A syntelog-based pan-genome provides insights into rice domestication and de-domestication [0.03%]
基于同源基因的水稻泛基因组揭示了栽培稻驯化和逆向驯化的遗传机制
Dongya Wu,Lingjuan Xie,Yanqing Sun et al.
Dongya Wu et al.
Background: Asian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the ev...
BEDwARS: a robust Bayesian approach to bulk gene expression deconvolution with noisy reference signatures [0.03%]
具有噪声参考信号的批量基因表达去卷积的稳健贝叶斯方法BEDwARS
Saba Ghaffari,Kelly J Bouchonville,Ehsan Saleh et al.
Saba Ghaffari et al.
Differential gene expression in bulk transcriptomics data can reflect change of transcript abundance within a cell type and/or change in the proportions of cell types. Expression deconvolution methods can help differentiate these scenarios....
Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes [0.03%]
利用scnRNA-seq转录组进行批量RNA-seq去卷积的有效方法
Francisco Avila Cobos,Mohammad Javad Najaf Panah,Jessica Epps et al.
Francisco Avila Cobos et al.
Background: RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, scnRNA-seq for short), can help characterize the composition of tissues a...
Genetic impacts on DNA methylation help elucidate regulatory genomic processes [0.03%]
基因对DNA甲基化的影响有助于阐明调控基因组过程
Sergio Villicaña,Juan Castillo-Fernandez,Eilis Hannon et al.
Sergio Villicaña et al.
Background: Pinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk. Resul...
vamos: variable-number tandem repeats annotation using efficient motif sets [0.03%]
利用高效的动机集进行VANS可变数串联重复序列注释
Jingwen Ren,Bida Gu,Mark J P Chaisson
Jingwen Ren
Roughly 3% of the human genome is composed of variable-number tandem repeats (VNTRs): arrays of motifs at least six bases. These loci are highly polymorphic, yet current approaches that define and merge variants based on alignment breakpoin...
ISLET: individual-specific reference panel recovery improves cell-type-specific inference [0.03%]
ISLET：个体特异性参考面板恢复可改善细胞类型特异性推断
Hao Feng,Guanqun Meng,Tong Lin et al.
Hao Feng et al.
We propose a statistical framework ISLET to infer individual-specific and cell-type-specific transcriptome reference panels. ISLET models the repeatedly measured bulk gene expression data, to optimize the usage of shared information within ...
Observational Study
Genome biology. 2023 Jul 26;24(1):174. DOI:10.1186/s13059-023-03014-8 2023
Ireneusz Stolarek,Michal Zenczak,Luiza Handschuh et al.
Ireneusz Stolarek et al.
Background: The appearance of Slavs in East-Central Europe has been the subject of an over 200-year debate driven by two conflicting hypotheses. The first assumes that Slavs came to the territory of contemporary Poland no...
Predicting disease severity in metachromatic leukodystrophy using protein activity and a patient phenotype matrix [0.03%]
基于蛋白质活性和患者表型矩阵的元猫跳色白质营养不良疾病严重程度预测
Marena Trinidad,Xinying Hong,Steven Froelich et al.
Marena Trinidad et al.
Background: Metachromatic leukodystrophy (MLD) is a lysosomal storage disorder caused by mutations in the arylsulfatase A gene (ARSA) and categorized into three subtypes according to age of onset. The functional effect of...
Zhiheng Liu,Giovanni Quinones-Valdez,Ting Fu et al.
Zhiheng Liu et al.
Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is significantly under-explored. Here, we ...
MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads [0.03%]
MSV：通过直接从读段推断并统一破裂端来揭示嵌套和复杂重排的模块化结构变异调用器
Markus Schmidt,Arne Kutzner
Markus Schmidt
Structural variant (SV) calling belongs to the standard tools of modern bioinformatics for identifying and describing alterations in genomes. Initially, this work presents several complex genomic rearrangements that reveal conceptual ambigu...