Genomic and epidemiological identification of Pseudomonas aeruginosa transmission chains and in hospital ICUs [0.03%]
利用基因组学和流行病学识别医院重症监护病房中恶臭假单胞菌的传播链
Lucia Graña-Miraglia,Xiaoyi Hu,Cheryl Volling et al.
Lucia Graña-Miraglia et al.
Background: Pseudomonas aeruginosa (PA) is an opportunistic pathogen that poses a significant threat to hospitalized patients, particularly in intensive care units (ICUs) due to its ability to contaminate the environment ...
Network-based framework for studying etiology and phenotypic diversity in primary ciliopathies [0.03%]
基于网络的原发性纤毛缺陷病致病机制和表型多样性的研究框架
Ellen M Aarts,Diederik S Laman Trip,Ruxandra Neatu et al.
Ellen M Aarts et al.
Feng Yan,Pedro L Baldoni,James Lancaster et al.
Feng Yan et al.
Introduction: Recently, de novo transcriptome assembly methods have been developed to utilise long-read data in cases where a reference genome is unavailable, such as in non-model organisms. Despite the potential of these...
saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval [0.03%]
saseR：通过调整偏移量实现快速且可扩展的RNA测序工具以解锁差异使用、异常剪接和表达获取功能
Alexandre Segers,Jeroen Gilis,Mattias Van Heetvelde et al.
Alexandre Segers et al.
RNA-seq data analysis relies on many different tools, each tailored to specific applications and coming with unique assumptions and limitations. Indeed, tools for differential transcript usage or rare disease diagnosis through splicing and ...
Non-disruptive in vitro monitoring of cellular states with cell-free DNA methylation [0.03%]
基于细胞游离DNA甲基化的体外细胞状态无扰监测技术
Anja Hess,Alexander Kovacsovics,Fabian Bachinger et al.
Anja Hess et al.
Individual CpG methylation signatures characterize each mammalian cell type, thereby offering a powerful readout for clinical and diagnostic applications. Here, we apply this principle to in vitro cellular systems, using cell-free DNA relea...
Joshua D Kapp,Ciara Wanket,Remy Nguyen et al.
Joshua D Kapp et al.
The small amount of fragmented DNA present in rootless hair shafts is unsuitable for many assays, including most PCR-based assays. Thus, rootless hair DNA is often overlooked in biomedical and forensic analysis. Here we apply methods for ef...
Sequence bias in chromatin fragmentation leads to misinterpretation of protein-DNA interactions in vivo [0.03%]
染色质断裂的序列偏向会导致对体内蛋白质- DNA 相互作用的误读
Laura Durán,Laura Rodríguez,Alicia García et al.
Laura Durán et al.
Genome regulation depends on the binding of regulatory proteins to chromatin. V-plots are widely used to assess the binding of transcription factors and other protein complexes to DNA in vivo. However, we show here that V-plots result from ...
Rapid genome modifications including chromosomal fusions and large-scale inversions are key features in Arctic codfish species [0.03%]
染色体融合和大规模倒位是北极 codfish 特有的快速基因组变化事件
Siv N K Hoff,Marius F Maurstad,Ole K Tørresen et al.
Siv N K Hoff et al.
Background: Genome evolvability involves activation of transposable elements (TEs) that result in novel genomic rearrangements, including translocations, deletions, duplications, as well as larger structural reorganizatio...
Predicting disease-specific histone modifications and functional effects of non-coding variants by leveraging DNA language models [0.03%]
利用DNA语言模型预测疾病特异性组蛋白修饰及非编码变异的功能效应
Xiaoyu Wang,Tong Pan,Sihan Chen et al.
Xiaoyu Wang et al.
Background: Epigenetic modifications play a vital role in the pathogenesis of human diseases, particularly neurodegenerative disorders such as Alzheimer's disease, where dysregulated histone modifications are strongly imp...
Modeling nascent transcription from chromatin landscape and structure with CLASTER [0.03%]
基于染色质景观和结构的新生转录建模研究(CLASTER模型)
Marc Pielies Avellí,Arnór Ingi Sigurdsson,Joaquim Ollé López et al.
Marc Pielies Avellí et al.
We present the Chromatin Landscape and Structure to Expression Regressor (CLASTER), an epigenetic-based deep neural network that can integrate different data modalities describing the chromatin landscape and its 3D structure. CLASTER effect...