Dr Louis du Plessis

Research Interests

I analyse signatures left in pathogen genomes by the spread and adaptation of infectious diseases. In particular, I am interested in the potential of phylodynamic methods to produce rapid and accurate inferences of key epidemiological parameters and inform public health policy during emerging and re-emerging infectious disease outbreaks. I also investigate the limitations of current methods and identify scenarios where inferences are unreliable. To address such biases, I aim to develop methods that draw on different data sources to improve the robustness and reliability of conclusions. Finally, I am interested in finding ways to better visualise and communicate results to both scientists and non-scientists alike. 

Selected Publications

Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kuhnert D, de Maio N, Matschiner M, Mendes FK, Muller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen DA, Siveroni I, Suchard M, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ (2019) BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis. PLoS Computational Biology. In press.

Vasylyeva TI, du Plessis L, Pineda-Peña AC, Kühnert D, LemeyP,  Vandamme AM, Gomes P, Camacho RJ, Pybus OG, Abecasis AB, Faria NR (2019) Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology. Journal of Infectious Diseases. In press.

Vasylyeva TI, Liulchuk M, du Plessis L, Fearnhill E, Zadorozhna V, Babii N, Scherbinska A, Novitsky V, Pybus OG, Faria NR (2019) The changing epidemiological profile of HIV-1 subtype B epidemic in Ukraine. AIDS Research and Human Retroviruses 35(2):155-163

Faria NR, Kraemer MUG, Hill SC, Goes de Jesus J, de Aguiar RS, Iani FCM, Xavier J, Quick J, du Plessis L, Dellicour S, Thézé J, Carvalho RDO , Baele G, Wu C-H, Silveira PP, Arruda MB, Pereira MA, Pereira GC, Lourenço J, Obolski U, Abade L, Vasylyeva TI, Giovanetti M, Yi D, Weiss DJ, Wint GRW, Shearer FM, Funk S, Nikolai B, Fonseca V, Adelino TER, Oliveira MAA, Silva MVF, Sacchetto L, Figueiredo PO, Rezende IM, Mello EM, Said RFC, Santos DA, Ferraz ML, Brito MG, Santana LF, Menezes MT, Brindeiro RM, Tanuri A, dos Santos FCP, Cunha MS, Nogueira JS, Rocco IM, da Costa AC, Komninakis SCV, Azevedo V, Chieppe AO, Araujo ESM, Mendonça MCL, dos Santos CC, dos Santos CD, Mares-Guia AM, Nogueira RMR, Sequeira PC, Abreu RG, Garcia MHO, Abreu AL, Okumoto O, Kroon EG, de Albuquerque CFC, Lewandowski K, Pullan ST, Carroll M, de Oliveira T, Sabino EC, Souza RP, Suchard MA, Lemey P, Trindade GS, Drumond BP, Filippis AMB, Loman NJ, Cauchemez S, Alcantara LCJ, Pybus OG(2018) Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science 361:894–99

Thézé J, Li T, du Plessis L, Bouquet J, Kraemer MUG, Somasekar S, Yu G, de Cesare M, Balmaseda A, Kuan G, Harris E, Wu CH, Ansari MA, Bowden R, Faria NR, Yagi S, Messenger S, Brooks T, Stone M, Bloch EM, Busch M, Muñoz-Medina JE, González-Bonilla CR, Wolinsky S, López S, Arias CF, Bonsall D, Chiu CY, Pybus OG (2018) Genomic epidemiology reconstructs the introduction and spread of Zika virus in Central America and Mexico. Cell host & microbe 23(6).

Möller S*, du Plessis L*, Stadler T (2018) The impact of the tree prior on estimating clock rates during epidemic outbreaks. Proceedings of the National Academy of Sciences of the United States of America 115(16):4200-4205

Schmid-Hempel P, Aebi M, Barribeau SM, Kitajima T, du Plessis L, Schmid-Hempel R, Zoller S (2018) The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees. PLoS ONE 13(1): e0189738. 

Barido-Sottani J*, Bošková V*, du Plessis L*, Kühnert D*, Magnus C*, Mitov V*, Müller NF*, Pecerska J*, Rasmussen DA*, Zhang C*, Drummond AJ, Heath TA, Pybus OG, Vaughan TG, Stadler T (2018) Taming the BEAST - A community teaching material resource for BEAST 2. Systematic Biology 67:170–4

Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET Jr, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MR, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG (2017) Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature 546:406-10 

du Plessis L, Leventhal GE, Bonhoeffer S (2016) How good Are statistical models at approximating complex fitness landscapes? Molecular Biology & Evolution 33:2454-6

du Plessis L, Stadler T (2015) Getting to the root of epidemic spread with phylodynamic analysis of genomic data. Trends in Microbiology 23:383-6 

Barribeau SM, Sadd BM, du Plessis L, Brown MJ, Buechel SD, Cappelle K, Carolan JC, Christiaens O, Colgan TJ, Erler S, Evans J, Helbing S, Karaus E, Lattorff HM, Marxer M, Meeus I, Näpflin K, Niu J, Schmid-Hempel R, Smagghe G, Waterhouse RM, Yu N, Zdobnov EM, Schmid-Hempel P (2015) A depauperate immune repertoire precedes evolution of sociality in bees. Genome Biology 16:83 

Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJ, Hasselmann M, Let al. (2015) The genomes of two key bumblebee species with primitive eusocial organization. Genome Biology 16:76 

Stadler T, Kühnert D, Rasmussen DA, du Plessis L (2014) Insights into the early epidemic spread of Ebola in Sierra Leone provided by viral sequence data. PLoS Currents DOI: 10.1371/currents.outbreaks.02bc6d927ecee7bbd33532ec8ba 6a25f

Barribeau SM, Sadd BM, du Plessis L, Schmid-Hempel P (2014) Gene expression differences underlying genotype-by-genotype specificity in a host-parasite system. Proceedings of the National Academy of Sciences of the United States of America 111(9):3496-3501 

du Plessis L, Škunca N, Dessimoz C (2011) The what, where, how and why of gene ontology--a primer for bioinformaticians. Briefings in Bioinformatics 12:723-35 

List of site pages