ENGEP: advancing spatial transcriptomics with accurate unmeasured gene expression prediction [0.03%]
ENGEP：通过精确的未测量基因表达预测推进空间转录组学的发展
Shi-Tong Yang,Xiao-Fei Zhang
Shi-Tong Yang
Imaging-based spatial transcriptomics techniques provide valuable spatial and gene expression information at single-cell resolution. However, their current capability is restricted to profiling a limited number of genes per sample, resultin...
Benchmarking splice variant prediction algorithms using massively parallel splicing assays [0.03%]
使用大规模并行剪接测定法对剪接变异预测算法进行评估
Cathy Smith,Jacob O Kitzman
Cathy Smith
Background: Variants that disrupt mRNA splicing account for a sizable fraction of the pathogenic burden in many genetic disorders, but identifying splice-disruptive variants (SDVs) beyond the essential splice site dinucle...
Noé Cochetel,Andrea Minio,Andrea Guarracino et al.
Noé Cochetel et al.
Background: Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability ...
scNAT: a deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles [0.03%]
scNAT：一种深度学习方法，用于整合配对的单细胞RNA和T细胞受体测序谱型
Biqing Zhu,Yuge Wang,Li-Ting Ku et al.
Biqing Zhu et al.
Many deep learning-based methods have been proposed to handle complex single-cell data. Deep learning approaches may also prove useful to jointly analyze single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scT...
Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data [0.03%]
Smoother：一种在空间组学数据中引入结构依赖性的统一模块化框架
Jiayu Su,Jean-Baptiste Reynier,Xi Fu et al.
Jiayu Su et al.
Spatial omics technologies can help identify spatially organized biological processes, but existing computational approaches often overlook structural dependencies in the data. Here, we introduce Smoother, a unified framework that integrate...
A time-resolved meta-analysis of consensus gene expression profiles during human T-cell activation [0.03%]
基于人类T细胞活化过程中共识基因表达谱的元分析
Michael Rade,Sebastian Böhlen,Vanessa Neuhaus et al.
Michael Rade et al.
Background: The coordinated transcriptional regulation of activated T-cells is based on a complex dynamic behavior of signaling networks. Given an external stimulus, T-cell gene expression is characterized by impulse and ...
Meta-Analysis
Genome biology. 2023 Dec 14;24(1):287. DOI:10.1186/s13059-023-03120-7 2023
Metabolic GWAS-based dissection of genetic basis underlying nutrient quality variation and domestication of cassava storage root [0.03%]
基于代谢GWAS的木薯储根营养品质变异和驯化遗传基础剖析
Zehong Ding,Lili Fu,Bin Wang et al.
Zehong Ding et al.
Background: Metabolites play critical roles in regulating nutritional qualities of plants, thereby influencing their consumption and human health. However, the genetic basis underlying the metabolite-based nutrient qualit...
Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets [0.03%]
利用单细胞RNA测序数据计算去卷积具有不同细胞大小的异质组织所面临的挑战与机遇
Sean K Maden,Sang Ho Kwon,Louise A Huuki-Myers et al.
Sean K Maden et al.
Deconvolution of cell mixtures in "bulk" transcriptomic samples from homogenate human tissue is important for understanding disease pathologies. However, several experimental and computational challenges impede transcriptomics-based deconvo...
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark [0.03%]
SQANTI-SIM：用于lrRNAseq评估的受控转录新颖性模拟器
Jorge Mestre-Tomás,Tianyuan Liu,Francisco Pardo-Palacios et al.
Jorge Mestre-Tomás et al.
Long-read RNA sequencing has emerged as a powerful tool for transcript discovery, even in well-annotated organisms. However, assessing the accuracy of different methods in identifying annotated and novel transcripts remains a challenge. Her...
Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers [0.03%]
工蜂和采蜜蜂肠道菌群的菌株水平多样性周转调节其功能特征
Gilles L C Baud,Aiswarya Prasad,Kirsten M Ellegaard et al.
Gilles L C Baud et al.
Background: Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain co...