EvoRMD: integrating biological context and evolutionary RNA language models for interpretable prediction of RNA modifications [0.03%]
具有生物学背景和进化RNA语言模型的EvoRMD在可解释的RNA修饰预测中的应用
Bo Wang,Hao Zhang,Taoyong Cui et al.
Bo Wang et al.
RNA modifications regulate post transcriptional gene expression, yet most computational methods model each modification independently and overlook competition among modification types at a single site. We present EvoRMD, a biologically cont...
Jointly-hic: joint decomposition of contact frequency maps captures salient features of genome architecture across tissues and development [0.03%]
联合hic解析法：组织和发育过程中捕获基因组结构显著特征的接触频率图的联合分解
Thomas Reimonn,Vedat O Yilmaz,Hoang Tran et al.
Thomas Reimonn et al.
Chromosome conformation capture methods, such as Hi-C, have been used to profile chromosome organization from a wide variety of biosamples and conditions; however, existing methods for analyzing such datasets have disadvantages for large-sc...
Ubiquitous impact of natural selection on nucleotide diversity in 178 species of primates [0.03%]
自然选择对178种灵长类动物核苷酸多态性的影响
Bjarke Meyer Pedersen,Juraj Bergman,Vasili Pankratov et al.
Bjarke Meyer Pedersen et al.
Background: Genetic diversity shows great variation across the genome. To investigate the major evolutionary forces causing this variation in primates, we analyse genomic diversity in 178 species in coordinates of the hum...
A mammalian genomic signature shaped by single nucleotide variants regulates transcriptome integrity and diversity [0.03%]
由单核苷酸变异调控的转录组稳定性和多样性的哺乳动物基因组标志
Jian Yang,Samuel Ogunsola,Jason Wong et al.
Jian Yang et al.
Background: Many functional features of mammalian genomic sequences remain poorly defined, especially how sequence motifs and genetic variants within non-coding regions (NCRs) regulate transcriptome integrity and diversit...
LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools [0.03%]
LEMMIv2：基准框架用于宏基因组和16S扩增子分析工具的评估及目录编制
Mathieu Seppey,Andres Benavides,Matthew R Berkeley et al.
Mathieu Seppey et al.
Metagenomics enables culture-independent investigation of microbial communities without prior knowledge of sample composition. However, sequence analysis is complex, and many computational strategies exist. Selecting among them is challengi...
BEstimate: a computational tool for the design and interpretation of CRISPR base editing experiments [0.03%]
BEstimate：一个用于CRISPR碱基编辑实验设计与解读的计算工具
Cansu Dinçer,Bo Fussing,Mathew J Garnett et al.
Cansu Dinçer et al.
CRISPR base editors enable scalable targeted DNA mutagenesis and are a powerful tool for analysing the function of variants of uncertain significance and disease modelling. Existing guide RNA (gRNA) design tools lack comprehensive functiona...
Highly efficient chromatin conformation capture with post-enrichment in single cells by HiChew [0.03%]
高效单细胞染色质构象捕获的HiChew方法
Zhichao Chen,Yeming Xie,Chen Zhang et al.
Zhichao Chen et al.
We present HiChew, a novel chromatin conformation capture method combining efficient sticky-end ligation with post-PCR methylation-based enrichment. HiChew achieves approximately 50% valid pair ratios compared to 8% for unenriched methods, ...
LCPAN: efficient variation graph construction using locally consistent parsing [0.03%]
基于局部一致解析的高效变体图构建(LCPAN)
Akmuhammet Ashyralyyev,Zülal Bingöl,Begüm Filiz Öz et al.
Akmuhammet Ashyralyyev et al.
Efficient and consistent string processing is critical in the exponentially growing genomic data era. Locally Consistent Parsing (LCP) addresses this need by partitioning an input genome string into short, exactly matching substrings ("core...
Author Correction: Spatiotemporal transcriptomics reveals key gene regulation for grain yield and quality in wheat [0.03%]
作者更正：时空转录组学揭示了小麦增产提质的关键基因调控
Xiaohui Li,Yiman Wan,Dongzhi Wang et al.
Xiaohui Li et al.
Published Erratum
Genome biology. 2026 Apr 23;27(1):142. DOI:10.1186/s13059-026-04065-3 2026
Geometry-aware graph attention networks to explain single-cell chromatin states and gene expression with SEAGALL [0.03%]
基于几何结构的图注意力网络解释单细胞染色质状态和基因表达(SEAGALL)
Gabriele Malagoli,Patrick Hanel,Anna Danese et al.
Gabriele Malagoli et al.
High-throughput single-cell sequencing is widely used to study cell identity. We present SEAGALL (Single-cell Explainable Geometry-Aware Graph Attention Learning pipeLine), a deep learning method to quantify the impact of molecular features...