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...
Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets [0.03%]
评估用于在多样本单细胞数据集中寻找特定条件原型细胞的差异丰度方法
Haidong Yi,Alec Plotkin,Natalie Stanley
Haidong Yi
Background: To analyze the large volume of data generated by single-cell technologies and to identify cellular correlates of particular clinical or experimental outcomes, differential abundance analyses are often applied....
The hazards of genotype imputation when mapping disease susceptibility variants [0.03%]
在绘制疾病易感变异时基因分型插补的危险性
Winston Lau,Aminah Ali,Hannah Maude et al.
Winston Lau et al.
Background: The cost-free increase in statistical power of using imputation to infer missing genotypes is undoubtedly appealing, but is it hazard-free? This case study of three type-2 diabetes (T2D) loci demonstrates that...
Current challenges and future of agricultural genomes to phenomes in the USA [0.03%]
美国农业基因组到表型组现状的当前挑战和未来发展前景
Christopher K Tuggle,Jennifer L Clarke,Brenda M Murdoch et al.
Christopher K Tuggle et al.
Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by improvements in identifying and measuring relevant trait variation in such populations across many environments (p...