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profileWilliam P. Hanage, Ph.D.

TitleAssociate Professor of Epidemiology
InstitutionHarvard T.H. Chan School of Public Health
DepartmentEpidemiology
AddressHarvard School of Public Health
Kresge Bldg 5th floor Room 506F
677 Huntington Ave
Boston MA 02115
Phone617/432-1282
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The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
R01AI106786     (HANAGE, WILLIAM)Jun 1, 2013 - May 31, 2018
NIH/NIAID
Ecological and genetic contributions to the spread of resistance in pneumococcus
Role: Principal Investigator

U54GM088558     (LIPSITCH, MARC)Sep 15, 2009 - Aug 31, 2019
NIH/NIGMS
MIDAS Center for Communicable Disease Dynamics
Role: Co-Principal Investigator

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Collapse selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Marttinen P, Hanage WP. Speciation trajectories in recombining bacterial species. PLoS Comput Biol. 2017 Jul 03; 13(7):e1005640. PMID: 28671999.
    View in: PubMed
  2. Yildirim I, Little BA, Finkelstein J, Lee G, Hanage WP, Shea K, Pelton SI. Surveillance of pneumococcal colonization and invasive pneumococcal disease reveals shift in prevalent carriage serotypes in Massachusetts' children to relatively low invasiveness. Vaccine. 2017 Jul 13; 35(32):4002-4009. PMID: 28645717.
    View in: PubMed
  3. Andam CP, Worby CJ, Gierke R, McGee L, Pilishvili T, Hanage WP. Penicillin Resistance of Nonvaccine Type Pneumococcus before and after PCV13 Introduction, United States. Emerg Infect Dis. 2017 Jun; 23(6):1012-1015. PMID: 28518018.
    View in: PubMed
  4. Mostowy R, Croucher NJ, Andam CP, Corander J, Hanage WP, Marttinen P. Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations. Mol Biol Evol. 2017 May 01; 34(5):1167-1182. PMID: 28199698.
    View in: PubMed
  5. Azarian T, Grant LR, Georgieva M, Hammitt LL, Reid R, Bentley SD, Goldblatt D, Santosham M, Weatherholtz R, Burbidge P, Goklish N, Thompson CM, Hanage WP, O'Brien KL, Lipsitch M. Association of Pneumococcal Protein Antigen Serology With Age and Antigenic Profile of Colonizing Isolates. J Infect Dis. 2017 03 01; 215(5):713-722. PMID: 28035010.
    View in: PubMed
  6. Andam CP, Mitchell PK, Callendrello A, Chang Q, Corander J, Chaguza C, McGee L, Beall BW, Hanage WP. Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States. J Clin Microbiol. 2017 Apr; 55(4):1104-1115. PMID: 28100596.
    View in: PubMed
  7. Cerqueira GC, Earl AM, Ernst CM, Grad YH, Dekker JP, Feldgarden M, Chapman SB, Reis-Cunha JL, Shea TP, Young S, Zeng Q, Delaney ML, Kim D, Peterson EM, O'Brien TF, Ferraro MJ, Hooper DC, Huang SS, Kirby JE, Onderdonk AB, Birren BW, Hung DT, Cosimi LA, Wortman JR, Murphy CI, Hanage WP. Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks. Proc Natl Acad Sci U S A. 2017 Jan 31; 114(5):1135-1140. PMID: 28096418.
    View in: PubMed
  8. Croucher NJ, Campo JJ, Le TQ, Liang X, Bentley SD, Hanage WP, Lipsitch M. Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening. Proc Natl Acad Sci U S A. 2017 Jan 17; 114(3):E357-E366. PMID: 28053228.
    View in: PubMed
  9. Harms K, Lunnan A, Hülter N, Mourier T, Vinner L, Andam CP, Marttinen P, Fridholm H, Hansen AJ, Hanage WP, Nielsen KM, Willerslev E, Johnsen PJ. Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms. Proc Natl Acad Sci U S A. 2016 Dec 27; 113(52):15066-15071. PMID: 27956618.
    View in: PubMed
  10. Chaguza C, Cornick JE, Harris SR, Andam CP, Bricio-Moreno L, Yang M, Yalcin F, Ousmane S, Govindpersad S, Senghore M, Ebruke C, Du Plessis M, Kiran AM, Pluschke G, Sigauque B, McGee L, Klugman KP, Turner P, Corander J, Parkhill J, Collard JM, Antonio M, von Gottberg A, Heyderman RS, French N, Kadioglu A, Hanage WP, Everett DB, Bentley SD. Understanding pneumococcal serotype 1 biology through population genomic analysis. BMC Infect Dis. 2016 Nov 08; 16(1):649. PMID: 27821148.
    View in: PubMed
  11. Chaguza C, Andam CP, Harris SR, Cornick JE, Yang M, Bricio-Moreno L, Kamng'ona AW, Parkhill J, French N, Heyderman RS, Kadioglu A, Everett DB, Bentley SD, Hanage WP. Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule. MBio. 2016 Sep 27; 7(5). PMID: 27677790.
    View in: PubMed
  12. Hanage WP. Not So Simple After All: Bacteria, Their Population Genetics, and Recombination. Cold Spring Harb Perspect Biol. 2016 Jul 01; 8(7). PMID: 27091940.
    View in: PubMed
  13. Azarian T, Daum RS, Petty LA, Steinbeck JL, Yin Z, Nolan D, Boyle-Vavra S, Hanage WP, Salemi M, David MZ. Intrahost Evolution of Methicillin-Resistant Staphylococcus aureus USA300 Among Individuals With Reoccurring Skin and Soft-Tissue Infections. J Infect Dis. 2016 Sep 15; 214(6):895-905. PMID: 27288537; PMCID: PMC4996148 [Available on 09/15/17].
  14. Numminen E, Gutmann M, Shubin M, Marttinen P, Méric G, van Schaik W, Coque TM, Baquero F, Willems RJ, Sheppard SK, Feil EJ, Hanage WP, Corander J. The impact of host metapopulation structure on the population genetics of colonizing bacteria. J Theor Biol. 2016 May 07; 396:53-62. PMID: 26916623.
    View in: PubMed
  15. Chang HH, Dordel J, Donker T, Worby CJ, Feil EJ, Hanage WP, Bentley SD, Huang SS, Lipsitch M. Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus. Genome Med. 2016 Feb 13; 8(1):18. PMID: 26873713; PMCID: PMC4752745.
  16. Hausdorff WP, Hanage WP. Interim results of an ecological experiment - Conjugate vaccination against the pneumococcus and serotype replacement. Hum Vaccin Immunother. 2016; 12(2):358-74. PMID: 26905681.
    View in: PubMed
  17. Chang Q, Lipsitch M, Hanage WP. Impact of Host Heterogeneity on the Efficacy of Interventions to Reduce Staphylococcus aureus Carriage. Infect Control Hosp Epidemiol. 2016 Feb; 37(2):197-204. PMID: 26598029; PMCID: PMC4760641.
  18. Marttinen P, Croucher NJ, Gutmann MU, Corander J, Hanage WP. Recombination produces coherent bacterial species clusters in both core and accessory genomes. Microb Genom. 2015 Nov; 1(5):e000038. PMID: 28348822.
    View in: PubMed
  19. Croucher NJ, Finkelstein JA, Pelton SI, Parkhill J, Bentley SD, Lipsitch M, Hanage WP. Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae. Sci Data. 2015; 2:150058. PMID: 26528397; PMCID: PMC4622223.
  20. Goldstein E, Greene SK, Olson DR, Hanage WP, Lipsitch M. Estimating the hospitalization burden associated with influenza and respiratory syncytial virus in New York City, 2003-2011. Influenza Other Respir Viruses. 2015 Sep; 9(5):225-33. PMID: 25980600; PMCID: PMC4548992.
  21. Mitchell PK, Lipsitch M, Hanage WP. Carriage burden, multiple colonization and antibiotic pressure promote emergence of resistant vaccine escape pneumococci. Philos Trans R Soc Lond B Biol Sci. 2015 Jun 05; 370(1670):20140342. PMID: 25918447; PMCID: PMC4424439.
  22. Li Y, Croucher NJ, Thompson CM, Trzcinski K, Hanage WP, Lipsitch M. Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity. BMC Genomics. 2015 May 09; 16:369. PMID: 25956132; PMCID: PMC4424882.
  23. Dallman TJ, Byrne L, Ashton PM, Cowley LA, Perry NT, Adak G, Petrovska L, Ellis RJ, Elson R, Underwood A, Green J, Hanage WP, Jenkins C, Grant K, Wain J. Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157. Clin Infect Dis. 2015 Aug 01; 61(3):305-12. PMID: 25888672; PMCID: PMC4542925.
  24. Méric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, Mikhail J, Harris LG, Wilkinson TS, Rolo J, Lamble S, Bray JE, Jolley KA, Hanage WP, Bowden R, Maiden MC, Mack D, de Lencastre H, Feil EJ, Corander J, Sheppard SK. Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis. Genome Biol Evol. 2015 Apr 16; 7(5):1313-28. PMID: 25888688; PMCID: PMC4453061.
  25. Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M, Hanage WP. Selective and genetic constraints on pneumococcal serotype switching. PLoS Genet. 2015 Mar; 11(3):e1005095. PMID: 25826208; PMCID: PMC4380333.
  26. Perron GG, Whyte L, Turnbaugh PJ, Goordial J, Hanage WP, Dantas G, Desai MM. Functional characterization of bacteria isolated from ancient arctic soil exposes diverse resistance mechanisms to modern antibiotics. PLoS One. 2015; 10(3):e0069533. PMID: 25807523; PMCID: PMC4373940.
  27. Chang HH, Cohen T, Grad YH, Hanage WP, O'Brien TF, Lipsitch M. Origin and proliferation of multiple-drug resistance in bacterial pathogens. Microbiol Mol Biol Rev. 2015 Mar; 79(1):101-16. PMID: 25652543; PMCID: PMC4402963.
  28. Chang Q, Stevenson AE, Croucher NJ, Lee GM, Pelton SI, Lipsitch M, Finkelstein JA, Hanage WP. Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced. BMC Infect Dis. 2015 Feb 18; 15:68. PMID: 25887323; PMCID: PMC4336693.
  29. Hilty M, Wüthrich D, Salter SJ, Engel H, Campbell S, Sá-Leão R, de Lencastre H, Hermans P, Sadowy E, Turner P, Chewapreecha C, Diggle M, Pluschke G, McGee L, Köseoglu Eser Ö, Low DE, Smith-Vaughan H, Endimiani A, Küffer M, Dupasquier M, Beaudoing E, Weber J, Bruggmann R, Hanage WP, Parkhill J, Hathaway LJ, Mühlemann K, Bentley SD. Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages. Genome Biol Evol. 2014 Dec 04; 6(12):3281-94. PMID: 25480686; PMCID: PMC4986459.
  30. Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD, Hanage WP. Diversification of bacterial genome content through distinct mechanisms over different timescales. Nat Commun. 2014 Nov 19; 5:5471. PMID: 25407023; PMCID: PMC4263131.
  31. Andam CP, Hanage WP. Mechanisms of genome evolution of Streptococcus. Infect Genet Evol. 2015 Jul; 33:334-42. PMID: 25461843; PMCID: PMC4430445.
  32. Worby CJ, Chang HH, Hanage WP, Lipsitch M. The distribution of pairwise genetic distances: a tool for investigating disease transmission. Genetics. 2014 Dec; 198(4):1395-404. PMID: 25313129; PMCID: PMC4256759.
  33. Hanage WP. Microbiology: Microbiome science needs a healthy dose of scepticism. Nature. 2014 Aug 21; 512(7514):247-8. PMID: 25143098.
    View in: PubMed
  34. Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR, Mather AE, Hanage WP, Goldblatt D, Nosten FH, Turner C, Turner P, Bentley SD, Parkhill J. Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes. PLoS Genet. 2014 Aug; 10(8):e1004547. PMID: 25101644; PMCID: PMC4125147.
  35. Chang Q, Wang W, Regev-Yochay G, Lipsitch M, Hanage WP. Antibiotics in agriculture and the risk to human health: how worried should we be? Evol Appl. 2015 Mar; 8(3):240-7. PMID: 25861382; PMCID: PMC4380918.
  36. Kemp MW, Lazarus BM, Perron GG, Hanage WP, Chapman E. Biomedical Ph.D. students enrolled in two elite universities in the United kingdom and the United States report adopting multiple learning relationships. PLoS One. 2014; 9(7):e103075. PMID: 25054473; PMCID: PMC4108381.
  37. Croucher NJ, Hanage WP, Harris SR, McGee L, van der Linden M, de Lencastre H, Sá-Leão R, Song JH, Ko KS, Beall B, Klugman KP, Parkhill J, Tomasz A, Kristinsson KG, Bentley SD. Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone. BMC Biol. 2014 Jun 23; 12:49. PMID: 24957517; PMCID: PMC4094930.
  38. Croucher NJ, Chewapreecha C, Hanage WP, Harris SR, McGee L, van der Linden M, Song JH, Ko KS, de Lencastre H, Turner C, Yang F, Sá-Leão R, Beall B, Klugman KP, Parkhill J, Turner P, Bentley SD. Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape. Genome Biol Evol. 2014 Jun 10; 6(7):1589-602. PMID: 24916661; PMCID: PMC4122920.
  39. Mostowy R, Croucher NJ, Hanage WP, Harris SR, Bentley S, Fraser C. Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution. PLoS Genet. 2014 May; 10(5):e1004300. PMID: 24786281; PMCID: PMC4006708.
  40. Sheppard SK, Cheng L, Méric G, de Haan CP, Llarena AK, Marttinen P, Vidal A, Ridley A, Clifton-Hadley F, Connor TR, Strachan NJ, Forbes K, Colles FM, Jolley KA, Bentley SD, Maiden MC, Hänninen ML, Parkhill J, Hanage WP, Corander J. Cryptic ecology among host generalist Campylobacter jejuni in domestic animals. Mol Ecol. 2014 May; 23(10):2442-51. PMID: 24689900; PMCID: PMC4237157.
  41. Worby CJ, Lipsitch M, Hanage WP. Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data. PLoS Comput Biol. 2014 Mar; 10(3):e1003549. PMID: 24675511; PMCID: PMC3967931.
  42. Grad YH, Kirkcaldy RD, Trees D, Dordel J, Harris SR, Goldstein E, Weinstock H, Parkhill J, Hanage WP, Bentley S, Lipsitch M. Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study. Lancet Infect Dis. 2014 Mar; 14(3):220-6. PMID: 24462211; PMCID: PMC4030102.
  43. Haggerty LS, Jachiet PA, Hanage WP, Fitzpatrick DA, Lopez P, O'Connell MJ, Pisani D, Wilkinson M, Bapteste E, McInerney JO. A pluralistic account of homology: adapting the models to the data. Mol Biol Evol. 2014 Mar; 31(3):501-16. PMID: 24273322; PMCID: PMC3935183.
  44. Lee GM, Kleinman K, Pelton SI, Hanage W, Huang SS, Lakoma M, Dutta-Linn M, Croucher NJ, Stevenson A, Finkelstein JA. Impact of 13-Valent Pneumococcal Conjugate Vaccination on Streptococcus pneumoniae Carriage in Young Children in Massachusetts. J Pediatric Infect Dis Soc. 2014 Mar; 3(1):23-32. PMID: 24567842; PMCID: PMC3933044.
  45. Katz LS, Petkau A, Beaulaurier J, Tyler S, Antonova ES, Turnsek MA, Guo Y, Wang S, Paxinos EE, Orata F, Gladney LM, Stroika S, Folster JP, Rowe L, Freeman MM, Knox N, Frace M, Boncy J, Graham M, Hammer BK, Boucher Y, Bashir A, Hanage WP, Van Domselaar G, Tarr CL. Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. MBio. 2013 Jul 02; 4(4). PMID: 23820394; PMCID: PMC3705451.
  46. Shepheard MA, Fleming VM, Connor TR, Corander J, Feil EJ, Fraser C, Hanage WP. Historical zoonoses and other changes in host tropism of Staphylococcus aureus, identified by phylogenetic analysis of a population dataset. PLoS One. 2013; 8(5):e62369. PMID: 23667472; PMCID: PMC3647051.
  47. Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM, Parkhill J, Bentley SD, Hanage WP, Lipsitch M. Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet. 2013 Jun; 45(6):656-63. PMID: 23644493; PMCID: PMC3725542.
  48. Hanage WP. Fuzzy species revisited. BMC Biol. 2013 Apr 15; 11:41. PMID: 23587266; PMCID: PMC3626887.
  49. Croucher NJ, Harris SR, Grad YH, Hanage WP. Bacterial genomes in epidemiology--present and future. Philos Trans R Soc Lond B Biol Sci. 2013 Mar 19; 368(1614):20120202. PMID: 23382424; PMCID: PMC3678326.
  50. Grad YH, Godfrey P, Cerquiera GC, Mariani-Kurkdjian P, Gouali M, Bingen E, Shea TP, Haas BJ, Griggs A, Young S, Zeng Q, Lipsitch M, Waldor MK, Weill FX, Wortman JR, Hanage WP. Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen. MBio. 2013 Jan 22; 4(1):e00452-12. PMID: 23341549; PMCID: PMC3551546.
  51. Polz MF, Alm EJ, Hanage WP. Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet. 2013 Mar; 29(3):170-5. PMID: 23332119; PMCID: PMC3760709.
  52. Castillo-Ramírez S, Corander J, Marttinen P, Aldeljawi M, Hanage WP, Westh H, Boye K, Gulay Z, Bentley SD, Parkhill J, Holden MT, Feil EJ. Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus. Genome Biol. 2012 Dec 27; 13(12):R126. PMID: 23270620; PMCID: PMC3803117.
  53. Grad YH, Lipsitch M, Griggs AD, Haas BJ, Shea TP, McCowan C, Montmayeur A, FitzGerald M, Wortman JR, Krogfelt KA, Bingen E, Weill FX, Tietze E, Flieger A, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP. Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany. Proc Natl Acad Sci U S A. 2012 Dec 26; 109(52):E3629-30. PMID: 23479789; PMCID: PMC3535640.
  54. Connor TR, Corander J, Hanage WP. Population subdivision and the detection of recombination in non-typable Haemophilus influenzae. Microbiology. 2012 Dec; 158(Pt 12):2958-64. PMID: 23038806; PMCID: PMC4083659.
  55. Sirén J, Hanage WP, Corander J. Inference on population histories by approximating infinite alleles diffusion. Mol Biol Evol. 2013 Feb; 30(2):457-68. PMID: 22993237; PMCID: PMC3548313.
  56. Willems RJ, Top J, van Schaik W, Leavis H, Bonten M, Sirén J, Hanage WP, Corander J. Restricted gene flow among hospital subpopulations of Enterococcus faecium. MBio. 2012; 3(4):e00151-12. PMID: 22807567; PMCID: PMC3413404.
  57. Scott JR, Hinds J, Gould KA, Millar EV, Reid R, Santosham M, O'Brien KL, Hanage WP. Nontypeable pneumococcal isolates among navajo and white mountain apache communities: are these really a cause of invasive disease? J Infect Dis. 2012 Jul 01; 206(1):73-80. PMID: 22536000; PMCID: PMC3415932.
  58. Salter SJ, Hinds J, Gould KA, Lambertsen L, Hanage WP, Antonio M, Turner P, Hermans PW, Bootsma HJ, O'Brien KL, Bentley SD. Variation at the capsule locus, cps, of mistyped and non-typable Streptococcus pneumoniae isolates. Microbiology. 2012 Jun; 158(Pt 6):1560-9. PMID: 22403189; PMCID: PMC3541774.
  59. 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. Pneumococcal carriage and antibiotic resistance in young children before 13-valent conjugate vaccine. Pediatr Infect Dis J. 2012 Mar; 31(3):249-54. PMID: 22173142; PMCID: PMC3288953.
  60. Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, Fitzgerald M, Godfrey P, Haas BJ, Murphy CI, 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-Møller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci U S A. 2012 Feb 21; 109(8):3065-70. PMID: 22315421; PMCID: PMC3286951.
  61. Scott JR, Hanage WP, Lipsitch M, Millar EV, Moulton LH, Hinds J, Reid R, Santosham M, O'Brien KL. Pneumococcal sequence type replacement among American Indian children: a comparison of pre- and routine-PCV7 eras. Vaccine. 2012 Mar 16; 30(13):2376-81. PMID: 22094283.
    View in: PubMed
  62. Corander J, Connor TR, O'Dwyer CA, Kroll JS, Hanage WP. Population structure in the Neisseria, and the biological significance of fuzzy species. J R Soc Interface. 2012 Jun 07; 9(71):1208-15. PMID: 22072450; PMCID: PMC3350722.
  63. Marttinen P, Hanage WP, Croucher NJ, Connor TR, Harris SR, Bentley SD, Corander J. Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res. 2012 Jan; 40(1):e6. PMID: 22064866; PMCID: PMC3245952.
  64. Hyams C, Opel S, Hanage W, Yuste J, Bax K, Henriques-Normark B, Spratt BG, Brown JS. Effects of Streptococcus pneumoniae strain background on complement resistance. PLoS One. 2011; 6(10):e24581. PMID: 22022358; PMCID: PMC3192701.
  65. Hanage WP, Bishop CJ, Lee GM, Lipsitch M, Stevenson A, Rifas-Shiman SL, Pelton SI, Huang SS, Finkelstein JA. Clonal replacement among 19A Streptococcus pneumoniae in Massachusetts, prior to 13 valent conjugate vaccination. Vaccine. 2011 Nov 08; 29(48):8877-81. PMID: 21964059; PMCID: PMC3221484.
  66. Willems RJ, Hanage WP, Bessen DE, Feil EJ. Population biology of Gram-positive pathogens: high-risk clones for dissemination of antibiotic resistance. FEMS Microbiol Rev. 2011 Sep; 35(5):872-900. PMID: 21658083; PMCID: PMC3242168.
  67. Donkor ES, Bishop CJ, Gould K, Hinds J, Antonio M, Wren B, Hanage WP. High levels of recombination among Streptococcus pneumoniae isolates from the Gambia. MBio. 2011; 2(3):e00040-11. PMID: 21693638; PMCID: PMC3119534.
  68. Hanage WP, Bishop CJ, Huang SS, Stevenson AE, Pelton SI, Lipsitch M, Finkelstein JA. Carried pneumococci in Massachusetts children: the contribution of clonal expansion and serotype switching. Pediatr Infect Dis J. 2011 Apr; 30(4):302-8. PMID: 21085049; PMCID: PMC3175614.
  69. Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, von Gottberg A, Song JH, Ko KS, Pichon B, Baker S, Parry CM, Lambertsen LM, Shahinas D, Pillai DR, Mitchell TJ, Dougan G, Tomasz A, Klugman KP, Parkhill J, Hanage WP, Bentley SD. Rapid pneumococcal evolution in response to clinical interventions. Science. 2011 Jan 28; 331(6016):430-4. PMID: 21273480; PMCID: PMC3648787.
  70. Yildirim I, Hanage WP, Lipsitch M, Shea KM, Stevenson A, Finkelstein J, Huang SS, Lee GM, Kleinman K, Pelton SI. Serotype specific invasive capacity and persistent reduction in invasive pneumococcal disease. Vaccine. 2010 Dec 16; 29(2):283-8. PMID: 21029807; PMCID: PMC3139683.
  71. Baker S, Hanage WP, Holt KE. Navigating the future of bacterial molecular epidemiology. Curr Opin Microbiol. 2010 Oct; 13(5):640-5. PMID: 20846899; PMCID: PMC2963795.
  72. Hanage WP, Finkelstein JA, Huang SS, Pelton SI, Stevenson AE, Kleinman K, Hinrichsen VL, Fraser C. Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete. Epidemics. 2010 Jun; 2(2):80-4. PMID: 21031138; PMCID: PMC2963072.
  73. 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. HIV-1 transmitting couples have similar viral load set-points in Rakai, Uganda. PLoS Pathog. 2010 May 06; 6(5):e1000876. PMID: 20463808; PMCID: PMC2865511.
  74. 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. Re-emergence of the type 1 pilus among Streptococcus pneumoniae isolates in Massachusetts, USA. Vaccine. 2010 Jul 05; 28(30):4842-6. PMID: 20434550; PMCID: PMC2897942.
  75. Hanage WP. Charles Darwin in modern epidemiology and public health: the celebration continues. J Epidemiol Community Health. 2011 Jan; 65(1):6-7. PMID: 19996353.
    View in: PubMed
  76. Colijn C, Cohen T, Fraser C, Hanage W, Goldstein E, Givon-Lavi N, Dagan R, Lipsitch M. What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae? J R Soc Interface. 2010 Jun 06; 7(47):905-19. PMID: 19940002; PMCID: PMC2871802.
  77. Tang J, Hanage WP, Fraser C, Corander J. Identifying currents in the gene pool for bacterial populations using an integrative approach. PLoS Comput Biol. 2009 Aug; 5(8):e1000455. PMID: 19662158; PMCID: PMC2713424.
  78. Lee GM, Huang SS, Rifas-Shiman SL, Hinrichsen VL, Pelton SI, Kleinman K, Hanage WP, Lipsitch M, McAdam AJ, Finkelstein JA. Epidemiology and risk factors for Staphylococcus aureus colonization in children in the post-PCV7 era. BMC Infect Dis. 2009 Jul 11; 9:110. PMID: 19594890; PMCID: PMC2716346.
  79. Huang SS, Hinrichsen VL, Stevenson AE, Rifas-Shiman SL, Kleinman K, Pelton SI, Lipsitch M, Hanage WP, Lee GM, Finkelstein JA. Continued impact of pneumococcal conjugate vaccine on carriage in young children. Pediatrics. 2009 Jul; 124(1):e1-11. PMID: 19564254; PMCID: PMC2782668.
  80. Hanage WP, Fraser C, Tang J, Connor TR, Corander J. Hyper-recombination, diversity, and antibiotic resistance in pneumococcus. Science. 2009 Jun 12; 324(5933):1454-7. PMID: 19520963.
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  81. 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. Pandemic potential of a strain of influenza A (H1N1): early findings. Science. 2009 Jun 19; 324(5934):1557-61. PMID: 19433588; PMCID: PMC3735127.
  82. Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP. The bacterial species challenge: making sense of genetic and ecological diversity. Science. 2009 Feb 06; 323(5915):741-6. PMID: 19197054.
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  83. Bishop CJ, Aanensen DM, Jordan GE, Kilian M, Hanage WP, Spratt BG. Assigning strains to bacterial species via the internet. BMC Biol. 2009 Jan 26; 7:3. PMID: 19171050; PMCID: PMC2636762.
  84. Hanage WP, Aanensen DM. Methods for data analysis. Methods Mol Biol. 2009; 551:287-304. PMID: 19521881.
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  85. Lipsitch M, Colijn C, Cohen T, Hanage WP, Fraser C. No coexistence for free: neutral null models for multistrain pathogens. Epidemics. 2009 Mar; 1(1):2-13. PMID: 21352747; PMCID: PMC3099423.
  86. Marttinen P, Baldwin A, Hanage WP, Dowson C, Mahenthiralingam E, Corander J. Bayesian modeling of recombination events in bacterial populations. BMC Bioinformatics. 2008 Oct 07; 9:421. PMID: 18840286; PMCID: PMC2579306.
  87. Melin MM, Hollingshead SK, Briles DE, Hanage WP, Lahdenkari M, Kaijalainen T, Kilpi TM, Käyhty HM. 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. Clin Vaccine Immunol. 2008 Oct; 15(10):1555-63. PMID: 18753340; PMCID: PMC2565924.
  88. 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. Streptococcus pneumoniae contains 3 rlrA pilus variants that are clonally related. J Infect Dis. 2008 Mar 15; 197(6):888-96. PMID: 18269316.
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  89. Hanage WP. Serotype-specific problems associated with pneumococcal conjugate vaccination. Future Microbiol. 2008 Feb; 3(1):23-30. PMID: 18230031.
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  90. Fraser C, Hollingsworth TD, Chapman R, de Wolf F, Hanage WP. Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis. Proc Natl Acad Sci U S A. 2007 Oct 30; 104(44):17441-6. PMID: 17954909; PMCID: PMC2077275.
  91. Hanage WP. Serotype replacement in invasive pneumococcal disease: where do we go from here? J Infect Dis. 2007 Nov 01; 196(9):1282-4. PMID: 17922390.
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  92. Pelton SI, Huot H, Finkelstein JA, Bishop CJ, Hsu KK, Kellenberg J, Huang SS, Goldstein R, Hanage WP. Emergence of 19A as virulent and multidrug resistant Pneumococcus in Massachusetts following universal immunization of infants with pneumococcal conjugate vaccine. Pediatr Infect Dis J. 2007 Jun; 26(6):468-72. PMID: 17529860.
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  93. Turner KM, Hanage WP, Fraser C, Connor TR, Spratt BG. Assessing the reliability of eBURST using simulated populations with known ancestry. BMC Microbiol. 2007 Apr 12; 7:30. PMID: 17430587; PMCID: PMC1865383.
  94. Fraser C, Hanage WP, Spratt BG. Recombination and the nature of bacterial speciation. Science. 2007 Jan 26; 315(5811):476-80. PMID: 17255503; PMCID: PMC2220085.
  95. Hanage WP, Huang SS, Lipsitch M, Bishop CJ, Godoy D, Pelton SI, Goldstein R, Huot H, Finkelstein JA. Diversity and antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae carriage isolates in the post-heptavalent conjugate vaccine era. J Infect Dis. 2007 Feb 01; 195(3):347-52. PMID: 17205472.
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  96. Hanage WP, Spratt BG, Turner KM, Fraser C. Modelling bacterial speciation. Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29; 361(1475):2039-44. PMID: 17062418; PMCID: PMC1764933.
  97. Hanage WP, Fraser C, Spratt BG. Sequences, sequence clusters and bacterial species. Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29; 361(1475):1917-27. PMID: 17062411; PMCID: PMC1764932.
  98. Porat N, Greenberg D, Givon-Lavi N, Shuval DS, Trefler R, Segev O, Hanage WP, Dagan R. The important role of nontypable Streptococcus pneumoniae international clones in acute conjunctivitis. J Infect Dis. 2006 Sep 01; 194(5):689-96. PMID: 16897669.
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  99. Wiles S, Hanage WP, Frankel G, Robertson B. Modelling infectious disease - time to think outside the box? Nat Rev Microbiol. 2006 Apr; 4(4):307-12. PMID: 16518420.
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  100. Hanage WP, Kaijalainen T, Saukkoriipi A, Rickcord JL, Spratt BG. A successful, diverse disease-associated lineage of nontypeable pneumococci that has lost the capsular biosynthesis locus. J Clin Microbiol. 2006 Mar; 44(3):743-9. PMID: 16517849; PMCID: PMC1393106.
  101. Fisher MC, Hanage WP, de Hoog S, Johnson E, Smith MD, White NJ, Vanittanakom N. Low effective dispersal of asexual genotypes in heterogeneous landscapes by the endemic pathogen Penicillium marneffei. PLoS Pathog. 2005 Oct; 1(2):e20. PMID: 16254598; PMCID: PMC1266309.
  102. Hanage WP, Fraser C, Spratt BG. The impact of homologous recombination on the generation of diversity in bacteria. J Theor Biol. 2006 Mar 21; 239(2):210-9. PMID: 16236325.
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  103. Hanage WP, Kaijalainen T, Herva E, Saukkoriipi A, Syrjänen R, Spratt BG. Using multilocus sequence data to define the pneumococcus. J Bacteriol. 2005 Sep; 187(17):6223-30. PMID: 16109964; PMCID: PMC1196147.
  104. Hanage WP, Fraser C, Spratt BG. Fuzzy species among recombinogenic bacteria. BMC Biol. 2005 Mar 07; 3:6. PMID: 15752428; PMCID: PMC554772.
  105. Fraser C, Hanage WP, Spratt BG. Neutral microepidemic evolution of bacterial pathogens. Proc Natl Acad Sci U S A. 2005 Feb 08; 102(6):1968-73. PMID: 15684071; PMCID: PMC548543.
  106. Hanage WP, Kaijalainen TH, Syrjänen RK, Auranen K, Leinonen M, Mäkelä PH, Spratt BG. Invasiveness of serotypes and clones of Streptococcus pneumoniae among children in Finland. Infect Immun. 2005 Jan; 73(1):431-5. PMID: 15618181; PMCID: PMC538975.
  107. Spratt BG, Hanage WP, Li B, Aanensen DM, Feil EJ. Displaying the relatedness among isolates of bacterial species -- the eBURST approach. FEMS Microbiol Lett. 2004 Dec 15; 241(2):129-34. PMID: 15598523.
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  108. Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol. 2004 Mar; 186(5):1518-30. PMID: 14973027; PMCID: PMC344416.
  109. Hanage WP, Auranen K, Syrjänen R, Herva E, Mäkelä PH, Kilpi T, Spratt BG. Ability of pneumococcal serotypes and clones to cause acute otitis media: implications for the prevention of otitis media by conjugate vaccines. Infect Immun. 2004 Jan; 72(1):76-81. PMID: 14688083; PMCID: PMC343969.
  110. Hanage WP, Cohen J. Stimulation of cytokine release and adhesion molecule expression by products of Viridans streptococci. J Infect Dis. 2002 Feb 01; 185(3):357-67. PMID: 11807718.
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  111. Spratt BG, Hanage WP, Feil EJ. The relative contributions of recombination and point mutation to the diversification of bacterial clones. Curr Opin Microbiol. 2001 Oct; 4(5):602-6. PMID: 11587939.
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