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Nikolaos Vakirlis

Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes
2020 · Nikolaos Vakirlis, Anne-Ruxandra Carvunis, et al. · eLife · 147
De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences
2020 · Nikolaos Vakirlis, Omer Acar, et al. · Nature Communications · 143
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A Molecular Portrait of De Novo Genes in Yeasts
2017 · Nikolaos Vakirlis, Alex S Hebert, et al. · Molecular Biology and Evolution · 130
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De novo birth of functional microproteins in the human lineage
2022 · Nikolaos Vakirlis, Zoe Vance, et al. · Cell Reports · 108
Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
2016 · Nikolaos Vakirlis, Véronique Sarilar, et al. · Genome Research · 96
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Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast
2024 · Élodie Caudal, Victor Loegler, et al. · Nature Genetics · 67
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Computational Prediction of De Novo Emerged Protein-Coding Genes
2018 · Nikolaos Vakirlis, Aoife McLysaght · Methods in molecular biology · 34
Interlaboratory Comparison Study on Ribodepleted Total RNA High-Throughput Sequencing for Plant Virus Diagnostics and Bioinformatic Competence
2021 · Yahya Z. A. Gaafar, Marcel Westenberg, et al. · Pathogens · 26
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Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
2024 · Nikolaos Vakirlis, Anne Kupczok · Genome Research · 24
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Ancestral Sequence Reconstruction as a Tool to Detect and Study De Novo Gene Emergence
2024 · Nikolaos Vakirlis, Omer Acar, et al. · Genome Biology and Evolution · 16
Degradation Determinants Are Abundant in Human Noncanonical Proteins and Minor Annotated Isoforms
2026 · Claudio Casola, Adekola Owoyemi, et al. · Genome Biology and Evolution · 12
Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains
2023 · Emilios Tassios, Christoforos Nikolaou, et al. · Molecular Biology and Evolution · 12
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Intergenic polyA/T tracts explain the propensity of yeast de novo genes to encode transmembrane domains
2025 · Nikolaos Vakirlis, Timothy Fuqua · Journal of Evolutionary Biology · 7
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De Novo Genes: Current Status and Future Goals
2025 · Claudio Casola, Victor Luria, et al. · Genome Biology and Evolution · 6
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Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon
2023 · Finn O Gehlert, Lisa Nickel, et al. · Nucleic Acids Research · 6
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The plasma membrane Cation binding protein 1 affects accumulation of Potato virus Y in pepper both at the systemic level and in protoplasts
2020 · Despoina Beris, Konstantinos Kotsaridis, et al. · Virus Research · 5
Evolution of gene repertoires and new genes in yeasts
2016 · Nikolaos Vakirlis · theses.fr (ABES) · 3
Machine learning can distinguish orphans that have resulted from sequence divergence beyond recognition
2025 · Emilios Tassios, Jori de Leuw, et al. · Bioinformatics Advances · 2
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Distinct chromosomal “niches” in the genome of Saccharomyces cerevisiae provide the background for genomic innovation and shape the fate of gene duplicates
2022 · Athanasia Stavropoulou, Emilios Tassios, et al. · NAR Genomics and Bioinformatics · 2
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Author Correction: De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences
2021 · Nikolaos Vakirlis, Omer Acar, et al. · Nature Communications · 2
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Author response: Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes
2020 · Nikolaos Vakirlis, Anne-Ruxandra Carvunis, et al. · eLife · 2
Evolutionary journey and characterisation of a novel pan‐gene associated with beer strains of Saccharomyces cerevisiae
2019 · Nikolaos Vakirlis, Chandre Monerawela, et al. · Yeast · 2
Evolutionary origins of protein novelty across an entire yeast subphylum
2026 · Emilios Tassios, Nikolaos Pirgelis, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 1
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Identification and Classification of Expressed Orphan Genes, Spurious Orphan Genes, and Conserved Genes in the Human Gut Microbiome
2026 · Chen Chen, Nikolaos Vakirlis, et al. · Genome Biology and Evolution · 1
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Emergence Biases in Molecular Evolution
2026 · Timothy Fuqua, Nikolaos Vakirlis · Genome Biology and Evolution · 1
Works count: 31
Citation count: 857
H-index: 12
I10-index: 12
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