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William Hanage

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Nicholas J Croucher; Yonatan H Grad; Simon R Harris; William P Hanage
Bacterial genomes in epidemiology--present and future.
Martin F Polz; Elizabeth Alm; William P Hanage
Horizontal gene transfer and the evolution of bacterial and archaeal population structure.
Jukka Sirén; William P Hanage; Jukka Corander
Inference on population histories by approximating infinite alleles diffusion.

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All Publications

2013: Nicholas J Croucher; Yonatan H Grad; Simon R Harris; William P Hanage
Bacterial genomes in epidemiology--present and future.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013;368(1614):20120202.
2013: Martin F Polz; Elizabeth Alm; William P Hanage
Horizontal gene transfer and the evolution of bacterial and archaeal population structure.
Trends in genetics : TIG 2013;29(3):170-5.
2013: Jukka Sirén; William P Hanage; Jukka Corander
Inference on population histories by approximating infinite alleles diffusion.
Molecular biology and evolution 2013;30(2):457-68.
2013: Marcus A Shepheard; Thomas R Connor; Jukka Corander; Edward J Feil; Vicki M Fleming; Christophe Fraser; William P Hanage
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.
2013: William P Hanage
Fuzzy species revisited.
BMC biology 2013;11():41.
2013: Yonatan H Grad; Allison Griggs; Brian J Haas; Edouard Bingen; Gustavo C Cerquiera; Paul Godfrey; Malika Gouali; Marc Lipsitch; Patricia Mariani-Kurkdjian; Terrence P Shea; Matthew K Waldor; François-Xavier Weill; Jennifer Wortman; Sarah Young; Qiandong Zeng; William P Hanage
Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen.
mBio 2013;4(1):e00452-12.
2012: Yonatan H Grad; Allison D Griggs; Brian J Haas; Edouard Bingen; Bruce W Birren; Michael FitzGerald; Antje Flieger; Deborah T Hung; Karen A Krogfelt; Eric S Lander; Marc Lipsitch; Caryn McCowan; Anna Montmayeur; Chad Nusbaum; Terrance P Shea; Erhard Tietze; François-Xavier Weill; Jennifer Wortman; William P Hanage
Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(52):E3629-30.
2012: Thomas Richard Connor; Jukka Corander; William P Hanage
Population subdivision and the detection of recombination in non-typable Haemophilus influenzae.
Microbiology (Reading, England) 2012;158(Pt 12):2958-64.
2012: Jennifer R Scott; Katherine A Gould; Jason Hinds; Eugene V Millar; Katherine L O'Brien; Raymond Reid; Mathuram Santosham; William P Hanage
Nontypeable pneumococcal isolates among navajo and white mountain apache communities: are these really a cause of invasive disease?
The Journal of infectious diseases 2012;206(1):73-80.
2012: Jukka Corander; J Simon Kroll; Clíona A O'dwyer; Thomas R Connor; William P Hanage
Population structure in the Neisseria, and the biological significance of fuzzy species.
Journal of the Royal Society, Interface / the Royal Society 2012;9(71):1208-15.
2012: S J Salter; P Turner; M Antonio; H J Bootsma; K A Gould; William P Hanage; P W M Hermans; J Hinds; L Lambertsen; Katherine L O'Brien; S D Bentley
Variation at the capsule locus, cps, of mistyped and non-typable Streptococcus pneumoniae isolates.
Microbiology (Reading, England) 2012;158(Pt 6):1560-9.
2012: Jennifer R Scott; Raymond Reid; Mathuram Santosham; William P Hanage; Jason Hinds; Marc Lipsitch; Eugene V Millar; Lawrence H Moulton; Katherine L O'Brien
Pneumococcal sequence type replacement among American Indian children: a comparison of pre- and routine-PCV7 eras.
Vaccine 2012;30(13):2376-81.
2012: Peter C Wroe; M Maya Dutta-Linn; Jonathan A Finkelstein; William P Hanage; Virginia L Hinrichsen; Ken Kleinman; Matthew Lakoma; Grace M Lee; Marc Lipsitch; Stephen I Pelton; Sheryl L Rifas-Shiman; Abbie E Stevenson; Susan S Huang
Pneumococcal carriage and antibiotic resistance in young children before 13-valent conjugate vaccine.
The Pediatric infectious disease journal 2012;31(3):249-54.
2012: Rob Willems; Marc Bonten; William P Hanage; Helen L Leavis; Jukka Sirén; Janetta Top; Willem van Schaik; Jukka Corander
Restricted gene flow among hospital subpopulations of Enterococcus faecium.
mBio 2012;3(4):e00151-12.
2012: Pekka Marttinen; Stephen D Bentley; Thomas R Connor; Nicholas J Croucher; William P Hanage; Simon R Harris; Jukka Corander
Detection of recombination events in bacterial genomes from large population samples.
Nucleic acids research 2012;40(1):e6.
2011: William P Hanage; S S Huang; G M Lee; Marc Lipsitch; Stephen I Pelton; Sheryl L Rifas-Shiman; A Stevenson; Cynthia J Bishop; J A Finkelstein
Clonal replacement among 19A Streptococcus pneumoniae in Massachusetts, prior to 13 valent conjugate vaccination.
Vaccine 2011;29(48):8877-81.
2011: William P Hanage; Cynthia J Bishop; Susan S Huang; Abbie E Stevenson; Stephen I Pelton; Marc Lipsitch; Jonathan A Finkelstein
Carried pneumococci in Massachusetts children: the contribution of clonal expansion and serotype switching.
The Pediatric infectious disease journal 2011;30(4):302-8.
2011: Nicholas J Croucher; Simon R Harris; Christophe Fraser; Michael A Quail; John Burton; Mark van der Linden; Lesley McGee; Anne Von Gottberg; Jae Hoon Song; Kwan Soo Ko; Bruno Pichon; Stephen Baker; Christopher M Parry; Lotte M Lambertsen; Dea Shahinas; Dylan R Pillai; Tim Mitchell; Gordon Dougan; Alexander Tomasz; keith klugman; Julian Parkhill; William P Hanage; Stephen D Bentley
Rapid pneumococcal evolution in response to clinical interventions.
Science (New York, N.Y.) 2011;331(6016):430-4.
2011: E S Donkor; M Antonio; Cynthia J Bishop; B Wren; J Hinds; K A Gould; William P Hanage
High levels of recombination among Streptococcus pneumoniae isolates from the Gambia.
mBio 2011;2(3):e00040-11.
2010: Inci Yildirim; William P Hanage; Marc Lipsitch; Kimberly M Shea; Abbie Stevenson; Jonathan Finkelstein; Susan S Huang; Grace M Lee; Ken Kleinman; S I Pelton
Serotype specific invasive capacity and persistent reduction in invasive pneumococcal disease.
Vaccine 2010;29(2):283-8.
2010: Stephen Baker; William P Hanage; Kathryn E Holt
Navigating the future of bacterial molecular epidemiology.
Current opinion in microbiology 2010;13(5):640-5.
2010: Gili Regev-Yochay; William P Hanage; Krzysztof Trzcinski; Sheryl L Rifas-Shiman; Grace Lee; Andrew Bessolo; Susan S Huang; Stephen I Pelton; Alexander J McAdam; Jonathan A Finkelstein; Marc Lipsitch; Richard Malley
Re-emergence of the type 1 pilus among Streptococcus pneumoniae isolates in Massachusetts, USA.
Vaccine 2010;28(30):4842-6.
2010: William P Hanage; Jonathan A Finkelstein; Susan S Huang; Stephen I Pelton; Abbie E Stevenson; Ken Kleinman; Virginia L Hinrichsen; Christophe Fraser
Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete.
Epidemics 2010;2(2):80-4.
2010: Deirdre Hollingsworth; Oliver Laeyendecker; George Shirreff; Christl A Donnelly; David Serwadda; Maria J Wawer; Noah Kiwanuka; Fred Nalugoda; Aleisha Collinson-Streng; Victor Ssempijja; William P Hanage; Thomas C Quinn; Ronald H Gray; Christophe Fraser
HIV-1 transmitting couples have similar viral load set-points in Rakai, Uganda.
PLoS pathogens 2010;6(5):e1000876.
2009: Jing Tang; William P Hanage; Christophe Fraser; Jukka Corander
Identifying currents in the gene pool for bacterial populations using an integrative approach.
PLoS computational biology 2009;5(8):e1000455.
2009: Susan S Huang; Virginia L Hinrichsen; Abbie E Stevenson; Sheryl L Rifas-Shiman; Ken Kleinman; Stephen I Pelton; Marc Lipsitch; William P Hanage; Grace M Lee; Jonathan A Finkelstein
Continued impact of pneumococcal conjugate vaccine on carriage in young children.
Pediatrics 2009;124(1):e1-11.
2009: Christophe Fraser; Christl A Donnelly; Simon Cauchemez; William P Hanage; Maria Van Kerkhove; Deirdre Hollingsworth; Jamie Griffin; Rebecca F Baggaley; Helen E Jenkins; Emily J Lyons; Thibaut Jombart; Wes R Hinsley; Nicholas C Grassly; Francois Balloux; Azra C Ghani; Neil M Ferguson; Andrew Rambaut; Oliver G Pybus; Hugo Lopez-Gatell; Celia M Alpuche-Aranda; Ietza Bojorquez Chapela; Ethel Palacios Zavala; Dulce Ma Espejo Guevara; Francesco Checchi; Erika Garcia; Stephane Hugonnet; Cathy Roth
Pandemic potential of a strain of influenza A (H1N1): early findings.
Science (New York, N.Y.) 2009;324(5934):1557-61.
2009: William P Hanage; Christophe Fraser; Jing Tang; Thomas Richard Connor; Jukka Corander
Hyper-recombination, diversity, and antibiotic resistance in pneumococcus.
Science (New York, N.Y.) 2009;324(5933):1454-7.
2009: Marc Lipsitch; Caroline Colijn; Ted Cohen; William P Hanage; Christophe Fraser
No coexistence for free: neutral null models for multistrain pathogens.
Epidemics 2009;1(1):2-13.
2009: Christophe Fraser; Eric J Alm; Martin F Polz; Brian G Spratt; William P Hanage
The bacterial species challenge: making sense of genetic and ecological diversity.
Science (New York, N.Y.) 2009;323(5915):741-6.
2009: Grace M Lee; Susan S Huang; Sheryl L Rifas-Shiman; Virginia L Hinrichsen; Stephen I Pelton; Ken Kleinman; William P Hanage; Marc Lipsitch; Alexander J McAdam; Jonathan A Finkelstein
Epidemiology and risk factors for Staphylococcus aureus colonization in children in the post-PCV7 era.
BMC infectious diseases 2009;9():110.
2009: William P Hanage; David M Aanensen
Methods for data analysis.
Methods in molecular biology (Clifton, N.J.) 2009;551():287-304.
2009: Cynthia J Bishop; David M Aanensen; Gregory E Jordan; Mogens Kilian; William P Hanage; Brian G Spratt
Assigning strains to bacterial species via the internet.
BMC biology 2009;7():3.
2008: Merit M Melin; Susan Kay Hollingshead; David E Briles; William P Hanage; Mika Lahdenkari; Tarja Kaijalainen; Terhi Kilpi; Helena M Käyhty
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.
Clinical and vaccine immunology : CVI 2008;15(10):1555-63.
2008: Monica Moschioni; Claudio Donati; Alessandro Muzzi; Vega Masignani; Stefano Censini; William P Hanage; Cynthia J Bishop; Joice Neves Reis; Staffan Normark; Birgitta Henriques Normark; Antonello Covacci; Rino Rappuoli; Michèle A Barocchi
Streptococcus pneumoniae contains 3 rlrA pilus variants that are clonally related.
The Journal of infectious diseases 2008;197(6):888-96.
2008: William P Hanage
Serotype-specific problems associated with pneumococcal conjugate vaccination.
Future microbiology 2008;3(1):23-30.
2008: Pekka Marttinen; Adam Baldwin; William P Hanage; Chris Dowson; Eshwar Mahenthiralingam; Jukka Corander
Bayesian modeling of recombination events in bacterial populations.
BMC bioinformatics 2008;9():421.
2007: William P Hanage
Serotype replacement in invasive pneumococcal disease: where do we go from here?
The Journal of infectious diseases 2007;196(9):1282-4.
2007: Christophe Fraser; Deirdre Hollingsworth; Ruth Chapman; Frank de Wolf; William P Hanage
Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(44):17441-6.
2007: Stephen I Pelton; Heather Huot; Jonathan A Finkelstein; Cynthia J Bishop; Katherine K Hsu; Joan Kellenberg; Susan S Huang; Richard Goldstein; William P Hanage
Emergence of 19A as virulent and multidrug resistant Pneumococcus in Massachusetts following universal immunization of infants with pneumococcal conjugate vaccine.
The Pediatric infectious disease journal 2007;26(6):468-72.
2007: William P Hanage; Susan S Huang; Marc Lipsitch; Cynthia J Bishop; Daniel Godoy; Stephen I Pelton; Richard Goldstein; Heather Huot; Jonathan A Finkelstein
Diversity and antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae carriage isolates in the post-heptavalent conjugate vaccine era.
The Journal of infectious diseases 2007;195(3):347-52.
2007: Christophe Fraser; William P Hanage; Brian G Spratt
Recombination and the nature of bacterial speciation.
Science (New York, N.Y.) 2007;315(5811):476-80.
2007: Katy Turner; William P Hanage; Christophe Fraser; Thomas R Connor; Brian G Spratt
Assessing the reliability of eBURST using simulated populations with known ancestry.
BMC microbiology 2007;7():30.
2006: William P Hanage; Brian G Spratt; Katy Turner; Christophe Fraser
Modelling bacterial speciation.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2006;361(1475):2039-44.
2006: William P Hanage; Christophe Fraser; Brian G Spratt
Sequences, sequence clusters and bacterial species.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2006;361(1475):1917-27.
2006: Nurith Porat; David Greenberg; Noga Givon-Lavi; Dror S Shuval; Ronit Trefler; Orit Segev; William P Hanage; Ron Dagan
The important role of nontypable Streptococcus pneumoniae international clones in acute conjunctivitis.
The Journal of infectious diseases 2006;194(5):689-96.
2006: Siouxsie Wiles; William P Hanage; Gad Frankel; Brian Robertson
Modelling infectious disease - time to think outside the box?
Nature reviews. Microbiology 2006;4(4):307-12.
2006: William P Hanage; Christophe Fraser; Brian G Spratt
The impact of homologous recombination on the generation of diversity in bacteria.
Journal of theoretical biology 2006;239(2):210-9.
2006: William P Hanage; Tarja Kaijalainen; Annika Saukkoriipi; J L Rickcord; Brian G Spratt
A successful, diverse disease-associated lineage of nontypeable pneumococci that has lost the capsular biosynthesis locus.
Journal of clinical microbiology 2006;44(3):743-9.
2005: Matthew C Fisher; William P Hanage; Sybren de Hoog; Elizabeth Johnson; Michael D Smith; Nicholas J White; Nongnuch Vanittanakom
Low effective dispersal of asexual genotypes in heterogeneous landscapes by the endemic pathogen Penicillium marneffei.
PLoS pathogens 2005;1(2):e20.
2005: William P Hanage; Tarja Kaijalainen; Elja Herva; Annika Saukkoriipi; Ritva Syrjänen; Brian G Spratt
Using multilocus sequence data to define the pneumococcus.
Journal of bacteriology 2005;187(17):6223-30.
2005: Christophe Fraser; William P Hanage; Brian G Spratt
Neutral microepidemic evolution of bacterial pathogens.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(6):1968-73.
2005: William P Hanage; Christophe Fraser; Brian G Spratt
Fuzzy species among recombinogenic bacteria.
BMC biology 2005;3():6.
2005: William P Hanage; Tarja Kaijalainen; Ritva Syrjänen; Kari Auranen; Maija Leinonen; P Helena Mäkelä; Brian G Spratt
Invasiveness of serotypes and clones of Streptococcus pneumoniae among children in Finland.
Infection and immunity 2005;73(1):431-5.
2004: Brian G Spratt; William P Hanage; Bao Li; David M Aanensen; Edward J Feil
Displaying the relatedness among isolates of bacterial species -- the eBURST approach.
FEMS microbiology letters 2004;241(2):129-34.
2004: Edward J Feil; Bao C Li; David M Aanensen; William P Hanage; Brian G Spratt
eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data.
Journal of bacteriology 2004;186(5):1518-30.
2004: William P Hanage; Kari Auranen; Ritva Syrjänen; Elja Herva; P Helena Mäkelä; Terhi Kilpi; Brian G Spratt
Ability of pneumococcal serotypes and clones to cause acute otitis media: implications for the prevention of otitis media by conjugate vaccines.
Infection and immunity 2004;72(1):76-81.
2001: Brian G Spratt; William P Hanage; Edward J Feil
The relative contributions of recombination and point mutation to the diversification of bacterial clones.
Current opinion in microbiology 2001;4(5):602-6.