DAGIP: alleviating cell-free DNA sequencing biases with optimal transport [0.03%]
DAGIP：用最优传输缓解无细胞DNA序列偏见
Antoine Passemiers,Stefania Tuveri,Tatjana Jatsenko et al.
Antoine Passemiers et al.
Cell-free DNA (cfDNA) is a rich source of biomarkers for various pathophysiological conditions. Preanalytical variables, such as the library preparation protocol or sequencing platform, are major confounders of cfDNA analysis. We present DA...
Genome assembly of the maize B chromosome provides insight into its epigenetic characteristics and effects on the host genome [0.03%]
玉米B染色体的基因组装为其表观遗传特性及其对宿主基因组的影响提供了见解
Qian Liu,Yang Liu,Congyang Yi et al.
Qian Liu et al.
Background: B chromosomes contribute to the genetic variation in numerous eukaryotes. Yet their genetic and epigenetic characteristics, as well as their effects on the host genome remain poorly understood. ...
Ultra-sensitive detection of transposon insertions across multiple families by transposable element display sequencing [0.03%]
转座子显示测序对多个家族转座子插入的超灵敏检测
Pol Vendrell-Mir,Basile Leduque,Leandro Quadrana
Pol Vendrell-Mir
Background: Mobilization of transposable elements (TEs) can generate large effect mutations. However, due to the difficulty of detecting new TE insertions in genomes and the typically rare occurrence of transposition, the...
Benchmarking single-cell cross-omics imputation methods for surface protein expression [0.03%]
单细胞交叉组学插补方法在表面蛋白表达方面的基准测试
Chen-Yang Li,Yong-Jia Hong,Bo Li et al.
Chen-Yang Li et al.
Background: Recent advances in single-cell multimodal omics sequencing have facilitated the simultaneous profiling of transcriptomes and surface proteomes within individual cells, offering insights into cellular functions...
Josep Biayna,Gabrijela Dumbović
Josep Biayna
Eukaryotic cells are highly structured and composed of multiple membrane-bound and membraneless organelles. Subcellular RNA localization is a critical regulator of RNA function, influencing various biological processes. At any given moment,...
CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis [0.03%]
在人类红细胞生成中CTCF特异地维持染色质可及性和基因表达所必需
Xue Yang,Li Cheng,Ye Xin et al.
Xue Yang et al.
Background: CTCF is considered as the most essential transcription factor regulating chromatin architecture and gene expression. However, genome-wide impact of CTCF on erythropoiesis has not been extensively investigated....
Admixture as a source for HLA variation in Neolithic European farming communities [0.03%]
新石器时代欧洲农作社区中HLA变异的混血来源
Nicolas Antonio da Silva,Onur Özer,Magdalena Haller-Caskie et al.
Nicolas Antonio da Silva et al.
Background: The northern European Neolithic is characterized by two major demographic events: immigration of early farmers from Anatolia at 7500 years before present, and their admixture with local western hunter-gatherer...
PRODE recovers essential and context-essential genes through neighborhood-informed scores [0.03%]
通过考虑邻近关系的分数来识别必需基因和条件性必需基因
Thomas Cantore,Paola Gasperini,Riccardo Bevilacqua et al.
Thomas Cantore et al.
Gene context-essentiality assessment supports precision oncology opportunities. The variability of gene effects inference from loss-of-function screenings across models and technologies limits identifying robust hits. We propose a computati...
Cross-species imputation and comparison of single-cell transcriptomic profiles [0.03%]
跨物种单细胞转录组谱的填充和比较
Ran Zhang,Mu Yang,Jacob Schreiber et al.
Ran Zhang et al.
Cross-species comparison and prediction of gene expression profiles are important to understand regulatory changes during evolution and to transfer knowledge learned from model organisms to humans. Single-cell RNA-seq (scRNA-seq) profiles e...
Comparative Study
Genome biology. 2025 Feb 26;26(1):40. DOI:10.1186/s13059-025-03493-x 2025
Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2 [0.03%]
使用GuideScan2进行基因组范围的CRISPR引导RNA设计和特异性分析
Henri Schmidt,Minsi Zhang,Dimitar Chakarov et al.
Henri Schmidt et al.
We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly design and analysis of individual gRNAs and gRNA libraries for targeting coding and non-coding r...