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Christophe Fraser

Senior Group Leader in Pathogen Dynamics

Education

Affiliations

Projects

Papers

Blanquart F, Lehtinen S, Lipsitch M, Fraser C. (2018). The evolution of antibiotic resistance in a structured host population. Journal of the Royal Society, Interface, 15(143)

Lehtinen S, Blanquart F, Croucher NJ, Turner P, Lipsitch M, Fraser C. (2017). Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage. Proceedings of the National Academy of Sciences of the United States of America, 114(5)

Blanquart F, Lehtinen S, Fraser C. (2017). . Proceedings. Biological sciences, 284(1855)

Li LM, Grassly NC, Fraser C. (2017). Quantifying Transmission Heterogeneity Using Both Pathogen Phylogenies and Incidence Time Series. Molecular biology and evolution, 34(11)

Mostowy RJ, Croucher NJ, De Maio N, Chewapreecha C, Salter SJ, Turner P, Aanensen DM, Bentley SD, Didelot X, Fraser C. (2017). Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination. Molecular biology and evolution, 34(10)

Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost SDW, Gall A, Gaiseitsiwe S, Grabowski M, Gray R, Guindon S, von Haeseler A, Kaleebu P, Kendall M, Kozlov A, Manasa J, Minh BQ, Moyo S, Novitsky V, Nsubuga R, Pillay S, Quinn TC, Serwadda D, Ssemwanga D, Stamatakis A, Trifinopoulos J, Wawer M, Leigh Brown A, de Oliveira T, Kellam P, Pillay D, Fraser C. (2017). HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences. AIDS research and human retroviruses, 33(11)

Blanquart F, Grabowski MK, Herbeck J, Nalugoda F, Serwadda D, Eller MA, Robb ML, Gray R, Kigozi G, Laeyendecker O, Lythgoe KA, Nakigozi G, Quinn TC, Reynolds SJ, Wawer MJ, Fraser C. (2016). A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda. Elife

Croucher NJ, Mostowy R, Wymant C, Turner P, Bentley SD, Fraser C. (2016). Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict. PLoS biology, 14(3)

Herbeck JT, Mittler JE, Gottlieb GS, Goodreau SM, Murphy JT, Cori A, Pickles M, Fraser C. (2016). Evolution of HIV virulence in response to widespread scale up of antiretroviral therapy: a modeling study. Virus evolution, 2(2)

Cori A, Pickles M, van Sighem A, Gras L, Bezemer D, Reiss P, Fraser C. (2015). CD4+ cell dynamics in untreated HIV-1 infection: overall rates, and effects of age, viral load, sex and calendar time. AIDS (London, England), 29(18)

Hollingsworth TD, Pilcher CD, Hecht FM, Deeks SG, Fraser C. (2015). High Transmissibility During Early HIV Infection Among Men Who Have Sex With Men-San Francisco, California. The Journal of infectious diseases, 211(11)

Li LM, Grassly NC, Fraser C. (2014). Genomic analysis of emerging pathogens: methods, application and future trends. Genome biology, 15(11)

Fraser C, Lythgoe K, Leventhal GE, Shirreff G, Hollingsworth TD, Alizon S, Bonhoeffer S. (2014). Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective. Science (New York, N.Y.), 343(6177)

Pelat C, Ferguson NM, White PJ, Reed C, Finelli L, Cauchemez S, Fraser C. (2014). Optimizing the precision of case fatality ratio estimates under the surveillance pyramid approach. American journal of epidemiology, 180(10)

Mostowy R, Croucher NJ, Hanage WP, Harris SR, Bentley S, Fraser C. (2014). Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution. PLoS genetics, 10(5)

Alizon S, Fraser C. (2013). Within-host and between-host evolutionary rates across the HIV-1 genome. Retrovirology

Lythgoe KA, Pellis L, Fraser C. (2013). Is HIV short-sighted? Insights from a multistrain nested model. Evolution; international journal of organic evolution, 67(10)

Shirreff G, Alizon S, Cori A, Günthard HF, Laeyendecker O, van Sighem A, Bezemer D, Fraser C. (2013). How effectively can HIV phylogenies be used to measure heritability?. Evolution, medicine, and public health, 2013(1)

Lythgoe KA, Fraser C. (2012). New insights into the evolutionary rate of HIV-1 at the within-host and epidemiological levels. Proceedings. Biological sciences, 279(1741)

van Sighem A, Jansen I, Bezemer D, De Wolf F, Prins M, Stolte I, Fraser C. (2012). Increasing sexual risk behaviour among Dutch men who have sex with men: mathematical models versus prospective cohort data. AIDS (London, England), 26(14)

de Silva E, Ferguson NM, Fraser C. (2012). Inferring pandemic growth rates from sequence data. Journal of the Royal Society, Interface, 9(73)

Shirreff G, Pellis L, Laeyendecker O, Fraser C. (2011). Transmission selects for HIV-1 strains of intermediate virulence: a modelling approach. PLoS computational biology, 7(10)

Fraser C, Cummings DA, Klinkenberg D, Burke DS, Ferguson NM. (2011). Influenza transmission in households during the 1918 pandemic. American journal of epidemiology, 174(5)

Pellis L, Ferguson NM, Fraser C. (2011). Epidemic growth rate and household reproduction number in communities of households, schools and workplaces. Journal of mathematical biology, 63(4)

Fraser C, Hollingsworth TD. (2010). Interpretation of correlations in setpoint viral load in transmitting couples. AIDS (London, England), 24(16)

Hollingsworth TD, Laeyendecker O, Shirreff G, Donnelly CA, Serwadda D, Wawer MJ, Kiwanuka N, Nalugoda F, Collinson-Streng A, Ssempijja V, Hanage WP, Quinn TC, Gray RH, Fraser C. (2010). HIV-1 transmitting couples have similar viral load set-points in Rakai, Uganda. PLoS pathogens, 6(5)

Baggaley RF, Fraser C. (2010). Modelling sexual transmission of HIV: testing the assumptions, validating the predictions. Current opinion in HIV and AIDS, 5(4)

Hanage WP, Finkelstein JA, Huang SS, Pelton SI, Stevenson AE, Kleinman K, Hinrichsen VL, Fraser C. (2010). Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete. Epidemics, 2(2)

Bezemer D, de Wolf F, Boerlijst MC, van Sighem A, Hollingsworth TD, Fraser C. (2010). 27 years of the HIV epidemic amongst men having sex with men in the Netherlands: an in depth mathematical model-based analysis. Epidemics, 2(2)

Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, Griffin J, Baggaley RF, Jenkins HE, Lyons EJ, Jombart T, Hinsley WR, Grassly NC, Balloux F, Ghani AC, Ferguson NM, Rambaut A, Pybus OG, Lopez-Gatell H, Alpuche-Aranda CM, Chapela IB, Zavala EP, Guevara DM, Checchi F, Garcia E, Hugonnet S, Roth C, . (2009). Pandemic potential of a strain of influenza A (H1N1): early findings. Science (New York, N.Y.), 324(5934)

Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP. (2009). The bacterial species challenge: making sense of genetic and ecological diversity. Science (New York, N.Y.), 323(5915)

Lipsitch M, Colijn C, Cohen T, Hanage WP, Fraser C. (2009). No coexistence for free: neutral null models for multistrain pathogens. Epidemics, 1(1)

Bezemer D, de Wolf F, Boerlijst MC, van Sighem A, Hollingsworth TD, Prins M, Geskus RB, Gras L, Coutinho RA, Fraser C. (2008). A resurgent HIV-1 epidemic among men who have sex with men in the era of potent antiretroviral therapy. AIDS (London, England), 22(9)

Pellis L, Ferguson NM, Fraser C. (2008). The relationship between real-time and discrete-generation models of epidemic spread. Mathematical biosciences, 216(1)

Grassly NC, Fraser C. (2008). Mathematical models of infectious disease transmission. Nature reviews. Microbiology, 6(6)

Hollingsworth TD, Anderson RM, Fraser C. (2008). HIV-1 transmission, by stage of infection. The Journal of infectious diseases, 198(5)

Fraser C, Hollingsworth TD, Chapman R, de Wolf F, Hanage WP. (2007). Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis. Proceedings of the National Academy of Sciences of the United States of America, 104(44)

Fraser C, Hanage WP, Spratt BG. (2007). Recombination and the nature of bacterial speciation. Science (New York, N.Y.), 315(5811)

Fraser C, Tomassini JE, Xi L, Golm G, Watson M, Giuliano AR, Barr E, Ault KA. (2007). Modeling the long-term antibody response of a human papillomavirus (HPV) virus-like particle (VLP) type 16 prophylactic vaccine. Vaccine, 25(21)

Fraser C. (2007). Estimating individual and household reproduction numbers in an emerging epidemic. PLoS One, 2(8)

Fraser C. (2007). Influenza pandemic vaccines: spread them thin?. PLoS medicine, 4(6)

Hanage WP, Spratt BG, Turner KM, Fraser C. (2006). Modelling bacterial speciation. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 361(1475)

Grassly NC, Fraser C. (2006). Seasonal infectious disease epidemiology. Proceedings. Biological sciences, 273(1600)

Fraser C. (2005). HIV recombination: what is the impact on antiretroviral therapy?. Journal of the Royal Society, Interface, 2(5)

Fraser C, Hanage WP, Spratt BG. (2005). Neutral microepidemic evolution of bacterial pathogens. Proceedings of the National Academy of Sciences of the United States of America, 102(6)

Fraser C, Riley S, Anderson RM, Ferguson NM. (2004). Factors that make an infectious disease outbreak controllable. Proceedings of the National Academy of Sciences of the United States of America, 101(16)

Garnett GP, Fraser C. (2003). Let it be sexual--selection, aggregation and distortion used to construct a case against sexual transmission. International journal of STD & AIDS, 14(11)

Fraser C, Ferguson NM, De Wolf F, Ghani AC, Garnett GP, Anderson RM. (2002). Antigen-driven T-cell turnover. Journal of theoretical biology, 219(2)