Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections [0.03%]
用于福尔马林固定石蜡包埋组织切片人宿主-病原体共定位研究的双空间解析转录组学
Hailey Sounart,Enikő Lázár,Yuvarani Masarapu et al.
Hailey Sounart et al.
Technologies to study localized host-pathogen interactions are urgently needed. Here, we present a spatial transcriptomics approach to simultaneously capture host and pathogen transcriptome-wide spatial gene expression information from huma...
GeneSegNet: a deep learning framework for cell segmentation by integrating gene expression and imaging [0.03%]
通过整合基因表达和图像的细胞分割深度学习框架GeneSegNet
Yuxing Wang,Wenguan Wang,Dongfang Liu et al.
Yuxing Wang et al.
When analyzing data from in situ RNA detection technologies, cell segmentation is an essential step in identifying cell boundaries, assigning RNA reads to cells, and studying the gene expression and morphological features of cells. We devel...
Single-cell metabolic profiling reveals subgroups of primary human hepatocytes with heterogeneous responses to drug challenge [0.03%]
单细胞代谢谱分析揭示初级人肝细胞亚群对药物刺激的异质性反应
Eva Sanchez-Quant,Maria Lucia Richter,Maria Colomé-Tatché et al.
Eva Sanchez-Quant et al.
Background: Xenobiotics are primarily metabolized by hepatocytes in the liver, and primary human hepatocytes are the gold standard model for the assessment of drug efficacy, safety, and toxicity in the early phases of dru...
The evolution and mutational robustness of chromatin accessibility in Drosophila [0.03%]
果蝇染色质可及性的进化及突变稳健性
Samuel Khodursky,Eric B Zheng,Nicolas Svetec et al.
Samuel Khodursky et al.
Background: The evolution of genomic regulatory regions plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems complicates...
Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue [0.03%]
基于数据驱动的总RNA表达基因鉴定以估计脑组织中异质细胞类型的RNA丰度
Louise A Huuki-Myers,Kelsey D Montgomery,Sang Ho Kwon et al.
Louise A Huuki-Myers et al.
We define and identify a new class of control genes for next-generation sequencing called total RNA expression genes (TREGs), which correlate with total RNA abundance in cell types of different sizes and transcriptional activity. We provide...
MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites [0.03%]
疟疾基因调控区功能解读的深度学习框架疟疾SED：解码疟原虫非编码变异的调控贡献
Chengqi Wang,Yibo Dong,Chang Li et al.
Chengqi Wang et al.
Malaria remains one of the deadliest infectious diseases. Transcriptional regulation effects of noncoding variants in this unusual genome of malaria parasites remain elusive. We developed a sequence-based, ab initio deep learning framework,...
Diego Garrido-Martín,Miquel Calvo,Ferran Reverter et al.
Diego Garrido-Martín et al.
The increasing availability of multidimensional phenotypic data in large cohorts of genotyped individuals requires efficient methods to identify genetic effects on multiple traits. Permutational multivariate analysis of variance (PERMANOVA)...
Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease [0.03%]
代谢组广泛分析揭露肠道微生物特征并暗示特定菌群功能在终末期肾病中的作用
Pan Zhang,Xifan Wang,Shenghui Li et al.
Pan Zhang et al.
Background: The gut microbiota plays a crucial role in regulating host metabolism and producing uremic toxins in patients with end-stage renal disease (ESRD). Our objective is to advance toward a holistic understanding of...
Robust, scalable, and informative clustering for diverse biological networks [0.03%]
稳健、可扩展且富含信息的算法在各种生物学网络中的聚类应用
Chris Gaiteri,David R Connell,Faraz A Sultan et al.
Chris Gaiteri et al.
Clustering molecular data into informative groups is a primary step in extracting robust conclusions from big data. However, due to foundational issues in how they are defined and detected, such clusters are not always reliable, leading to ...
Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants [0.03%]
植物基因体中动态的DNA甲基化周转与增强的基因表达可塑性相关
Clara J Williams,Dawei Dai,Kevin A Tran et al.
Clara J Williams et al.
Background: In several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA...