Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes [0.03%]
基于真实世界跨生境宏基因组数据的生物信息学病毒识别工具评测
Ling-Yi Wu,Yasas Wijesekara,Gonçalo J Piedade et al.
Ling-Yi Wu et al.
Background: As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identif...
Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods [0.03%]
Demuxafy：通过整合多种单细胞解复用和双拷贝检测方法改进滴度分配
Drew Neavin,Anne Senabouth,Himanshi Arora et al.
Drew Neavin et al.
Recent innovations in single-cell RNA-sequencing (scRNA-seq) provide the technology to investigate biological questions at cellular resolution. Pooling cells from multiple individuals has become a common strategy, and droplets can subsequen...
Machine-learning analysis reveals an important role for negative selection in shaping cancer aneuploidy landscapes [0.03%]
机器学习分析揭示了癌症非整倍体景观形成中的负选择重要作用
Juman Jubran,Rachel Slutsky,Nir Rozenblum et al.
Juman Jubran et al.
Background: Aneuploidy, an abnormal number of chromosomes within a cell, is a hallmark of cancer. Patterns of aneuploidy differ across cancers, yet are similar in cancers affecting closely related tissues. The selection p...
Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes [0.03%]
Scoary2：基于微生物基因组的表型多组学数据的快速关联分析
Thomas Roder,Grégory Pimentel,Pascal Fuchsmann et al.
Thomas Roder et al.
Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genomic data is challenging, leaving...
Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies [0.03%]
评估和改进长读长元基因组组装中细菌含量的表示方法并加以改善
Xiaowen Feng,Heng Li
Xiaowen Feng
Background: In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We ...
scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing [0.03%]
科幻ATAC序：使用组合流体索引进行大规模单细胞染色质可及性测序
Xuan Zhang,Alexandre P Marand,Haidong Yan et al.
Xuan Zhang et al.
Single-cell ATAC-seq has emerged as a powerful approach for revealing candidate cis-regulatory elements genome-wide at cell-type resolution. However, current single-cell methods suffer from limited throughput and high costs. Here, we presen...
A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline [0.03%]
基于图形的基因组变异分型算法的全面基准测试，用于植物基因组以创建准确的集成管道
Ze-Zhen Du,Jia-Bao He,Wen-Biao Jiao
Ze-Zhen Du
Background: Although sequencing technologies have boosted the measurement of the genomic diversity of plant crops, it remains challenging to accurately genotype millions of genetic variants, especially structural variatio...
SuperCellCyto: enabling efficient analysis of large scale cytometry datasets [0.03%]
超细胞cyto：实现大规模流式细胞数据集的有效分析
Givanna H Putri,George Howitt,Felix Marsh-Wakefield et al.
Givanna H Putri et al.
Advancements in cytometry technologies have enabled quantification of up to 50 proteins across millions of cells at single cell resolution. Analysis of cytometry data routinely involves tasks such as data integration, clustering, and dimens...
PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization [0.03%]
基于概率矩阵分解的单细胞基因调控网络推理方法PMF-GRN
Claudia Skok Gibbs,Omar Mahmood,Richard Bonneau et al.
Claudia Skok Gibbs et al.
Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorization for Gene Regulatory Network...
Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement [0.03%]
Domestication 和改良过程中DNA甲基化增加促进梨果实提早成熟
Bobo Song,Jinshan Yu,Xiaolong Li et al.
Bobo Song et al.
Background: DNA methylation is an essential epigenetic modification. However, its contribution to trait changes and diversity in the domestication of perennial fruit trees remains unknown. ...