2025

  1. Julia Haag, Alexandros Stamatakis: "Pythia 2.0: New Data, New Prediction Model, New Features", biorXiv preprint, 2025.
  2. Noah A Wahl, Georgios D Koutsovoulos, Ben Bettisworth, Alexandros Stamatakis: "raxtax: A k-mer-based non-Bayesian Taxonomic Classifier", biorXiv preprint, 2025.
  3. Julia Haag, Alexander I. Jordan, Alexandros Stamatakis: "Pandora: A Tool to Estimate Dimensionality Reduction Stability of Genotype Data" Open Access: Bioinformatics Advances, March 2025.
  4. Ben Bettisworth, Nikolaos Psonis, Nikos Poulakakis, Pavlos Pavlidis, Alexandros Stamatakis: "Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads", Open Access: Molecular Biology and Evolution, 2025.

2024

  1. Alexandros Stamatakis, Panagiotis Tsakalides, Melina Tamiolaki: "Necessary reforms in the Greek academic system", Frontiers in Political Science open access link, 2024.
  2. Jason Charamis, Sofia Balaska, Panagiotis Ioannidis, Vít Dvořák, Konstantinos Mavridis, Mary Ann McDowell, Pavlos Pavlidis, René Feyereisen, Petr Volf, John Vontas: "Comparative Genomics Uncovers the Evolutionary Dynamics of Detoxification and Insecticide Target Genes Across 11 Phlebotomine Sand Flies", Genome Biology and Evolution open access link
  3. Tom A Williams, Adrian A Davin, Lénárd L Szánthó, Alexandros Stamatakis, Noah A Wahl, Ben J Woodcroft, Rochelle M Soo, Laura Eme, Paul O Sheridan, Cecile Gubry-Rangin, Anja Spang, Philip Hugenholtz, Gergely J Szöllősi: "Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution", The ISME Journal - Multidisciplinary Journal of Microbial Ecology open access link, 2024.
  4. Anastasis Togkousidis, Alexandros Stamatakis, Olivier Gascuel: "Much Ado About Nothing: Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to evade (Over-)optimization", preprint on bioRxiv, 2024.
  5. Lukas Hübner, Alexandros Stamatakis: "Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests", preprint on bioRxiv, Conference Proceedings Version, 2024, accepted for publication at WABI2024.
  6. Nikolaos Psonis, Despoina Vassou, Argyro Nafplioti, Eugenia Tabakaki, Pavlos Pavlidis, Alexandros Stamatakis, Nikos Poulakakis: "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 Journal pre-proof, 2024.
  7. 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: "Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region", Molecular Phylogenetics and Evolution, on-line pre-proof, 2024.
  8. Luise Häuser, Gerhard Jäger, Alexandros Stamatakis: "Computational Approaches for Integrating out Subjectivity in Cognate Synonym Selection", Accepted for publication in Proceedings of SCiL 2024 at UC Irvine, California, US, June 2024. preprint on arXiv
  9. 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, Joel Cracraft, Metin Balaban, Uyen Mai, Guangji Chen, Rongsheng Gao, Chengran Zhou, Yulong Xie, Zijian Huang, Zhen Cao, Zhi Yan, Huw A. Ogilvie, Luay Nakhleh, Bent Lindow, Benoit Morel, Jon Fjeldså, Peter A. Hosner, Rute R. da Fonseca, Bent Petersen, Joseph A. Tobias, Tamás Székely, Jonathan David Kennedy, Andrew Hart Reeve, Andras Liker, Martin Stervander, Agostinho Antunes, Dieter Thomas Tietze, Mads Bertelsen, Fumin Lei, Carsten Rahbek, Gary R. Graves, Mikkel H. Schierup, Tandy Warnow, Edward L. Braun, M. Thomas P. Gilbert, Erich D. Jarvis, Siavash Mirarab, Guojie Zhang: "Complexity of avian evolution revealed by family-level genomes" Nature, 2024.
  10. Benoit Morel, Tom A. William, Alexandros Stamatakis, Gergely Szollosi: "AleRax: A tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer and loss." Bioinformatics, 2024.
  11. Alexey Kozlov, Alexandros Stamatakis: "EcoFreq: Compute with Cheaper, Cleaner Energy via Carbon-aware Power Scaling", accepted for publication in Proceedings of ISC High Performance, Hamburg, May, 2024. paper link
  12. Julius Wiegert, Julia Haag, Dimitri Hoehler, Alexandros Stamatakis: "Predicting Phylogenetic Bootstrap Values via Machine Learning", Molecular Biology and Evolution, October 2024.
  13. Luise Häuser, Gerhard Jäger, Taraka Rama, Johann-Mattis List, Alexandros Stamatakis: "Are Sounds Sound for Phylogenetic Reconstruction?", Proceedings of SIGTYP2024 , BEST PAPER AWARD, Malta, March, 2024.
  14. Melina Tamiolaki, Alexandros Stamatakis: "Substanziell unterfinanziert - Probleme der griechischen Forschungslandschaft", Forschung und Lehre,1:42-43, 2024.
  15. Johanna Trost, Julia Haag, Dimitri Hoehler, Luca Nesterenko, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau: "Simulations of Sequence Evolution: How (Un)realistic They Are and Why" , Molecular Biology and Evolution, 2024.

2023

  1. Julia Haag, Lukas Hübner, Alexey M. Kozlov, Alexandros Stamatakis: "The Free Lunch is not over yet—systematic exploration of numerical thresholds in maximum likelihood phylogenetic inference." Bioinformatics Advances 3, no. 1 (2023): vbad124.
  2. Anastasis Togkousidis, Olga Chernomor, Alexandros Stamatakis: "Parallel Inference of Phylogenetic Stands with Gentrius", 2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). IEEE, 2023.
  3. Tom A. Williams, Adrian A. Davin, Benoit Morel, Lenard L. Szantho, Anja Spang, Alexandros Stamatakis, Philip Hugenholtz, Gergely J. Szollosi: "Parameter estimation and species tree rooting using ALE and GeneRax" , Genome Biology and Evolution, evad134, 2023.
  4. Anastasis Togkousidis, Alexey M. Kozlov, Julia Haag, Dimitri Höhler, Alexandros Stamatakis: "Adaptive RAxML-NG: Accelerating Phylogenetic inference under Maximum Likelihood using dataset difficulty", biorXiv preprint, 2023.
  5. Tom A. Williams, Adrian A. Davin, Benoit Morel, Lenard L. Szantho, Anja Spang, Alexandros Stamatakis, Philip Hugenholtz, Gergely J. Szollosi: "The power and limitations of species tree-aware phylogenetics", biorXiv preprint, 2023.
  6. Ben Bettisworth, Alexander I. Jordan, Alexandros Stamatakis: "Phylourny: efficiently calculating elimination tournament win probabilities via phylogenetic methods", open access, Statistics and Computing:33(80), 2023.