Imperial College London

DrThibautJombart

Faculty of MedicineSchool of Public Health

Senior Lecturer
 
 
 
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Contact

 

+44 (0)20 7594 3658t.jombart Website

 
 
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Location

 

UG11Norfolk PlaceSt Mary's Campus

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Summary

 

Publications

Publication Type
Year
to

74 results found

Jombart T, Kamvar ZN, Cai J, Pulliam J, Chisholm S, Fitzjohn R, Schumacher J, Bhatia Set al., 2019, reconhub/incidence: Incidence version 1.7.0

Incidence can now handle standardised weeks starting on any day thanks to the aweek package :tada:library(incidence)library(ggplot2)library(cowplot)d <- as.Date("2019-03-11") + -7:6setNames(d, weekdays(d))#> Monday Tuesday Wednesday Thursday Friday #> "2019-03-04" "2019-03-05" "2019-03-06" "2019-03-07" "2019-03-08" #> Saturday Sunday Monday Tuesday Wednesday #> "2019-03-09" "2019-03-10" "2019-03-11" "2019-03-12" "2019-03-13" #> Thursday Friday Saturday Sunday #> "2019-03-14" "2019-03-15" "2019-03-16" "2019-03-17"imon <- incidence(d, "mon week") # also ISO weekitue <- incidence(d, "tue week")iwed <- incidence(d, "wed week")ithu <- incidence(d, "thu week")ifri <- incidence(d, "fri week")isat <- incidence(d, "sat week")isun <- incidence(d, "sun week") # also MMWR week and EPI weekpmon <- plot(imon, show_cases = TRUE, labels_week = FALSE)ptue <- plot(itue, show_cases = TRUE, labels_week = FALSE)pwed <- plot(iwed, show_cases = TRUE, labels_week = FALSE)pthu <- plot(ithu, show_cases = TRUE, labels_week = FALSE)pfri <- plot(ifri, show_cases = TRUE, labels_week = FALSE)psat <- plot(isat, show_cases = TRUE, labels_week = FALSE)psun <- plot(isun, show_cases = TRUE, labels_week = FALSE)s <- scale_x_date(limits = c(as.Date("2019-02-26"), max(d) + 7L))plot_grid(pmon + s,ptue + s,pwed + s,pthu + s,pfri + s,psat + s,psun + s)multi-weeks/months/years can now be handledlibrary(incidence)library(outbreaks)d <- ebola_sim_clean$linelist$date_of_onseth <- ebola_sim_clean$linelist$hospitalplot(incidence(d, interval = "1 epiweek", group = h))plot(incidence(d, interval = "2 epiweeks", group = h))plot(incide

SOFTWARE

Campbell F, Cori A, Ferguson N, Jombart Tet al., 2019, Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data., PLoS Comput Biol, Vol: 15

There exists significant interest in developing statistical and computational tools for inferring 'who infected whom' in an infectious disease outbreak from densely sampled case data, with most recent studies focusing on the analysis of whole genome sequence data. However, genomic data can be poorly informative of transmission events if mutations accumulate too slowly to resolve individual transmission pairs or if there exist multiple pathogens lineages within-host, and there has been little focus on incorporating other types of outbreak data. We present here a methodology that uses contact data for the inference of transmission trees in a statistically rigorous manner, alongside genomic data and temporal data. Contact data is frequently collected in outbreaks of pathogens spread by close contact, including Ebola virus (EBOV), severe acute respiratory syndrome coronavirus (SARS-CoV) and Mycobacterium tuberculosis (TB), and routinely used to reconstruct transmission chains. As an improvement over previous, ad-hoc approaches, we developed a probabilistic model that relates a set of contact data to an underlying transmission tree and integrated this in the outbreaker2 inference framework. By analyzing simulated outbreaks under various contact tracing scenarios, we demonstrate that contact data significantly improves our ability to reconstruct transmission trees, even under realistic limitations on the coverage of the contact tracing effort and the amount of non-infectious mixing between cases. Indeed, contact data is equally or more informative than fully sampled whole genome sequence data in certain scenarios. We then use our method to analyze the early stages of the 2003 SARS outbreak in Singapore and describe the range of transmission scenarios consistent with contact data and genetic sequence in a probabilistic manner for the first time. This simple yet flexible model can easily be incorporated into existing tools for outbreak reconstruction and should permit a bet

JOURNAL ARTICLE

Kamvar Z, Cai J, Pulliam JRC, Schumacher J, Jombart Tet al., 2019, Epidemic curves made easy using the R package incidence

The epidemiological curve (epicurve) is one of the simplest yet most useful tools used by field epidemiologists, modellers, and decision makers for assessing the dynamics of infectious disease epidemics. Here, we present the free, open-source package incidence for the R programming language, which allows users to easily compute, handle, and visualise epicurves from unaggregated linelist data. This package was built in accordance with the development guidelines of the R Epidemics Consortium (RECON), which aim to ensure robustness and reliability through extensive automated testing, documentation, and good coding practices. As such, it fills an important gap in the toolbox for outbreak analytics using the R software, and provides a solid building block for further developments in infectious disease modelling. incidence is available from https://www.repidemicsconsortium.org/incidence .

JOURNAL ARTICLE

Jombart T, Kamvar ZN, Cai J, Pulliam J, Chisholm S, Fitzjohn R, Schumacher J, Bhatia Set al., 2019, reconhub/incidence 1.5

☣:chart_with_upwards_trend::chart_with_downwards_trend:☣ Compute and visualise incidence

SOFTWARE

Jombart T, Kamvar Z, Cai J, Chisholm S, Fitzjohn R, Schumacher J, Bhatia Set al., 2018, reconhub/incidence: Incidence version 1.5.3

This is a patch release that fixes an issue with handling single-group incidence curves.You can install this version like so:remotes::install_github("reconhub/incidence@1.5.3")

SOFTWARE

Cori A, Nouvellet P, Garske T, Bourhy H, Nakoune E, Jombart Tet al., 2018, A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies, PLOS COMPUTATIONAL BIOLOGY, Vol: 14, ISSN: 1553-7358

JOURNAL ARTICLE

Campbell F, Didelot X, Fitzjohn R, Ferguson N, Cori A, Jombart Tet al., 2018, outbreaker2: a modular platform for outbreak reconstruction, BMC BIOINFORMATICS, Vol: 19, ISSN: 1471-2105

JOURNAL ARTICLE

Moraga P, Dorigatti I, Kamvar Z, Piatkowski P, Toikkanen S, Nagraj VP, Donnelly C, Jombart Tet al., 2018, epiflows: an R package for risk assessment of travel-related spread of disease

As international travel increases worldwide, new surveillance tools are needed to help identify locations where diseases are most likely to be spread and prevention measures need to be implemented. In this paper we present epiflows, an R package for risk assessment of travel-related spread of disease. epiflows produces estimates of the expected number of symptomatic and/or asymptomatic infections that could be introduced to other locations from the source of infection. Estimates (average and confidence intervals) of the number of infections introduced elsewhere are obtained by integrating data on the cumulative number of cases reported, population movement, length of stay and information on the distributions of the incubation and infectious periods of the disease. The package also provides tools for geocoding and visualization. We illustrate the use of epiflows by assessing the risk of travel-related spread of yellow fever cases in Southeast Brazil in December 2016 to May 2017.

JOURNAL ARTICLE

Nagraj VP, Randhawa N, Campbell F, Crellen T, Sudre B, Jombart Tet al., 2018, epicontacts: Handling, visualisation and analysis of epidemiological contacts

Epidemiological outbreak data is often captured in line list and contact format to facilitate contact tracing for outbreak control. epicontacts is an R package that provides a unique data structure for combining these data into a single object in order to facilitate more efficient visualisation and analysis. The package incorporates interactive visualisation functionality as well as network analysis techniques. Originally developed as part of the Hackout3 event, it is now developed, maintained and featured as part of the R Epidemics Consortium (RECON). The package is available for download from the Comprehensive R Archive Network (CRAN) and GitHub .

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Beugin M-P, Gayet T, Pontier D, Devillard S, Jombart Tet al., 2018, A fast likelihood solution to the genetic clustering problem, METHODS IN ECOLOGY AND EVOLUTION, Vol: 9, Pages: 1006-1016, ISSN: 2041-210X

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Nouvellet P, Cori A, Garske T, Blake IM, Dorigatti I, Hinsley W, Jombart T, Mills HL, Nedjati-Gilani G, Van Kerkhove MD, Fraser C, Donnelly CA, Ferguson NM, Riley Set al., 2018, A simple approach to measure transmissibility and forecast incidence, EPIDEMICS, Vol: 22, Pages: 29-35, ISSN: 1755-4365

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Dupuis JR, Bremer FT, Jombart T, Sim SB, Geib SMet al., 2018, mvmapper: Interactive spatial mapping of genetic structures, MOLECULAR ECOLOGY RESOURCES, Vol: 18, Pages: 362-367, ISSN: 1755-098X

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Campbell F, Strang C, Ferguson N, Cori A, Jombart Tet al., 2018, When are pathogen genome sequences informative of transmission events?, PLOS PATHOGENS, Vol: 14, ISSN: 1553-7366

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Montano V, Jombart T, 2017, An Eigenvalue test for spatial principal component analysis, BMC BIOINFORMATICS, Vol: 18, ISSN: 1471-2105

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Jombart T, Kendall M, Almagro-Garcia J, Colijn Cet al., 2017, treespace: Statistical exploration of landscapes of phylogenetic trees, MOLECULAR ECOLOGY RESOURCES, Vol: 17, Pages: 1385-1392, ISSN: 1755-098X

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Cori A, Donnelly CA, Dorigatti I, Ferguson NM, Fraser C, Garske T, Jombart T, Nedjati-Gilani G, Nouvellet P, Riley S, Van Kerkhove MD, Mills HL, Blake IMet al., 2017, Key data for outbreak evaluation: building on the Ebola experience, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 372, ISSN: 0962-8436

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Garske T, Cori A, Ariyarajah A, Blake IM, Dorigatti I, Eckmanns T, Fraser C, Hinsley W, Jombart T, Mills HL, Nedjati-Gilani G, Newton E, Nouvellet P, Perkins D, Riley S, Schumacher D, Shah A, Van Kerkhove MD, Dye C, Ferguson NM, Donnelly CAet al., 2017, Heterogeneities in the case fatality ratio in the West African Ebola outbreak 2013-2016, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 372, ISSN: 0962-8436

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Bertranpetit E, Jombart T, Paradis E, Pena H, Dubey J, Su C, Mercier A, Devillard S, Ajzenberg Det al., 2017, Phylogeography of Toxoplasma gondii points to a South American origin, INFECTION GENETICS AND EVOLUTION, Vol: 48, Pages: 150-155, ISSN: 1567-1348

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Inns T, Ashton PM, Herrera-Leon S, Lighthill J, Foulkes S, Jombart T, Rehman Y, Fox A, Dallman T, De Pinna E, Browning L, Coia JE, Edeghere O, Vivancos Ret al., 2017, Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis, EPIDEMIOLOGY AND INFECTION, Vol: 145, Pages: 289-298, ISSN: 0950-2688

JOURNAL ARTICLE

Jombart T, Archer F, Schliep K, Kamvar Z, Harris R, Paradis E, Goudet J, Lapp Het al., 2017, apex: phylogenetics with multiple genes, MOLECULAR ECOLOGY RESOURCES, Vol: 17, Pages: 19-26, ISSN: 1755-098X

JOURNAL ARTICLE

Paradis E, Gosselin T, Grunwald NJ, Jombart T, Manel S, Lapp Het al., 2017, Towards an integrated ecosystem of R packages for the analysis of population genetic data, MOLECULAR ECOLOGY RESOURCES, Vol: 17, Pages: 1-4, ISSN: 1755-098X

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Paradis E, Gosselin T, Goudet J, Jombart T, Schliep Ket al., 2017, Linking genomics and population genetics with R, MOLECULAR ECOLOGY RESOURCES, Vol: 17, Pages: 54-66, ISSN: 1755-098X

JOURNAL ARTICLE

Clare FC, Halder JB, Daniel O, Bielby J, Semenov MA, Jombart T, Loyau A, Schmeller DS, Cunningham AA, Rowcliffe M, Garner TWJ, Bosch J, Fisher MCet al., 2016, Climate forcing of an emerging pathogenic fungus across a montane multi-host community, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 371, ISSN: 0962-8436

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Agua-Agum J, Ariyarajah A, Aylward B, Bawo L, Bilivogui P, Blake IM, Brennan RJ, Cawthorne A, Cleary E, Clement P, Conteh R, Cori A, Dafae F, Dahl B, Dangou J-M, Diallo B, Donnelly CA, Dorigatti I, Dye C, Eckmanns T, Fallah M, Ferguson NM, Fiebig L, Fraser C, Garske T, Gonzalez L, Hamblion E, Hamid N, Hersey S, Hinsley W, Jambei A, Jombart T, Kargbo D, Keita S, Kinzer M, George FK, Godefroy B, Gutierrez G, Kannangarage N, Mills HL, Moller T, Meijers S, Mohamed Y, Morgan O, Nedjati-Gilani G, Newton E, Nouvellet P, Nyenswah T, Perea W, Perkins D, Riley S, Rodier G, Rondy M, Sagrado M, Savulescu C, Schafer IJ, Schumacher D, Seyler T, Shah A, Van Kerkhove MD, Wesseh CS, Yoti Zet al., 2016, Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study, PLOS MEDICINE, Vol: 13, ISSN: 1549-1676

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Agua-Agum J, Allegranzi B, Ariyarajah A, Aylward RB, Blake IM, Barboza P, Bausch D, Brennan RJ, Clement P, Coffey P, Cori A, Donnelly CA, Dorigatti I, Drury P, Durski K, Dye C, Eckmanns T, Ferguson NM, Fraser C, Garcia E, Garske T, Gasasira A, Gurry C, Gutierrez GJ, Hamblion E, Hinsley W, Holden R, Holmes D, Hugonnet S, Jombart T, Kelley E, Santhana R, Mahmoud N, Mills HL, Mohamed Y, Musa E, Naidoo D, Nedjati-Gilani G, Newton E, Norton I, Nouvellet P, Perkins D, Perkins M, Riley S, Schumacher D, Shah A, Minh T, Varsaneux O, Van Kerkhove MDet al., 2016, After Ebola in West Africa - Unpredictable Risks, Preventable Epidemics, NEW ENGLAND JOURNAL OF MEDICINE, Vol: 375, Pages: 587-596, ISSN: 0028-4793

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Cauchemez S, Nouvellet P, Cori A, Jombart T, Garske T, Clapham H, Moore S, Mills HL, Salje H, Collins C, Rodriquez-Barraquer I, Riley S, Truelove S, Algarni H, Alhakeem R, AlHarbi K, Turkistani A, Aguas RJ, Cummings DAT, Van Kerkhove MD, Donnelly CA, Lessler J, Fraser C, Al-Barrak A, Ferguson NMet al., 2016, Unraveling the drivers of MERS-CoV transmission, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 113, Pages: 9081-9086, ISSN: 0027-8424

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Dallman T, Inns T, Jombart T, Ashton P, Loman N, Chatt C, Messelhaeusser U, Rabsch W, Simon S, Nikisins S, Bernard H, le Hello S, da-Silva NJ, Kornschober C, Mossong J, Hawkey P, De Pinna E, Grant K, Cleary Pet al., 2016, Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network, MICROBIAL GENOMICS, Vol: 2, ISSN: 2057-5858

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Finnie TJR, South A, Bento A, Sherrard-Smith E, Jombart Tet al., 2016, EpiJSON: A unified data-format for epidemiology, EPIDEMICS, Vol: 15, Pages: 20-26, ISSN: 1755-4365

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Lessler J, Salje H, Van Kerkhove MD, Ferguson NM, Cauchemez S, Rodriquez-Barraquer I, Hakeem R, Jombart T, Aguas R, Al-Barrak A, Cummings DATet al., 2016, Estimating the Severity and Subclinical Burden of Middle East Respiratory Syndrome Coronavirus Infection in the Kingdom of Saudi Arabia, AMERICAN JOURNAL OF EPIDEMIOLOGY, Vol: 183, Pages: 657-663, ISSN: 0002-9262

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Agua-Agum J, Ariyarajah A, Blake IM, Cori A, Donnelly CA, Dorigatti I, Dye C, Eck-Manns T, Ferguson NM, Fraser C, Garske T, Hinsley W, Jombart T, Mills HL, Nedjati-Gilani G, Newton E, Nouvellet P, Perkins D, Riley S, Schumacher D, Shah A, Thomas LJ, Van Kerkhove MDet al., 2016, Ebola Virus Disease among Male and Female Persons in West Africa, NEW ENGLAND JOURNAL OF MEDICINE, Vol: 374, Pages: 96-98, ISSN: 0028-4793

JOURNAL ARTICLE

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