Disc-Hub: a python package for benchmarking machine learning strategies in DIA-MS identification [0.03%]
盘式中心：一种用于DIA-MS识别中机器学习策略基准测试的python包
Yiwen Yu,Xiaohui Wu,Jian Song
Yiwen Yu
Motivation: Accurate analysis of data-independent acquisition (DIA) mass spectrometry data relies on machine learning to distinguish target peptides from decoy peptides. Different DIA identification engines adopt distinct...
HeraNorm: an R shiny application for identifying optimal endogenous controls for miRNA and RNA assays in qPCR and ddPCR [0.03%]
HeraNorm：一款用于识别miRNA和RNA测定中qPCR和ddPCR内源对照的R Shiny应用程序
Yao Hu,Xiaochun Xu,Yirong Shen et al.
Yao Hu et al.
Motivation: Normalization is a critical step in quantitative PCR (qPCR) and droplet digital PCR (ddPCR) experiments to ensure accurate and reproducible gene expression analysis. However, commonly used endogenous controls ...
PSO-FeatureFusion: a general framework for fusing heterogeneous features via particle swarm optimization [0.03%]
PSO-特征融合：一种基于粒子群优化的异构特征融合通用框架
Raziyeh Masumshah,Changiz Eslahchi
Raziyeh Masumshah
Motivation: Integrating heterogeneous biological data is a central challenge in bioinformatics, especially when modeling complex relationships among entities such as drugs, diseases, and molecular features. Existing metho...
GeoGenIE: a deep learning approach to predict geographic provenance of biodiversity samples from genomic SNPs [0.03%]
GeoGenIE：一种利用基因组SNP预测生物多样性样本地理来源的深度学习方法
Bradley T Martin,Zachery D Zbinden,Michael E Douglas et al.
Bradley T Martin et al.
Motivation: Determining geographic origin of samples is a common objective in wildlife management, forensics, and conservation. Current methods often assume evolutionary models or require extensive reference datasets, whi...
In silico analysis of insect-associated bacterial phytases reveals optimal biochemical properties and function in poultry gut condition [0.03%]
昆虫相关细菌植酸酶的计算机分析揭示了其在禽类肠道条件下的最优生化特性及功能
Olyad Erba Urgessa,Ketema Tafess Tulu,Mesfin Tafesse Gemeda et al.
Olyad Erba Urgessa et al.
Motivation: Insect guts may harbor phytase-producing bacteria applicable in poultry nutrition, but only Serratia sp. TN49 and its histidine acid phytase (AEQ29498.1) have been studied for this purpose. Therefore, AEQ29498...
Computational strategies in tumor phylogenetics: evaluating multimodal integration and methodological trade-offs across study designs [0.03%]
肿瘤表型组学中的计算策略：评估跨研究设计的多模态整合和方法替代方案
Chenghan Jiang,Zhe Wang,Ruoyu Wang et al.
Chenghan Jiang et al.
Motivation: Tumor clonal evolution represents a dynamic ecosystem underpinned by genetic alterations and Darwinian selection, posing major challenges due to intratumoral heterogeneity and therapy resistance. Although comp...
OncotreeVIS-an interactive graphical user interface for visualizing mutation tree cohorts [0.03%]
OncotreeVIS-用于可视化突变树种群的交互式图形用户界面
Monica-Andreea Baciu-Drăgan,Niko Beerenwinkel
Monica-Andreea Baciu-Drăgan
Summary: In recent years, developments in single-cell next-generation sequencing technology and computational methodology have made it possible to reconstruct, with increasing precision, the evolutionary history of tumors...
Revealing tissue architecture through the hypercomplex Fourier analysis of spatial transcriptomics data [0.03%]
通过空间转录组数据的超复数傅立叶分析揭示组织结构
Hildreth Robert Frost
Hildreth Robert Frost
Motivation: We present an approach for analyzing spatial transcriptomics (ST) data using a quaternion-domain discrete Fourier transform. Quaternions are four-dimensional hypercomplex numbers that have been primarily emplo...
Benchmarking of variant pathogenicity prediction methods using a population genetics approach [0.03%]
基于人群遗传学的方法评估变异致病性预测工具性能
Mikhail Gudkov,Loïc Thibaut,Steven Monger et al.
Mikhail Gudkov et al.
Motivation: Variant pathogenicity predictors are essential for identifying new associations between genetic variants and rare diseases. However, despite the availability of numerous predictors, there is no clear consensus...
Nextpie: a web-based reporting tool and database for reproducible nextflow pipelines [0.03%]
下一代管道的网络报告工具及数据库：可重复使用的nextflow管道
Bishwa Ghimire,Nicholas Booth,Tapio Lönnberg et al.
Bishwa Ghimire et al.
Motivation: High-throughput genomic data analysis consists of the inexorably intertwined inputs and outputs of a vast array of bioinformatic analysis tools. To guarantee streamlined and reproducible analyses, the often co...