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GenArk: towards a million UCSC genome browsers
Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome...
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Navigation and Use of Custom Tracks within the Axolotl Genome Browser
The availability of the chromosome-scale axolotl genome sequences has made it possible to explore genome evolution, perform cross-species...
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JBrowse 2: a modular genome browser with views of synteny and structural variation
We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary...
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Along the Bos taurus genome, uncover candidate imprinting control regions
BackgroundIn mammals, Imprinting Control Regions (ICRs) regulate a subset of genes in a parent-of-origin-specific manner. In both human and mouse,...
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Finding and Verifying Enhancers for Endothelial-Expressed Genes
Identification and analysis of enhancers for endothelial-expressed genes can provide crucial information regarding their upstream transcriptional...
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Galbase: a comprehensive repository for integrating chicken multi-omics data
BackgroundMulti-omics data can provide a stereoscopic view to explore potential causal variations and genes, as well as underlying genetic mechanisms...
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Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks
BackgroundGenome browsers are widely used for locating interesting genomic regions, but their interactive use is obviously limited to inspecting...
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Molecular characterization of de novo ring chromosome 21 in a child with seizures, growth retardation, and multiple congenital anomalies
The ring chromosome 21[r(21)] syndrome is a rare disorder, and mainly occurs as a de novo event. However, a wide variation of the phenotype has been...
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Helicobacter pylori Infection Mediates Inflammation and Tumorigenesis-Associated Genes Through miR-155-5p: An Integrative Omics and Bioinformatics-Based Investigation
Helicobacter pylori ( H. pylori ) is a major human pathogenic bacterium that survives in the gastric mucosa. The aim of this study is to evaluate the...
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Cistrome Data Browser and Toolkit: analyzing human and mouse genomic data using compendia of ChIP-seq and chromatin accessibility data
The Cistrome Data Browser (DB) at the website (cistrome.org/db) provides about 56,000 published human and mouse ChIP-seq, DNase-seq, and ATAC-seq...
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Genomic resources for rhesus macaques (Macaca mulatta)
Rhesus macaques ( Macaca mulatta ) are among the most extensively studied of nonhuman primates. This species has been the subject of many...
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GENCODE Annotation for the Human and Mouse Genome: A User Perspective
The GENCODE project provides comprehensive annotation of the functional elements in human and mouse genomes with high accuracy. The annotations are...
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A novel transcript variant of human G-protein coupled estrogen receptor
The G-protein coupled estrogen receptor ( GPER ) mediates short-term non-genomic effects of estrogen in diverse cell types and tissues. According to...
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Integrative multiomics and weighted network approach reveals the prognostic role of RPS7 in lung squamous cell carcinoma pathogenesis
Lung cancer is one of the most commonly occurring malignant cancers with the highest rate of mortality globally. Difference between lung squamous...
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CRISPR-Cas9-Mediated Bioluminescent Tagging of Endogenous Proteins by Fluorescent Protein-Assisted Cell Sorting
Oncogenic fusion genes are attractive therapeutic targets because of their tumor-specific expression and central “driver” roles in various human...
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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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RetroSeeker reveals the characteristics, expression, and evolution of a large set of novel retrotransposons
Retrotransposons are highly prevalent in most animals and account for more than 35% of the human genome. However, the prevalence, biogenesis...
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Determining the Compaction State of Genes Using DNA FISH
DNA fluorescence in situ hybridization (FISH) enables the visualization of chromatin architecture and the interactions between genomic loci at a...
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Purification of Circular RNAs Using Poly(A) Tailing Followed by RNase R Digestion
Thousands of eukaryotic protein-coding genes can be alternatively spliced to yield linear mRNAs and circular RNAs (circRNAs). Some circRNAs...