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...
Higher order repeat structures reflect diverging evolutionary paths in maize centromeres and knobs [0.03%]
高级重复结构反映了玉米着丝粒和 knobs 中日益分化的发展道路
Rebecca D Piri,Mingyu Wang,M Cinta Romay et al.
Rebecca D Piri et al.
Background: Highly repetitive tandem repeat arrays, known as satellite DNAs, are enriched in low-recombination regions such as centromeres. Satellite arrays often contain complex internal structures called higher-order re...
Haplotype-aware segmentation with HapASeg increases accuracy of detecting homolog-specific somatic copy number alterations [0.03%]
基于 haplotype 的染色体结构变异分割算法可提高同源染色体特异的拷贝数突变检测精度
Oliver Priebe,Ron Solan,Conor Messer et al.
Oliver Priebe et al.
Somatic copy number alterations (sCNAs) drive cancer initiation, progression, resistance, and metastasis. Furthering our understanding of sCNAs requires substantially larger cohorts. Most tumors available for sequencing are preserved with f...
Hidden in plain sight: illuminating the tRNA landscape by sequencing [0.03%]
无处不在却又隐藏天下的tRNA组学及其测序研究
Katherine Marlow,Zhangli Su
Katherine Marlow
Transfer RNAs (tRNAs) are essential for decoding mRNAs into proteins and are increasingly recognized as dynamic regulators of gene expression. Their function is shaped by intricate layers of post-transcriptional processing, modification, am...
PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns [0.03%]
高效的计算模型模拟时空基因表达模式-PreTSA模型
Haotian Zhuang,Zhicheng Ji
Haotian Zhuang
Modeling temporal and spatial gene expression patterns in large-scale single-cell and spatial transcriptomics data is a computationally intensive task. We present PreTSA, a method that offers computational efficiency in modeling these patte...
Genome co-adaptation and the evolution of methicillin resistant Staphylococcus aureus [0.03%]
金黄色葡萄球菌甲氧西林耐药株的基因组共同适应性演化
Seungwon Ko,Elizabeth A Cummins,William Monteith et al.
Seungwon Ko et al.
Background: Antimicrobial resistance in bacterial pathogens is a major threat to global health, rendering standard treatments ineffective and increasing the risk of severe infection or death. Resistance is often conferred...
DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase [0.03%]
DMN-SEQ通过5-甲基胞嘧啶脱氨酶富集DNA低甲基化区域用于生物标志物发现
Yiding Wang,Yang Li,Chang Ye et al.
Yiding Wang et al.
Various methods have been developed for 5-methylcytosine (5mC) sequencing; however, effective ways to enrich hypomethylated DNA regions have been limited. Here, we describe the DEMETER-assisted 5-Methylcytosine Nicking sequencing (DMN-seq) ...