Author

L. du Plessis

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Evolutionary Biology· 4 Microbiology· 2

Signature Assays, Organisms & Methods

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Approach:statistical model· 6 Assay:whole-genome sequencing· 4 Research Focus:phylogenetics / evolution· 3 Organism:virus· 2 Research Focus:chromatin & epigenetic regulation· 1 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

A. Rambaut· 3 shared J. McCrone· 2 shared O. Pybus· 2 shared T. Stadler· 2 shared V. Hill· 2 shared A. A. Fisher· 1 shared A. Carabelli· 1 shared A. Gavryushkina· 1 shared

Activity by Year

2018-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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3 shared papersEvolutionary Biology

A. Rambaut

Mutual co-authors in cluster

Author profile →

6 papers

Recent·Most cited

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

C. Judge, T. Vaughan, T. Russell, S. Abbott, L. du Plessis, T. Stadler, O. Brady, S. Hill

EpiFusion improves estimation of outbreak dynamics by integrating phylodynamic and epidemiological data using particle filtering, enhancing accuracy and efficiency in large, poorly sampled epidemics.

bioRxiv · Dec 18, 2023Evolutionary Biology

Insights into Treponema pallidum genomics from modern and ancient genomes using a novel mapping strategy

M. Pla-Diaz, G. Akguel, M. Molak, L. du Plessis, H. Panagiotopoulou, K. Doan, W. Bogdanowicz, P. Dabrowski, M. Oziemblowski, B. Kwiatkowska, J. Szczurowski, J. Grzelak, N. Arora, K. Majander, F. Gonzalez-Candelas, V. Schuenemann

This study evaluates the impact of reference genome choice on phylogenetic analysis of Treponema pallidum using a novel multiple-reference mapping strategy and ancient genomes.

bioRxiv · Feb 8, 2023 · PreprintMicrobiology

The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK

V. Hill, L. du Plessis, T. P. A. Peacock, D. Aggarwal, A. Carabelli, R. Colquhoun, N. Ellaby, E. Gallagher, N. Groves, B. Jackson, J. McCrone, A. N. O'Toole, A. Price, T. Sanderson, E. Scher, , A. Rambaut

This study investigates the origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 (Alpha) in the UK, finding that a chronically-infected immunocompetent individual likely drove its rapid mutation and spread.

bioRxiv · Mar 8, 2022Evolutionary Biology

Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing

S. Dellicour, S. Lequime, B. Vrancken, M. S. Gill, P. Bastide, K. Gangavarapu, N. L. Matteson, Y. Tan, L. du Plessis, A. A. Fisher, M. I. Nelson, M. Gilbert, M. A. Suchard, K. G. Andersen, N. D. Grubaugh, , P. Lemey

This study uses phylogeographic and phylodynamic methods to test hypotheses about West Nile virus dispersal and genetic diversity, finding temperature influences on spread and no strong evidence for migratory bird flyway restriction.

bioRxiv · Sep 19, 2020 · PreprintEvolutionary Biology

A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology

A. Rambaut, E. C. Holmes, V. Hill, A. OToole, J. McCrone, C. Ruis, L. du Plessis, O. Pybus

This paper proposes a dynamic nomenclature system for SARS-CoV-2 to improve genomic epidemiology by tracking active lineages and their spread.

bioRxiv · Apr 17, 2020Microbiology

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

R. Bouckaert, T. G. Vaughan, J. Barido-Sottani, S. Duchene, M. Fourment, A. Gavryushkina, J. Heled, G. Jones, D. Kuhnert, N. de Maio, M. Matschiner, F. K. Mendes, N. Muller, H. A. Ogilvie, L. du Plessis, , A. J. Drummond

The paper describes new developments in the BEAST 2.5 software platform for Bayesian evolutionary analysis, expanding joint inference over multiple data types and complex phylodynamics.

bioRxiv · Nov 19, 2018Evolutionary Biology