Imbalanced chromatin distribution in cellular senescence specifies paraspeckle dynamics [0.03%]
染色质分布不平衡控制衰老细胞中寄生 speck 动态变化机制研究
Joonwoo Lee,Jinmi Choi,Jeongeun Park et al.
Joonwoo Lee et al.
Cellular senescence is accompanied by extensive genomic reorganization, such as senescence-associated heterochromatin foci and expanded interchromatin compartments, to ultimately affect gene expression. Here, we demonstrate that chromatin s...
CLDN10-driven lineage decision in an amnion and primordial germ cell progenitor at the amnion-epiblast boundary in primates [0.03%]
灵长类胚胎原条和羊膜交界区的羊膜及生殖细胞祖细胞分化路径中的 Claudin 10 线粒决定作用
Nikola Sekulovski,Amber E Carleton,Anusha Rengarajan et al.
Nikola Sekulovski et al.
Background: A growing body of evidence from primate embryos as well as in vitro systems supports the notion that amnion and primordial germ cell (PGC) lineage progressing cells share a common precursor. ...
U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis [0.03%]
U-FISH：一种用于基于影像的空间组学分析和AI辅助的FISH诊断的荧光点检测器
Weize Xu,Huaiyuan Cai,Qian Zhang et al.
Weize Xu et al.
Imaging-based spatial-omics advances biomedical discoveries with subcellular resolution and high sensitivity, but accurately identifying signal spots from diverse images remains challenging. We develop U-FISH, a deep learning method that en...
Mammalian conservation of endogenous G-quadruplex reveals their associations with complex traits [0.03%]
内源性G-四链体的哺乳动物保守性及其与复杂性状之间的关联
Ze-Hao Zhang,Zi-Yan Wang,Cong-Hui Li et al.
Ze-Hao Zhang et al.
Background: DNA G-quadruplexes (G4s) are four-stranded DNA structures. Endogenous G-quadruplexes (eG4s) have been identified as pivotal regulatory elements for gene expression in the human genome. The measurement of evolu...
Chemoreceptor family in plant-associated bacteria responds preferentially to the plant signal molecule glycerol 3-phosphate [0.03%]
植物相关细菌中的化学感受器家族偏好性地响应植物信号分子甘油-3-磷酸
Félix Velando,Jiawei Xing,Roberta Genova et al.
Félix Velando et al.
Background: Chemotaxis to plant compounds is frequently the initial step for the colonization of plants by bacteria. Plant pathogens and plant-associated bacteria contain approximately twice as many chemoreceptors as the ...
Integrated phenomic and genomic analyses unveil modes of altered phenotypic plasticity during wheat improvement [0.03%]
集成表型组和基因组分析揭示了小麦改良过程中表型可塑性变化的模式
Linqian Han,Xiaoming Wang,Ryan Benke et al.
Linqian Han et al.
Background: Wheat has a critical role in global food security. During the improvement of wheat from landraces to cultivars, a suite of traits has been modified for higher yields. However, changing patterns of wheat in res...
Deep tissue profiling of Populus stem at single nucleus level reveals uncharacterized cell types and cell-specific gene regulatory networks [0.03%]
单细胞核水平深入鉴定杨树茎的细胞类型及特异基因表达网络
Henry W Schmidt,Daniel Conde,Wendell J Pereira et al.
Henry W Schmidt et al.
Background: Single-cell genomics is revolutionizing plant developmental biology, enabling the transcriptome profiling of individual cells and their lineage relationships. However, plant cell walls polymers hamper the diss...
Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner [0.03%]
通过TranSigner准确分配长RNA测序读段以增强转录组表达定量
Hyun Joo Ji,Mihaela Pertea
Hyun Joo Ji
Long-read RNA sequencing captures transcripts at full lengths, but existing methods for transcriptome profiling using long-read data often produce inconsistent transcript identification and quantification results. Here, we introduce TranSig...
DelSIEVE: cell phylogeny modeling of single nucleotide variants and deletions from single-cell DNA sequencing data [0.03%]
利用单细胞DNA测序数据对单核苷酸变异和缺失进行细胞谱系建模：DelSieve方法
Senbai Kang,Nico Borgsmüller,Monica Valecha et al.
Senbai Kang et al.
With rapid advancements in single-cell DNA sequencing (scDNA-seq), various computational methods have been developed to study evolution and call variants on single-cell level. However, modeling deletions remains challenging because they aff...
Hongyan Gao,Bowen Li,Zihan Guo et al.
Hongyan Gao et al.
As important mobile elements in prokaryotes, prophages shape the genomic context of their hosts and regulate the structure of bacterial populations. However, it is challenging to precisely identify prophages through computational methods. H...