Bayesian multi-study non-negative matrix factorization for mutational signatures [0.03%]
用于突变特征的多研究非负矩阵因子分解的贝叶斯方法
Isabella N Grabski,Lorenzo Trippa,Giovanni Parmigiani
Isabella N Grabski
Mutational signatures are typically identified from tumor genome sequencing data using non-negative matrix factorization (NMF). However, existing NMF techniques only decompose a single dataset, limiting rigorous comparisons of signatures ac...
Benjamin J Livesey,Mihaly Badonyi,Mafalda Dias et al.
Benjamin J Livesey et al.
Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human genetic variation, as well as in other applications like protein e...
Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data with miRTalk [0.03%]
基于miRTalk的单细胞转录组数据的外泌体衍生miRNA介导的细胞间通讯推断方法
Xin Shao,Lingqi Yu,Chengyu Li et al.
Xin Shao et al.
MicroRNAs are released from cells in extracellular vesicles (EVs), representing an essential mode of cell-cell communication (CCC) via a regulatory effect on gene expression. Single-cell RNA-sequencing technologies have ushered in an era of...
Post-cleavage target residence determines asymmetry in non-homologous end joining of Cas12a-induced DNA double strand breaks [0.03%]
crispr-cas12a介导的dna双链断裂非同源末端连接修复途径中非对称性形成机制研究
Ruo-Dan Chen,Yi Yang,Kun-Ming Liu et al.
Ruo-Dan Chen et al.
Background: After Cas12a cleaves its DNA target, it generates a DNA double strand break (DSB) with two compatible 5'-staggered ends. The Cas12a-gRNA complex remains at the protospacer adjacent motif (PAM)-proximal end (PP...
Genomic evidence for low genetic diversity but purging of strong deleterious variants in snow leopards [0.03%]
基因组证据表明雪豹遗传多样性较低但强烈有害变异被清除
Lin Yang,Hong Jin,Qien Yang et al.
Lin Yang et al.
Background: Long-term persistence of species with low genetic diversity is the focus of widespread attention in conservation biology. The snow leopard, Panthera uncia, is a big cat from high-alpine regions of Asia. Howeve...
Spatiotemporal transcriptomics reveals key gene regulation for grain yield and quality in wheat [0.03%]
时空转录组揭示了影响小麦产量和质量的关键基因调控机制
Xiaohui Li,Yiman Wan,Dongzhi Wang et al.
Xiaohui Li et al.
Background: Cereal grain size and quality are critical agronomic traits in crop production. Wheat grain development is governed by intricate regulatory networks that require precise spatiotemporal coordination of gene exp...
TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks [0.03%]
TFProfiler：一种广泛测量转录因子活性并识别机制上不同的网络的转录因子推理方法
Taylor Jones,Rutendo F Sigauke,Lynn Sanford et al.
Taylor Jones et al.
TF Profiler is a method of inferring transcription factor (TF) regulatory activity, i.e., when a TF is present and actively participating in the regulation of transcription, directly from nascent sequencing assays such as PRO-seq and GRO-se...
Filtering cells with high mitochondrial content depletes viable metabolically altered malignant cell populations in cancer single-cell studies [0.03%]
根据癌症单细胞研究过滤高线粒体含量的细胞可耗尽活的代谢改变的恶性细胞群
Josephine Yates,Agnieszka Kraft,Valentina Boeva
Josephine Yates
Background: Single-cell transcriptomics has transformed our understanding of cellular diversity, yet noise from technical artifacts and low-quality cells can obscure key biological signals. A common practice is filtering ...
The histone acetyltransferase CBP participates in regulating the DNA damage response through ATM after double-strand breaks [0.03%]
CBP组蛋白乙酰转移酶通过ATM参与DNA双链断裂后的损伤修复反应调节作用
Wafaa S Ramadan,Samrein B M Ahmed,Iman M Talaat et al.
Wafaa S Ramadan et al.
Background: Spatial and temporal control of DNA damage response pathways after DNA damage is crucial for maintenance of genomic stability. Ataxia telangiectasia mutated (ATM) protein plays a central role in DNA damage res...
MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles [0.03%]
基于生物原理的可解释多组学数据集成的深度原型分析（MIDAA）
Salvatore Milite,Giulio Caravagna,Andrea Sottoriva
Salvatore Milite
High-throughput multi-omic molecular profiling allows the probing of biological systems at unprecedented resolution. However, integrating and interpreting high-dimensional, sparse, and noisy multimodal datasets remains challenging. Deriving...