A nucleoporin-associated signaling cascade controls plant immunity via histone modification [0.03%]
与核孔蛋白相关信号通路通过组蛋白修饰控制植物免疫反应
Leiwen Pan,Shun Peng,Yuehui Zhang et al.
Leiwen Pan et al.
Background: Plants undergo massive transcriptional reprogramming upon pathogen infection. The transcription factors SAR DEFICIENT1 (SARD1) and CAM-BINDING PROTEIN 60-LIKE G (CBP60g) are master regulators of this process. ...
SpatPPI: a geometric deep learning model for predicting protein-protein interactions involving intrinsically disordered regions [0.03%]
基于几何的深度学习模型预测内在无序区域的蛋白质-蛋白质相互作用
Zeyu Xu,Yanhao Zhu,Jiyun Han et al.
Zeyu Xu et al.
Intrinsically disordered proteins and regions (IDRs) lack stable 3D structures, posing challenges for interaction prediction. We present SpatPPI, a geometric deep learning model tailored for IDPPI prediction. SpatPPI leverages structural cu...
Silent mutations in coding regions of Hepatitis C virus affect patterns of HCV RNA structures and attenuate viral replication and pathogenesis [0.03%]
丙型肝炎病毒的编码区沉默突变会影响HCV RNA结构模式并减弱病毒复制和致病性
Roba Dabour,Shaked Bergman,Zohar Zafrir et al.
Roba Dabour et al.
Background: Vaccines based on live attenuated viruses are the most effective strategy for controlling infections, since they elicit long-lasting natural and effective immune response, but entail challenges for safety and ...
Hai-Jun Liu,Jingxian Fu,Shuhua Xu et al.
Hai-Jun Liu et al.
The prevalence of synthetic associations in GWAS, where non-causal variants become significant by tagging multiple undetected causal variants and not necessarily in strong linkage disequilibrium with any single one, remains unexplored. We i...
Cisformer: a scalable cross-modality generation framework for decoding transcriptional regulation at single-cell resolution [0.03%]
基于单细胞分辨率解码转录调控的可扩展跨模式生成框架
Luzhang Ji,Qihang Zou,Ke Tang et al.
Luzhang Ji et al.
Single-cell multiomic technologies enable the joint analysis of different modalities, but face challenges due to experimental complexity. Current computational methods for single-cell cross-modality translation lack biological interpretabil...
xCell 2.0: robust algorithm for cell type proportion estimation predicts response to immune checkpoint blockade [0.03%]
xCell 2.0：稳健的算法可估算细胞类型比例，预测对免疫检查点抑制剂的反应
Almog Angel,Loai Naom,Shir Nabet-Levy et al.
Almog Angel et al.
Background: Accurate estimation of cell type proportions from bulk gene expression data is essential for understanding the cellular heterogeneity underlying complex tissues and diseases. Here, we introduce xCell 2.0, an a...
Jialu Wu,Qing Ye,Yilin Wang et al.
Jialu Wu et al.
Background: Single-cell foundation models (scFMs) have emerged as powerful tools for integrating heterogeneous datasets and exploring biological systems. Despite high expectations, their ability to extract unique biologic...
Incorporating additive genetic effects and linkage disequilibrium information to discover gene-environment interactions using BV-LDER-GE [0.03%]
利用BV-LDER-GE模型发现基因-环境互作效应并整合加性遗传效应和连锁不平衡信息
Zihan Dong,Wei Jiang,Jiangnan Shen et al.
Zihan Dong et al.
Uncovering environmental factors interacting with genetic factors to influence complex traits is important in genetic epidemiology and disease etiology. We introduce BiVariate Linkage-Disequilibrium Eigenvalue Regression for Gene-Environmen...
Unico: a unified model for cell-type resolution genomics from heterogeneous omics data [0.03%]
基于组学数据的单细胞分辨率基因组学统一模型_UNICO
Zeyuan Johnson Chen,Elior Rahmani,Eran Halperin
Zeyuan Johnson Chen
Most population-scale genomic datasets collected to date consist of "bulk" samples obtained from heterogeneous tissues, reflecting mixtures of different cell types. We introduce Unico, a Unified cross-omics computational method designed to ...
GWAS-informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density [0.03%]
基于GWAS的数据库整合及非编码CRISPRi筛选揭示骨密度遗传病因
Mitchell Conery,James A Pippin,Yadav Wagley et al.
Mitchell Conery et al.
Background: Over 1100 independent signals have been identified with genome-wide association studies (GWAS) for bone mineral density (BMD), a key risk factor for mortality-increasing fragility fractures; however, the effec...