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Predicting Microbe-Disease Association via Tripartite Network and Relation Graph Convolutional Network
Many evidences show that microbes play vital roles in human health and diseases. Thus, predicting microbe-disease associations is helpful for disease...
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Plant and fungal species interactions differ between aboveground and belowground habitats in mountain forests of eastern China
Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between...
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Spike sorting with Kilosort4
Spike sorting is the computational process of extracting the firing times of single neurons from recordings of local electrical fields. This is an...
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Persistent Homology for RNA Data Analysis
Molecular representations are of great importance for machine learning models in RNA data analysis. Essentially, efficient molecular descriptors or...
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Exploring fish functional trait assemblages in Eastern Mediterranean rivers: a study across multiple scales using network analysis
Functional traits of river fish assemblages have rarely been studied in the Eastern Mediterranean region. A dataset of 254 Greek electrofished...
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The modular biochemical reaction network structure of cellular translation
Translation is an essential attribute of all living cells. At the heart of cellular operation, it is a chemical information decoding process that...
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A Multi-perspective Model for Protein–Ligand-Binding Affinity Prediction
AbstractGathering information from multi-perspective graphs is an essential issue for many applications especially for protein–ligand-binding...
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MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
Structural variant (SV) calling belongs to the standard tools of modern bioinformatics for identifying and describing alterations in genomes....
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ppiGReMLIN: a graph mining based detection of conserved structural arrangements in protein-protein interfaces
BackgroundProtein-protein interactions (PPIs) are fundamental in many biological processes and understanding these interactions is key for a myriad...
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Centrality Analysis of Protein–Protein Interaction Networks Using R
Proteins are structural and functional components of cells. They interact with each other to drive specific cellular functions. The physical and...
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Predicting links between tumor samples and genes using 2-Layered graph based diffusion approach
BackgroundDetermining the association between tumor sample and the gene is demanding because it requires a high cost for conducting genetic...
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The global integrative network: integration of signaling and metabolic pathways
The crosstalk between signaling and metabolic pathways has been known to play key roles in human diseases and plant biological processes. The...
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Graph regularized L2,1-nonnegative matrix factorization for miRNA-disease association prediction
BackgroundThe aberrant expression of microRNAs is closely connected to the occurrence and development of a great deal of human diseases. To study...
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Genetic Analysis by Targeted Misexpression and Gene Silencing
Analysis of gene function is crucial for understanding the mechanism of biological processes. Critical clues to gene functions in vivo can be...
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Application of Graphs in a One Health Framework
The One Health framework, which advocates the crucial interconnection between environmental, animal, and human health and well-being, is becoming of...
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Identifying potential association on gene-disease network via dual hypergraph regularized least squares
BackgroundIdentifying potential associations between genes and diseases via biomedical experiments must be the time-consuming and expensive research...
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MetaCarvel: linking assembly graph motifs to biological variants
Reconstructing genomic segments from metagenomics data is a highly complex task. In addition to general challenges, such as repeats and sequencing...
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scEvoNet: a gradient boosting-based method for prediction of cell state evolution
BackgroundExploring the function or the developmental history of cells in various organisms provides insights into a given cell type's core molecular...
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The network structure of intertidal meiofaunal communities from environmental DNA metabarcoding surveys in Northwest Iberia
The identification of patterns and mechanisms behind species’ distribution is one of the major challenges in ecology, having important outcomes for...
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ACCBN: ant-Colony-clustering-based bipartite network method for predicting long non-coding RNA–protein interactions
BackgroundLong non-coding RNA (lncRNA) studies play an important role in the development, invasion, and metastasis of the tumor. The analysis and...
