Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads [0.03%]
长RNA序列读取中保留的内含子在样本匹配的短读取中无法可靠检测到
Julianne K David,Sean K Maden,Mary A Wood et al.
Julianne K David et al.
Background: There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but relia...
Gene flow and introgression are pervasive forces shaping the evolution of bacterial species [0.03%]
基因流动和渗入是塑造细菌物种演化的普遍力量
Awa Diop,Ellis L Torrance,Caroline M Stott et al.
Awa Diop et al.
Background: Although originally thought to evolve clonally, studies have revealed that most bacteria exchange DNA. However, it remains unclear to what extent gene flow shapes the evolution of bacterial genomes and maintai...
A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships [0.03%]
一个全球高密度的染色质相互作用网络揭示了功能性的长距离和跨染色体关系
Ruchi Lohia,Nathan Fox,Jesse Gillis
Ruchi Lohia
Background: Chromatin contacts are essential for gene-expression regulation; however, obtaining a high-resolution genome-wide chromatin contact map is still prohibitively expensive owing to large genome sizes and the quad...
Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples [0.03%]
利用肿瘤正常配对参考样本进行个性化基因组组装以准确发现癌症体细胞突变
Chunlin Xiao,Zhong Chen,Wanqiu Chen et al.
Chunlin Xiao et al.
Background: The use of a personalized haplotype-specific genome assembly, rather than an unrelated, mosaic genome like GRCh38, as a reference for detecting the full spectrum of somatic events from cancers has long been ad...
Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques [0.03%]
利用转录组定量技术估计污水中SARS-CoV-2的谱系丰度
Jasmijn A Baaijens,Alessandro Zulli,Isabel M Ott et al.
Jasmijn A Baaijens et al.
Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in...
Sheng Hu Qian,Lu Chen,Yu-Li Xiong et al.
Sheng Hu Qian et al.
Background: Pseudogenes are excellent markers for genome evolution, which are emerging as crucial regulators of development and disease, especially cancer. However, systematic functional characterization and evolution of ...
Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus [0.03%]
全面转录变异分析揭示了油菜种子含油量的基因网络调控机制
Zengdong Tan,Yan Peng,Yao Xiong et al.
Zengdong Tan et al.
Background: Regulation of gene expression plays an essential role in controlling the phenotypes of plants. Brassica napus (B. napus) is an important source for the vegetable oil in the world, and the seed oil content is a...
Mapping responsive genomic elements to heat stress in a maize diversity panel [0.03%]
将玉米多样性群体中的热应激响应基因组元件定位于基因图谱上
Zhikai Liang,Zachary A Myers,Dominic Petrella et al.
Zhikai Liang et al.
Background: Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approaches to effectively uncover the genomic region that regulates distinct responsive patte...
Deciphering the impact of genetic variation on human polyadenylation using APARENT2 [0.03%]
利用APARENT2破译遗传变异对人类多聚腺苷酸化的影响
Johannes Linder,Samantha E Koplik,Anshul Kundaje et al.
Johannes Linder et al.
Background: 3'-end processing by cleavage and polyadenylation is an important and finely tuned regulatory process during mRNA maturation. Numerous genetic variants are known to cause or contribute to human disorders by di...
The landscape of hervRNAs transcribed from human endogenous retroviruses across human body sites [0.03%]
人类内源性逆转录病毒转录的hervRNAs在人体各部位的分布特征
Jianqi She,Minghao Du,Zhanzhan Xu et al.
Jianqi She et al.
Background: Human endogenous retroviruses (HERVs), the remnants of ancient retroviruses, account for 8% of the human genome, but most have lost their transcriptional abilities under physiological conditions. However, moun...