Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis
BMC » Genome Biology
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5d ago
Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants ..read more
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Genomic hallmarks and therapeutic implications of G0 cell cycle arrest in cancer
BMC » Genome Biology
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5d ago
Therapy resistance in cancer is often driven by a subpopulation of cells that are temporarily arrested in a non-proliferative G0 state, which is difficult to capture and whose mutational drivers remain largely ..read more
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Inferring cell-type-specific causal gene regulatory networks during human neurogenesis
BMC » Genome Biology
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5d ago
Genetic variation influences both chromatin accessibility, assessed in chromatin accessibility quantitative trait loci (caQTL) studies, and gene expression, assessed in expression QTL (eQTL) studies. Genetic v ..read more
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Pervasive tandem duplications and convergent evolution shape coral genomes
BMC » Genome Biology
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5d ago
Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central ..read more
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Mutscan—a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data
BMC » Genome Biology
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5d ago
Multiplexed assays of variant effect (MAVE) experimentally measure the effect of large numbers of sequence variants by selective enrichment of sequences with desirable properties followed by quantification by ..read more
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A survey of mapping algorithms in the long-reads era
BMC » Genome Biology
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5d ago
It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the seed-and-extend fra ..read more
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Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans
BMC » Genome Biology
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2w ago
The variation in the rate at which humans age may be rooted in early events acting through the genomic regions that are influenced by such events and subsequently are related to health phenotypes in later life ..read more
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Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability
BMC » Genome Biology
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2w ago
Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect importa ..read more
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Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications
BMC » Genome Biology
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2w ago
Predicting the impact of coding and noncoding variants on splicing is challenging, particularly in non-canonical splice sites, leading to missed diagnoses in patients. Existing splice prediction tools are comp ..read more
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RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches
BMC » Genome Biology
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2w ago
We present RabbitTClust, a fast and memory-efficient genome clustering tool based on sketch-based distance estimation. Our approach enables efficient processing of large-scale datasets by combining dimensional ..read more
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