Srr2-dependent SOX2 levels govern the chromatin and transcriptional landscape of adult neural stem cell fate decisions in mouse [0.03%]
Srr2依赖的SOX2水平决定小鼠成年神经干细胞命运决定过程中的染色质和转录景观
Sara Cruces-Salguero,Antonio Jordán-Pla,Ana Domingo-Muelas et al.
Sara Cruces-Salguero et al.
Background: Stem cell maintenance and lineage commitment in the nervous system require precise regulation of transcription factors, with SOX2 serving as a pivotal regulator. SOX2 expression is controlled by multiple enhan...
Tumoral switch in NUMB splicing changes essential transcription pathways and induces malignant properties in tumour cells [0.03%]
NUMB剪接转换的肿瘤性变化影响了重要的转录途径并诱导了肿瘤细胞的恶性表现
José Manuel García-Heredia,Sara M Ortega-Campos,Amancio Carnero
José Manuel García-Heredia
Background: Emerging evidence indicates that cancer is associated with widespread splicing alterations that generate tumour-specific isoforms. One example is NUMB, an evolutionarily conserved adaptor protein, which produc...
MLMarker: a machine learning framework for tissue inference and biomarker discovery [0.03%]
基于机器学习的组织推理和生物标志物发现框架MLMarker
Tine Claeys,Sam van Puyenbroeck,Kris Gevaert et al.
Tine Claeys et al.
MLMarker is a machine learning tool that computes continuous tissue similarity scores for proteomics data, addressing the challenge of interpreting complex or sparse datasets. Trained on 34 healthy tissues, its Random Forest model generates...
UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity [0.03%]
联合循环：一种用于跨相关Hi-C数据集调用染色质环的工作流程，具有更高的特异性和灵敏度
Jiangyuan Liu,Johan H Gibcus,Job Dekker
Jiangyuan Liu
Chromatin loop calling from chromatin interaction data often exhibits substantial variability across related samples. We present UnionLoops, a computational workflow for chromatin loop calling across multiple related samples. UnionLoops int...
Spatiotemporal transcriptomic analysis during cold ischemic injury to the murine kidney reveals compartment-specific changes [0.03%]
冷缺血损伤下小鼠肾脏时空转录组分析揭示隔室特异性变化
Srujan Singh,Shishir Kumar Patel,Ryo Matsuura et al.
Srujan Singh et al.
Background: Kidney transplantation is the preferred treatment strategy for end-stage kidney disease. Deceased donor kidneys usually undergo cold storage until kidney transplantation, leading to cold ischemia injury that m...
GenOT: generative optimal transport enables spatiotemporal interpolation and generation in cross-platform spatial transcriptomics [0.03%]
基于生成最优传输的跨平台空间转录组时空插值和生成方法研究
Rui Wang,Xinxin Liu,Linlin Zhuo et al.
Rui Wang et al.
Spatial transcriptomics technologies have revolutionized the analysis of spatial gene expression, yet integrating spatial information and generating data across heterogeneous samples remain challenging. We present GenOT, a generative framew...
Deciphering the mosaic genome of sugarcane cultivars through polyploid admixture inference with AdmixPoly [0.03%]
通过AdmixPoly进行甘蔗栽培品种多倍体杂交推断以解读其镶嵌基因组
Simon Rio,Franck Gauthier,Olivier Garsmeur et al.
Simon Rio et al.
Background: Characterizing population structure and admixture events between ancestral groups plays a key role in understanding the evolutionary history of species and crops. Most tools for inferring admixture have been d...
OTTR-seq profiling reveals dynamic tRNA modification landscapes across diverse archaeal species [0.03%]
基于OTTR-seq的表征揭示了广泛古菌种类中动态tRNA修饰图谱
Jesse S Leavitt,Henry T Moore,Thomas J Santangelo et al.
Jesse S Leavitt et al.
Background: Transfer RNA (tRNA) modifications are essential for structural integrity, decoding fidelity, and stress adaptation, yet their evolutionary dynamics remain poorly characterized in archaea. Here, we apply Ordere...
James M Holt,Christopher T Saunders,Egor Dolzhenko et al.
James M Holt et al.
Variant benchmarking is critical in assessing the accuracy of genomic secondary pipelines. However, traditional benchmarking tools that require exact genotype matches inject biases from variant representation and are ill-suited for tandem r...
Gapless and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres [0.03%]
连续性和阶段性的基因组组装揭示了烟草半保持染色体在全四倍体化后的分化
Weikai Chen,Shaoying Chen,Jingxuan Wang et al.
Weikai Chen et al.
Common tobacco (Nicotiana tabacum) is an economically important crop worldwide whose allotetraploid genome remains incompletely assembled. We present a 4.2-Gb telomere-to-telomere, gap-free, and phased genome assembly. This assembly reveals...