From Foundations of Phylodynamics to New Applications in Cell Biology

Project Information

PhyCogy

Grant agreement ID: 101001077

DOI

10.3030/101001077

EC signature date 20 January 2021

Start date 1 June 2021

End date 31 May 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 999 540,00

EU contribution

€ 1 999 540,00

Coordinated by

EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Switzerland

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

Open Research Data Pilot (1)

Data Management Plan

Data Management Plan DMP

Publications

Thesis and dissertations (2)

Beyond the Binary: Generalised Trees for Phylodynamics

Author(s): Stolz, Ugne; id_orcid0000-0001-8610-9397
Published in: Issue 3, 2024
Publisher: ETH Zürich

Phylogenetic Methods in Single-Cell Biology

Author(s): Sophie Seidel
Published in: NO JOURNAL TITLE, 2024
Publisher: ETH Zürich
DOI: 10.3929/ethz-b-000674908

Peer reviewed articles (13)

TiDeTree: a Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data

Author(s): Sophie Seidel; Tanja Stadler
Published in: Proceedings of the Royal Society B: Biological Sciences, Issue 1986, 2022, ISSN 0962-8452
Publisher: Royal Society of London
DOI: 10.1098/rspb.2022.1844

Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations

Author(s): Jérémie Scire, Joëlle Barido-Sottani, Denise Kühnert, Timothy G. Vaughan, Tanja Stadler
Published in: Viruses, 2022, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14081648

EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering

Author(s): Ciara Judge, Timothy Vaughan, Timothy Russell, Sam Abbott, Louis du Plessis, Tanja Stadler, Oliver Brady, Sarah Hill
Published in: PLOS Computational Biology, Issue 20, 2024, Page(s) e1012528, ISSN 1553-7358
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/journal.pcbi.1012528

Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data

Author(s): Timothy G Vaughan, Tanja Stadler
Published in: Molecular Biology and Evolution, Issue 42, 2025, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaf130

HIV co-infection is associated with reduced Mycobacterium tuberculosis transmissibility in sub-Saharan Africa

Author(s): Etthel M. Windels, Eddie M. Wampande, Moses L. Joloba, W. Henry Boom, Galo A. Goig, Helen Cox,Jerry Hella, Sonia Borrell, Sebastien Gagneux, Daniela Brites, Tanja Stadler
Published in: PLOS Pathogens, 2024, ISSN 1553-7374
Publisher: PLOS
DOI: 10.1371/journal.ppat.1011675

The lives of cells, recorded

Author(s): Amjad Askary, Wei Chen, Junhong Choi, Lucia Y. Du, Michael B. Elowitz, James A. Gagnon, Alexander F. Schier, Sophie Seidel, Jay Shendure, Tanja Stadler, Martin Tran
Published in: Nature Reviews Genetics, Issue 26, 2025, Page(s) 203-222, ISSN 1471-0056
Publisher: Nature Publishing Group
DOI: 10.1038/s41576-024-00788-w

Strategies for resolving cellular phylogenies from sequential lineage tracing data

Author(s): Nicola Mulberry, Tanja Stadler
Published in: Theoretical Population Biology, Issue 168, 2026, Page(s) 32-43, ISSN 0040-5809
Publisher: Academic Press
DOI: 10.1016/j.tpb.2026.01.001

The Fossilized Birth–Death Model Is Identifiable

Author(s): Kate Truman, Timothy G Vaughan, Alex Gavryushkin, Alexandra “Sasha” Gavryushkina
Published in: Systematic Biology, Issue 74, 2025, Page(s) 112-123, ISSN 1063-5157
Publisher: Taylor & Francis
DOI: 10.1093/sysbio/syae058

Estimating epidemic dynamics with genomic and time series data

Author(s): Alexander E. Zarebski, Antoine Zwaans, Bernardo Gutierrez, Louis du Plessis, Oliver G. Pybus
Published in: Journal of The Royal Society Interface, Issue 22, 2025, ISSN 1742-5662
Publisher: The Royal Society
DOI: 10.1098/rsif.2024.0632

Estimating pathogen spread using structured coalescent and birth–death models: A quantitative comparison

Author(s): Sophie Seidel, Tanja Stadler, Timothy G. Vaughan
Published in: Epidemics, Issue 49, 2025, Page(s) 100795, ISSN 1755-4365
Publisher: Elsevier BV
DOI: 10.1016/j.epidem.2024.100795

Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages

Author(s): Etthel M. Windels, Cecilia Valenzuela Agüí, Bouke C. de Jong, Conor J. Meehan, Chloé Loiseau, Galo A. Goig, Michaela Zwyer, Sonia Borrell, Daniela Brites, Sebastien Gagneux, Tanja Stadler
Published in: Epidemics, Issue 51, 2025, Page(s) 100821, ISSN 1755-4365
Publisher: Elsevier BV
DOI: 10.1016/j.epidem.2025.100821

A Bayesian phylodynamic inference framework for single-cell CRISPR/Cas9 lineage tracing barcode data with dependent target sites

Author(s): A. Zwaans, S. Seidel, M. Manceau, T. Stadler
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, Issue 380, 2025, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2023.0318

Phylodynamic estimation of the within-host evolutionary rate of extended-spectrum beta-lactamase-producing Enterobacterales

Author(s): Etthel M. Windels, Lisandra Aguilar-Bultet, Isabelle Vock, Laura Maurer Pekerman, Sarah Tschudin-Sutter, Tanja Stadler
Published in: Microbial Genomics, Issue 11, 2025, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.001499

Other (9)

Integrating Transmission Dynamics and Pathogen Evolution Through a Bayesian Approach

Author(s): Ugne Stolz, Tana Stadler, Timothy G. Vaughan
Published in: bioRxiv, 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.04.15.589468

The Fossilised Birth-Death Model is Identifiable

Author(s): Kate Truman, Timothy G. Vaughan, Alex Gavryushkin, Alexandra Gavryushkina
Published in: bioRxiv, 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.02.08.579547

Single-cell phylodynamics reveal rapid late-stage colorectal cancer expansions

Author(s): Joao M Alves, Kylie Chen, Sonia Prado-López, Nuria Estévez-Gómez, Pilar Alvariño, Juana Alonso, Monica Valecha, Laura Tomás, Antoine Zwaans, Ugnė Stolz, Tanja Stadler, Debora Chantada, José Manuel Cameselle-Teijeiro, Alexei Drummond, David Posada
Published in: biorxiv, 2026
Publisher: openRxiv
DOI: 10.1101/2025.11.25.690378

Assessing the inference of single-cell phylogenies and population dynamics from genetic lineage tracing data

Author(s): Julia Pilarski, Tanja Stadler, Sophie Seidel
Published in: bioRxiv, 2026
Publisher: openRxiv
DOI: 10.1101/2025.01.08.631854

Bayesian phylodynamics of early vertebrate development in BEAST 2

Author(s): Antoine Zwaans, Sophie Seidel, Marc Manceau, Tanja Stadler
Published in: bioRxiv, 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.07.04.601658

Strategies for resolving cellular phylogenies from sequential lineage tracing data

Author(s): Nicola Mulberry, Tanja Stadler
Published in: bioRxiv, 2026
Publisher: openRxiv
DOI: 10.1101/2025.01.14.632902

Bayesian phylodynamics for developmental biology: incorporating age-dependence

Author(s): Nicola Mulberry, Julia Pilarski, Jana Dinger, Tanja Stadler
Published in: bioRxiv, 2026
Publisher: openRxiv
DOI: 10.1101/2025.08.28.672870

Enhancing Evolutionary Timelines: The Impact of Stratigraphic Range Information on Phylogenetic Inference

Author(s): Ugnė Stolz, Alexandra Gavryushkina, Timothy G. Vaughan, Tanja Stadler, Bethany J. Allen
Published in: bioRxiv, 2026
Publisher: openRxiv
DOI: 10.1101/2025.04.17.649084

EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering

Author(s): Ciara Judge, Timothy G. Vaughan, Timothy Russel, Sam Abbott, Louis du Plessis, Tanja Stadler, Oliver Brady, Sarah Hill
Published in: bioRxiv, 2024
Publisher: Cold Sprint Harbor Laboratory
DOI: 10.1101/2023.12.18.572106

Non-peer reviewed articles (1)

"""A mathematical theory of evolution"": phylogenetic models dating back 100 years"

Author(s): Noah A. Rosenberg, Tanja Stadler, Mike Steel
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, Issue 380, 2025, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2023.0297