Tài liệu miễn phí Sinh học
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Cobolt: Integrative analysis of multimodal single-cell sequencing data
A growing number of single-cell sequencing platforms enable joint profiling of multiple omics from the same cells. We present Cobolt, a novel method that not only allows for analyzing the data from joint-modality platforms, but provides a coherent framework for the integration of multiple datasets measured on different modalities.
4/6/2023 5:29:34 AM +00:00
Programmed genomic instability regulates neural transdifferentiation of human brain microvascular pericytes
Transdifferentiation describes transformation in vivo of specialized cells from one lineage into another. While there is extensive literature on forced induction of lineage reprogramming in vitro, endogenous mechanisms that govern transdifferentiation remain largely unknown.
4/6/2023 5:29:24 AM +00:00
Single-cell characterization of CRISPRmodified transcript isoforms with nanopore sequencing
We developed a single-cell approach to detect CRISPR-modified mRNA transcript structures. This method assesses how genetic variants at splicing sites and splicing factors contribute to alternative mRNA isoforms.
4/6/2023 5:29:13 AM +00:00
Flimma: A federated and privacy-aware tool for differential gene expression analysis
Aggregating transcriptomics data across hospitals can increase sensitivity and robustness of differential expression analyses, yielding deeper clinical insights. As data exchange is often restricted by privacy legislation, meta-analyses are frequently employed to pool local results.
4/6/2023 5:29:01 AM +00:00
Benchmarking UMI-based single-cell RNA-seq preprocessing workflows
Single-cell RNA-sequencing (scRNA-seq) technologies and associated analysis methods have rapidly developed in recent years. This includes preprocessing methods, which assign sequencing reads to genes to create count matrices for downstream analysis.
4/6/2023 5:28:51 AM +00:00
A benchmark of structural variation detection by long reads through a realistic simulated model
Accurate simulations of structural variation distributions and sequencing data are crucial for the development and benchmarking of new tools. We develop Sim-it, a straightforward tool for the simulation of both structural variation and long-read data.
4/6/2023 5:28:41 AM +00:00
Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing
The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods. Here, we use single-molecule nascent RNA sequencing to characterize the various forms of transient RNAs during termination at genome-wide scale in wildtype Arabidopsis and in atxrn3, fpa, and met1 mutants.
4/6/2023 5:28:28 AM +00:00
A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease
Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development
4/6/2023 5:28:19 AM +00:00
Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases
Alternative splicing (AS) is an important aspect of gene regulation. Nevertheless, its role in molecular processes and pathobiology is far from understood. A roadblock is that tools for the functional analysis of AS-set events are lacking.
4/6/2023 5:28:10 AM +00:00
An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes
We have developed an efficient and inexpensive pipeline for streamlining large-scale collection and genome sequencing of bacterial isolates. Evaluation of this method involved a worldwide research collaboration focused on the model organism Salmonella enterica, the 10KSG consortium.
4/6/2023 5:28:02 AM +00:00
ATRX regulates glial identity and the tumor microenvironment in IDH-mutant glioma
Recent single-cell transcriptomic studies report that IDH-mutant gliomas share a common hierarchy of cellular phenotypes, independent of genetic subtype. However, the genetic differences between IDH-mutant glioma subtypes are prognostic, predictive of response to chemotherapy, and correlate with distinct tumor microenvironments.
4/6/2023 5:27:46 AM +00:00
An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila
Enhancers are non-coding regions of the genome that control the activity of target genes. Recent efforts to identify active enhancers experimentally and in silico have proven effective. While these tools can predict the locations of enhancers with a high degree of accuracy, the mechanisms underpinning the activity of enhancers are often unclear.
4/6/2023 5:27:38 AM +00:00
A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit
Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh. We generate RNA-seq data from the developing fruits of 206 pear cultivars with a wide range of stone cell contents and use a systems genetics approach to integrate co-expression networks and expression quantitative trait loci (eQTLs) to characterize the regulatory mechanisms controlling lignocellulose formation in the stone cells of pear fruits.
4/6/2023 5:27:30 AM +00:00
NMD abnormalities during brain development in the Fmr1-knockout mouse model of fragile X syndrome
Fragile X syndrome (FXS) is an intellectual disability attributable to loss of fragile X protein (FMRP). We previously demonstrated that FMRP binds mRNAs targeted for nonsense-mediated mRNA decay (NMD) and that FMRP loss results in hyperactivated NMD and inhibition of neuronal differentiation in human stem cells.
4/6/2023 5:27:22 AM +00:00
Accurate long-read de novo assembly evaluation with Inspector
Long-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors. We present Inspector, a reference-free long-read de novo assembly evaluator which faithfully reports types of errors and their precise locations
4/6/2023 5:27:10 AM +00:00
Comprehensive characterization of singlecell full-length isoforms in human and mouse with long-read sequencing
A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in single cells.
4/6/2023 5:26:59 AM +00:00
Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity
Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassava is a staple crop in Africa and other tropical regions and has a highly heterozygous genome.
4/6/2023 5:26:42 AM +00:00
TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations
Topologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs has been shown to depend on cohesin in a loop-extrusion mechanism.
4/6/2023 5:26:30 AM +00:00
Sex without crossing over in the yeast Saccharomycodes ludwigii
Intermixing of genomes through meiotic reassortment and recombination of homologous chromosomes is a unifying theme of sexual reproduction in eukaryotic organisms and is considered crucial for their adaptive evolution.
4/6/2023 5:26:20 AM +00:00
Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations
Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis. Results: Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/B compartments, topologically associated domains (TADs), and widespread chromatin interactions.
4/6/2023 5:26:07 AM +00:00
A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits
Common walnut (Juglans regia L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control of its adaptation and agronomic traits remain largely unexplored.
4/6/2023 5:25:55 AM +00:00
Lamin C is required to establish genome organization after mitosis
The dynamic 3D organization of the genome is central to gene regulation and development. The nuclear lamina influences genome organization through the tethering of lamina-associated domains (LADs) to the nuclear periphery.
4/6/2023 5:25:40 AM +00:00
IRFinder-S: A comprehensive suite to discover and explore intron retention
Accurate quantification and detection of intron retention levels require specialized software. Building on our previous software, we create a suite of tools called IRFinder-S, to analyze and explore intron retention events in multiple samples.
4/6/2023 5:25:33 AM +00:00
Promotech: A general tool for bacterial promoter recognition
Promoters are genomic regions where the transcription machinery binds to initiate the transcription of specific genes. Computational tools for identifying bacterial promoters have been around for decades. However, most of these tools were designed to recognize promoters in one or few bacterial species.
4/6/2023 5:25:26 AM +00:00
Phasebook: Haplotype-aware de novo assembly of diploid genomes from long reads
Haplotype-aware diploid genome assembly is crucial in genomics, precision medicine, and many other disciplines. Long-read sequencing technologies have greatly improved genome assembly. However, current long-read assemblers are either reference based, so introduce biases, or fail to capture the haplotype diversity of diploid genomes.
4/6/2023 5:25:14 AM +00:00
DNA methylation-calling tools for Oxford Nanopore sequencing: A survey and human epigenome-wide evaluation
Nanopore long-read sequencing technology greatly expands the capacity of long-range, single-molecule DNA-modification detection. A growing number of analytical tools have been developed to detect DNA methylation from nanopore sequencing reads.
4/6/2023 5:25:03 AM +00:00
Effects of sequence motifs in the yeast 3′ untranslated region determined from massively parallel assays of random sequences
The 3′ untranslated region (UTR) plays critical roles in determining the level of gene expression through effects on activities such as mRNA stability and translation. Functional elements within this region have largely been identified through analyses of native genes, which contain multiple co-evolved sequence features.
4/6/2023 5:24:52 AM +00:00
A global screening identifies chromatinenriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation
Cellular RNA-binding proteins (RBPs) have multiple roles in posttranscriptional control, and some are shown to bind DNA. However, the global localization and the general chromatin-binding ability of RBPs are not wellcharacterized and remain undefined in hematopoietic cells.
4/6/2023 5:24:41 AM +00:00
Global properties of regulatory sequences are predicted by transcription factor recognition mechanisms
Mammalian genomes contain millions of putative regulatory sequences, which are delineated by binding of multiple transcription factors. The degree to which spacing and orientation constraints among transcription factor binding sites contribute to the recognition and identity of regulatory sequence is an unresolved but important question that impacts our understanding of genome function and evolution.
4/6/2023 5:24:32 AM +00:00
Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation
Alternative cleavage and polyadenylation (APA), an RNA processing event, occurs in over 70% of human protein-coding genes. APA results in mRNA transcripts with distinct 3′ ends. Most APA occurs within 3′ UTRs, which harbor regulatory elements that can impact mRNA stability, translation, and localization.
4/6/2023 5:24:24 AM +00:00