Urinary Proteomics: Biological Foundations, Analytical Frameworks, and Clinical Translation Across Human Diseases [0.03%]
Fanjie Meng,Yuxuan Xiao,Xincheng Li et al.
Fanjie Meng et al.
Urinary proteomics has swiftly emerged as a formidable tool for the identification of non-invasive biomarkers and the surveillance of diseases. The progression in high-resolution mass spectrometry and data-independent acquisition techniques...
Metabolomics Identified Caloric Restriction-associated Glycerophospholipid Alterations in ApoE-/- Mice [0.03%]
Zi-Yu Wei,He-Ping Wang,Song Tang et al.
Zi-Yu Wei et al.
Caloric restriction (CR) improves metabolic health and reduces the risk of aging-related vascular diseases. However, the systematic metabolic reprogramming associated with CR remains unclear. To address this, we performed multi-tissue metab...
Variant Calling in the Dark Genome: Benchmarking SNV Calls in the Flanks of Structural Variants [0.03%]
Ningxin Dang,Peng Jia,Jiadong Lin et al.
Ningxin Dang et al.
Single nucleotide variant calling protocols routinely discard calls in the regions immediately flanking structural variants (often 50 bp either side) because it is technically challenging to call them accurately. Although there are undoubte...
StarFunc: Fusing Template-based and Deep Learning Approaches for Accurate Protein Function Prediction [0.03%]
StarFunc：融合模板和深度学习方法进行精确的蛋白质功能预测
Chengxin Zhang,Quancheng Liu,Lydia Freddolino
Chengxin Zhang
Deep learning has significantly advanced the development of high-performance methods for protein function prediction. Nonetheless, even for state-of-the-art deep learning approaches, template information remains an indispensable component i...
MetaDIA: A DDA-free Database Reduction Strategy for DIA Human Gut Metaproteomics [0.03%]
一种无DDA的数据库缩减策略用于人类肠道宏蛋白组中的DIA代谢组学研究
Haonan Duan,Zhibin Ning,Zhongzhi Sun et al.
Haonan Duan et al.
Microbiomes, especially within the gut, are complex and may comprise hundreds of species. The identification of peptides in metaproteomics presents a substantial challenge, as it involves matching peptides to mass spectra within an enormous...
Evaluating AlphaFold Tools and Related Scoring Functions for Protein-peptide Complex Prediction [0.03%]
评估AlphaFold工具及相关打分函数预测蛋白质-肽复合物的能力
Negin Manshour,Jarett Zida Ren,Farzaneh Esmaili et al.
Negin Manshour et al.
Determining the three-dimensional structures of protein-peptide complexes is crucial for elucidating biological processes and designing peptide-based drugs. Protein-peptide docking has become essential for predicting complex structures. Alp...
CD4+ T cells in Type 1 Diabetes: Inferring Stage-specific Dysregulation from scRNA-seq [0.03%]
单细胞RNA测序推断1型糖尿病患者CD4+T细胞的特征性调控变化
Dmitry I Tychinin,Ekaterina S Petriaikina,Olga A Antonova et al.
Dmitry I Tychinin et al.
Deciphering the cellular and molecular mechanisms of type 1 diabetes (T1D) has long been a central goal in immunology. Here, we perform a large-scale single-cell transcriptomic analysis of peripheral blood mononuclear cells from children wi...
Human Single-cell Atlas Analysis Reveals Heterogeneous Endothelial Signaling [0.03%]
人类单细胞图谱分析揭示异质性内皮信号转导
Zimo Zhu,Rongbin Zheng,Yang Yu et al.
Zimo Zhu et al.
Endothelial cells (ECs) play complex roles across tissues and vessel types. Yet, systematic investigations of EC heterogeneity in the combined context of vessel type and tissue microenvironment are still largely lacking. We integrated over ...
Granulin+ Macrophages Promote Lineage Plasticity in Prostate Cancer Through Paracrine Signaling Loops [0.03%]
granulin+巨噬细胞通过旁分泌信号环促进前列腺癌的系谱可塑性
Zhipeng Zhu,Mi Zhang,Ying Song et al.
Zhipeng Zhu et al.
While lineage plasticity is a well-established driver of therapy resistance in prostate cancer, the role of tumor-infiltrating immune cells in mediating phenotype switching remains poorly understood. Here, we employed single-cell multi-omic...
Single-cell RNA Sequencing Discovered Subtypes Associated with Angiogenesis and Propranolol Treatment in Infantile Hemangioma [0.03%]
单细胞RNA测序发现与血管形成和普萘洛尔治疗相关的婴幼儿血管瘤亚型
Qiang Chen,Liuqing Yang,Sili Ni et al.
Qiang Chen et al.
Infantile hemangioma (IH), a benign vascular tumor of infancy, is characterized by rapid postnatal growth and subsequent spontaneous resolution. Although propranolol, initially developed for cardiovascular disorders, is the primary treatmen...