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adephylo: new tools for investigating the phylogenetic signal in biological traits.
Jombart T, Balloux F, Dray S. Jombart T, et al. Bioinformatics. 2010 Aug 1;26(15):1907-9. doi: 10.1093/bioinformatics/btq292. Epub 2010 Jun 4. Bioinformatics. 2010. PMID: 20525823
adegenet: a R package for the multivariate analysis of genetic markers.
Jombart T. Jombart T. Bioinformatics. 2008 Jun 1;24(11):1403-5. doi: 10.1093/bioinformatics/btn129. Epub 2008 Apr 8. Bioinformatics. 2008. PMID: 18397895
Spatiotemporal dynamics in the early stages of the 2009 A/H1N1 influenza pandemic.
Jombart T, Eggo RM, Dodd P, Balloux F. Jombart T, et al. PLoS Curr. 2009 Aug 31;1:RRN1026. doi: 10.1371/currents.rrn1026. PLoS Curr. 2009. PMID: 20025199 Free PMC article.
Putting phylogeny into the analysis of biological traits: a methodological approach.
Jombart T, Pavoine S, Devillard S, Pontier D. Jombart T, et al. J Theor Biol. 2010 Jun 7;264(3):693-701. doi: 10.1016/j.jtbi.2010.03.038. Epub 2010 Mar 31. J Theor Biol. 2010. PMID: 20361983
Reconstructing disease outbreaks from genetic data: a graph approach.
Jombart T, Eggo RM, Dodd PJ, Balloux F. Jombart T, et al. Heredity (Edinb). 2011 Feb;106(2):383-90. doi: 10.1038/hdy.2010.78. Epub 2010 Jun 16. Heredity (Edinb). 2011. PMID: 20551981 Free PMC article.
adegenet 1.3-1: new tools for the analysis of genome-wide SNP data.
Jombart T, Ahmed I. Jombart T, et al. Bioinformatics. 2011 Nov 1;27(21):3070-1. doi: 10.1093/bioinformatics/btr521. Epub 2011 Sep 16. Bioinformatics. 2011. PMID: 21926124 Free PMC article.
CONTACT: t.jombart@imperial.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
CONTACT: t.jombart@imperial.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data.
Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, Ferguson N. Jombart T, et al. PLoS Comput Biol. 2014 Jan;10(1):e1003457. doi: 10.1371/journal.pcbi.1003457. Epub 2014 Jan 23. PLoS Comput Biol. 2014. PMID: 24465202 Free PMC article.
OutbreakTools: a new platform for disease outbreak analysis using the R software.
Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X, Fraser C, Frost S, Hens N, Hugues J, Höhle M, Opatowski L, Rambaut A, Ratmann O, Soubeyrand S, Suchard MA, Wallinga J, Ypma R, Ferguson N. Jombart T, et al. Epidemics. 2014 Jun;7(100):28-34. doi: 10.1016/j.epidem.2014.04.003. Epub 2014 Apr 18. Epidemics. 2014. PMID: 24928667 Free PMC article.
Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting.
Tong SY, Holden MT, Nickerson EK, Cooper BS, Köser CU, Cori A, Jombart T, Cauchemez S, Fraser C, Wuthiekanun V, Thaipadungpanit J, Hongsuwan M, Day NP, Limmathurotsakul D, Parkhill J, Peacock SJ. Tong SY, et al. Genome Res. 2015 Jan;25(1):111-8. doi: 10.1101/gr.174730.114. Epub 2014 Dec 9. Genome Res. 2015. PMID: 25491771 Free PMC article.
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