Tài liệu miễn phí Sinh học
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SynthEx: A synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling
Changes in the quantity of genetic material, known as somatic copy number alterations (CNAs), can drive tumorigenesis. Many methods exist for assessing CNAs using microarrays, but considerable technical issues limit current CNA calling based upon DNA sequencing. We present SynthEx, a novel tool for detecting CNAs from whole exome and genome sequencing.
4/6/2023 6:57:09 AM +00:00
Are cells from a snowman realistic? Cryopreserved tissues as a source for single-cell RNA-sequencing experiments
A recently published study in Genome Biology shows that cells isolated from cryopreserved tissues are a reliable source of genetic material for single-cell RNA-sequencing experiments.
4/6/2023 6:57:02 AM +00:00
CancerLocator: Non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA
We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously infers the proportions and the tissue-of-origin of tumor-derived cell-free DNA in a blood sample using genome-wide DNA methylation data.
4/6/2023 6:56:55 AM +00:00
Genomic history of the origin and domestication of common bean unveils its closest sister species
Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants.
4/6/2023 6:56:48 AM +00:00
DeepCpG: Accurate prediction of single-cell DNA methylation states using deep learning
Recent technological advances have enabled DNA methylation to be assayed at single-cell resolution. However, current protocols are limited by incomplete CpG coverage and hence methods to predict missing methylation states are critical to enable genome-wide analyses. We report DeepCpG, a computational approach based on deep neural networks to predict methylation states in single cells.
4/6/2023 6:56:41 AM +00:00
CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data
Most existing dimensionality reduction and clustering packages for single-cell RNA-seq (scRNA-seq) data deal with dropouts by heavy modeling and computational machinery. Here, we introduce CIDR (Clustering through Imputation and Dimensionality Reduction), an ultrafast algorithm that uses a novel yet very simple implicit imputation approach to alleviate the impact of dropouts in scRNA-seq data in a principled manner.
4/6/2023 6:56:30 AM +00:00
Dietary restriction protects from ageassociated DNA methylation and induces epigenetic reprogramming of lipid metabolism
Dietary restriction (DR), a reduction in food intake without malnutrition, increases most aspects of health during aging and extends lifespan in diverse species, including rodents. However, the mechanisms by which DR interacts with the aging process to improve health in old age are poorly understood.
4/6/2023 6:56:19 AM +00:00
Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment
Global but predictable changes impact the DNA methylome as we age, acting as a type of molecular clock. This clock can be hastened by conditions that decrease lifespan, raising the question of whether it can also be slowed, for example, by conditions that increase lifespan. Mice are particularly appealing organisms for studies of mammalian aging; however, epigenetic clocks have thus far been formulated only in humans.
4/6/2023 6:56:13 AM +00:00
Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions
Age-associated epigenetic changes are implicated in aging. Notably, age-associated DNA methylation changes comprise a so-called aging “clock”, a robust biomarker of aging. However, while genetic, dietary and drug interventions can extend lifespan, their impact on the epigenome is uncharacterised.
4/6/2023 6:56:04 AM +00:00
IRFinder: Assessing the impact of intron retention on mammalian gene expression
Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle.
4/6/2023 6:55:57 AM +00:00
MeDeCom: Discovery and quantification of latent components of heterogeneous methylomes
It is important for large-scale epigenomic studies to determine and explore the nature of hidden confounding variation, most importantly cell composition. We developed MeDeCom as a novel reference-free computational framework that allows the decomposition of complex DNA methylomes into latent methylation components and their proportions in each sample.
4/6/2023 6:55:50 AM +00:00
Functional implications of Neandertal introgression in modern humans
Admixture between early modern humans and Neandertals approximately 50,000–60,000 years ago has resulted in 1.5–4% Neandertal ancestry in the genomes of present-day non-Africans. Evidence is accumulating that some of these archaic alleles are advantageous for modern humans, while others are deleterious; however, the major mechanism by which these archaic alleles act has not been fully explored.
4/6/2023 6:55:44 AM +00:00
Knocking out consumer concerns and regulator’s rules: Efficient use of CRISPR/Cas ribonucleoprotein complexes for genome editing in cereals
Selection-free genome editing using Cas9 ribonucleoprotein embryo bombardment has been achieved for maize and wheat. This is a breakthrough that should make new breeding technologies more acceptable for worldwide use.
4/6/2023 6:55:37 AM +00:00
Post-transcriptional regulation of fruit ripening and disease resistance in tomato by the vacuolar protease SlVPE3
Proteases represent one of the most abundant classes of enzymes in eukaryotes and are known to play key roles in many biological processes in plants. However, little is known about their functions in fruit ripening and disease resistance, which are unique to flowering plants and required for seed maturation and dispersal.
4/6/2023 6:55:28 AM +00:00
Cepip: Context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes
It remains challenging to predict regulatory variants in particular tissues or cell types due to highly context-specific gene regulation. By connecting large-scale epigenomic profiles to expression quantitative trait loci (eQTLs) in a wide range of human tissues/cell types, we identify critical chromatin features that predict variant regulatory potential.
4/6/2023 6:55:20 AM +00:00
Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes
Hirschsprung disease (HSCR), which is congenital obstruction of the bowel, results from a failure of enteric nervous system (ENS) progenitors to migrate, proliferate, differentiate, or survive within the distal intestine. Previous studies that have searched for genes underlying HSCR have focused on ENS-related pathways and genes not fitting the current knowledge have thus often been ignored.
4/6/2023 6:55:13 AM +00:00
Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome
The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific genetic changes to gene expression, DNA methylation, and histone marks but these investigations have only been carried out in a limited set of samples.
4/6/2023 6:55:03 AM +00:00
Accurate and equitable medical genomic analysis requires an understanding of demography and its influence on sample size and ratio
In a recent study, Petrovski and Goldstein reported that (non-Finnish) Europeans have significantly fewer nonsynonymous singletons in Online Mendelian Inheritance in Man (OMIM) disease genes compared with Africans, Latinos, South Asians, East Asians, and other unassigned non-Europeans.
4/6/2023 6:54:56 AM +00:00
Single-cell transcriptome conservation in cryopreserved cells and tissues
A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains transcripts in viable single cells, allowing one to disconnect time and place of sampling from subsequent processing steps.
4/6/2023 6:54:49 AM +00:00
Mouse genomic screen reveals novel host regulator of metastasis
Tumor cells have to overcome challenges in the host tissue microenvironment to metastasize successfully to distant organs. In a recent Nature study, a genome-wide functional screen demonstrated that deficiency of the sphingosine-1-phoshate (S1P) transporter gene Spns2 in endothelium increased immune-mediated cell killing by T cells and natural killer (NK) cells, thereby suppressing metastatic colonization.
4/6/2023 6:54:43 AM +00:00
DdClone: Joint statistical inference of clonal populations from single cell and bulk tumour sequencing data
Next-generation sequencing (NGS) of bulk tumour tissue can identify constituent cell populations in cancers and measure their abundance. This requires computational deconvolution of allelic counts from somatic mutations, which may be incapable of fully resolving the underlying population structure.
4/6/2023 6:54:35 AM +00:00
EpiG: Statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data
The study of epigenetic heterogeneity at the level of individual cells and in whole populations is the key to understanding cellular differentiation, organismal development, and the evolution of cancer. We develop a statistical method, epiG, to infer and differentiate between different epi-allelic haplotypes, annotated with CpG methylation status and DNA polymorphisms, from whole-genome bisulfite sequencing data, and nucleosome occupancy from NOMe-seq data.
4/6/2023 6:54:27 AM +00:00
Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons
Cotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyploidization and are cultivated worldwide. Although the overall genetic diversity between these two cultivated species has been studied with limited accessions, their population structure and genetic variations remain largely unknown.
4/6/2023 6:54:20 AM +00:00
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most methods of detecting an allelic imbalance assume diploid genomes.
4/6/2023 6:54:08 AM +00:00
Efficient precise knockin with a double cut HDR donor after CRISPR/Cas9-mediated double-stranded DNA cleavage
Precise genome editing via homology-directed repair (HDR) after double-stranded DNA (dsDNA) cleavage facilitates functional genomic research and holds promise for gene therapy. However, HDR efficiency remains low in some cell types, including some of great research and clinical interest, such as human induced pluripotent stem cells (iPSCs).
4/6/2023 6:53:58 AM +00:00
The birth of a human-specific neural gene by incomplete duplication and gene fusion
Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks.
4/6/2023 6:53:51 AM +00:00
RNAs competing for microRNAs mutually influence their fluctuations in a highly non-linear microRNA-dependent manner in single cells
Distinct RNA species may compete for binding to microRNAs (miRNAs). This competition creates an indirect interaction between miRNA targets, which behave as miRNA sponges and eventually influence each other’s expression levels. Theoretical predictions suggest that not only the mean expression levels of targets but also the fluctuations around the means are coupled through miRNAs.
4/6/2023 6:53:44 AM +00:00
Software tools for visualizing Hi-C data
High-throughput assays for measuring the three-dimensional (3D) configuration of DNA have provided unprecedented insights into the relationship between DNA 3D configuration and function. Data interpretation from assays such as ChIA-PET and Hi-C is challenging because the data is large and cannot be easily rendered using standard genome browsers.
4/6/2023 6:53:36 AM +00:00
Human disease genomics: From variants to biology
The central objectives of human genetic research are to identify the sequence variation that plays a causal role in the development of disease, and then to use this information to generate insights into the biology of health and disease that can support clinical translation.
4/6/2023 6:53:30 AM +00:00
RNF40 regulates gene expression in an epigenetic context-dependent manner
Monoubiquitination of H2B (H2Bub1) is a largely enigmatic histone modification that has been linked to transcriptional elongation. Because of this association, it has been commonly assumed that H2Bub1 is an exclusively positively acting histone modification and that increased H2Bub1 occupancy correlates with increased gene expression. In contrast, depletion of the H2B ubiquitin ligases RNF20 or RNF40 alters the expression of only a subset of genes.
4/6/2023 6:53:22 AM +00:00