Development, or differentiation/proliferation, could be autonomous or regulatory. The classic example of C. elegans development was generally considered an exception, whereas the development of most other animals are believed to be mostly regulatory. This conjecture was, however, never formally tested. We aimed to assess the autonomous/regulatory component of the development of animals by reconstruction of the developmental cell lineage tree.

18 of the amino acids were each encoded by more than one codon, but the synonymous codons were not used with equal frequency, a phenomenone known as the "codon usage bias". It is commonly accepted that the evolution of codon usage bias was underlied by mutation, drift and selection. We explored the relative contribution of chance (mutation and drift) and necessity (selection) in determining the codon usage bias of cells and genes.

More than 40 years ago, Vogal proposed the "error catastrophe" hypothesis to explain the phenomenone of aging.  Others have proposed "mutation catastrophe" hypothesis to further include the possible influence by mutation. These and other theories have connected stochastic errors in expression of genetic information with aging. We tried to futher explore this connection and identify key mediators underlying such connection, using phenotypic data of mutation rate and translational error rate, in combination of genotype of yeast strains.

The same RNA molecular can fold into different secondary structure, especially when the folding is interfered by different trans-regulatory factors met at different stages of its life. E.g., during transcription, template DNA strand might competitively inhibit RNA folding; During translation, ribosomes might preclude certain fragments of mRNA from folding. We assessed the specificity and function of such differential foldings using high-throughput sequencing data of RNA secondary structures.