Z-scores outperform similar methods for analyzing CRISPR paralog synthetic lethality screens [0.03%]
与CRISPR旁系同源物合成致死筛查分析的类似方法相比，Z分数的表现更佳
Juihsuan Chou,Nazanin Esmaeili Anvar,Reem Elghaish et al.
Juihsuan Chou et al.
Genetic screens offer a promising strategy for identifying tumor-specific therapeutic targets, but single-gene knockout screens often miss functionally redundant paralogs. Multiplex Cas9 and Cas12a CRISPR systems have been deployed to assay...
Maximum likelihood inference of time-scaled cell lineage trees with mixed-type missing data using LAML [0.03%]
基于混合型缺失数据的细胞谱系树的时间尺度的最大似然推断方法LAML
Gillian Chu,Uyen Mai,Henri Schmidt et al.
Gillian Chu et al.
Dynamic lineage tracing technologies combine genome editing with single-cell sequencing to track cell divisions. We introduce Lineage Analysis via Maximum Likelihood (LAML) to infer a maximum likelihood time-resolved cell lineage tree under...
Automated integration of multi-slice spatial transcriptomics data in 2D and 3D using VR-Omics [0.03%]
基于VR-Omics的多模态空间转录组大数据自动化二维和三维整合分析
Denis Bienroth,Natalie Charitakis,Dillon Wong et al.
Denis Bienroth et al.
The field of spatial transcriptomics is rapidly evolving, with increasing sample complexity, resolution, and tissue size. Yet the field lacks comprehensive and intuitive solutions for automated integration and analysis of multi-slice data i...
Deciphering gene regulatory programs in mouse embryonic skin through single-cell multiomics analysis [0.03%]
通过单细胞多组学分析解码小鼠胚胎皮肤基因调控程序
Qiuting Deng,Pengfei Cai,Yingjie Luo et al.
Qiuting Deng et al.
Background: Cell type-specific transcriptional heterogeneity in embryonic mouse skin is well-documented, but few studies have investigated the regulatory mechanisms. Here, we present high-throughput single-cell chromatin ...
The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes [0.03%]
水螅的动态基因组及动物染色体中古活跃重复序列组合
Koto Kon-Nanjo,Tetsuo Kon,Tracy Chih-Ting Koubkova Yu et al.
Koto Kon-Nanjo et al.
Background: Many metazoan genomes are characterized by highly conserved chromosomal homologies that predate the ancient origin of this clade. This conservation has been tested by expansions of selfish DNA elements, in par...
A BAC-guided haplotype assembly pipeline increases the resolution of the virus resistance locus CMD2 in cassava [0.03%]
一种BAC指导的基因型组装管线提高了 cassava 对病毒CMD2 位点解析度
Luc Cornet,Syed Shan-E-Ali Zaidi,Jia Li et al.
Luc Cornet et al.
Background: Cassava is an important crop for food security in the tropics where its production is jeopardized by several viral diseases, including the cassava mosaic disease (CMD) which is endemic in Sub-Saharan Africa an...
Kelly Yichen Li,Qin Cao,Savio Ho-Chit Chow et al.
Kelly Yichen Li et al.
Background: Transcriptional enhancers usually, but not always, regulate genes within the same topologically associating domain (TAD). We hypothesize that this incomplete insulation is partially due to three-dimensional st...
Geometric Diagrams of Genomes: constructing a visual grammar for 3D genomics [0.03%]
基因组的几何图谱：构建三维基因组的视觉语法
Carla Molins-Pitarch,Jonathan Khao,Santiago Bonet et al.
Carla Molins-Pitarch et al.
Advances in the field of three-dimensional (3D) genomics have revealed an ever-expanding array of architectural features that were unknown only a few years ago. Just as ribbon diagrams integrate spatial and symbolic representation to commun...
Jeremy A Arbesfeld,Estelle Y Da,James S Stevenson et al.
Jeremy A Arbesfeld et al.
Background: Experimental data from functional assays have a critical role in interpreting the impact of genetic variants. Assay data must be unambiguously mapped to a reference genome to make it accessible, but it is ofte...
spCLUE: a contrastive learning approach to unified spatial transcriptomics analysis across single-slice and multi-slice data [0.03%]
基于对比学习的空间转录组学跨单切片和多切片数据统一分析方法
Xiang Wang,Wei Vivian Li,Hongwei Li
Xiang Wang
Advances in spatial transcriptomics demand new tools to integrate data across tissue slices and identify consistent spatial domains. We introduce spCLUE, a comprehensive framework combining multi-view graph network, contrastive learning, at...