Tài liệu miễn phí Sinh học
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AFLAP: Assembly-free linkage analysis pipeline using k-mers from genome sequencing data
Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly.
4/6/2023 5:54:09 AM +00:00
G-quadruplexes are transcription factor binding hubs in human chromatin
The binding of transcription factors (TF) to genomic targets is critical in the regulation of gene expression. Short, double-stranded DNA sequence motifs are routinely implicated in TF recruitment, but many questions remain on how binding site specificity is governed.
4/6/2023 5:54:00 AM +00:00
Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication
Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood.
4/6/2023 5:53:51 AM +00:00
Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach
X-chromosomal genes contribute to sex differences, in particular during early development, when both X chromosomes are active in females. Double X-dosage shifts female pluripotent cells towards the naive stem cell state by increasing pluripotency factor expression, inhibiting the differentiation-promoting MAP kinase (MAPK) signaling pathway, and delaying differentiation.
4/6/2023 5:53:39 AM +00:00
Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes
Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes.
4/6/2023 5:53:27 AM +00:00
Prevention of acquired sensorineural hearing loss in mice by in vivo Htra2 gene editing
Aging, noise, infection, and ototoxic drugs are the major causes of human acquired sensorineural hearing loss, but treatment options are limited. CRISPR/ Cas9 technology has tremendous potential to become a new therapeutic modality for acquired non-inherited sensorineural hearing loss.
4/6/2023 5:53:16 AM +00:00
Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved alternative splicing nonsense-mediated decay pathways
Alternative splicing, which generates multiple mRNA isoforms from single genes, is crucial for the regulation of eukaryotic gene expression. The flux through competing splicing pathways cannot be determined by traditional RNA-Seq, however, because different mRNA isoforms can have widely differing decay rates.
4/6/2023 5:53:05 AM +00:00
Histone lactylation drives oncogenesis by facilitating m6 A reader protein YTHDF2 expression in ocular melanoma
Histone lactylation, a metabolic stress-related histone modification, plays an important role in the regulation of gene expression during M1 macrophage polarization. However, the role of histone lactylation in tumorigenesis remains unclear.
4/6/2023 5:52:50 AM +00:00
PCIP-seq: Simultaneous sequencing of integrated viral genomes and their insertion sites with long reads
The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells.
4/6/2023 5:52:42 AM +00:00
Microbiome meta-analysis and crossdisease comparison enabled by the SIAMCAT machine learning toolbox
The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software is scarce, and overoptimistic evaluation and limited cross-study generalization are prevailing issues.
4/6/2023 5:52:34 AM +00:00
Identification of pathogenic variants in cancer genes using base editing screens with editing efficiency correction
Millions of nucleotide variants are identified through cancer genome sequencing and it is clinically important to identify the pathogenic variants among them. By introducing base substitutions at guide RNA target regions in the genome, CRISPR-Cas9-based base editors provide the possibility for evaluating a large number of variants in their genomic context.
4/6/2023 5:52:20 AM +00:00
Kssd: Sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis
Here, we develop k -mer substring space decomposition (Kssd), a sketching technique which is significantly faster and more accurate than current sketching methods. We show that it is the only method that can be used for large-scale dataset comparisons at population resolution on simulated and real data.
4/6/2023 5:52:10 AM +00:00
ACME dissociation: A versatile cell fixationdissociation method for single-cell transcriptomics
Single-cell sequencing technologies are revolutionizing biology, but they are limited by the need to dissociate live samples. Here, we present ACME (ACetic-MEthanol), a dissociation approach for single-cell transcriptomics that simultaneously fixes cells. ACME-dissociated cells have high RNA integrity, can be cryopreserved multiple times, and are sortable and permeable.
4/6/2023 5:52:02 AM +00:00
SRSF3 and SRSF7 modulate 3′UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels
Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3′ untranslated regions (3′UTRs). We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export.
4/6/2023 5:51:53 AM +00:00
Simplitigs as an efficient and scalable representation of de Bruijn graphs
Here, we introduce simplitigs as a compact, efficient, and scalable representation, and ProphAsm, a fast algorithm for their computation. For the example of assemblies of model organisms and two bacterial pan-genomes, we compare simplitigs to unitigs, the best existing representation, and demonstrate that simplitigs provide a substantial improvement in the cumulative sequence length and their number.
4/6/2023 5:51:42 AM +00:00
A benchmark for RNA-seq deconvolution analysis under dynamic testing environments
Deconvolution analyses have been widely used to track compositional alterations of cell types in gene expression data. Although a large number of novel methods have been developed, due to a lack of understanding of the effects of modeling assumptions and tuning parameters, it is challenging for researchers to select an optimal deconvolution method suitable for the targeted biological conditions.
4/6/2023 5:51:32 AM +00:00
FlsnRNA-seq: Protoplasting-free full-length single-nucleus RNA profiling in plants
The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we present a protoplasting-free approach, flsnRNA-seq, for large-scale full-length RNA profiling at a single-nucleus level in plants using isolated nuclei.
4/6/2023 5:51:19 AM +00:00
Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes
A-to-I RNA editing diversifies the transcriptome and has multiple downstream functional effects. Genetic variation contributes to RNA editing variability between individuals and has the potential to impact phenotypic variability.
4/6/2023 5:51:05 AM +00:00
Comprehensive identification of somatic nucleotide variants in human brain tissue
Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers.
4/6/2023 5:50:55 AM +00:00
Homopolish: A method for the removal of systematic errors in nanopore sequencing by homologous polishing
Nanopore sequencing has been widely used for the reconstruction of microbial genomes. Owing to higher error rates, errors on the genome are corrected via neural networks trained by Nanopore reads. However, the systematic errors usually remain uncorrected. This paper designs a model that is trained by homologous sequences for the correction of Nanopore systematic errors.
4/6/2023 5:50:46 AM +00:00
Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders
People with neurodegenerative disorders show diverse clinical syndromes, genetic heterogeneity, and distinct brain pathological changes, but studies report overlap between these features. DNA methylation (DNAm) provides a way to explore this overlap and heterogeneity as it is determined by the combined effects of genetic variation and the environment.
4/6/2023 5:50:37 AM +00:00
A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis
Frequent activation of the co-transcriptional factor YAP is observed in a large number of solid tumors. Activated YAP associates with enhancer loci via TEAD4-DNA-binding protein and stimulates cancer aggressiveness.
4/6/2023 5:50:26 AM +00:00
ADAR1 is a new target of METTL3 and plays a pro-oncogenic role in glioblastoma by an editing-independent mechanism
N6 -methyladenosine (m6A) and adenosine-to-inosine (A-to-I) RNA editing are two of the most abundant RNA modification events affecting adenosines in mammals. Both these RNA modifications determine mRNA fate and play a pivotal role in tumor development and progression.
4/6/2023 5:50:09 AM +00:00
My personal mutanome: A computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype
Massive genome sequencing data have inspired new challenges in personalized treatments and facilitated oncological drug discovery. We present a comprehensive database, My Personal Mutanome (MPM), for accelerating the development of precision cancer medicine protocols.
4/6/2023 5:50:01 AM +00:00
Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2
Macrophages are innate immune cells with diverse functional and molecular phenotypes. This diversity is largely unexplored at the level of single-cell proteomes because of the limitations of quantitative single-cell protein analysis.
4/6/2023 5:49:31 AM +00:00
ReSeq simulates realistic Illumina high-throughput sequencing data
In high-throughput sequencing data, performance comparisons between computational tools are essential for making informed decisions at each step of a project. Simulations are a critical part of method comparisons, but for standard Illumina sequencing of genomic DNA, they are often oversimplified, which leads to optimistic results for most tools.
4/6/2023 5:49:22 AM +00:00
GeneWalk identifies relevant gene functions for a biological context using network representation learning
A bottleneck in high-throughput functional genomics experiments is identifying the most important genes and their relevant functions from a list of gene hits. Gene Ontology (GO) enrichment methods provide insight at the gene set level.
4/6/2023 5:49:12 AM +00:00
LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals.
4/6/2023 5:48:48 AM +00:00
Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals
Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression.
4/6/2023 5:48:40 AM +00:00
Evolutionary conservation and divergence of the human brain transcriptome
Mouse models have allowed for the direct interrogation of genetic effects on molecular, physiological, and behavioral brain phenotypes. However, it is unknown to what extent neurological or psychiatric traits may be human- or primate-specific and therefore which components can be faithfully recapitulated in mouse models.
4/6/2023 5:48:18 AM +00:00