A Burak Gulhan,Richard Burhans,Robert Harris et al.
A Burak Gulhan et al.
Advances in sequencing and assembly allow the creation of thousands of genome assemblies. However, producing multiple alignments required for their analysis lags behind due to the time-consuming process of pairwise alignment, typically perf...
Phased epigenomics and methylation inheritance in a historical Vitis vinifera hybrid [0.03%]
历史山葡萄杂交品种的分阶段表观基因组和甲基化继承
Noé Cochetel,Amanda M Vondras,Rosa Figueroa-Balderas et al.
Noé Cochetel et al.
Background: Epigenetic modifications, such as DNA methylation, regulate transcription and influence key biological traits. While many efforts were made to understand their stability in annual crops, their long-term persis...
Runxin Gao,Minrong Guo,Shiping Luan et al.
Runxin Gao et al.
Multivalent interactions between proteins with intrinsically disordered regions or prion-like domains can drive liquid-liquid phase separation (LLPS) and form membraneless condensates essential for diverse cellular functions. Here, we predi...
Eric Kernfeld,Yunxiao Yang,Joshua S Weinstock et al.
Eric Kernfeld et al.
Diverse machine learning methods promise to forecast gene expression changes in response to novel genetic perturbations. However, these methods' accuracy is not well characterized. We created a benchmarking platform that combines a panel of...
Comparative Study
Genome biology. 2025 Nov 17;26(1):388. DOI:10.1186/s13059-025-03840-y 2025
PRC1-mediated H2A.Zub promotes gene expression by preventing H3.1K27me1 incorporation in Arabidopsis [0.03%]
拟南芥中由PRC1介导的H2A.Zub通过防止H3.1K27me1的结合促进基因表达
Fernando Baile,Javier Antúnez-Sánchez,José Gutiérrez-Marcos et al.
Fernando Baile et al.
Background: PcG complexes are pivotal in orchestrating the transition from embryonic to vegetative development in plants. However, the mechanisms underlying the gene expression reprogramming that takes place during this d...
Integrative analysis of RNA binding proteins identifies DDX55 as a novel regulator of 3'UTR isoform diversity [0.03%]
整合分析RNA结合蛋白鉴定DDX55为调控3'UTR多样性新型调节因子
Matthew R Gazzara,Timothy Cater,Michael J Mallory et al.
Matthew R Gazzara et al.
Background: The 3' untranslated regions (3'UTRs) of mRNAs play a critical role in controlling gene expression and function because they contain binding sites for microRNAs and RNA binding proteins (RBPs) that alter mRNA s...
Uli-epic: profiling RNA modifications from ultra-low input samples [0.03%]
Uli-Epic：从超低输入样品中对RNA修饰进行剖析
Weizhi He,Chu Xu,Wen Chen et al.
Weizhi He et al.
High-throughput sequencing with chemical labeling enables robust, transcriptome-wide detection of RNA modifications at single-nucleotide resolution. However, these methods typically require substantial RNA amounts due to harsh treatments. W...
Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus [0.03%]
泛基因组结构变异模式反映了油菜的进化分化
Nazanin P Afsharyan,Agnieszka A Golicz,Rod J Snowdon
Nazanin P Afsharyan
Background: Understanding genetic diversity is crucial for enhancing crop productivity. This study explores species-wide genome structural variation (SV) and its role in intraspecific and ecogeographical diversification o...
HydraRNA: a hybrid architecture based full-length RNA language model [0.03%]
HydraRNA：一种全长度 RNA 语言模型的混合架构
Guipeng Li,Feifei Jiang,Junhao Zhu et al.
Guipeng Li et al.
Background: RNA, an essential component of the central dogma of molecular biology, plays versatile roles in all cellular processes. RNA large language models (LLMs) are emerging as powerful methods in RNA research to deci...
Translational regulation plasticity shapes wheat grain adaptation to heat stress [0.03%]
翻译调控的可塑性塑造了小麦籽粒对高温胁迫的适应性
Yongming Chen,Yiwen Guo,Mengsi Ma et al.
Yongming Chen et al.
Background: Extremely high temperatures due to global warming are increasingly threatening crop production, and plants have evolved highly sophisticated mechanisms to respond to harsh environmental stresses and survive. A...