Bill Hanage
Dr. Hanage employs a mix of theoretical and laboratory work to research the evolution and epidemiology of infectious disease. After his PhD, he engaged in post doctoral study at the University of Oxford and Imperial College London, before being awarded a Royal Society University Research Fellowship. Prior to joining CCDD he was a Reader in the department of Infectious Disease Epidemiology at Imperial College London.
Dr. Hanage has worked extensively developing multilocus sequence typing (MLST; www.mlst.net) and analysis (MLSA) for the study of bacterial pathogens and species, as well as means of analyzing data developed using this method. Along with his more theoretical projects he has worked on both bacterial (Neisseria, Streptococci) and viral pathogens (HIV-1, H1N1 influenza). He is particularly interested in using an evolutionary framework such as methods derived from population genetics to inform epidemiology. He has acted as an advisor to Glaxo SmithKline and the World Health Organisation.
Pneumococcal carriage and antibiotic resistance in young children before 13-valent conjugate vaccine
Wroe PC, Lee GM, Finkelstein JA, Pelton SI, Hanage WP, Lipsitch M, Stevenson AE, Rifas-Shiman SL, Kleinman K, Dutta-Linn MM, Hinrichsen VL, Lakoma M, Huang SS
Pediatr Infect Dis J 2012 Mar.
Pneumococcal sequence type replacement among American Indian children: a comparison of pre- and routine-PCV7 eras
Scott JR, Hanage WP, Lipsitch M, Millar EV, Moulton LH, Hinds J, Reid R, Santosham M, O'Brien KL
Vaccine 2012 Mar.
Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011
Grad Y, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, FitzGerald M, Godfrey P, Haas BJ, Murphy C, Russ C, Sykes S, Walker BJ, Wortman JR, Young S, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, DeSmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-Moller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP.
PNAS 2012 Feb.
Detection of recombination events in bacterial genomes from large population samples
Marttinen P, Hanage WP, Croucher NJ, Connor TR, Harris SR, Bentley SD, Corander J
Nucleic Acids Res 2012 Jan.
Clonal replacement among 19A Streptococcus pneumoniae in Massachusetts, prior to 13 valent conjugate vaccination
Hanage WP, Bishop CJ, Lee GM, Lipsitch M, Stevenson A, Rifas-Shiman SL, Pelton SI, Huang SS, Finkelstein JA
Vaccine 2011 Nov.
Population biology of Gram-positive pathogens: high-risk clones for dissemination of antibiotic resistance
Willems RJ, Hanage WP, Bessen DE, Feil EJ
FEMS Microbiol Rev 2011 Sep.
Carried pneumococci in Massachusetts children: the contribution of clonal expansion and serotype switching
Hanage WP, Bishop CJ, Huang SS, Stevenson AE, Pelton SI, Lipsitch M, Finkelstein JA
Pediatr Infect Dis J 2011 Apr.
Serotype specific invasive capacity and persistent reduction in invasive pneumococcal disease
Yildirim I, Hanage WP, Lipsitch M, Shea KM, Stevenson A, Finkelstein J, Huang SS, Lee GM, Kleinman K, Pelton SI
Vaccine 2010 Dec.
Re-remergence of the type 1 pilus among Streptococcus pneumoniae isolates in Massachusetts, USA
Regev-Yochay G, Hanage WP, Trzcinski K, Rifas-Shiman SL, Lee G, Bessolo A, Huang SS, Pelton SI, McAdam AJ, Finkelstein JA, Lipsitch M, Malley R
Vaccine 2010 Jul.
HIV-1 transmitting couples have similar viral load set-points in Rakai, Uganda
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.
PLoS Pathog 2010 May
Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete
Hanage WP, Finkelstein JA, Huang SS, Pelton SI, Stevenson AE, Kleinman K, Hinrichsen VL, Fraser C.
Epidemics 2010 Mar.
Identifying currents in the gene pool for bacterial populations using an integrative approach
Tang J, Hanage WP, Fraser C, Corander J
PLoS Computational Biology 2009 Aug.
Pandemic potential of a strain of influenza A (H1N1): early findings
Fraser C, Donnelly CA, Cauchemez S, Hanage B, 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, Apluche-Aranda CM, Chapela IB, Zavala EP, Guevara DM, Checchi F, Garcia E, Hugonnet S, Roth C..
Science 2009 Jul.
Epidemiology and risk factors for Staphylococcus aureus colonization in children in the post-PCV7 era
Lee GM, Huang SS, Rifas-Shiman SL, Hinrichsen VL, Pelton SI, Kleinman K, Hanage WP, Lipsitch M, McAdam AJ, Finkelstein J...
BMC Infectious Diseases 2009 Jul.
Continued impact of pneumococcal conjugate vaccine on carriage in young children
Huang SS, Hinrichsen VL, Stevenson AE, Rifas-Shiman SL, Kleinman K, Pelton SI, Lipsitch M, Hanage WP, Lee G, Finkelstein J.
Pediatrics 2009 Jul.
Pandemic potential of a strain of influenza A (H1N1): early findings
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
Science 2009 Jun.
Hyper-recombination, diversity, and antibiotic resistance in pneumococcus
Hanage WP, Fraser C, Tang J, Connor TR, Corander J
Science 2009 Jun.
No coexistence for free: neutral null models for multistrain pathogens
Epidemics 2009 Mar.
The bacterial species challenge: making sense of genetic and ecological diversity
Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP.
Science 2009 Feb.
Assigning strains to bacterial species via the internet
Bishop CJ, Aanensen DM, Jordan GE, Kilian M, Hanage WP, Spratt BG.
BMC Biology 2009 Jan.
Charles Darwin in modern epidemiology and public health – the celebration continues
J Epidemiol Community Health 2009
Distribution of pneumococcal surface protein A families 1 and 2 among Streptococcus pneumoniae isolates from children in Finland who had acute otitis media or were nasopharyngeal carriers
Melin MM, Hollingshead SK, Briles DE, Hanage WP, Lahdenkari M, Kaijalainen T, Kilpi TM, Kayhty HM
Clin Vaccine Immunol 2008 Oct.
Bayesian modeling of recombination events in bacterial populations
Marttinen P, Baldwin A, Hanage WP, Dowson C, Mahenthiralingam E, Corander J
BMC Bioinformatics 2008 Oct.
Streptococcus pneumoniae contains 3 rlrA pilus variants that are clonally related
Moschioni M, Donati C, Muzzi A, Masignani V, Censini S, Hanage WP, Bishop CJ, Reis JN, Normark S, Henriques-Normark B, Covacci A, Rappuoli R, Barocchi MA.
J Infect Dis 2008 Mar.
Serotype-specific problems associated with pneumococcal conjugate vaccination
Future Microbiol. 2008 Feb.
Serotype replacement in invasive pneumococcal disease: where do we go from here?
J Infect Dis 2007 Nov.
Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis
Fraser C, Hollingsworth TD, Chapman R, de Wolf F, Hanage WP
Proc Natl Acad Sci U S A 2007 Oct.
Emergence of 19A as virulent and multidrug resistant Pneumococcus in Massachusetts following universal immunization of infants with pneumococcal conjugate vaccine
Pelton SI, Huot H, Finkelstein JA, Bishop CJ, Hsu KK, Kellenberg J, Huang SS, Goldstein R, Hanage W
Pediatr Infect Dis J 2007 Jun.
Assessing the reliability of eBURST using simulated populations with known ancestry
Turner KM, Hanage WP, Fraser C, Connor TR
BMC Microbiol 2007 Apr.
Diversity and antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae carriage isolates in the post-heptavalent conjugate vaccine era
Hanage WP, Huang SS, Lipsitch M, Bishop CJ, Godoy D, Pelton SI, Goldstein R, Huot H, Finkelstein J.
Journal of Infectious Diseases 2007 Feb.
Modelling bacterial speciation
Hanage WP, Fraser C, Turner K, Spratt BG.
Philos Trans R Soc Lond B Biol Sci 2006 Nov.
Sequences, sequence clusters and bacterial species
Hanage B, Fraser C, Spratt BG
Philos Trans R Soc Lond B Biol Sci 2006 Nov.
Modelling infectious disease - time to think outside the box?
Wiles S, Hanage WP, Frankel G, Robertson B
Nat Rev Microbiol 2006 Apr.
The impact of homologous recombination on the generation of diversity in bacteria
Hanage WP, Fraser C, Spratt BG
Journal of Theoretical Biology 2006 Mar.
A successful, diverse disease-associated lineage of nontypeable pneumococci that has lost the capsular biosynthesis locus
Hanage WP, Kaijalainen T, Saukkoriipi A, Rickcord J, Spratt BG
Journal of Clinical Microbiology 2006 Mar.
Low effective dispersal of asexual genotypes in heterogeneous landscapes by the endemic pathogen Penicillium marneffei
Fisher MC, Hanage WP, de Hoog S, Johnson E, Smith MD, White NJ, Vanittanakom N.
PLoS Pathogens 2005 Oct.
Using multilocus sequence data to define the pneumococcus
Hanage WP, Kaijalainen T, Herva E, Saukkoriipi A, Syrjänen R, Spratt BG
J Bacteriol 2005 Sep.
Neutral microepidemic evolution of bacterial pathogens
Fraser C, Hanage WP, Spratt BG
Proc Natl Acad Sci USA 2005 Feb.
Invasiveness of serotypes and clones of Streptococcus pneumoniae among children in Finland
Hanage WP, Kaijalainen TH, Syrjänen RK, Auranen K, Leinonen M, Makela PH, Spratt BG.
Infect Immun 2005 Jan.
Displaying the relatedness among isolates of bacterial species -- the eBURST approach
Spratt BG, Hanage WP, Li B, Aanensen DM, Feil EJ
FEMS Microbiol Lett 2004 Dec.
eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data
Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG...
J Bacteriol 2004 Mar.
Ability of pneumococcal serotypes and clones to cause acute otitis media: implications for the prevention of otitis media by conjugate vaccines
Hanage WP, Auranen K, Syrjanen R, Herva E, Makela PH, Kilpi T, Spratt BG
Infect Immun 2004 Jan.
Stimulation of cytokine release and adhesion molecule expression by products of viridans streptococci
Hanage WP, Cohen J
J Infect Dis 2002 Feb.
The relative contributions of recombination and point mutation to the diversification of bacterial clones
Spratt BG, Hanage WP, Feil EJ
Curr Opin Microbiol 2001 Oct.