De novo reconstruction of cell interaction landscapes from single-cell spatial transcriptome data with DeepLinc [0.03%]
基于单细胞空间转录组数据的DeepLinc脱 novo重建细胞互作图谱方法
Runze Li,Xuerui Yang
Runze Li
Based on a deep generative model of variational graph autoencoder (VGAE), we develop a new method, DeepLinc (deep learning framework for Landscapes of Interacting Cells), for the de novo reconstruction of cell interaction networks from sing...
Implicating effector genes at COVID-19 GWAS loci using promoter-focused Capture-C in disease-relevant immune cell types [0.03%]
利用疾病相关免疫细胞中的启动子聚焦型Capture-C鉴定COVID-19基因组广泛关联研究位点上的效应因子基因
Matthew C Pahl,Carole Le Coz,Chun Su et al.
Matthew C Pahl et al.
Background: SARS-CoV-2 infection results in a broad spectrum of COVID-19 disease, from mild or no symptoms to hospitalization and death. COVID-19 disease severity has been associated with some pre-existing conditions and ...
Jan Dohmen,Artem Baranovskii,Jonathan Ronen et al.
Jan Dohmen et al.
Tumors are complex tissues of cancerous cells surrounded by a heterogeneous cellular microenvironment with which they interact. Single-cell sequencing enables molecular characterization of single cells within the tumor. However, cell annota...
3D genome organization in the epithelial-mesenchymal transition spectrum [0.03%]
上皮间质转化谱系中的三维基因组结构与功能关系研究进展
Qing You Pang,Tuan Zea Tan,Vignesh Sundararajan et al.
Qing You Pang et al.
Background: The plasticity along the epithelial-mesenchymal transition (EMT) spectrum has been shown to be regulated by various epigenetic repertoires. Emerging evidence of local chromatin conformation changes suggests th...
NT-seq: a chemical-based sequencing method for genomic methylome profiling [0.03%]
NT-seq：一种基于化学的用于基因组甲基化组分析的测序方法
Xuwen Li,Shiyuan Guo,Yan Cui et al.
Xuwen Li et al.
DNA methylation plays vital roles in both prokaryotes and eukaryotes. There are three forms of DNA methylation in prokaryotes: N6-methyladenine (6mA), N4-methylcytosine (4mC), and 5-methylcytosine (5mC). Although many sequencing methods hav...
Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection [0.03%]
全面评估差异ChIP-seq工具，指导最佳算法选择
Thomas Eder,Florian Grebien
Thomas Eder
Background: The analysis of chromatin binding patterns of proteins in different biological states is a main application of chromatin immunoprecipitation followed by sequencing (ChIP-seq). A large number of algorithms and ...
Interspecific hybridization in tomato influences endogenous viral sRNAs and alters gene expression [0.03%]
番茄种间杂交影响内源病毒sRNAs并改变基因表达
Sara Lopez-Gomollon,Sebastian Y Müller,David C Baulcombe
Sara Lopez-Gomollon
Background: Hybridization is associated with the activation of transposable elements and changes in the patterns of gene expression leading to phenotypic changes. However, the underlying mechanisms are not well understood...
Peiyao Zhao,Jiaqiang Zhu,Ying Ma et al.
Peiyao Zhao et al.
Background: Spatial transcriptomics are a set of new technologies that profile gene expression on tissues with spatial localization information. With technological advances, recent spatial transcriptomics data are often i...
Identifying common transcriptome signatures of cancer by interpreting deep learning models [0.03%]
通过解释深度学习模型来识别癌症的共同转录组标志物
Anupama Jha,Mathieu Quesnel-Vallières,David Wang et al.
Anupama Jha et al.
Background: Cancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have been genetically associated with cancer or shown to directly contribute t...
Eirini Christodoulaki,Viola Nolte,Wei-Yun Lai et al.
Eirini Christodoulaki et al.
Background: Pleiotropy describes the phenomenon in which a gene affects multiple phenotypes. The extent of pleiotropy is still disputed, mainly because of issues of inadequate power of analyses. A further challenge is tha...