scPriorGraph: constructing biosemantic cell-cell graphs with prior gene set selection for cell type identification from scRNA-seq data [0.03%]
基于先验基因集选择的单细胞类型识别的生物语义细胞互作网络构建（scPriorGraph）
Xiyue Cao,Yu-An Huang,Zhu-Hong You et al.
Xiyue Cao et al.
Cell type identification is an indispensable analytical step in single-cell data analyses. To address the high noise stemming from gene expression data, existing computational methods often overlook the biologically meaningful relationships...
Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria [0.03%]
环节动物甲基组揭示了两侧对称动物发育和衰老相关表观遗传退化的祖先现象
Kero Guynes,Luke A Sarre,Allan M Carrillo-Baltodano et al.
Kero Guynes et al.
Background: DNA methylation in the form of 5-methylcytosine (5mC) is the most abundant base modification in animals. However, 5mC levels vary widely across taxa. While vertebrate genomes are hypermethylated, in most inver...
Current genomic deep learning models display decreased performance in cell type-specific accessible regions [0.03%]
当前的基因组深度学习模型在特定细胞类型可访问区域的表现较差
Pooja Kathail,Richard W Shuai,Ryan Chung et al.
Pooja Kathail et al.
Background: A number of deep learning models have been developed to predict epigenetic features such as chromatin accessibility from DNA sequence. Model evaluations commonly report performance genome-wide; however, cis re...
MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data [0.03%]
矩阵和分析元数据标准，以促进单细胞数据的协调性和可重复性
Irzam Sarfraz,Yichen Wang,Amulya Shastry et al.
Irzam Sarfraz et al.
Many datasets are being produced by consortia that seek to characterize healthy and disease tissues at single-cell resolution. While biospecimen and experimental information is often captured, detailed metadata standards related to data mat...
aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph [0.03%]
基于优化自适应k近邻图的单细胞和空间转录组聚类（AKNNO）
Jia Li,Yu Shyr,Qi Liu
Jia Li
Typical clustering methods for single-cell and spatial transcriptomics struggle to identify rare cell types, while approaches tailored to detect rare cell types gain this ability at the cost of poorer performance for grouping abundant ones....
Epigenomic identification of vernalization cis-regulatory elements in winter wheat [0.03%]
冬季小麦春化 cis 调控元件的表观基因组鉴定
Yanhong Liu,Pan Liu,Lifeng Gao et al.
Yanhong Liu et al.
Background: Winter wheat undergoes vernalization, a process activated by prolonged exposure to low temperatures. During this phase, flowering signals are generated and transported to the apical meristems, stimulating the ...
Modelling the demographic history of human North African genomes points to a recent soft split divergence between populations [0.03%]
人类北非基因组的人口历史模型指向种群最近的软分裂分歧事件
Jose M Serradell,Jose M Lorenzo-Salazar,Carlos Flores et al.
Jose M Serradell et al.
Background: North African human populations present a complex demographic scenario due to the presence of an autochthonous genetic component and population substructure, plus extensive gene flow from the Middle East, Euro...
Phospholipase-mediated phosphate recycling during plant leaf senescence [0.03%]
植物叶片衰老期间的磷脂酶介导的磷酸盐循环回收
Bao Yang,Zengdong Tan,Jiayu Yan et al.
Bao Yang et al.
Background: Phosphorus is a macronutrient necessary for plant growth and development and its availability and efficient use affect crop yields. Leaves are the largest tissue that uses phosphorus in plants, and membrane ph...
Mining alternative splicing patterns in scRNA-seq data using scASfind [0.03%]
利用scASfind在单细胞RNA测序数据中挖掘选择性拼接模式
Yuyao Song,Guillermo Parada,Jimmy Tsz Hang Lee et al.
Yuyao Song et al.
Single-cell RNA-seq (scRNA-seq) is widely used for transcriptome profiling, but most analyses focus on gene-level events, with less attention devoted to alternative splicing. Here, we present scASfind, a novel computational method to allow ...
scCross: a deep generative model for unifying single-cell multi-omics with seamless integration, cross-modal generation, and in silico exploration [0.03%]
SCCROSS：一种深层生成模型，用于统一单细胞多组学数据的无缝整合、跨模式生成和计算机模拟探索
Xiuhui Yang,Koren K Mann,Hao Wu et al.
Xiuhui Yang et al.
Single-cell multi-omics data reveal complex cellular states, providing significant insights into cellular dynamics and disease. Yet, integration of multi-omics data presents challenges. Some modalities have not reached the robustness or cla...