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) ...
A geometric deep learning framework for genome-wide prediction of enzyme turnover number [0.03%]
一种用于全基因组预测酶转化数的几何深度学习框架
Tong Pan,Xin Cui,Huan Yee Koh et al.
Tong Pan et al.
Background: Enzyme turnover numbers (Kcat) are fundamental kinetic constants that quantify enzymatic efficiency. Systematic studies of Kcat are essential for characterizing the mechanisms underlying proteomic composition ...
Dissecting the genetic architecture of seed-related traits in Brassica napus by integrating multi-omics analysis and VIS-NIR hyperspectral imaging [0.03%]
基于组学整合和VIS-NIR高光谱成像技术解析油菜籽相关性状的遗传结构
Zengdong Tan,Yunhao Liu,Xiaowei Wu et al.
Zengdong Tan et al.
Background: Brassica napus (B. napus) is globally important oilseed crop, yet traditional approaches for phenotyping of seed traits are labor-intensive and destructive. ...
ICE: robust detection of cellular senescence from weak single-cell signatures using imputation-based marker refinement [0.03%]
利用基于插补的标记优化法从单细胞微弱信号中稳健地检测细胞衰老事件
Peng Xu,Hantao Zhang,Siyao Zhu et al.
Peng Xu et al.
Detecting senescent cells from single-cell RNA-seq data remains challenging due to the weak and non-specific expression of canonical markers. Here, we demonstrate that simple expansion of these low-signal marker sets does not improve detect...
Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants [0.03%]
多条道路通向植物染色体相互作用：植物转录因子结合的图谱构建与解析
Moonia Ammari,Aanchal Choudhary,Mark Zander
Moonia Ammari
Elucidating transcription factor (TF) function is essential for advancing our understanding and manipulation of the mechanisms that orchestrate gene expression programs underlying plant growth, development, and resilience. Defining the geno...