Benchmarking cell-type deconvolution in cross-platform transcriptomic data [0.03%]
跨平台转录组数据中细胞类型去卷积的基准测试
Aakanksha Singh,Pinar Cakmak,Jennifer H Lun et al.
Aakanksha Singh et al.
Background: Transcriptomic data from diverse measurement technologies are widely used to study tissue heterogeneity. Cell-type deconvolution, which resolves mixed transcriptomic signals into cellular components, is a key ...
Interpretable distillation reveals that deep learning splicing models suffer from pervasive confounders and blind spots [0.03%]
可解释的知识蒸馏表明深度学习拼接模型存在广泛的混淆因素和盲点问题
Simon Liu,Wenjing Zhang,Oded Regev
Simon Liu
Background: Predicting RNA splicing from genomic sequence is a crucial task for understanding gene regulation and interpreting genetic variation. Recent deep learning advancements have led to splicing prediction algorithm...
Ancient genomics study reveals low HLA diversity in eastern hunter-gatherers [0.03%]
古基因组研究显示东部狩猎采集者的HLA多样性较低
Onur Özer,Nicolas Antonio da Silva,Magdalena Haller-Caskie et al.
Onur Özer et al.
Background: Eastern hunter-gatherers (EHG) contributed varying proportions of genetic ancestry to many modern Europeans. However, how this contribution shaped the human leukocyte antigen (HLA) gene diversity remains unexp...
Comprehensive benchmarking of RNA velocity methods across single-cell datasets [0.03%]
跨单细胞数据集的RNA速度方法全面基准测试
Yida Wu,Chuihan Kong,Xu Liao et al.
Yida Wu et al.
Background: RNA velocity provides a powerful framework for inferring cellular dynamics from single-cell RNA sequencing data. The rapid proliferation of computational methods within this field has prompted a need for syste...
Xi-Tong Zhu,Xinyan Lu,Zengxin Zhang et al.
Xi-Tong Zhu et al.
Background: Fusion transcripts, first characterized in cancer, have been increasingly reported in plants with the expansion of next-generation sequencing. However, their prevalence and biological relevance remain highly d...
IDEAL-Age: an interpretable deep learning framework for single-cell resolution profiling of immunological aging [0.03%]
理想年龄：一种解释性深度学习框架，用于免疫衰老的单细胞分辨率分析
Yin Xu,Zhengchao Luo,Kai He et al.
Yin Xu et al.
Immunosenescence increases susceptibility to infection and reduces vaccine responsiveness, yet bulk transcriptomic clocks obscure the cellular heterogeneity underlying this process. Here, we present IDEAL-Age, an interpretable deep learning...
Comparative assessment of large language models for microbial phenotype assignment [0.03%]
大型语言模型在微生物表型分配中的比较评估
Philipp C Münch,Nasim Safaei,René Mreches et al.
Philipp C Münch et al.
Background: Large language models (LLMs) are increasingly used to extract knowledge from text, yet their coverage and reliability in biology remain unclear. Microbial phenotypes are especially important to assess, as comp...
Comparative Study
Genome biology. 2026 Jul 23;27(1):235. DOI:10.1186/s13059-026-04207-7 2026
Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer [0.03%]
解码染色质三维结构揭示前列腺癌分层基因调控下的不同增强子类型
Huan Cao,Zexun Wu,Baixi Ji et al.
Huan Cao et al.
Background: The transcription process is controlled by non-coding regulatory elements, more than 70% of which are putative enhancers. These enhancers comprise over 600,000 regions and are marked by histone modifications. ...
Genomic and cytogenetic evidence for divergence and speciation in geladas [0.03%]
基因组和细胞遗传学证据揭示了胶猴的分化和物种形成过程
Brooklynn R Scott,Ferehiwot Ayele,Alemayehu Lemma et al.
Brooklynn R Scott et al.
Background: Chromosomal rearrangements can play an important role in shaping patterns of genomic divergence and speciation, yet their evolutionary context is still largely unclear, as such events are rare and challenging ...
Targeted chromosomal sequencing of wild bonobos identifies a genetically distinct subpopulation east of the Lomami river [0.03%]
目标染色体测序揭示倭黑猩西
Mar Crego-Walters,Sebastian Cuadros-Espinoza,Irune Ruiz-Gartzia et al.
Mar Crego-Walters et al.
Background: Bonobos (Pan paniscus), an endangered species, have for decades been genetically understudied, partly due to difficulties in obtaining high-quality samples. The study of their genome is important not only for ...