Tài liệu miễn phí Sinh học
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Trends and challenges in computational RNA biology
Recent years have witnessed a profound shift in our understanding of RNA biology. Several novel biochemical and sequencing techniques are producing vast amounts of data that fundamentally challenge the textbook view of RNA as a simple intermediate step of gene expression, revealing a wealth of unexpected new roles and shedding light on the complexity of the RNA world.
4/6/2023 6:49:01 AM +00:00
IMP: A pipeline for reproducible referenceindependent integrated metagenomic and metatranscriptomic analyses
Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data.
4/6/2023 6:48:53 AM +00:00
Fruitful analysis of sex chromosomes reveals X-treme genetic diversity
The evolution of sex chromosomes has occurred many times in highly divergent taxa. The bulk of the research that has shaped our expectations for their evolutionary path has focused on model organisms that have older sex chromosomes; In these organisms, the two sex chromosomes are highly differentiated from each other in form and function.
4/6/2023 6:48:45 AM +00:00
A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence
In cancer, mutually exclusive or co-occurring somatic alterations across genes can suggest functional interactions. Existing tests for such patterns make the unrealistic assumption of identical gene alteration probabilities across tumors. We present Discrete Independence Statistic Controlling for Observations with Varying Event Rates (DISCOVER), a novel test that is more sensitive than other methods and controls its false positive rate.
4/6/2023 6:48:38 AM +00:00
DIVAN: Accurate identification of noncoding disease-specific risk variants using multi-omics profiles
Understanding the link between non-coding sequence variants, identified in genome-wide association studies, and the pathophysiology of complex diseases remains challenging due to a lack of annotations in non-coding regions.
4/6/2023 6:48:30 AM +00:00
Autosomal genetic control of human gene expression does not differ across the sexes
Despite their nearly identical genomes, males and females differ in risk, incidence, prevalence, severity and age-at-onset of many diseases. Sexual dimorphism is also seen in human autosomal gene expression, and has largely been explored by examining the contribution of genotype-by-sex interactions to variation in gene expression.
4/6/2023 6:48:23 AM +00:00
New insights into the generation and role of de novo mutations in health and disease
Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing studies of parent–offspring trios have provided the first insights into the number and distribution of these de novo mutations in health and disease, pointing to risk factors that increase their number in the offspring.
4/6/2023 6:48:16 AM +00:00
Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing
Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. The molecular nature of DTCs remains elusive, as well as when and from where in the tumor they originate.
4/6/2023 6:48:09 AM +00:00
Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes.
4/6/2023 6:48:02 AM +00:00
The continuum of causality in human genetic disorders
Studies of human genetic disorders have traditionally followed a reductionist paradigm. Traits are defined as Mendelian or complex based on family pedigree and population data, whereas alleles are deemed rare, common, benign, or deleterious based on their population frequencies.
4/6/2023 6:47:56 AM +00:00
Whole genome sequence analysis of serum amino acid levels
Blood levels of amino acids are important biomarkers of disease and are influenced by synthesis, protein degradation, and gene–environment interactions. Whole genome sequence analysis of amino acid levels may establish a paradigm for analyzing quantitative risk factors.
4/6/2023 6:47:49 AM +00:00
Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort
Disorders of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or phenotypic sex is atypical. Clinical management of DSD is often difficult and currently only 13% of patients receive an accurate clinical genetic diagnosis.
4/6/2023 6:47:39 AM +00:00
Patterns of ribosomal protein expression specify normal and malignant human cells
Ribosomes are highly conserved molecular machines whose core composition has traditionally been regarded as invariant. However, recent studies have reported intriguing differences in the expression of some ribosomal proteins (RPs) across tissues and highly specific effects on the translation of individual mRNAs.
4/6/2023 6:47:33 AM +00:00
Revisiting the morbid genome of Mendelian disorders
The pathogenicity of many Mendelian variants has been challenged by large-scale sequencing efforts. However, many rare and benign “disease mutations” are difficult to analyze due to their rarity. The Saudi Arabian variome is enriched for homozygosity due to inbreeding, a key advantage that can be exploited for the critical examination of previously published variants.
4/6/2023 6:47:25 AM +00:00
Functional and regulatory profiling of energy metabolism in fission yeast
The control of energy metabolism is fundamental for cell growth and function and anomalies in it are implicated in complex diseases and ageing. Metabolism in yeast cells can be manipulated by supplying different carbon sources: Yeast grown on glucose rapidly proliferates by fermentation, analogous to tumour cells growing by aerobic glycolysis, whereas on non-fermentable carbon sources metabolism shifts towards respiration.
4/6/2023 6:47:18 AM +00:00
Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease
Genome-wide association studies (GWAS) have revealed many susceptibility loci for complex genetic diseases. For most loci, the causal genes have not been identified. Currently, the identification of candidate genes is predominantly based on genes that localize close to or within identified loci.
4/6/2023 6:47:09 AM +00:00
Characterizing the morbid genome of ciliopathies
Ciliopathies are clinically diverse disorders of the primary cilium. Remarkable progress has been made in understanding the molecular basis of these genetically heterogeneous conditions; However, our knowledge of their morbid genome, pleiotropy, and variable expressivity remains incomplete.
4/6/2023 6:46:56 AM +00:00
Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans
The 2’-5’ oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; Yet, strong evidence of positive selection in the OAS region is still lacking.
4/6/2023 6:46:44 AM +00:00
Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery
The relationship between monogenic and polygenic forms of epilepsy is poorly understood and the extent to which the genetic and acquired epilepsies share common pathways is unclear. Here, we use an integrated systems-level analysis of brain gene expression data to identify molecular networks disrupted in epilepsy
4/6/2023 6:46:32 AM +00:00
TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells
Ten-eleven translocation (TET) enzymes oxidise DNA methylation as part of an active demethylation pathway. Despite extensive research into the role of TETs in genome regulation, little is known about their effect on transposable elements (TEs), which make up nearly half of the mouse and human genomes.
4/6/2023 6:46:22 AM +00:00
Extremely low nucleotide diversity in the X-linked region of papaya caused by a strong selective sweep
The papaya Y-linked region showed clear population structure, resulting in the detection of the ancestral male population that domesticated hermaphrodite papayas were selected from. The same populations were used to study nucleotide diversity and population structure in the X-linked region.
4/6/2023 6:46:13 AM +00:00
A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes
Most gene prediction methods detect coding sequences from transcriptome assemblies in the absence of closely related reference genomes. Such methods are of limited application due to high transcript fragmentation and extensive assembly errors, which may lead to redundant or false coding sequence predictions.
4/6/2023 6:46:06 AM +00:00
Understanding rare and common diseases in the context of human evolution
The wealth of available genetic information is allowing the reconstruction of human demographic and adaptive history. Demography and purifying selection affect the purge of rare, deleterious mutations from the human population, whereas positive and balancing selection can increase the frequency of advantageous variants, improving survival and reproduction in specific environmental conditions.
4/6/2023 6:45:59 AM +00:00
Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures
Tumor-infiltrating immune cells have been linked to prognosis and response to immunotherapy; however, the levels of distinct immune cell subsets and the signals that draw them into a tumor, such as the expression of antigen presenting machinery genes, remain poorly characterized.
4/6/2023 6:45:50 AM +00:00
Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features
The human lung tissue microbiota remains largely uncharacterized, although a number of studies based on airway samples suggest the existence of a viable human lung microbiota. Here we characterized the taxonomic and derived functional profiles of lung microbiota in 165 non-malignant lung tissue samples from cancer patients.
4/6/2023 6:45:41 AM +00:00
Precise genome-wide mapping of single nucleosomes and linkers in vivo
We developed a chemical cleavage method that releases single nucleosome dyad-containing fragments, allowing us to precisely map both single nucleosomes and linkers with high accuracy genome-wide in yeast.
4/6/2023 6:45:29 AM +00:00
A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog
The accurate description of ancestry is essential to interpret, access, and integrate human genomics data, and to ensure that these benefit individuals from all ancestral backgrounds. However, there are no established guidelines for the representation of ancestry information. Here we describe a framework for the accurate and standardized description of sample ancestry, and validate it by application to the NHGRI-EBI GWAS Catalog.
4/6/2023 6:45:22 AM +00:00
A panoramic view of RNA modifications: Exploring new frontiers
Methods for transcriptome-wide analyses of RNA modifications—highlighted as the 'Method of the Year 2016' by Nature Methods—have recently revealed highly dynamic 'epitranscriptomes', in which RNA modifications regulate gene activities and cellular phenotypes in health and disease.
4/6/2023 6:45:15 AM +00:00
The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages
Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment. Results: In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara.
4/6/2023 6:45:07 AM +00:00
Genome-wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys
Previous studies showed that the majority of developmental genes are devoid of DNA methylation at promoters even when they are repressed. Such hypomethylated regions at developmental genes are unusually large and extend well beyond proximal promoters, forming DNA methylation valleys (DMVs) or DNA methylation canyons.
4/6/2023 6:44:55 AM +00:00