T-ChroNet: Time-aware chromatin network reconstruction to detect dynamic regulatory programs in longitudinal epigenetic dataset [0.03%]
基于时间感知染色质网络重建的纵向表观遗传数据集中动态调控程序检测方法:T-CHRONET
Stefano Di Giovenale,Ottavio Lischio,Clelia Cortile et al.
Stefano Di Giovenale et al.
Networks are widely applied to investigate relationships among individual components of complex biological systems. Recent application of biological networks, such as gene co-expression networks and gene regulatory networks, has been instru...
Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graphs [0.03%]
Lancet 2：基于联合多样本局部组装图的改善和加速体细胞变异调用
Rajeeva Lochan Musunuri,Bryan Zhu,Wayne E Clarke et al.
Rajeeva Lochan Musunuri et al.
Here, we present Lancet2, an open-source somatic variant caller designed to improve detection of small variants in short-read sequencing data. Lancet2 introduces significant enhancements, including: (i) Improved variant discovery and genoty...
SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics [0.03%]
基于高分辨率空间转录组学的空间邻域和差异表达分析
Jinming Cheng,Pierce Kah Hoe Chow,Nan Liu
Jinming Cheng
Spatial transcriptomics technologies such as Xenium, MERFISH, and Visium HD enable high-resolution profiling of gene expression while preserving tissue architecture. However, most computational methods for spatial analysis do not explicitly...
A birth certificate for data to improve findability, accountability, and traceability [0.03%]
数据的出生证：提升查找性、问责性和可追溯性
Rongbin Li,Avisha Das,Yuntao Yang et al.
Rongbin Li et al.
Data quality is the foundational to scientific research and the rapid advancement of artificial intelligence. Ensuring data quality, provenance, and reproducibility requires robust mechanisms for traceability and accountability from the mom...
Correction to 'Eduomics: a Nextflow pipeline to simulate -omics data for education' [0.03%]
关于"Eduomics：用于教育的模拟-组学数据Nextflow管道"的更正
[This corrects the article DOI: 10.1093/nar/lqag029.]. © The Author(s) 2026. Published by Oxford University Press.
Published Erratum
NAR genomics and bioinformatics. 2026 Apr 2;8(2):lqag038. DOI:10.1093/nargab/lqag038 2026
systemPipeR: a multipurpose workflow management system for reproducible data analysis [0.03%]
系统管道器：用于可重复数据分析的多功能工作流管理系统
Le Zhang,Daniela Cassol,Brendan Gongol et al.
Le Zhang et al.
Workflow management systems (WMS) are essential for creating and automating multi-step data analyses and ensuring the reproducibility of biological insights. Although numerous WMS solutions exist, few provide deep integration of command-lin...
Henrique M Dias,Guilherme Y A Sagawa,Vladimir J Torres-Rodriguez et al.
Henrique M Dias et al.
Understanding orthologous and homeologous relationships among genes informs how evolution and artificial selection have shaped plant genomes of related species to adapt to different niches and produce diverse phenotypes. Grasses are ecologi...
G/C-ending and synonymous codon bias define functional translational programs that shape human tissue and cancer proteomes [0.03%]
G/C结尾和同义密码偏爱性定义了塑造人类组织和癌症蛋白质组的功能翻译程序
Sherif Rashad,Kuniyasu Niizuma
Sherif Rashad
Codon usage bias is a fundamental feature of the genetic code, yet its impact on messenger RNA translation is incompletely defined. Here, we integrate comparative genomics, human tissue proteomes, large cancer cell line, and patient cancer ...
Optimizing genomic language models for promoter prediction: a comparative study of tokenization and cross-species learning [0.03%]
优化基因组语言模型进行启动子预测：词元化和跨物种学习的比较研究
Eyal Hadad,Noia Kogman,Lina Golan et al.
Eyal Hadad et al.
Large Language Models (LLMs) are increasingly applied to genomic tasks, yet core challenges remain concerning tokenization, evaluation, and data scarcity. This study focuses on promoter classification and systematically evaluates four token...
Comparative Study
NAR genomics and bioinformatics. 2026 Mar 12;8(1):lqag025. DOI:10.1093/nargab/lqag025 2026
gplasCC: classification and recovery of plasmids from short-read sequencing data for any bacterial species [0.03%]
GPLASCC：从短读序列数据中对任意细菌物种的质粒进行分类和恢复
Julian A Paganini,Jesse J Kerkvliet,Oscar Jordan et al.
Julian A Paganini et al.
Plasmids play a pivotal role in the spread of antibiotic resistance genes. Accurately reconstructing plasmids often requires long-read sequencing, but bacterial genomic data in publicly accessible repositories have historically been derived...