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Integrative analysis of genomic and epigenomic regulation reveals miRNA mediated tumor heterogeneity and immune evasion in lower grade glioma
The expression dysregulation of microRNAs (miRNA) has been widely reported during cancer development, however, the underling mechanism remains...
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tRigon: an R package and Shiny App for integrative (path-)omics data analysis
BackgroundPathomics facilitates automated, reproducible and precise histopathology analysis and morphological phenoty**. Similar to molecular...
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Integrative transcriptome-wide analysis of atopic dermatitis for drug repositioning
Atopic dermatitis (AD) is one of the most common inflammatory skin diseases, which significantly impact the quality of life. Transcriptome-wide...
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TCGAplot: an R package for integrative pan-cancer analysis and visualization of TCGA multi-omics data
BackgroundPan-cancer analysis examines both the commonalities and heterogeneity among genomic and cellular alterations across numerous types of...
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Integrative analysis of green ash phloem transcripts and proteins during an emerald ash borer infestation
BackgroundEmerald ash borer ( Agrilus planipennis ; EAB) is an Asian insect species that has been invasive to North America for 20 years. During this...
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Prioritization of risk genes in colorectal cancer by integrative analysis of multi-omics data and gene networks
Genome-wide association studies (GWASs) have identified over 140 colorectal cancer (CRC)-associated loci; however, target genes at the majority of...
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A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs
A comprehensive and precise definition of the pluripotency gene regulatory network (PGRN) is crucial for clarifying the regulatory mechanisms in...
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RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data
BackgroundMassive amounts of data are produced by combining next-generation sequencing with complex biochemistry techniques to characterize...
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Integrative analysis reveals associations between oral microbiota dysbiosis and host genetic and epigenetic aberrations in oral cavity squamous cell carcinoma
Dysbiosis of the human oral microbiota has been reported to be associated with oral cavity squamous cell carcinoma (OSCC) while the host-microbiota...
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Complex strategies: an integrative analysis of contests in Siamese fighting fish
BackgroundAnimals use contests to attain resources and employ strategic decisions to minimise contest costs. These decisions are defined by...
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Integrative transcriptome analysis uncovers common components containing CPS2 regulated by maize lncRNA GARR2 in gibberellin response
Main conclusionThe combined transcriptome outcome provides an important clue to the regulatory cascade centering on lncRNA GARR2 and CPS2 gene in GA...
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HyperGCN: an effective deep representation learning framework for the integrative analysis of spatial transcriptomics data
BackgroundAdvances of spatial transcriptomics technologies enabled simultaneously profiling gene expression and spatial locations of cells from the...
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The HADDOCK2.4 web server for integrative modeling of biomolecular complexes
Interactions between macromolecules, such as proteins and nucleic acids, are essential for cellular functions. Experimental methods can fail to...
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Genome-wide meta-analysis, functional genomics and integrative analyses implicate new risk genes and therapeutic targets for anxiety disorders
Anxiety disorders are the most prevalent mental disorders. However, the genetic etiology of anxiety disorders remains largely unknown. Here we...
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Dictionary learning for integrative, multimodal and scalable single-cell analysis
Map** single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most...
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Accurate and efficient integrative reference-informed spatial domain detection for spatial transcriptomics
Spatially resolved transcriptomics (SRT) studies are becoming increasingly common and large, offering unprecedented opportunities in map** complex...
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Integrative Learning to Combine Individualized Treatment Rules from Multiple Randomized Trials
Using individualized treatment rules (ITRs) to tailor treatment to individual patient’s characteristics and intermediate responses holds promise to...
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Integrative analysis reveals a lineage-specific circular RNA landscape for adipo-osteogenesis of human mesenchymal stem cells
BackgroundThe balance between osteogenesis and adipogenesis of mesenchymal stem cells (MSCs) is critical to skeletal development and diseases. As a...
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Predicting Papillary Renal Cell Carcinoma Prognosis Using Integrative Analysis of Histopathological Images and Genomic Data
Renal cell carcinoma (RCC) is a common malignant tumor of the adult kidney, with the papillary subtype (pRCC) as the second most frequent. There is a...