Tài liệu miễn phí Sinh học
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An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression
The gut microbiome, a key constituent of the colonic environment, has been implicated as an important modulator of human health. The eukaryotic epigenome is postulated to respond to environmental stimuli through alterations in chromatin features and, ultimately, gene expression.
4/6/2023 6:44:46 AM +00:00
Kourami: Graph-guided assembly for novel human leukocyte antigen allele discovery
Accurate typing of human leukocyte antigen (HLA) is important because HLA genes play important roles in immune responses and disease genesis. Previously available computational methods are database-matching approaches and their outputs are inherently limited by the completeness of already known types, making them unsuitable for discovery of novel alleles.
4/6/2023 6:44:38 AM +00:00
Bystro: Rapid online variant annotation and natural-language filtering at whole-genome scale
The search engine dramatically simplifies complex filtering tasks that previously required programming experience or specialty command-line programs. Critically, Bystro’s annotation and filtering capabilities are orders of magnitude faster than previous solutions, saving weeks of processing time for large experiments.
4/6/2023 6:44:31 AM +00:00
Antisense suppression of the nonsense mediated decay factor Upf3b as a potential treatment for diseases caused by nonsense mutations
About 11% of all human genetic diseases are caused by nonsense mutations that generate premature translation termination codons (PTCs) in messenger RNAs (mRNA). PTCs not only lead to the production of truncated proteins, but also often result in decreased mRNA abundance due to nonsense-mediated mRNA decay (NMD).
4/6/2023 6:44:24 AM +00:00
A reproducibility-based computational framework identifies an inducible, enhanced antiviral state in dendritic cells from HIV-1 elite controllers
Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protection. Here, we explore this hypothesis by applying single-cell RNA-sequencing to examine viral responses among the dendritic cells (DCs) of three elite controllers (ECs) of HIV-1 infection.
4/6/2023 6:44:16 AM +00:00
Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells
Canonical Wnt/beta-catenin signalling regulates self-renewal and lineage selection within the mammalian epidermis. Although the transcriptional response of keratinocytes that receive a Wnt signal is well characterized, little is known about the mechanism by which keratinocytes in proximity to the Wnt-receiving cell are co-opted to undergo a change in cell fate.
4/6/2023 6:44:05 AM +00:00
Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha
In plants, the existence and possible role of epigenetic reprogramming has been questioned because of the occurrence of stably inherited epialleles. Evidence suggests that epigenetic reprogramming does occur during land plant reproduction, but there is little consensus on the generality and extent of epigenetic reprogramming in plants.
4/6/2023 6:43:56 AM +00:00
SCANPY: Large-scale single-cell gene expression data analysis
SCANPY is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks.
4/6/2023 6:43:43 AM +00:00
RNA virus interference via CRISPR/Cas13a system in plants
CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleaving single-stranded RNA (ssRNA) molecules of the phage genome.
4/6/2023 6:43:36 AM +00:00
FineMAV: Prioritizing candidate genetic variants driving local adaptations in human populations
We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated “gold standard” positively selected variants and simulations.
4/6/2023 6:43:29 AM +00:00
Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers
Enhancers are modular regulatory elements that are central to the spatial and temporal regulation of gene expression. Bidirectional transcription initiating at enhancers has been proposed to mark active enhancers and as such has been utilized to experimentally identify active enhancers de novo.
4/6/2023 6:43:22 AM +00:00
Adaptation of Arabidopsis thaliana to the Yangtze River basin
Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms adapt to climate changes is a crucial biological question that is still largely unanswered.
4/6/2023 6:43:14 AM +00:00
The proBAM and proBed standard formats: Enabling a seamless integration of genomics and proteomics data
On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative, we introduce here two novel standard data formats, proBAM and proBed, that have been developed to address the current challenges of integrating mass spectrometry-based proteomics data with genomics and transcriptomics information in proteogenomics studies.
4/6/2023 6:43:04 AM +00:00
SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells
Endogenous retroviruses (ERVs), which are responsible for 10% of spontaneous mouse mutations, are kept under control via several epigenetic mechanisms. The H3K9 histone methyltransferase SETDB1 is essential for ERV repression in embryonic stem cells (ESCs), with DNA methylation also playing an important role.
4/6/2023 6:42:58 AM +00:00
Single-cell RNA-seq study determines the ontogeny of macrophages in glioblastomas
Tumor heterogeneity is determined by both heterogeneous tumor cells and a complex tumor microenvironment. Profiling of different types of cells from among the complex cell population in the tumor microenvironment, as well as determining their lineage and their phenotypes, is critical for researchers to understand how such cells interact with tumor cells.
4/6/2023 6:42:48 AM +00:00
Epigenetic supersimilarity of monozygotic twin pairs
Monozygotic twins have long been studied to estimate heritability and explore epigenetic influences on phenotypic variation. The phenotypic and epigenetic similarities of monozygotic twins have been assumed to be largely due to their genetic identity.
4/6/2023 6:42:40 AM +00:00
From forensic epigenetics to forensic epigenomics: Broadening DNA investigative intelligence
Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment.
4/6/2023 6:42:34 AM +00:00
DE-kupl: Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition
We introduce a k-mer-based computational protocol, DE-kupl, for capturing local RNA variation in a set of RNA-seq libraries, independently of a reference genome or transcriptome. DE-kupl extracts all k-mers with differential abundance directly from the raw data files.
4/6/2023 6:42:23 AM +00:00
DotAligner: Identification and clustering of RNA structure motifs
The diversity of processed transcripts in eukaryotic genomes poses a challenge for the classification of their biological functions. Sparse sequence conservation in non-coding sequences and the unreliable nature of RNA structure predictions further exacerbate this conundrum.
4/6/2023 6:42:11 AM +00:00
Stranger in a strange land: The experiences of immigrant researchers
International collaborations are key to advancing scientific research globally and often require mobility on the part of researchers. Migration of scientists enables the spread of ideas and skills around the world, giving researchers the opportunity to follow the best resources.
4/6/2023 6:42:04 AM +00:00
Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline
The 3′ untranslated regions (UTRs) of mRNAs play a major role in post-transcriptional regulation of gene expression. Selection of transcript cleavage and polyadenylation sites is a dynamic process that produces multiple transcript isoforms for the same gene within and across different cell types.
4/6/2023 6:41:56 AM +00:00
The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD transcription-competent complex
Circular RNAs are a class of endogenous RNAs with various functions in eukaryotic cells. Worthy of note, circular RNAs play a critical role in cancer. Currently, nothing is known about their role in head and neck squamous cell carcinoma (HNSCC). The identification of circular RNAs in HNSCC might become useful for diagnostic and therapeutic strategies in HNSCC.
4/6/2023 6:41:48 AM +00:00
MICRA: An automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization through reads analysis.
4/6/2023 6:41:39 AM +00:00
Systems-epigenomics inference of transcription factor activity implicates arylhydrocarbon-receptor inactivation as a key event in lung cancer development
Diverse molecular alterations associated with smoking in normal and precursor lung cancer cells have been reported, yet their role in lung cancer etiology remains unclear. A prominent example is hypomethylation of the aryl hydrocarbon-receptor repressor (AHRR) locus, which is observed in blood and squamous epithelial cells of smokers, but not in lung cancer.
4/6/2023 6:41:30 AM +00:00
Balancing selection and trans-specific polymorphisms
Balancing selection maintains variation for evolution. A recent study investigated the extent of balancing selection in two Brassicaceae species and highlighted its importance for adaptation.
4/6/2023 6:41:23 AM +00:00
PureCLIP: Capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data
The iCLIP and eCLIP techniques facilitate the detection of protein–RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases.
4/6/2023 6:41:17 AM +00:00
Intergenic disease-associated regions are abundant in novel transcripts
Genotyping of large populations through genome-wide association studies (GWAS) has successfully identified many genomic variants associated with traits or disease risk. Unexpectedly, a large proportion of GWAS single nucleotide polymorphisms (SNPs) and associated haplotype blocks are in intronic and intergenic regions, hindering their functional evaluation.
4/6/2023 6:41:09 AM +00:00
Single-cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment
Tumor-associated macrophages (TAMs) are abundant in gliomas and immunosuppressive TAMs are a barrier to emerging immunotherapies. It is unknown to what extent macrophages derived from peripheral blood adopt the phenotype of brain-resident microglia in pre-treatment gliomas.
4/6/2023 6:40:56 AM +00:00
Experimental design and quantitative analysis of microbial community multiomics
Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed.
4/6/2023 6:40:46 AM +00:00
Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species
Drosophila melanogaster has one of best-described transcriptomes of any multicellular organism. Nevertheless, the paucity of 3′-sequencing data in this species precludes comprehensive assessment of alternative polyadenylation (APA), which is subject to broad tissue-specific control.
4/6/2023 6:40:33 AM +00:00