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Evaluation of network-guided random forest for disease gene discovery
BackgroundGene network information is believed to be beneficial for disease module and pathway identification, but has not been explicitly utilized...
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Characterization of a lipid droplet and endoplasmic reticulum stress related gene risk signature to evaluate the clinical and biological value in hepatocellular carcinoma
IntroductionLipid metabolism and endoplasmic reticulum (ER) stress play an important role in the progression and metastasis of hepatocellular...
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ENGEP: advancing spatial transcriptomics with accurate unmeasured gene expression prediction
Imaging-based spatial transcriptomics techniques provide valuable spatial and gene expression information at single-cell resolution. However, their...
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scGIST: gene panel design for spatial transcriptomics with prioritized gene sets
A critical challenge of single-cell spatial transcriptomics (sc-ST) technologies is their panel size. Being based on fluorescence in situ...
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A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis
DNA methylation has been utilized for target gene silencing in plants. However, it is not well understood whether other silencing pathways can be...
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A novel graph-based k-partitioning approach improves the detection of gene-gene correlations by single-cell RNA sequencing
BackgroundGene expression is regulated by transcription factors, cofactors, and epigenetic mechanisms. Coexpressed genes indicate similar functional...
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Unifying duplication episode clustering and gene-species map** inference
We present a novel problem, called MetaEC, which aims to infer gene-species assignments in a collection of partially leaf-labeled gene trees labels...
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PriPath: identifying dysregulated pathways from differential gene expression via grou**, scoring, and modeling with an embedded feature selection approach
BackgroundCell homeostasis relies on the concerted actions of genes, and dysregulated genes can lead to diseases. In living organisms, genes or their...
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An overview of detecting gene-trait associations by integrating GWAS summary statistics and eQTLs
Detecting genes that affect specific traits (such as human diseases and crop yields) is important for treating complex diseases and improving crop...
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Gene expression and survival analysis study of KIAA0101 gene revealed its prognostic and diagnostic importance in breast cancer
Breast cancer (BC) is the most frequent cancer affecting women worldwide. High-throughput genomic platforms and microarray-based gene expression...
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Gene count normalization in single-cell imaging-based spatially resolved transcriptomics
BackgroundRecent advances in imaging-based spatially resolved transcriptomics (im-SRT) technologies now enable high-throughput profiling of targeted...
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Synechococcus nitrogen gene loss in iron-limited ocean regions
Synechococcus are the most abundant cyanobacteria in high latitude regions and are responsible for an estimated 17% of annual marine net primary...
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Harissa: Stochastic Simulation and Inference of Gene Regulatory Networks Based on Transcriptional Bursting
Gene regulatory networks, as a powerful abstraction for describing complex biological interactions between genes through their expression products...
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Dietary macronutrient composition impacts gene regulation in adipose tissue
Diet is a key lifestyle component that influences metabolic health through several factors, including total energy intake and macronutrient...
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Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis
IntroductionStaphylococcus aureus is a gram-positive bacterium that causes serious infection. With the increasing resistance of bacteria to current...
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EGFR Pathway-Based Gene Signatures of Druggable Gene Mutations in Melanoma, Breast, Lung, and Thyroid Cancers
AbstractEGFR , BRAF , PIK3CA , and KRAS genes play major roles in EGFR pathway, and accommodate activating mutations that predict response to many...
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MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge
Messenger RNA (mRNA) has an essential role in the protein production process. Predicting mRNA expression levels accurately is crucial for...
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Sr65: a widely effective gene for stem rust resistance in wheat
Key messageSr65 in chromosome 1A of Indian wheat landrace Hango-2 is a potentially useful all-stage resistance gene that currently protects wheat...
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The Goldfish Genome and Its Utility for Understanding Gene Regulation and Vertebrate Body Morphology
Goldfish, widely viewed as an ornamental fish, is a member of Cyprinidae family and has a very long history in research for both genetics and...
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Approaches to Marker Gene Identification from Single-Cell RNA-Sequencing Data
The advent of next-generation sequencing techniques, such as single-cell RNA-sequencing (scRNA-seq), has drastically increased the amount of data...