Tài liệu miễn phí Sinh học
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RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k-mer-based lowest common ancestor taxonomic classification. We present three major findings: the number of new species added to the NCBI RefSeq database greatly outpaces the number of new genera; as a result, more reads are classified with newer database versions, but fewer are classified at the species level; and Bayesian-based re-estimation mitigates this effect but struggles with novel genomes.
4/6/2023 10:44:04 PM +00:00
Holo-Seq: Single-cell sequencing of holo-transcriptome
Current single-cell RNA-seq approaches are hindered by preamplification bias, loss of strand of origin information, and the inability to observe small-RNA and mRNA dual transcriptomes. Here, we introduce a single-cell holotranscriptome sequencing (Holo-Seq) that overcomes all three hurdles.
4/6/2023 10:43:54 PM +00:00
Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages
Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there are two major clades, Complexa and Robusta, but the genomic bases of significant differences between them remain unclear.
4/6/2023 10:43:46 PM +00:00
Alternative polyadenylation factors link cell cycle to migration
In response to a wound, fibroblasts are activated to migrate toward the wound, to proliferate and to contribute to the wound healing process. We hypothesize that changes in pre-mRNA processing occurring as fibroblasts enter the proliferative cell cycle are also important for promoting their migration.
4/6/2023 10:43:38 PM +00:00
Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes
The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation.
4/6/2023 10:43:30 PM +00:00
Evolutionary and developmental dynamics of sex-biased gene expression in common frogs with proto-Y chromosomes
The patterns of gene expression on highly differentiated sex chromosomes differ drastically from those on autosomes, due to sex-specific patterns of selection and inheritance. As a result, X chromosomes are often enriched in female-biased genes (feminization) and Z chromosomes in male-biased genes (masculinization).
4/6/2023 10:43:23 PM +00:00
SCoPE-MS: Mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation
Some exciting biological questions require quantifying thousands of proteins in single cells. To achieve this goal, we develop Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS) and validate its ability to identify distinct human cancer cell types based on their proteomes. We use SCoPE-MS to quantify over a thousand proteins in differentiating mouse embryonic stem cells.
4/6/2023 10:43:16 PM +00:00
PINES: Phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants
Functional characterization of the noncoding genome is essential for biological understanding of gene regulation and disease. Here, we introduce the computational framework PINES (Phenotype-Informed Noncoding Element Scoring), which predicts the functional impact of noncoding variants by integrating epigenetic annotations in a phenotype-dependent manner.
4/6/2023 10:43:08 PM +00:00
Modularity of genes involved in local adaptation to climate despite physical linkage
Linkage among genes experiencing different selection pressures can make natural selection less efficient. Theory predicts that when local adaptation is driven by complex and non-covarying stresses, increased linkage is favored for alleles with similar pleiotropic effects, with increased recombination favored among alleles with contrasting pleiotropic effects.
4/6/2023 10:42:55 PM +00:00
Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes
Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evolutionary history.
4/6/2023 10:42:47 PM +00:00
PHLI-seq: Constructing and visualizing cancer genomic maps in 3D by phenotypebased high-throughput laser-aided isolation and sequencing
Spatial mapping of genomic data to tissue context in a high-throughput and high-resolution manner has been challenging due to technical limitations. Here, we describe PHLI-seq, a novel approach that enables high-throughput isolation and genome-wide sequence analysis of single cells or small numbers of cells to construct genomic maps within cancer tissue in relation to the images or phenotypes of the cells.
4/6/2023 10:42:39 PM +00:00
SKESA: Strategic k-mer extension for scrupulous assemblies
SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity, handles low-level contamination in reads, is fast, and produces an identical assembly for the same input when assembled multiple times with the same or different compute resources.
4/6/2023 10:42:31 PM +00:00
Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
The phenotypes of cancer cells are driven in part by somatic structural variants. Structural variants can initiate tumors, enhance their aggressiveness, and provide unique therapeutic opportunities. Whole-genome sequencing of tumors can allow exhaustive identification of the specific structural variants present in an individual cancer, facilitating both clinical diagnostics and the discovery of novel mutagenic mechanisms.
4/6/2023 10:42:24 PM +00:00
CRISPhieRmix: A hierarchical mixture model for CRISPR pooled screens
Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortunately, two problems exist, particularly for CRISPRi/a screens: variability in guide efficiency and large rare off-target effects.
4/6/2023 10:42:17 PM +00:00
Clust: Automatic extraction of optimal coexpressed gene clusters from gene expression data
Identifying co-expressed gene clusters can provide evidence for genetic or physical interactions. Thus, co-expression clustering is a routine step in large-scale analyses of gene expression data. We show that commonly used clustering methods produce results that substantially disagree and that do not match the biological expectations of coexpressed gene clusters.
4/6/2023 10:42:08 PM +00:00
SeqOthello: Querying RNA-seq experiments at scale
We present SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq experiments. It takes SeqOthello only 5 min and 19.1 GB memory to conduct a global survey of 11,658 fusion events against 10,113 TCGA Pan-Cancer RNA-seq datasets.
4/6/2023 10:42:01 PM +00:00
CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
Recent experimental efforts of CRISPR-Cas9 systems have shown that off-target binding and cleavage are a concern for the system and that this is highly dependent on the selected guide RNA (gRNA) design. Computational predictions of off-targets have been proposed as an attractive and more feasible alternative to tedious experimental efforts.
4/6/2023 10:41:48 PM +00:00
Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence
Histone lysine acylations by short-chain fatty acids are distinct from the widely studied histone lysine acetylation in chromatin, although both modifications are regulated by primary metabolism in mammalian cells. It remains unknown whether and how histone acylation and acetylation interact to regulate gene expression in plants that have distinct regulatory pathways of primary metabolism.
4/6/2023 10:41:39 PM +00:00
CRISPR-induced exon skipping is dependent on premature termination codon mutations
In previous studies, CRISPR/Cas9 was shown to induce unexpected exon skipping; however, the mechanism by which this phenomenon is triggered is controversial. By analyzing 22 gene-edited rabbit lines generated using CRISPR/Cas9, we provide evidence of exon skipping at high frequency in premature termination codon-mutated rabbits but not in the rabbits with a premature termination codon mutation in exon 1 rabbits with non-frameshift or missense mutations.
4/6/2023 10:41:28 PM +00:00
Live imaging and tracking of genome regions in CRISPR/dCas9 knock-in mice
CRISPR/dCas9 is a versatile tool that can be used to recruit various effectors and fluorescent molecules to defined genome regions where it can modulate genetic and epigenetic markers, or track the chromatin dynamics in live cells. In vivo applications of CRISPR/dCas9 in animals have been challenged by delivery issues. We generate and characterize a mouse strain with dCas9-EGFP ubiquitously expressed in various tissues.
4/6/2023 10:41:18 PM +00:00
Manipulating plant RNA-silencing pathways to improve the gene editing efficiency of CRISPR/Cas9 systems
The CRISPR/Cas9 system, composed of a single-guide RNA for target recognition and a Cas9 protein for DNA cleavage, has the potential to revolutionize agriculture as well as medicine. Even though extensive work has been done to improve the gene editing activity of CRISPR/Cas9, little is known about the regulation of this bacterial system in eukaryotic host cells, especially at the post-transcriptional level.
4/6/2023 10:41:08 PM +00:00
Ankyrin domain encoding genes from an ancient horizontal transfer are functionally integrated into Nasonia developmental gene regulatory networks
How regulatory networks incorporate additional components and how novel genes are functionally integrated into well-established developmental processes are two important and intertwined questions whose answers have major implications for understanding the evolution of development.
4/6/2023 10:40:58 PM +00:00
Reduced intrinsic DNA curvature leads to increased mutation rate
Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1–7-bp scale, but cis elements remain poorly characterized. The lack of understanding regarding why different sequences have different mutation rates hampers our ability to identify positive selection in evolution and to identify driver mutations in tumorigenesis.
4/6/2023 10:40:52 PM +00:00
Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation
The importance of transcription factors (TFs) and epigenetic modifications in the control of gene expression is widely accepted. However, causal relationships between changes in TF binding, histone modifications, and gene expression during the response to extracellular stimuli are not well understood. Here, we analyze the ordering of these events on a genome-wide scale in dendritic cells in response to lipopolysaccharide (LPS) stimulation.
4/6/2023 10:40:45 PM +00:00
A novel long noncoding RNA HOXC-AS3 mediates tumorigenesis of gastric cancer by binding to YBX1
Recently, increasing evidence shows that long noncoding RNAs (lncRNAs) play a significant role in human tumorigenesis. However, the function of lncRNAs in human gastric cancer remains largely unknown.
4/6/2023 10:40:34 PM +00:00
Genes reveal traces of common recent demographic history for most of the Uralicspeaking populations
The genetic origins of Uralic speakers from across a vast territory in the temperate zone of North Eurasia have remained elusive. Previous studies have shown contrasting proportions of Eastern and Western Eurasian ancestry in their mitochondrial and Y chromosomal gene pools.
4/6/2023 10:40:22 PM +00:00
Conservation of biodiversity in the genomics era
“Conservation genomics” encompasses the idea that genome-scale data will improve the capacity of resource managers to protect species. Although genetic approaches have long been used in conservation research, it has only recently become tractable to generate genome-wide data at a scale that is useful for conservation.
4/6/2023 10:40:11 PM +00:00
The 3D Genome Browser: A web-based browser for visualizing 3D genome organization and long-range chromatin interactions
Our browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure.
4/6/2023 10:40:02 PM +00:00
Harnessing accurate non-homologous end joining for efficient precise deletion in CRISPR/Cas9-mediated genome editing
Many applications of CRISPR/Cas9-mediated genome editing require Cas9-induced non-homologous end joining (NHEJ), which was thought to be error prone. However, with directly ligatable ends, Cas9-induced DNA double strand breaks may be repaired preferentially by accurate NHEJ.
4/6/2023 10:39:54 PM +00:00
ABLE: Blockwise site frequency spectra for inferring complex population histories and recombination
We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide multi-locus data (for example, RADSeq) and can also accommodate arbitrarily large samples.
4/6/2023 10:39:45 PM +00:00