MOTIVATION: The emergence of abundant biological networks, which benefit from the development of advanced high-throughput techniques, contributes to describing and modeling complex internal interactions among biological entities such as genes and pro...
Independent component analysis (ICA) of bacterial transcriptomes has emerged as a powerful tool for obtaining co-regulated, independently-modulated gene sets (iModulons), inferring their activities across a range of conditions, and enabling their ass...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
Single-cell RNAseq is an emerging technology that allows the quantification of gene expression in individual cells. In plants, single-cell sequencing technology has been applied to generate root cell expression maps under many experimental conditions...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
Bioinformatics tools and resources are valuable for the analysis of data sets focusing on programmed cell death. This chapter discusses methods for the generation of gene sets as well as enrichment analysis using publicly available databases.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
Epistasis detection is a hot topic in bioinformatics due to its relevance to the detection of specific phenotypic traits and gene-gene interactions. Here, we present a step-by-step protocol to apply Epi-GTBN, a machine learning-based method based on ...
The BioGateway App is a plugin for the Cytoscape network editor, allowing users to interactively build biological networks by querying the Biogateway Resource Description Framework (RDF) triple store. BioGateway contains information from several cura...
Gene set analysis (GSA) is one of the methods of choice for analyzing the results of current omics studies; however, it has been mainly developed to analyze mRNA (microarray, RNA-Seq) data. The following review includes an update regarding general me...
MOTIVATION: Although long non-coding RNAs (lncRNAs) have limited capacity for encoding proteins, they have been verified as biomarkers in the occurrence and development of complex diseases. Recent wet-lab experiments have shown that lncRNAs function ...
Recent advances in genomic technologies have generated data on large-scale protein-DNA interactions and open chromatin regions for many eukaryotic species. How to identify condition-specific functions of transcription factors using these data has bec...
Join thousands of healthcare professionals staying informed about the latest AI breakthroughs in medicine. Get curated insights delivered to your inbox.