Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells [0.03%]
单细胞转录适应的普遍性和基因调控约束
Ian A Mellis,Madeline E Melzer,Nicholas Bodkin et al.
Ian A Mellis et al.
Background: Cells and tissues have a remarkable ability to adapt to genetic perturbations via a variety of molecular mechanisms. Nonsense-induced transcriptional compensation, a form of transcriptional adaptation, has rec...
Benchmarking clustering, alignment, and integration methods for spatial transcriptomics [0.03%]
空间转录组学聚类、配准和整合方法的基准测试
Yunfei Hu,Manfei Xie,Yikang Li et al.
Yunfei Hu et al.
Background: Spatial transcriptomics (ST) is advancing our understanding of complex tissues and organisms. However, building a robust clustering algorithm to define spatially coherent regions in a single tissue slice and a...
Inferring clonal somatic mutations directed by X chromosome inactivation status in single cells [0.03%]
利用单细胞分析X染色体失活状态推断克隆来源的体细胞性染色体突变
Ilke Demirci,Anton J M Larsson,Xinsong Chen et al.
Ilke Demirci et al.
Analysis of clonal dynamics in human tissues is enabled by somatic genetic variation. Here, we show that analysis of mitochondrial mutations in single cells is dramatically improved in females when using X chromosome inactivation to select ...
Pelin Icer Baykal,Paweł Piotr Łabaj,Florian Markowetz et al.
Pelin Icer Baykal et al.
In biomedical research, validating a scientific discovery hinges on the reproducibility of its experimental results. However, in genomics, the definition and implementation of reproducibility remain imprecise. We argue that genomic reproduc...
Creating large-scale genetic diversity in Arabidopsis via base editing-mediated deep artificial evolution [0.03%]
通过碱基编辑介导的深度人工进化在拟南芥中创建大规模遗传多样性
Xiang Wang,Wenbo Pan,Chao Sun et al.
Xiang Wang et al.
Background: Base editing is a powerful tool for artificial evolution to create allelic diversity and improve agronomic traits. However, the great evolutionary potential for every sgRNA target has been overlooked. And ther...
Transcriptional and epigenetic characterization of a new in vitro platform to model the formation of human pharyngeal endoderm [0.03%]
一个新型的体外平台的转录和表观遗传特征鉴定 该平台可用于模拟人类咽部内胚层的形成
Andrea Cipriano,Alessio Colantoni,Alessandro Calicchio et al.
Andrea Cipriano et al.
Background: The Pharyngeal Endoderm (PE) is an extremely relevant developmental tissue, serving as the progenitor for the esophagus, parathyroids, thyroids, lungs, and thymus. While several studies have highlighted the im...
Microsatellite instability at U2AF-binding polypyrimidic tract sites perturbs alternative splicing during colorectal cancer initiation [0.03%]
U2AF结合的多嘧啶片段位点微卫星不稳定性在结直肠癌发生过程中干扰可变剪接
Vincent Jonchère,Hugo Montémont,Enora Le Scanf et al.
Vincent Jonchère et al.
Background: Microsatellite instability (MSI) due to mismatch repair deficiency (dMMR) is common in colorectal cancer (CRC). These cancers are associated with somatic coding events, but the noncoding pathophysiological imp...
Duc Quang Le,Tien Anh Nguyen,Son Hoang Nguyen et al.
Duc Quang Le et al.
Pangenome inference is an indispensable step in bacterial genomics, yet its scalability poses a challenge due to the rapid growth of genomic collections. This paper presents PanTA, a software package designed for constructing pangenomes of ...
DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants [0.03%]
DNA结合因子印记和增强子RNA可识别功能性非编码遗传变异
Simon C Biddie,Giovanna Weykopf,Elizabeth F Hird et al.
Simon C Biddie et al.
Background: Genome-wide association studies (GWAS) have revealed a multitude of candidate genetic variants affecting the risk of developing complex traits and diseases. However, the highlighted regions are typically in th...
STdGCN: spatial transcriptomic cell-type deconvolution using graph convolutional networks [0.03%]
基于图卷积网络的Spatial转录组细胞类型去卷积方法研究（STdGCN）
Yawei Li,Yuan Luo
Yawei Li
Spatially resolved transcriptomics integrates high-throughput transcriptome measurements with preserved spatial cellular organization information. However, many technologies cannot reach single-cell resolution. We present STdGCN, a graph mo...