Bioinformatics is a field of biological studies that makes heavy use of computational resources as a key element of its methodology, as well as a reference to specific analysis “pipelines” that are repeatedly used in genomics. Common uses of bioinformatics include the identification of candidate genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim of better understanding the genetic basis of disease, unique adaptations, desirable properties (especially in agricultural species), or differences between populations. In a less formal way, bioinformatics also tries to understand the organizational principles within nucleic acid and protein sequences.
Ethylene & Light Transcriptional Meta-analysis
In this meta-analysis, we overlay data from multiple experiments with ethylene treatment in roots, but with plants grown under different lighting conditions, to compare and contrast ethylene response under these light contexts. For more info, see the publication:
Harkey et al. (2019) Light modulates ethylene synthesis, signaling, and downstream transcriptional networks to control plant development. Front. in Plant Sci. 10:1094.
Methods for analysis at GitHub
TF DEACoN
TF DEACoN (Transcription Factor Discovery by Enrichment Analysis of Coexpression Networks) is a tool developed in the Muday lab to allow for the prediction of transcription factor regulators from a list of coexpressed genes in Arabidopsis. For more info, see the publication:
Harkey et al. (2020) A new tool for discovering transcriptional regulators of co-expressed genes predicts gene regulatory networks that mediate ethylene-controlled root development. in silico Plants. 2(1):diaa006