Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR [0.03%]
通过ViCAR改进表观遗传特征和三维染色质结构的联合绘制
Sean M Flynn,Somdutta Dhir,Krzysztof Herka et al.
Sean M Flynn et al.
Methods to measure chromatin contacts at genomic regions bound by histone modifications or proteins are important tools to investigate chromatin organization. However, such methods do not capture the possible involvement of other epigenomic...
RNAseqCovarImpute: a multiple imputation procedure that outperforms complete case and single imputation differential expression analysis [0.03%]
RNAseqCovarImpute：一种优于完全事例和单次估算的差异表达分析的方法
Brennan H Baker,Sheela Sathyanarayana,Adam A Szpiro et al.
Brennan H Baker et al.
Missing covariate data is a common problem that has not been addressed in observational studies of gene expression. Here, we present a multiple imputation method that accommodates high dimensional gene expression data by incorporating princ...
Enhlink infers distal and context-specific enhancer-promoter linkages [0.03%]
Enhlink 推断远距离和特异性情境下的增强子-启动子关联
Olivier B Poirion,Wulin Zuo,Catrina Spruce et al.
Olivier B Poirion et al.
Enhlink is a computational tool for scATAC-seq data analysis, facilitating precise interrogation of enhancer function at the single-cell level. It employs an ensemble approach incorporating technical and biological covariates to infer condi...
Feng Zhang,Chenkun Yang,Hao Guo et al.
Feng Zhang et al.
Background: UV-B, an important environmental factor, has been shown to affect the yield and quality of rice (Oryza sativa) worldwide. However, the molecular mechanisms underlying the response to UV-B stress remain elusive...
NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs [0.03%]
一种新型的奈米孔直接RNA测序方法（NERD-SEQ），可扩展非编码RNA的表达谱
Luke Saville,Li Wu,Jemaneh Habtewold et al.
Luke Saville et al.
Non-coding RNAs (ncRNAs) are frequently documented RNA modification substrates. Nanopore Technologies enables the direct sequencing of RNAs and the detection of modified nucleobases. Ordinarily, direct RNA sequencing uses polyadenylation se...
Gut microbiota contributes to high-altitude hypoxia acclimatization of human populations [0.03%]
肠道微生物组有助于人类适应高原低氧环境
Qian Su,Dao-Hua Zhuang,Yu-Chun Li et al.
Qian Su et al.
Background: The relationship between human gut microbiota and high-altitude hypoxia acclimatization remains highly controversial. This stems primarily from uncertainties regarding both the potential temporal changes in th...
Contribution of homoeologous exchange to domestication of polyploid Brassica [0.03%]
亚倍体交换在家畜育种中的贡献以芸苔属为例
Tianpeng Wang,Aalt D J van Dijk,Ranze Zhao et al.
Tianpeng Wang et al.
Background: Polyploidy is widely recognized as a significant evolutionary force in the plant kingdom, contributing to the diversification of plants. One of the notable features of allopolyploidy is the occurrence of homoe...
Seqrutinator: scrutiny of large protein superfamily sequence datasets for the identification and elimination of non-functional homologues [0.03%]
Seqrutinator：鉴定和剔除非功能同源物的大型蛋白质超家族序列数据集筛查软件
Agustín Amalfitano,Nicolás Stocchi,Hugo Marcelo Atencio et al.
Agustín Amalfitano et al.
Seqrutinator is an objective, flexible pipeline that removes sequences with sequencing and/or gene model errors and sequences from pseudogenes from complex, eukaryotic protein superfamilies. Testing Seqrutinator on major superfamilies BAHD,...
Real-time identification of epistatic interactions in SARS-CoV-2 from large genome collections [0.03%]
从大型基因组集合中实时识别SARS-CoV-2的表型相互作用效应
Gabriel Innocenti,Maureen Obara,Bibiana Costa et al.
Gabriel Innocenti et al.
Background: The emergence of the SARS-CoV-2 virus has highlighted the importance of genomic epidemiology in understanding the evolution of pathogens and guiding public health interventions. The Omicron variant in particul...
Current limitations in predicting mRNA translation with deep learning models [0.03%]
深度学习模型预测蛋白质合成的局限性
Niels Schlusser,Asier González,Muskan Pandey et al.
Niels Schlusser et al.
Background: The design of nucleotide sequences with defined properties is a long-standing problem in bioengineering. An important application is protein expression, be it in the context of research or the production of mR...