Unravelling the thread of Podarcis omics; insights into the genome and transcriptome of the Cretan wall lizard
Genes & Genomics· 2026DOI Manos Stratakis, Panagiotis Ioannidis, Iliana Bista, Dominic Absolon, Will Eagles, Shane McCarthy, Amy Denton, Petros Lymberakis, Nikos Poulakakis
A systematic exploration of current limitations of cognate-based phylogenetic inference
Open Research Europe· 2025DOI Häuser, Luise; Jäger, Gerhard; Stamatakis, Alexandros
Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization
Systematic Biology· 2025DOI Anastasis Togkousidis; Alexandros Stamatakis; Olivier Gascuel
Advances and challenges in understanding evolution through genome comparison: meeting report of the European Molecular Biology Organization (EMBO) lecture course “Evolutionary and Comparative Genomics”
Bioinformatics Advances· 2025DOI Athina Gavriilidou, Alexandros Stamatakis, Anne Kupczok, Iliana Bista, Chris D Jiggins, Rosa Fernández, Eirini Skourtanioti, Grigoris Amoutzias, Daniela Delneri, Nikos Kyrpides, Christoforos Nikolaou, Alexandros A Pittis, Tereza Manousaki, Nikolaos Vakirlis
bigrig: A range simulator for the DEC[+J] model
biorvix preprint· 2025DOI Ben Bettisworth, Alexis Stamatakis
Pandora: A Tool to Estimate Dimensionality Reduction Stability of Genotype Data
Bioinformatics Advances· 2025DOI Julia Haag; Alexander I. Jordan; Alexandros Stamatakis
Performance assessment of phylogenetic inference tools using PhyloSmew
Bioinformatics Advances· 2025DOI Dimitri Höhler, Julia Haag, Alexey M Kozlov, Benoit Morel, Alexandros Stamatakis
raxtax: a k-mer-based non-Bayesian taxonomic classifier
Noah A Wahl , Georgios Koutsovoulos , Ben Bettisworth , Alexandros Stamatakis
Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads
Molecular Biology and Evolution· 2025DOI Ben Bettisworth; Nikolaos Psonis; Nikos Poulakakis; Pavlos Pavlidis; Alexandros Stamatakis
AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss
Benoit Morel, Tom A Williams, Alexandros Stamatakis, Gergely J Szöllősi
Are Sounds Sound for Phylogenetic Reconstruction?
-· 2024
Luise Häuser, Gerhard Jäger, Taraka Rama, Johann-Mattis List, Alexandros Stamatakis
Comparative Genomics Uncovers the Evolutionary Dynamics of Detoxification and Insecticide Target Genes Across 11 Phlebotomine Sand Flies
Genome Biology and Evolution· 2024DOI Jason Charamis, Sofia Balaska, Panagiotis Ioannidis, Vít Dvořák, Konstantinos Mavridis, Mary Ann McDowell, Pavlos Pavlidis, René Feyereisen, Petr Volf, John Vontas
Complexity of avian evolution revealed by family-level genomes
Josefin Stiller, Shaohong Feng, Al-Aabid Chowdhury, Iker Rivas-González, David A. Duchêne, Qi Fang, Yuan Deng, Alexey Kozlov, Alexandros Stamatakis, Santiago Claramunt, Jacqueline M. T. Nguyen, Simon Y. W. Ho, Brant C. Faircloth, Julia Haag, Peter Houde,
Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region
Molecular Phylogenetics and Evolution· 2024DOI Panayiota Kotsakiozi, Aglaia Antoniou, Nikolaos Psonis, Κostas Sagonas, Emmanouela Karameta, Çetin Ilgaz, Yusuf Kumlutaş, Aziz Avcı, Daniel Jablonski, Diego Darriba, Alexandros Stamatakis, Petros Lymberakis, Nikos Poulakakis
EcoFreq: Compute with Cheaper, Cleaner Energy via Carbon-aware Power Scaling
ISC High Performance 2024 Research Paper Proceedings· 2024DOI Alexey Kozlov, Alexandros Stamatakis
Forensic Science International: Genetics
Forensic Science International: Genetics· 2024DOI Psonis, Nikolaos and Vassou, Despoina and Nafplioti, Argyro and Tabakaki, Eugenia and Pavlidis, Pavlos and Stamatakis, Alexandros and Poulakakis, Nikos,
Identification of the 18 World War II executed citizens of Adele, Rethymnon, Crete using an ancient DNA approach and low coverage genomes
Forensic Science International: Genetics· 2024DOI Nikolaos Psonis, Despoina Vassou, Argyro Nafplioti, Eugenia Tabakaki, Pavlos Pavlidis, Alexandros Stamatakis, Nikos Poulakakis
Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests
Lukas Hübner; Alexandros Stamatakis
Necessary reforms in the Greek academic system
Frontiers in Political Science· 2024DOI Alexandros Stamatakis; Alexandros Stamatakis; Alexandros Stamatakis; Panagiotis Tsakalides; Panagiotis Tsakalides; Melina Tamiolaki; Melina Tamiolaki; Melina Tamiolaki
Pandora: A Tool to Estimate Dimensionality Reduction Stability of Genotype Data
biorXiv preprint· 2024
Julia Haag, Alexander I. Jordan, Alexandros Stamatakis
Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution
The ISME Journal· 2024DOI Williams, Tom A.; Davin, Adrian A.; Szánthó, Lénárd L.; Stamatakis, Alexandros; Wahl, Noah A.; Woodcroft, Ben J.; Soo, Rochelle M.; Eme, Laura; Sheridan, Paul O.; Gubry-Rangin, Cecile; Spang, Anja; Hugenholtz, Philip; Szöllősi, Gergely J.
Predicting Phylogenetic Bootstrap Values via Machine Learning
bioRxiv preprint· 2024
Julius Wiegert, Julia Haag, Dimitri Hoehler, Alexandros Stamatakis
Simulations of Sequence Evolution: How (Un)realistic They Are and Why
Molecular Biology and Evolution,· 2024DOI Johanna Trost, Julia Haag, Dimitri Höhler, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau Author Notes
Adaptive RAxML-NG: Accelerating Phylogenetic Inference under Maximum Likelihood using Dataset Difficulty
Molecular Biology and Evolution· 2023DOI Anastasis Togkousidis, Oleksiy M Kozlov, Julia Haag, Dimitri Höhler, Alexandros Stamatakis
Parallel Inference of Phylogenetic Stands with Gentrius
2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)· 2023DOI Anastasis Togkousidis; Olga Chernomor; Alexandros Stamatakis
Parameter Estimation and Species Tree Rooting Using ALE and GeneRax
Genome Biology and Evolution· 2023DOI Tom A Williams; Adrián A Davín; Benoit Morel; Lénárd L Szánthó; Anja Spang; Alexandros Stamatakis; Philip Hugenholtz; Gergely J Szöllősi
Phylourny: efficiently calculating elimination tournament win probabilities via phylogenetic methods
Statistics and Computing· 2023DOI Ben Bettisworth, Alexander I. Jordan & Alexandros Stamatakis
The power and limitations of species tree-aware phylogenetics
Evolutionary Biology· 2023DOI Tom A. Williams, Adrian A. Davin, Benoit Morel, Lenard L. Szantho, Anja Spang, Alexandros Stamatakis, Philip Hugenholtz, Gergely J. Szollosi
The Free Lunch is not over yet – Systematic Exploration of Numerical Thresholds in Phylogenetic Inference
Bioinformatics Advances· 2022DOI Julia Haag; Lukas Hübner; Alexey M. Kozlov; Alexandros Stamatakis