Tài liệu miễn phí Sinh học
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Conbase: A software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
Accurate variant calling and genotyping represent major limiting factors for downstream applications of single-cell genomics. Here, we report Conbase for the identification of somatic mutations in single-cell DNA sequencing data.
4/6/2023 10:26:20 PM +00:00
Interactive roles of chromatin regulation and circadian clock function in plants
Circadian rhythms in transcription ultimately result in oscillations of key biological processes. Understanding how transcriptional rhythms are generated in plants provides an opportunity for fine-tuning growth, development, and responses to the environment.
4/6/2023 10:26:09 PM +00:00
BRB-seq: Ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing
Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3′ cDNA libraries for dozens of samples, requiring just 2 hours of hands-on time.
4/6/2023 10:26:03 PM +00:00
Alevin efficiently estimates accurate gene abundances from dscRNA-seq data
We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting.
4/6/2023 10:25:56 PM +00:00
Tandem-genotypes: Robust detection of tandem repeat expansions from long DNA reads
Tandemly repeated DNA is highly mutable and causes at least 31 diseases, but it is hard to detect pathogenic repeat expansions genome-wide. Here, we report robust detection of human repeat expansions from careful alignments of long but error-prone (PacBio and nanopore) reads to a reference genome.
4/6/2023 10:25:49 PM +00:00
TAD fusion score: Discovery and ranking the contribution of deletions to genome structure
Deletions that fuse two adjacent topologically associating domains (TADs) can cause severe developmental disorders. We provide a formal method to quantify deletions based on their potential disruption of the three-dimensional genome structure, denoted as the TAD fusion score.
4/6/2023 10:25:42 PM +00:00
Melissa: Bayesian clustering and imputation of single-cell methylomes
Measurements of single-cell methylation are revolutionizing our understanding of epigenetic control of gene expression, yet the intrinsic data sparsity limits the scope for quantitative analysis of such data.
4/6/2023 10:25:35 PM +00:00
PAGA: Graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
Single-cell RNA-seq quantifies biological heterogeneity across both discrete cell types and continuous cell transitions. Partition-based graph abstraction (PAGA) provides an interpretable graph-like map of the arising data manifold, based on estimating connectivity of manifold partitions (https://github.com/theislab/paga).
4/6/2023 10:25:26 PM +00:00
EmptyDrops: Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
Droplet-based single-cell RNA sequencing protocols have dramatically increased the throughput of single-cell transcriptomics studies. A key computational challenge when processing these data is to distinguish libraries for real cells from empty droplets.
4/6/2023 10:25:19 PM +00:00
Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors
Histone acetylation plays a central role in gene regulation and is sensitive to the levels of metabolic intermediates. However, predicting the impact of metabolic alterations on acetylation in pathological conditions is a significant challenge. Here, we present a genome-scale network model that predicts the impact of nutritional environment and genetic alterations on histone acetylation.
4/6/2023 10:25:12 PM +00:00
Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome
The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.
4/6/2023 10:25:03 PM +00:00
Analysis of error profiles in deep nextgeneration sequencing data
Sequencing errors are key confounding factors for detecting low-frequency genetic variants that are important for cancer molecular diagnosis, treatment, and surveillance using deep next-generation sequencing (NGS). However, there is a lack of comprehensive understanding of errors introduced at various steps of a conventional NGS workflow, such as sample handling, library preparation, PCR enrichment, and sequencing. In this study, we use current NGS technology to systematically investigate these questions.
4/6/2023 10:24:49 PM +00:00
Measuring the reproducibility and quality of Hi-C data
Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to perform and involve multiple complex experimental steps; thus, accurate methods for measuring the quality and reproducibility of Hi-C data are essential to determine whether the output should be used further in a study.
4/6/2023 10:24:40 PM +00:00
Reproducible inference of transcription factor footprints in ATAC-seq and DNaseseq datasets using protocol-specific bias modeling
DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBSs) in regulatory regions through footprinting.
4/6/2023 10:24:33 PM +00:00
MMSplice: Modular modeling improves the predictions of genetic variant effects on splicing
Predicting the effects of genetic variants on splicing is highly relevant for human genetics. We describe the framework MMSplice (modular modeling of splicing) with which we built the winning model of the CAGI5 exon skipping prediction challenge. T
4/6/2023 10:24:26 PM +00:00
Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells
Protein recoding by RNA editing is required for normal health and evolutionary adaptation. However, de novo induction of RNA editing in response to environmental factors is an uncommon phenomenon. While APOBEC3A edits many mRNAs in monocytes and macrophages in response to hypoxia and interferons, the physiological significance of such editing is unclear.
4/6/2023 10:24:19 PM +00:00
Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants
The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention.
4/6/2023 10:24:11 PM +00:00
Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
Human selection has a long history of transforming crop genomes. Peach (Prunus persica) has undergone more than 5000 years of domestication that led to remarkable changes in a series of agronomically important traits, but genetic bases underlying these changes and the effects of artificial selection on genomic diversity are not well understood.
4/6/2023 10:24:04 PM +00:00
Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma
Adenosine-to-inosine (A-to-I) RNA editing is an essential post-transcriptional mechanism mediated by ADAR enzymes that have been recently associated with cancer. Here, we characterize the inosinome signature in normal brain and de novo glioblastoma (GBM) using new metrics that re-stratify GBM patients according to their editing profiles and indicate this post-transcriptional event as a possible molecular mechanism for sexual dimorphism in GBM.
4/6/2023 10:23:55 PM +00:00
Assessing taxonomic metagenome profilers with OPAL
The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenient visualizations.
4/6/2023 10:23:47 PM +00:00
Clonealign: Statistical integration of independent single-cell RNA and DNA sequencing data from human cancers
Measuring gene expression of tumor clones at single-cell resolution links functional consequences to somatic alterations. Without scalable methods to simultaneously assay DNA and RNA from the same single cell, parallel single-cell DNA and RNA measurements from independent cell populations must be mapped for genome-transcriptome association.
4/6/2023 10:23:40 PM +00:00
Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity
Alternative splicing is a key regulatory mechanism in eukaryotic cells and increases the effective number of functionally distinct gene products. Using bulk RNA sequencing, splicing variation has been studied across human tissues and in genetically diverse populations.
4/6/2023 10:23:34 PM +00:00
Identification of transcription factor binding sites using ATAC-seq
Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq.
4/6/2023 10:23:24 PM +00:00
DStruct: Identifying differentially reactive regions from RNA structurome profiling data
RNA biology is revolutionized by recent developments of diverse high-throughput technologies for transcriptomewide profiling of molecular RNA structures. RNA structurome profiling data can be used to identify differentially structured regions between groups of samples.
4/6/2023 10:23:13 PM +00:00
I-Boost: An integrative boosting approach for predicting survival time with multiple genomics platforms
We propose a statistical boosting method, termed I-Boost, to integrate multiple types of high-dimensional genomics data with clinical data for predicting survival time. I-Boost provides substantially higher prediction accuracy than existing methods.
4/6/2023 10:23:06 PM +00:00
CellFishing.jl: An ultrafast and scalable cell search method for single-cell RNA sequencing
Recent technical improvements in single-cell RNA sequencing (scRNA-seq) have enabled massively parallel profiling of transcriptomes, thereby promoting large-scale studies encompassing a wide range of cell types of multicellular organisms.
4/6/2023 10:22:57 PM +00:00
Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates
Recent studies have revealed thousands of A-to-I RNA editing events in primates, but the origination and general functions of these events are not well addressed. Results: Here, we perform a comparative editome study in human and rhesus macaque and uncover a substantial proportion of macaque A-to-I editing sites that are genomically polymorphic in some animals or encoded as noneditable nucleotides in human.
4/6/2023 10:22:50 PM +00:00
Structural rearrangements generate cellspecific, gene-independent CRISPR-Cas9 loss of fitness effects
CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functional consequences of CRISPR-Cas9 gene-editing has not yet been assessed.
4/6/2023 10:22:43 PM +00:00
Modeling double strand break susceptibility to interrogate structural variation in cancer
Structural variants (SVs) are known to play important roles in a variety of cancers, but their origins and functional consequences are still poorly understood. Many SVs are thought to emerge from errors in the repair processes following DNA double strand breaks (DSBs).
4/6/2023 10:22:32 PM +00:00
NCBoost classifies pathogenic non-coding variants in Mendelian diseases through supervised learning on purifying selection signals in humans
State-of-the-art methods assessing pathogenic non-coding variants have mostly been characterized on common disease-associated polymorphisms, yet with modest accuracy and strong positional biases. In this study, we curated 737 high-confidence pathogenic non-coding variants associated with monogenic Mendelian diseases.
4/6/2023 10:22:25 PM +00:00