An Atlas of Variant Effects to understand the genome at nucleotide resolution [0.03%]
一个变异效应图谱，在核苷酸分辨率下理解基因组
Douglas M Fowler,David J Adams,Anna L Gloyn et al.
Douglas M Fowler et al.
Sequencing has revealed hundreds of millions of human genetic variants, and continued efforts will only add to this variant avalanche. Insufficient information exists to interpret the effects of most variants, limiting opportunities for pre...
Pei Ni,Yidi Zhao,Ximeng Zhou et al.
Pei Ni et al.
Prime editing is limited by low efficiency in plants. Here, we develop an upgraded engineered plant prime editor in hexaploid wheat, ePPEplus, by introducing a V223A substitution into reverse transcriptase in the ePPEmax* architecture. ePPE...
RAD21 is the core subunit of the cohesin complex involved in directing genome organization [0.03%]
RAD21是染色体粘连复合体的重要组成蛋白，参与基因组高级结构的维持与调控
Yuao Sun,Xin Xu,Wenxue Zhao et al.
Yuao Sun et al.
Background: The ring-shaped cohesin complex is an important factor for the formation of chromatin loops and topologically associating domains (TADs) by loop extrusion. However, the regulation of association between cohesi...
Ha Vu,Jason Ernst
Ha Vu
A large-scale application of the "stacked modeling" approach for chromatin state discovery previously provides a single "universal" chromatin state annotation of the human genome based jointly on data from many cell and tissue types. Here, ...
Panhematopoietic RNA barcoding enables kinetic measurements of nucleate and anucleate lineages and the activation of myeloid clones following acute platelet depletion [0.03%]
全血细胞RNA条形码能够对造血有核和无核谱系的动态变化以及急性血小板耗竭后髓系克隆活化进行测量
Edyta E Wojtowicz,Jayna J Mistry,Vladimir Uzun et al.
Edyta E Wojtowicz et al.
Background: Platelets and erythrocytes constitute over 95% of all hematopoietic stem cell output. However, the clonal dynamics of HSC contribution to these lineages remains largely unexplored. ...
ExplaiNN: interpretable and transparent neural networks for genomics [0.03%]
ExplaiNN：基因组学的可解释透明神经网络
Gherman Novakovsky,Oriol Fornes,Manu Saraswat et al.
Gherman Novakovsky et al.
Deep learning models such as convolutional neural networks (CNNs) excel in genomic tasks but lack interpretability. We introduce ExplaiNN, which combines the expressiveness of CNNs with the interpretability of linear models. ExplaiNN can pr...
Human papillomavirus integration transforms chromatin to drive oncogenesis [0.03%]
人乳头瘤病毒的整合会转化染色体以驱动肿瘤发生
Mehran Karimzadeh,Christopher Arlidge,Ariana Rostami et al.
Mehran Karimzadeh et al.
Background: Human papillomavirus (HPV) drives almost all cervical cancers and up to 70% of head and neck cancers. Frequent integration into the host genome occurs predominantly in tumorigenic types of HPV. We hypothesize ...
DCATS: differential composition analysis for flexible single-cell experimental designs [0.03%]
DCATS：灵活的单细胞实验设计的差异组成分析
Xinyi Lin,Chuen Chau,Kun Ma et al.
Xinyi Lin et al.
Differential composition analysis - the identification of cell types that have statistically significant changes in abundance between multiple experimental conditions - is one of the most common tasks in single cell omic data analysis. Howe...
Transcriptome- and proteome-wide association studies nominate determinants of kidney function and damage [0.03%]
转录组和蛋白质组的全尺度关联研究确定了肾功能和损伤的决定因素
Pascal Schlosser,Jingning Zhang,Hongbo Liu et al.
Pascal Schlosser et al.
Background: The pathophysiological causes of kidney disease are not fully understood. Here we show that the integration of genome-wide genetic, transcriptomic, and proteomic association studies can nominate causal determi...
scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics [0.03%]
基于深度学习的稳健推理和准确预测细胞动力学模型
Qian Li
Qian Li
Despite the continued efforts, a batch-insensitive tool that can both infer and predict the developmental dynamics using single-cell genomics is lacking. Here, I present scTour, a novel deep learning architecture to perform robust inference...