Tài liệu miễn phí Sinh học
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A benchmark of batch-effect correction methods for single-cell RNA sequencing data
Large-scale single-cell transcriptomic datasets generated using different technologies contain batchspecific systematic variations that present a challenge to batch-effect removal and data integration. With continued growth expected in scRNA-seq data, achieving effective batch integration with available computational resources is crucial.
4/6/2023 5:58:49 AM +00:00
Compacting a synthetic yeast chromosome arm
Redundancy is a common feature of genomes, presumably to ensure robust growth under different and changing conditions. Genome compaction, removing sequences nonessential for given conditions, provides a novel way to understand the core principles of life.
4/6/2023 5:58:41 AM +00:00
The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication
As a perennial crop, oil-Camellia possesses a long domestication history and produces high-quality seed oil that is beneficial to human health. Camellia oleifera Abel. is a sister species to the tea plant, which is extensively cultivated for edible oil production.
4/6/2023 5:58:30 AM +00:00
SWISS: Multiplexed orthogonal genome editing in plants with a Cas9 nickase and engineered CRISPR RNA scaffolds
We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deaminase and adenosine deaminase to Cas9 nickase target sites to generate multiplexed base editing.
4/6/2023 5:58:19 AM +00:00
Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer
Muscle-invasive bladder cancers are characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival.
4/6/2023 5:58:09 AM +00:00
Knockout of circRNAs by base editing backsplice sites of circularized exons
Many circular RNAs (circRNAs) are produced from back-splicing of exons of precursor mRNAs and are generally co-expressed with cognate linear RNAs. Methods for circRNA-specific knockout are lacking, largely due to sequence overlaps between forms. Here, we use base editors (BEs) for circRNA depletion.
4/6/2023 5:58:00 AM +00:00
SquiggleNet: Real-time, direct classification of nanopore signals
We present SquiggleNet, the first deep-learning model that can classify nanopore reads directly from their electrical signals. SquiggleNet operates faster than DNA passes through the pore, allowing real-time classification and read ejection. Using 1 s of sequencing data, the classifier achieves significantly higher accuracy than base calling followed by sequence alignment.
4/6/2023 5:57:52 AM +00:00
SpatialDWLS: Accurate deconvolution of spatial transcriptomic data
Recent development of spatial transcriptomic technologies has made it possible to characterize cellular heterogeneity with spatial information. However, the technology often does not have sufficient resolution to distinguish neighboring cell types.
4/6/2023 5:57:44 AM +00:00
Role of epigenetics in unicellular to multicellular transition in Dictyostelium
The evolution of multicellularity is a critical event that remains incompletely understood. We use the social amoeba, Dictyostelium discoideum, one of the rare organisms that readily transits back and forth between both unicellular and multicellular stages, to examine the role of epigenetics in regulating multicellularity.
4/6/2023 5:57:35 AM +00:00
Embryo CHH hypermethylation is mediated by RdDM and is autonomously directed in Brassica rapa
RNA-directed DNA methylation (RdDM) initiates cytosine methylation in all contexts and maintains asymmetric CHH methylation. Mature plant embryos show one of the highest levels of CHH methylation, and it has been suggested that RdDM is responsible for this hypermethylation.
4/6/2023 5:57:24 AM +00:00
A generalization of t-SNE and UMAP to single-cell multimodal omics
Emerging single-cell technologies profile multiple types of molecules within individual cells. A fundamental step in the analysis of the produced high-dimensional data is their visualization using dimensionality reduction techniques such as t-SNE and UMAP.
4/6/2023 5:57:17 AM +00:00
MARS: Leveraging allelic heterogeneity to increase power of association testing
In standard genome-wide association studies (GWAS), the standard association test is underpowered to detect associations between loci with multiple causal variants with small effect sizes.
4/6/2023 5:57:10 AM +00:00
Ten-eleven translocation protein 1 modulates medulloblastoma progression
Medulloblastoma (MB) is the most common malignant pediatric brain tumor that originates in the cerebellum and brainstem. Frequent somatic mutations and deregulated expression of epigenetic regulators in MB highlight the substantial role of epigenetic alterations.
4/6/2023 5:57:01 AM +00:00
Cotton pan-genome retrieves the lost sequences and genes during domestication and selection
Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components.
4/6/2023 5:56:52 AM +00:00
Intergenic RNA mainly derives from nascent transcripts of known genes
Eukaryotic genomes undergo pervasive transcription, leading to the production of many types of stable and unstable RNAs. Transcription is not restricted to regions with annotated gene features but includes almost any genomic context. Currently, the source and function of most RNAs originating from intergenic regions in the human genome remain unclear.
4/6/2023 5:56:41 AM +00:00
Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana
How species can adapt to abrupt environmental changes, particularly in the absence of standing genetic variation, is poorly understood and a pressing question in the face of ongoing climate change.
4/6/2023 5:56:30 AM +00:00
Genetic impacts on DNA methylation: Research findings and future perspectives
Multiple recent studies highlight that genetic variants can have strong impacts on a significant proportion of the human DNA methylome. Methylation quantitative trait loci, or meQTLs, allow for the exploration of biological mechanisms that underlie complex human phenotypes, with potential insights for human disease onset and progression.
4/6/2023 5:56:22 AM +00:00
Promoter G-quadruplex folding precedes transcription and is controlled by chromatin
Four-stranded G-quadruplexes (G4s) are DNA secondary structures in the human genome that are primarily found in active promoters associated with elevated transcription. Here, we explore the relationship between the folding of promoter G4s, transcription and chromatin state.
4/6/2023 5:56:15 AM +00:00
Drosophila primary microRNA-8 encodes a microRNA-encoded peptide acting in parallel of miR-8
Recent genome-wide studies of many species reveal the existence of a myriad of RNAs differing in size, coding potential and function. Among these are the long non-coding RNAs, some of them producing functional small peptides via the translation of short ORFs.
4/6/2023 5:56:04 AM +00:00
Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures
The 3D organization of the chromatin fiber in cell nuclei plays a key role in the regulation of gene expression. Genome-wide techniques to score DNADNA contacts, such as Hi-C, reveal the partitioning of chromosomes into epigenetically defined active and repressed compartments and smaller “topologically associated” domains.
4/6/2023 5:55:56 AM +00:00
PseudotimeDE: Inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data
To investigate molecular mechanisms underlying cell state changes, a crucial analysis is to identify differentially expressed (DE) genes along the pseudotime inferred from single-cell RNA-sequencing data. However, existing methods do not account for pseudotime inference uncertainty, and they have either ill-posed p-values or restrictive models.
4/6/2023 5:55:41 AM +00:00
HDAC4 degradation during senescence unleashes an epigenetic program driven by AP-1/p300 at selected enhancers and super-enhancers
Cellular senescence is a permanent state of replicative arrest defined by a specific pattern of gene expression. The epigenome in senescent cells is sculptured in order to sustain the new transcriptional requirements, particularly at enhancers and super-enhancers.
4/6/2023 5:55:32 AM +00:00
Functional mapping of androgen receptor enhancer activity
Androgen receptor (AR) is critical to the initiation, growth, and progression of prostate cancer. Once activated, the AR binds to cis-regulatory enhancer elements on DNA that drive gene expression. Yet, there are 10–100× more binding sites than differentially expressed genes.
4/6/2023 5:55:25 AM +00:00
Best practices on the differential expression analysis of multi-species RNA-seq
Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics.
4/6/2023 5:55:12 AM +00:00
Complete vertebrate mitogenomes reveal widespread repeats and gene duplications
Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.
4/6/2023 5:55:03 AM +00:00
Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits
DNA methylation dynamics in the brain are associated with normal development and neuropsychiatric disease and differ across functionally distinct brain regions. Previous studies of genome-wide methylation differences among human brain regions focus on limited numbers of individuals and one to two brain regions.
4/6/2023 5:54:54 AM +00:00
The impact of cell type and context-dependent regulatory variants on human immune traits
The vast majority of trait-associated variants identified using genome-wide association studies (GWAS) are noncoding, and therefore assumed to impact gene regulation. However, the majority of trait-associated loci are unexplained by regulatory quantitative trait loci (QTLs).
4/6/2023 5:54:46 AM +00:00
PD-L1 lncRNA splice isoform promotes lung adenocarcinoma progression via enhancing c-Myc activity
Although using a blockade of programmed death-ligand 1 (PD-L1) to enhance T cell immune responses shows great promise in tumor immunotherapy, the immune-checkpoint inhibition strategy is limited for patients with solid tumors.
4/6/2023 5:54:36 AM +00:00
Determination of complete chromosomal haplotypes by bulk DNA sequencing
Haplotype phase represents the collective genetic variation between homologous chromosomes and is an essential feature of non-haploid genomes. Here we describe a computational strategy to reliably determine complete whole-chromosome haplotypes using a combination of bulk long-range sequencing and Hi-C sequencing.
4/6/2023 5:54:25 AM +00:00
Personalized genome structure via single gamete sequencing
Genetic maps have been fundamental to building our understanding of disease genetics and evolutionary processes. The gametes of an individual contain all of the information required to perform a de novo chromosome-scale assembly of an individual’s genome, which historically has been performed with populations and pedigrees.
4/6/2023 5:54:18 AM +00:00