Tài liệu miễn phí Sinh học
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The chromatin remodeler Ino80 mediates RNAPII pausing site determination
Promoter-proximal pausing of RNA polymerase II (RNAPII) is a critical step for the precise regulation of gene expression. Despite the apparent close relationship between promoter-proximal pausing and nucleosome, the role of chromatin remodeler governing this step has mainly remained elusive.
4/6/2023 5:24:14 AM +00:00
Biologically relevant transfer learning improves transcription factor binding prediction
Deep learning has proven to be a powerful technique for transcription factor (TF) binding prediction but requires large training datasets. Transfer learning can reduce the amount of data required for deep learning, while improving overall model performance, compared to training a separate model for each new task.
4/6/2023 5:24:04 AM +00:00
KrasG12D induces changes in chromatin territories that differentially impact early nuclear reprogramming in pancreatic cells
Pancreatic ductal adenocarcinoma initiation is most frequently caused by Kras mutations. Results: Here, we apply biological, biochemical, and network biology methods to validate GEMM-derived cell models using inducible KrasG12D expression. We describe the time-dependent, chromatin remodeling program that impacts function during early oncogenic signaling.
4/6/2023 5:23:54 AM +00:00
SRCP: A comprehensive pipeline for accurate annotation and quantification of circRNAs
Here we describe a new integrative approach for accurate annotation and quantification of circRNAs named Short Read circRNA Pipeline (SRCP). Our strategy involves two steps: annotation of validated circRNAs followed by a quantification step. We show that SRCP is more sensitive than other individual pipelines and allows for more comprehensive quantification of a larger number of differentially expressed circRNAs.
4/6/2023 5:23:46 AM +00:00
Gut bacterial metabolites modulate endoplasmic reticulum stress
The endoplasmic reticulum (ER) is a membranous organelle that maintains proteostasis and cellular homeostasis, controlling the fine balance between health and disease. Dysregulation of the ER stress response has been implicated in intestinal inflammation associated with inflammatory bowel disease (IBD), a chronic condition characterized by changes to the mucosa and alteration of the gut microbiota.
4/6/2023 5:23:39 AM +00:00
LightGBM: Accelerated genomically designed crop breeding through ensemble learning
LightGBM is an ensemble model of decision trees for classification and regression prediction. We demonstrate its utility in genomic selection-assisted breeding with a large dataset of inbred and hybrid maize lines.
4/6/2023 5:23:30 AM +00:00
ACE: A probabilistic model for characterizing gene-level essentiality in CRISPR screens
High-throughput CRISPR-Cas9 knockout screens are widely used to evaluate gene essentiality in cancer research. Here we introduce a probabilistic modeling framework, Analysis of CRISPR-based Essentiality (ACE), that accounts for multiple sources of variation in CRISPR-Cas9 screens and enables new statistical tests for essentiality.
4/6/2023 5:23:23 AM +00:00
Chromatin accessibility and regulatory vocabulary across indicine cattle tissues
: Spatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions across different tissues and developmental stages is led by large international collaborative efforts mostly focusing on model organisms, such as ENCODE.
4/6/2023 5:23:10 AM +00:00
Genomic insight into balancing high yield, good quality, and blast resistance of japonica rice
Balancing the yield, quality and resistance to disease is a daunting challenge in crop breeding due to the negative relationship among these traits. Large-scale genomic landscape analysis of germplasm resources is considered to be an efficient approach to dissect the genetic basis of the complex traits.
4/6/2023 5:23:00 AM +00:00
PRINCESS: Comprehensive detection of haplotype resolved SNVs, SVs, and methylation
Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV, methylation, or phasing of SNV; however, only the combination of variants provides a comprehensive insight into the sample and thus enables novel findings in biology or medicine.
4/6/2023 5:22:48 AM +00:00
Mapping the evolving landscape of superenhancers during cell differentiation
Super-enhancers are clusters of enhancer elements that play critical roles in the maintenance of cell identity. Current investigations on super-enhancers are centered on the established ones in static cell types. How super-enhancers are established during cell differentiation remains obscure.
4/6/2023 5:22:37 AM +00:00
Revisiting genetic artifacts on DNA methylation microarrays exposes novel biological implications
Illumina DNA methylation microarrays enable epigenome-wide analysis vastly used for the discovery of novel DNA methylation variation in health and disease. However, the microarrays’ probe design cannot fully consider the vast human genetic diversity, leading to genetic artifacts.
4/6/2023 5:22:25 AM +00:00
Trycycler: Consensus long-read assemblies for bacterial genomes
While long-read sequencing allows for the complete assembly of bacterial genomes, long-read assemblies contain a variety of errors. Here, we present Trycycler, a tool which produces a consensus assembly from multiple input assemblies of the same genome. Benchmarking showed that Trycycler assemblies contained fewer errors than assemblies constructed with a single tool.
4/6/2023 5:22:18 AM +00:00
The influence of the gut microbiome on BCG-induced trained immunity
The bacillus Calmette-Guérin (BCG) vaccine protects against tuberculosis and heterologous infections but elicits high inter-individual variation in specific and nonspecific, or trained, immune responses. While the gut microbiome is increasingly recognized as an important modulator of vaccine responses and immunity in general, its potential role in BCG-induced protection is largely unknown.
4/6/2023 5:21:58 AM +00:00
Genomic basis underlying the metabolome-mediated drought adaptation of maize
Drought is a major environmental disaster that causes crop yield loss worldwide. Metabolites are involved in various environmental stress responses of plants. However, the genetic control of metabolomes underlying crop environmental stress adaptation remains elusive.
4/6/2023 5:21:48 AM +00:00
Evaluation of some aspects in supervised cell type identification for single-cell RNAseq: Classifier, feature selection, and reference construction
Cell type identification is one of the most important questions in single-cell RNA sequencing (scRNA-seq) data analysis. With the accumulation of public scRNA-seq data, supervised cell type identification methods have gained increasing popularity due to better accuracy, robustness, and computational performance.
4/6/2023 5:21:40 AM +00:00
PUMAS: Fine-tuning polygenic risk scores with GWAS summary statistics
Polygenic risk scores (PRSs) have wide applications in human genetics research, but often include tuning parameters which are difficult to optimize in practice due to limited access to individual-level data. Here, we introduce PUMAS, a novel method to fine-tune PRS models using summary statistics from genome-wide association studies (GWASs).
4/6/2023 5:21:33 AM +00:00
H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha
Polycomb repressive complex 1 (PRC1) and PRC2 are chromatin regulators maintaining transcriptional repression. The deposition of H3 lysine 27 trimethylation (H3K27me3) by PRC2 is known to be required for transcriptional repression, whereas the contribution of H2A ubiquitination (H2Aub) in the Polycomb repressive system remains unclear in plants.
4/6/2023 5:21:24 AM +00:00
LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology
Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and bioinformatic resources in approximately 7 days and using one long-read sequencing technology.
4/6/2023 5:21:13 AM +00:00
Gramtools enables multiscale variation analysis with genome graphs
Genome graphs allow very general representations of genetic variation; depending on the model and implementation, variation at different length-scales (single nucleotide polymorphisms (SNPs), structural variants) and on different sequence backgrounds can be incorporated with different levels of transparency.
4/6/2023 5:21:02 AM +00:00
Pandora: Nucleotide-resolution bacterial pan-genomics with reference graphs
We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which analyze SNPs in just the core genome have unsatisfactory limitations.
4/6/2023 5:20:51 AM +00:00
NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks
Long-read sequencing enables variant detection in genomic regions that are considered difficult-to-map by short-read sequencing. To fully exploit the benefits of longer reads, here we present a deep learning method NanoCaller, which detects SNPs using long-range haplotype information, then phases long reads with called SNPs and calls indels with local realignment.
4/6/2023 5:20:42 AM +00:00
Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila
Variation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remains largely unknown.
4/6/2023 5:20:33 AM +00:00
AMULET: A novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data
Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniquely aligned reads across the genome to effectively detect multiplets. We evaluate the method by generating snATAC-seq data in the human blood and pancreatic islet samples.
4/6/2023 5:20:22 AM +00:00
Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation
Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgression, we investigate six wild Vitis species that are native to the Southwestern United States and useful for breeding grapevine (V. vinifera) rootstocks.
4/6/2023 5:20:14 AM +00:00
Acute depletion of CTCF rewires genomewide chromatin accessibility
The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studies. However, acute depletion of CTCF globally reduces chromatin interactions but does not significantly alter transcription.
4/6/2023 5:20:03 AM +00:00
NucHMM: A method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality
We develop a novel computational method, NucHMM, to identify functional nucleosome states associated with cell type-specific combinatorial histone marks and nucleosome organization features such as phasing, spacing and positioning. We test it on publicly available MNase-seq and ChIP-seq data in MCF7, H1, and IMR90 cells and identify 11 distinct functional nucleosome states.
4/6/2023 5:19:53 AM +00:00
Systematic functional interrogation of human pseudogenes using CRISPRi
The human genome encodes over 14,000 pseudogenes that are evolutionary relics of protein-coding genes and commonly considered as nonfunctional. Emerging evidence suggests that some pseudogenes may exert important functions.
4/6/2023 5:19:42 AM +00:00
Deterministic transition of enterotypes shapes the infant gut microbiome at an early age
The succession of the gut microbiota during the first few years plays a vital role in human development. We elucidate the characteristics and alternations of the infant gut microbiota to better understand the correlation between infant health and microbiota maturation.
4/6/2023 5:19:35 AM +00:00
Effective control of large deletions after double-strand breaks by homologydirected repair and dsODN insertion
After repairing double-strand breaks (DSBs) caused by CRISPR-Cas9 cleavage, genomic damage, such as large deletions, may have pathogenic consequences. : We show that large deletions are ubiquitous but are dependent on editing sites and cell types. Human primary T cells display more significant deletions than hematopoietic stem and progenitor cells (HSPCs), whereas we observe low levels in induced pluripotent stem cells (iPSCs).
4/6/2023 5:19:26 AM +00:00