Field-crop transcriptome models are enhanced by measurements in systematically controlled environments [0.03%]
系统控制环境下的测量可改进田间作物转录组模型
Yoichi Hashida,Daisuke Kyogoku,Suguru E Tanaka et al.
Yoichi Hashida et al.
Background: Plants in the field respond to seasonal and diel changes in various environmental factors such as irradiance and temperature. We previously developed a statistical model that predicts rice gene expression from...
ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations [0.03%]
一种RNA和DNA三级结构基序识别的算法ARTEM：碱基对排列变化下的结构 motifs 寻找方法
Eugene F Baulin,Davyd R Bohdan,Dawid Kowalski et al.
Eugene F Baulin et al.
Non-coding RNA functions are largely defined by their 3D structures, which consist of recurrent building blocks, tertiary motifs. The computational motif search problem remains largely unsolved, as standard approaches are restrained by sequ...
TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis [0.03%]
TRFill：协同使用HiFi和Hi-C测序可准确组装串联重复序列以进行群体水平分析
Huaming Wen,Jinbao Yang,Xianjia Zhao et al.
Huaming Wen et al.
The highly repetitive content of eukaryotic genomes, including long tandem repeats, segmental duplications, and centromeres, makes haplotype-resolved genome assembly hard. Repeat sequences introduce gaps or mis-joins in the assemblies. We i...
David P Hirst,Morgane Térézol,Laura Cantini et al.
David P Hirst et al.
Joint matrix factorization is popular for extracting lower dimensional representations of multi-omics data but loses effectiveness with limited samples. Addressing this limitation, we introduce MOTL (Multi-Omics Transfer Learning), a framew...
Purifying selection shapes the dynamics of P-element invasion in Drosophila simulans populations [0.03%]
净化选择决定Drosophila simulans种群中P元素入侵的动力学过程
Anna M Langmüller,Benjamin C Haller,Viola Nolte et al.
Anna M Langmüller et al.
Background: Transposable elements (TEs) are DNA sequences that can move within a host genome. Many new TE insertions have deleterious effects on their host and are therefore removed by purifying selection. The genomic dis...
Comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchi [0.03%]
对荔枝果实品质的全基因组和表型综合分析揭示了其遗传基础
Qian Yan,Junting Feng,Jiezhen Chen et al.
Qian Yan et al.
Background: Litchi, an economically important fruit crop in Southeast Asia, is renowned for its distinctive flavor and nutrient value, but its genetic diversity and genetic basis underlying fruit quality regulation remain...
Explainable deep learning for stratified medicine in inflammatory bowel disease [0.03%]
深度学习在炎症性肠病分层医学中的可解释性研究
Nora Verplaetse,Piero Fariselli,Yves Moreau et al.
Nora Verplaetse et al.
Moving from a one-size-fits-all to an individual approach in precision medicine requires a deeper understanding of disease molecular mechanisms. Especially in heterogeneous complex diseases such as inflammatory bowel disease (IBD), better m...
Modeling combinatorial regulation from single-cell multi-omics provides regulatory units underpinning cell type landscape using cRegulon [0.03%]
基于单细胞多组学的组合调控建模利用cRegulon提供细胞类型景观背后的调节单元
Zhanying Feng,Xi Chen,Zhana Duren et al.
Zhanying Feng et al.
Advances in single-cell technology enable large-scale generation of omics data, promising for clarifying gene regulatory networks governing different cell type/states. Nonetheless, prevailing methods fail to account for universal and reusab...
Joint representation and visualization of derailed cell states with Decipher [0.03%]
利用Decipher对脱轨细胞状态的联合表示和可视化
Achille Nazaret,Joy Linyue Fan,Vincent-Philippe Lavallée et al.
Achille Nazaret et al.
Biological insights often depend on comparing conditions such as disease and health. Yet, we lack effective computational tools for integrating single-cell genomics data across conditions or characterizing transitions from normal to deviant...
A base editing platform for the correction of cancer driver mutations unmasks conserved p53 transcription programs [0.03%]
基于编辑的癌症驱动突变矫正平台揭示了保守的p53转录程序
Pascal Wang,Rituparno Sen,Frank Buchholz et al.
Pascal Wang et al.
Background: Understanding the role of cancer hotspot mutations is essential for unraveling mechanisms of tumorigenesis and identifying therapeutic vulnerabilities. Correcting cancer mutations with base editing is a novel,...