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...
GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation [0.03%]
GET_PANGENES：从植物基因组比对中调用基因组以确认存在性-缺失变异
Bruno Contreras-Moreira,Shradha Saraf,Guy Naamati et al.
Bruno Contreras-Moreira et al.
Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define pangenes, which summarize a sp...
CEGA: a method for inferring natural selection by comparative population genomic analysis across species [0.03%]
CEGA：通过比较种群基因组分析来推断自然选择的方法
Shilei Zhao,Lianjiang Chi,Hua Chen
Shilei Zhao
We developed maximum likelihood method for detecting positive selection or balancing selection using multilocus or genomic polymorphism and divergence data from two species. The method is especially useful for investigating natural selectio...
Hiram Clawson,Brian T Lee,Brian J Raney et al.
Hiram Clawson et al.
Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our establi...
MBE: model-based enrichment estimation and prediction for differential sequencing data [0.03%]
基于模型的差分测序数据的富集估计和预测算法研究(MBE)
Akosua Busia,Jennifer Listgarten
Akosua Busia
Characterizing differences in sequences between two conditions, such as with and without drug exposure, using high-throughput sequencing data is a prevalent problem involving quantifying changes in sequence abundances, and predicting such d...