omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data [0.03%]
OmniDeConv：批量RNA序列数据使用和基准单细胞信息脱卷的统一框架
Alexander Dietrich,Lorenzo Merotto,Konstantin Pelz et al.
Alexander Dietrich et al.
Background: In silico cell-type deconvolution from bulk transcriptomics data is a powerful technique to gain insights into the cellular composition of complex tissues. While first-generation methods used precomputed expre...
Multiomics profiling reveals the adaptive responses of largemouth bass to high temperature stress [0.03%]
多组学分析揭示了大口黑鲈对高温胁迫的适应性响应
Wenzhi Guan,Yongqing Yu,Jinpeng Zhang et al.
Wenzhi Guan et al.
Background: Largemouth bass (Micropterus salmoides) is among the most economically important freshwater fish species. High temperature is a major abiotic stressor, leading to increased mortality and significant economic l...
Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types [0.03%]
使用真实的数据评估去卷积方法，以获得稳健的预后见解
Minghan Li,Yuqing Su,Yizhou Tang et al.
Minghan Li et al.
Background: Deconvolution of bulk RNA-expression data unlocks the cellular complexity of cancer, yet traditional pseudobulk benchmarks may not always be reliable in real-world settings where absolute cell proportions are ...
Harmonizing single-cell 3D genome data with STARK and scNucleome [0.03%]
利用STARK和scNucleome对齐单细胞三维基因组数据
Wen-Jie Jiang,KangWen Cai,YuanChen Sun et al.
Wen-Jie Jiang et al.
Single-cell three-dimensional genome sequencing (sc3DG-seq) reveals genome regulation and heterogeneity in various biological processes, but a universal analysis tool is lacking. Here we present STARK, a versatile toolkit for processing, qu...
Comprehensive assessment of activity, specificity, and safety of hypercompact TnpB systems for gene editing [0.03%]
全面评估超紧凑TnpB系统在基因编辑中的活性、特异性及安全性
Changchang Xin,Guanghai Xiang,Shiwei Cao et al.
Changchang Xin et al.
Background: As the ancestor of CRISPR-Cas12 nucleases, TnpB represents the most compact gene editing tool currently available. Recent studies have identified multiple TnpB systems with gene editing activity in mammalian c...
Dissecting the contribution of transposable elements to interphase chromosome structure [0.03%]
染色体转座子元件对间期染色体结构的贡献分解
Liyang Shi,Zhen Xiao,Xuemeng Zhou et al.
Liyang Shi et al.
Background: Transposable elements (TEs) occupy nearly half of the human genome and play diverse biological roles. Despite their abundance, the extent to which TEs contribute to three-dimensional (3D) genome structure rema...
Alesha A Hatton,Robert F Hillary,Daniel L McCartney et al.
Alesha A Hatton et al.
Background: While height is a highly heritable trait with strong polygenic prediction, previous studies have postulated that minimal variation of its individual differences can be captured by DNA methylation (DNAm). We in...
Genomic basis underlying alternative transcripts-mediated drought tolerance in maize [0.03%]
基于转录本可变剪切的玉米抗旱性状的遗传基础分析
Shulin Hao,Suwen Han,Zhenghua He et al.
Shulin Hao et al.
Background: Drought is a major abiotic stress that affects the growth and yield of maize. Alternative transcripts are crucial in abiotic stress responses in plants. However, the genetic basis of alternative transcripts me...
CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model [0.03%]
CLAMP：使用染色质可及性语言模型预测多种物种中特定蛋白质介导的染色体环化区域
Zhijie He,Yu Sun,Hao Li et al.
Zhijie He et al.
Emerging DNA language models provide powerful tools to address the challenge of accurately predicting chromatin loops, fundamental structures governing 3D genome organization and gene regulation. Here we present CLAMP, which utilizes a deep...
TSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data [0.03%]
TSniffer：通过RNA测序数据无偏倚地鉴定RNA编辑位点和量化编辑活性
Maike Herrmann,Yvonne Krebs,Francisco M Acosta et al.
Maike Herrmann et al.
RNA editing by adenosine deaminases acting on RNA (ADARs) is an essential cellular process performed by three enzymes in mammals: ADAR1-p150, ADAR1-p110, and ADAR2, demonstrating different target specificity and selectivity. Here we describ...