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Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index
MotivationAlignment of reads to a reference genome sequence is one of the key steps in the analysis of human whole-genome sequencing data obtained...
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Cancer mutationscape: revealing the link between modular restructuring and intervention efficacy among mutations
There is increasing evidence that biological systems are modular in both structure and function. Complex biological signaling networks such as gene...
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Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling
Immunoglobulins (Ig), which exist either as B-cell receptors (BCR) on the surface of B cells or as antibodies when secreted, play a key role in the...
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METASEED: a novel approach to full-length 16S rRNA gene reconstruction from short read data
BackgroundWith the emergence of Oxford Nanopore technology, now the on-site sequencing of 16S rRNA from environments is available. Due to the error...
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expHRD: an individualized, transcriptome-based prediction model for homologous recombination deficiency assessment in cancer
BackgroundHomologous recombination deficiency (HRD) stands as a clinical indicator for discerning responsive outcomes to platinum-based chemotherapy...
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Building RadiologyNET: an unsupervised approach to annotating a large-scale multimodal medical database
BackgroundThe use of machine learning in medical diagnosis and treatment has grown significantly in recent years with the development of...
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A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques
BackgroundThe growing abundance of in vitro omics data, coupled with the necessity to reduce animal testing in the safety assessment of chemical...
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SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies
BackgroundSimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well...
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Transcriptome- and DNA methylation-based cell-type deconvolutions produce similar estimates of differential gene expression and differential methylation
BackgroundChanging cell-type proportions can confound studies of differential gene expression or DNA methylation (DNAm) from peripheral blood...
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OBSERVE: guidelines for the refinement of rodent cancer models
Existing guidelines on the preparation (Planning Research and Experimental Procedures on Animals: Recommendations for Excellence (PREPARE)) and...
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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...