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...
Mapping snoRNA-target RNA interactions in an RNA-binding protein-dependent manner with chimeric eCLIP [0.03%]
利用嵌合eCLIP以RNA结合蛋白依赖性方式绘制snoRNA-靶标RNA相互作用图
Zhuoyi Song,Bongmin Bae,Simon Schnabl et al.
Zhuoyi Song et al.
Background: Small nucleolar RNAs (snoRNAs) are non-coding RNAs that function in ribosome and spliceosome biogenesis, primarily by guiding modifying enzymes to specific sites on ribosomal RNA (rRNA) and spliceosomal RNA (s...
Digital sequencing is improved by using structured unique molecular identifiers [0.03%]
使用结构化独特分子标识符改进数字测序技术
Peter Micallef,Manuel Luna Santamaría,Mandy Escobar et al.
Peter Micallef et al.
Digital sequencing uses unique molecular identifiers (UMIs) to correct for polymerase induced errors and amplification biases. Here, we design 19 different structured UMIs to minimize the capacity of primers to form non-specific PCR product...
Batch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns [0.03%]
使用Crescendo批量校正单细胞空间转录组计数数据可改善空间基因模式的可视化和检测
Nghia Millard,Jonathan H Chen,Mukta G Palshikar et al.
Nghia Millard et al.
Spatial transcriptomics facilitates gene expression analysis of cells in their spatial anatomical context. Batch effects hinder visualization of gene spatial patterns across samples. We present the Crescendo algorithm to correct for batch e...
Transposable elements may enhance antiviral resistance in HIV-1 elite controllers [0.03%]
可转座元件或能提高HIV-1优秀控制者抗病毒抵抗力
Manvendra Singh,Sabrina M Leddy,Luis Pedro Iñiguez et al.
Manvendra Singh et al.
Background: Less than 0.5% of people living with HIV-1 are elite controllers (ECs)-individuals who maintain undetectable plasma viremia without antiretroviral therapy, despite having replication-competent viral reservoirs...
Genomic signals of ecogeographic adaptation in a wild relative are associated with improved wheat performance under drought stress [0.03%]
野生近缘种中与干旱胁迫下小麦性能改善相关的生态地理适应基因组信号
Moses Nyine,Dwight Davidson,Elina Adhikari et al.
Moses Nyine et al.
Background: Prioritizing wild relative diversity for improving crop adaptation to emerging drought-prone environments is challenging. Here, we combine the genome-wide environmental scans (GWES) in wheat diploid ancestor A...