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gcplyr: an R package for microbial growth curve data analysis
BackgroundCharacterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of...
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ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing
BackgroundStructural variations play an important role in bacterial genomes. They can mediate genome adaptation quickly in response to the external...
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Computational gastronomy: capturing culinary creativity by making food computable
Cooking, a quintessential creative pursuit, holds profound significance for individuals, communities, and civilizations. Food and cooking transcend...
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Ensemble Machine Learning and Predicted Properties Promote Antimicrobial Peptide Identification
AbstractThe emergence of antibiotic-resistant microbes raises a pressing demand for novel alternative treatments. One promising alternative is the...
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A comprehensive review of computational cell cycle models in guiding cancer treatment strategies
This article reviews the current knowledge and recent advancements in computational modeling of the cell cycle. It offers a comparative analysis of...
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Deepvirusclassifier: a deep learning tool for classifying SARS-CoV-2 based on viral subtypes within the coronaviridae family
PurposeIn this study, we present DeepVirusClassifier, a tool capable of accurately classifying Severe Acute Respiratory Syndrome Coronavirus 2...
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Filter bank temporally local multivariate synchronization index for SSVEP-based BCI
BackgroundMultivariate synchronization index (MSI) has been successfully applied for frequency detection in steady state visual evoked potential...
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Unraveling Brain Synchronisation Dynamics by Explainable Neural Networks using EEG Signals: Application to Dyslexia Diagnosis
AbstractThe electrical activity of the neural processes involved in cognitive functions is captured in EEG signals, allowing the exploration of the...
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SGCP: a spectral self-learning method for clustering genes in co-expression networks
BackgroundA widely used approach for extracting information from gene expression data employs the construction of a gene co-expression network and...
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Unsupervised modeling of mutational landscapes of adeno-associated viruses viability
Adeno-associated viruses 2 (AAV2) are minute viruses renowned for their capacity to infect human cells and akin organisms. They have recently emerged...
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Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2
BackgroundFungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with...
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Observing isolated synaptic vesicle association and fusion ex vivo
Here, we present a protocol for isolating functionally intact glutamatergic synaptic vesicles from whole-mouse brain tissue and using them in a...
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Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure
AbstractProtein complexes perform diverse biological functions, and obtaining their three-dimensional structure is critical to understanding and...
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A Novel Detection Method for High-Order SNP Epistatic Interactions Based on Explicit-Encoding-Based Multitasking Harmony Search
To elucidate the genetic basis of complex diseases, it is crucial to discover the single-nucleotide polymorphisms (SNPs) contributing to disease...
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Identification of immune-associated biomarkers of diabetes nephropathy tubulointerstitial injury based on machine learning: a bioinformatics multi-chip integrated analysis
BackgroundDiabetic nephropathy (DN) is a major microvascular complication of diabetes and has become the leading cause of end-stage renal disease...
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Revisiting the evolution of bow-tie architecture in signaling networks
Bow-tie architecture is a layered network structure that has a narrow middle layer with multiple inputs and outputs. Such structures are widely seen...
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MetaV: A Pioneer in feature Augmented Meta-Learning Based Vision Transformer for Medical Image Classification
Image classification, a fundamental task in computer vision, faces challenges concerning limited data handling, interpretability, improved feature...
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Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue
Spatial epigenetic map** of tissues enables the study of gene regulation programs and cellular functions with the dependency on their local tissue...
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penalizedclr: an R package for penalized conditional logistic regression for integration of multiple omics layers
BackgroundThe matched case–control design, up until recently mostly pertinent to epidemiological studies, is becoming customary in biomedical...
