As of November 2017, I have decided to promote open, transparent publishing, i.e. publishing in which:

  • papers are freely available to the community
  • reviews are fully published
  • referees are explicitly named

I no longer review for, edit for, or submit my research papers to journals which do no fulfil these criteria.

Statistics

These were last updated on the 07-01-2019.

web of science:

  • citations: 7,857
  • h-index: 28

Google scholar:

  • citations: 10,510
  • h-index: 31
  • h10-index: 49

List of publications

This list was last updated on the 07-01-2019.

  • Polonsky JA, Baidjoe A, Kamvar ZN, Cori A, Durski K, Edmunds JW, Eggo RM, Funk S, Kaiser L, Keating P, le Polain de Waroux O, Marks M, Moraga P, Morgan O, Nouvellet P, Ratnayake R, Roberts CH, Whitworth J & Jombart T (accepted). Outbreak analytics: a developing data science for informing the response to emerging pathogens Philosophical Transactions B
  • Cori A, Nouvellet P, Garske T, Bourhy H, Nakouné E & Jombart T (accepted). A graph-based evidence synthesis approach to detecting outbreak clusters: an application to dog rabies PLoS Computational Biology
  • Campbell F, Didelot X, FitzJohn R, Ferguson N, Cori A & Jombart T (2018). outbreaker2: a modular platform for outbreak reconstruction BMC Bioinformatics doi:10.1186/s12859-018-2330-z
  • Campbell, F., Strang, C., Ferguson, N., Cori, A. & Jombart, T. (2018). When are pathogen genome sequences informative of transmission events? PLoS Pathogens doi:10.1371/journal.ppat.1006885
  • Montano, V., & Jombart, T. (2017). An Eigenvalue test for spatial principal component analysis. BMC Bioinformatics, 18(1), 562. doi:10.1186/s12859-017-1988-y
  • Paradis, E., Gosselin, T., Grunwald, N. J., Jombart, T., Manel, S., & Lapp, H. (2017). Towards an integrated ecosystem of R packages for the analysis of population genetic data. Molecular Ecology Resources, 17(1), 1-4. doi:10.1111/1755-0998.12636
  • Dupuis, J. R., Bremer, F. T., Jombart, T., Sim, S. B., & Geib, S. M. (2017). mvmapper: Interactive spatial mapping of genetic structures.. Mol Ecol Resour. doi:10.1111/1755-0998.12724
  • Jombart, T., Kendall, M., Almagro-Garcia, J., & Colijn, C. (2017). treespace: Statistical exploration of landscapes of phylogenetic trees. Molecular Ecology Resources, 17(6), 1385-1392. doi:10.1111/1755-0998.12676
  • Cori, A., Donnelly, C. A., Dorigatti, I., Ferguson, N. M., Fraser, C., Garske, T., ... Blake, I. M. (2017). Key data for outbreak evaluation: building on the Ebola experience. Philosophical Transactions of the Royal Society B-Biological Sciences, 372(1721), 14 pages. doi:10.1098/rstb.2016.0371
  • Garske, T., Cori, A., Ariyarajah, A., Blake, I. M., Dorigatti, I., Eckmanns, T., ... Donnelly, C. A. (2017). Heterogeneities in the case fatality ratio in the West African Ebola outbreak 2013-2016. Philosophical Transactions of the Royal Society B-Biological Sciences, 372(1721), 9 pages. doi:10.1098/rstb.2016.0308
  • Nouvellet, P., Cori, A., Garske, T., Blake, I. M., Dorigatti, I., Hinsley, W., ... Riley, S. (2017). A simple approach to measure transmissibility and forecast incidence.. Epidemics. doi:10.1016/j.epidem.2017.02.012
  • Bertranpetit, E., Jombart, T., Paradis, E., Pena, H., Dubey, J., Su, C., ... Ajzenberg, D. (2017). Phylogeography of Toxoplasma gondii points to a South American origin. Infection Genetics and Evolution, 48, 150-155. doi:10.1016/j.meegid.2016.12.020
  • Agua-Agum, J., Ariyarajah, A., Aylward, B., Bawo, L., Bilivogui, P., Blake, I. M., ... Yoti, Z. (2016). Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study. PLoS Medicine, 13(11), 23 pages. doi:10.1371/journal.pmed.1002170
  • Inns, T., Ashton, P. M., Herrera-Leon, S., Lighthill, J., Foulkes, S., Jombart, T., ... Vivancos, R. (2017). Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis. EPIDEMIOLOGY AND INFECTION, 145(2), 289-298. doi:10.1017/S0950268816001941
  • Clare, F. C., Halder, J. B., Daniel, O., Bielby, J., Semenov, M. A., Jombart, T., ... Fisher, M. C. (2016). Climate forcing of an emerging pathogenic fungus across a montane multi-host community. Philosophical Transactions of the Royal Society B-Biological Sciences, 371(1709), 8 pages. doi:10.1098/rstb.2015.0454
  • Paradis, E., Gosselin, T., Goudet, J., Jombart, T., & Schliep, K. (2017). Linking genomics and population genetics with R. Molecular Ecology Resources, 17(1), 54-66. doi:10.1111/1755-0998.12577
  • Dallman, T., Inns, T., Jombart, T., Ashton, P., Loman, N., Chatt, C., ... Cleary, P. (2016). Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network.. Microb Genom, 2(8), e000070. doi:10.1099/mgen.0.000070
  • Jombart, T., Archer, F., Schliep, K., Kamvar, Z., Harris, R., Paradis, E., ... Lapp, H. (2017). apex: phylogenetics with multiple genes. MOLECULAR ECOLOGY RESOURCES, 17(1), 19-26. doi:10.1111/1755-0998.12567
  • Agua-Agum, J., Allegranzi, B., Ariyarajah, A., Aylward, R. B., Blake, I. M., Barboza, P., ... Van Kerkhove, M. D. (2016). After Ebola in West Africa - Unpredictable Risks, Preventable Epidemics. NEW ENGLAND JOURNAL OF MEDICINE, 375(6), 587-596. doi:10.1056/NEJMsr1513109
  • Cauchemez, S., Nouvellet, P., Cori, A., Jombart, T., Garske, T., Clapham, H., ... Ferguson, N. M. (2016). Unraveling the drivers of MERS-CoV transmission. Proceedings of the National Academy of Sciences of the United States of America, 113(32), 9081-9086. doi:10.1073/pnas.1519235113
  • Lessler, J., Salje, H., Van Kerkhove, M. D., Ferguson, N. M., Cauchemez, S., Rodriquez-Barraquer, I., ... Cummings, D. A. T. (2016). Estimating the Severity and Subclinical Burden of Middle East Respiratory Syndrome Coronavirus Infection in the Kingdom of Saudi Arabia. American Journal of Epidemiology, 183(7), 657-663. doi:10.1093/aje/kwv452
  • Agua-Agum, J., Ariyarajah, A., Blake, I. M., Cori, A., Donnelly, C. A., Dorigatti, I., ... Van Kerkhove, M. D. (2016). Ebola Virus Disease among Male and Female Persons in West Africa. New England Journal of Medicine, 374(1), 96-98. doi:10.1056/NEJMc1510305
  • Karkey, A., Jombart, T., Walker, A. W., Thompson, C. N., Torres, A., Dongol, S., ... Baker, S. (2016). The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water. PLoS Neglected Tropical Diseases, 10(1), 18 pages. doi:10.1371/journal.pntd.0004346
  • Finnie, T. J. R., South, A., Bento, A., Sherrard-Smith, E., & Jombart, T. (2016). EpiJSON: A unified data-format for epidemiology. EPIDEMICS, 15, 20-26. doi:10.1016/j.epidem.2015.12.002
  • Nouvellet, P., Garske, T., Mills, H. L., Nedjati-Gilani, G., Hinsley, W., Blake, I. M., ... Ferguson, N. M. (2015). The role of rapid diagnostics in managing Ebola epidemics. Nature, 528(7580), S109-S116. doi:10.1038/nature16041
  • Jombart, T., Kendall, M. L., Almagro-Garcia, J., & Colijn, C. (2015). treespace (Version 1.0.0) [Computer Software].
  • Weinert, L. A., Chaudhuri, R. R., Wang, J., Peters, S. E., Corander, J., Jombart, T., ... Maskell, D. J. (2015). Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis (vol 6, 6740, 2015). NATURE COMMUNICATIONS, 6, 1 page. doi:10.1038/ncomms8272
  • Weinert, L. A., Chaudhuri, R. R., Wang, J., Peters, S. E., Corander, J., Jombart, T., ... Maskell, D. J. (2015). Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. NATURE COMMUNICATIONS, 6, 9 pages. doi:10.1038/ncomms7740
  • Agua-Agum, J., Ariyarajah, A., Blake, I. M., Cori, A., Donnelly, C. A., Dorigatti, I., ... Van Kerkhove, M. D. (2015). Ebola Virus Disease among Children in West Africa. NEW ENGLAND JOURNAL OF MEDICINE, 372(13), 1274-1277. doi:10.1056/NEJMc1415318
  • Hao, C. T., Karkey, A., Duy, P. T., Boinett, C. J., Cain, A. K., Ellington, M., ... Baker, S. (2015). A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae. EMBO Molecular Medicine, 7(3), 227-239.
  • West African Ebola Epidemic after One Year - Slowing but Not Yet under Control (2015). New England Journal of Medicine, 372(6), 584-587. doi:10.1056/NEJMc1414992
  • Tong, S. Y. C., Holden, M. T. G., Nickerson, E. K., Cooper, B. S., Koeser, C. U., Cori, A., ... Peacock, S. J. (2015). Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting. GENOME RESEARCH, 25(1), 111-118. doi:10.1101/gr.174730.114
  • Nhung, N. T., Cuong, N. V., Campbell, J., Hoa, N. T., Bryant, J. E., Truc, V. N. T., ... Carrique-Mas, J. (2015). High Levels of Antimicrobial Resistance among Escherichia coli Isolates from Livestock Farms and Synanthropic Rats and Shrews in the Mekong Delta of Vietnam. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 81(3), 812-820. doi:10.1128/AEM.03366-14
  • Aylward, B., Barboza, P., Bawo, L., Bertherat, E., Bilivogui, P., Blake, I., ... Yoti, Z. (2014). Ebola Virus Disease in West Africa - The First 9 Months of the Epidemic and Forward Projections. NEW ENGLAND JOURNAL OF MEDICINE, 371(16), 1481-1495. doi:10.1056/NEJMoa1411100
  • Mita, T., & Jombart, T. (2015). Patterns and dynamics of genetic diversity in Plasmodium falciparum: What past human migrations tell us about malaria. Parasitology International, 64(3), 238-243. doi:10.1016/j.parint.2014.09.007
  • Devillard, S., Jombart, T., Leger, F., Pontier, D., Say, L., & Ruette, S. (2014). How reliable are morphological and anatomical characters to distinguish European wildcats, domestic cats and their hybrids in France?. Journal of Zoological Systematics and Evolutionary Research, 52(2), 154-162. doi:10.1111/jzs.12049
  • Jombart, T., Aanensen, D. M., Baguelin, M., Birrell, P., Cauchemez, S., Camacho, A., ... Ferguso, N. (2014). OutbreakTools: A new platform for disease outbreak analysis using the R software. EPIDEMICS, 7, 28-34. doi:10.1016/j.epidem.2014.04.003
  • Jombart, T., Cori, A., Didelot, X., Cauchemez, S., Fraser, C., & Ferguson, N. (2014). Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data. PLOS COMPUTATIONAL BIOLOGY, 10(1), 14 pages. doi:10.1371/journal.pcbi.1003457
  • Tanabe, K., Jombart, T., Horibe, S., Palacpac, N. M. Q., Honma, H., Tachibana, S. -I., ... Mita, T. (2013). Plasmodium falciparum mitochondrial genetic diversity exhibits isolation-by-distance patterns supporting a sub-Saharan African origin. MITOCHONDRION, 13(6), 630-636. doi:10.1016/j.mito.2013.08.008
  • Chadeau-Hyam, M., Campanella, G., Jombart, T., Bottolo, L., Portengen, L., Vineis, P., ... Vermeulen, R. C. H. (2013). Deciphering the complex: Methodological overview of statistical models to derive OMICS-based biomarkers. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS, 54(7), 542-557. doi:10.1002/em.21797
  • Huyse, T., Van den Broeck, F., Jombart, T., Webster, B. L., Diaw, O., Volckaert, F. A. M., ... Polman, K. (2013). Regular treatments of praziquantel do not impact on the genetic make-up of Schistosoma mansoni in Northern Senegal. INFECTION GENETICS AND EVOLUTION, 18, 100-105. doi:10.1016/j.meegid.2013.05.007
  • Tanabe, K., Mita, T., Palacpac, N. M. Q., Arisue, N., Tougan, T., Kawai, S., ... Horii, T. (2013). Within-population genetic diversity of Plasmodium falciparum vaccine candidate antigens reveals geographic distance from a Central sub-Saharan African origin. VACCINE, 31(9), 1334-1339. doi:10.1016/j.vaccine.2012.12.039
  • Cui, Y., Yu, C., Yan, Y., Li, D., Li, Y., Jombart, T., ... Yang, R. (2013). Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proceedings of the National Academy of Sciences of the United States of America, 110(2), 577-582. doi:10.1073/pnas.1205750110
  • Muenkemueller, T., Lavergne, S., Bzeznik, B., Dray, S., Jombart, T., Schiffers, K., & Thuiller, W. (2012). How to measure and test phylogenetic signal. Methods in Ecology and Evolution, 3(4), 743-756. doi:10.1111/j.2041-210X.2012.00196.x
  • Dray, S., Pelissier, R., Couteron, P., Fortin, M. -J., Legendre, P., Peres-Neto, P. R., ... Wagner, H. H. (2012). Community ecology in the age of multivariate multiscale spatial analysis. ECOLOGICAL MONOGRAPHS, 82(3), 257-275. doi:10.1890/11-1183.1
  • Yalcindag, E., Elguero, E., Arnathau, C., Durand, P., Akiana, J., Anderson, T. J., ... Prugnolle, F. (2012). Multiple independent introductions of Plasmodium falciparum in South America. Proceedings of the National Academy of Sciences of the United States of America, 109(2), 511-516. doi:10.1073/pnas.1119058109
  • Dray, S., & Jombart, T. (2011). revisiting guerry's data: introducing spatial constraints in multivariate analysis. Snnals of Applied Statistics, 5(4), 2278-2299. doi:10.1214/10-AOAS356
  • Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, S., Albrechtsen, A., ... Willerslev, E. (2011). An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. SCIENCE, 334(6052), 94-98. doi:10.1126/science.1211177
  • Jombart, T., & Ahmed, I. (2011). adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. BIOINFORMATICS, 27(21), 3070-3071. doi:10.1093/bioinformatics/btr521
  • Morelli, G., Song, Y., Mazzoni, C. J., Eppinger, M., Roumagnac, P., Wagner, D. M., ... Achtman, M. (2010). Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. NATURE GENETICS, 42(12), 1140-+. doi:10.1038/ng.705
  • Jombart, T., Devillard, S., & Balloux, F. (2010). Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC GENETICS, 11, 15 pages. doi:10.1186/1471-2156-11-94
  • Tanabe, K., Mita, T., Jombart, T., Eriksson, A., Horibe, S., Palacpac, N., ... Balloux, F. (2010). Plasmodium falciparum Accompanied the Human Expansion out of Africa. CURRENT BIOLOGY, 20(14), 1283-1289. doi:10.1016/j.cub.2010.05.053
  • Jombart, T., Eggo, R. M., Dodd, P. J., & Balloux, F. (2011). Reconstructing disease outbreaks from genetic data: a graph approach. HEREDITY, 106(2), 383-390. doi:10.1038/hdy.2010.78
  • Jombart, T., Balloux, F., & Dray, S. (2010). adephylo: new tools for investigating the phylogenetic signal in biological traits. BIOINFORMATICS, 26(15), 1907-1909. doi:10.1093/bioinformatics/btq292
  • Jombart, T., Pavoine, S., Devillard, S., & Pontier, D. (2010). Putting phylogeny into the analysis of biological traits: A methodological approach. JOURNAL OF THEORETICAL BIOLOGY, 264(3), 693-701. doi:10.1016/j.jtbi.2010.03.038
  • Nuebel, U., Dordel, J., Kurt, K., Strommenger, B., Westh, H., Shukla, S. K., ... Witte, W. (2010). A Timescale for Evolution, Population Expansion, and Spatial Spread of an Emerging Clone of Methicillin-Resistant Staphylococcus aureus. PLOS PATHOGENS, 6(4), 12 pages. doi:10.1371/journal.ppat.1000855
  • Balloux, F., Handley, L. -J. L., Jombart, T., Liu, H., & Manica, A. (2009). Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 276(1672), 3447-3455. doi:10.1098/rspb.2009.0752
  • Fraser, C., Donnelly, C. A., Cauchemez, S., Hanage, W. P., Van Kerkhove, M. D., Hollingsworth, T. D., ... Ferguson, N. M. (2009). Influenza: Making Privileged Data Public Response. SCIENCE, 325(5944), 1072-1073. doi:10.1126/science.325_1072b
  • Fraser, C., Donnelly, C. A., Cauchemez, S., Hanage, W. P., Van Kerkhove, M. D., Hollingsworth, T. D., ... Roth, C. (2009). Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings. SCIENCE, 324(5934), 1557-1561. doi:10.1126/science.1176062
  • Jombart, T., Pontier, D., & Dufour, A. -B. (2009). Genetic markers in the playground of multivariate analysis. HEREDITY, 102(4), 330-341. doi:10.1038/hdy.2008.130
  • Jombart, T., Dray, S., & Dufour, A. -B. (2009). Finding essential scales of spatial variation in ecological data: a multivariate approach. ECOGRAPHY, 32(1), 161-168. doi:10.1111/j.1600-0587.2008.05567.x
  • Jombart, T., Eggo, R. M., Dodd, P., & Balloux, F. (2009). Spatiotemporal dynamics in the early stages of the 2009 A/H1N1 influenza pandemic.. PLoS Curr, 1, RRN1026.
  • Devillard, S., Jombart, T., & Pontier, D. (2009). Revealing cryptic genetic structuring in an urban population of stray cats (Felis silvestris catus). MAMMALIAN BIOLOGY, 74(1), 59-71. doi:10.1016/j.mambio.2008.01.001
  • Christophe, F., Christl, A. D., Cauchemez, S., Hanage, W. P., Van Kerkhove, M. D., Hollingsworth, T. D., ... Ferguson, N. M. (2009). Response. Science, 325(5944), 1072-1073.
  • Jombart, T., Devillard, S., Dufour, A. -B., & Pontier, D. (2008). Revealing cryptic spatial patterns in genetic variability by a new multivariate method. HEREDITY, 101(1), 92-103. doi:10.1038/hdy.2008.34
  • Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. BIOINFORMATICS, 24(11), 1403-1405. doi:10.1093/bioinformatics/btn129
  • Laloe, D., Jombart, T., Dufour, A. -B., & Moazami-Goudarzi, K. (2007). Consensus genetic structuring and typological value of markers using multiple co-inertia analysis. GENETICS SELECTION EVOLUTION, 39(5), 545-567. doi:10.1051/gse:2007021