E. Tassios, *C. Nikolaou, & *N. Vakirlis. Intergenic regions of Saccharomycotina yeasts are enriched in potential to encode transmembrane domains. Molecular Biology and Evolution msad059 (2023) doi: 10.1093/molbev/msad059.
N. Vakirlis*, Z. Vance, Kate M. Duggan, A. McLysaght*, De novo birth of functional microproteins in the human lineage. Cell Reports, 41(12), (2022) doi: 10.1016/j.celrep.2022.111808
A. Stavropoulou, E. Tassios, M. Kalyva, M. Georgoulopoulos, N. Vakirlis, I. Iliopoulos, C. Nikolaou. Distinct chromosomal “niches” in the genome of Saccharomyces cerevisiae provide the background for genomic innovation and shape the fate of gene duplicates. NAR Genomics and Bioinformatics. 4(4):lqac086, (2022) doi: 10.1093/nargab/lqac086
N. Vakirlis, A.-R. Carvunis, A. McLysaght, Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes. eLife. 9, e53500 (2020). doi: 10.7554/eLife.53500
N. Vakirlis, O. Acar, B. Hsu, N. Castilho Coelho, S. B. Van Oss, A. Wacholder, K. Medetgul-Ernar, R. W. Bowman, C. P. Hines, J. Iannotta, S. B. Parikh, A. McLysaght, C. J. Camacho, A. F. O’Donnell, T. Ideker, A.-R. Carvunis, De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nature Communications. 11, 1–18 (2020). doi:10.1038/s41467-020-14500-z
N. Vakirlis, A. S. Hebert, D. A. Opulente, G. Achaz, C. T. Hittinger, G. Fischer, J. J. Coon, I. Lafontaine, A Molecular Portrait of De Novo Genes in Yeasts. Mol Biol Evol. 35, 631–645 (2018). doi:10.1093/molbev/msx315