Strengthening Computational Biodiversity Research in Greece

Información del proyecto

Comp-Biodiv-GR

Identificador del acuerdo de subvención: 101087081

DOI

10.3030/101087081

Fecha de la firma de la CE 8 Noviembre 2022

Fecha de inicio 1 Enero 2023

Fecha de finalización 31 Diciembre 2027

Financiado con arreglo a

• Widening participation and spreading excellence

Coste total

€ 2 400 000,00

Aportación de la UE

€ 2 400 000,00

Coordinado por

IDRYMA TECHNOLOGIAS KAI EREVNAS
Greece

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

Documents, reports (3)

Report on newly established collaborations with regional and international networks
Curricula of regional training activities of regional talents
Report on COME Summer Schools, International Conferences, Workshops

Report on COME Summer Schools, International Conferences, Workshops

Websites, patent fillings, videos etc. (1)

Separate Project/BCG website

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

Other (1)

Published Position Paper

Publicaciones

Peer reviewed articles (24)

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

Autores: 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
Publicado en: Molecular Phylogenetics and Evolution, Edición 197:108091, 2024, ISSN 1095-9513
Editor: Elsevier science
DOI: 10.1016/j.ympev.2024.108091

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

Autores: Anastasis Togkousidis; Alexandros Stamatakis; Olivier Gascuel
Publicado en: Systematic Biology, 2025, ISSN 2692-8205
Editor: Oxford Academic
DOI: 10.1093/SYSBIO/SYAF043

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

Autores: Noah A Wahl , Georgios Koutsovoulos , Ben Bettisworth , Alexandros Stamatakis
Publicado en: Bioinformatics,, Edición 41, 12, 2025, ISSN 1367-4811
Editor: Oxford academic
DOI: 10.1093/BIOINFORMATICS/BTAF620

Complexity of avian evolution revealed by family-level genomes

Autores: 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,
Publicado en: Nature, 2024, ISSN 1476-4687
Editor: 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

Autores: Manos Stratakis, Panagiotis Ioannidis, Iliana Bista, Dominic Absolon, Will Eagles, Shane McCarthy, Amy Denton, Petros Lymberakis, Nikos Poulakakis
Publicado en: Genes & Genomics, Edición 48, 2026, ISSN 1976-9571
Editor: 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

Autores: 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.
Publicado en: The ISME Journal, 2024, ISSN 1751-7370
Editor: Oxford Academic
DOI: 10.5445/IR/1000173538

Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests

Autores: Lukas Hübner; Alexandros Stamatakis
Publicado en: ISSN: 1868-8969, 2024, ISSN 1868-8969
Editor: 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

Autores: Nikolaos Psonis, Despoina Vassou, Argyro Nafplioti, Eugenia Tabakaki, Pavlos Pavlidis, Alexandros Stamatakis, Nikos Poulakakis
Publicado en: Forensic Science International: Genetics, Edición 71, 2024, ISSN 1872-4973
Editor: Elsevier BV
DOI: 10.1016/J.FSIGEN.2024.103060

Performance assessment of phylogenetic inference tools using PhyloSmew

Autores: Dimitri Höhler, Julia Haag, Alexey M Kozlov, Benoit Morel, Alexandros Stamatakis
Publicado en: Bioinformatics Advances, Edición 5, 2025, ISSN 2635-0041
Editor: Oxford University Press (OUP)
DOI: 10.1093/BIOADV/VBAF300

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

Autores: Julia Haag; Lukas Hübner; Alexey M. Kozlov; Alexandros Stamatakis
Publicado en: Bioinformatics Advances, 2022, ISSN 2635-0041
Editor: Oxford Academics
DOI: 10.1101/2022.07.13.499893

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

Autores: Anastasis Togkousidis, Oleksiy M Kozlov, Julia Haag, Dimitri Höhler, Alexandros Stamatakis
Publicado en: Molecular Biology and Evolution, Edición Volume 40, Edición 10, 2023, ISSN 1537-1719
Editor: Oxford Academic
DOI: 10.1093/molbev/msad227

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

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

Parameter Estimation and Species Tree Rooting Using ALE and GeneRax

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

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

Autores: Johanna Trost, Julia Haag, Dimitri Höhler, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau Author Notes
Publicado en: Molecular Biology and Evolution,, Edición Volume 41, Edición 1, 2024, ISSN 1537-1719
Editor: Oxford Academic
DOI: 10.1093/molbev/msad277

Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads

Autores: Ben Bettisworth; Nikolaos Psonis; Nikos Poulakakis; Pavlos Pavlidis; Alexandros Stamatakis
Publicado en: Molecular Biology and Evolution, 2025, ISSN 1537-1719
Editor: Oxford Academic
DOI: 10.1093/MOLBEV/MSAF006

Forensic Science International: Genetics

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

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

Autores: Häuser, Luise; Jäger, Gerhard; Stamatakis, Alexandros
Publicado en: Open Research Europe, 2025, ISSN 2732-5121
Editor: Open Research Europe
DOI: 10.12688/OPENRESEUROPE.20351.3

Necessary reforms in the Greek academic system

Autores: Alexandros Stamatakis; Alexandros Stamatakis; Alexandros Stamatakis; Panagiotis Tsakalides; Panagiotis Tsakalides; Melina Tamiolaki; Melina Tamiolaki; Melina Tamiolaki
Publicado en: Frontiers in Political Science, 2024, ISSN 2673-3145
Editor: frontiers
DOI: 10.5445/IR/1000177163

Phylourny: efficiently calculating elimination tournament win probabilities via phylogenetic methods

Autores: Ben Bettisworth, Alexander I. Jordan & Alexandros Stamatakis
Publicado en: Statistics and Computing, 2023, ISSN 0960-3174
Editor: 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

Autores: Benoit Morel, Tom A Williams, Alexandros Stamatakis, Gergely J Szöllősi
Publicado en: Bioinformatics, Edición Volume 40, Edición 4, 2024, ISSN 1367-4811
Editor: 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”

Autores: 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
Publicado en: Bioinformatics Advances, Edición 5, 2025, ISSN 2635-0041
Editor: Oxford University Press (OUP)
DOI: 10.1093/BIOADV/VBAF223

Predicting Phylogenetic Bootstrap Values via Machine Learning

Autores: Wiegert, Julius; Höhler, Dimitri; Haag, Julia; Stamatakis, Alexandros; Rzhetsky, Andrey
Publicado en: Molecular Biology and Evolution, 2024, ISSN 1537-1719
Editor: Oxford Academic
DOI: 10.1101/2024.03.04.583288

The power and limitations of species tree-aware phylogenetics

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

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

Autores: Julia Haag; Alexander I. Jordan; Alexandros Stamatakis
Publicado en: Bioinformatics Advances, 2025, ISSN 2635-0041
Editor: Oxford Academic
DOI: 10.1093/BIOADV/VBAF040

Conference proceedings (3)

Parallel Inference of Phylogenetic Stands with Gentrius

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

Are Sounds Sound for Phylogenetic Reconstruction?

Autores: Luise Häuser, Gerhard Jäger, Taraka Rama, Johann-Mattis List, Alexandros Stamatakis
Publicado en: -, 2024, ISSN 2331-8422
Editor: Arxiv

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

Autores: Alexey Kozlov, Alexandros Stamatakis
Publicado en: ISC High Performance 2024 Research Paper Proceedings, Edición pp. 1-12, 2024, ISBN 978-3-9826336-0-2
Editor: Prometeus GmbH
DOI: 10.23919/ISC.2024.10528928.

Other (3)

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

Autores: Ben Bettisworth, Alexis Stamatakis
Publicado en: biorvix preprint, 2025, ISSN 2692-8205
Editor: biorvix
DOI: 10.1101/2025.11.24.690345

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

Autores: Julia Haag, Alexander I. Jordan, Alexandros Stamatakis
Publicado en: biorXiv preprint, 2024, ISSN 2692-8205
Editor: bioRxiv

Predicting Phylogenetic Bootstrap Values via Machine Learning

Autores: Julius Wiegert, Julia Haag, Dimitri Hoehler, Alexandros Stamatakis
Publicado en: bioRxiv preprint, 2024, ISSN 2692-8205
Editor: bioRxiv