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Frontiers in Bioinformatics
Scopus
ISSN 2673-7647 · Frontiers Media S.A. · 811 artikel di indeks
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Artikel Jurnal
IRMKD: an application of instance relation matrix in plant disease recognition
BackgroundThe recognition and prevention of plant diseases is very important to the growth process. At present, neural networks have achieved good results in plant disease identification, but the development of convolutional neural networks has brought a large number of network parameters and long…
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Benchmarking multiple gene ontology enrichment tools reveals high biological significance, ranking, and stringency heterogeneity among datasets
Functional enrichment analysis (FEA) provides biological meaning from lists of differentially expressed genes and proteins obtained through omics experiments. FEA tools can employ numerous statistical methods and rely on different pathway databases. In this sense, Overrepresentation Analysis (ORA)…
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Essential nucleic acid omics: a theoretical foundation for early-stage users
Modern biology often relies on the analysis of entire sets of molecules (omics). A subset of omics uses nucleic acid sequencing to reconstruct genomes and profile gene expression. Novel findings and existing data are contextualized by databases, which have been growing exponentially due to falling…
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Identification and bioinformatics analysis of a novel member of the lumbrokinase gene family in earthworms
BackgroundLumbrokinase is a novel antithrombotic drug isolated and purified from earthworms and used in the treatment of stroke and cardiovascular disease. However, to date, there has been no systematic classification of lumbrokinase genes.MethodsIn this study, a new member of the lumbrokinase gene…
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Applications of AI to single-cell and spatial transcriptomics: current state-of-the-art and challenges
Artificial intelligence (AI) has become a common tool for bioinformatics, with hundreds of methods published in recent years. Due to the training data demands of deep-learning algorithms, high-throughput single-cell and spatial transcriptomics is one of the most popular areas for these…
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TRANSAID: a hybrid deep learning framework for translation site prediction with integrated biological feature scoring
IntroductionTranslation initiation and termination are critical regulatory checkpoints in protein synthesis, yet accurate computational prediction of their sites remains challenging due to training data biases and the complexity of full-length transcripts.MethodsTo address these limitations, we…
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Evaluating transcriptomic integration for cyanobacterial constraint-based metabolic modelling
Metabolic modelling has wide-ranging applications, including for the improved production of high-value compounds, understanding complex diseases and analysing microbial community interactions. Integrating transcriptomic data with genome-scale metabolic models is crucial for deepening our…
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Mutational insights and in silico characterization of NEK family kinases in OSCC patients from the Pakistani population
IntroductionOral squamous cell carcinoma (OSCC) is a prevalent malignancy characterized by aggressive behavior, poor prognosis, and limited therapeutic options. Mutations in the NIMA-related kinase (NEK) family are increasingly implicated in tumorigenesis across various cancers. However, their…
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GPXplore: an intelligent computational framework for precise gene promoter extraction
Efficient and precise extraction of gene promoter regions is vital for understanding gene regulation, with broad implications in gene editing, functional genomics, and disease research. However, existing tools often fall short in scalability, usability and performance. To address these limitations…
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Machine learning-based QSAR and molecular modeling of phytocompounds in Barleria buxifolia L. as a potential aldose reductase inhibitor
IntroductionThe traditional medicinal plant Barleria buxifolia L is well-known for its pharmacological properties. This study aims to predict the binding affinity of bioactive compounds obtained from B. buxifolia towards significant molecular targets associated with diabetes mellitus. The polyol…
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A system-wide investigation into the phosphoregulatory network of TNIK and its cellular implications
IntroductionTNIK (Traf2- and Nck-interacting kinase) is a serine/threonine kinase that plays a crucial role in cytoskeletal organization, Wnt pathway activation, and cancer progression. Recent studies have implicated the role of TNIK in oncogenic signaling pathways and neuropsychiatric regulation…
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Identification of key genes in chickpea transcriptomics and the development of ChickpeaOmicsR as a comprehensive resource to advance breeding and genomic studies
IntroductionChickpea (Cicer arietinum L.) is a key legume crop and a major source of dietary protein in developing countries, yet its productivity is constrained by multiple biotic and abiotic stresses. Advances in RNA-seq and whole-genome sequencing enable detailed exploration of stress-responsive…
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Network pharmacology refined with non-ubiquity and decoy-controlled molecular docking reveals insights into Moringa oleifera phytochemicals targeting insulin resistance
Moringa oleifera phytochemicals were predicted to target insulin resistance proteins using a modified network pharmacology and molecular docking approach. Two hundred ninety M. oleifera phytochemicals with their aglycones, acetylase and myrosinase degradation products were compiled from literature…
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An explainable-AI framework reveals novel lncRNAs specific for breast cancer subtypes
BackgroundLong non-coding RNAs (lncRNAs) have emerged as important regulators in cancer biology; yet their potential for cancer subtyping remains underexplored particularly in the context of large-scale, multi-class supervised classification frameworks, due to limited publicly available data or…
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Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank
The cryogenic sample-electron microscopy (cryoEM) field has generated significant amounts of 3D Electron Microscopy (3DEM) volumetric data and associated metadata, now comprehensively archived in the Electron Microscopy Data Bank (EMDB - www.emdatabank.org) and the Electron Microscopy Public Image…
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Repurposing AI for protein interactions and dynamics: opportunities, limitations, and lessons
Understanding protein interactions and dynamics of biological systems is central in drug discovery. Advances in artificial intelligence (AI) have expanded the scope of predictive learning for complex biological systems. Repurposing current gold-standard AI algorithms for structural and biological…
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SimpleKANSleepNet: a Kolmogorov–Arnold network based sleep stage classification method
A novel Kolmogorov–Arnold Network (KAN) based machine learning model is proposed for the automatic sleep stage classification task. The redefined architecture of the Multilayer Perceptron (MLP) aims to build a more flexible model by using learnable activation functions. In this study, an effective…
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Integrated experimental and computational insights into the anti-inflammatory potential of flower-derived exosome-like nanoparticles targeting the NF-κB pathway
IntroductionDysregulated inflammation underlies numerous chronic pathologies, with the NF-κB p65–p50 heterodimer acting as a pivotal transcriptional regulator that mediates different inflammatory responses. Consequently, inhibiting NF-κB nuclear translocation has emerged as a promising strategy in…
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Unveiling the potential of apigenin and kaempferol against colon cancer: an integrated network pharmacology and docking approach
BackgroundColon cancer is one of the prevalent and deadly malignancies, requiring advanced treatment strategies.MethodsIMPPAT database, drug-likeliness, bioavailability scores, and Lipinski/Ghosh rules were utilized to screen the phytochemicals. STITCH, SwissTargetPrediction, CTD, and GeneCards…