HAK-actin, a U-ExM-compatible probe to image the actin cytoskeleton [0.03%]
兼容U-ExM的成像肌动蛋白细胞骨架的探针HAK-actin
Olivier Mercey,Luc Reymond,Florent Lemaître et al.
Olivier Mercey et al.
Expansion microscopy (ExM) enables super-resolution imaging by physically enlarging biological samples. While ExM has been successfully applied to study the intracellular microtubule cytoskeleton, reliable probes for visualizing actin fiber...
A tri-modal contrastive learning framework for protein representation learning [0.03%]
一种用于蛋白质表征学习的三模式对比学习框架
Li Zhang,Han Guo,Leah Schaffer et al.
Li Zhang et al.
Protein foundation models, particularly protein language models, have shown strong success in learning meaningful protein representations using transformer architectures pretrained on large-scale datasets through self-supervised learning. T...
Differential expression analysis in single-cell and spatial RNA-seq without model assumptions [0.03%]
无需模型假设的单细胞和空间RNA测序差异表达分析
Gennady Margolin,Andrew Tang,Sergey Leikin
Gennady Margolin
Gene up(down)regulation findings in single-cell and spatial RNA sequencing can be inconsistent despite remarkable progress in technology. Inconsistent findings in high-quality samples raise concerns about assumptions behind widely accepted ...
ProtFI, an efficient frailty-trained proteomics-based biomarker of aging, robustly predicts age-related decline [0.03%]
基于蛋白质组学的脆弱性训练生物标志物ProtFI可有效预测衰老相关的生理功能下降
Swier Garst,Lieke Kuiper,Erik van den Akker et al.
Swier Garst et al.
Many molecular aging biomarkers have been developed to capture heterogeneity in individual aging rates. Yet, systematic comparison of the modeling choices underlying these biomarkers has been limited. In this study, we trained aging biomark...
Spatial mapping of microbial communities by an integrated automation platform of sequential FISH [0.03%]
基于序贯FISH技术的自动化平台进行微生物群落空间分布映射
Zhaohui Cao,Wenlong Zuo,Lanxiang Wang et al.
Zhaohui Cao et al.
Spatial mapping of microbial communities at single-cell resolution is opening up dimensions to understand microbiome organization and function. However, current fluorescence in situ hybridization (FISH) methods for microbiomes are limited b...
Cellular-state control using ribozyme-scaffolded miRNA-sensing and CRISPR-mediated actuation [0.03%]
基于核糖酶支架的miRNA检测和CRISPR激活的细胞状态控制
Taek Kang,Leonidas Bleris
Taek Kang
Cellular transitions between states are fundamental to development, adaptation, and pathological processes, but monitoring and guiding these transitions using endogenous signals remain challenging. MicroRNAs (miRNAs) represent a powerful mo...
R-PLA enables enhanced detection of R-loops in mammalian cells using proximity ligation [0.03%]
邻近连接使能在哺乳动物细胞中使用R-PLA增强检测R环
Anthony Sanchez,Jullian O Perren,Meili Aiello et al.
Anthony Sanchez et al.
R-loops are key nucleic acid structures involved in many biological processes including DNA damage responses. Here, we develop a method for detecting and visualizing R-loops using fluorescence microscopy by combining S9.6 and RNaseH1 antibo...
A lightweight TcrLM model predicts T cell receptor and epitope binding specificity [0.03%]
轻量级的TcrLM模型预测T细胞受体和表位结合特异性
Chenpeng Yu,Xing Fang,Shiye Tian et al.
Chenpeng Yu et al.
Immune responses depend on specific interactions between T cell receptors (TCRs) and peptides presented by antigen-presenting cells (APCs). The vast diversity of the TCR repertoire makes accurate prediction of TCR-antigen binding specificit...
A high-speed attention network for MHC-bound peptide identification and 3D modeling [0.03%]
基于高阶张量卷积网络的脑疾病诊断模型及图嵌入方法研究
Coos A B Baakman,Giulia Crocioni,Cunliang Geng et al.
Coos A B Baakman et al.
We developed SwiftMHC, an ultra-fast and accurate structure-based framework for peptide-MHC (pMHC) modeling and binding affinity prediction. Using task-specific deep learning trained on physics-derived synthetic data, SwiftMHC predicts pMHC...
Multiscale domain identification for spatial transcriptomics via persistent homology [0.03%]
基于持久同调的空序转录组学多尺度域识别
Perry Beamer,Zixuan Cang
Perry Beamer
Spatial transcriptomics (ST) measures gene expression at a set of spatial locations in a tissue. Communities of nearby cells that express similar genes form spatial domains. Specialized clustering algorithms have been developed to identify ...