A comprehensive study of genetic regulation and disease associations of plasma circulatory microRNAs using population-level data [0.03%]
基于人群队列的血浆循环微小核糖核酸遗传调控和疾病相关性研究
Rima Mustafa,Michelle M J Mens,Arno van Hilten et al.
Rima Mustafa et al.
Background: MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression. Perturbations in plasma miRNA levels are known to impact disease risk and have potential as disease biomarkers...
Scalable identification of lineage-specific gene regulatory networks from metacells with NetID [0.03%]
基于元细胞的谱系特异性基因调控网络可扩展识别方法NetID
Weixu Wang,Yichen Wang,Ruiqi Lyu et al.
Weixu Wang et al.
The identification of gene regulatory networks (GRNs) is crucial for understanding cellular differentiation. Single-cell RNA sequencing data encode gene-level covariations at high resolution, yet data sparsity and high dimensionality hamper...
MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge [0.03%]
MHConstructor：一种高效解决MHC拼接难题的软体方案
Kristen J Wade,Rayo Suseno,Kerry Kizer et al.
Kristen J Wade et al.
The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short-read, de novo assembly algorit...
Multi-omics reveals lactylation-driven regulatory mechanisms promoting tumor progression in oral squamous cell carcinoma [0.03%]
多组学揭示乳酰化驱动的促进口腔鳞状细胞癌进展的调控机制
Fengyang Jing,Lijing Zhu,Jianyun Zhang et al.
Fengyang Jing et al.
Background: Lactylation, a post-translational modification, is increasingly recognized for its role in cancer progression. This study investigates its prevalence and impact in oral squamous cell carcinoma (OSCC). ...
HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data [0.03%]
一种分层的贝叶斯交互模型：估计细胞特异性甲基化定量特征位点，结合来自细胞分类鸟枪法测序数据的先验条件(HBI模型)
Youshu Cheng,Biao Cai,Hongyu Li et al.
Youshu Cheng et al.
Methylation quantitative trait loci (meQTLs) quantify the effects of genetic variants on DNA methylation levels. However, most published studies utilize bulk methylation datasets composed of different cell types and limit our understanding ...
Malick Ndiaye,Silvia Prieto-Baños,Lucy M Fitzgerald et al.
Malick Ndiaye et al.
The exponential increase in sequencing data calls for conceptual and computational advances to extract useful biological insights. One such advance, minimizers, allows for reducing the quantity of data handled while maintaining some of its ...
The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation [0.03%]
核糖体谱分析揭示了酵母广泛而多样的翻译景观
Chris Papadopoulos,Hugo Arbes,David Cornu et al.
Chris Papadopoulos et al.
Background: Pervasive translation is a widespread phenomenon that plays a critical role in the emergence of novel microproteins, but the diversity of translation patterns contributing to their generation remains unclear. ...
SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data [0.03%]
基于空间条形码转录组数据的细胞类型去卷积的混合机器学习和回归方法(SDePER)
Yunqing Liu,Ningshan Li,Ji Qi et al.
Yunqing Liu et al.
Spatial barcoding-based transcriptomic (ST) data require deconvolution for cellular-level downstream analysis. Here we present SDePER, a hybrid machine learning and regression method to deconvolve ST data using reference single-cell RNA seq...
scCTS: identifying the cell type-specific marker genes from population-level single-cell RNA-seq [0.03%]
scCTS：从群体水平单细胞RNA序列中识别特定细胞类型的标记基因
Luxiao Chen,Zhenxing Guo,Tao Deng et al.
Luxiao Chen et al.
Single-cell RNA-sequencing (scRNA-seq) provides gene expression profiles of individual cells from complex samples, facilitating the detection of cell type-specific marker genes. In scRNA-seq experiments with multiple donors, the population ...
zMAP toolset: model-based analysis of large-scale proteomic data via a variance stabilizing z-transformation [0.03%]
zMAP工具集：基于模型的大规模蛋白质组数据的方差稳定z转换分析
Xiuqi Gui,Jing Huang,Linjie Ruan et al.
Xiuqi Gui et al.
Isobaric labeling-based mass spectrometry (ILMS) has been widely used to quantify, on a proteome-wide scale, the relative protein abundance in different biological conditions. However, large-scale ILMS data sets typically involve multiple r...