Improved modeling of RNA-binding protein motifs in an interpretable neural model of RNA splicing [0.03%]
在可解释的RNA剪接神经模型中改进RNA结合蛋白基序的建模
Kavi Gupta,Chenxi Yang,Kayla McCue et al.
Kavi Gupta et al.
Sequence-specific RNA-binding proteins (RBPs) play central roles in splicing decisions. Here, we describe a modular splicing architecture that leverages in vitro-derived RNA affinity models for 79 human RBPs and the annotated human genome t...
Evaluating spatially variable gene detection methods for spatial transcriptomics data [0.03%]
空间转录组学数据中空间可变基因检测方法的评估
Carissa Chen,Hani Jieun Kim,Pengyi Yang
Carissa Chen
Background: The identification of genes that vary across spatial domains in tissues and cells is an essential step for spatial transcriptomics data analysis. Given the critical role it serves for downstream data interpret...
Liang Yang,Jiali Lyu,Xi Li et al.
Liang Yang et al.
Background: Deletion of haploinsufficient genes or duplication of triplosensitive ones results in phenotypic effects in a concentration-dependent manner, and the mechanisms underlying these dosage-sensitive effects remain...
Chromatin activity identifies differential gene regulation across human ancestries [0.03%]
染色质活性识别人类不同祖源之间的差异基因调控
Kade P Pettie,Maxwell Mumbach,Amanda J Lea et al.
Kade P Pettie et al.
Background: Current evidence suggests that cis-regulatory elements controlling gene expression may be the predominant target of natural selection in humans and other species. Detecting selection acting on these elements i...
scSNV-seq: high-throughput phenotyping of single nucleotide variants by coupled single-cell genotyping and transcriptomics [0.03%]
scSNV-seq：通过结合单细胞基因分型和转录组学对单核苷酸变异进行高通量表型分析
Sarah E Cooper,Matthew A Coelho,Magdalena E Strauss et al.
Sarah E Cooper et al.
CRISPR screens with single-cell transcriptomic readouts are a valuable tool to understand the effect of genetic perturbations including single nucleotide variants (SNVs) associated with diseases. Interpretation of these data is currently li...
ARMC5 controls the degradation of most Pol II subunits, and ARMC5 mutation increases neural tube defect risks in mice and humans [0.03%]
ARMC5 控制大多数 RNA 聚合酶 II 亚基的降解，ARMC5 突变会增加小鼠和人类神经管缺陷的风险
Hongyu Luo,Linjiang Lao,Kit Sing Au et al.
Hongyu Luo et al.
Background: Neural tube defects (NTDs) are caused by genetic and environmental factors. ARMC5 is part of a novel ubiquitin ligase specific for POLR2A, the largest subunit of RNA polymerase II (Pol II). ...
ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features [0.03%]
ChIPr：从2D染色质特征准确预测凝聚素介导的3D基因组组织结构
Ahmed Abbas,Khyati Chandratre,Yunpeng Gao et al.
Ahmed Abbas et al.
The three-dimensional genome organization influences diverse nuclear processes. Here we present Chromatin Interaction Predictor (ChIPr), a suite of regression models based on deep neural networks, random forest, and gradient boosting to pre...
Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions [0.03%]
Niche-DE：空间转录组学数据中的生态位差异基因表达分析识别上下文依赖的细胞间相互作用
Kaishu Mason,Anuja Sathe,Paul R Hess et al.
Kaishu Mason et al.
Existing methods for analysis of spatial transcriptomic data focus on delineating the global gene expression variations of cell types across the tissue, rather than local gene expression changes driven by cell-cell interactions. We propose ...
RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9 [0.03%]
RNA结合蛋白RBM5通过激活致癌蛋白HOXA9在急性髓性白血病中起着重要作用
Mengli Zhang,Judith Hyle,Xiaowen Chen et al.
Mengli Zhang et al.
Background: The oncogenic protein HOXA9 plays a critical role in leukemia transformation and maintenance, and its aberrant expression is a hallmark of most aggressive acute leukemia. Although inhibiting the upstream regul...
Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration [0.03%]
通过混合效应机器学习和数据集成改进来自耗竭筛选的细菌CRISPRi引导效率预测
Yanying Yu,Sandra Gawlitt,Lisa Barros de Andrade E Sousa et al.
Yanying Yu et al.
CRISPR interference (CRISPRi) is the leading technique to silence gene expression in bacteria; however, design rules remain poorly defined. We develop a best-in-class prediction algorithm for guide silencing efficiency by systematically inv...