A survey of computational approaches for characterizing microbial interactions in microbial mats [0.03%]
用于表征微生物被膜中微生物相互作用的计算方法综述
Vanesa L Perillo,Michael Nute,Nicolae Sapoval et al.
Vanesa L Perillo et al.
In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the facto...
cuteFC: regenotyping structural variants through an accurate and efficient force-calling method [0.03%]
cuteFC：通过准确高效的强制调用方法对结构变异进行重分型
Tao Jiang,Shuqi Cao,Yadong Liu et al.
Tao Jiang et al.
Long-read sequencing technologies have great potential for the comprehensive discovery of structural variations (SVs). However, accurate genotype assignment for SVs remains challenging due to unavoidable sequencing errors, limited coverage,...
Cancer gene identification from RNA variant allelic frequencies using RVdriver [0.03%]
基于RNA变异等位基因频率的癌症驱动基因识别算法RVdriver
James R M Black,Thomas P Jones,Carlos Martínez-Ruiz et al.
James R M Black et al.
Existing approaches to identifying cancer genes rely overwhelmingly on DNA sequencing data. Here, we introduce RVdriver, a computational tool that leverages paired bulk genomic and transcriptomic data to classify RNA variant allele frequenc...
Engineering novel CRISPRi repressors for highly efficient mammalian gene regulation [0.03%]
高效的哺乳动物基因调控的新型CRISPR干扰阻遏物工程化
Andrew Kristof,Krithika Karunakaran,Christopher Allen et al.
Andrew Kristof et al.
Background: CRISPR interference (CRISPRi), the repurposing of the RNA-guided endonuclease dCas9 as a programmable transcriptional repressor, allows highly specific repression (knockdown) of gene expression. CRISPRi platfo...
MINGLE: a mutual information-based interpretable framework for automatic cell type annotation in single-cell chromatin accessibility data [0.03%]
Siyu Li,Yifan Huang,Shengquan Chen
Siyu Li
Single-cell chromatin accessibility sequencing (scCAS) has proven invaluable for investigating the intricate landscape of epigenomic heterogeneity. We propose MINGLE, a mutual information-based interpretable framework that leverages cellula...
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...