Linking signalling and miRNA networks with vertebrate evolution
Title: Linking signalling and miRNA networks with vertebrate evolution
SNIC Project: SNIC 2013/1-303
Project Type: SNAC Medium
Principal Investigator: Lukasz Huminiecki <>
Affiliation: SU
Duration: 2013-11-17 – 2014-12-01
Classification: 10610 10615 10609


We propose computational analysis of global patterns of gene and genome duplications in vertebrates, and their consequences for signal transduction, and microRNA (miRNA) network evolution, as well as expression pattern evolution. We would like to use pathway databases and freely available genomic, expression, and miRNA datasets, to infer architectural changes of the animal signal transduction and miRNA networks after small scale duplications (SSDs) and whole genome duplications (WGDs). Quantification of the patterns of nonfunctionalization, subfunctionalization, and neofunctionalization will enhance our understanding of the evolutionary forces driving duplicate retention. The identification of the shared animal developmental toolkit is one of the most significant and fundamental discoveries in biology, and we designate the toolkit to be a focus area investigated besides the global perspective. Rich supply of data generated by the genomics community and freely available in public domain, as well as bioinformatics expertise established over many years through working in several top labs, guarantee feasibility of this study. Proof of feasibility has been already generated with published studies on the evolution of the transforming growth factor-beta pathway (Huminiecki, Goldovsky et al. 2009), and global analysis of the rewiring of the vertebrate signal transduction engine following 2R-WGD (Huminiecki and Heldin 2010).