Tài liệu miễn phí Sinh học
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RaGOO: Fast and accurate reference-guided scaffolding of draft genomes
We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecules are constructed, RaGOO identifies structural variants, including those spanning sequencing gaps.
4/6/2023 9:06:52 AM +00:00
Structural variant calling: The long and the short of it
Recent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases, regulation of gene expression, ethnic diversity, and large-scale chromosome evolution—giving rise to the differences within populations and among species
4/6/2023 9:06:46 AM +00:00
Soil domestication by rice cultivation results in plant-soil feedback through shifts in soil microbiota
Soils are a key component of agricultural productivity, and soil microbiota determine the availability of many essential plant nutrients. Agricultural domestication of soils, that is, the conversion of previously uncultivated soils to a cultivated state, is frequently accompanied by intensive monoculture, especially in the developing world.
4/6/2023 9:06:38 AM +00:00
Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families
The ocean microbiome represents one of the largest microbiomes and produces nearly half of the primary energy on the planet through photosynthesis or chemosynthesis. Using recent advances in marine genomics, we explore new applications of oceanic metagenomes for protein structure and function prediction.
4/6/2023 9:06:31 AM +00:00
SEPATH: Benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Human tissue is increasingly being whole genome sequenced as we transition into an era of genomic medicine. With this arises the potential to detect sequences originating from microorganisms, including pathogens amid the plethora of human sequencing reads.
4/6/2023 9:06:24 AM +00:00
Global impact of somatic structural variation on the DNA methylome of human cancers
Genomic rearrangements exert a heavy influence on the molecular landscape of cancer. New analytical approaches integrating somatic structural variants (SSVs) with altered gene features represent a framework by which we can assign global significance to a core set of genes, analogous to established methods that identify genes non-randomly targeted by somatic mutation or copy number alteration.
4/6/2023 9:06:13 AM +00:00
Birth, expansion, and death of VCYcontaining palindromes on the human Y chromosome
Large palindromes (inverted repeats) make up substantial proportions of mammalian sex chromosomes, often contain genes, and have high rates of structural variation arising via ectopic recombination. As a result, they underlie many genomic disorders.
4/6/2023 9:06:06 AM +00:00
Quantitative MNase-seq accurately maps nucleosome occupancy levels
Micrococcal nuclease (MNase) is widely used to map nucleosomes. However, its aggressive endo-/exo-nuclease activities make MNase-seq unreliable for determining nucleosome occupancies, because cleavages within linker regions produce oligo- and mono-nucleosomes, whereas cleavages within nucleosomes destroy them.
4/6/2023 9:05:59 AM +00:00
The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation
Cells have evolved quality control mechanisms to ensure protein homeostasis by detecting and degrading aberrant mRNAs and proteins. A common source of aberrant mRNAs is premature polyadenylation, which can result in non-functional protein products.
4/6/2023 9:05:45 AM +00:00
IMAGE: High-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis
Identifying genetic variants that are associated with methylation variation—an analysis commonly referred to as methylation quantitative trait locus (mQTL) mapping—is important for understanding the epigenetic mechanisms underlying genotype-trait associations.
4/6/2023 9:05:39 AM +00:00
MetaCell: Analysis of single-cell RNA-seq data using K-nn graph partitions
We describe a methodology for partitioning scRNA-seq datasets into metacells: disjoint and homogenous groups of profiles that could have been resampled from the same cell. Unlike clustering analysis, our algorithm specializes at obtaining granular as opposed to maximal groups.
4/6/2023 9:05:31 AM +00:00
Benchmark of computational methods for predicting microRNA-disease associations
A series of miRNA-disease association prediction methods have been proposed to prioritize potential disease-associated miRNAs. Independent benchmarking of these methods is warranted to assess their effectiveness and robustness.
4/6/2023 9:05:24 AM +00:00
The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance
Robustness and evolutionary stability of gene expression in the human genome are established by an array of redundant enhancers. Results: Using Hi-C data in multiple cell lines, we report a comprehensive map of promoters and active enhancers connected by chromatin contacts, spanning 9000 enhancer chains in 4 human cell lines associated with 2600 human genes.
4/6/2023 9:05:17 AM +00:00
Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny
Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates.
4/6/2023 9:05:10 AM +00:00
Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation
DNA methylation (DNAm) is a critical regulator of both development and cellular identity and shows unique patterns in neurons. To better characterize maturational changes in DNAm patterns in these cells, we profile the DNAm landscape at single-base resolution across the first two decades of human neocortical development in NeuN+ neurons using whole-genome bisulfite sequencing and compare them to non-neurons (primarily glia) and prenatal homogenate cortex.
4/6/2023 9:05:03 AM +00:00
DESE: Estimating driver tissues by selective expression of genes associated with complex diseases or traits
The driver tissues or cell types in which susceptibility genes initiate diseases remain elusive. We develop a unified framework to detect the causal tissues of complex diseases or traits according to selective expression of diseaseassociated genes in genome-wide association studies (GWASs).
4/6/2023 9:04:55 AM +00:00
Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency
Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency.
4/6/2023 9:04:48 AM +00:00
Reproducible biomedical benchmarking in the cloud: Lessons from crowd-sourced data challenges
Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. But ensuring that the methods evaluated are reproducible and reusable is complicated by the diversity of software architectures, input and output file formats, and computing environments.
4/6/2023 9:04:41 AM +00:00
Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles
Birds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day and owls (Strigiformes) hunting by night.
4/6/2023 9:04:34 AM +00:00
Genomic GPS: Using genetic distance from individuals to public data for genomic analysis without disclosing personal genomes
Genomic global positioning system (GPS) applies the multilateration technique commonly used in the GPS to genomic data. In the framework we present here, investigators calculate genetic distances from their samples to reference samples, which are from data held in the public domain, and share this information with others.
4/6/2023 9:04:27 AM +00:00
MetaCarvel: Linking assembly graph motifs to biological variants
Reconstructing genomic segments from metagenomics data is a highly complex task. In addition to general challenges, such as repeats and sequencing errors, metagenomic assembly needs to tolerate the uneven depth of coverage among organisms in a community and differences between nearly identical strains.
4/6/2023 9:04:19 AM +00:00
Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease
Diarrhea is the second leading cause of death in children under 5 years of age. Enhanced understanding of causal pathways, pathogenesis, and sequelae of diarrhea is urgently needed. Although the gut microbiota is believed to play a role in susceptibility to diarrheal diseases, our understanding of this association remains incomplete.
4/6/2023 9:04:12 AM +00:00
MITRE: Inferring features from microbiota time-series data linked to host status
Longitudinal studies are crucial for discovering causal relationships between the microbiome and human disease. We present MITRE, the Microbiome Interpretable Temporal Rule Engine, a supervised machine learning method for microbiome time-series analysis that infers human-interpretable rules linking changes in abundance of clades of microbes over time windows to binary descriptions of host status, such as the presence/absence of disease.
4/6/2023 9:04:05 AM +00:00
Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes
In ruminants, early rumen development is vital for efficient fermentation that converts plant materials to human edible food such as milk and meat. Here, we investigate the extent and functional basis of host-microbial interactions regulating rumen development during the first 6 weeks of life.
4/6/2023 9:03:57 AM +00:00
Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center
Two of the most important pathogens contributing to the global rise in antimicrobial resistance (AMR) are Klebsiella pneumoniae and Enterobacter cloacae. Despite this, most of our knowledge about the changing patterns of disease caused by these two pathogens is based on studies with limited timeframes that provide few insights into their population dynamics or the dynamics in AMR elements that they can carry.
4/6/2023 9:03:50 AM +00:00
A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types
Semi-automated genome annotation methods such as Segway take as input a set of genome-wide measurements such as of histone modification or DNA accessibility and output an annotation of genomic activity in the target cell type. Here we present annotations of 164 human cell types using 1615 data sets.
4/6/2023 9:03:43 AM +00:00
AlleleAnalyzer: A tool for personalized and allele-specific sgRNA design
The CRISPR/Cas system is a highly specific genome editing tool capable of distinguishing alleles differing by even a single base pair. Target sites might carry genetic variations that are not distinguishable by sgRNA designing tools based on one reference genome.
4/6/2023 9:03:37 AM +00:00
An enhanced genetic model of colorectal cancer progression history
The classical genetic model of colorectal cancer presents APC mutations as the earliest genomic alterations, followed by KRAS and TP53 mutations. However, the timing and relative order of clonal expansion and other types of genomic alterations, such as genomic rearrangements, are still unclear.
4/6/2023 9:03:28 AM +00:00
TOAST: Improving reference-free cell composition estimation by cross-cell type differential analysis
In the analysis of high-throughput data from complex samples, cell composition is an important factor that needs to be accounted for. Except for a limited number of tissues with known pure cell type profiles, a majority of genomics and epigenetics data relies on the “reference-free deconvolution” methods to estimate cell composition.
4/6/2023 9:03:18 AM +00:00
Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis
Circadian rhythms modulate growth and development in all organisms through interlocking transcriptional-translational feedback loops. The transcriptional loop involves chromatin modifications of central circadian oscillators in mammals and plants.
4/6/2023 9:03:11 AM +00:00