Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework [0.03%]
Splice_sim：一种用于RNA测序模拟和评估的核苷酸转换框架
Niko Popitsch,Tobias Neumann,Arndt von Haeseler et al.
Niko Popitsch et al.
Nucleotide conversion RNA sequencing techniques interrogate chemical RNA modifications in cellular transcripts, resulting in mismatch-containing reads. Biases in mapping the resulting reads to reference genomes remain poorly understood. We ...
A feedback loop driven by H3K9 lactylation and HDAC2 in endothelial cells regulates VEGF-induced angiogenesis [0.03%]
内皮细胞中的H3K9乳酸化和HDAC2反馈回路调控VEGF诱导的血管生成
Wei Fan,Shuhao Zeng,Xiaotang Wang et al.
Wei Fan et al.
Background: Vascular endothelial growth factor (VEGF) is one of the most powerful proangiogenic factors and plays an important role in multiple diseases. Increased glycolytic rates and lactate accumulation are associated ...
scHolography: a computational method for single-cell spatial neighborhood reconstruction and analysis [0.03%]
基于计算的单细胞空间微环境重构与分析方法（scholography）
Yuheng C Fu,Arpan Das,Dongmei Wang et al.
Yuheng C Fu et al.
Spatial transcriptomics has transformed our ability to study tissue complexity. However, it remains challenging to accurately dissect tissue organization at single-cell resolution. Here we introduce scHolography, a machine learning-based me...
Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons [0.03%]
替代剪接与无效介导的降解在小鼠神经元发育过程中协调下调非神经元基因表达
Anna Zhuravskaya,Karen Yap,Fursham Hamid et al.
Anna Zhuravskaya et al.
Background: The functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-mediated decay (NMD) can modulate transcript abundance. Previous studies have identifie...
Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome [0.03%]
评估NGS技术和生物信息学工具在超二倍体癌症基因组中检测体细胞拷贝数变异的能力
Daniall Masood,Luyao Ren,Cu Nguyen et al.
Daniall Masood et al.
Background: Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of therapeutic treatments. Using data sets established in our previous study,...
An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs [0.03%]
整合单细胞RNA测序的神经母细胞瘤肿瘤和临床前模型地图揭示了不同的间质样基因表达程序
Richard H Chapple,Xueying Liu,Sivaraman Natarajan et al.
Richard H Chapple et al.
Background: Neuroblastoma is a common pediatric cancer, where preclinical studies suggest that a mesenchymal-like gene expression program contributes to chemotherapy resistance. However, clinical outcomes remain poor, imp...
Author Correction: Legal aspects of privacy-enhancing technologies in genome-wide association studies and their impact on performance and feasibility [0.03%]
作者更正：基因组范围关联研究中增强隐私技术的法律方面及其对性能和可行性的影晌
Alissa Brauneck,Louisa Schmalhorst,Stefan Weiss et al.
Alissa Brauneck et al.
Published Erratum
Genome biology. 2024 Jun 18;25(1):160. DOI:10.1186/s13059-024-03311-w 2024
DNA methylation variations underlie lettuce domestication and divergence [0.03%]
甲基化修饰在莴苣 Domestication 和分化过程中的作用
Shuai Cao,Nunchanoke Sawettalake,Ping Li et al.
Shuai Cao et al.
Background: Lettuce (Lactuca sativa L.) is an economically important vegetable crop worldwide. Lettuce is believed to be domesticated from a single wild ancestor Lactuca serriola and subsequently diverged into two major m...
Beyond benchmarking and towards predictive models of dataset-specific single-cell RNA-seq pipeline performance [0.03%]
超越基准建立具有预测性的单细胞RNA测序数据集特异性工作流程性能模型
Cindy Fang,Alina Selega,Kieran R Campbell
Cindy Fang
Background: The advent of single-cell RNA-sequencing (scRNA-seq) has driven significant computational methods development for all steps in the scRNA-seq data analysis pipeline, including filtering, normalization, and clus...
LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA [0.03%]
基于线性扩增的亚硫酸氢盐测序技术(LABS): 用于从游离DNA中进行超高灵敏度癌症检测
Xiao-Long Cui,Ji Nie,Houxiang Zhu et al.
Xiao-Long Cui et al.
Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limitations impede clinical application. Most assays necessitate substantial DNA inputs, posing challenges. Additionally, ...