Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet [0.03%]
用扩展的表观遗传字母来模拟甲基敏感的转录因子序列模式
Coby Viner,Charles A Ishak,James Johnson et al.
Coby Viner et al.
Background: Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified bases. Curren...
GTax: improving de novo transcriptome assembly by removing foreign RNA contamination [0.03%]
GTax：通过去除外来RNA污染来改善从头转录组组装
Roberto Vera Alvarez,David Landsman
Roberto Vera Alvarez
The cost and complexity of generating a complete reference genome means that many organisms lack an annotated reference. An alternative is to use a de novo reference transcriptome. This technology is cost-effective but is susceptible to off...
Hamid Kian Gaikani,Monika Stolar,Divya Kriti et al.
Hamid Kian Gaikani et al.
The history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model re...
Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets [0.03%]
评估用于在多样本单细胞数据集中寻找特定条件原型细胞的差异丰度方法
Haidong Yi,Alec Plotkin,Natalie Stanley
Haidong Yi
Background: To analyze the large volume of data generated by single-cell technologies and to identify cellular correlates of particular clinical or experimental outcomes, differential abundance analyses are often applied....
The hazards of genotype imputation when mapping disease susceptibility variants [0.03%]
在绘制疾病易感变异时基因分型插补的危险性
Winston Lau,Aminah Ali,Hannah Maude et al.
Winston Lau et al.
Background: The cost-free increase in statistical power of using imputation to infer missing genotypes is undoubtedly appealing, but is it hazard-free? This case study of three type-2 diabetes (T2D) loci demonstrates that...
Current challenges and future of agricultural genomes to phenomes in the USA [0.03%]
美国农业基因组到表型组现状的当前挑战和未来发展前景
Christopher K Tuggle,Jennifer L Clarke,Brenda M Murdoch et al.
Christopher K Tuggle et al.
Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by improvements in identifying and measuring relevant trait variation in such populations across many environments (p...
Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies [0.03%]
对评论的回应：会计多样化可移动元素景观对于开发和评估准确的从头注释策略至关重要
Shujun Ou,Ning Jiang,Candice N Hirsch et al.
Shujun Ou et al.
Genetic effects of sequence-conserved enhancer-like elements on human complex traits [0.03%]
类似增强子的序列保守元件对人类复杂性状的遗传影响
Xiang Zhu,Shining Ma,Wing Hung Wong
Xiang Zhu
Background: The vast majority of findings from human genome-wide association studies (GWAS) map to non-coding sequences, complicating their mechanistic interpretations and clinical translations. Non-coding sequences that ...
FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases [0.03%]
FORGEdb：一种用于识别复杂疾病的功能变异、靶基因及机制的工具
Charles E Breeze,Eric Haugen,María Gutierrez-Arcelus et al.
Charles E Breeze et al.
The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to identify potential biological mecha...
Author Correction: Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression [0.03%]
作者更正：六倍体小麦中通过同源介导的染色体间相互作用，在多倍化和渗入后形成特定亚基因组区域
Jizeng Jia,Yilin Xie,Jingfei Cheng et al.
Jizeng Jia et al.
Published Erratum
Genome biology. 2024 Jan 2;25(1):5. DOI:10.1186/s13059-023-03154-x 2024