SMART: spatial transcriptomics deconvolution using marker-gene-assisted topic model [0.03%]
基于标记基因主题模型的空间转录组去卷积方法
Chen Xi Yang,Don D Sin,Raymond T Ng
Chen Xi Yang
While spatial transcriptomics offer valuable insights into gene expression patterns within the spatial context of tissue, many technologies do not have a single-cell resolution. Here, we present SMART, a marker gene-assisted deconvolution m...
EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data [0.03%]
EpiCHAOS：量化单细胞数据表观基因组异质性的度量标准
Katherine Kelly,Michael Scherer,Martina Maria Braun et al.
Katherine Kelly et al.
Epigenetic heterogeneity is a fundamental property of biological systems and is recognized as a potential driver of tumor plasticity and therapy resistance. Single-cell epigenomics technologies have been widely employed to study epigenetic ...
Chromatin loops gather targets of upstream regulators together for efficient gene transcription regulation during vernalization in wheat [0.03%]
基于小麦春化过程中染色质环形成高效基因转录调控的上游调节因子靶点聚集机制研究
Yanyan Liu,Xintong Xu,Chao He et al.
Yanyan Liu et al.
Background: Plants respond to environmental stimuli by altering gene transcription that is highly related with chromatin status, including histone modification, chromatin accessibility, and three-dimensional chromatin int...
Functional screening reveals genetic dependencies and diverging cell cycle control in atypical teratoid rhabdoid tumors [0.03%]
功能筛选揭示了非典型畸胎样/横纹肌样瘤的遗传依赖性和不同的细胞周期控制机制
Daniel J Merk,Foteini Tsiami,Sophie Hirsch et al.
Daniel J Merk et al.
Background: Atypical teratoid rhabdoid tumors (ATRT) are incurable high-grade pediatric brain tumors. Despite intensive research efforts, the prognosis for ATRT patients under currently established treatment protocols is ...
MoCHI: neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data [0.03%]
MoCHI：利用神经网络拟合可解释模型并从深度点突变扫描数据中量化能量、能级耦合、上位效应和别构作用
Andre J Faure,Ben Lehner
Andre J Faure
We present MoCHI, a tool to fit interpretable models using deep mutational scanning data. MoCHI infers free energy changes, as well as interaction terms (energetic couplings) for specified biophysical models, including from multimodal pheno...
HTAD: a human-in-the-loop framework for supervised chromatin domain detection [0.03%]
基于监督学习的染色质拓扑域检测的人机交互框架
Wei Shen,Ping Zhang,Yiwei Jiang et al.
Wei Shen et al.
Topologically associating domains (TADs) are essential units of genome architecture, influencing transcriptional regulation and diseases. Despite numerous methods proposed for TAD identification, it remains challenging due to complex backgr...
Genetic-by-age interaction analyses on complex traits in UK Biobank and their potential to identify effects on longitudinal trait change [0.03%]
英国生物样本库复杂性状的基因年龄交互作用分析及其识别纵向表型变化效应的潜力
Thomas W Winkler,Simon Wiegrebe,Janina M Herold et al.
Thomas W Winkler et al.
Background: Genome-wide association studies (GWAS) have identified thousands of loci for disease-related human traits in cross-sectional data. However, the impact of age on genetic effects is underacknowledged. Also, iden...
Publisher Correction: Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing [0.03%]
出版更正：标记小麦中的大型CNV区块可利用超低覆盖率测序增强种质资源的数字化
Jianxia Niu,Wenxi Wang,Zihao Wang et al.
Jianxia Niu et al.
Published Erratum
Genome biology. 2024 Nov 25;25(1):298. DOI:10.1186/s13059-024-03442-0 2024
Hierarchical annotation of eQTLs by H-eQTL enables identification of genes with cell type-divergent regulation [0.03%]
分级的eQTL注释可实现H-eQTL方法对具有细胞类型特异性调控基因的识别
Pawel F Przytycki,Katherine S Pollard
Pawel F Przytycki
While context-type-specific regulation of genes is largely determined by cis-regulatory regions, attempts to identify cell type-specific eQTLs are complicated by the nested nature of cell types. We present hierarchical eQTL (H-eQTL), a netw...
scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes [0.03%]
scStatDyn：通过建模单细胞水平的表达变化解码药物反应性肿瘤细胞状态动力学
Wenbo Guo,Xinqi Li,Dongfang Wang et al.
Wenbo Guo et al.
Understanding tumor cell heterogeneity and plasticity is crucial for overcoming drug resistance. Single-cell technologies enable analyzing cell states at a given condition, but catenating static cell snapshots to characterize dynamic drug r...