Diego Garrido-Martín,Miquel Calvo,Ferran Reverter et al.
Diego Garrido-Martín et al.
The increasing availability of multidimensional phenotypic data in large cohorts of genotyped individuals requires efficient methods to identify genetic effects on multiple traits. Permutational multivariate analysis of variance (PERMANOVA)...
Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease [0.03%]
代谢组广泛分析揭露肠道微生物特征并暗示特定菌群功能在终末期肾病中的作用
Pan Zhang,Xifan Wang,Shenghui Li et al.
Pan Zhang et al.
Background: The gut microbiota plays a crucial role in regulating host metabolism and producing uremic toxins in patients with end-stage renal disease (ESRD). Our objective is to advance toward a holistic understanding of...
Robust, scalable, and informative clustering for diverse biological networks [0.03%]
稳健、可扩展且富含信息的算法在各种生物学网络中的聚类应用
Chris Gaiteri,David R Connell,Faraz A Sultan et al.
Chris Gaiteri et al.
Clustering molecular data into informative groups is a primary step in extracting robust conclusions from big data. However, due to foundational issues in how they are defined and detected, such clusters are not always reliable, leading to ...
Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants [0.03%]
植物基因体中动态的DNA甲基化周转与增强的基因表达可塑性相关
Clara J Williams,Dawei Dai,Kevin A Tran et al.
Clara J Williams et al.
Background: In several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA...
The landscape of cell-free mitochondrial DNA in liquid biopsy for cancer detection [0.03%]
液体活检中细胞游离线粒体DNA在癌症检测中的作用及挑战
Ymke van der Pol,Norbert Moldovan,Jip Ramaker et al.
Ymke van der Pol et al.
Background: Existing methods to detect tumor signal in liquid biopsy have focused on the analysis of nuclear cell-free DNA (cfDNA). However, non-nuclear cfDNA and in particular mitochondrial DNA (mtDNA) has been understud...
scIBD: a self-supervised iterative-optimizing model for boosting the detection of heterotypic doublets in single-cell chromatin accessibility data [0.03%]
scIBD：一种自监督迭代优化模型，可增强单细胞染色质可及性数据中异类双重峰的检测能力
Wenhao Zhang,Rui Jiang,Shengquan Chen et al.
Wenhao Zhang et al.
Application of the widely used droplet-based microfluidic technologies in single-cell sequencing often yields doublets, introducing bias to downstream analyses. Especially, doublet-detection methods for single-cell chromatin accessibility s...
MCProj: metacell projection for interpretable and quantitative use of transcriptional atlases [0.03%]
MCProj：用于解释性和定量使用转录图集的元细胞投影
Oren Ben-Kiki,Akhiad Bercovich,Aviezer Lifshitz et al.
Oren Ben-Kiki et al.
We describe MCProj-an algorithm for analyzing query scRNA-seq data by projections over reference single-cell atlases. We represent the reference as a manifold of annotated metacell gene expression distributions. We then interpret query meta...
HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing [0.03%]
HycDemux：纳米孔测序中准确的条形码样本解复用的混合无监督方法
Renmin Han,Junhai Qi,Yang Xue et al.
Renmin Han et al.
DNA barcodes enable Oxford Nanopore sequencing to sequence multiple barcoded DNA samples on a single flow cell. DNA sequences with the same barcode need to be grouped together through demultiplexing. As the number of samples increases, accu...
Large sample size and nonlinear sparse models outline epistatic effects in inflammatory bowel disease [0.03%]
大样本量和非线性稀疏模型揭示炎症性肠病的基因互作效应
Nora Verplaetse,Antoine Passemiers,Adam Arany et al.
Nora Verplaetse et al.
Background: Despite clear evidence of nonlinear interactions in the molecular architecture of polygenic diseases, linear models have so far appeared optimal in genotype-to-phenotype modeling. A key bottleneck for such mod...
Genomic variant benchmark: if you cannot measure it, you cannot improve it [0.03%]
基因变异基准：如果不进行测量，则无法改善它
Sina Majidian,Daniel Paiva Agustinho,Chen-Shan Chin et al.
Sina Majidian et al.
Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future challenges. However, they depen...