Gaetan De Waele,Gerben Menschaert,Willem Waegeman
Gaetan De Waele
Transformers pre-trained on single-cell transcriptomic data have recently been applied to a series of tasks, earning them the title of foundation models. However, recent benchmarks indicate that current iterations of single-cell foundation ...
InteRRact: a web server for the interactive exploration and comparison of transcriptome-wide RNA-RNA interactions [0.03%]
InteRRact：一个用于探索和比较转录组范围内的RNA-RNA相互作用的网络服务器
Egor Semenchenko,Jingwen Luo,Volodymyr Tsybulskyi et al.
Egor Semenchenko et al.
RNA-RNA interactions (RRI) can now be probed on a transcriptome-wide scale using proximity ligation methods such as SPLASH, PARIS, LIGR-seq, RIC-seq, and others. While individual pipelines for computationally processing the corresponding ra...
Comparative Study
NAR genomics and bioinformatics. 2026 Aug 20;8(3):lqag089. DOI:10.1093/nargab/lqag089 2026
TandemTwister: scalable genotyping and advanced visualization of tandem repeats [0.03%]
TandemTwister：串联重复的可扩展基因分型和高级可视化技术
Lion Ward Al Raei,Maryam Ghareghani,M-Hossein Moeinzadeh et al.
Lion Ward Al Raei et al.
Tandem repeats (TRs) are genomic regions consisting of consecutively repeated units with variable copy numbers and possible mutations. They are used in DNA fingerprinting and have been implicated in complex traits and genetic disorders, inc...
The PhageExpressionAtlas reveals shared and unique transcriptional patterns across phage-host interactions [0.03%]
噬菌体表达图谱揭示了噬菌体-宿主相互作用中共享和独特的转录模式
Maik Wolfram-Schauerte,Caroline Trust,Nils Waffenschmidt et al.
Maik Wolfram-Schauerte et al.
Time-resolved transcriptomic profiling has been used to study phage-host interactions for more than a decade. However, the resulting datasets are not readily accessible for custom re-analysis, and resources are lacking that provide standard...
Systematic evaluation of the heterogeneity of topologically associating domain boundaries in a large genomic context in humans [0.03%]
在人类基因组的大范围内对拓扑关联域边界异质性进行系统评估
Ying Sun,Niels Tommerup,Lars Juhl Jensen et al.
Ying Sun et al.
Topologically associating domains (TADs) are generally considered as a homogeneous basic units of genome folding, which is critical for transcriptional regulation. However, recent studies indicate that both the TAD domain structures and the...
Integrating heterogeneity into topologically associating domain boundary prediction in large genomic context in human [0.03%]
在人类基因组的大背景下将异质性整合到拓扑相关域边界预测中
Ying Sun,Lars Juhl Jensen,Niels Tommerup et al.
Ying Sun et al.
A fundamental understanding of genome organization relies on accurately annotating topologically associating domains (TADs) and their boundaries. This is crucial for understanding how cis-regulatory elements regulate gene expression. To go ...
Etiology-guided mutational signature learning from DNA repair knockouts in cell lines using supervised NMF [0.03%]
基于细胞系DNA修复敲除的监督NMF指导的病因突变标志学习方法
Sander Goossens,Yasin I Tepeli,Colm Seale et al.
Sander Goossens et al.
Many tumours show deficiencies in DNA damage response (DDR), not only driving tumorigenesis but also exposing vulnerabilities with therapeutic potential. Assessing which patients might benefit from DDR-targeting therapy requires knowledge o...
Unveiling the terra cognita of sequence spaces using Cartesian projection of asymmetric distances [0.03%]
基于非对称距离的笛卡尔投影揭示序列空间的新知之地
Alban Ramette
Alban Ramette
Visualizing relationships within massive biological datasets remains a significant challenge, particularly as sequence length and volume increase. We introduce CAPASYDIS (Cartesian Projections of Asymmetric Distances), a scalable approach d...
The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance [0.03%]
长读RNA测序的前景：降低等位基因不平衡分析中的偏差
Nadja Nolte,Marko Petek,Pablo Angulo Lara et al.
Nadja Nolte et al.
Inaccurate allele and gene expression counts due to map bias and genome ambiguity lead to high false positive and false negative rates in studies of allelic imbalance. We demonstrate that long read RNA sequencing (RNA-seq) and straightforwa...
Correction to 'A landscape of metallophore synthesis and uptake potential of the genus Staphylococcus' [0.03%]
关于“金属配体合成和摄取能力的地景图——葡萄球菌属”的更正通知
[This corrects the article DOI: 10.1093/nargab/lqaf183.]. © The Author(s) 2026. Published by Oxford University Press.
Published Erratum
NAR genomics and bioinformatics. 2026 Jul 30;8(3):lqag091. DOI:10.1093/nargab/lqag091 2026