Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data [0.03%]
Transipedia.org：基于k-mer的大规模RNA测序数据集的探索及其在癌症数据分析中的应用
Chloé Bessière,Haoliang Xue,Benoit Guibert et al.
Chloé Bessière et al.
Indexing techniques relying on k-mers have proven effective in searching for RNA sequences across thousands of RNA-seq libraries, but without enabling direct RNA quantification. We show here that arbitrary RNA sequences can be quantified in...
Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation [0.03%]
对SETD2、NSD1、NSD2、NSD3和ASH1L的系统扰动揭示了它们在组蛋白H3K36甲基化中的不同贡献
Gerry A Shipman,Reinnier Padilla,Cynthia Horth et al.
Gerry A Shipman et al.
Background: Methylation of histone 3 lysine 36 (H3K36me) has emerged as an essential epigenetic component for the faithful regulation of gene expression. Despite its importance in development and disease, how the molecula...
Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing [0.03%]
基于单细胞链特异性测序的二倍体基因组组装图形分型方法研究
Mir Henglin,Maryam Ghareghani,William T Harvey et al.
Mir Henglin et al.
Haplotype information is crucial for biomedical and population genetics research. However, current strategies to produce de novo haplotype-resolved assemblies often require either difficult-to-acquire parental data or an intermediate haplot...
Susanna Sawyer,Pere Gelabert,Benjamin Yakir et al.
Susanna Sawyer et al.
Reconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage si...
Drought-responsive dynamics of H3K9ac-marked 3D chromatin interactions are integrated by OsbZIP23-associated super-enhancer-like promoter regions in rice [0.03%]
OsobZIP23相关超级启动子区域整合水稻H3K9ac标记的三维染色质交互作用应对干旱胁迫的动态变化
Yu Chang,Jiahan Liu,Minrong Guo et al.
Yu Chang et al.
Background: In response to drought stress (DS), plants undergo complex processes that entail significant transcriptome reprogramming. However, the intricate relationship between the dynamic alterations in the three-dimens...
Spatiotemporal modeling reveals high-resolution invasion states in glioblastoma [0.03%]
时空建模揭示了胶质母细胞瘤高分辨率的入侵状态
Varsha Thoppey Manoharan,Aly Abdelkareem,Gurveer Gill et al.
Varsha Thoppey Manoharan et al.
Background: Diffuse invasion of glioblastoma cells through normal brain tissue is a key contributor to tumor aggressiveness, resistance to conventional therapies, and dismal prognosis in patients. A deeper understanding o...
DEMINING: A deep learning model embedded framework to distinguish RNA editing from DNA mutations in RNA sequencing data [0.03%]
基于RNA测序数据的RNA编辑与DNA突变区分的深度学习模型嵌入框架
Zhi-Can Fu,Bao-Qing Gao,Fang Nan et al.
Zhi-Can Fu et al.
Precise calling of promiscuous adenosine-to-inosine RNA editing sites from transcriptomic datasets is hindered by DNA mutations and sequencing/mapping errors. Here, we present a stepwise computational framework, called DEMINING, to distingu...
Hao Wang,William Torous,Boying Gong et al.
Hao Wang et al.
Increasingly, scRNA-Seq studies explore cell populations across different samples and the effect of sample heterogeneity on organism's phenotype. However, relatively few bioinformatic methods have been developed which adequately address the...
Integrated large-scale metagenome assembly and multi-kingdom network analyses identify sex differences in the human nasal microbiome [0.03%]
整合宏基因组拼接和多王国网络分析鉴定人类鼻微生物组性别差异
Yanmei Ju,Zhe Zhang,Mingliang Liu et al.
Yanmei Ju et al.
Background: Respiratory diseases impose an immense health burden worldwide. Epidemiological studies have revealed extensive disparities in the incidence and severity of respiratory tract infections between men and women. ...
Optimizing and benchmarking polygenic risk scores with GWAS summary statistics [0.03%]
基于GWAS汇总统计数据的多基因风险评分的优化与基准测试
Zijie Zhao,Tim Gruenloh,Meiyi Yan et al.
Zijie Zhao et al.
Background: Polygenic risk score (PRS) is a major research topic in human genetics. However, a significant gap exists between PRS methodology and applications in practice due to often unavailable individual-level data for...