Optimizing bioinformatic workflows to extract clinically usable gene expression data from targeted tumor RNA sequencing panels: comparison with total RNA-seq in cancer samples [0.03%]
通过靶向肿瘤RNA测序 panel 提取临床可用基因表达数据的生物信息工作流优化：与癌症样本中的总RNA-seq比较
Xiaokang Pan,Ashley Patton,Yi Seok Chang et al.
Xiaokang Pan et al.
Motivation: Targeted RNA sequencing (RNA-seq) is widely used to detect gene fusions in tumors but clinical use of expression data from panels in fusion-negative cases has been limited. Differential gene expression (DGE) p...
Amand Floriaan Schmidt,Nikita Hukerikar,Chris Finan et al.
Amand Floriaan Schmidt et al.
Motivation: Computational visualizations are prevalent in all disciplines of biomedical science, from wet-lab research, through clinical science to population health and epidemiology. While matplotlib and seaborn are esta...
A latent factor framework to organize regulatory and metabolic programs inferred from scRNA-seq [0.03%]
一种潜在因素框架 用于组织从单细胞RNA测序推断的调节和代谢程序
Chiara Napoli,Francesco Bardozzo,Suraj Verma et al.
Chiara Napoli et al.
Motivation: Single-cell RNA sequencing enables high-resolution characterization of transcriptional heterogeneity, but provides only a partial view of the regulatory and metabolic processes associated with cellular states....
Generation of peptide detectability datasets from single DIA experiment for prediction model fine-tuning [0.03%]
从单次DIA实验生成肽段检测数据集以优化预测模型微调
Léo Schneider,Julie Flecheux,Zied Bouyahia et al.
Léo Schneider et al.
Motivation: Accurate prediction of peptide detectability in mass spectrometry-based proteomics is critical for improving both protein identification and quantification. Current models generally estimate detectability from...
Integrative multi-omics analysis identifies methylation-associated lncRNAs FAM83A-AS2 and AC012213.1 as candidate prognostic markers in lung adenocarcinoma [0.03%]
整合多组学分析鉴定出甲基化相关的长链非编码RNA FAM83A-AS2 和 AC012213.1 是肺腺癌预后标志物的候选分子
Syed Muktadir Al Sium,Mahafujul Islam Quadery Tonmoy,Dhirendra Nath Barman et al.
Syed Muktadir Al Sium et al.
Motivation: The Motivation: Long non-coding RNAs (lncRNAs) are important regulators of gene expression and are increasingly implicated in cancer. However, the extent to which aberrant DNA methylation is associated with ln...
The 15th ISCB Student Wikipedia Competition: past, present and future perspectives [0.03%]
第十五届ISCB学生维基百科竞赛：过去、现在和未来的视角
Alastair M Kilpatrick,Audra Anjum,Dan DeBlasio et al.
Alastair M Kilpatrick et al.
The International Society for Computational Biology (ISCB) Student Wikipedia Competition, now in its 15th edition, has become a cornerstone initiative for promoting open educational resources in computational biology. Launched in 2012, the ...
Enhancing feature selection for ordinal outcomes using resampling-based sparse linear discriminant analysis [0.03%]
基于重采样的稀疏线性判别分析在有序结果特征选择中的应用增强
Yin Liu,Ryan Wang,Dong Si
Yin Liu
Motivation: High-dimensional biomedical datasets with ordinal outcomes-such as cancer stages or treatment responses-pose significant challenges for feature selection due to strong predictor correlations and limited sample...
TPdsm: a method based on TabPFN for prediction of deleterious synonymous mutations [0.03%]
基于TabPFN的有害同义突变预测方法TPdsm
Bing Zeng,Min Hu,Zhonghui Cui et al.
Bing Zeng et al.
Motivation: Assessing the deleteriousness of synonymous mutations is of considerable importance for understanding human health, and the development of corresponding prediction methods offers a rapid and efficient approach...
EvoSubster: a pipeline for evolutionary inference of single- and double-base substitution spectra [0.03%]
EvoSubster：一种用于单碱基和双碱基替换谱系进化推理的流水线系统
Mariko Nakagawa,Martin C Frith
Mariko Nakagawa
Motivation: Mutational processes differ widely across the tree of life, yet most existing resources focus on somatic mutations in humans or on a limited set of well-studied species. ...
scPD: a Python package for inferring continuous population dynamics from single-cell snapshot data [0.03%]
scPD：一个从单细胞快照数据中推断连续种群动态的Python包
Yusong Yin,Hong Qi,Huan Hu
Yusong Yin
Summary: Quantitative inference of developmental dynamics from single-cell snapshot data is essential for disentangling differentiation and proliferation processes. The pseudodynamics framework provides a principled appro...