Characterization of the transposable element landscape shaping the Ectocarpus genome [0.03%]
表征转座子景观塑造Ectocarpus基因组的特性
Erica Dinatale,Rory J Craig,Claudia Martinho et al.
Erica Dinatale et al.
Background: Comprising up to 90% of eukaryotic genomes, transposable elements (TEs) are mobile genetic units that play fundamental roles in evolution. Brown algae, one of the most complex multicellular eukaryotic groups t...
Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation [0.03%]
支链氨基酸饥饿期间密码子特异性核糖体停滞重塑了翻译动力学
Lina Worpenberg,Cédric Gobet,Felix Naef
Lina Worpenberg
Background: Cells regulate protein synthesis in response to fluctuating nutrient availability through mechanisms that affect both translation initiation and elongation. Branched-chain amino acids, leucine, isoleucine, and...
Hybrid BAG-seq: DNA and RNA from the same single nucleus reveals interactions between genomic and transcriptomic landscapes in human tumor samples [0.03%]
混合BAG-seq：来自同一单个细胞核的DNA和RNA揭示了人类肿瘤样本中基因组和转录组景观之间的相互作用
Siran Li,Joan Alexander,Jude Kendall et al.
Siran Li et al.
We introduce hybrid BAG-seq: a high-throughput, multi-omic method that simultaneously captures DNA and RNA from single nuclei. We apply this protocol to 65,499 single nuclei from samples of five uterine cancer patients and validate the clus...
Machine learning and statistical inference in microbial population genomics [0.03%]
机器学习和统计推理在微生物群体基因组学中的应用
Samuel K Sheppard,Nicolas Arning,David W Eyre et al.
Samuel K Sheppard et al.
The availability of large genome datasets has changed the microbiology research landscape. Analyzing such data requires computationally demanding analyses, and new approaches have come from different data analysis philosophies. Machine lear...
SNPmanifold: detecting single-cell clonality and lineages from single-nucleotide variants using binomial variational autoencoder [0.03%]
基于二项式变分自编码器的单核苷酸变异检测单细胞克隆性和谱系（SNPmanifold）
Hoi Man Chung,Yuanhua Huang
Hoi Man Chung
Single-nucleotide-variant (SNV) clone assignment of high-covariance single-cell lineage tracing data remains a challenge due to hierarchical mutation structure and many missing signals. We develop SNPmanifold, a Python package that learns a...
Single-nucleus transcriptomics revealed auxin-driven mechanisms of wood plasticity to enhance severe drought tolerance in poplar [0.03%]
单细胞基因组学揭示了木素生物合成途径的关键作用：杨树应对极端干旱的耐受机制
Daniela Gómez-Soto,Wendell J Pereira,Alejandro Piedrabuena-Díaz et al.
Daniela Gómez-Soto et al.
Background: Drought significantly affects forests and woody crops by limiting their growth, increasing their susceptibility to diseases, and reducing productivity. Wood anatomical plasticity is a crucial adaptive mechanis...
Differential regulation of mesoscale chromosome conformations in osteoblasts and osteosarcoma [0.03%]
骨细胞和骨肉瘤中对介观尺度染色体构象的调控不同
Madhoolika Bisht,Yu-Chieh Chung,Siou-Luan He et al.
Madhoolika Bisht et al.
Background: Chromosome conformation within the nucleus is essential for genome function. These have primarily been studied at the scale of loops and compartments, or at lower spatial resolution using traditional in situ h...
Genome of the green-head ant, Rhytidoponera metallica, reveals mechanisms of toxin evolution in a genetically hyper-diverse eusocial species [0.03%]
绿头蚁金属蚁基因组揭示了高度遗传多样性物种中的毒素进化机制
Anders Isaksen,Pedro G Nachtigall,Robin A Araya et al.
Anders Isaksen et al.
Background: While ants are textbook examples of eusocial animals in which altruistic behavior is maintained through kin selection, several ants form genetically diverse colonies that challenge this concept. One example is...
Interaction of plant-derived metabolites and rhizobiome functions enhances drought stress tolerance [0.03%]
植物衍生代谢物与根系微生物组功能的互作可提高干旱胁迫耐受性
Anna Kazarina,Soumyadev Sarkar,Bryttan Adams et al.
Anna Kazarina et al.
Background: Plants have evolved alongside microbes, enabling plants to better cope with abiotic and biotic stress. Interactions between plant roots and local soil microbes are critical for environmental adaptation and pla...
High-resolution genome assembly reveals retrotransposon-mediated centromere dynamics in rye [0.03%]
高质量基因组组装揭示了黑麦中逆转录转座子介导的着丝粒动态变化
Congyang Yi,Qian Liu,Congle Zhu et al.
Congyang Yi et al.
Background: The genome of rye, Secale cereale, is distinguished by large repetitive regions including subtelomeric heterochromatin and retrotransposon-dominant centromeres, which contrast with the satellite-repeat-based c...