MNMST: topology of cell networks leverages identification of spatial domains from spatial transcriptomics data [0.03%]
基于空间转录组数据的空间结构域识别构建细胞网络拓扑结构
Yu Wang,Zaiyi Liu,Xiaoke Ma
Yu Wang
Advances in spatial transcriptomics provide an unprecedented opportunity to reveal the structure and function of biology systems. However, current algorithms fail to address the heterogeneity and interpretability of spatial transcriptomics ...
Author Correction: Epiphany: predicting Hi-C contact maps from 1D epigenomic signals [0.03%]
作者更正：Epiphany：从1D表观基因信号预测Hi-C接触图
Rui Yang,Arnav Das,Vianne R Gao et al.
Rui Yang et al.
Published Erratum
Genome biology. 2024 May 23;25(1):132. DOI:10.1186/s13059-024-03281-z 2024
scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data [0.03%]
scCDC：一种在单细胞和单核RNA测序数据中检测和校正基因特异性污染的计算方法
Weijian Wang,Yihui Cen,Zezhen Lu et al.
Weijian Wang et al.
In droplet-based single-cell and single-nucleus RNA-seq assays, systematic contamination of ambient RNA molecules biases the quantification of gene expression levels. Existing methods correct the contamination for all genes globally. Howeve...
In vivo rescue of genetic dilated cardiomyopathy by systemic delivery of nexilin [0.03%]
遗传性扩张型心肌病的体内治疗：通过全身递送nexilin救援遗传性扩张型心肌病
Yanjiao Shao,Canzhao Liu,Hsin-Kai Liao et al.
Yanjiao Shao et al.
Background: Dilated cardiomyopathy (DCM) is one of the most common causes of heart failure. Multiple identified mutations in nexilin (NEXN) have been suggested to be linked with severe DCM. However, the exact association ...
Identification of the RSX interactome in a marsupial shows functional coherence with the Xist interactome during X inactivation [0.03%]
识别有袋动物RSX互作蛋白组 萨克斯激酶型互相作用组在X灭活过程中的功能一致性
Kim L McIntyre,Shafagh A Waters,Ling Zhong et al.
Kim L McIntyre et al.
The marsupial specific RSX lncRNA is the functional analogue of the eutherian specific XIST, which coordinates X chromosome inactivation. We characterized the RSX interactome in a marsupial representative (the opossum Monodelphis domestica)...
Author Correction: Trans-ancestral genome-wide association study of longitudinal pubertal height growth and shared heritability with adult health outcomes [0.03%]
作者更正：纵向青春生长发育的跨祖先系全基因组关联研究及其与成人健康结果的共有遗传性
Jonathan P Bradfeld,Rachel L Kember,Anna Ulrich et al.
Jonathan P Bradfeld et al.
Published Erratum
Genome biology. 2024 May 21;25(1):129. DOI:10.1186/s13059-024-03276-w 2024
Genome-wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression [0.03%]
全基因组复制叉停滞/暂停位点的鉴定及RNA聚合酶II转录与DNA复制进展之间的相互作用
Patricia Rojas,Jianming Wang,Giovanni Guglielmi et al.
Patricia Rojas et al.
Background: DNA replication progression can be affected by the presence of physical barriers like the RNA polymerases, leading to replication stress and DNA damage. Nonetheless, we do not know how transcription influences...
Biologically informed NeuralODEs for genome-wide regulatory dynamics [0.03%]
基于生物信息的神经ODE模型用于全基因组调控动力学研究
Intekhab Hossain,Viola Fanfani,Jonas Fischer et al.
Intekhab Hossain et al.
Background: Gene regulatory network (GRN) models that are formulated as ordinary differential equations (ODEs) can accurately explain temporal gene expression patterns and promise to yield new insights into important cell...
Conditional knockdown of OsMLH1 to improve plant prime editing systems without disturbing fertility in rice [0.03%]
水稻条件性敲除OsMLH1以改进植物Prime编辑系统而不影响其育性
Xiaoshuang Liu,Dongfang Gu,Yiru Zhang et al.
Xiaoshuang Liu et al.
Background: High-efficiency prime editing (PE) is desirable for precise genome manipulation. The activity of mammalian PE systems can be largely improved by inhibiting DNA mismatch repair by coexpressing a dominant-negati...
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data [0.03%]
HATCHet2：从肿瘤批量测序数据中推断克隆和单体型特异性的拷贝数
Matthew A Myers,Brian J Arnold,Vineet Bansal et al.
Matthew A Myers et al.
Bulk DNA sequencing of multiple samples from the same tumor is becoming common, yet most methods to infer copy-number aberrations (CNAs) from this data analyze individual samples independently. We introduce HATCHet2, an algorithm to identif...