Tài liệu miễn phí Sinh học
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Single-cell ATAC-seq signal extraction and enhancement with SCATE
Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology for analyzing genome-wide regulatory landscapes in single cells. Single-cell ATAC-seq data are sparse and noisy, and analyzing such data is challenging.
4/6/2023 6:17:29 AM +00:00
An evolutionary driver of interspersed segmental duplications in primates
The complex interspersed pattern of segmental duplications in humans is responsible for rearrangements associated with neurodevelopmental disease, including the emergence of novel genes important in human brain evolution.
4/6/2023 6:17:20 AM +00:00
HBA-DEALS: Accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis
We present Hierarchical Bayesian Analysis of Differential Expression and ALternative Splicing (HBA-DEALS), which simultaneously characterizes differential expression and splicing in cohorts. HBA-DEALS attains state of the art or better performance for both expression and splicing and allows genes to be characterized as having differential gene expression, differential alternative splicing, both, or neither.
4/6/2023 6:17:13 AM +00:00
Sierra: Discovery of differential transcript usage from polyA-captured single-cell RNA-seq data
High-throughput single-cell RNA-seq (scRNA-seq) is a powerful tool for studying gene expression in single cells. Most current scRNA-seq bioinformatics tools focus on analysing overall expression levels, largely ignoring alternative mRNA isoform expression. We present a computational pipeline, Sierra, that readily detects differential transcript usage from data generated by commonly used polyA-captured scRNA-seq technology.
4/6/2023 6:17:03 AM +00:00
The regulatory landscape of early maize inflorescence development
The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments.
4/6/2023 6:16:53 AM +00:00
Cell type-specific genome scans of DNA methylation divergence indicate an important role for transposable elements
In population genomics, genetic diversity measures play an important role in genome scans for divergent sites. In population epigenomics, comparable tools are rare although the epigenome can vary at several levels of organization.
4/6/2023 6:16:44 AM +00:00
Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III
The relationship between transcription and the 3D chromatin structure is debated. Multiple studies have shown that transcription affects global Cohesin binding and 3D genome structures. However, several other studies have indicated that inhibited transcription does not alter chromatin conformations.
4/6/2023 6:16:31 AM +00:00
Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity
Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for large metagenomic data sets that exploits the sparsity of DNA assembly graphs to efficiently extract subgraphs surrounding an inferred genome.
4/6/2023 6:16:23 AM +00:00
Identification of cell type-specific methylation signals in bulk whole genome bisulfite sequencing data
The traditional approach to studying the epigenetic mechanism CpG methylation in tissue samples is to identify regions of concordant differential methylation spanning multiple CpG sites (differentially methylated regions).
4/6/2023 6:16:15 AM +00:00
Single-cell transcriptome and antigenimmunoglobin analysis reveals the diversity of B cells in non-small cell lung cancer
Malignant transformation and progression of cancer are driven by the coevolution of cancer cells and their dysregulated tumor microenvironment (TME). Recent studies on immunotherapy demonstrate the efficacy in reverting the anti-tumoral function of T cells, highlighting the therapeutic potential in targeting certain cell types in TME. However, the functions of other immune cell types remain largely unexplored.
4/6/2023 6:16:04 AM +00:00
3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize
Maize ears and tassels are two separate types of inflorescence which are initiated by similar developmental processes but gradually develop distinct architectures. However, coordinated trans and cis regulation of differentially expressed genes determining ear and tassel architecture within the 3D genome context is largely unknown.
4/6/2023 6:15:53 AM +00:00
Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis
Stable gene repression is essential for normal growth and development. Polycomb repressive complexes 1 and 2 (PRC1&2) are involved in this process by establishing monoubiquitination of histone 2A (H2Aub1) and subsequent trimethylation of lysine 27 of histone 3 (H3K27me3).
4/6/2023 6:15:42 AM +00:00
3DeFDR: Statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data
An important unanswered question in chromatin biology is the extent to which long-range looping interactions change across developmental models, genetic perturbations, drug treatments, and disease states. Computational tools for rigorous assessment of cell type-specific loops across multiple biological conditions are needed.
4/6/2023 6:15:30 AM +00:00
Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life
Repeat-induced point (RIP) mutation in Neurospora crassa degrades transposable elements by targeting repeats with C→T mutations. Whether RIP affects core genomic sequence in important ways is unknown.
4/6/2023 6:15:24 AM +00:00
Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs
Mapping of allele-specific DNA methylation (ASM) can be a post-GWAS strategy for localizing regulatory sequence polymorphisms (rSNPs). The advantages of this approach, and the mechanisms underlying ASM in normal and neoplastic cells, remain to be clarified.
4/6/2023 6:15:13 AM +00:00
Analysis of endothelial-to-haematopoietic transition at the single cell level identifies cell cycle regulation as a driver of differentiation
Haematopoietic stem cells (HSCs) first arise during development in the aorta-gonad-mesonephros (AGM) region of the embryo from a population of haemogenic endothelial cells which undergo endothelial-to-haematopoietic transition (EHT). Despite the progress achieved in recent years, the molecular mechanisms driving EHT are still poorly understood, especially in human where the AGM region is not easily accessible.
4/6/2023 6:15:05 AM +00:00
Enhanced Integrated Gradients: Improving interpretability of deep learning models using splicing codes as a case study
Despite the success and fast adaptation of deep learning models in biomedical domains, their lack of interpretability remains an issue. Here, we introduce Enhanced Integrated Gradients (EIG), a method to identify significant features associated with a specific prediction task. Using RNA splicing prediction as well as digit classification as case studies, we demonstrate that EIG improves upon the original Integrated Gradients method and produces sets of informative features.
4/6/2023 6:14:58 AM +00:00
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
An important challenge in pre-processing data from droplet-based single-cell RNA sequencing protocols is distinguishing barcodes associated with real cells from those binding background reads. Existing methods test barcodes individually and consequently do not leverage the strong cell-to-cell correlation present in most datasets.
4/6/2023 6:14:50 AM +00:00
Analysis of transcript-deleterious variants in Mendelian disorders: Implications for RNAbased diagnostics
At least 50% of patients with suspected Mendelian disorders remain undiagnosed after whole-exome sequencing (WES), and the extent to which noncoding variants that are not captured by WES contribute to this fraction is unclear. Whole transcriptome sequencing is a promising supplement to WES, although empirical data on the contribution of RNA analysis to the diagnosis of Mendelian diseases on a large scale are scarce.
4/6/2023 6:14:39 AM +00:00
Dynamic rewiring of the human interactome by interferon signaling
The type I interferon (IFN) response is an ancient pathway that protects cells against viral pathogens by inducing the transcription of hundreds of IFNstimulated genes. Comprehensive catalogs of IFN-stimulated genes have been established across species and cell types by transcriptomic and biochemical approaches, but their antiviral mechanisms remain incompletely characterized.
4/6/2023 6:14:28 AM +00:00
Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping
To investigate the epigenetic and transcriptional mechanisms of coronary artery disease (CAD) risk, as well as the functional regulation of chromatin structure and function, we create a catalog of genetic variants associated with three stages of transcriptional cis-regulation in primary human coronary artery vascular smooth muscle cells (HCASMCs).
4/6/2023 6:14:18 AM +00:00
Systematic assessment of tissue dissociation and storage biases in singlecell and single-nucleus RNA-seq workflows
Single-cell RNA sequencing has been widely adopted to estimate the cellular composition of heterogeneous tissues and obtain transcriptional profiles of individual cells. Multiple approaches for optimal sample dissociation and storage of single cells have been proposed as have single-nuclei profiling methods.
4/6/2023 6:14:11 AM +00:00
Assembly and annotation of an Ashkenazi human reference genome
Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very small sample of the human population.
4/6/2023 6:14:04 AM +00:00
MAUDE: Inferring expression changes in sorting-based CRISPR screens
Improved methods are needed to model CRISPR screen data for interrogation of genetic elements that alter reporter gene expression readout. We create MAUDE (Mean Alterations Using Discrete Expression) for quantifying the impact of guide RNAs on a target gene’s expression in a pooled, sorting-based expression screen. MAUDE quantifies guide-level effects by modeling the distribution of cells across sorting expression bins.
4/6/2023 6:13:52 AM +00:00
Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing
Investigating genome evolution in response to therapy is difficult in human tissue samples. To address this challenge, we develop an unbiased wholegenome plasma DNA sequencing approach that concurrently measures genomic copy number and exome mutations from archival cryostored plasma samples.
4/6/2023 6:13:41 AM +00:00
CICERO: A versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data
To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate ranking. CICERO outperforms commonly used methods, achieving a 95% detection rate for 184 independently validated driver fusions including internal tandem duplications and other noncanonical events in 170 pediatric cancer transcriptomes.
4/6/2023 6:13:34 AM +00:00
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations
Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been carried out.
4/6/2023 6:13:23 AM +00:00
InstaGRAAL: Chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder
Continuous developments in DNA sequencing technologies aim at alleviating the technical challenges that limit the ability to assemble sequence data into full-length chromosomes. Conventional assembly programs and pipelines often encounter difficulties to close gaps in draft genome assemblies introduced by regions enriched in repeated elements.
4/6/2023 6:13:15 AM +00:00
Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae
The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyces cerevisiae, a preinitiation complex (PIC) comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs.
4/6/2023 6:13:07 AM +00:00
SURF: Integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins
Advances in high-throughput profiling of RNA-binding proteins (RBPs) have resulted in CLIP-seq datasets coupled with transcriptome profiling by RNA-seq. However, analysis methods that integrate both types of data are lacking.
4/6/2023 6:12:59 AM +00:00