Saswat K Mohanty,Francesca Chiaromonte,Kateryna D Makova
Saswat K Mohanty
Background: G-quadruplexes (G4s) are non-canonical DNA structures that can form at approximately 1% of the human genome. They facilitate genomic instability by increasing point mutations and structural variation. Numerous...
Plasmids, prophages, and defense systems are depleted from plant microbiota genomes [0.03%]
植物微生物基因组中耗尽了质粒、前噬菌体和防御系统
Avi Bograd,Yaara Oppenheimer-Shaanan,Asaf Levy
Avi Bograd
Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. Here, we compare 38,912 bacterial genomes ...
Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors [0.03%]
通过SEU-TCA整合单细胞和空间转录组学揭示早期心脏祖细胞的空间起源
Jingjing He,Yi Yang,Rui Jiang et al.
Jingjing He et al.
Obtaining single-cell spatial information remains a challenge in spatial transcriptomics. Here we develop SEU-TCA, a method that leverages transfer component analysis to improve single-cell spatial mapping accuracy. Application to multiple ...
A dynamic histone-based chromatin regulatory toolkit underpins genome and developmental evolution in an invertebrate clade [0.03%]
动态的组蛋白介导的染色质调控体系在无脊椎动物门类中推动基因组和发育的进化
Francisco M Martín-Zamora,Joby Cole,Rory D Donnellan et al.
Francisco M Martín-Zamora et al.
Background: The dynamic addition and removal of posttranslational modifications on eukaryotic histones define regulatory regions that play a central role in genome and chromatin biology. However, our understanding of thes...
spaMGCN: a graph convolutional network with autoencoder for spatial domain identification using multi-scale adaptation [0.03%]
基于多尺度自适应自动编码器的图卷积网络的空间领域识别方法研究
Tianjiao Zhang,Hongfei Zhang,Zhongqian Zhao et al.
Tianjiao Zhang et al.
Spatial domain identification is crucial in spatial transcriptomics analysis. Existing methods excel with continuous and clustered distributions but struggle with discrete ones. We present spaMGCN, an innovative approach specifically design...
TORC: Target-Oriented Reference Construction for supervised cell-type identification in scRNA-seq [0.03%]
基于目标导向参考构建的单细胞转录组监督分类方法研究
Xin Wei,Wenjing Ma,Zhijin Wu et al.
Xin Wei et al.
Cell-type identification is a crucial step in single cell RNA-seq (scRNA-seq) data analysis, for which supervised methods are preferred due to their accuracy and efficiency. Performance is highly dependent on the quality of the reference da...
DNA G-quadruplex structures act as functional elements in α- and β-globin enhancers [0.03%]
DNA G-四链体结构作为α-和β-血红蛋白增强子中的功能元件
Colm Doyle,Krzysztof Herka,Sean M Flynn et al.
Colm Doyle et al.
Background: Enhancer elements interact with target genes at a distance to modulate their expression, but the molecular details of enhancer-promoter interaction are incompletely understood. G-quadruplex DNA secondary struc...
Identifying associations of de novo noncoding variants with autism through integration of gene expression, sequence, and sex information [0.03%]
通过基因表达、序列和性别信息的整合来识别自闭症的新发非编码变异关联
Runjia Li,Jason Ernst
Runjia Li
Background: Whole-genome sequencing (WGS) data has facilitated genome-wide identification of rare noncoding variants. However, elucidating these variants' associations with complex diseases remains challenging. A previous...
Transcriptional analysis of metastatic hormone-naïve prostate cancer primary tumor biopsies reveals a relevant role for SOX11 in prostate cancer cell dissemination [0.03%]
转录分析转移性非去势前列腺癌的活检标本发现SOX11在前列腺癌细胞播散中具有相关作用
Natalia Martin-Martin,Saioa Garcia-Longarte,Jon Corres-Mendizabal et al.
Natalia Martin-Martin et al.
Background: Metastatic hormone-naïve prostate cancer (mHNPC) is an infrequent form of this tumor type that is characterized by metastasis at the time of diagnosis and accounts for up to 50% of prostate cancer-related dea...
A resource for whole-body gene expression map of human tissues based on integration of single cell and bulk transcriptomics [0.03%]
基于单细胞和批量转录组学整合的人类组织全基因表达图谱资源
Mengnan Shi,Loren Méar,Max Karlsson et al.
Mengnan Shi et al.
New technologies enable single-cell transcriptome analysis, mapping genome-wide expression across the human body. Here, we present an extended analysis of protein-coding genes in all major human tissues and organs, combining single-cell and...