Large-scale multi-trait genome-wide analysis for inflammatory bowel disease reveals new insights into its molecular mechanisms and emphasizes the roles of systemic immune regulation [0.03%]
Zijun Zhu,Lei Shi,Hailong Li et al.
Zijun Zhu et al.
Inflammatory bowel disease (IBD) is a hereditary and chronic inflammatory condition affecting the gastrointestinal tract, with two main subphenotypes: Crohn's disease (CD) and ulcerative colitis (UC). Most IBD-related genetic associations a...
Ming-Xiao Zhao,Hua-Huan Cai,Qiang Chen et al.
Ming-Xiao Zhao et al.
Protein N-phosphorylation represents one of the principal forms of protein phosphorylation modifications, which has been extensively identified in both prokaryotes and eukaryotes. However, significant knowledge gaps persist regarding its fu...
QTFPred: robust high-performance quantum machine learning modeling that predicts main and cooperative transcription factor bindings with base resolution [0.03%]
QTFPred：一种鲁棒的高性能量子机器学习建模方法，可进行基于碱基的主转录因子和协同转录因子结合位点预测
Taichi Matsubara,Shuto Machida,Samuel Papa Kwesi Owusu et al.
Taichi Matsubara et al.
Deep learning has become an essential tool for identifying transcription factor (TF) binding sites, yet conventional approaches often struggle with limited training data for specific TFs. Here, we introduce QTFPred (Quantum-based TF Predict...
Transcriptome Transformer: improving patient survival prediction via multitask learning of transcriptomic and clinical features [0.03%]
基于临床和基因表达数据的多任务学习改善患者生存预测
Bonil Koo,Inyoung Sung,Sangseon Lee et al.
Bonil Koo et al.
Accurate survival prediction is essential in healthcare as it guides treatment strategies and improves patient outcomes. While clinical features provide valuable prognostic information, they often fail to represent the molecular complexity ...
Introducing a foundational sequence transformer for range adaptive nucleotide decoding (STRAND) [0.03%]
介绍一种用于范围自适应核苷酸解码的基础序列变压器（STRAND）
Shant Ayanian,Collin Osborne,Clark Xu et al.
Shant Ayanian et al.
The advent of high-throughput sequencing has led to an exponential increase in genomic data, highlighting the need for efficient and accurate models to analyze and interpret this information. In this study, we introduce a novel, exomic foun...
Single-cell omics arena: evaluation of large language models for automatic cell-type annotations on single-cell omics data via RNA-seq bridging [0.03%]
单细胞组学领域：通过RNA序列桥接评估大型语言模型在单细胞组学数据自动细胞类型注释中的应用
Junhao Liu,Siwei Xu,Yongxian Wu et al.
Junhao Liu et al.
The single-cell sequencing revolution enables simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues. Among all the analysis s...
From genomic signals to prediction tools: a critical feature analysis and rigorous benchmark for phage-host prediction [0.03%]
从基因组信号到预测工具：噬菌体-宿主预测的批判性特征分析和严格的基准测试
Jiayu Shang,Cheng Peng,Jiaojiao Guan et al.
Jiayu Shang et al.
Accurate prediction of virus-host interactions is critical for understanding viral ecology and developing applications like phage therapy. However, the growing number of computational tools has created a complex landscape, making direct per...
Data-driven strategies for drug repurposing: insights, recommendations, and case studies [0.03%]
数据驱动的药物再定位策略：见解、建议和案例研究
Susanna Savander,Nurettin Nusret Curabaz,Amna Mumtaz Abbasi et al.
Susanna Savander et al.
Drug discovery is a complex, time-intensive, and costly process, often requiring more than a decade and substantial financial investment to bring a single therapeutic to market. Drug repurposing, the systematic identification of new indicat...
LogicSR: prior-guided symbolic regression for gene regulatory network inference from single-cell transcriptomics data [0.03%]
基于单细胞转录组数据的基因调控网络推理的先验引导符号回归逻辑sr：来自单细胞 transcriptomics 数据的基因调控网络推理的先验引导符号回归
Dezhen Zhang,Zhi-Ping Liu,Rui Gao
Dezhen Zhang
Deciphering gene regulatory mechanisms from high-dimensional biology data remains a central challenge in modern systems biology, despite the growing availability of single-cell datasets. The difficulty stems partly from the sparsity and noi...
BridgeSyn: a bridging fusion framework for drug combination synergy prediction [0.03%]
桥接融合框架用于药物组合协同效应预测
Qingyu Wang,Suwan Mao,Xiaoyan Liu et al.
Qingyu Wang et al.
Drug combination is a promising therapeutic strategy for complex diseases. However, only a small fraction of potential drug combinations exhibit true synergistic effects, making the prediction of drug synergy a critical yet challenging task...