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Identification of gene-level methylation for disease prediction
DNA methylation is an epigenetic alteration that plays a fundamental part in governing gene regulatory processes. The DNA methylation mechanism...
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SEDA 2024 update: enhancing the SEquence DAtaset builder for seamless integration into automated data analysis pipelines
BackgroundThe initial version of SEDA assists life science researchers without programming skills with the preparation of DNA and protein sequence...
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A functional gene module identification algorithm in gene expression data based on genetic algorithm and gene ontology
Since genes do not function individually, the gene module is considered an important tool for interpreting gene expression profiles. In order to...
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Multimodality Tests for Gene-Based Identification of Oncological Patients
Personalized medicine in cancer treatment is based on knowledge of the RNA levels of a set of genes that are deregulated as a consequence of the...
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Improved Regularized Multi-class Logistic Regression for Gene Classification with Optimal Kernel PCA and HC Algorithm
A significant challenge in high-dimensional and big data analysis is related to the classification and prediction of the variables of interest. The...
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The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L
BackgroundTheobroma cacao , the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a...
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Biclustering analysis on tree-shaped time-series single cell gene expression data of Caenorhabditis elegans
BackgroundIn recent years, gene clustering analysis has become a widely used tool for studying gene functions, efficiently categorizing genes with...
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Develo** an SNP dataset for efficiently evaluating soybean germplasm resources using the genome sequencing data of 3,661 soybean accessions
BackgroundSingle nucleotide polymorphism (SNP) markers play significant roles in accelerating breeding and basic crop research. Several soybean SNP...
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Large-scale omics dataset of polymer degradation provides robust interpretation for microbial niche and succession on different plastisphere
While biodegradable polymers have received increased attention due to the recent marine plastic problem, few studies have compared microbiomes and...
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Protein-Coding Gene Families in Prokaryote Genome Comparisons
The identification of orthologous genes is relevant for comparative genomics, phylogenetic analysis, and functional annotation. There are many...
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Particulate matter-induced gene expression patterns in human-derived cells based on 11 public gene expression datasets
BackgroundExposure to particulate matter (PM) and house dust mite (HDM) can change the expression patterns of inflammation-, oxidative stress-, and...
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Gene Networks Inference by Reinforcement Learning
Gene Regulatory Networks inference from gene expression data is an important problem in systems biology field, involving the estimation of gene-gene...
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Label-aware distance mitigates temporal and spatial variability for clustering and visualization of single-cell gene expression data
Clustering and visualization are essential parts of single-cell gene expression data analysis. The Euclidean distance used in most distance-based...
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The Global Soil Mycobiome consortium dataset for boosting fungal diversity research
Fungi are highly important biotic components of terrestrial ecosystems, but we still have a very limited understanding about their diversity and...
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Identifying Gene Markers Associated with Cell Subpopulations
An important point of the analysis of a single-cell RNA experiment is the identification of the key elements, i.e., genes, characterizing each cell...
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dgfr: an R package to assess sequence diversity of gene families
BackgroundGene families are groups of homologous genes that often have similar biological functions. These families are formed by gene duplication...
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Inferring circadian gene regulatory relationships from gene expression data with a hybrid framework
BackgroundThe central biological clock governs numerous facets of mammalian physiology, including sleep, metabolism, and immune system regulation....
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Genome-Wide Prediction of Disease Resistance Gene Analogs in Flax
Flax (Linum usitatissimum L.) is an important crop as the sources of fiber and seed oil. Annually, various pathogens cause significant loss to flax...
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Building High-Confidence Gene Regulatory Networks by Integrating Validated TF–Target Gene Interactions Using ConnecTF
Many methods are now available to identify or predict the target genes of transcription factors (TFs) in plants. These include experimental...
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A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset
BackgroundSingle-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and...
