CrossFilt: a cross-species filtering tool that eliminates alignment bias in comparative genomics studies of primates [0.03%]
CrossFilt：一种跨物种筛选工具可消除灵长类动物比较基因组学研究中的比对偏倚效应
Kenneth A Barr,Yoav Gilad
Kenneth A Barr
Comparative functional genomic studies are often affected by biased read mapping across species due to inter-species differences in genome structure, sequence composition, and annotation quality. We developed CrossFilt, a filtering strategy...
Machine learning predictions surpass individual mRNAs as a proxy of single-cell protein expression [0.03%]
机器学习预测超越单个mRNA成为单细胞蛋白表达的替代指标
Josephine Fisher,Oliver Wood,Samuel Bullers et al.
Josephine Fisher et al.
Background: Expansive repositories of scRNA-seq data are now available. These are often analysed assuming that mRNA abundance reflects expression of the cognate protein. However, post-transcriptional/translational regulat...
SVScope improves somatic structural variations detection via graph-genome optimization [0.03%]
基于图形基因组优化改进体细胞结构变异检测
Kailing Tu,Qilin Zhang,Yang Li et al.
Kailing Tu et al.
Somatic structural variations (SVs) are critical in cancer genomes, yet their detection from long-read sequencing remains challenging due to alignment errors in repetitive regions. We develop SVScope, leveraging full-length reads and local ...
Single-cell and spatial transcriptomics in Phragmites australis reveal the association of B chromosomes with plant invasiveness [0.03%]
单细胞和空间转录组揭示芦苇染色体与植物入侵性的关联
Cui Wang,James Ord,Mengxiao Yan et al.
Cui Wang et al.
Background: Invasive plants pose a major threat to global biodiversity, yet the molecular and genomic mechanisms underlying their success remain poorly understood. Here, we investigate the invasion of the common reed Phra...
SpaNiche: spatial niche analysis to explore colocalization patterns and cellular interactions in spatial transcriptomics data [0.03%]
SpaNiche：探索空间转录组学数据中共定位模式和细胞相互作用的空间生态位分析
Siyuan Huang,Qinghua Ran,Junjie Tang et al.
Siyuan Huang et al.
We propose a computational framework for spatial niche analysis (SpaNiche) in spatial transcriptomics data to uncover colocalization patterns and infer potential ligand-receptor interactions. SpaNiche leverages graph-regularized joint non-n...
Full-DIA enables complete single-cell proteomics from diaPASEF using deep learning [0.03%]
基于深度学习的diaPASEF数据驱动完整单细胞蛋白质组学分析
Jian Song,Amanda Momenzadeh,Hebin Liu et al.
Jian Song et al.
diaPASEF improves ion utilization and sensitivity by synchronizing quadrupole isolation with trapped ion mobility separation, making it suitable for single-cell proteomics. We present Full-DIA, a deep learning-driven software that enhances ...
The SMARCA4 subunit of the SWI/SNF complex prevents genome instability at G quadruplexes [0.03%]
SWI/SNF复合物的SMARCA4亚基可防止G四联体处的基因组不稳定性
Alison Harrod,Hugang Feng,Nagham Ghaddar et al.
Alison Harrod et al.
Background: G-quadruplex (G4) structures are secondary structures that can form in guanine-rich single stranded DNA sequences. These play important roles in biological processes such as regulation of gene expression but c...
A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection [0.03%]
用于illumina测序仪的双色荧光染料化学物质的一个周期序列人工产物及其对体细胞变异检测的影响
Beverly J Fu,Vinayak V Viswanadham,Dominika Maziec et al.
Beverly J Fu et al.
Background: The sequencing-by-synthesis technology by Illumina, Inc. enables efficient and scalable readouts of mutations from genomic data. To enhance sequencing speed and efficiency, Illumina has shifted from the four-c...
Benchmarking component choices for unpaired single cell RNA and epigenomic integration [0.03%]
配对单细胞RNA和表观基因组整合的基准组件选择
Fnu Naqing,Qiuyue Yuan,Zhana Duren
Fnu Naqing
Background: Single-cell multi-omics sequencing technologies enable profiling various cellular aspects, offering valuable biological insights. Integrating unpaired multi-omics data, which involves profiling different modal...
Prediction of plant phase-separating proteins using positive-unlabeled learning [0.03%]
基于正负样本学习的植物相分离蛋白预测方法
Ran Fu,Yisu Tian,Hui Ren et al.
Ran Fu et al.
Liquid-liquid phase separation regulates biological processes through dynamic condensates. Despite its significance, experimentally validated phase-separating proteins in plants remain limited, complicating predictions. We overcome this gap...