CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model [0.03%]
CLAMP：使用染色质可及性语言模型预测多种物种中特定蛋白质介导的染色体环化区域
Zhijie He,Yu Sun,Hao Li et al.
Zhijie He et al.
Emerging DNA language models provide powerful tools to address the challenge of accurately predicting chromatin loops, fundamental structures governing 3D genome organization and gene regulation. Here we present CLAMP, which utilizes a deep...
TSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data [0.03%]
TSniffer：通过RNA测序数据无偏倚地鉴定RNA编辑位点和量化编辑活性
Maike Herrmann,Yvonne Krebs,Francisco M Acosta et al.
Maike Herrmann et al.
RNA editing by adenosine deaminases acting on RNA (ADARs) is an essential cellular process performed by three enzymes in mammals: ADAR1-p150, ADAR1-p110, and ADAR2, demonstrating different target specificity and selectivity. Here we describ...
An inflammatory and quiescent HSC subpopulation expands with age in humans [0.03%]
人年龄增长时体内炎症和静止的造血干细胞亚群会增多
Ksenia R Safina,Basit Salik,Dylan Kotliar et al.
Ksenia R Safina et al.
Aging of the blood system impacts systemic health and can be traced to hematopoietic stem cells (HSCs). Despite multiple reports on human HSC aging, a unified map detailing their molecular age-related changes is lacking. We developed a cons...
Neighborhood nonnegative matrix factorization identifies patterns and spatially-variable genes in large-scale spatial transcriptomics data [0.03%]
邻域非负矩阵分解可识别大规模空间转录组学数据中的模式和空间变异基因
Ragnhild Laursen,Han Chen,Jack Demaray et al.
Ragnhild Laursen et al.
Single-cell proteomics of Arabidopsis leaf mesophyll reveals dynamic protein responses to water-deficit stress [0.03%]
拟南芥叶片叶肉单细胞蛋白质组揭示了蛋白质对缺水胁迫的动态响应
James M Fulcher,Pranav Dawar,Vimal Kumar Balasubramanian et al.
James M Fulcher et al.
Background: The application of single-cell omics tools to biological systems can provide unique insights into diverse cellular populations and their heterogeneous responses to internal and external perturbations. Thus far...
Exploring differences in the human gut microbiome between Han Chinese and non-Chinese populations [0.03%]
汉族人群与非汉族群肠道微生物组的差异性研究
Jingjing Wang,Zhenmiao Zhang,Yang Chen et al.
Jingjing Wang et al.
Background: The human gut microbiota exhibits significant diversity across populations, influenced by factors such as geography, diet, and lifestyle, particularly between the Han Chinese and non-Chinese populations. While...
Tracing bronze to iron age population dynamics in Northwest Xinjiang using ancient time-series genomic data [0.03%]
利用古代时间序列基因组数据探究新疆西北部青铜至铁器时代的人口动态变化
Xue Zhao,Daxuan Zhang,Bing Sun et al.
Xue Zhao et al.
Background: Northwestern Xinjiang is situated at the confluence of the central Eurasian Steppe, the Inner Asian Mountain Corridor and the Tianshan mountains, and is home to rich archaeological, cultural and genetic divers...
Ancient DNA study provides clues to leprosy susceptibility in medieval Europe [0.03%]
古DNA研究为中世纪欧洲患麻风病的易感性提供线索
Joanna H Romeyer-Dherbey,Amke Caliebe,Onur Ӧzer et al.
Joanna H Romeyer-Dherbey et al.
Background: Leprosy is a chronic infectious disease caused by Mycobacterium leprae (M. leprae) that reached an epidemic scale in the Middle Ages. Nowadays, the disease is absent in Europe and host genetic influences have ...
FSBLUP: a novel strategy of fusion similarity matrix construction via optimally integrating intermediate omics data to enhance genomic prediction [0.03%]
FSBLUP：通过中间组学数据优化构建相似矩阵以增强基因组预测的新策略
Yahui Xue,Lei Zhou,Yue Zhuo et al.
Yahui Xue et al.
The increasing availability of multi-omics data is promising in enhancing genomic prediction in breeding and human genetics. However, integrating multi-omics data into genomic prediction models remains challenging due to complex relationshi...
Non-negative matrix factorization and deconvolution as a dual simplex problem [0.03%]
非负矩阵分解与脱.convolution作为一种双simplex问题
Denis Kleverov,Ekaterina Aladyeva,Alexey Serdyukov et al.
Denis Kleverov et al.
Background: Non-negative matrix factorization is a powerful linear algebra tool used in multiple areas of data analysis, including computational biology. Despite numerous optimization methods devised for non-negative matr...