A novel explainable deep-learning approach for network analysis of epistatic interactions [0.03%]
一种新颖的可解释深度学习方法用于分析上位性相互作用的网络
Andrea Mastropietro,Georgios Markopoulos,Evangelos Evangelou et al.
Andrea Mastropietro et al.
Epistatic interactions of gene loci often determine complex trait phenotypes and may indicate the underlying molecular mechanisms of traits and diseases. Yet, the inference of epistatic interactions and gene-gene networks remains challengin...
RAZOR: a database of PCR primers targeting human respiratory viruses [0.03%]
针对人类呼吸道病毒的PCR引物数据库(RAZOR)
Hunter M Gill,Quoseena Mir,Rajneesh Srivastava et al.
Hunter M Gill et al.
Respiratory viruses like SARS-CoV-2, Influenza A, and others represent a considerable threat to public health, infecting millions of people annually. Previous respiratory virus outbreaks have demonstrated the value of polymerase chain react...
NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data [0.03%]
NGSTroubleFinder：一种检测和量化人类NGS数据中的污染和亲缘关系的工具
Samuel Valentini,Tecla Venturelli,Xavier Gallego et al.
Samuel Valentini et al.
Quality control constitutes a critical component of any next-generation sequencing (NGS) pipeline; however, most existing pipelines emphasize technical quality assessment (e.g. read quality, alignment metrics, duplication rates) while overl...
SM3DD with segmented PCA: a comprehensive method for interpreting 3D spatial transcriptomics [0.03%]
用于解释3D空间转录组学的SM3DD与分段PCA：一种全面的方法
Tony Blick,Aaron Kilgallon,James Monkman et al.
Tony Blick et al.
We developed Standardised Minimum 3D Distance (SM3DD), an entirely cell segmentation/annotation-free approach to the analysis of spatial RNA datasets, using it to compare lung tissue from 16 clinically normal individuals to that of 18 SARS-...
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