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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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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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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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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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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...
