PCA outperforms popular hidden variable inference methods for molecular QTL mapping [0.03%]
在分子QTL图谱绘制方面，PCA的表现优于流行的隐变量推理方法
Heather J Zhou,Lei Li,Yumei Li et al.
Heather J Zhou et al.
Background: Estimating and accounting for hidden variables is widely practiced as an important step in molecular quantitative trait locus (molecular QTL, henceforth "QTL") analysis for improving the power of QTL identific...
KAGE: fast alignment-free graph-based genotyping of SNPs and short indels [0.03%]
基于图形的SNP和短插入删除基因分型工具KAGE
Ivar Grytten,Knut Dagestad Rand,Geir Kjetil Sandve
Ivar Grytten
Genotyping is a core application of high-throughput sequencing. We present KAGE, a genotyper for SNPs and short indels that is inspired by recent developments within graph-based genome representations and alignment-free methods. KAGE uses a...
Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin [0.03%]
基于MMUPHin的元分析微生物群落和炎症性肠病中的族群结构发现
Siyuan Ma,Dmitry Shungin,Himel Mallick et al.
Siyuan Ma et al.
Microbiome studies of inflammatory bowel diseases (IBD) have achieved a scale for meta-analysis of dysbioses among populations. To enable microbial community meta-analyses generally, we develop MMUPHin for normalization, statistical meta-an...
Meta-Analysis
Genome biology. 2022 Oct 3;23(1):208. DOI:10.1186/s13059-022-02753-4 2022
Eva Galle,Chee-Wai Wong,Adhideb Ghosh et al.
Eva Galle et al.
Background: Histone lactylation has been recently described as a novel histone post-translational modification linking cellular metabolism to epigenetic regulation. ...
Parental genomes segregate into distinct blastomeres during multipolar zygotic divisions leading to mixoploid and chimeric blastocysts [0.03%]
父母本基因组在多极受精卵分裂过程中进入不同的卵裂球导致合子嵌合体的形成
Tine De Coster,Heleen Masset,Olga Tšuiko et al.
Tine De Coster et al.
Background: During normal zygotic division, two haploid parental genomes replicate, unite and segregate into two biparental diploid blastomeres. Results: ...
MBD5 and MBD6 stabilize the BAP1 complex and promote BAP1-dependent cancer [0.03%]
MBD5和MBD6稳定BAP1复合物并促进BAP1依赖性肿瘤发生
Natsumi Tsuboyama,Aileen Patricia Szczepanski,Zibo Zhao et al.
Natsumi Tsuboyama et al.
Background: BRCA1-associated protein 1 (BAP1) is an ubiquitin carboxy-terminal hydrolase, which forms a multi-protein complex with different epigenetic factors, such as ASXL1-3 and FOXK1/2. At the chromatin level, BAP1 ca...
Widespread false gene gains caused by duplication errors in genome assemblies [0.03%]
基因重复错误导致基因组组装中普遍存在假基因增益现象
Byung June Ko,Chul Lee,Juwan Kim et al.
Byung June Ko et al.
Background: False duplications in genome assemblies lead to false biological conclusions. We quantified false duplications in popularly used previous genome assemblies for platypus, zebra finch, and Anna's Hummingbird, an...
False gene and chromosome losses in genome assemblies caused by GC content variation and repeats [0.03%]
基因组装配中由GC含量变化和重复序列导致的假阴性基因和染色体丢失事件
Juwan Kim,Chul Lee,Byung June Ko et al.
Juwan Kim et al.
Background: Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as com...
Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis [0.03%]
单细胞多组学分析揭示小鼠早期器官发育期间动态DNA甲基化与细胞命运决定之间的关联
Stephen J Clark,Ricard Argelaguet,Tim Lohoff et al.
Stephen J Clark et al.
Background: Perturbation of DNA methyltransferases (DNMTs) and of the active DNA demethylation pathway via ten-eleven translocation (TET) methylcytosine dioxygenases results in severe developmental defects and embryonic l...
Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice [0.03%]
全基因组测序揭示经典近交系小鼠 Domestication的遗传机制
Ming Liu,Caixia Yu,Zhichao Zhang et al.
Ming Liu et al.
Background: The laboratory mouse was domesticated from the wild house mouse. Understanding the genetics underlying domestication in laboratory mice, especially in the widely used classical inbred mice, is vital for studie...