Chenxi Zhou,Max Brown,Mark Blaxter;Darwin Tree of Life Project Consortium;Shane A McCarthy et al.
Chenxi Zhou et al.
Plant organelle genomes, particularly large mitochondrial genomes with complex repeats, present significant challenges for assembly. The advent of long-read sequencing enables the assembly of complete genomes, but problems of resolving alte...
scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data [0.03%]
基于质谱的单细胞蛋白质组学数据的理解：线性模型的应用（SCPlainer）
Christophe Vanderaa,Laurent Gatto
Christophe Vanderaa
Analyzing mass spectrometry (MS)-based single-cell proteomics (SCP) data faces important challenges inherent to MS-based technologies and single-cell experiments. We present scplainer, a principled and standardized approach for extracting m...
scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3' scRNA-seq data [0.03%]
基于reads1保留的单细胞3′端测序数据的精确多聚腺苷酸位点检测及其可选使用分析方法(scTail)
Ruiyan Hou,Yuanhua Huang
Ruiyan Hou
The first-strand reads (often reads 1) of three-prime single-cell RNA-seq (3' scRNA-seq) can contain informative cDNA for analysis of polyadenylation sites (PAS), but are often overlooked or trimmed. Here, we describe a computational method...
Identification of replicative aging and inflammatory aging signatures via whole-genome CRISPRi screens [0.03%]
通过全基因组CRISPRi筛选鉴定复制衰老和炎症衰老标志物
Lingling Wu,Xiang Zhu,Yanxia Liu et al.
Lingling Wu et al.
Background: Aging is a major risk factor for chronic diseases and cancer. Cellular aging, particularly in adult stem cells, offers a high-throughput framework for dissecting the molecular mechanisms of aging. ...
Chromosome-level genome assembly of the autotetraploid yellow pitaya provides novel insights into evolution of trait patterning in pitaya species with different ploidy [0.03%]
自四倍体黄皮刺茄染色体水平基因组组装提供新视角理解不同倍性刺茄物种中特性的演化规律
Qamar U Zaman,Ali Raza,Liu Hui et al.
Qamar U Zaman et al.
Background: Yellow pitaya (Selenicereus megalanthus, 2n = 4x = 44) breeding remains severely hindered due to the lack of a reference genome. Results: ...
Effects of chromosome number reduction on mitotic and meiotic stability in fission yeast [0.03%]
染色体数目减少对裂殖酵母有丝分裂和减数分裂稳定性的效应
Yueyue Jiang,Yanze Jian,Lingyun Nie et al.
Yueyue Jiang et al.
Background: Genetic information is stored on multiple chromosomes in eukaryotic organisms and is passed on to offspring through cell division. How chromosome number influences cell division and chromosome segregation is n...
Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals [0.03%]
长读段检测低甲基化拟南芥个体的体细胞转座元件动员事件
Andrea Movilli,Svitlana Sushko,Fernando A Rabanal et al.
Andrea Movilli et al.
Background: Because transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypomethylated plants. It is...
SpaSEG: unsupervised deep learning for multi-task analysis of spatially resolved transcriptomics [0.03%]
SpaSEG：无监督深度学习在空间分辨转录组学多任务分析中的应用
Yong Bai,Xiangyu Guo,Keyin Liu et al.
Yong Bai et al.
Spatially resolved transcriptomics (SRT) for characterizing spatial cellular heterogeneities in tissue environments requires systematic analytical approaches to elucidate gene expression variations within their physiological context. Here, ...
Björn E Langer,Andreia Amaral,Marie-Odile Baudement et al.
Björn E Langer et al.
Standardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two...
Artificial chromosome reorganization reveals high plasticity of the budding and fission yeast genomes [0.03%]
人工染色体重组揭示出芽和裂殖酵母基因组的高度可塑性
Xueting Zhu,Shaochun Liu,Tiantian Ye et al.
Xueting Zhu et al.
Background: The genome of a eukaryotic cell is usually organized on a set of chromosomes. Recently, karyotype engineering has been applied to various organisms, but whether and to what extent a naturally evolved genome ca...