Interaction network
View article: STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets Open
Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein …
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The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest Open
Much of the complexity within cells arises from functional and regulatory interactions among proteins. The core of these interactions is increasingly known, but novel interactions continue to be discovered, and the information remains scat…
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Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts Open
The Drug-Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that provides information on drug-gene interactions and druggable genes from publications, databases, and other web-based sources. Drug, gene, and interaction data…
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Network-based prediction of drug combinations Open
Drug combinations, offering increased therapeutic efficacy and reduced toxicity, play an important role in treating multiple complex diseases. Yet, our ability to identify and validate effective combinations is limited by a combinatorial e…
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pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks Open
Pathway analysis is often the first choice for studying the mechanisms underlying a phenotype. However, conventional methods for pathway analysis do not take into account complex protein-protein interaction information, resulting in incomp…
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Interaction rewiring and the rapid turnover of plant–pollinator networks Open
Whether species interactions are static or change over time has wide‐reaching ecological and evolutionary consequences. However, species interaction networks are typically constructed from temporally aggregated interaction data, thereby im…
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New insights into the interplay between long non‐coding RNAs and RNA‐binding proteins in cancer Open
With the development of proteomics and epigenetics, a large number of RNA‐binding proteins (RBPs) have been discovered in recent years, and the interaction between long non‐coding RNAs (lncRNAs) and RBPs has also received increasing attent…
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SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis Open
Living cells are made up of individual parts, i.e. the genome, the proteins, the RNA and lipid molecules as well as the metabolites and ions. However, life depends on the functional interaction among these components which is often organiz…
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Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets Open
Significance Large-scale biological network analyses often use concepts used in social networks analysis (e.g. finding “communities,” “hubs,” etc.). However, mathematically advanced engineering concepts have only been applied to analyze sm…
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Network Medicine in the Age of Biomedical Big Data Open
Network medicine is an emerging area of research dealing with molecular and genetic interactions, network biomarkers of disease, and therapeutic target discovery. Large-scale biomedical data generation offers a unique opportunity to assess…
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DyNet: visualization and analysis of dynamic molecular interaction networks Open
Summary : The ability to experimentally determine molecular interactions on an almost proteome-wide scale under different conditions is enabling researchers to move from static to dynamic network analysis, uncovering new insights into how …
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Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks Open
Biological networks are often used to represent complex biological systems, which can contain several types of entities. Analysis and visualization of such networks is supported by the Cytoscape software tool and its many apps. While earli…
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Mechanisms underlying the therapeutic effects of Qingfeiyin in treating acute lung injury based on GEO datasets, network pharmacology and molecular docking Open
This study successfully predict the effective components and potential targets and pathways involved in the treatment of ALI for QFY. We provided a novel strategy for future research of molecular mechanisms of QFY in ALI treatment. Moreove…
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Network-based integration of multi-omics data for prioritizing cancer genes Open
Motivation Several molecular events are known to be cancer-related, including genomic aberrations, hypermethylation of gene promoter regions and differential expression of microRNAs. These aberration events are very heterogeneous across tu…
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OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space Open
Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. How…
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systemsDock: a web server for network pharmacology-based prediction and analysis Open
We present systemsDock, a web server for network pharmacology-based prediction and analysis, which permits docking simulation and molecular pathway map for comprehensive characterization of ligand selectivity and interpretation of ligand a…
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One Time of Interaction May Not Be Enough: Go Deep with an Interaction-over-Interaction Network for Response Selection in Dialogues Open
Currently, researchers have paid great attention to retrieval-based dialogues in open-domain. In particular, people study the problem by investigating context-response matching for multi-turn response selection based on publicly recognized…
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Inferring Interaction Networks From Multi-Omics Data Open
A major goal in systems biology is a comprehensive description of the entirety of all complex interactions between different types of biomolecules-also referred to as the interactome-and how these interactions give rise to higher, cellular…
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Opposed latitudinal patterns of network‐derived and dietary specialization in avian plant–frugivore interaction systems Open
Latitudinal patterns of biodiversity have been studied for centuries, but it is only during the last decades that species interaction networks have been used to examine the proposed latitudinal gradient of biotic specialization. These stud…
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HAPPENN is a novel tool for hemolytic activity prediction for therapeutic peptides which employs neural networks Open
The growing prevalence of resistance to antibiotics motivates the search for new antibacterial agents. Antimicrobial peptides are a diverse class of well-studied membrane-active peptides which function as part of the innate host defence sy…
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LncRRIsearch: A Web Server for lncRNA-RNA Interaction Prediction Integrated With Tissue-Specific Expression and Subcellular Localization Data Open
Long non-coding RNAs (lncRNAs) play critical roles in various biological processes, but the function of the majority of lncRNAs is still unclear. One approach for estimating a function of a lncRNA is the identification of its interaction t…
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Identification of hub genes and potential molecular mechanisms in gastric cancer by integrated bioinformatics analysis Open
Objective Gastric cancer (GC) is the fourth most common cause of cancer-related deaths in the world. In the current study, we aim to identify the hub genes and uncover the molecular mechanisms of GC. Methods The expression profiles of the …
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Constructing prediction models from expression profiles for large scale lncRNA–miRNA interaction profiling Open
Motivation The interaction of miRNA and lncRNA is known to be important for gene regulations. However, not many computational approaches have been developed to analyze known interactions and predict the unknown ones. Given that there are n…
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Morphological trait matching shapes plant–frugivore networks across the Andes Open
Interactions between resource and consumer species are organized in ecological networks. Species interactions in these networks are influenced by the functional traits of the interacting partners, but the generality of trait‐based interact…
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Drug Target Protein-Protein Interaction Networks: A Systematic Perspective Open
The identification and validation of drug targets are crucial in biomedical research and many studies have been conducted on analyzing drug target features for getting a better understanding on principles of their mechanisms. But most of t…
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iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery Open
Computational tools for multiomics data integration have usually been designed for unsupervised detection of multiomics features explaining large phenotypic variations. To achieve this, some approaches extract latent signals in heterogeneo…
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<i>In silico</i> analyses for potential key genes associated with gastric cancer Open
Background Understanding hub genes involved in gastric cancer (GC) metastasis could lead to effective approaches to diagnose and treat cancer. In this study, we aim to identify the hub genes and investigate the underlying molecular mechani…
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Interactome-based approaches to human disease Open
Recent advances in high-throughput technologies have created exciting opportunities for systematically investigating the molecular basis of human disease. In addition to a growing catalog of disease-associated genetic variations, we can no…
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Gradient Boosting Decision Tree-Based Method for Predicting Interactions Between Target Genes and Drugs Open
Determining the target genes that interact with drugs-drug-target interactions-plays an important role in drug discovery. Identification of drug-target interactions through biological experiments is time consuming, laborious, and costly. T…
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Network pharmacology based research into the effect and mechanism of Yinchenhao Decoction against Cholangiocarcinoma Open
Background Cholangiocarcinoma refers to an epithelial cell malignancy with poor prognosis. Yinchenhao decoction (YCHD) showed positive effects on cancers, and associations between YCHD and cholangiocarcinoma remain unclear. This study aime…