Tài liệu miễn phí Sinh học
Download Tài liệu học tập miễn phí Sinh học
Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome
Structural variation (SV) influences genome organization and contributes to human disease. However, the complete mutational spectrum of SV has not been routinely captured in disease association studies.
4/6/2023 6:53:11 AM +00:00
Transcriptomic signatures shaped by cell proportions shed light on comparative developmental biology
Comparative transcriptomics can answer many questions in developmental and evolutionary developmental biology. Most transcriptomic studies start by showing global patterns of variation in transcriptomes that differ between species or organs through developmental time. However, little is known about the kinds of expression differences that shape these patterns.
4/6/2023 6:53:04 AM +00:00
Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types
A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability. Our data highlight the importance of transcriptional and epigenetic variability for the key role of neutrophils as the first responders to inflammatory stimuli.
4/6/2023 6:52:57 AM +00:00
The genome landscape of indigenous African cattle
The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African farming systems.
4/6/2023 6:52:46 AM +00:00
Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus
The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model.
4/6/2023 6:52:35 AM +00:00
Genome-wide mapping of 5- hydroxymethyluracil in the eukaryote parasite Leishmania
5-Hydroxymethyluracil (5hmU) is a thymine base modification found in the genomes of a diverse range of organisms. To explore the functional importance of 5hmU, we develop a method for the genome-wide mapping of 5hmU-modified loci based on a chemical tagging strategy for the hydroxymethyl group.
4/6/2023 6:52:28 AM +00:00
Correcting for cell-type effects in DNA methylation studies: Reference-based method outperforms latent variable approaches in empirical studies
Based on an extensive simulation study, McGregor and colleagues recently recommended the use of surrogate variable analysis (SVA) to control for the confounding effects of cell-type heterogeneity in DNA methylation association studies in scenarios where no cell-type proportions are available.
4/6/2023 6:52:19 AM +00:00
Discovery and functional prioritization of Parkinson’s disease candidate genes from large-scale whole exome sequencing
Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson’s disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants.
4/6/2023 6:52:03 AM +00:00
Chrom3D: Three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts
Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational modeling framework that simulates positions of topologically-associated domains (TADs) relative to each other and to the nuclear periphery.
4/6/2023 6:51:51 AM +00:00
Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species
The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants.
4/6/2023 6:51:41 AM +00:00
Single Cas9 nickase induced generation of NRAMP1 knockin cattle with reduced offtarget effects
The CRISPR-Cas9 system is a widely utilized platform for transgenic animal production in various species, although its off-target effects should be addressed. Several applications of this tool have been proposed in model animals but remain insufficient for transgenic livestock production.
4/6/2023 6:51:34 AM +00:00
Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies
We present a set of statistical methods for the analysis of DNA methylation microarray data, which account for tumor purity. These methods are an extension of our previously developed method for purity estimation; Our updated method is flexible, efficient, and does not require data from reference samples or matched normal controls.
4/6/2023 6:51:28 AM +00:00
Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies
Identification of single nucleotide polymorphisms (SNPs) associated with gene expression levels, known as expression quantitative trait loci (eQTLs), may improve understanding of the functional role of phenotype-associated SNPs in genome-wide association studies (GWAS).
4/6/2023 6:51:20 AM +00:00
GAVIN: Gene-Aware Variant INterpretation for medical sequencing
We present Gene-Aware Variant INterpretation (GAVIN), a new method that accurately classifies variants for clinical diagnostic purposes. Classifications are based on gene-specific calibrations of allele frequencies from the ExAC database, likely variant impact using SnpEff, and estimated deleteriousness based on CADD scores for >3000 genes.
4/6/2023 6:51:14 AM +00:00
Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome
Respiratory illness caused by viral infection is associated with the development and exacerbation of childhood asthma. Little is known about the effects of respiratory viral infections in the absence of illness. Using quantitative PCR (qPCR) for common respiratory viruses and for two genes known to be highly upregulated in viral infections (CCL8/CXCL11), we screened 92 asthmatic and 69 healthy children without illness for respiratory virus infections.
4/6/2023 6:51:08 AM +00:00
Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain
Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosine (m5C).
4/6/2023 6:51:01 AM +00:00
iRegNet3D: Three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations
The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-DNA and chromatinchromatin interactions for the analysis of both coding and non-coding disease-associated mutations to obtain mechanistic insights into their functional impact.
4/6/2023 6:50:54 AM +00:00
Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus
In 2014, Western Africa experienced an unanticipated explosion of Ebola virus infections. What distinguishes fatal from non-fatal outcomes remains largely unknown, yet is key to optimising personalised treatment strategies.
4/6/2023 6:50:46 AM +00:00
Allele-specific analysis of cell fusionmediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation
Inactivation of one X chromosome is established early in female mammalian development and can be reversed in vivo and in vitro when pluripotency factors are re-expressed. The extent of reactivation along the inactive X chromosome (Xi) and the determinants of locus susceptibility are, however, poorly understood.
4/6/2023 6:50:39 AM +00:00
Gut microbial degradation of organophosphate insecticides-induces glucose intolerance via gluconeogenesis
Organophosphates are the most frequently and largely applied insecticide in the world due to their biodegradable nature. Gut microbes were shown to degrade organophosphates and cause intestinal dysfunction.
4/6/2023 6:50:31 AM +00:00
Single-cell epigenomic variability reveals functional cancer heterogeneity
Cell-to-cell heterogeneity is a major driver of cancer evolution, progression, and emergence of drug resistance. Epigenomic variation at the single-cell level can rapidly create cancer heterogeneity but is difficult to detect and assess functionally.
4/6/2023 6:50:24 AM +00:00
Controlling bias and inflation in epigenome- and transcriptome-wide association studies using the empirical null distribution
We show that epigenome- and transcriptome-wide association studies (EWAS and TWAS) are prone to significant inflation and bias of test statistics, an unrecognized phenomenon introducing spurious findings if left unaddressed. Neither GWAS-based methodology nor state-of-the-art confounder adjustment methods completely remove bias and inflation.
4/6/2023 6:50:13 AM +00:00
Insights into the design and interpretation of iCLIP experiments
Ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) identifies the sites on RNAs that are in direct contact with RNA-binding proteins (RBPs). Several variants of CLIP exist, which require different computational approaches for analysis.
4/6/2023 6:50:04 AM +00:00
Identifying aggressive prostate cancer foci using a DNA methylation classifier
Slow-growing prostate cancer (PC) can be aggressive in a subset of cases. Therefore, prognostic tools to guide clinical decision-making and avoid overtreatment of indolent PC and undertreatment of aggressive disease are urgently needed. PC has a propensity to be multifocal with several different cancerous foci per gland.
4/6/2023 6:49:56 AM +00:00
Human sex development: Targeted technologies to improve diagnosis
A new study of disorders of sex development presents an improved targeted next-generation sequencing approach for their diagnosis. Disorders of (or differences in) sex development (DSD) are a broad range of conditions that can affect reproductive development and function in humans.
4/6/2023 6:49:45 AM +00:00
Methylome evolution in plants
Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time.
4/6/2023 6:49:37 AM +00:00
The genome of the Gulf pipefish enables understanding of evolutionary innovations
Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuing these molecular phenomena underlying phenotypic evolution.
4/6/2023 6:49:28 AM +00:00
Ten years of the Genomics of Common Diseases: “The end of the beginning”
The first meeting in the Genomics of Common Diseases series was held just after the publication of the first successful genome-wide association analyses (GWAS), when optimism for the genomic dissection of common complex traits and diseases was high.
4/6/2023 6:49:21 AM +00:00
TET enzymes: Double agents in the transposable element–host genome conflict
The mouse genome is replete with retrotransposon sequences, from evolutionarily young elements with mutagenic potential that must be controlled, to inactive molecular fossils whose sequences can be domesticated over evolutionary time to benefit the host genome.
4/6/2023 6:49:15 AM +00:00
Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0.
4/6/2023 6:49:07 AM +00:00