Asymmetric integration of various cancer datasets for identifying risk-associated variants and genes [0.03%]
基于多种癌症数据集的非对称整合以鉴定相关变异和基因
Ruixuan Wang,Lam Tran,Benjamin Brennan et al.
Ruixuan Wang et al.
Motivation: Cancer genomic research provides an opportunity to identify cancer risk-associated genes, but often suffers from undesirable low statistical power due to a limited sample size. Integrated analysis with differe...
ProtFun: a protein function prediction model using graph attention networks with a protein large language model [0.03%]
基于图注意力网络和蛋白质大语言模型的蛋白质功能预测模型ProtFun
Muhammed Talo,Serdar Bozdag
Muhammed Talo
Motivation: Understanding protein functions facilitates the identification of the underlying causes of many diseases and guides the research for discovering new therapeutic targets and medications. With the advancement of...
Deconvolution and phylogeny inference of diverse variant types integrating bulk DNA-seq with single-cell RNA-seq [0.03%]
利用单细胞RNA测序和批量DNA测序综合分析多种变异类型及其系统发育关系
Nishat Anjum Bristy,Russell Schwartz
Nishat Anjum Bristy
Motivation: Reconstructing clonal lineage trees ("tumor phylogenetics") has become a core tool of cancer genomics. Earlier approaches based on bulk DNA sequencing (DNA-seq) have largely given way to single-cell DNA-seq (s...
Advances and challenges in understanding evolution through genome comparison: meeting report of the European Molecular Biology Organization (EMBO) lecture course "Evolutionary and Comparative Genomics" [0.03%]
通过基因组比较理解进化所面临的挑战和前景：欧洲分子生物学组织（EMBO）讲习班“进化与比较基因组学”会议报告
Athina Gavriilidou,Alexandros Stamatakis,Anne Kupczok et al.
Athina Gavriilidou et al.
This perspective outlines emerging trends, key challenges, and future opportunities in evolutionary and comparative genomics. Our starting point are the topics presented at the 2024 EMBO Early Career Lecture Course "Evolutionary and Compara...
Synthetic data-driven AI approach for fetal chromosomal aneuploidies detection [0.03%]
基于合成数据的AI方法在胎儿染色体异常检测中的应用研究
Changhoe Hwang,Krishna Prasad Adhikari,Gyeongin Oh et al.
Changhoe Hwang et al.
Motivation: A major limitation in the development of fetal chromosomal aneuploidy detection technologies lies in the scarcity of real positive data. To address this issue, we propose a novel methodology to generate virtua...
KinMethyl: robust methylation detection in prokaryotic SMRT sequencing via kinetic signal modeling and deep feature integration [0.03%]
KinMethyl：通过动力学信号建模和深度特征整合在原核生物SMRT测序中进行稳健的甲基化检测
Jichen Zhang,Yutaka Saito
Jichen Zhang
Motivation: Accurate detection of 5-methylcytosine (5mC) from PacBio single-molecule real-time (SMRT) sequencing remains challenging in prokaryotes due to weak kinetic signals and motif diversity. ...
tBN-CSDI: a time-varying blue noise-based diffusion model for time-series imputation [0.03%]
基于时变蓝噪声的时间序列插补扩散模型
Graham Bishop,Tong Si,Isabelle Luebbert et al.
Graham Bishop et al.
Motivation: Missing data imputation remains a critical challenge in high-dimensional time-series data analysis, where traditional methods often struggle to capture complex nonlinear dependencies inherent in sequential dat...
Anna Špačková,Nina Kadášová,Ivana Hutařová Vařeková et al.
Anna Špačková et al.
Motivation: Cytochrome P450 proteins play a crucial role in human metabolism, ranging from hormone production to drug metabolism. While multiple commonly known variants have known effects on the individual cytochrome P450...
TAILcaller: an R package for analyzing differences in poly(A) tail length for Oxford Nanopore RNA sequencing [0.03%]
TAILCaller：一个R语言软件包用于分析牛津纳米孔RNA测序中多聚(A)尾长度的差异
Mateusz Maździarz,Łukasz Paukszto,Jakub Sawicki
Mateusz Maździarz
Motivation: Changes in poly(A) tail length were identified as a key post-transcriptional mechanism that controls protein synthesis. The length of the poly(A) tail was shown to directly impact mRNA stability and translatio...
SocialViruses: integrating quantitative phage-bacteria and phage-phage interaction networks for rational cocktail design [0.03%]
社会病毒：定量噬菌体-细菌和噬菌体-噬菌体相互作用网络的整合以进行理性的鸡尾酒设计
Felipe Molina,Manuel Menor-Flores,Miguel A Vega-Rodríguez
Felipe Molina
Motivation: Phage therapy is emerging as a promising alternative to antibiotics in biomedical research, highlighting the growing need for computational tools to rationally design effective phage cocktails. However, its cl...