Evaluating microbial network inference methods: moving beyond synthetic data with reproducibility-driven benchmarks [0.03%]
超越合成数据的可重复性驱动基准评估微生物网络推理方法
Zahra Ghaeli,Rosa Aghdam,Changiz Eslahchi
Zahra Ghaeli
Background: Microbial network inference is an essential approach for revealing complex interactions within microbial communities. However, the lack of experimentally validated gold standards presents a significant obstacl...
GPU-accelerated MitoGraph for high-throughput three-dimensional mitochondrial morphology analysis [0.03%]
基于GPU加速的MitoGraph高通量三维线粒体形态分析方法
Siddharth Nahar,Zichen Wang,Eric Arkfeld et al.
Siddharth Nahar et al.
MitoGraph is a widely used tool for the automated segmentation of mitochondrial networks in three-dimensional (3D) fluorescence microscopy. However, the emergence of advanced live-cell microscopes such as lattice light-sheet microscopy (LLS...
EMD-HVG: a normalization-independent method for highly variable gene selection based on Earth mover's distance [0.03%]
基于地球 movers 距离的归一化独立的高度可变基因选择方法(Earth movers距离高变量基因选择的规范化独立方法)
Chunfang Peng,Guobin Li,Jiamiao Wu et al.
Chunfang Peng et al.
Background: Identifying highly variable genes (HVGs) is a critical step in single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) analyses. Conventional approaches typically rely on normalization to adjus...
MetaServe: a lightweight, metadata-aware governance and delivery layer for pre-publication research omics data [0.03%]
元数据感知的预出版组学研究数据治理和交付轻量级层次结构_MetaServe
Yizhuo Shen,Jianpeng Sheng,Pengcheng Yan
Yizhuo Shen
Background: Institutional research teams and core facilities routinely manage pre-publication omics datasets that span heterogeneous file types, nested project structures, and multiple downstream uses. Public repositories...
Circtools 2.0: a comprehensive framework for enhanced circular RNA bioinformatics [0.03%]
Circtools 2.0：增强的环形RNA生物信息学全面框架
Shubhada R Kulkarni,Walker J Compton Mellon,Felix Wiedmann et al.
Shubhada R Kulkarni et al.
Background: Circular RNAs (circRNAs) play a pivotal role in gene regulation, acting as transcriptional modulators at various cellular levels and exhibit remarkable specificity across cell types and developmental stages. D...
GOATEA: gene set enrichment analysis in R with shiny interactive visualizations [0.03%]
GOATEA：使用Shiny交互式可视化在R中进行基因集合富集分析
Maurits A W Unkel,Jeff A Beeler,Steven A Kushner et al.
Maurits A W Unkel et al.
Background: High-throughput genomic and proteomic technologies are used to study biological systems by performing differential expression analysis across various experimental conditions. Geneset Ordinal Association Test (...
A causal reinforcement learning framework for reliable gene regulatory network inference [0.03%]
一种可靠的基因调控网络推理的因果强化学习框架
Ruirui Ji,Wenzhuo Zhang,Yi Geng et al.
Ruirui Ji et al.
Background: Gene regulatory network inference is crucial for revealing the mechanisms of cellular functions and the causal mechanisms of disease occurrence. However, traditional correlation-based methods struggle to ident...
Marijo Šimunović,Lovro Vrček,Mile Šikić et al.
Marijo Šimunović et al.
Background: Modern sequencing technologies have enabled the reconstruction of complete mammalian genomes from telomere to telomere. However, scaling this achievement to thousands of species and population-level studies re...
Genestrip: exact and efficient read classification for selected groups of organisms [0.03%]
基因条形码：针对选定生物群体的精确高效读序分类方法
Daniel Pfeifer,Markus Graf,Clas Rurik
Daniel Pfeifer
Background: The consumption of main memory resources is a significant burden in k-mer-based metagenomic analysis when creating related databases but also when performing (unique) k-mer-counting and read classification. Ge...
MuSA: a Nextflow pipeline for deep, reproducible annotation and clinical ranking of genomic variants [0.03%]
MuSA：一个用于深度、可重复的基因组变异注释和临床排序的Nextflow流水线
D Scognamiglio,E Bonetti,A Moroni et al.
D Scognamiglio et al.
Background: Accurate clinical interpretation of genetic variants requires integration of functional predictions, evolutionary constraint, population allele frequencies, and clinical evidence from heterogeneous resources. ...