Dr William P Hanage

Publications


Journals

  • Hollingsworth TD; Laeyendecker O; Shirreff G; Donnelly CA; Serwadda D; Wawer MJ; Kiwanuka N; Nalugoda F; et alCollinson-Streng A; Ssempijja V; Hanage WP; Quinn TC; Gray RH; Fraser C. (May 2010). HIV-1 transmitting couples have similar viral load set-points in Rakai, Uganda. PLoS Pathog. 6:e1000876. DOI Open Access copy.
  • Regev-Yochay G; Hanage WP; Trzcinski K; Rifas-Shiman SL; Lee G; Bessolo A; Huang SS; Pelton SI; et alMcAdam AJ; Finkelstein JA; Lipsitch M; Malley R. (5 Jul 2010). Re-emergence of the type 1 pilus among Streptococcus pneumoniae isolates in Massachusetts, USA. Vaccine. 28:4842-4846. DOI.
  • Hanage WP. (5 Feb 2010). The New Foundations of Evolution On the Tree of Life. SCIENCE. 327:645-646. DOI.
  • Hanage WP. (Jan 2011). Charles Darwin in modern epidemiology and public health: the celebration continues. J Epidemiol Community Health. 65:6-7. DOI.
  • Tang J; Hanage WP; Fraser C; Corander J. (Aug 2009). Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach. PLOS COMPUT BIOL. 5. DOI.
  • Fraser C; Donnelly CA; Cauchemez S; Hanage WP; Van Kerkhove MD; Hollingsworth TD; Griffin J; Baggaley RF; et alJenkins HE; Lyons EJ; Jombart T; Hinsley WR; Grassly NC; Balloux F; Ghani AC; Rambaut A; Ferguson NM. (28 Aug 2009). Influenza: Making Privileged Data Public Response. SCIENCE. 325:1072-1073.
  • Lee GM; Huang SS; Rifas-Shiman SL; Hinrichsen VL; Pelton SI; Kleinman K; Hanage WP; Lipsitch M; et alMcAdam AJ; Finkelstein JA. (11 Jul 2009). Epidemiology and risk factors for Staphylococcus aureus colonization in children in the post-PCV7 era. BMC INFECT DIS. 9. DOI.
  • Huang SS; Hinrichsen VL; Stevenson AE; Rifas-Shiman SL; Kleinman K; Pelton SI; Lipsitch M; Hanage WP; et alLee GM; Finkelstein JA. (Jul 2009). Continued Impact of Pneumococcal Conjugate Vaccine on Carriage in Young Children. PEDIATRICS. 124:E1-E11. DOI.
  • Fraser C; Donnelly CA; Cauchemez S; Hanage WP; Van Kerkhove MD; Hollingsworth TD; Griffin J; Baggaley RF; et alJenkins 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 DME; Checchi F; Garcia E; Hugonnet S; Roth C; WHO Rapid Pandemic Assessment Coll. (19 Jun 2009). Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings. SCIENCE. 324:1557-1561. DOI.
  • Hanage WP; Fraser C; Tang J; Connor TR; Corander J. (12 Jun 2009). Hyper-Recombination, Diversity, and Antibiotic Resistance in Pneumococcus. SCIENCE. 324:1454-1457. DOI.
  • Hanage WP; Aanensen DM. (2009). Methods for data analysis. Methods Mol Biol. 551:287-304. DOI.
  • Bishop CJ; Aanensen DM; Jordan GE; Kilian M; Hanage WP; Spratt BG. (26 Jan 2009). Assigning strains to bacterial species via the internet. BMC BIOL. 7. DOI.
  • Fraser C; Alm EJ; Polz MF; Spratt BG; Hanage WP. (6 Feb 2009). The bacterial species challenge: making sense of genetic and ecological diversity. Science. 323:741-746. DOI.
  • Marttinen P; Baldwin A; Hanage WP; Dowson C; Mahenthiralingam E; Corander J. (7 Oct 2008). Bayesian modeling of recombination events in bacterial populations. BMC BIOINFORMATICS. 9. DOI.
  • Melin MM; Hollingshead SK; Briles DE; Hanage WP; Lahdenkari M; Kaijalainen T; Kilpi TM; Kayhty HM. (Oct 2008). 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. 15:1555-1563. DOI.
  • Moschioni M; Donati C; Muzzi A; Masignani V; Censini S; Hanage WP; Bishop CJ; Reis JN; et alNormark S; Henriques-Normark B; Covacci A; Rappuoli R; Barocchi MA. (15 Mar 2008). Streptococcus pneumoniae contains 3 rlrA pilus variants that are clonally related. JOURNAL OF INFECTIOUS DISEASES. 197:888-896. DOI.
  • Hanage WP. (Feb 2008). Serotype-specific problems associated with pneumococcal conjugate vaccination. Future Microbiol. 3:23-30. DOI.
  • Hanage WP. (1 Nov 2007). Serotype replacement in invasive pneumococcal disease: where do we go from here?. J Infect Dis. 196:1282-1284. DOI.
  • Fraser C; Hollingsworth D; Chapman D; de Wolf F; Hanage WP. (2007). Variation in HIV-1 set-point viral load: Epidemiological analysis and an evolutionary hypothesis. Proc Natl Acad Sci USA. In press.
  • Pelton SI; Huot H; Finkelstein JA; Bishop CJ; Hsu KK; Kellenberg J; Huang SS; Goldstein R; et alHanage WP. (Jun 2007). Emergence of 19A as virulent and multidrug resistant Pneumococcus in Massachusetts following universal immunization of infants with pneumococcal conjugate vaccine. Pediatr Infect Dis J. 26:468-472. DOI.
  • Turner KM; Hanage WP; Fraser C; Connor TR; Spratt BG. (2007). Assessing the reliability of eBURST using simulated populations with known ancestry. BMC Microbiol. 7:30. DOI.
  • Fraser C; Hanage WP; Spratt BG. (26 Jan 2007). Recombination and the nature of bacterial speciation. Science. 315:476-480. DOI.
  • Hanage WP; Huang SS; Lipsitch M; Bishop CJ; Godoy D; Pelton SI; Goldstein R; Huot H; et alFinkelstein JA. (1 Feb 2007). Diversity and antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae carriage isolates in the post-heptavalent conjugate vaccine era. J Infect Dis. 195:347-352. DOI.
  • Fisher MC; Hanage WP; de Hoog S; Johnson E; Smith MD; White NJ; Vanittanakom N. (Oct 2005). Low effective dispersal of asexual genotypes in heterogeneous landscapes by the endemic pathogen Penicillium marneffei. PLOS PATHOG. 1:159-165. DOI Open Access copy.
  • Hanage WP; Fraser C; Spratt BG. (29 Nov 2006). Sequences, sequence clusters and bacterial species. Philos Trans R Soc Lond B Biol Sci. 361:1917-1927. DOI.
  • Hanage WP; Spratt BG; Turner KM; Fraser C. (29 Nov 2006). Modelling bacterial speciation. Philos Trans R Soc Lond B Biol Sci. 361:2039-2044. DOI.
  • Porat N; Greenberg D; Givon-Lavi N; Shuval DS; Trefler R; Segev O; Hanage WP; Dagan R. (1 Sep 2006). The important role of nontypable Streptococcus pneumoniae international clones in acute conjunctivitis. J Infect Dis. 194:689-696. DOI.
  • Hanage WP; Kaijalainen T; Saukkoriipi A; Rickcord JL; Spratt BG. (Mar 2006). A successful, diverse disease-associated lineage of nontypeable pneumococci that has lost the capsular biosynthesis locus. J Clin Microbiol. 44:743-749. DOI.
  • Wiles S; Hanage WP; Frankel G; Robertson B. (Apr 2006). Modelling infectious disease - time to think outside the box?. Nat Rev Microbiol. 4:307-312. DOI.
  • Hanage WP; Fraser C; Spratt BG. (21 Mar 2006). The impact of homologous recombination on the generation of diversity in bacteria. J Theor Biol. 239:210-219. DOI.
  • Hanage WP; Fraser C; Spratt BG. (2005). Fuzzy species among recombinogenic bacteria. BMC Biol. 3:6. DOI.
  • Hanage WP; Kaijalainen T; Herva E; Saukkoriipi A; Syrjänen R; Spratt BG. (Sep 2005). Using multilocus sequence data to define the pneumococcus. J Bacteriol. 187:6223-6230. DOI.
  • Fraser C; Hanage WP; Spratt BG. (8 Feb 2005). Neutral microepidemic evolution of bacterial pathogens. Proc Natl Acad Sci U S A. 102:1968-1973. DOI.
  • Hanage WP; Kaijalainen TH; Syrjänen RK; Auranen K; Leinonen M; Mäkelä PH; Spratt BG. (Jan 2005). Invasiveness of serotypes and clones of Streptococcus pneumoniae among children in Finland. Infect Immun. 73:431-435. DOI.
  • Spratt BG; Hanage WP; Li B; Aanensen DM; Feil EJ. (15 Dec 2004). Displaying the relatedness among isolates of bacterial species -- the eBURST approach. FEMS Microbiol Lett. 241:129-134. DOI.
  • Feil EJ; Li BC; Aanensen DM; Hanage WP; Spratt BG. (Mar 2004). eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol. 186:1518-1530.
  • Hanage WP; Auranen K; Syrjänen R; Herva E; Mäkelä PH; Kilpi T; Spratt BG. (Jan 2004). Ability of pneumococcal serotypes and clones to cause acute otitis media: implications for the prevention of otitis media by conjugate vaccines. Infect Immun. 72:76-81.
  • Hanage WP; Cohen J. (1 Feb 2002). Stimulation of cytokine release and adhesion molecule expression by products of Viridans streptococci. J Infect Dis. 185:357-367. DOI.
  • Spratt BG; Hanage WP; Feil EJ. (Oct 2001). The relative contributions of recombination and point mutation to the diversification of bacterial clones. Curr Opin Microbiol. 4:602-606.

Chapters in books

  • Spratt BG; Fraser C; Hanage WP. Exploring genetic relatedness, patterns of evolutionary descent, and the population genetics of bacterial pathogens using multilocus sequence typing. In Encyclopedia of Infectious Diseases: Modern Methodologies. Tibayrenc M (ed). Wiley (2007).
  • Spratt BG; Hanage WP; Brueggemann AB. Evolutionary and population biology of Streptococcus pneumoniae. In The Pneumococcus. 119-135. Tuomanen (ed); Mitchell EI (ed); Morrison TJ (ed); Spratt DA (ed); BG (ed). ASM Press (2004).
  • Hanage WP; Feil EJ; Brueggemann AB; Spratt BG. Multilocus sequence typing: strain characterization, population biology, and patterns of evolutionary descent. In Molecular Microbiology: Diagnostic Principles and Practice. new (ed). (2004).

Conferences

  • Hyams CJ; Opel S; Yuste J; Hanage WP; Henriques-Normark B; Wesier JN; Brown JS; Spratt BG. INVASIVE CAPSULAR SEROTYPES OF STREPTOCOCCUS PNEUMONIAE ARE RELATIVELY RESISTANT TO COMPLEMENT COMPARED WITH NON-INVASIVE SEROTYPES. 63:A52-A52. (Dec 2008).
  • Moschioni M; Donati C; Muzzi A; Masignani V; Censini S; Hanage WP; Bishop CJ; Reis JN; et alNormark S; Henriques-Normark B; Covacci A; Rappuoli R; Barocchi MA. Streptococcus pneumoniae contains 3 rlrA pilus variants that are clonally related. Symposium on Novel Opportunities to Develop Vaccines to Control Antibiotic Resistant Bacteria: From the Trials Back to the Laboratory. 197:888-896. (15 Mar 2008).
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