Strengthening Computational Biodiversity Research in Greece

Informazioni relative al progetto

Comp-Biodiv-GR

ID dell’accordo di sovvenzione: 101087081

DOI

10.3030/101087081

Data della firma CE 8 Novembre 2022

Data di avvio 1 Gennaio 2023

Data di completamento 31 Dicembre 2027

Finanziato da

• Widening participation and spreading excellence

Costo totale

€ 2 400 000,00

Contributo UE

€ 2 400 000,00

Coordinato da

IDRYMA TECHNOLOGIAS KAI EREVNAS
Greece

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

Websites, patent fillings, videos etc. (1)

Separate Project/BCG website

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

Pubblicazioni

Peer reviewed articles (23)

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

Autori: 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
Pubblicato in: Molecular Phylogenetics and Evolution, Numero 197:108091, 2024, ISSN 1095-9513
Editore: Elsevier science
DOI: 10.1016/j.ympev.2024.108091

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

Autori: Anastasis Togkousidis; Alexandros Stamatakis; Olivier Gascuel
Pubblicato in: Systematic Biology, 2025, ISSN 2692-8205
Editore: Oxford Academic
DOI: 10.1093/SYSBIO/SYAF043

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

Autori: Noah A Wahl , Georgios Koutsovoulos , Ben Bettisworth , Alexandros Stamatakis
Pubblicato in: Bioinformatics,, Numero 41, 12, 2025, ISSN 1367-4811
Editore: Oxford academic
DOI: 10.1093/BIOINFORMATICS/BTAF620

Complexity of avian evolution revealed by family-level genomes

Autori: 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,
Pubblicato in: Nature, 2024, ISSN 1476-4687
Editore: 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

Autori: Manos Stratakis, Panagiotis Ioannidis, Iliana Bista, Dominic Absolon, Will Eagles, Shane McCarthy, Amy Denton, Petros Lymberakis, Nikos Poulakakis
Pubblicato in: Genes & Genomics, Numero 48, 2026, ISSN 1976-9571
Editore: 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

Autori: 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.
Pubblicato in: The ISME Journal, 2024, ISSN 1751-7370
Editore: Oxford Academic
DOI: 10.5445/IR/1000173538

Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests

Autori: Lukas Hübner; Alexandros Stamatakis
Pubblicato in: ISSN: 1868-8969, 2024, ISSN 1868-8969
Editore: 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

Autori: Nikolaos Psonis, Despoina Vassou, Argyro Nafplioti, Eugenia Tabakaki, Pavlos Pavlidis, Alexandros Stamatakis, Nikos Poulakakis
Pubblicato in: Forensic Science International: Genetics, Numero 71, 2024, ISSN 1872-4973
Editore: Elsevier BV
DOI: 10.1016/J.FSIGEN.2024.103060

Performance assessment of phylogenetic inference tools using PhyloSmew

Autori: Dimitri Höhler, Julia Haag, Alexey M Kozlov, Benoit Morel, Alexandros Stamatakis
Pubblicato in: Bioinformatics Advances, Numero 5, 2025, ISSN 2635-0041
Editore: Oxford University Press (OUP)
DOI: 10.1093/BIOADV/VBAF300

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

Autori: Julia Haag; Lukas Hübner; Alexey M. Kozlov; Alexandros Stamatakis
Pubblicato in: Bioinformatics Advances, 2022, ISSN 2635-0041
Editore: Oxford Academics
DOI: 10.1101/2022.07.13.499893

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

Autori: Anastasis Togkousidis, Oleksiy M Kozlov, Julia Haag, Dimitri Höhler, Alexandros Stamatakis
Pubblicato in: Molecular Biology and Evolution, Numero Volume 40, Numero 10, 2023, ISSN 1537-1719
Editore: Oxford Academic
DOI: 10.1093/molbev/msad227

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

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

Parameter Estimation and Species Tree Rooting Using ALE and GeneRax

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

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

Autori: Johanna Trost, Julia Haag, Dimitri Höhler, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau Author Notes
Pubblicato in: Molecular Biology and Evolution,, Numero Volume 41, Numero 1, 2024, ISSN 1537-1719
Editore: Oxford Academic
DOI: 10.1093/molbev/msad277

Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads

Autori: Ben Bettisworth; Nikolaos Psonis; Nikos Poulakakis; Pavlos Pavlidis; Alexandros Stamatakis
Pubblicato in: Molecular Biology and Evolution, 2025, ISSN 1537-1719
Editore: Oxford Academic
DOI: 10.1093/MOLBEV/MSAF006

Forensic Science International: Genetics

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

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

Autori: Häuser, Luise; Jäger, Gerhard; Stamatakis, Alexandros
Pubblicato in: Open Research Europe, 2025, ISSN 2732-5121
Editore: Open Research Europe
DOI: 10.12688/OPENRESEUROPE.20351.3

Necessary reforms in the Greek academic system

Autori: Alexandros Stamatakis; Alexandros Stamatakis; Alexandros Stamatakis; Panagiotis Tsakalides; Panagiotis Tsakalides; Melina Tamiolaki; Melina Tamiolaki; Melina Tamiolaki
Pubblicato in: Frontiers in Political Science, 2024, ISSN 2673-3145
Editore: frontiers
DOI: 10.5445/IR/1000177163

Phylourny: efficiently calculating elimination tournament win probabilities via phylogenetic methods

Autori: Ben Bettisworth, Alexander I. Jordan & Alexandros Stamatakis
Pubblicato in: Statistics and Computing, 2023, ISSN 0960-3174
Editore: 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

Autori: Benoit Morel, Tom A Williams, Alexandros Stamatakis, Gergely J Szöllősi
Pubblicato in: Bioinformatics, Numero Volume 40, Numero 4, 2024, ISSN 1367-4811
Editore: 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”

Autori: 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
Pubblicato in: Bioinformatics Advances, Numero 5, 2025, ISSN 2635-0041
Editore: Oxford University Press (OUP)
DOI: 10.1093/BIOADV/VBAF223

The power and limitations of species tree-aware phylogenetics

Autori: Tom A. Williams, Adrian A. Davin, Benoit Morel, Lenard L. Szantho, Anja Spang, Alexandros Stamatakis, Philip Hugenholtz, Gergely J. Szollosi
Pubblicato in: Evolutionary Biology, 2023, ISSN 2692-8205
Editore: biorXiv
DOI: 10.1101/2023.03.17.533068

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

Autori: Julia Haag; Alexander I. Jordan; Alexandros Stamatakis
Pubblicato in: Bioinformatics Advances, 2025, ISSN 2635-0041
Editore: Oxford Academic
DOI: 10.1093/BIOADV/VBAF040

Conference proceedings (3)

Parallel Inference of Phylogenetic Stands with Gentrius

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

Are Sounds Sound for Phylogenetic Reconstruction?

Autori: Luise Häuser, Gerhard Jäger, Taraka Rama, Johann-Mattis List, Alexandros Stamatakis
Pubblicato in: -, 2024, ISSN 2331-8422
Editore: Arxiv

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

Autori: Alexey Kozlov, Alexandros Stamatakis
Pubblicato in: ISC High Performance 2024 Research Paper Proceedings, Numero pp. 1-12, 2024, ISBN 978-3-9826336-0-2
Editore: Prometeus GmbH
DOI: 10.23919/ISC.2024.10528928.

Other (3)

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

Autori: Ben Bettisworth, Alexis Stamatakis
Pubblicato in: biorvix preprint, 2025, ISSN 2692-8205
Editore: biorvix
DOI: 10.1101/2025.11.24.690345

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

Autori: Julia Haag, Alexander I. Jordan, Alexandros Stamatakis
Pubblicato in: biorXiv preprint, 2024, ISSN 2692-8205
Editore: bioRxiv

Predicting Phylogenetic Bootstrap Values via Machine Learning

Autori: Julius Wiegert, Julia Haag, Dimitri Hoehler, Alexandros Stamatakis
Pubblicato in: bioRxiv preprint, 2024, ISSN 2692-8205
Editore: bioRxiv