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Christophe Fraser

Senior Group Leader in Pathogen Dynamics

Education

Affiliations

Projects

Papers

Ferretti L, Wymant C, Kendall M, Zhao L, Nurtay A, Abeler-Dörner L, Parker M, Bonsall D, Fraser C. (2020). Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing. Science (New York, N.Y.)

El Bouzidi K, Kemp SA, Datir RP, Murtala-Ibrahim F, Aliyu A, Kwaghe V, Frampton D, Roy S, Breuer J, Sabin CA, Ogbanufe O, Charurat ME, Bonsall D, Golubchik T, Fraser C, Dakum P, Ndembi N, Gupta RK. (2020). High prevalence of integrase mutation L74I in West African HIV-1 subtypes prior to integrase inhibitor treatment. The Journal of antimicrobial chemotherapy

Bbosa N, Ssemwanga D, Ssekagiri A, Xi X, Mayanja Y, Bahemuka U, Seeley J, Pillay D, Abeler-Dörner L, Golubchik T, Fraser C, Kaleebu P, Ratmann O. (2020). Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda. Viruses, 12(3)

Bonsall D, Golubchik T, de Cesare M, Limbada M, Kosloff B, MacIntyre-Cockett G, Hall M, Wymant C, Ansari MA, Abeler-Dörner L, Schaap A, Brown A, Barnes E, Piwowar-Manning E, Eshleman S, Wilson E, Emel L, Hayes R, Fidler S, Ayles H, Bowden R, Fraser C,. (2020). A comprehensive genomics solution for HIV surveillance and clinical monitoring in low income settings. Journal of clinical microbiology

Fogel JM, Bonsall D, Cummings V, Bowden R, Golubchik T, de Cesare M, Wilson EA, Gamble T, Del Rio C, Batey DS, Mayer KH, Farley JE, Hughes JP, Remien RH, Beyrer C, Fraser C, Eshleman SH. (2020). Performance of a high-throughput next-generation sequencing method for analysis of HIV drug resistance and viral load. The Journal of antimicrobial chemotherapy

Parker MJ, Fraser C, Abeler-Dörner L, Bonsall D. (2020). Ethics of instantaneous contact tracing using mobile phone apps in the control of the COVID-19 pandemic. Journal of medical ethics

Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Esquivel Gomez LR, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh Brown AJ. (2020). Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus evolution, 6(1)

Lehtinen S, Chewapreecha C, Lees J, Hanage WP, Lipsitch M, Croucher NJ, Bentley SD, Turner P, Fraser C, Mostowy RJ. (2020). Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae. Science advances, 6(21)

Lehtinen S, Chewapreecha C, Lees J, Hanage WP, Lipsitch M, Croucher NJ, Bentley SD, Turner P, Fraser C, Mostowy RJ. (2020). . Science advances, 6(21)

Ratmann O, Grabowski MK, Hall M, Golubchik T, Wymant C, Abeler-Dörner L, Bonsall D, Hoppe A, Brown AL, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C, . (2019). Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis. Nature communications, 10(1)

Le Vu S, Ratmann O, Delpech V, Brown AE, Gill ON, Tostevin A, Dunn D, Fraser C, Volz EM. (2019). HIV-1 Transmission Patterns in Men Who Have Sex with Men: Insights from Genetic Source Attribution Analysis. AIDS research and human retroviruses, 35(9)

Hall MD, Holden MT, Srisomang P, Mahavanakul W, Wuthiekanun V, Limmathurotsakul D, Fountain K, Parkhill J, Nickerson EK, Peacock SJ, Fraser C. (2019). Improved characterisation of MRSA transmission using within-host bacterial sequence diversity. eLife, (8)

Abeler-Dörner L, Grabowski MK, Rambaut A, Pillay D, Fraser C, . (2019). PANGEA-HIV 2: Phylogenetics And Networks for Generalised Epidemics in Africa. Current opinion in HIV and AIDS, 14(3)

Lehtinen S, Blanquart F, Lipsitch M, Fraser C, . (2019). On the evolutionary ecology of multidrug resistance in bacteria. PLoS pathogens, 15(5)

Ryu S, Cowling BJ, Wu P, Olesen S, Fraser C, Sun DS, Lipsitch M, Grad YH. (2019). Case-based surveillance of antimicrobial resistance with full susceptibility profiles. JAC-antimicrobial resistance, 1(3)

Volz EM, Le Vu S, Ratmann O, Tostevin A, Dunn D, Orkin C, O'Shea S, Delpech V, Brown A, Gill N, Fraser C, . (2018). Molecular Epidemiology of HIV-1 Subtype B Reveals Heterogeneous Transmission Risk: Implications for Intervention and Control. The Journal of infectious diseases, 217(10)

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)

Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Croucher NJ, Hall M, Hillebregt M, Ong SH, Ratmann O, Albert J, Bannert N, Fellay J, Fransen K, Gourlay A, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Cornelissen M, Kellam P, Reiss P, Fraser C, . (2018). Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver. Virus evolution, 4(1)

Blanquart F, Lehtinen S, Fraser C. (2017). An evolutionary model to predict the frequency of antibiotic resistance under seasonal antibiotic use, and an application to Streptococcus pneumoniae. Proceedings. Biological sciences, 284(1855)

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 S. (2018). A simple approach to measure transmissibility and forecast incidence. Epidemics, (22)

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)

Didelot X, Fraser C, Gardy J, Colijn C. (2017). Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks. Molecular biology and evolution, 34(4)

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)

Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D'Ambrozio J, Dellicour S, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A. (2017). Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature, 544(7650)

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 IM. (2017). Key data for outbreak evaluation: building on the Ebola experience. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 372(1721)

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 CA. (2017). Heterogeneities in the case fatality ratio in the West African Ebola outbreak 2013-2016. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 372(1721)

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)

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

Le Vu S, Ratmann O, Delpech V, Brown AE, Gill ON, Tostevin A, Fraser C, Volz EM. (2018). Comparison of cluster-based and source-attribution methods for estimating transmission risk using large HIV sequence databases. Epidemics, (23)

Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C, . (2017). Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe. PLoS biology, 15(6)

Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain AS, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon AF, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C, . (2017). Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison. Molecular biology and evolution, 34(1)

Wymant C, Hall M, Ratmann O, Bonsall D, Golubchik T, de Cesare M, Gall A, Cornelissen M, Fraser C, . (2018). PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity. Molecular biology and evolution, 35(3)

Cobey S, Baskerville EB, Colijn C, Hanage W, Fraser C, Lipsitch M. (2017). Host population structure and treatment frequency maintain balancing selection on drug resistance. Journal of the Royal Society, Interface, 14(133)

Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C, . (2017). Correction: Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe. PLoS biology, 15(7)

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 DA, Van Kerkhove MD, Donnelly CA, Lessler J, Fraser C, Al-Barrak A, Ferguson NM. (2016). Unraveling the drivers of MERS-CoV transmission. Proceedings of the National Academy of Sciences of the United States of America, 113(32)

Agua-Agum J, Ariyarajah A, Blake IM, Cori A, Donnelly CA, Dorigatti I, Dye C, Eckmanns 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 MD. (2016). Ebola Virus Disease among Male and Female Persons in West Africa. The New England journal of medicine, 374(1)

Ratmann O, van Sighem A, Bezemer D, Gavryushkina A, Jurriaans S, Wensing A, de Wolf F, Reiss P, Fraser C, . (2016). Sources of HIV infection among men having sex with men and implications for prevention. Science translational medicine, 8(320)

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, (5)

Pinsent A, Fraser C, Ferguson NM, Riley S. (2016). A systematic review of reported reassortant viral lineages of influenza A. BMC infectious diseases, (16)

Lythgoe KA, Blanquart F, Pellis L, Fraser C. (2016). Large Variations in HIV-1 Viral Load Explained by Shifting-Mosaic Metapopulation Dynamics. PLoS biology, 14(10)

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)

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 JM, 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 Z. (2016). Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study. PLoS medicine, 13(11)

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)

Agua-Agum J, Ariyarajah A, Blake IM, Cori A, Donnelly CA, Dorigatti I, Dye C, Eckmanns T, Ferguson NM, Fowler RA, Fraser C, Garske T, Hinsley W, Jombart T, Mills HL, Murthy S, Nedjati Gilani G, Nouvellet P, Pelletier L, Riley S, Schumacher D, Shah A, Van Kerkhove MD. (2015). Ebola virus disease among children in West Africa. The New England journal of medicine, 372(13)

Lipsitch M, Donnelly CA, Fraser C, Blake IM, Cori A, Dorigatti I, Ferguson NM, Garske T, Mills HL, Riley S, Van Kerkhove MD, Hernán MA. (2015). Potential Biases in Estimating Absolute and Relative Case-Fatality Risks during Outbreaks. PLoS neglected tropical diseases, 9(7)

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)

Nouvellet P, Garske T, Mills HL, Nedjati-Gilani G, Hinsley W, Blake IM, Van Kerkhove MD, Cori A, Dorigatti I, Jombart T, Riley S, Fraser C, Donnelly CA, Ferguson NM. (2015). The role of rapid diagnostics in managing Ebola epidemics. Nature, 528(7580)

Bezemer D, Cori A, Ratmann O, van Sighem A, Hermanides HS, Dutilh BE, Gras L, Rodrigues Faria N, van den Hengel R, Duits AJ, Reiss P, de Wolf F, Fraser C, . (2015). Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis. PLoS medicine, 12(11)

Agua-Agum J, Ariyarajah A, Aylward B, Blake IM, Brennan R, Cori A, Donnelly CA, Dorigatti I, Dye C, Eckmanns T, Ferguson NM, Formenty P, Fraser C, Garcia E, Garske T, Hinsley W, Holmes D, Hugonnet S, Iyengar S, Jombart T, Krishnan R, Meijers S, Mills HL, Mohamed Y, Nedjati-Gilani G, Newton E, Nouvellet P, Pelletier L, Perkins D, Riley S, Sagrado M, Schnitzler J, Schumacher D, Shah A, Van Kerkhove MD, Varsaneux O, Wijekoon Kannangarage N. (2015). West African Ebola epidemic after one year--slowing but not yet under control. The New England journal of medicine, 372(6)

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)

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)

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)

Cori A, Ayles H, Beyers N, Schaap A, Floyd S, Sabapathy K, Eaton JW, Hauck K, Smith P, Griffith S, Moore A, Donnell D, Vermund SH, Fidler S, Hayes R, Fraser C, . (2014). HPTN 071 (PopART): a cluster-randomized trial of the population impact of an HIV combination prevention intervention including universal testing and treatment: mathematical model. PLoS One, 9(1)

Kucharski A, Mills H, Pinsent A, Fraser C, Van Kerkhove M, Donnelly CA, Riley S. (2014). Distinguishing Between Reservoir Exposure and Human-to-Human Transmission for Emerging Pathogens Using Case Onset Data. PLoS currents, (6)

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. (2014). OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics, (7)

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)

Eaton JW, Menzies NA, Stover J, Cambiano V, Chindelevitch L, Cori A, Hontelez JA, Humair S, Kerr CC, Klein DJ, Mishra S, Mitchell KM, Nichols BE, Vickerman P, Bakker R, Bärnighausen T, Bershteyn A, Bloom DE, Boily MC, Chang ST, Cohen T, Dodd PJ, Fraser C, Gopalappa C, Lundgren J, Martin NK, Mikkelsen E, Mountain E, Pham QD, Pickles M, Phillips A, Platt L, Pretorius C, Prudden HJ, Salomon JA, van de Vijver DA, de Vlas SJ, Wagner BG, White RG, Wilson DP, Zhang L, Blandford J, Meyer-Rath G, Remme M, Revill P, Sangrujee N, Terris-Prestholt F, Doherty M, Shaffer N, Easterbrook PJ, Hirnschall G, Hallett TB. (2014). Health benefits, costs, and cost-effectiveness of earlier eligibility for adult antiretroviral therapy and expanded treatment coverage: a combined analysis of 12 mathematical models. The Lancet. Global health, 2(1)

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)

Robinson K, Fyson N, Cohen T, Fraser C, Colijn C. (2013). How the dynamics and structure of sexual contact networks shape pathogen phylogenies. PLoS computational biology, 9(6)

Cauchemez S, Fraser C, Van Kerkhove MD, Donnelly CA, Riley S, Rambaut A, Enouf V, van der Werf S, Ferguson NM. (2014). Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility. The Lancet. Infectious diseases, 14(1)

Cori A, Ferguson NM, Fraser C, Cauchemez S. (2013). A new framework and software to estimate time-varying reproduction numbers during epidemics. American journal of epidemiology, 178(9)

Eaton JW, Menzies NA, Stover J, Cambiano V, Chindelevitch L, Cori A, Hontelez JA, Humair S, Kerr CC, Klein DJ, Mishra S, Mitchell KM, Nichols BE, Vickerman P, Bakker R, Bärnighausen T, Bershteyn A, Bloom DE, Boily MC, Chang ST, Cohen T, Dodd PJ, Fraser C, Gopalappa C, Lundgren J, Martin NK, Mikkelsen E, Mountain E, Pham QD, Pickles M, Phillips A, Platt L, Pretorius C, Prudden HJ, Salomon JA, van de Vijver DA, de Vlas SJ, Wagner BG, White RG, Wilson DP, Zhang L, Blandford J, Meyer-Rath G, Remme M, Revill P, Sangrujee N, Terris-Prestholt F, Doherty M, Shaffer N, Easterbrook PJ, Hirnschall G, Hallett TB. (2013). Health benefits, costs, and cost-effectiveness of earlier eligibility for adult antiretroviral therapy and expanded treatment coverage: a combined analysis of 12 mathematical models. The Lancet. Global health, 2(1)

Shepheard MA, Fleming VM, Connor TR, Corander J, Feil EJ, Fraser C, Hanage WP. (2013). Historical zoonoses and other changes in host tropism of Staphylococcus aureus, identified by phylogenetic analysis of a population dataset. PLoS One, 8(5)

Alizon S, Fraser C. (2013). Within-host and between-host evolutionary rates across the HIV-1 genome. Retrovirology, (10)

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)

Ratmann O, Donker G, Meijer A, Fraser C, Koelle K. (2012). Phylodynamic inference and model assessment with approximate bayesian computation: influenza as a case study. PLoS computational biology, 8(12)

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)

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

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)

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)

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)

Opatowski L, Fraser C, Griffin J, de Silva E, Van Kerkhove MD, Lyons EJ, Cauchemez S, Ferguson NM. (2011). Transmission characteristics of the 2009 H1N1 influenza pandemic: comparison of 8 Southern hemisphere countries. PLoS pathogens, 7(9)

Truscott J, Fraser C, Cauchemez S, Meeyai A, Hinsley W, Donnelly CA, Ghani A, Ferguson N. (2012). Essential epidemiological mechanisms underpinning the transmission dynamics of seasonal influenza. Journal of the Royal Society, Interface, 9(67)

Müller V, Fraser C, Herbeck JT. (2011). A strong case for viral genetic factors in HIV virulence. Viruses, 3(3)

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

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)

Van Kerkhove MD, Asikainen T, Becker NG, Bjorge S, Desenclos JC, dos Santos T, Fraser C, Leung GM, Lipsitch M, Longini IM Jr., McBryde ES, Roth CE, Shay DK, Smith DJ, Wallinga J, White PJ, Ferguson NM, Riley S, . (2010). Studies needed to address public health challenges of the 2009 H1N1 influenza pandemic: insights from modeling. PLoS medicine, 7(6)

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)

Cauchemez S, Donnelly CA, Reed C, Ghani AC, Fraser C, Kent CK, Finelli L, Ferguson NM. (2009). Household transmission of 2009 pandemic influenza A (H1N1) virus in the United States. The New England journal of medicine, 361(27)

Truscott J, Fraser C, Hinsley W, Cauchemez S, Donnelly C, Ghani A, Ferguson N, Meeyai A. (2009). Quantifying the transmissibility of human influenza and its seasonal variation in temperate regions. PLoS currents, (1)

Colijn C, Cohen T, Fraser C, Hanage W, Goldstein E, Givon-Lavi N, Dagan R, Lipsitch M. (2010). What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae?. Journal of the Royal Society, Interface, 7(47)

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)

Hanage WP, Fraser C, Tang J, Connor TR, Corander J. (2009). Hyper-recombination, diversity, and antibiotic resistance in pneumococcus. Science (New York, N.Y.), 324(5933)

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)

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

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

Halloran ME, Ferguson NM, Eubank S, Longini IM Jr., Cummings DA, Lewis B, Xu S, Fraser C, Vullikanti A, Germann TC, Wagener D, Beckman R, Kadau K, Barrett C, Macken CA, Burke DS, Cooley P. (2008). Modeling targeted layered containment of an influenza pandemic in the United States. Proceedings of the National Academy of Sciences of the United States of America, 105(12)

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

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

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

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

Ferguson NM, Cummings DA, Fraser C, Cajka JC, Cooley PC, Burke DS. (2006). Strategies for mitigating an influenza pandemic. Nature, 442(7101)

Hanage WP, Fraser C, Spratt BG. (2006). Sequences, sequence clusters and bacterial species. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 361(1475)

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)

Wu JT, Riley S, Fraser C, Leung GM. (2006). Reducing the impact of the next influenza pandemic using household-based public health interventions. PLoS medicine, 3(9)

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

Hanage WP, Fraser C, Spratt BG. (2006). The impact of homologous recombination on the generation of diversity in bacteria. Journal of theoretical biology, 239(2)

Hanage WP, Fraser C, Spratt BG. (2005). Fuzzy species among recombinogenic bacteria. BMC biology, (3)

Ferguson NM, Cummings DA, Cauchemez S, Fraser C, Riley S, Meeyai A, Iamsirithaworn S, Burke DS. (2005). Strategies for containing an emerging influenza pandemic in Southeast Asia. Nature, 437(7056)

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)

Ferguson NM, Fraser C, Donnelly CA, Ghani AC, Anderson RM. (2004). Public health. Public health risk from the avian H5N1 influenza epidemic. Science (New York, N.Y.), 304(5673)

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)

Riley S, Fraser C, Donnelly CA, Ghani AC, Abu-Raddad LJ, Hedley AJ, Leung GM, Ho LM, Lam TH, Thach TQ, Chau P, Chan KP, Lo SV, Leung PY, Tsang T, Ho W, Lee KH, Lau EM, Ferguson NM, Anderson RM. (2003). Transmission dynamics of the etiological agent of SARS in Hong Kong: impact of public health interventions. Science (New York, N.Y.), 300(5627)

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)