Jessica Powell,Andrea Talenti,Andressa Fisch et al.
Jessica Powell et al.
Background: Understanding the variation between well and poorly adapted cattle breeds to local environments and pathogens is essential for breeding cattle with improved climate and disease-resistant phenotypes. Although c...
SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors [0.03%]
探索染色质景观和先驱因子作用的工具
Wuming Gong,Nikita Dsouza,Daniel J Garry
Wuming Gong
Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. Currently, no method specifically detects differential chromatin accessibility. Here, SeATAC uses a conditional variati...
Graph construction method impacts variation representation and analyses in a bovine super-pangenome [0.03%]
图形构建方法影响牛超泛基因组的变异表示和分析
Alexander S Leonard,Danang Crysnanto,Xena M Mapel et al.
Alexander S Leonard et al.
Background: Several models and algorithms have been proposed to build pangenomes from multiple input assemblies, but their impact on variant representation, and consequently downstream analyses, is largely unknown. ...
Brian C Lin,Upendra Katneni,Katarzyna I Jankowska et al.
Brian C Lin et al.
Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous SNVs are previously considered to be "silent," but mounting evidence has revealed that these variants can cause RNA and protein changes and are implicated i...
SPUMONI 2: improved classification using a pangenome index of minimizer digests [0.03%]
改进的分类方法：使用最小化子摘要的泛基因组索引的SPUMONI 2版本
Omar Y Ahmed,Massimiliano Rossi,Travis Gagie et al.
Omar Y Ahmed et al.
Genomics analyses use large reference sequence collections, like pangenomes or taxonomic databases. SPUMONI 2 is an efficient tool for sequence classification of both short and long reads. It performs multi-class classification using a nove...
Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability [0.03%]
元分析（单细胞方法）基准评估发现可扩展性和互操作性的必要性
Anthony Sonrel,Almut Luetge,Charlotte Soneson et al.
Anthony Sonrel et al.
Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect important steps of analysis pipelines,...
Meta-Analysis
Genome biology. 2023 May 17;24(1):119. DOI:10.1186/s13059-023-02962-5 2023
Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications [0.03%]
Introme 准确预测编码和非编码变异对基因剪接的影响及其临床应用价值
Patricia J Sullivan,Velimir Gayevskiy,Ryan L Davis et al.
Patricia J Sullivan et al.
Predicting the impact of coding and noncoding variants on splicing is challenging, particularly in non-canonical splice sites, leading to missed diagnoses in patients. Existing splice prediction tools are complementary but knowing which to ...
RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches [0.03%]
兔兔TClust：基于最小哈希算法实现千万量级细菌基因组的快速聚类分析
Xiaoming Xu,Zekun Yin,Lifeng Yan et al.
Xiaoming Xu et al.
We present RabbitTClust, a fast and memory-efficient genome clustering tool based on sketch-based distance estimation. Our approach enables efficient processing of large-scale datasets by combining dimensionality reduction techniques with s...
Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data [0.03%]
基于标记基因的细胞类型解卷积的空间转录组学数据的概率模型 Celloscope
Agnieszka Geras,Shadi Darvish Shafighi,Kacper Domżał et al.
Agnieszka Geras et al.
Spatial transcriptomics maps gene expression across tissues, posing the challenge of determining the spatial arrangement of different cell types. However, spatial transcriptomics spots contain multiple cells. Therefore, the observed signal ...
Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans [0.03%]
表观基因组分析鉴定出亲本印记甲基化与人类衰老速度相关性
Chenhao Gao,Carmen Amador,Rosie M Walker et al.
Chenhao Gao et al.
Background: The variation in the rate at which humans age may be rooted in early events acting through the genomic regions that are influenced by such events and subsequently are related to health phenotypes in later life...