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Below is a list of review articles from the lab. For a listing and summary of primary publications, check the sub-pages: [1] genomics of DNA repair failures; [2] transcriptome quality control; [3] predicting cancer evolution; and [4] automated gene function inference
[review article] To NMD or Not To NMD: Nonsense-Mediated mRNA Decay in Cancer and Other Genetic Diseases. F Supek, B Lehner, R Lindeboom (2020) Trends in Genetics.
Genomic analyses have quantified the importance of known and novel 'rules of nonsense-mediated mRNA decay (NMD)', allowing accurate prediction of whether premature termination codon (PTC)-containing mRNAs are degraded or not. NMD can both aggravate and alleviate the effects of PTCs that cause genetic disease, and this varies across both diseases and individuals. NMD frequently inactivates tumor suppressor genes and silences the expression of neoantigens.
[review article] Scales and mechanisms of somatic mutation rate variation across the human genome. F Supek and B Lehner. DNA Repair special issue Cutting-edge Perspectives in Genomic Maintenance VI.
Either an increase in the global mutation rate or a redistribution of mutations from inactive to active DNA can increase the rate at which consequential mutations are acquired. Environmental carcinogens and intrinsic mechanisms operating in tumor cells can cause cancer by this second mechanism: by specifically increasing the mutation rate in active regions of the genome.
[review article] The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function. F Supek. (2016) J Mol Evol.
Comparative analyses of genomes, from bacteria across fungi to humans and human tumors have revealed many links between genes' biological roles and the accrual of synonymous mutations. The evolutionary trace of codon bias patterns across homologous genes may be examined to learn about a gene’s relevance to various phenotypes, or, more generally, its function in the cell.