Tài liệu miễn phí Sinh học
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Alignment and mapping methodology influence transcript abundance estimation
The accuracy of transcript quantification using RNA-seq data depends on many factors, such as the choice of alignment or mapping method and the quantification model being adopted. While the choice of quantification model has been shown to be important, considerably less attention has been given to comparing the effect of various read alignment approaches on quantification accuracy.
4/6/2023 5:38:55 AM +00:00
A novel antiviral lncRNA, EDAL, shields a T309 O-GlcNAcylation site to promote EZH2 lysosomal degradation
The central nervous system (CNS) is vulnerable to viral infection, yet few host factors in the CNS are known to defend against invasion by neurotropic viruses. Long noncoding RNAs (lncRNAs) have been revealed to play critical roles in a wide variety of biological processes and are highly abundant in the mammalian brain, but their roles in defending against invasion of pathogens into the CNS remain unclear.
4/6/2023 5:38:44 AM +00:00
Variation around the dominant viral genome sequence contributes to viral load and outcome in patients with Ebola virus disease
Viral load is a major contributor to outcome in patients with Ebola virus disease (EVD), with high values leading to a fatal outcome. Evidence from the 2013–2016 Ebola virus (EBOV) outbreak indicated that different genotypes of the virus can have different phenotypes in patients.
4/6/2023 5:38:36 AM +00:00
CSS: Cluster similarity spectrum integration of single-cell genomics data
It is a major challenge to integrate single-cell sequencing data across experiments, conditions, batches, time points, and other technical considerations. New computational methods are required that can integrate samples while simultaneously preserving biological information.
4/6/2023 5:38:28 AM +00:00
Fine-tuning sugar content in strawberry
Fine-tuning quantitative traits for continuous subtle phenotypes is highly advantageous. We engineer the highly conserved upstream open reading frame (uORF) of FvebZIPs1.1 in strawberry (Fragaria vesca), using base editor A3A-PBE. Seven novel alleles are generated.
4/6/2023 5:38:20 AM +00:00
Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction
Compared to proteins, glycans, and lipids, much less is known about RNAs on the cell surface. We develop a series of technologies to test for any nuclearencoded RNAs that are stably attached to the cell surface and exposed to the extracellular space, hereafter called membrane-associated extracellular RNAs (maxRNAs).
4/6/2023 5:38:08 AM +00:00
Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs
Quantifying the genetic heterogeneity of a cell population is essential to understanding of biological systems. We develop a universal method to label individual DNA molecules for single-base-resolution haplotype-resolved quantitative characterization of diverse types of rare variants, with frequency as low as 4 × 10−5 , using both short- or long-read sequencing platforms.
4/6/2023 5:37:58 AM +00:00
RNA G-quadruplex structures exist and function in vivo in plants
Guanine-rich sequences are able to form complex RNA structures termed RNA G-quadruplexes in vitro. Because of their high stability, RNA Gquadruplexes are proposed to exist in vivo and are suggested to be associated with important biological relevance.
4/6/2023 5:37:50 AM +00:00
Transcriptional regulatory networks of tumor-associated macrophages that drive malignancy in mesenchymal glioblastoma
Glioblastoma (GBM) is a complex disease with extensive molecular and transcriptional heterogeneity. GBM can be subcategorized into four distinct subtypes; tumors that shift towards the mesenchymal phenotype upon recurrence are generally associated with treatment resistance, unfavorable prognosis, and the infiltration of pro-tumorigenic macrophages.
4/6/2023 5:37:43 AM +00:00
COCOA: Coordinate covariation analysis of epigenetic heterogeneity
A key challenge in epigenetics is to determine the biological significance of epigenetic variation among individuals. We present Coordinate Covariation Analysis (COCOA), a computational framework that uses covariation of epigenetic signals across individuals and a database of region sets to annotate epigenetic heterogeneity.
4/6/2023 5:37:32 AM +00:00
PipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools
Single-cell RNA-sequencing (scRNAseq) and the set of attached analysis methods are evolving fast, with more than 560 software tools available to the community, roughly half of which are dedicated to tasks related to data processing such as clustering, ordering, dimension reduction, or normalization.
4/6/2023 5:37:19 AM +00:00
Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies
Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a novel tool for reference-free assembly evaluation based on efficient k-mer set operations.
4/6/2023 5:37:03 AM +00:00
A systematic evaluation of single-cell RNA-sequencing imputation methods
The rapid development of single-cell RNA-sequencing (scRNA-seq) technologies has led to the emergence of many methods for removing systematic technical noises, including imputation methods, which aim to address the increased sparsity observed in single-cell data.
4/6/2023 5:36:55 AM +00:00
The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication
A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera).
4/6/2023 5:36:44 AM +00:00
Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis
Many computational methods have been developed recently to analyze single-cell RNA-seq (scRNA-seq) data. Several benchmark studies have compared these methods on their ability for dimensionality reduction, clustering, or differential analysis, often relying on default parameters.
4/6/2023 5:36:35 AM +00:00
EPISCORE: Cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data
Cell type heterogeneity presents a challenge to the interpretation of epigenome data, compounded by the difficulty in generating reliable single-cell DNA methylomes for large numbers of cells and samples. We present EPISCORE, a computational algorithm that performs virtual microdissection of bulk tissue DNA methylation data at single cell-type resolution for any solid tissue.
4/6/2023 5:36:28 AM +00:00
Primo: Integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits
To provide a comprehensive mechanistic interpretation of how known trait-associated SNPs affect complex traits, we propose a method, Primo, for integrative analysis of GWAS summary statistics with multiple sets of omics QTL summary statistics from different cellular conditions or studies.
4/6/2023 5:36:16 AM +00:00
DNA polymerase stalling at structured DNA constrains the expansion of short tandem repeats
Short tandem repeats (STRs) contribute significantly to de novo mutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their repetitive sequences induce DNA polymerase slippage and stalling, leading to length and sequence variation.
4/6/2023 5:36:05 AM +00:00
AuthentiCT: A model of ancient DNA damage to estimate the proportion of present-day DNA contamination
Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses.
4/6/2023 5:35:58 AM +00:00
A vast resource of allelic expression data spanning human tissues
Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level.
4/6/2023 5:35:50 AM +00:00
PSCAN: Spatial scan tests guided by protein structures improve complex disease gene discovery and signal variant detection
Germline disease-causing variants are generally more spatially clustered in protein 3-dimensional structures than benign variants. Motivated by this tendency, we develop a fast and powerful protein-structure-based scan (PSCAN) approach for evaluating gene-level associations with complex disease and detecting signal variants.
4/6/2023 5:35:43 AM +00:00
GBAT: A gene-based association test for robust detection of trans-gene regulation
The observation that disease-associated genetic variants typically reside outside of exons has inspired widespread investigation into the genetic basis of transcriptional regulation. While associations between the mRNA abundance of a gene and its proximal SNPs (cis-eQTLs) are now readily identified, identification of high-quality distal associations (trans-eQTLs) has been limited by a heavy multiple testing burden and the proneness to false-positive signals.
4/6/2023 5:35:34 AM +00:00
Methods for copy number aberration detection from single-cell DNA-sequencing data
Copy number aberrations (CNAs), which are pathogenic copy number variations (CNVs), play an important role in the initiation and progression of cancer. Single-cell DNA-sequencing (scDNAseq) technologies produce data that is ideal for inferring CNAs.
4/6/2023 5:35:24 AM +00:00
Integrative analyses of single-cell transcriptome and regulome using MAES TRO
MAESTRO provides functions for preprocessing, alignment, quality control, expression and chromatin accessibility quantification, clustering, differential analysis, and annotation. By modeling gene regulatory potential from chromatin accessibilities at the single-cell level, MAESTRO outperforms the existing methods for integrating the cell clusters between scRNAseq and scATAC-seq.
4/6/2023 5:35:13 AM +00:00
The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
RNA-binding proteins (RBPs) function as master regulators of gene expression. Alterations in RBP expression and function are often observed in cancer and influence critical pathways implicated in tumor initiation and growth. Identification and characterization of oncogenic RBPs and their regulatory networks provide new opportunities for targeted therapy.
4/6/2023 5:35:06 AM +00:00
Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference
DNA methylation is a key epigenetic modification in human development and disease, yet there is limited understanding of its highly coordinated regulation. Here, we identify 818 genes that affect DNA methylation patterns in blood using large-scale population genomics data.
4/6/2023 5:34:48 AM +00:00
Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx
Population structure among study subjects may confound genetic association studies, and lack of proper correction can lead to spurious findings. The Genotype-Tissue Expression (GTEx) project largely contains individuals of European ancestry, but the v8 release also includes up to 15% of individuals of non-European ancestry.
4/6/2023 5:34:41 AM +00:00
A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex
Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present.
4/6/2023 5:34:33 AM +00:00
ContamLD: Estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium
We report a method called ContamLD for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA.
4/6/2023 5:34:24 AM +00:00
Long-read-based human genomic structural variation detection with cuteSV
Long-read sequencing is promising for the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high yields and performance simultaneously due to the complex SV signatures implied by noisy long reads.
4/6/2023 5:34:14 AM +00:00