Evidence map›Paper›PMID 39253641›Full record

ArticleArXiv2024

On the importance of assessing topological convergence in Bayesian phylogenetic inference.

Marius Brusselmans, Luiz Max Carvalho, Samuel L Hong, Jiansi Gao, Frederick A Matsen, Andrew Rambaut, Philippe Lemey, Marc A Suchard, Gytis Dudas, Guy Baele

Abstract readPreprint
In one paragraph

Article in ArXiv, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Marius BrusselmansDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
Luiz Max CarvalhoSchool of Applied Mathematics, Getulio Vargas Foundation, Praia de Botafogo, 190, 22250-900, Rio de Janeiro, Brazil.
Samuel L HongDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
Jiansi GaoComputational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
Frederick A MatsenHoward Hughes Medical Institute, Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.ORCID 0000-0003-0607-6025
Andrew RambautInstitute of Ecology and Evolution, University of Edinburgh, Edinburgh, EH9, 3FL, UK.
Philippe LemeyDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
Marc A SuchardDepartment of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA.
Gytis DudasInstitute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
Guy BaeleDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.ORCID 0000-0002-1915-7732

Funding

Fast and flexible Bayesian phylogenetics via modern machine learningR01AI162611 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI MATSEN, FREDERICK ALBERT · 2021 to 2025
$3.8M
Statistical Innovation to Integrate Sequences and Phenotypes for Scalable Phylodynamic InferenceR01AI153044 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Marc A. Suchard · 2021 to 2026
$2.4M
NIAID NIH HHS R01 AI153044NIAID NIH HHS R01 AI162611Wellcome Trust
6 · The paper itself

Abstract

Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution. These algorithms require careful evaluation of the quality of the generated samples. Within the field of phylogenetics, one frequently adopted diagnostic approach is to evaluate the

Indexed as

Bayesian inferenceconvergenceEBOVeffective sample sizeHIVmixingphylodynamicsphylogeneticstopologies

Identifiers

PMID39253641
PMCPMC11383445

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.