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William P. Hanage, Ph.D.

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Overview
I am an Associate Professor of Epidemiology in the department of Epidemiology, and a faculty member in the Center for Communicable Disease Dynamics. I employ a mix of theoretical and laboratory work to research the evolution and epidemiology of infectious disease. After my PhD, I did post doctoral study at the University of Oxford and Imperial College London, before being awarded a Royal Society University Research Fellowship. Prior to joining the Center for Communicable Disease Dynamics, I was a Reader in the department of Infectious Disease Epidemiology at Imperial College London. There I 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. I am particularly interested in using an evolutionary framework such as methods derived from population genetics to inform epidemiology. In 2012 I received the Fleming Prize for research in Microbiology and was the recipient of a 2012 ICAAC Young Investigator Award from the American Society for Microbiology.

Research
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.
  1. R01AI128344 (HANAGE, WILLIAM) Jun 26, 2017 - May 31, 2022
    NIH
    Deep sequencing of pathogens to precisely define transmission networks using rare variants
    Role: Principal Investigator
  2. R01AI106786 (HANAGE, WILLIAM) Jun 1, 2013 - May 31, 2020
    NIH
    Ecological and genetic contributions to the spread of resistance in pneumococcus
    Role: Principal Investigator
  3. U54GM088558 (LIPSITCH, MARC) Sep 15, 2009 - Sep 19, 2014
    NIH
    MIDAS Center for Communicable Disease Dynamics
    Role: Co-Principal Investigator

Featured Content

Bibliographic
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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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Che Y, Yang Y, Xu X, Brinda K, Polz MF, Hanage WP, Zhang T. Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes. Proc Natl Acad Sci U S A. 2021 Feb 09; 118(6). PMID: 33526659.
    Citations:    Fields:    
  2. Tran TN, Wikle N, Albert J, Inam H, Strong E, Brinda K, Leighow SM, Yang F, Hossain S, Pritchard JR, Chan P, Hanage WP, Hanks EM, Boni MF. Optimal SARS-CoV-2 vaccine allocation using real-time seroprevalence estimates in Rhode Island and Massachusetts. medRxiv. 2021 Jan 15. PMID: 33469599.
    Citations:    
  3. Harrow GL, Lees JA, Hanage WP, Lipsitch M, Corander J, Colijn C, Croucher NJ. Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. ISME J. 2021 Jan 06. PMID: 33408365.
    Citations:    Fields:    
  4. Lemieux JE, Siddle KJ, Shaw BM, Loreth C, Schaffner SF, Gladden-Young A, Adams G, Fink T, Tomkins-Tinch CH, Krasilnikova LA, DeRuff KC, Rudy M, Bauer MR, Lagerborg KA, Normandin E, Chapman SB, Reilly SK, Anahtar MN, Lin AE, Carter A, Myhrvold C, Kemball ME, Chaluvadi S, Cusick C, Flowers K, Neumann A, Cerrato F, Farhat M, Slater D, Harris JB, Branda JA, Hooper D, Gaeta JM, Baggett TP, O'Connell J, Gnirke A, Lieberman TD, Philippakis A, Burns M, Brown CM, Luban J, Ryan ET, Turbett SE, LaRocque RC, Hanage WP, Gallagher GR, Madoff LC, Smole S, Pierce VM, Rosenberg E, Sabeti PC, Park DJ, MacInnis BL. Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science. 2021 02 05; 371(6529). PMID: 33303686.
    Citations: 1     Fields:    Translation:HumansPHPublic Health
  5. Levin AT, Hanage WP, Owusu-Boaitey N, Cochran KB, Walsh SP, Meyerowitz-Katz G. Assessing the age specificity of infection fatality rates for COVID-19: systematic review, meta-analysis, and public policy implications. Eur J Epidemiol. 2020 Dec; 35(12):1123-1138. PMID: 33289900.
    Citations: 5     Fields:    Translation:HumansPHPublic Health
  6. Goldenfeld M, Nir-Paz R, Segal G, Bar-On E, Mendelson E, Mandelboim M, Wolf DG, Marom EM, Israely T, Achdout H, Rahav G, Hanage WP, Regev-Yochay G. Characteristics of Clinically Asymptomatic Patients with SARS-CoV-2 Infections, Case Series. Prehosp Disaster Med. 2021 Feb; 36(1):125-128. PMID: 33198831.
    Citations: 1     Fields:    Translation:Humans
  7. Choi B, Choudhary MC, Regan J, Sparks JA, Padera RF, Qiu X, Solomon IH, Kuo HH, Boucau J, Bowman K, Adhikari UD, Winkler ML, Mueller AA, Hsu TY, Desjardins M, Baden LR, Chan BT, Walker BD, Lichterfeld M, Brigl M, Kwon DS, Kanjilal S, Richardson ET, Jonsson AH, Alter G, Barczak AK, Hanage WP, Yu XG, Gaiha GD, Seaman MS, Cernadas M, Li JZ. Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host. N Engl J Med. 2020 12 03; 383(23):2291-2293. PMID: 33176080.
    Citations: 14     Fields:    Translation:Humans
  8. Hanage WP, Testa C, Chen JT, Davis L, Pechter E, Seminario P, Santillana M, Krieger N. COVID-19: US federal accountability for entry, spread, and inequities-lessons for the future. Eur J Epidemiol. 2020 Nov; 35(11):995-1006. PMID: 33136249.
    Citations: 4     Fields:    Translation:HumansPHPublic Health
  9. Krieger N, Testa C, Hanage WP, Chen JT. US racial and ethnic data for COVID-19 cases: still missing in action. Lancet. 2020 11 07; 396(10261):e81. PMID: 33169681.
    Citations: 4     Fields:    Translation:HumansCellsPHPublic Health
  10. Azarian T, Martinez PP, Arnold BJ, Qiu X, Grant LR, Corander J, Fraser C, Croucher NJ, Hammitt LL, Reid R, Santosham M, Weatherholtz RC, Bentley SD, O'Brien KL, Lipsitch M, Hanage WP. Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae. PLoS Biol. 2020 10; 18(10):e3000878. PMID: 33091022.
    Citations: 1     Fields:    Translation:Cells
  11. Alwan NA, Burgess RA, Ashworth S, Beale R, Bhadelia N, Bogaert D, Dowd J, Eckerle I, Goldman LR, Greenhalgh T, Gurdasani D, Hamdy A, Hanage WP, Hodcroft EB, Hyde Z, Kellam P, Kelly-Irving M, Krammer F, Lipsitch M, McNally A, McKee M, Nouri A, Pimenta D, Priesemann V, Rutter H, Silver J, Sridhar D, Swanton C, Walensky RP, Yamey G, Ziauddeen H. Scientific consensus on the COVID-19 pandemic: we need to act now. Lancet. 2020 10 31; 396(10260):e71-e72. PMID: 33069277.
    Citations: 14     Fields:    Translation:HumansCellsPHPublic Health
  12. Lemieux JE, Siddle KJ, Shaw BM, Loreth C, Schaffner SF, Gladden-Young A, Adams G, Fink T, Tomkins-Tinch CH, Krasilnikova LA, DeRuff KC, Rudy M, Bauer MR, Lagerborg KA, Normandin E, Chapman SB, Reilly SK, Anahtar MN, Lin AE, Carter A, Myhrvold C, Kemball ME, Chaluvadi S, Cusick C, Flowers K, Neumann A, Cerrato F, Farhat M, Slater D, Harris JB, Branda J, Hooper D, Gaeta JM, Baggett TP, O'Connell J, Gnirke A, Lieberman TD, Philippakis A, Burns M, Brown CM, Luban J, Ryan ET, Turbett SE, LaRocque RC, Hanage WP, Gallagher GR, Madoff LC, Smole S, Pierce VM, Rosenberg E, Sabeti PC, Park DJ, Maclnnis BL. Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events. medRxiv. 2020 Aug 25. PMID: 32869040.
    Citations:    
  13. Hanage WP, Vincent VI, Low NM. Seroprevalence of SARS-CoV-2 in Hong Kong returnees. Lancet Microbe. 2020 Aug; 1(4):e147. PMID: 33521713.
    Citations:    
  14. Wu F, Zhang J, Xiao A, Gu X, Lee WL, Armas F, Kauffman K, Hanage W, Matus M, Ghaeli N, Endo N, Duvallet C, Poyet M, Moniz K, Washburne AD, Erickson TB, Chai PR, Thompson J, Alm EJ. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases. mSystems. 2020 Jul 21; 5(4). PMID: 32694130.
    Citations: 75     
  15. Grubaugh ND, Hanage WP, Rasmussen AL. Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. Cell. 2020 08 20; 182(4):794-795. PMID: 32697970.
    Citations: 56     Fields:    Translation:HumansCellsPHPublic Health
  16. Kogan NE, Clemente L, Liautaud P, Kaashoek J, Link NB, Nguyen AT, Lu FS, Huybers P, Resch B, Havas C, Petutschnig A, Davis J, Chinazzi M, Mustafa B, Hanage WP, Vespignani A, Santillana M. An Early Warning Approach to Monitor COVID-19 Activity with Multiple Digital Traces in Near Real-Time. ArXiv. 2020 Jul 01. PMID: 32676518.
    Citations:    
  17. Villabona-Arenas CJ, Hanage WP, Tully DC. Phylogenetic interpretation during outbreaks requires caution. Nat Microbiol. 2020 07; 5(7):876-877. PMID: 32427978.
    Citations: 16     Fields:    Translation:HumansCellsPHPublic Health
  18. Hanage WP, Shelburne SA. Streptococcus pyogenes With Reduced Susceptibility to ß-Lactams: How Big an Alarm Bell? Clin Infect Dis. 2020 Jun 24; 71(1):205-206. PMID: 31630163.
    Citations: 1     Fields:    
  19. Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bonneau R, Brown MA, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, Hanage WP, Huang KH, Lee WL, Matus M, McElroy KA, Nagler J, Rhode SF, Santillana M, Tucker JA, Wuertz S, Zhao S, Thompson J, Alm EJ. SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases. medRxiv. 2020 Jun 23. PMID: 32607521.
    Citations:    
  20. Lehtinen S, Chewapreecha C, Lees J, Hanage WP, Lipsitch M, Croucher NJ, Bentley SD, Turner P, Fraser C, Mostowy RJ. Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae. Sci Adv. 2020 May; 6(21):eaaz6137. PMID: 32671212.
    Citations:    Fields:    
  21. Lee RS, Hanage WP. Reproducibility in science: important or incremental? Lancet Microbe. 2020 Jun; 1(2):e59-60. PMID: 32835329.
    Citations:    
  22. Senghore M, Savi MK, Gnangnon B, Hanage WP, Okeke IN. Leveraging Africa's preparedness towards the next phase of the COVID-19 pandemic. Lancet Glob Health. 2020 07; 8(7):e884-e885. PMID: 32416768.
    Citations: 8     Fields:    Translation:HumansPHPublic Health
  23. Miller JC, Qiu X, Hanage WP. The risk of SARS-CoV-2 transmission in the healthcare setting and potential impact of cohorting strategies. medRxiv. 2020 Apr 23. PMID: 32511644.
    Citations:    
  24. MacFadden DR, Coburn B, Brinda K, Corbeil A, Daneman N, Fisman D, Lee RS, Lipsitch M, McGeer A, Melano RG, Mubareka S, Hanage WP. Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli. Antimicrob Agents Chemother. 2020 04 21; 64(5). PMID: 32152083.
    Citations:    Fields:    
  25. Kraemer MUG, Yang CH, Gutierrez B, Wu CH, Klein B, Pigott DM, du Plessis L, Faria NR, Li R, Hanage WP, Brownstein JS, Layan M, Vespignani A, Tian H, Dye C, Pybus OG, Scarpino SV. The effect of human mobility and control measures on the COVID-19 epidemic in China. Science. 2020 05 01; 368(6490):493-497. PMID: 32213647.
    Citations: 267     Fields:    Translation:HumansCellsPHPublic Health
  26. Chaguza C, Heinsbroek E, Gladstone RA, Tafatatha T, Alaerts M, Peno C, Cornick JE, Musicha P, Bar-Zeev N, Kamng'ona A, Kadioglu A, McGee L, Hanage WP, Breiman RF, Heyderman RS, French N, Everett DB, Bentley SD. Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data. Clin Infect Dis. 2020 03 17; 70(7):1294-1303. PMID: 31094423.
    Citations: 1     Fields:    Translation:HumansCells
  27. Kraemer MUG, Yang CH, Gutierrez B, Wu CH, Klein B, Pigott DM, du Plessis L, Faria NR, Li R, Hanage WP, Brownstein JS, Layan M, Vespignani A, Tian H, Dye C, Cauchemez S, Pybus OG, Scarpino SV. The effect of human mobility and control measures on the COVID-19 epidemic in China. medRxiv. 2020 Mar 06. PMID: 32511452.
    Citations:    
  28. Brinda K, Callendrello A, Ma KC, MacFadden DR, Charalampous T, Lee RS, Cowley L, Wadsworth CB, Grad YH, Kucherov G, O'Grady J, Baym M, Hanage WP. Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing. Nat Microbiol. 2020 03; 5(3):455-464. PMID: 32042129.
    Citations: 9     Fields:    Translation:HumansCells
  29. Lee RS, Proulx JF, McIntosh F, Behr MA, Hanage WP. Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing. Elife. 2020 Feb 04; 9. PMID: 32014110.
    Citations: 5     Fields:    
  30. Arnold B, Sohail M, Wadsworth C, Corander J, Hanage WP, Sunyaev S, Grad YH. Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen. Mol Biol Evol. 2020 02 01; 37(2):417-428. PMID: 31589312.
    Citations: 3     Fields:    Translation:Cells
  31. Hanage WP, Lewnard JA. Pneumococcal conjugate vaccines in different settings - Authors' reply. Lancet Infect Dis. 2019 12; 19(12):1284. PMID: 31782391.
    Citations:    Fields:    Translation:Humans
  32. MacFadden DR, Hanage WP. Potential for Erosion of Efficacy in Noninferiority Trials of Decreasing Duration of Antibiotic Therapy. Clin Infect Dis. 2019 09 13; 69(7):1262. PMID: 30726884.
    Citations: 2     Fields:    Translation:Humans
  33. MacFadden DR, Fisman DN, Hanage WP, Lipsitch M. The Relative Impact of Community and Hospital Antibiotic Use on the Selection of Extended-spectrum Beta-lactamase-producing Escherichia coli. Clin Infect Dis. 2019 06 18; 69(1):182-188. PMID: 30462185.
    Citations: 3     Fields:    Translation:HumansCells
  34. MacFadden DR, Melano RG, Coburn B, Tijet N, Hanage WP, Daneman N. Comparing Patient Risk Factor-, Sequence Type-, and Resistance Locus Identification-Based Approaches for Predicting Antibiotic Resistance in Escherichia coli Bloodstream Infections. J Clin Microbiol. 2019 06; 57(6). PMID: 30894438.
    Citations: 3     Fields:    Translation:HumansCellsPHPublic Health
  35. Hanage WP. Two Health or Not Two Health? That Is the Question. mBio. 2019 04 09; 10(2). PMID: 30967467.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  36. Mitchell PK, Azarian T, Croucher NJ, Callendrello A, Thompson CM, Pelton SI, Lipsitch M, Hanage WP. Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13. Microb Genom. 2019 02; 5(2). PMID: 30777813.
    Citations: 1     Fields:    Translation:HumansCellsPHPublic Health
  37. Lewnard JA, Hanage WP. Making sense of differences in pneumococcal serotype replacement. Lancet Infect Dis. 2019 06; 19(6):e213-e220. PMID: 30709666.
    Citations: 10     Fields:    Translation:HumansCells
  38. Campo JJ, Le TQ, Pablo JV, Hung C, Teng AA, Tettelin H, Tate A, Hanage WP, Alderson MR, Liang X, Malley R, Lipsitch M, Croucher NJ. Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination. Elife. 2018 12 28; 7. PMID: 30592459.
    Citations: 9     Fields:    Translation:HumansCTClinical Trials
  39. Azarian T, Mitchell PK, Georgieva M, Thompson CM, Ghouila A, Pollard AJ, von Gottberg A, du Plessis M, Antonio M, Kwambana-Adams BA, Clarke SC, Everett D, Cornick J, Sadowy E, Hryniewicz W, Skoczynska A, Moïsi JC, McGee L, Beall B, Metcalf BJ, Breiman RF, Ho PL, Reid R, O'Brien KL, Gladstone RA, Bentley SD, Hanage WP. Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci. PLoS Pathog. 2018 11; 14(11):e1007438. PMID: 30475919.
    Citations: 8     Fields:    Translation:HumansCells
  40. Hanage WP. From bacterial genomics to clinical epidemiology: an interview with Bill Hanage. BMC Biol. 2018 11 01; 16(1):122. PMID: 30382834.
    Citations:    Fields:    
  41. Martin MA, Lee RS, Cowley LA, Gardy JL, Hanage WP. Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission. Microb Genom. 2018 10; 4(10). PMID: 30303479.
    Citations: 8     Fields:    Translation:HumansCellsPHPublic Health
  42. Chang Q, Abuelaish I, Biber A, Jaber H, Callendrello A, Andam CP, Regev-Yochay G, Hanage WP. Genomic epidemiology of meticillin-resistant Staphylococcus aureus ST22 widespread in communities of the Gaza Strip, 2009. Euro Surveill. 2018 08; 23(34). PMID: 30153881.
    Citations: 3     Fields:    Translation:HumansCells
  43. Cowley LA, Petersen FC, Junges R, Jimson D Jimenez M, Morrison DA, Hanage WP. Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae. PLoS Genet. 2018 06; 14(6):e1007410. PMID: 29897968.
    Citations: 9     Fields:    Translation:Cells
  44. Azarian T, Grant LR, Arnold BJ, Hammitt LL, Reid R, Santosham M, Weatherholtz R, Goklish N, Thompson CM, Bentley SD, O'Brien KL, Hanage WP, Lipsitch M. The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome. PLoS Pathog. 2018 04; 14(4):e1006966. PMID: 29617440.
    Citations: 9     Fields:    Translation:HumansCellsPHPublic Health
  45. MacFadden DR, McGeer A, Athey T, Perusini S, Olsha R, Li A, Eshaghi A, Gubbay JB, Hanage WP. Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15. Emerg Infect Dis. 2018 03; 24(3):492-497. PMID: 29460729.
    Citations: 5     Fields:    Translation:HumansCellsPHPublic Health
  46. Arnold BJ, Gutmann MU, Grad YH, Sheppard SK, Corander J, Lipsitch M, Hanage WP. Weak Epistasis May Drive Adaptation in Recombining Bacteria. Genetics. 2018 03; 208(3):1247-1260. PMID: 29330348.
    Citations: 11     Fields:    Translation:Cells
  47. Worby CJ, Lipsitch M, Hanage WP. Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data. Am J Epidemiol. 2017 Nov 15; 186(10):1209-1216. PMID: 29149252.
    Citations: 20     Fields:    Translation:HumansPHPublic Health
  48. Corander J, Fraser C, Gutmann MU, Arnold B, Hanage WP, Bentley SD, Lipsitch M, Croucher NJ. Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. Nat Ecol Evol. 2017 Dec; 1(12):1950-1960. PMID: 29038424.
    Citations: 35     Fields:    Translation:Cells
  49. Lee GM, Kleinman K, Pelton S, Lipsitch M, Huang SS, Lakoma M, Dutta-Linn M, Rett M, Hanage WP, Finkelstein JA. Immunization, Antibiotic Use, and Pneumococcal Colonization Over a 15-Year Period. Pediatrics. 2017 Nov; 140(5). PMID: 28978716.
    Citations: 8     Fields:    Translation:HumansCellsPHPublic Health
  50. Cobey S, Baskerville EB, Colijn C, Hanage W, Fraser C, Lipsitch M. Host population structure and treatment frequency maintain balancing selection on drug resistance. J R Soc Interface. 2017 08; 14(133). PMID: 28835542.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  51. Chaguza C, Cornick JE, Andam CP, Gladstone RA, Alaerts M, Musicha P, Peno C, Bar-Zeev N, Kamng'ona AW, Kiran AM, Msefula CL, McGee L, Breiman RF, Kadioglu A, French N, Heyderman RS, Hanage WP, Bentley SD, Everett DB. Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi. Vaccine. 2017 08 16; 35(35 Pt B):4594-4602. PMID: 28711389.
    Citations: 11     Fields:    Translation:HumansCellsPHPublic Health
  52. Marttinen P, Hanage WP. Speciation trajectories in recombining bacterial species. PLoS Comput Biol. 2017 Jul; 13(7):e1005640. PMID: 28671999.
    Citations: 7     Fields:    Translation:Cells
  53. 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 07 13; 35(32):4002-4009. PMID: 28645717.
    Citations: 8     Fields:    Translation:HumansCells
  54. 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 06; 23(6):1012-1015. PMID: 28518018.
    Citations: 2     Fields:    Translation:HumansCellsPHPublic Health
  55. 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 05 01; 34(5):1167-1182. PMID: 28199698.
    Citations: 40     Fields:    Translation:Cells
  56. 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.
    Citations: 9     Fields:    Translation:Humans
  57. 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 04; 55(4):1104-1115. PMID: 28100596.
    Citations: 12     Fields:    Translation:HumansCells
  58. 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 01 31; 114(5):1135-1140. PMID: 28096418.
    Citations: 45     Fields:    Translation:HumansCellsPHPublic Health
  59. 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 01 17; 114(3):E357-E366. PMID: 28053228.
    Citations: 21     Fields:    Translation:HumansCells
  60. 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 12 27; 113(52):15066-15071. PMID: 27956618.
    Citations: 1     Fields:    Translation:HumansCells
  61. 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 11 08; 16(1):649. PMID: 27821148.
    Citations: 9     Fields:    Translation:HumansCells
  62. 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.
    Citations: 22     Fields:    
  63. Hanage WP. Not So Simple After All: Bacteria, Their Population Genetics, and Recombination. Cold Spring Harb Perspect Biol. 2016 07 01; 8(7). PMID: 27091940.
    Citations: 16     Fields:    Translation:Cells
  64. 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 09 15; 214(6):895-905. PMID: 27288537.
    Citations: 13     Fields:    Translation:HumansCells
  65. 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.
    Citations: 4     Fields:    Translation:Cells
  66. 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.
    Citations: 9     Fields:    Translation:HumansCells
  67. 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.
    Citations: 15     Fields:    Translation:HumansCellsPHPublic Health
  68. 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.
    Citations: 1     Fields:    Translation:HumansCells
  69. 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.
    Citations: 11     Fields:    
  70. 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.
    Citations: 21     Fields:    Translation:HumansCells
  71. 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.
    Citations: 17     Fields:    Translation:Humans
  72. 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.
    Citations: 12     Fields:    Translation:HumansCells
  73. 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.
    Citations: 5     Fields:    Translation:AnimalsCells
  74. 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.
    Citations: 62     Fields:    Translation:HumansCellsPHPublic Health
  75. 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.
    Citations: 44     Fields:    Translation:Cells
  76. 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.
    Citations: 28     Fields:    Translation:HumansCells
  77. 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.
    Citations: 39     Fields:    Translation:CellsPHPublic Health
  78. 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.
    Citations: 45     Fields:    Translation:HumansCells
  79. 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.
    Citations: 11     Fields:    Translation:HumansCells
  80. 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, Eser ÖK, 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 12 04; 6(12):3281-94. PMID: 25480686.
    Citations: 29     Fields:    Translation:HumansCells
  81. 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.
    Citations: 75     Fields:    Translation:Cells
  82. Andam CP, Hanage WP. Mechanisms of genome evolution of Streptococcus. Infect Genet Evol. 2015 Jul; 33:334-42. PMID: 25461843.
    Citations: 27     Fields:    Translation:HumansAnimalsCellsPHPublic Health
  83. 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.
    Citations: 16     Fields:    Translation:HumansCellsPHPublic Health
  84. Hanage WP. Microbiology: Microbiome science needs a healthy dose of scepticism. Nature. 2014 Aug 21; 512(7514):247-8. PMID: 25143098.
    Citations: 49     Fields:    Translation:HumansAnimals
  85. 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.
    Citations: 71     Fields:    Translation:HumansCells
  86. 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.
    Citations: 70     
  87. 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.
    Citations:    Fields:    Translation:Humans
  88. 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.
    Citations: 43     Fields:    Translation:HumansCellsPHPublic Health
  89. 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.
    Citations: 42     Fields:    Translation:HumansCells
  90. 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.
    Citations: 43     Fields:    Translation:Cells
  91. 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.
    Citations: 43     Fields:    Translation:AnimalsCells
  92. 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.
    Citations: 57     Fields:    Translation:HumansCellsPHPublic Health
  93. 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.
    Citations: 89     Fields:    Translation:HumansCells
  94. 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.
    Citations: 17     Fields:    Translation:Humans
  95. 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.
    Citations: 34     Fields:    
  96. 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.
    Citations: 66     Fields:    Translation:HumansCellsPHPublic Health
  97. 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.
    Citations: 17     Fields:    Translation:HumansAnimalsCells
  98. 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.
    Citations: 169     Fields:    Translation:HumansCellsPHPublic Health
  99. Hanage WP. Fuzzy species revisited. BMC Biol. 2013 Apr 15; 11:41. PMID: 23587266.
    Citations: 10     Fields:    Translation:AnimalsCells
  100. 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.
    Citations: 24     Fields:    Translation:Cells
  101. 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.
    Citations: 26     Fields:    Translation:HumansCells
  102. 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.
    Citations: 122     Fields:    Translation:Cells
  103. 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.
    Citations: 49     Fields:    Translation:Cells
  104. 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.
    Citations: 3     Fields:    Translation:HumansCellsPHPublic Health
  105. Connor TR, Corander J, Hanage WP. Population subdivision and the detection of recombination in non-typable Haemophilus influenzae. Microbiology (Reading). 2012 Dec; 158(Pt 12):2958-2964. PMID: 23038806.
    Citations: 7     Translation:Cells
  106. 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.
    Citations: 3     Fields:    Translation:Cells
  107. 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.
    Citations: 75     Fields:    Translation:HumansAnimalsCells
  108. 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.
    Citations: 16     Fields:    Translation:HumansCells
  109. Salter SJ, Hinds J, Gould KA, Lambertsen L, Hanage WP, Antonio M, Turner P, Hermans PWM, Bootsma HJ, O'Brien KL, Bentley SD. Variation at the capsule locus, cps, of mistyped and non-typable Streptococcus pneumoniae isolates. Microbiology (Reading). 2012 Jun; 158(Pt 6):1560-1569. PMID: 22403189.
    Citations: 40     Translation:HumansCells
  110. 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.
    Citations: 29     Fields:    Translation:HumansCells
  111. 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.
    Citations: 113     Fields:    Translation:HumansCellsPHPublic Health
  112. 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.
    Citations: 8     Fields:    Translation:HumansCells
  113. 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.
    Citations: 18     Fields:    Translation:Cells
  114. 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.
    Citations: 114     Fields:    Translation:Cells
  115. 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.
    Citations: 10     Fields:    Translation:HumansCells
  116. 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.
    Citations: 25     Fields:    Translation:HumansCellsPHPublic Health
  117. 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.
    Citations: 61     Fields:    Translation:HumansCells
  118. 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.
    Citations: 20     Fields:    Translation:HumansCells
  119. 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.
    Citations: 33     Fields:    Translation:HumansCells
  120. 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.
    Citations: 449     Fields:    Translation:HumansCells
  121. 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.
    Citations: 38     Fields:    Translation:HumansCells
  122. Baker S, Hanage WP, Holt KE. Navigating the future of bacterial molecular epidemiology. Curr Opin Microbiol. 2010 Oct; 13(5):640-5. PMID: 20846899.
    Citations: 25     Fields:    Translation:Cells
  123. 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.
    Citations: 55     Fields:    Translation:HumansCellsPHPublic Health
  124. 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.
    Citations: 59     Fields:    Translation:HumansCells
  125. 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.
    Citations: 28     Fields:    Translation:HumansCells
  126. 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.
    Citations:    Fields:    Translation:HumansPHPublic Health
  127. 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.
    Citations: 30     Fields:    Translation:HumansCells
  128. 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.
    Citations: 44     Fields:    Translation:Cells
  129. 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.
    Citations: 18     Fields:    Translation:HumansCells
  130. 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.
    Citations: 121     Fields:    Translation:HumansCells
  131. 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.
    Citations: 96     Fields:    Translation:Cells
  132. 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.
    Citations: 628     Fields:    Translation:HumansCellsPHPublic Health
  133. 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.
    Citations: 141     Fields:    Translation:Cells
  134. 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.
    Citations: 93     Fields:    Translation:Cells
  135. Hanage WP, Aanensen DM. Methods for data analysis. Methods Mol Biol. 2009; 551:287-304. PMID: 19521881.
    Citations: 1     Fields:    Translation:HumansCells
  136. 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.
    Citations: 45     Fields:    Translation:HumansCells
  137. 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.
    Citations: 18     Fields:    Translation:Cells
  138. 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.
    Citations: 12     Fields:    Translation:HumansCells
  139. 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.
    Citations: 43     Fields:    Translation:HumansCells
  140. Hanage WP. Serotype-specific problems associated with pneumococcal conjugate vaccination. Future Microbiol. 2008 Feb; 3(1):23-30. PMID: 18230031.
    Citations: 25     Fields:    Translation:HumansAnimalsCells
  141. 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.
    Citations: 155     Fields:    Translation:HumansCells
  142. 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.
    Citations: 10     Fields:    Translation:HumansCellsPHPublic Health
  143. 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.
    Citations: 103     Fields:    Translation:HumansCells
  144. 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.
    Citations: 76     Fields:    Translation:Cells
  145. Fraser C, Hanage WP, Spratt BG. Recombination and the nature of bacterial speciation. Science. 2007 Jan 26; 315(5811):476-80. PMID: 17255503.
    Citations: 197     Fields:    Translation:Cells
  146. 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.
    Citations: 45     Fields:    Translation:HumansCellsPHPublic Health
  147. 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.
    Citations: 44     Fields:    Translation:Cells
  148. 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.
    Citations: 51     Fields:    Translation:Cells
  149. 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.
    Citations: 12     Fields:    Translation:HumansCells
  150. 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.
    Citations: 21     Fields:    Translation:HumansAnimalsCellsPHPublic Health
  151. 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.
    Citations: 27     Fields:    Translation:HumansCells
  152. 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.
    Citations: 19     Fields:    
  153. 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.
    Citations: 56     Fields:    Translation:Cells
  154. 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.
    Citations: 46     Fields:    Translation:Cells
  155. Hanage WP, Fraser C, Spratt BG. Fuzzy species among recombinogenic bacteria. BMC Biol. 2005 Mar 07; 3:6. PMID: 15752428.
    Citations: 107     Fields:    Translation:Cells
  156. 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.
    Citations: 62     Fields:    Translation:HumansCells
  157. 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.
    Citations: 59     Fields:    Translation:HumansCells
  158. 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.
    Citations: 80     Fields:    Translation:HumansCells
  159. 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.
    Citations: 761     Fields:    Translation:HumansCells
  160. 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.
    Citations: 28     Fields:    Translation:HumansCells
  161. 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.
    Citations: 3     Fields:    Translation:HumansCells
  162. 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.
    Citations: 60     Fields:    Translation:HumansCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.