Epigenomic analysis reveals a dynamic and context-specific macrophage enhancer landscape associated with innate immune activation and tolerance [0.03%]
表观基因组分析揭示了与先天免疫活化和耐受相关的动态且具有特定环境的巨噬细胞增强子景观
Ping Zhang,Harindra E Amarasinghe,Justin P Whalley et al.
Ping Zhang et al.
Background: Chromatin states and enhancers associate gene expression, cell identity and disease. Here, we systematically delineate the acute innate immune response to endotoxin in terms of human macrophage enhancer activi...
Comprehensive benchmarking of CITE-seq versus DOGMA-seq single cell multimodal omics [0.03%]
CITE-seq与DOGMA-seq单细胞多模态组学的全面基准测试
Zhongli Xu,Elisa Heidrich-O&#x;Hare,Wei Chen et al.
Zhongli Xu et al.
The recently developed method TEA-seq and similar DOGMA-seq single cell trimodal omics assays provide unprecedented opportunities for understanding cell biology, but independent evaluation is lacking. We explore the utility of DOGMA-seq com...
SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning [0.03%]
SeqScreen：通过集成学习准确而敏感地筛选致病序列的功能性筛查方法
Advait Balaji,Bryce Kille,Anthony D Kappell et al.
Advait Balaji et al.
The COVID-19 pandemic has emphasized the importance of accurate detection of known and emerging pathogens. However, robust characterization of pathogenic sequences remains an open challenge. To address this need we developed SeqScreen, whic...
An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics [0.03%]
基于蛋白质基因组学的分析及其如何以及何时通过转录本信息缩减蛋白数据库来增强真核生物蛋白质组学研究的实例考察
Laura Fancello,Thomas Burger
Laura Fancello
Background: Proteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases. However, empirical observations reveal that these la...
Nadav Brandes,Omer Weissbrod,Michal Linial
Nadav Brandes
Genetic studies of human traits have revolutionized our understanding of the variation between individuals, and yet, the genetics of most traits is still poorly understood. In this review, we highlight the major open problems that need to b...
SCADIE: simultaneous estimation of cell type proportions and cell type-specific gene expressions using SCAD-based iterative estimating procedure [0.03%]
基于SCAD的迭代估计程序同时估算细胞类型比例和特定细胞类型的基因表达（SCADIE）
Daiwei Tang,Seyoung Park,Hongyu Zhao
Daiwei Tang
A challenge in bulk gene differential expression analysis is to differentiate changes due to cell type-specific gene expression and cell type proportions. SCADIE is an iterative algorithm that simultaneously estimates cell type-specific gen...
Gene fusion as an important mechanism to generate new genes in the genus Oryza [0.03%]
基因融合是水稻属物种产生新基因的重要机制
Yanli Zhou,Chengjun Zhang,Li Zhang et al.
Yanli Zhou et al.
Background: Events of gene fusion have been reported in several organisms. However, the general role of gene fusion as part of new gene origination remains unknown. ...
Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome [0.03%]
虚拟ChIP-seq技术：通过转录组学学习预测转录因子的结合位点
Mehran Karimzadeh,Michael M Hoffman
Mehran Karimzadeh
Existing methods for computational prediction of transcription factor (TF) binding sites evaluate genomic regions with similarity to known TF sequence preferences. Most TF binding sites, however, do not resemble known TF sequence motifs, an...
CONET: copy number event tree model of evolutionary tumor history for single-cell data [0.03%]
单细胞数据的肿瘤进化历史的拷贝数事件树模型(CONET)
Magda Markowska,Tomasz Cąkała,BłaŻej Miasojedow et al.
Magda Markowska et al.
Copy number alterations constitute important phenomena in tumor evolution. Whole genome single-cell sequencing gives insight into copy number profiles of individual cells, but is highly noisy. Here, we propose CONET, a probabilistic model f...
Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets [0.03%]
多发性硬化遗传学分析鉴定出B和CD4+T细胞为主要亚群
Michael H Guo,Prashanth Sama,Brenna A LaBarre et al.
Michael H Guo et al.
Background: Multiple sclerosis (MS) is an autoimmune condition of the central nervous system with a well-characterized genetic background. Prior analyses of MS genetics have identified broad enrichments across peripheral ...