iDNA-ABF: multi-scale deep biological language learning model for the interpretable prediction of DNA methylations [0.03%]
基于多尺度深度生物语言学习模型的DNA甲基化可解释预测方法(iDNA-ABF)
Junru Jin,Yingying Yu,Ruheng Wang et al.
Junru Jin et al.
In this study, we propose iDNA-ABF, a multi-scale deep biological language learning model that enables the interpretable prediction of DNA methylations based on genomic sequences only. Benchmarking comparisons show that our iDNA-ABF outperf...
Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D [0.03%]
单细胞Hi-C数据的标准化与去噪方法BandNorm和scVI-3D
Ye Zheng,Siqi Shen,Sündüz Keleş
Ye Zheng
Single-cell high-throughput chromatin conformation capture methodologies (scHi-C) enable profiling of long-range genomic interactions. However, data from these technologies are prone to technical noise and biases that hinder downstream anal...
Global early replication disrupts gene expression and chromatin conformation in a single cell cycle [0.03%]
全局早期复制扰乱单个细胞周期中的基因表达和染色质构象
Miguel M Santos,Mark C Johnson,Lukáš Fiedler et al.
Miguel M Santos et al.
Background: The early embryonic divisions of many organisms, including fish, flies, and frogs, are characterized by a very rapid S-phase caused by high rates of replication initiation. In somatic cells, S-phase is much lo...
scGWAS: landscape of trait-cell type associations by integrating single-cell transcriptomics-wide and genome-wide association studies [0.03%]
scGWAS：通过整合单细胞转录组范围和全基因组关联研究建立性状-细胞类型关联图谱
Peilin Jia,Ruifeng Hu,Fangfang Yan et al.
Peilin Jia et al.
Background: The rapid accumulation of single-cell RNA sequencing (scRNA-seq) data presents unique opportunities to decode the genetically mediated cell-type specificity in complex diseases. Here, we develop a new method, ...
Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes [0.03%]
人类和大猿中假常染色体区系1的进化动态分析
Juraj Bergman,Mikkel Heide Schierup
Juraj Bergman
Background: The pseudoautosomal region 1 (PAR1) is a 2.7 Mb telomeric region of human sex chromosomes. PAR1 has a crucial role in ensuring proper segregation of sex chromosomes during male meiosis, exposing it to extreme ...
Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information [0.03%]
通过整合单细胞RNA测序数据和空间信息评估细胞间相互作用方法
Zhaoyang Liu,Dongqing Sun,Chenfei Wang
Zhaoyang Liu
Background: Cell-cell interactions are important for information exchange between different cells, which are the fundamental basis of many biological processes. Recent advances in single-cell RNA sequencing (scRNA-seq) en...
Dissemination of circulating tumor cells at night: role of sleep or circadian rhythm? [0.03%]
循环肿瘤细胞的夜间扩散：由睡眠还是昼夜节律引起？
Yves Dauvilliers,Frédéric Thomas,Catherine Alix-Panabières
Yves Dauvilliers
Author Correction: Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG [0.03%]
作者更正：单细胞多组基因表达和染色质可及性数据的调控分析与scREG
Zhana Duren,Fengge Chang,Fnu Naqing et al.
Zhana Duren et al.
Published Erratum
Genome biology. 2022 Oct 13;23(1):213. DOI:10.1186/s13059-022-02786-9 2022
A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes [0.03%]
低成本基因组学工作流程可在微生物群落中实现分离株筛选和菌株水平分析
Jon G Sanders,Weiwei Yan,Deus Mjungu et al.
Jon G Sanders et al.
Earth's environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput...
Enhanced mitochondrial DNA editing in mice using nuclear-exported TALE-linked deaminases and nucleases [0.03%]
利用核输出TALE连接脱氨酶和核酸酶进行小鼠线粒体DNA增强编辑
Seonghyun Lee,Hyunji Lee,Gayoung Baek et al.
Seonghyun Lee et al.
We present two methods for enhancing the efficiency of mitochondrial DNA (mtDNA) editing in mice with DddA-derived cytosine base editors (DdCBEs). First, we fused DdCBEs to a nuclear export signal (DdCBE-NES) to avoid off-target C-to-T conv...