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Quantifying the proportion of different cell types in the human cortex using DNA methylation profiles
BackgroundDue to interindividual variation in the cellular composition of the human cortex, it is essential that covariates that capture these...
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meth-SemiCancer: a cancer subtype classification framework via semi-supervised learning utilizing DNA methylation profiles
BackgroundIdentification of the cancer subtype plays a crucial role to provide an accurate diagnosis and proper treatment to improve the clinical...
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Inferring gene expression from cell-free DNA fragmentation profiles
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have...
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Inferring Protein-DNA Binding Profiles at Interspersed Repeats Using HiChIP and PAtChER
Alignment of short-read sequencing data to interspersed genomic repeats, such as transposable elements, can be problematic. This is especially true...
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Mitochondrial DNA sequences and transcriptomic profiles for elucidating the genetic underpinnings of cisplatin responsiveness in oral squamous cell carcinoma
ObjectivesFunctional genetic variation plays an important role in predicting patients’ response to chemotherapeutic agents. A growing catalogue of...
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Shifting the pH profiles of Staphylococcus epidermidis lipase (SEL) and Staphylococcus hyicus lipase (SHL) through generating chimeric lipases by DNA shuffling strategy
Enzymes are often required to function in a particular reaction condition by the industrial procedure. In order to identify critical residues...
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High temperature influences DNA methylation and transcriptional profiles in sea urchins (Strongylocentrotus intermedius)
BackgroundDNA methylation plays an important role in life processes by affecting gene expression, but it is still unclear how DNA methylation is...
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Mitochondrial supplementation of Sus scrofa metaphase II oocytes alters DNA methylation and gene expression profiles of blastocysts
BackgroundMitochondrial DNA (mtDNA) copy number in oocytes correlates with oocyte quality and fertilisation outcome. The introduction of additional...
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Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification
Chelex-based DNA extractions are well suited for student DNA barcoding research because they are simple, safe, and inexpensive and can be performed...
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Detection of Latent DNA Using a DNA Binding Dye
Latent DNA can be deposited every time a person holds or touches an item. This “touch DNA” can be crucial evidence if the item is of forensic...
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Different low-nitrogen-stress regimes result in distinct DNA-methylation patterns, metabolic profiles, and morpho-physiological changes in rice
AimsDNA methylation and demethylation are epigenetic responses to abiotic stresses. The aims of this study were to i) identify alterations in the DNA...
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An Algorithm for Pairwise DNA Sequences Alignment
A challenge in data analysis in bioinformatics is to offer integrated and modern access to the progressively increasing volume of data, as well as...
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Dynamic profiles of DNA methylation and the interaction with histone acetylation during fiber cell initiation of Gossypium hirsutum
BackgroundFiber, as the main product of cotton, provides main raw material for the textile industry. Many key factors have been revealed...
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Forensic DNA Investigation
Forensic DNA evidence is assisting in resolving crime and is now commonly used in most countries. It assists in exonerating the innocent,...
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Cybersecurity Across the DNA-Digital Boundary: DNA Samples to Genomic Data
Technological advances in biotechnology, especially next-generation DNA sequencing and direct-to-consumer genoty**, have created exponentially more...
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Exploring TRF2-Dependent DNA Distortion Through Single-DNA Manipulation Studies
TRF2 is a component of shelterin, a telomere-specific protein complex that protects the ends of mammalian chromosomes from DNA damage signaling and...
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Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host
BackgroundProducing animal protein while reducing the animal’s impact on the environment, e.g., through improved feed efficiency and lowered methane...
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Circulating cell-free DNA fragmentation is a stepwise and conserved process linked to apoptosis
BackgroundCirculating cell-free DNA (cfDNA) is a pool of short DNA fragments mainly released from apoptotic hematopoietic cells. Nevertheless, the...
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Single-cell DNA methylation sequencing by combinatorial indexing and enzymatic DNA methylation conversion
BackgroundDNA methylation is a critical molecular mark involved in cellular differentiation and cell-specific processes. Single-cell whole genome DNA...
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DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts
BackgroundDNA methylation is an important epigenetic modification which has numerous roles in modulating genome function. Its levels are spatially...
