Antisense transcription can induce expression memory via stable promoter repression [0.03%]
反义转录可通过稳定地抑制启动子来诱导表达记忆
Verena Mutzel,Till Schwämmle,Svearike Oeverdieck et al.
Verena Mutzel et al.
Background: The capacity of cells to retain a memory of previous signals enables acquisition of unique fates and adaptation to their environment. The underlying gene expression memory can arise from mutual repression of t...
Elise Amblard,Vadim Bertrand,Hugo Barbot et al.
Elise Amblard et al.
Background: Tumour heterogeneity significantly affects cancer progression and therapeutic response, yet quantifying it from bulk molecular data remains challenging. Deconvolution algorithms, which estimate cell type propo...
ST-FFPE-mIF: integrating spatial transcriptomics and multiplex immunofluorescence in formalin-fixed paraffin-embedded tissues using Stereo-seq [0.03%]
ST-FFPE-mIF：利用Stereo-seq在福尔马林固定石蜡包埋组织中整合空间转录组学和多重免疫荧光技术
Xue Zhang,Meng Zhang,Yuan Xu et al.
Xue Zhang et al.
While Stereo-seq-FFPE captures spatial gene expression in formalin-fixed paraffin-embedded (FFPE) samples, it is limited to transcriptomic data. Here, we introduce ST-FFPE-mIF, a protocol that integrates eight-plex immunofluorescence staini...
Spatial transcriptomic alignment, integration, and 3D reconstruction by STAIR [0.03%]
基于STAIR的空间转录组对齐、整合和三维重建方法
Yuanyuan Yu,Zhi Xie
Yuanyuan Yu
Merging multiple slices into a unified 3D atlas is a significant challenge in spatial transcriptomics. Here, we introduce STAIR, an end-to-end solution for alignment, integration, and 3D reconstruction. STAIR employs a heterogeneous graph a...
Nikol Chantzi,Ilias Georgakopoulos-Soares
Nikol Chantzi
Background: Short tandem repeats (STRs) are widespread, dynamic repetitive elements with a number of biological functions and relevance to human diseases, genome plasticity and adaptation. However, their prevalence across...
A single-cell atlas of RNA alternative splicing in the glioma-immune ecosystem [0.03%]
胶质瘤免疫生态系统中的单细胞RNA选择性可变剪接图谱
Xiao Song,Deanna Tiek,Minghui Lu et al.
Xiao Song et al.
Background: Single-cell analysis has refined our understanding of cellular heterogeneity in glioma, yet RNA alternative splicing, a critical layer of transcriptome regulation, remains underexplored at single-cell resoluti...
A systematic evaluation of highly variable gene selection methods for single-cell RNA-sequencing [0.03%]
单细胞RNA测序的高可变基因选择方法的系统评估
Ruzhang Zhao,Jiuyao Lu,Yuzi Li et al.
Ruzhang Zhao et al.
Selecting highly variable genes (HVGs) is a critical step in single-cell RNA sequencing data analysis. We benchmark 47 HVG selection methods across 19 datasets, 18 evaluation criteria, and 5,358 settings. Hybrid methods – mixtures of multi...
Correction: iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis [0.03%]
纠正：iNOME-seq：在阿拉伯芥中同时进行染色体可及性、核小体定位、DNA结合蛋白位点和DNA甲基化的全基因组测绘（体内）
Nosheen Hussain,Ryan Merritt,Julia Engelhorn et al.
Nosheen Hussain et al.
Published Erratum
Genome biology. 2025 Dec 10;26(1):423. DOI:10.1186/s13059-025-03888-w 2025
Transcriptional dynamics and chromatin accessibility in the regulation of shade-responsive genes in Arabidopsis [0.03%]
拟南芥荫蔽响应基因的转录动力学和染色质可及性调节研究
Sandi Paulišić,Alessandra Boccaccini,René Dreos et al.
Sandi Paulišić et al.
Background: Open chromatin regions host DNA regulatory motifs that are accessible to transcription factors and the transcriptional machinery. In Arabidopsis, responses to light are heavily regulated at the transcriptional...
Ancient genomes give insight into 160,000 years of East Asian population dynamics and biological adaptation [0.03%]
古代基因组揭示东亚16万年的群体动态和生物适应性
Guanglin He,Yuntao Sun,Shuhan Duan et al.
Guanglin He et al.
Advances in ancient DNA research have transformed our understanding of human evolution, admixture-driven adaptation, and genetic underpinnings of traits. However, the evolutionary dynamics of Paleolithic and Neolithic East Asian remain frag...