scParser: sparse representation learning for scalable single-cell RNA sequencing data analysis [0.03%]
可扩展单细胞RNA测序数据分析的稀疏表示学习方法(scParser)
Kai Zhao,Hon-Cheong So,Zhixiang Lin
Kai Zhao
The rapid rise in the availability and scale of scRNA-seq data needs scalable methods for integrative analysis. Though many methods for data integration have been developed, few focus on understanding the heterogeneous effects of biological...
Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets [0.03%]
测序数据中被忽视的低质量病人样本影响已发表的相关临床重要数据的可重复性
Maximilian Sprang,Jannik Möllmann,Miguel A Andrade-Navarro et al.
Maximilian Sprang et al.
Background: Reproducibility is a major concern in biomedical studies, and existing publication guidelines do not solve the problem. Batch effects and quality imbalances between groups of biological samples are major facto...
StaVia: spatially and temporally aware cartography with higher-order random walks for cell atlases [0.03%]
基于高阶随机游走的空间时间和高阶随机行走的细胞图谱感知制图法
Shobana V Stassen,Minato Kobashi,Edmund Y Lam et al.
Shobana V Stassen et al.
Single-cell atlases pose daunting computational challenges pertaining to the integration of spatial and temporal information and the visualization of trajectories across large atlases. We introduce StaVia, a computational framework that syn...
Benchmarking computational methods for single-cell chromatin data analysis [0.03%]
单细胞染色质数据计算方法的基准测试
Siyuan Luo,Pierre-Luc Germain,Mark D Robinson et al.
Siyuan Luo et al.
Background: Single-cell chromatin accessibility assays, such as scATAC-seq, are increasingly employed in individual and joint multi-omic profiling of single cells. As the accumulation of scATAC-seq and multi-omics dataset...
Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation [0.03%]
综合网络建模方法揭示神经分化过程中的动态增强子-启动子相互作用
William DeGroat,Fumitaka Inoue,Tal Ashuach et al.
William DeGroat et al.
Background: Increasing evidence suggests that a substantial proportion of disease-associated mutations occur in enhancers, regions of non-coding DNA essential to gene regulation. Understanding the structures and mechanism...
Associating transcription factors to single-cell trajectories with DREAMIT [0.03%]
基于DREAMIT的转录因子单细胞轨迹关联分析方法
Nathan D Maulding,Lucas Seninge,Joshua M Stuart
Nathan D Maulding
Inferring gene regulatory networks from single-cell RNA-sequencing trajectories has been an active area of research yet methods are still needed to identify regulators governing cell transitions. We developed DREAMIT (Dynamic Regulation of ...
The GC-content at the 5' ends of human protein-coding genes is undergoing mutational decay [0.03%]
人类蛋白质编码基因的5'端GC含量正在经历突变衰退
Yi Qiu,Yoon Mo Kang,Christopher Korfmann et al.
Yi Qiu et al.
Background: In vertebrates, most protein-coding genes have a peak of GC-content near their 5' transcriptional start site (TSS). This feature promotes both the efficient nuclear export and translation of mRNAs. Despite the...
SynGAP: a synteny-based toolkit for gene structure annotation polishing [0.03%]
基于同线性的基因结构注释修饰工具包SYNGAP
Fengqi Wu,Yingxiao Mai,Chengjie Chen et al.
Fengqi Wu et al.
Genome sequencing has become a routine task for biologists, but the challenge of gene structure annotation persists, impeding accurate genomic and genetic research. Here, we present a bioinformatics toolkit, SynGAP (Synteny-based Gene struc...
READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics [0.03%]
READv2：考古基因组学中先进且用户友好的生物亲缘关系检测方法
Erkin Alaçamlı,Thijessen Naidoo,Merve N Güler et al.
Erkin Alaçamlı et al.
The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient D...
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...