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...
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet [0.03%]
用扩展的表观遗传字母来模拟甲基敏感的转录因子序列模式
Coby Viner,Charles A Ishak,James Johnson et al.
Coby Viner et al.
Background: Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified bases. Curren...
GTax: improving de novo transcriptome assembly by removing foreign RNA contamination [0.03%]
GTax：通过去除外来RNA污染来改善从头转录组组装
Roberto Vera Alvarez,David Landsman
Roberto Vera Alvarez
The cost and complexity of generating a complete reference genome means that many organisms lack an annotated reference. An alternative is to use a de novo reference transcriptome. This technology is cost-effective but is susceptible to off...
Hamid Kian Gaikani,Monika Stolar,Divya Kriti et al.
Hamid Kian Gaikani et al.
The history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model re...