Xinling Li,Peng Qiu
Xinling Li
For sequencing-based spatial transcriptomics data, the gene-spot count matrix is highly sparse. This feature is similar to scRNA-seq. The goal of this paper is to identify whether there exist genes that are frequently under-detected in Visi...
Construction of a multi-tissue compound-target interaction network of Qingfei Paidu decoction in COVID-19 treatment based on deep learning and transcriptomic analysis [0.03%]
基于深度学习和转录组分析的新冠治疗麻杏石甘汤多组织复杂靶标作用网络构建研究
Xia Li,Xuetong Zhao,Xinjian Yu et al.
Xia Li et al.
The Qingfei Paidu decoction (QFPDD) is a widely acclaimed therapeutic formula employed nationwide for the clinical management of coronavirus disease 2019 (COVID-19). QFPDD exerts a synergistic therapeutic effect, characterized by its multi-...
Body plan evolvability: The role of variability in gene regulatory networks [0.03%]
基因调控网络中的变异性在身体计划演化发育中的作用
Alexander V Spirov,Ekaterina M Myasnikova,David M Holloway
Alexander V Spirov
Recent computational modeling of early fruit fly (Drosophila) development has characterized the degree to which gene regulation networks can be robust to natural variability. In the first few hours of development, broad spatial gradients of...
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data [0.03%]
一种新的基于残差网络的MNN方法从scRNA序列数据中消除批次效应（NDMNN）
Yupeng Ma,Yongzhen Pei
Yupeng Ma
The rapid development of single-cell RNA sequencing (scRNA-seq) technology has generated vast amounts of data. However, these data often exhibit batch effects due to various factors such as different time points, experimental personnel, and...
Gtie-Rt: A comprehensive graph learning model for predicting drugs targeting metabolic pathways in human [0.03%]
GTIE-RT：一种用于预测药物靶向人类代谢途径的全面图谱学习模型
Hayat Ali Shah,Juan Liu,Zhihui Yang
Hayat Ali Shah
Drugs often target specific metabolic pathways to produce a therapeutic effect. However, these pathways are complex and interconnected, making it challenging to predict a drug's potential effects on an organism's overall metabolism. The map...
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations [0.03%]
一种新的基于NGS的可映射性偏差处理方法以灵敏地检测DNA改变
Rituparna Sinha,Rajat Kumar Pal,Rajat Kumar De
Rituparna Sinha
A turning point in cancer research is the introduction of massively parallel sequencing technology which greatly reduced the cost and time for genome sequencing. This enhanced the scope for detecting and analyzing the role of structural alt...
Utilization of systematic error-assessment software to improve phylogenetic accuracy [0.03%]
利用系统误差评估软件提高谱系发育准确性
Hayeon Kim,Junghwan Lee,Mikyeong Je et al.
Hayeon Kim et al.
Unlike classical systems based on the use of morphological data, modern phylogenetic analyses use genetic information to construct phylogenetic trees. Ongoing research in the field of phylogenetics is evaluating the accuracy of phylogenetic...
PfgPDI: Pocket feature-enabled graph neural network for protein-drug interaction prediction [0.03%]
基于口袋特征的药物-蛋白作用预测图神经网络
Yiqian Zhang,Changjian Zhou
Yiqian Zhang
Biomolecular interaction recognition between ligands and proteins is an essential task, which largely enhances the safety and efficacy in drug discovery and development stage. Studying the interaction between proteins and ligands can improv...
MoRF_ESM: Prediction of MoRFs in disordered proteins based on a deep transformer protein language model [0.03%]
基于深度变压器蛋白质语言模型的无序蛋白MORF预测（MoRF_ESM）
Chun Fang,Jiasheng He,Hayato Yamana
Chun Fang
Molecular recognition features (MoRFs) are particular functional segments of disordered proteins, which play crucial roles in regulating the phase transition of membrane-less organelles and frequently serve as central sites in cellular inte...
Rajiv Karbhal,Sangeeta Sawant,Urmila Kulkarni-Kale
Rajiv Karbhal
Enzymes catalyze diverse biochemical reactions and are building blocks of cellular and metabolic pathways. Data and metadata of enzymes are distributed across databases and are archived in various formats. The enzyme databases provide utili...