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...
Cotton pedigree genome reveals restriction of cultivar-driven strategy in cotton breeding [0.03%]
棉花亲本基因组揭示了育种策略的局限性
Shang Liu,Dongyun Zuo,Hailiang Cheng et al.
Shang Liu et al.
Background: Many elite genes have been identified from the available cotton genomic data, providing various genetic resources for gene-driven breeding. However, backbone cultivar-driven breeding is the most widely applied...
DNA methylation modulated genetic variant effect on gene transcriptional regulation [0.03%]
DNA甲基化调节遗传变异对基因转录调控的作用
Yong Zeng,Rahi Jain,Magnus Lam et al.
Yong Zeng et al.
Background: Expression quantitative trait locus (eQTL) analysis has emerged as an important tool in elucidating the link between genetic variants and gene expression, thereby bridging the gap between risk SNPs and associa...
Pediatric glioma histone H3.3 K27M/G34R mutations drive abnormalities in PML nuclear bodies [0.03%]
组蛋白H3.3 K27M和G34R突变引起胶质瘤细胞PML核小体异常
Hsiao P J Voon,Linda Hii,Andrew Garvie et al.
Hsiao P J Voon et al.
Background: Point mutations in histone variant H3.3 (H3.3K27M, H3.3G34R) and the H3.3-specific ATRX/DAXX chaperone complex are frequent events in pediatric gliomas. These H3.3 point mutations affect many chromatin modific...
GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins [0.03%]
GCLiPP：用于构建RNA结合蛋白高分辨率占用图的全局交联和蛋白质纯化方法
Wandi S Zhu,Adam J Litterman,Harshaan S Sekhon et al.
Wandi S Zhu et al.
GCLiPP is a global RNA interactome capture method that detects RNA-binding protein (RBP) occupancy transcriptome-wide. GCLiPP maps RBP-occupied sites at a higher resolution than phase separation-based techniques. GCLiPP sequence tags corres...