Strengthening Computational Biodiversity Research in Greece

Project Information

Comp-Biodiv-GR

Grant agreement ID: 101087081

DOI

10.3030/101087081

EC signature date 8 November 2022

Start date 1 January 2023

End date 31 December 2027

Funded under

• Widening participation and spreading excellence

Total cost

€ 2 400 000,00

EU contribution

€ 2 400 000,00

Coordinated by

IDRYMA TECHNOLOGIAS KAI EREVNAS
Greece

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Websites, patent fillings, videos etc. (1)

Separate Project/BCG website

Set up of initial separate web page for BCG and the project completed.

Publications

Peer reviewed articles (23)

Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region

Author(s): 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
Published in: Molecular Phylogenetics and Evolution, Issue 197:108091, 2024, ISSN 1095-9513
Publisher: Elsevier science
DOI: 10.1016/j.ympev.2024.108091

Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization

Author(s): Anastasis Togkousidis; Alexandros Stamatakis; Olivier Gascuel
Published in: Systematic Biology, 2025, ISSN 2692-8205
Publisher: Oxford Academic
DOI: 10.1093/SYSBIO/SYAF043

raxtax: a k-mer-based non-Bayesian taxonomic classifier

Author(s): Noah A Wahl , Georgios Koutsovoulos , Ben Bettisworth , Alexandros Stamatakis
Published in: Bioinformatics,, Issue 41, 12, 2025, ISSN 1367-4811
Publisher: Oxford academic
DOI: 10.1093/BIOINFORMATICS/BTAF620

Complexity of avian evolution revealed by family-level genomes

Author(s): 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,
Published in: Nature, 2024, ISSN 1476-4687
Publisher: Springer nature
DOI: 10.1038/s41586-024-07323-1

Unravelling the thread of Podarcis omics; insights into the genome and transcriptome of the Cretan wall lizard

Author(s): Manos Stratakis, Panagiotis Ioannidis, Iliana Bista, Dominic Absolon, Will Eagles, Shane McCarthy, Amy Denton, Petros Lymberakis, Nikos Poulakakis
Published in: Genes & Genomics, Issue 48, 2026, ISSN 1976-9571
Publisher: Springer Science and Business Media LLC
DOI: 10.1007/S13258-025-01676-1

Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution

Author(s): 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.
Published in: The ISME Journal, 2024, ISSN 1751-7370
Publisher: Oxford Academic
DOI: 10.5445/IR/1000173538

Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests

Author(s): Lukas Hübner; Alexandros Stamatakis
Published in: ISSN: 1868-8969, 2024, ISSN 1868-8969
Publisher: Dagstuhl Publishing
DOI: 10.5445/IR/1000174546/PRE

Identification of the 18 World War II executed citizens of Adele, Rethymnon, Crete using an ancient DNA approach and low coverage genomes

Author(s): Nikolaos Psonis, Despoina Vassou, Argyro Nafplioti, Eugenia Tabakaki, Pavlos Pavlidis, Alexandros Stamatakis, Nikos Poulakakis
Published in: Forensic Science International: Genetics, Issue 71, 2024, ISSN 1872-4973
Publisher: Elsevier BV
DOI: 10.1016/J.FSIGEN.2024.103060

Performance assessment of phylogenetic inference tools using PhyloSmew

Author(s): Dimitri Höhler, Julia Haag, Alexey M Kozlov, Benoit Morel, Alexandros Stamatakis
Published in: Bioinformatics Advances, Issue 5, 2025, ISSN 2635-0041
Publisher: Oxford University Press (OUP)
DOI: 10.1093/BIOADV/VBAF300

The Free Lunch is not over yet – Systematic Exploration of Numerical Thresholds in Phylogenetic Inference

Author(s): Julia Haag; Lukas Hübner; Alexey M. Kozlov; Alexandros Stamatakis
Published in: Bioinformatics Advances, 2022, ISSN 2635-0041
Publisher: Oxford Academics
DOI: 10.1101/2022.07.13.499893

Adaptive RAxML-NG: Accelerating Phylogenetic Inference under Maximum Likelihood using Dataset Difficulty

Author(s): Anastasis Togkousidis, Oleksiy M Kozlov, Julia Haag, Dimitri Höhler, Alexandros Stamatakis
Published in: Molecular Biology and Evolution, Issue Volume 40, Issue 10, 2023, ISSN 1537-1719
Publisher: Oxford Academic
DOI: 10.1093/molbev/msad227

Comparative Genomics Uncovers the Evolutionary Dynamics of Detoxification and Insecticide Target Genes Across 11 Phlebotomine Sand Flies

Author(s): Jason Charamis, Sofia Balaska, Panagiotis Ioannidis, Vít Dvořák, Konstantinos Mavridis, Mary Ann McDowell, Pavlos Pavlidis, René Feyereisen, Petr Volf, John Vontas
Published in: Genome Biology and Evolution, Issue 16, 2024, ISSN 1759-6653
Publisher: Oxford University Press (OUP)
DOI: 10.1093/GBE/EVAE186

Parameter Estimation and Species Tree Rooting Using ALE and GeneRax

Author(s): Tom A Williams; Adrián A Davín; Benoit Morel; Lénárd L Szánthó; Anja Spang; Alexandros Stamatakis; Philip Hugenholtz; Gergely J Szöllősi
Published in: Genome Biology and Evolution, 2023, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.5445/ir/1000161500

Simulations of Sequence Evolution: How (Un)realistic They Are and Why

Author(s): Johanna Trost, Julia Haag, Dimitri Höhler, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau Author Notes
Published in: Molecular Biology and Evolution,, Issue Volume 41, Issue 1, 2024, ISSN 1537-1719
Publisher: Oxford Academic
DOI: 10.1093/molbev/msad277

Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads

Author(s): Ben Bettisworth; Nikolaos Psonis; Nikos Poulakakis; Pavlos Pavlidis; Alexandros Stamatakis
Published in: Molecular Biology and Evolution, 2025, ISSN 1537-1719
Publisher: Oxford Academic
DOI: 10.1093/MOLBEV/MSAF006

Forensic Science International: Genetics

Author(s): Psonis, Nikolaos and Vassou, Despoina and Nafplioti, Argyro and Tabakaki, Eugenia and Pavlidis, Pavlos and Stamatakis, Alexandros and Poulakakis, Nikos,
Published in: Forensic Science International: Genetics, 2024, ISSN 1872-4973
Publisher: Elsevier BV
DOI: 10.1016/J.FSIGEN.2024.10306

A systematic exploration of current limitations of cognate-based phylogenetic inference

Author(s): Häuser, Luise; Jäger, Gerhard; Stamatakis, Alexandros
Published in: Open Research Europe, 2025, ISSN 2732-5121
Publisher: Open Research Europe
DOI: 10.12688/OPENRESEUROPE.20351.3

Necessary reforms in the Greek academic system

Author(s): Alexandros Stamatakis; Alexandros Stamatakis; Alexandros Stamatakis; Panagiotis Tsakalides; Panagiotis Tsakalides; Melina Tamiolaki; Melina Tamiolaki; Melina Tamiolaki
Published in: Frontiers in Political Science, 2024, ISSN 2673-3145
Publisher: frontiers
DOI: 10.5445/IR/1000177163

Phylourny: efficiently calculating elimination tournament win probabilities via phylogenetic methods

Author(s): Ben Bettisworth, Alexander I. Jordan & Alexandros Stamatakis
Published in: Statistics and Computing, 2023, ISSN 0960-3174
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11222-023-10246-y

AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss

Author(s): Benoit Morel, Tom A Williams, Alexandros Stamatakis, Gergely J Szöllősi
Published in: Bioinformatics, Issue Volume 40, Issue 4, 2024, ISSN 1367-4811
Publisher: Oxford Academic
DOI: 10.1093/bioinformatics/btae162

Advances and challenges in understanding evolution through genome comparison: meeting report of the European Molecular Biology Organization (EMBO) lecture course “Evolutionary and Comparative Genomics”

Author(s): 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
Published in: Bioinformatics Advances, Issue 5, 2025, ISSN 2635-0041
Publisher: Oxford University Press (OUP)
DOI: 10.1093/BIOADV/VBAF223

The power and limitations of species tree-aware phylogenetics

Author(s): Tom A. Williams, Adrian A. Davin, Benoit Morel, Lenard L. Szantho, Anja Spang, Alexandros Stamatakis, Philip Hugenholtz, Gergely J. Szollosi
Published in: Evolutionary Biology, 2023, ISSN 2692-8205
Publisher: biorXiv
DOI: 10.1101/2023.03.17.533068

Pandora: A Tool to Estimate Dimensionality Reduction Stability of Genotype Data

Author(s): Julia Haag; Alexander I. Jordan; Alexandros Stamatakis
Published in: Bioinformatics Advances, 2025, ISSN 2635-0041
Publisher: Oxford Academic
DOI: 10.1093/BIOADV/VBAF040

Conference proceedings (3)

Parallel Inference of Phylogenetic Stands with Gentrius

Author(s): Anastasis Togkousidis; Olga Chernomor; Alexandros Stamatakis
Published in: 2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2023, ISBN 979-8-3503-1199-0
Publisher: IEEEXplore
DOI: 10.1109/IPDPSW59300.2023.00035

Are Sounds Sound for Phylogenetic Reconstruction?

Author(s): Luise Häuser, Gerhard Jäger, Taraka Rama, Johann-Mattis List, Alexandros Stamatakis
Published in: -, 2024, ISSN 2331-8422
Publisher: Arxiv

EcoFreq: Compute with Cheaper, Cleaner Energy via Carbon-aware Power Scaling

Author(s): Alexey Kozlov, Alexandros Stamatakis
Published in: ISC High Performance 2024 Research Paper Proceedings, Issue pp. 1-12, 2024, ISBN 978-3-9826336-0-2
Publisher: Prometeus GmbH
DOI: 10.23919/ISC.2024.10528928.

Other (3)

bigrig: A range simulator for the DEC[+J] model

Author(s): Ben Bettisworth, Alexis Stamatakis
Published in: biorvix preprint, 2025, ISSN 2692-8205
Publisher: biorvix
DOI: 10.1101/2025.11.24.690345

Pandora: A Tool to Estimate Dimensionality Reduction Stability of Genotype Data

Author(s): Julia Haag, Alexander I. Jordan, Alexandros Stamatakis
Published in: biorXiv preprint, 2024, ISSN 2692-8205
Publisher: bioRxiv

Predicting Phylogenetic Bootstrap Values via Machine Learning

Author(s): Julius Wiegert, Julia Haag, Dimitri Hoehler, Alexandros Stamatakis
Published in: bioRxiv preprint, 2024, ISSN 2692-8205
Publisher: bioRxiv