Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions [0.03%]
基于计数的基因集合富集分析方法应对基因组区域进行基因集合富集分析
Christopher T Lee,Raymond G Cavalcante,Chee Lee et al.
Christopher T Lee et al.
Gene set enrichment (GSE) testing enhances the biological interpretation of ChIP-seq data and other large sets of genomic regions. Our group has previously introduced two GSE methods for genomic regions: ChIP-Enrich for narrow regions and B...
BATCAVE: calling somatic mutations with a tumor- and site-specific prior [0.03%]
BATCAVE：使用肿瘤和部位特异性先验调用体细胞突变
Brian K Mannakee,Ryan N Gutenkunst
Brian K Mannakee
Detecting somatic mutations withins tumors is key to understanding treatment resistance, patient prognosis and tumor evolution. Mutations at low allelic frequency, those present in only a small portion of tumor cells, are particularly diffi...
JASS: command line and web interface for the joint analysis of GWAS results [0.03%]
JASS：GWPS结果联合分析的命令行和网络接口
Hanna Julienne,Pierre Lechat,Vincent Guillemot et al.
Hanna Julienne et al.
Genome-wide association study (GWAS) has been the driving force for identifying association between genetic variants and human phenotypes. Thousands of GWAS summary statistics covering a broad range of human traits and diseases are now publ...
Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation [0.03%]
少数SINE迹象：尽管翻译水平升高但Alu元件几乎没有生物学相关的证据
Laura Martinez-Gomez,Federico Abascal,Irwin Jungreis et al.
Laura Martinez-Gomez et al.
Transposable elements colonize genomes and with time may end up being incorporated into functional regions. SINE Alu elements, which appeared in the primate lineage, are ubiquitous in the human genome and more than a thousand overlap annota...
A novel use of random priming-based single-strand library preparation for whole genome sequencing of formalin-fixed paraffin-embedded tissue samples [0.03%]
一种基于随机引物的单链文库构建技术用于石蜡包埋组织样本全基因组测序的新方法
Emily A Saunderson,Ann-Marie Baker,Marc Williams et al.
Emily A Saunderson et al.
The desire to analyse limited amounts of biological material, historic samples and rare cell populations has collectively driven the need for efficient methods for whole genome sequencing (WGS) of limited amounts of poor quality DNA. Most p...
Characterization of novel primary miRNA transcription units in human cells using Bru-seq nascent RNA sequencing [0.03%]
利用Bru-seq新生RNA测序技术表征人类细胞中的新型主要微小RNA转录单位
Karan Bedi,Michelle T Paulsen,Thomas E Wilson et al.
Karan Bedi et al.
MicroRNAs (miRNAs) are key contributors to gene regulatory networks. Because miRNAs are processed from RNA polymerase II transcripts, insight into miRNA regulation requires a comprehensive understanding of the regulation of primary miRNA tr...
Analysis of the structural variability of topologically associated domains as revealed by Hi-C [0.03%]
Hi-C揭示的拓扑相关结构域的结构变异分析
Natalie Sauerwald,Akshat Singhal,Carl Kingsford
Natalie Sauerwald
Three-dimensional chromosome structure plays an integral role in gene expression and regulation, replication timing, and other cellular processes. Topologically associated domains (TADs), building blocks of chromosome structure, are genomic...
SProtFP: a machine learning-based method for functional classification of small ORFs in prokaryotes [0.03%]
基于机器学习的模式对原核生物小ORF的功能分类方法SProtFP
Small proteins (≤100 amino acids) play important roles across all life forms, ranging from unicellular bacteria to higher organisms. In this study, we have developed SProtFP which is a machine learning-based method for functional annotatio...
Consistent features observed in structural probing data of eukaryotic RNAs [0.03%]
对真核RNA结构探测数据中一致特征的观察
Understanding RNA structure is crucial for elucidating its regulatory mechanisms. With the recent commercialization of messenger RNA vaccines, the profound impact of RNA structure on stability and translation efficiency has become increasin...
Benchmarking of methods that identify alternative polyadenylation events in single-/multiple-polyadenylation site genes [0.03%]
单/多聚腺苷酸化位点基因中鉴定替代性poly(A)位点方法的评估研究
Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that diversifies gene expression by generating messenger RNA isoforms with varying 3' untranslated regions. Accurate identification and quantification of trans...