Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters [0.03%]
人类基因组中广泛存在的等位特异性拓扑结构域并不局限于印迹基因簇
Stephen Richer,Yuan Tian,Stefan Schoenfelder et al.
Stephen Richer et al.
Background: There is widespread interest in the three-dimensional chromatin conformation of the genome and its impact on gene expression. However, these studies frequently do not consider parent-of-origin differences, suc...
CeDAR: incorporating cell type hierarchy improves cell type-specific differential analyses in bulk omics data [0.03%]
CeDAR：通过引入细胞类型层次结构改进批量组学数据中的细胞类型特异性差异分析
Luxiao Chen,Ziyi Li,Hao Wu
Luxiao Chen
Bulk high-throughput omics data contain signals from a mixture of cell types. Recent developments of deconvolution methods facilitate cell type-specific inferences from bulk data. Our real data exploration suggests that differential express...
correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes [0.03%]
Correctkin：一种从低覆盖率的古人类基因组中推断高达四亲缘关系的优化方法
Emil Nyerki,Tibor Kalmár,Oszkár Schütz et al.
Emil Nyerki et al.
Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence in...
The genetic and evolutionary basis of gene expression variation in East Africans [0.03%]
东非人基因表达变异的基因和进化基础
Derek E Kelly,Shweta Ramdas,Rong Ma et al.
Derek E Kelly et al.
Background: Mapping of quantitative trait loci (QTL) associated with molecular phenotypes is a powerful approach for identifying the genes and molecular mechanisms underlying human traits and diseases, though most studies...
DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology [0.03%]
DIMPLE：探索进化、疾病和生物学中蛋白质变异的深度插入、删除和错义突变库
Christian B Macdonald,David Nedrud,Patrick Rockefeller Grimes et al.
Christian B Macdonald et al.
Insertions and deletions (indels) enable evolution and cause disease. Due to technical challenges, indels are left out of most mutational scans, limiting our understanding of them in disease, biology, and evolution. We develop a low cost an...
Using protein-per-mRNA differences among human tissues in codon optimization [0.03%]
利用人类组织中密码子优化的蛋白质每mRNA差异
Xavier Hernandez-Alias,Hannah Benisty,Leandro G Radusky et al.
Xavier Hernandez-Alias et al.
Background: Codon usage and nucleotide composition of coding sequences have profound effects on protein expression. However, while it is recognized that different tissues have distinct tRNA profiles and codon usages in th...
Pitfalls and opportunities for applying latent variables in single-cell eQTL analyses [0.03%]
单细胞eQTL分析中应用潜在变量的陷阱与机遇
Angli Xue,Seyhan Yazar,Drew Neavin et al.
Angli Xue et al.
Using latent variables in gene expression data can help correct unobserved confounders and increase statistical power for expression quantitative trait Loci (eQTL) detection. The probabilistic estimation of expression residuals (PEER) and p...
Author Correction: scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured [0.03%]
题图纠正：scDesign2：一种生成高保真单细胞基因表达计数数据（捕获基因相关性）的透明模拟器
Tianyi Sun,Dongyuan Song,Wei Vivian Li et al.
Tianyi Sun et al.
Published Erratum
Genome biology. 2023 Feb 22;24(1):32. DOI:10.1186/s13059-023-02884-2 2023
FixItFelix: improving genomic analysis by fixing reference errors [0.03%]
_FIX_it_FELIX_:修复参考基因组错误以改进基因组分析
Sairam Behera,Jonathon LeFaive,Peter Orchard et al.
Sairam Behera et al.
The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors impact the variant calling of 33 protein-coding genes, including ...
Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events [0.03%]
Not1和Not4通过相反作用决定mRNA的可溶性并以此调控协同转译事件的动力学过程
George Allen,Benjamin Weiss,Olesya O Panasenko et al.
George Allen et al.
Background: The Ccr4-Not complex is mostly known as the major eukaryotic deadenylase. However, several studies have uncovered roles of the complex, in particular of the Not subunits, unrelated to deadenylation and relevan...