Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries [0.03%]
层次化交织Bloom过滤器：实现超快的大规模序列近似查找
Svenja Mehringer,Enrico Seiler,Felix Droop et al.
Svenja Mehringer et al.
We present a novel data structure for searching sequences in large databases: the Hierarchical Interleaved Bloom Filter (HIBF). It is extremely fast and space efficient, yet so general that it could serve as the underlying engine for many a...
Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis [0.03%]
拟南芥热应力诱导的转录记忆的基因组和表观基因组决定因素
Christian Kappel,Thomas Friedrich,Vicky Oberkofler et al.
Christian Kappel et al.
Background: Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants...
Inferring cell-type-specific causal gene regulatory networks during human neurogenesis [0.03%]
人类神经发生过程中推断细胞类型特异性因果基因调控网络
Nil Aygün,Dan Liang,Wesley L Crouse et al.
Nil Aygün et al.
Background: Genetic variation influences both chromatin accessibility, assessed in chromatin accessibility quantitative trait loci (caQTL) studies, and gene expression, assessed in expression QTL (eQTL) studies. Genetic v...
Genomic hallmarks and therapeutic implications of G0 cell cycle arrest in cancer [0.03%]
癌症中G0细胞周期阻滞的基因组特征及治疗意义
Anna J Wiecek,Stephen J Cutty,Daniel Kornai et al.
Anna J Wiecek et al.
Background: Therapy resistance in cancer is often driven by a subpopulation of cells that are temporarily arrested in a non-proliferative G0 state, which is difficult to capture and whose mutational drivers remain largely...
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