CpG island turnover events predict evolutionary changes in enhancer activity [0.03%]
CpG岛的转变事件可预测增强子活性的进化变化
Acadia A Kocher,Emily V Dutrow,Severin Uebbing et al.
Acadia A Kocher et al.
Background: Genetic changes that modify the function of transcriptional enhancers have been linked to the evolution of biological diversity across species. Multiple studies have focused on the role of nucleotide substitut...
Leaf: an ultrafast filter for population-scale long-read SV detection [0.03%]
叶氏法：一种超快的群体规模长读长结构变异检测滤器
Chenxu Pan,Knut Reinert
Chenxu Pan
Advances in sequencing technology have facilitated population-scale long-read structural variant (SV) detection. Arguably, one of the main challenges in population-scale analysis is developing effective computational pipelines. Here, we pre...
Legal aspects of privacy-enhancing technologies in genome-wide association studies and their impact on performance and feasibility [0.03%]
基因组范围关联研究中增强隐私技术的法律问题及其对性能和可行性的的影响
Alissa Brauneck,Louisa Schmalhorst,Stefan Weiss et al.
Alissa Brauneck et al.
Genomic data holds huge potential for medical progress but requires strict safety measures due to its sensitive nature to comply with data protection laws. This conflict is especially pronounced in genome-wide association studies (GWAS) whi...
Gene count normalization in single-cell imaging-based spatially resolved transcriptomics [0.03%]
单细胞成像的空间分辨转录组学中的基因计数标准化
Lyla Atta,Kalen Clifton,Manjari Anant et al.
Lyla Atta et al.
Background: Recent advances in imaging-based spatially resolved transcriptomics (im-SRT) technologies now enable high-throughput profiling of targeted genes and their locations in fixed tissues. Normalization of gene expr...
FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe [0.03%]
利用已知蛋白质体系预测蛋白质折叠路径的新算法FoldPAthreader的研发及应用
Kailong Zhao,Pengxin Zhao,Suhui Wang et al.
Kailong Zhao et al.
Protein folding has become a tractable problem with the significant advances in deep learning-driven protein structure prediction. Here we propose FoldPAthreader, a protein folding pathway prediction method that uses a novel folding force f...
CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes [0.03%]
基于单分子DNA甲基化单倍型的多种细胞类型的概率模型CELFI-E-ISH
Irene Unterman,Dana Avrahami,Efrat Katsman et al.
Irene Unterman et al.
Deconvolution methods infer quantitative cell type estimates from bulk measurement of mixed samples including blood and tissue. DNA methylation sequencing measures multiple CpGs per read, but few existing deconvolution methods leverage this...
Author Correction: The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans [0.03%]
作者更正：人类衰老甲基化组及其与癌症、衰老和胚系基因变异的关系
Robert Lowe,Marita G Overhoff,Sreeram V Ramagopalan et al.
Robert Lowe et al.
Published Erratum
Genome biology. 2024 Jun 10;25(1):150. DOI:10.1186/s13059-024-03295-7 2024
Structural variant landscapes reveal convergent signatures of evolution in sheep and goats [0.03%]
结构变异景观揭示了羊和山羊进化中的趋同特征
Ji Yang,Dong-Feng Wang,Jia-Hui Huang et al.
Ji Yang et al.
Background: Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level refere...
TMO-Net: an explainable pretrained multi-omics model for multi-task learning in oncology [0.03%]
基于多组学的肿瘤多任务学习预训练模型TMO-Net
Feng-Ao Wang,Zhenfeng Zhuang,Feng Gao et al.
Feng-Ao Wang et al.
Cancer is a complex disease composing systemic alterations in multiple scales. In this study, we develop the Tumor Multi-Omics pre-trained Network (TMO-Net) that integrates multi-omics pan-cancer datasets for model pre-training, facilitatin...
DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts [0.03%]
转录因子结合区域的DNA甲基化特征及其功能和进化特征
Martina Rimoldi,Ning Wang,Jilin Zhang et al.
Martina Rimoldi et al.
Background: DNA methylation is an important epigenetic modification which has numerous roles in modulating genome function. Its levels are spatially correlated across the genome, typically high in repressed regions but lo...