Pan-S-locus analysis reveals insights into the origin and evolution of self-incompatibility in the orange subfamily [0.03%]
泛S位点分析揭示了橙亚科自交不亲和性的起源与进化的新见解
Jianbing Hu,Zezhen Du,Chenchen Liu et al.
Jianbing Hu et al.
Background: Self-incompatibility is controlled by a highly polymorphic supergene complex, the S-locus, which is structurally complex, rich in repetitive sequences, and varies in length from hundreds of kilobases to tens o...
Sol Moe Lee,David C Goldberg,Cameron Cloud et al.
Sol Moe Lee et al.
Background: DNA cytosine modifications, including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), are key epigenetic regulators with distinct functions. Dissecting the ternary code (C, 5mC, 5hmC) across tissues...
High-precision cell-type mapping and annotation of single-cell spatial transcriptomics with STAMapper [0.03%]
基于STAMapper的单细胞空间转录组高精度细胞类型定位与注释
Qunlun Shen,Kangning Dong,Shuqin Zhang et al.
Qunlun Shen et al.
In this paper, we develop a heterogeneous graph neural network, STAMapper, to transfer the cell-type labels from single-cell RNA-sequencing (scRNA-seq) data to single-cell spatial transcriptomics (scST) data. We collect 81 scST datasets con...
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...