From Foundations of Phylodynamics to New Applications in Cell Biology

Información del proyecto

PhyCogy

Identificador del acuerdo de subvención: 101001077

DOI

10.3030/101001077

Fecha de la firma de la CE 20 Enero 2021

Fecha de inicio 1 Junio 2021

Fecha de finalización 31 Mayo 2026

Financiado con arreglo a

• EXCELLENT SCIENCE - European Research Council (ERC)

Coste total

€ 1 999 540,00

Aportación de la UE

€ 1 999 540,00

Coordinado por

EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Switzerland

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

Open Research Data Pilot (1)

Data Management Plan

Data Management Plan DMP

Publicaciones

Thesis and dissertations (2)

Beyond the Binary: Generalised Trees for Phylodynamics

Autores: Stolz, Ugne; id_orcid0000-0001-8610-9397
Publicado en: Edición 3, 2024
Editor: ETH Zürich

Phylogenetic Methods in Single-Cell Biology

Autores: Sophie Seidel
Publicado en: NO JOURNAL TITLE, 2024
Editor: 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

Autores: Sophie Seidel; Tanja Stadler
Publicado en: Proceedings of the Royal Society B: Biological Sciences, Edición 1986, 2022, ISSN 0962-8452
Editor: Royal Society of London
DOI: 10.1098/rspb.2022.1844

Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations

Autores: Jérémie Scire, Joëlle Barido-Sottani, Denise Kühnert, Timothy G. Vaughan, Tanja Stadler
Publicado en: Viruses, 2022, ISSN 1999-4915
Editor: 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

Autores: Ciara Judge, Timothy Vaughan, Timothy Russell, Sam Abbott, Louis du Plessis, Tanja Stadler, Oliver Brady, Sarah Hill
Publicado en: PLOS Computational Biology, Edición 20, 2024, Página(s) e1012528, ISSN 1553-7358
Editor: Public Library of Science (PLoS)
DOI: 10.1371/journal.pcbi.1012528

Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data

Autores: Timothy G Vaughan, Tanja Stadler
Publicado en: Molecular Biology and Evolution, Edición 42, 2025, ISSN 0737-4038
Editor: Oxford University Press
DOI: 10.1093/molbev/msaf130

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

Autores: 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
Publicado en: PLOS Pathogens, 2024, ISSN 1553-7374
Editor: PLOS
DOI: 10.1371/journal.ppat.1011675

The lives of cells, recorded

Autores: 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
Publicado en: Nature Reviews Genetics, Edición 26, 2025, Página(s) 203-222, ISSN 1471-0056
Editor: Nature Publishing Group
DOI: 10.1038/s41576-024-00788-w

Strategies for resolving cellular phylogenies from sequential lineage tracing data

Autores: Nicola Mulberry, Tanja Stadler
Publicado en: Theoretical Population Biology, Edición 168, 2026, Página(s) 32-43, ISSN 0040-5809
Editor: Academic Press
DOI: 10.1016/j.tpb.2026.01.001

The Fossilized Birth–Death Model Is Identifiable

Autores: Kate Truman, Timothy G Vaughan, Alex Gavryushkin, Alexandra “Sasha” Gavryushkina
Publicado en: Systematic Biology, Edición 74, 2025, Página(s) 112-123, ISSN 1063-5157
Editor: Taylor & Francis
DOI: 10.1093/sysbio/syae058

Estimating epidemic dynamics with genomic and time series data

Autores: Alexander E. Zarebski, Antoine Zwaans, Bernardo Gutierrez, Louis du Plessis, Oliver G. Pybus
Publicado en: Journal of The Royal Society Interface, Edición 22, 2025, ISSN 1742-5662
Editor: The Royal Society
DOI: 10.1098/rsif.2024.0632

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

Autores: Sophie Seidel, Tanja Stadler, Timothy G. Vaughan
Publicado en: Epidemics, Edición 49, 2025, Página(s) 100795, ISSN 1755-4365
Editor: Elsevier BV
DOI: 10.1016/j.epidem.2024.100795

Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages

Autores: 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
Publicado en: Epidemics, Edición 51, 2025, Página(s) 100821, ISSN 1755-4365
Editor: 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

Autores: A. Zwaans, S. Seidel, M. Manceau, T. Stadler
Publicado en: Philosophical Transactions of the Royal Society B: Biological Sciences, Edición 380, 2025, ISSN 0962-8436
Editor: 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

Autores: Etthel M. Windels, Lisandra Aguilar-Bultet, Isabelle Vock, Laura Maurer Pekerman, Sarah Tschudin-Sutter, Tanja Stadler
Publicado en: Microbial Genomics, Edición 11, 2025, ISSN 2057-5858
Editor: Microbiology Society
DOI: 10.1099/mgen.0.001499

Other (9)

Integrating Transmission Dynamics and Pathogen Evolution Through a Bayesian Approach

Autores: Ugne Stolz, Tana Stadler, Timothy G. Vaughan
Publicado en: bioRxiv, 2024
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.04.15.589468

The Fossilised Birth-Death Model is Identifiable

Autores: Kate Truman, Timothy G. Vaughan, Alex Gavryushkin, Alexandra Gavryushkina
Publicado en: bioRxiv, 2024
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.02.08.579547

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

Autores: 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
Publicado en: biorxiv, 2026
Editor: openRxiv
DOI: 10.1101/2025.11.25.690378

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

Autores: Julia Pilarski, Tanja Stadler, Sophie Seidel
Publicado en: bioRxiv, 2026
Editor: openRxiv
DOI: 10.1101/2025.01.08.631854

Bayesian phylodynamics of early vertebrate development in BEAST 2

Autores: Antoine Zwaans, Sophie Seidel, Marc Manceau, Tanja Stadler
Publicado en: bioRxiv, 2024
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.07.04.601658

Strategies for resolving cellular phylogenies from sequential lineage tracing data

Autores: Nicola Mulberry, Tanja Stadler
Publicado en: bioRxiv, 2026
Editor: openRxiv
DOI: 10.1101/2025.01.14.632902

Bayesian phylodynamics for developmental biology: incorporating age-dependence

Autores: Nicola Mulberry, Julia Pilarski, Jana Dinger, Tanja Stadler
Publicado en: bioRxiv, 2026
Editor: openRxiv
DOI: 10.1101/2025.08.28.672870

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

Autores: Ugnė Stolz, Alexandra Gavryushkina, Timothy G. Vaughan, Tanja Stadler, Bethany J. Allen
Publicado en: bioRxiv, 2026
Editor: 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

Autores: Ciara Judge, Timothy G. Vaughan, Timothy Russel, Sam Abbott, Louis du Plessis, Tanja Stadler, Oliver Brady, Sarah Hill
Publicado en: bioRxiv, 2024
Editor: 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"

Autores: Noah A. Rosenberg, Tanja Stadler, Mike Steel
Publicado en: Philosophical Transactions of the Royal Society B: Biological Sciences, Edición 380, 2025, ISSN 0962-8436
Editor: Royal Society of London
DOI: 10.1098/rstb.2023.0297