Publications

C. Casola, A. Owoyemi, N. Vakirlis
Degradation determinants are abundant in human noncanonical proteins.
BiorXiv (2024).

E. Caudal, V. Loegler, F. Dutreux, N. Vakirlis, E. Teyssonnière, C. Caradec, A. Friedrich, J. Hou, J. Schacherer
Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast.
Nature Genetics 56, 1278–1287 (2024).

N. Vakirlis*, O. Acar, V. Cherupally, A.-R. Carvunis*
Ancestral Seaquence Reconstruction as a tool to detect and study de novo gene emergence.
Genome Biology and Evolution (2024).

N. Vakirlis*, A. Kupczok*
Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins.
Genome Research 34, 888–903 (2024).

F.O. Gehlert, L. Nickel, N. Vakirlis, K. Hammerschmidt, H.I. Vargas Gebauer, C. Kießling, A. Kupczok, R.A. Schmitz
Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon.
Nucleic Acids Research (2023).

E. Tassios, C. Nikolaou*, N. Vakirlis*
Intergenic regions of Saccharomycotina yeasts are enriched in potential to encode transmembrane domains.
Molecular Biology and Evolution (2023).

N. Vakirlis*, Z. Vance, Kate M. Duggan, A. McLysaght*
De novo birth of functional microproteins in the human lineage.
Cell Reports 41 (2022).

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 (2022).

N. Vakirlis, A.-R. Carvunis, A. McLysaght
Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes.
eLife 9 (2020).

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).