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OGRE: calculate, visualize, and analyze overlap between genomic input regions and public annotations
BackgroundModern genome sequencing leads to an ever-growing collection of genomic annotations. Combining these elements with a set of input regions...
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Methylation of Regulatory Regions of DNA Repair Genes in Carotid Atherosclerosis
AbstractThe status of DNA methylation in the human genome changes during the pathogenesis of common diseases and acts as a predictor of life...
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Cumulative effects of weakly repressive regulatory regions in the 3’ UTR maintain PD-1 expression homeostasis in mammals
PD-1 has become a common target for cancer treatment. However, the molecular regulation of PD-1 expression homeostasis remains unclear. Here we...
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Genomic regions, candidate genes, and pleiotropic variants associated with physiological and anatomical indicators of heat stress response in lactating sows
BackgroundHeat stress (HS) poses significant threats to the sustainability of livestock production. Genetically improving heat tolerance could...
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Genome-wide association study unravels genomic regions associated with chlorophyll fluorescence parameters in wheat (Triticum aestivum L.) under different sowing conditions
Key messageGenome-wide association study identified 205 significant marker–trait associations for chlorophyll fluorescence parameters in wheat....
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Deciphering the regulatory syntax of genomic DNA with deep learning
An organism’s genome contains many sequence regions that perform diverse functions. Examples of such regions include genes, promoters, enhancers, and...
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Methods for Functional Characterization of Genetic Polymorphisms of Non-Coding Regulatory Regions of the Human Genome
AbstractCurrently, numerous associations between genetic polymorphisms and various diseases have been characterized through the Genome-Wide...
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Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits
Although the genetic correlations between complex traits have been estimated for more than a century, only recently we have started to map and...
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Fishing for Developmental Regulatory Regions: Zebrafish Tissue-Specific ATAC-seq
Interactions between transcription factors and regulatory DNA can be described by gene regulatory networks. These networks provide a systems-level...
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Boosting tissue-specific prediction of active cis-regulatory regions through deep learning and Bayesian optimization techniques
BackgroundCis-regulatory regions (CRRs) are non-coding regions of the DNA that fine control the spatio-temporal pattern of transcription; they are...
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Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes
Complex gene regulatory mechanisms underlie differentiation and reprogramming. Contemporary single-cell lineage-tracing (scLT) methods use expressed,...
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Genome wide association analysis of root hair traits in rice reveals novel genomic regions controlling epidermal cell differentiation
BackgroundGenome wide association (GWA) studies demonstrate linkages between genetic variants and traits of interest. Here, we tested associations...
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In Embryo Gene Reporter Assays for Evaluation of Cis-Regulatory Regions
Gene expression reporter assays measure the relevance of cis-regulatory elementsCis-regulatory elements and DNA-binding proteins in modulating...
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Genetic impacts on DNA methylation help elucidate regulatory genomic processes
BackgroundPinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk.
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Combined linkage analysis and association map** identifies genomic regions associated with yield-related and drought-tolerance traits in wheat (Triticum aestivum L.)
Key messageCombined linkage analysis and association map** identified genomic regions associated with yield and drought tolerance, providing...
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Combined strategy employing MutMap and RNA-seq reveals genomic regions and genes associated with complete panicle exsertion in rice
Complete panicle exsertion (CPE) in rice is an important determinant of yield and a desirable trait in breeding. However, the genetic basis of CPE in...
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Combined population transcriptomic and genomic analysis reveals cis-regulatory differentiation of non-coding RNAs in maize
Key messageLong intergenic non-coding RNA (lincRNA), cis -acting expression quantitative trait locus ( cis -eQTL), maize, regulatory evolution.
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The genomic regions and candidate genes associated with drought tolerance and yield-related traits in foxtail millet: an integrative meta-analysis approach
Drought stress is one of the most significant limiting factors limiting crop productions. Foxtail millet ( Setaria italica ) is among the most...
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Identification of Genomic Regions for Deep-Water Resistance in Rice for Efficient Weed Control with Reduced Herbicide Use
Deep-water (DW) management in rice fields is a promising technique for efficient control of paddy weeds with reduced herbicide use. Maintaining a...
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Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization
BackgroundAs genomic studies continue to implicate non-coding sequences in disease, testing the roles of these variants requires insights into the...
