MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment [0.03%]
基于Snakemake的模块化基因组组装和注释自动化工作流及其质量评估工具（MoGAAAP）
Dirk-Jan M van Workum,Kuntal K Dey,Alexander Kozik et al.
Dirk-Jan M van Workum et al.
With the current speed of sequencing, there is a desire for standardized and automated genome assembly and annotation to produce high-quality genomes as input for comparative (pan)genomics. Therefore, we created a convenience pipeline using...
Eukan: a fully automated nuclear genome annotation pipeline for less studied and divergent eukaryotes [0.03%]
Eukan：一个全自动的核基因组注释流程用于研究较少且较远古真核生物
Matt Sarrasin,Gertraud Burger,B Franz Lang
Matt Sarrasin
Here, we introduce a new annotation pipeline, called Eukan, designed to deliver reliably high-quality results across a broad range of eukaryotes. First, experimental evidence is automatically leveraged to refine predictions, specifically, R...
CAMP: a modular metagenomics analysis system for integrated multistep data exploration [0.03%]
基于模块化的元基因组分析系统用于多步集成数据探索(CAMP)
Lauren Mak,Braden Tierney,Wei Wei et al.
Lauren Mak et al.
Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific meth...
FLYNC: a machine-learning-driven framework for discovering long noncoding RNAs in Drosophila melanogaster [0.03%]
FLYNC：一种用于在果蝇中发现长链非编码RNA的机器学习框架
Ricardo F Dos Santos,Tiago Baptista,Graça S Marques et al.
Ricardo F Dos Santos et al.
Noncoding RNAs have increasingly recognized roles in critical molecular mechanisms of disease. However, the noncoding genome of Drosophila melanogaster, one of the most powerful disease model organisms, has been understudied. Here, we prese...
nf-core/crisprseq: a versatile pipeline for comprehensive analysis of CRISPR gene editing and screening assays [0.03%]
nf-core/crisprseq：一种用于CRISPR基因编辑和筛选测定的全面分析的灵活工作流程
Júlia Mir-Pedrol,Laurence Kuhlburger,Marta Sanvicente-García et al.
Júlia Mir-Pedrol et al.
In recent years, CRISPR technology has become widely applied in scientific research, being simpler, cheaper, and more precise than previous gene-editing techniques. This editing technology can be used for various applications, such as gene ...
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins [0.03%]
AlphaFold和ESMFold单体蛋白和二聚体蛋白预测精度的比较评估
Sanjeet Kumar Mahtha,Sureshkumar Venkadesan,Debasisa Mohanty
Sanjeet Kumar Mahtha
We have evaluated the prediction accuracy of three different tools, deep-learning-based AlphaFold2, AlphaFold3, and large language model-based ESMFold, utilizing the experimentally derived structures deposited in the Protein Data Bank betwe...
Comparative Study
NAR genomics and bioinformatics. 2026 Jan 16;8(1):lqag002. DOI:10.1093/nargab/lqag002 2026
SyMetrics: an integrated machine learning model for evaluating the pathogenicity of synonymous variants in the human genome [0.03%]
SyMetrics：一种用于评估人类基因组同义变异致病性的集成机器学习模型
Linnaeus Bundalian,Martina Schmidt Strnadová,Felix Garten et al.
Linnaeus Bundalian et al.
Synonymous single nucleotide variants (sSNVs), traditionally seen as neutral, are now recognized for their biological impact. To assess their relevance, we developed SyMetrics, a framework that integrates predictors of splicing, RNA stabili...
RNA-KG v2.0: an RNA-centered Knowledge Graph with Properties [0.03%]
RNA-KG v2.0：一种具有属性的以RNA为中心的知识图谱
Emanuele Cavalleri,Paolo Perlasca,Marco Mesiti
Emanuele Cavalleri
RNA-KG is a recently developed biomedical knowledge graph that integrates the interactions involving coding and non-coding RNA molecules extracted from public data sources. It can be used to support the classification of new molecules, iden...
OmNI: a modular open-source framework for interactive multi-omics data integration and visualization [0.03%]
OmNI：一个模块化的开源框架，用于交互式的多组学数据整合和可视化
Grace Potter,Jacob A Beierle,Camron Bryant et al.
Grace Potter et al.
Omics Notebook Interactive (OmNI) is an R-based, open-source, and modular framework engineered for streamlined multi-omics data integration and analysis across diverse data types, incorporating interactive visualizations at each processing ...
Insights into the architecture of earthworm metallothionein genes, powered by long-read genomics and transcriptomics [0.03%]
基于长读长基因组学和转录组学的蚯蚓金属硫蛋白基因结构研究
Maxim A Karpov,Stephen Short,Peter Kille et al.
Maxim A Karpov et al.
The metal-handling metallothionein gene family is subjected to a strong selection pressure in earthworms inhabiting metalliferous soils. The resultant single nucleotide polymorphisms and structural variants within metallothionein's characte...