Ke Xu,Yu Xu,Zirui Wang et al.
Ke Xu et al.
Spatially resolved transcriptomics (SRT) data provide critical insights into gene expression patterns within tissue contexts, necessitating effective methods for identifying spatial domains. We introduce stDyer, an end-to-end deep learning ...
catGRANULE 2.0: accurate predictions of liquid-liquid phase separating proteins at single amino acid resolution [0.03%]
catGRANULE 2.0：以单氨基酸分辨率准确预测液-液相分离蛋白
Michele Monti,Jonathan Fiorentino,Dimitrios Miltiadis-Vrachnos et al.
Michele Monti et al.
Liquid-liquid phase separation (LLPS) enables the formation of membraneless organelles, essential for cellular organization and implicated in diseases. We introduce catGRANULE 2.0 ROBOT, an algorithm integrating physicochemical properties a...
A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome [0.03%]
利用完整参考基因组对现代人类中尼安德特人序列的精化分析
Shen-Ao Liang,Tianxin Ren,Jiayu Zhang et al.
Shen-Ao Liang et al.
Background: Leveraging long-read sequencing technologies, the first complete human reference genome, T2T-CHM13, corrects assembly errors in previous references and resolves the remaining 8% of the genome. While studies on...
Unveiling the role of chromosome structure morphology on gene function through chromosome conformation analysis [0.03%]
通过染色体构象分析揭示染色体结构形态在基因功能中的作用
Yuxiang Zhan,Asli Yildirim,Lorenzo Boninsegna et al.
Yuxiang Zhan et al.
Single-cell chromosome conformations vary significantly among individual cells. We introduce a two-step dimensionality reduction method for density-based, unsupervised clustering of single-cell 3D chromosome structures from simulations or m...
Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles [0.03%]
出版更正：ENCODE 填充挑战：跨细胞类型表观遗传学特征填充方法的关键评估
Jacob Matthew Schreiber,Carles A Boix,Jin Wook Lee et al.
Jacob Matthew Schreiber et al.
Published Erratum
Genome biology. 2025 Feb 13;26(1):31. DOI:10.1186/s13059-025-03494-w 2025
PANE: fast and reliable ancestral reconstruction on ancient genotype data with non-negative least square and principal component analysis [0.03%]
基于非负最小二乘和主成分分析的古基因数据快速可靠的谱系重建（PANE）
Luciana de Gennaro,Ludovica Molinaro,Alessandro Raveane et al.
Luciana de Gennaro et al.
The history of human populations has been strongly shaped by admixture events, contributing to patterns of observed genetic diversity across populations. In this study, we introduce the Principal component Ancestry proportions using NNLS Es...
Multi-omics analysis in primary T cells elucidates mechanisms behind disease-associated genetic loci [0.03%]
多组学分析在原代T细胞中的作用阐明与疾病相关遗传位点背后的机制
Chenfu Shi,Danyun Zhao,Jake Butler et al.
Chenfu Shi et al.
Background: Genome-wide association studies (GWAS) have uncovered the genetic basis behind many diseases and conditions. However, most of these genetic loci affect regulatory regions, making the interpretation challenging...
Long-read sequencing and genome assembly of natural history collection samples and challenging specimens [0.03%]
利用自然历史收藏样本和难以处理的样品进行长读测序和基因组组装
Bernhard Bein,Ioannis Chrysostomakis,Larissa S Arantes et al.
Bernhard Bein et al.
Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblie...
Dynamic changes in 3D chromatin structure during male gametogenesis in Arabidopsis thaliana [0.03%]
拟南芥雄配子体发生过程中染色质三维结构的动态变化
Zhihan Song,Qimin Xia,Minqi Yang et al.
Zhihan Song et al.
Background: Chromatin higher-order structure plays an important role in genome stability maintenance and gene transcriptional regulation; however, the dynamics of the three-dimensional (3D) chromatin in male gametophytes ...
Niklas Müller-Bötticher,Shashwat Sahay,Roland Eils et al.
Niklas Müller-Bötticher et al.
Clustering can identify the natural structure that is inherent to measured data. For single-cell omics, clustering finds cells with similar molecular phenotype after which cell types are annotated. Leiden clustering is one of the algorithms...