Genome Biology
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Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains
Genome Biology - Tập 21 - Trang 1-19 - 2020
CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. We carry out an experimental and computational study that exploits the natural genetic variation ac......
methylCC: technology-independent estimation of cell type composition using differentially methylated regions
Genome Biology - Tập 20 - Trang 1-13 - 2019
A major challenge in the analysis of DNA methylation (DNAm) data is variability introduced from intra-sample cellular heterogeneity, such as whole blood which is a convolution of DNAm profiles across a unique cell type. When this source of variability is confounded with an outcome of interest, if unaccounted for, false positives ensue. Current methods to estimate the cell type proportions in whole......
Old soldiers never die ....
Genome Biology - Tập 13 - Trang 1-3 - 2012
An ancestral supersoldier phenotype of Pheidole ants can be recovered when selection for supersoldiers re-emerges, indicating that the developmental potential for caste pathways is retained.
Predicting the sites of metastases
Genome Biology - Tập 6 - Trang 1-4 - 2005
Transplantation of human breast cancer cells into immunodeficient mice together with gene-expression microarray studies has recently identified genes implicated in the tissue tropism of breast-cancer metastasis. Such signatures of site-specific metastatic capabilities might allow the targeting of therapy to likely sites of metastasis.
Author Correction: Towards accurate and reliable resolution of structural variants for clinical diagnosis
Genome Biology - Tập 23 - Trang 1-2 - 2022
An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding
Genome Biology - Tập 22 - Trang 1-25 - 2021
Transcription factor (TF) binding specificity is determined via a complex interplay between the transcription factor’s DNA binding preference and cell type-specific chromatin environments. The chromatin features that correlate with transcription factor binding in a given cell type have been well characterized. For instance, the binding sites for a majority of transcription factors display concurre......
Integrating whole transcriptome sequence data and public databases for analysis of somatic mutations in tumors
Genome Biology - Tập 12 - Trang 1-27 - 2011
RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.)
Genome Biology - Tập 12 - Trang 1-19 - 2011
Whole genome duplication is a common evolutionary event in plants. Bread wheat (Triticum aestivum L.) is a good model to investigate the impact of paleo- and neoduplications on the organization and function of modern plant genomes. We performed an RNA sequencing-based inference of the grain filling gene network in bread wheat and identified a set of 37,695 non-redundant sequence clusters, which is......
Genome-wide mapping of the sixth base
Genome Biology - Tập 12 - Trang 1-3 - 2011
Mapping of 5-hydroxylmethylcytosine in mammalian genomes has unveiled its unique role in the epigenetic regulation of gene expression. See Research article: http://genomebiology.com/2011/12/6/R54
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