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 22-12-2017.

web of science:

  • citations: 6,381
  • h-index: 26

Google scholar:

  • citations: 8,574
  • h-index: 28
  • h10-index: 43

List of publications

This list was last updated on the 04-11-2018.

  • 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