statistical variables on the two real networks are considered. …”
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Molecular-genetic pathways of hepatitis C virus regulation of the expression of cellular factors PREB and PLA2G4C, which play an important role in virus replication by E. L. Mishchenko, A. A. Makarova, E. A. Antropova, A. S. Venzel, T. V. Ivanisenko, P. S. Demenkov, V. A. Ivanisenko

“…We assumed that NS3 could inhibit the function of host transcription factor (TF) NOTCH1 by protein-protein interaction, leading to upregulation of PREB and PLA2G4C. …”
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Structural information in therapeutic peptides: Emerging applications in biomedicine by Valentín Iglesias, Oriol Bárcenas, Carlos Pintado‐Grima, Michał Burdukiewicz, Salvador Ventura

“…This trend stems from their cost‐effectiveness and reduced immunogenicity, compared to antibodies or recombinant proteins, but also from their ability to dock and interfere with large protein–protein interaction surfaces, and their higher specificity and better biocompatibility relative to organic molecules. …”
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Exploring Drug Targets in Isoprenoid Biosynthetic Pathway for Plasmodium falciparum by Tabish Qidwai, Farrukh Jamal, Mohd Y. Khan, Bechan Sharma

“…For more comprehensive analysis, antimalarial drug-protein interaction has been covered.…”
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Structure‐based computational design of antibody mimetics: challenges and perspectives by Elton J. F. Chaves, Danilo F. Coêlho, Carlos H. B. Cruz, Emerson G. Moreira, Júlio C. M. Simões, Manassés J. Nascimento‐Filho, Roberto D. Lins

“…We discuss the intricacies of different computational protein–protein interaction design strategies, showcased by selected successful cases in the literature. …”
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CD163, a novel receptor for TNF, was revealed in situ by proximity ligation assay by Alexandre Cousin, Myriam Oger, Aymar de Jenlis, Audrey Lejart, Laure Barbier, Diane Riccobono, Xavier Holy, Anne-Laure Favier, Krisztina Nikovics

“…Our study compared co-localization using the Proximity Ligation Assay (PLA), a recently developed in situ protein-protein interaction technique. In an inflamed porcine lung model, we demonstrated the efficacy of PLA in detecting interactions between tumor necrosis factor (TNF) and its receptors TNFR1 and TNFR2. …”
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Comparison of Protein Acetyltransferase Action of CRTAase with the Prototypes of HAT by Prija Ponnan, Ajit Kumar, Prabhjot Singh, Prachi Gupta, Rini Joshi, Marco Gaspari, Luciano Saso, Ashok K. Prasad, Ramesh C. Rastogi, Virinder S. Parmar, Hanumantharao G. Raj

“…The autoacetylation of CR like that of HATs was found to enhance protein-protein interaction. CR like HAT-1, CBP, and p300 mediated the acylation of RP utilizing acetyl CoA and propionyl CoA as the substrates. …”
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Plasma Membrane Targeting of Protocadherin 15 Is Regulated by the Golgi-Associated Chaperone Protein PIST by Hongyun Nie, Yueyue Liu, Xiaolei Yin, Huiren Cao, Yanfei Wang, Wei Xiong, Yushuang Lin, Zhigang Xu

“…Here we show that PIST, a Golgi-associated, PDZ domain-containing protein, interacts with PCDH15. The interaction is mediated by the PDZ domain of PIST and the C-terminal PDZ domain-binding interface (PBI) of PCDH15. …”
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Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary Disease by Seokjin Ham, Yeon-Mok Oh, Tae-Young Roh

“…Differentially expressed or co-expressed genes in the protein interaction subnetworks were linked with mitochondrial dysfunction and the immune response, as expected. …”
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DYRK1A (Dual-Specificity Tyrosine-Phosphorylated and -Regulated Kinase 1A): A Gene with Dosage Effect During Development and Neurogenesis by M. Dierssen, M. Martínez de Lagrán

“…The large number of protein interaction and putative substrates described for DYRK1A suggest multiple pathways and functions to be involved in its developmental function. …”
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Activation Mechanism of LRRK2 and Its Cellular Functions in Parkinson’s Disease by Katharina E. Rosenbusch, Arjan Kortholt

“…LRRK2 belongs to the group of Roco proteins which are characterized by the presence of a Ras-like G-domain (Roc), a C-terminal of Roc domain (COR), a kinase, and several protein-protein interaction domains. Roco proteins exhibit a complex activation mechanism involving intramolecular signaling, dimerization, and substrate/effector binding. …”
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Intraneuronal binding of amyloid beta with reelin-Implications for the onset of Alzheimer's disease. by Asgeir Kobro-Flatmoen, Stig W Omholt

“…In a rat model used to study AD, it was recently shown that in layer II neurons of the anteriolateral entorhinal cortex expressing high levels of the glycoprotein reelin (Re+alECLII neurons), reelin and Aβ engage in a direct protein-protein interaction. If reelin functions as a sink for intracellular Aβ and if the binding to reelin makes Aβ physiologically inert, it implies that reelin can prevent the neuron from being exposed to the harmful effects typically associated with increased levels of oligomeric Aβ. …”
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Using Network Pharmacology to Explore the Mechanism of Panax notoginseng in the Treatment of Myocardial Fibrosis by Jingxue Han, Jingyi Hou, Yu Liu, Peng Liu, Tingting Zhao, Xinwei Wang

“…Targets of MF were then screened to select common targets and construct a protein-protein interaction network. This was followed by Gene Ontology and pathway enrichment analyses. …”
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TNIP1 in Autoimmune Diseases: Regulation of Toll-like Receptor Signaling by Rambon Shamilov, Brian J. Aneskievich

“…In addition to earlier foundational reports of TNIP1 SNPs in human autoimmune diseases and TNIP1 protein-protein interaction with receptor regulating proteins, more recent studies have identified new potential interaction partners and signaling pathways likely modulated by TNIP1. …”
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The Identification of Immune-Related Biomarkers for Osteoarthritis Immunotherapy Based on Single-Cell RNA Sequencing Analysis by Zhe Tan, Rong Chen, Hanyu Lin, Hong Wang

“…In addition, the Venn diagram was applied to evaluate the genes that are involved in OA and immune-related genes. The protein-protein interaction analysis was further conducted to explore the hub genes. …”
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Uncover the Underlying Mechanism of Drug-Induced Myopathy by Using Systems Biology Approaches by Dong Li, Aixin Li, Hairui Zhou, Xi Wang, Peng Li, Sheng Bi, Yang Teng

“…In this study, we curated the comprehensive DIM drug list based on structured labeling products (SPLs) and carried out the analysis based on chemical structure space, drug protein interaction, side effect space, and transcriptomic profiling space. …”
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A Network-Based Approach to Explore the Mechanism and Bioactive Compounds of Erzhi Pill against Metabolic Dysfunction-Associated Fatty Liver Disease by Shaojie Huang, Fei Mu, Fei Li, Wenjun Wang, Haixia Chen, Lu Lei, Yang Ma, Yi Ding, Jingwen Wang

“…This was carried out through target prediction, protein-protein interaction (PPI) network construction, gene ontology, KEGG pathway enrichment, and molecular docking. …”
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