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William Hanage

Associate Professor

Education

Affiliations

Projects

MIDAS CENTER FOR COMMUNICABLE DISEASE DYNAMICS

National Institutes of Health, National Institute of General Medical Sciences
People: Laura White, Ted Cohen, William Hanage, Rene Niehus, Ben Cowling, Tyler Brown, Joseph Wu, Mauricio Santillana Guzman, Joseph Lewnard, Aimee Taylor, Ayesha Mahmud, Pablo Martinez de Salazar, Lerato Magosi, Edward Goldstein, Christine Tedijanto, Tigist Menkir, Sze Man Leung, Hsiao-Han Chang, Caroline Buckee, Pamela Martinez, Marc Lipsitch
2009 – 2020

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Papers

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. (2020). The effect of human mobility and control measures on the COVID-19 epidemic in China. Science (New York, N.Y.)

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. (2020). SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases. medRxiv : the preprint server for health sciences

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. (2020). Scientific consensus on the COVID-19 pandemic: we need to act now. Lancet

B?inda 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. (2020). Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing. Nature microbiology

MacFadden DR, Coburn B, B?inda K, Corbeil A, Daneman N, Fisman D, Lee RS, Lipsitch M, McGeer A, Melano RG, Mubareka S, Hanage WP. (2020). Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli. Antimicrobial agents and chemotherapy

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. (2020). The effect of human mobility and control measures on the COVID-19 epidemic in China. medRxiv : the preprint server for health sciences

Lee RS, Proulx JF, McIntosh F, Behr MA, Hanage WP. (2020). revealed by deep sequencing. eLife, (9)

Hanage WP, Testa C, Chen JT, Davis L, Pechter E, Seminario P, Santillana M, Krieger N. (2020). COVID-19: US federal accountability for entry, spread, and inequities-lessons for the future. European journal of epidemiology

Kraemer Moritz U.G., Yang Chia-Hung, Gutierrez Bernardo, Wu Chieh-Hsi, Klein Brennan, Pigott David M., group open COVID-19 data working, Plessis Louis du, Faria Nuno R, Li Ruoran, Hanage William P., Brownstein John S, Layan Maylis, Vespignani Alessandro, Tian Huaiyu, Dye Christopher, Cauchemez Simon, Pybus Oliver, Scarpino Samuel V. (2020). The effect of human mobility and control measures on the COVID-19 epidemic in China. Cold Spring Harbor Laboratory Press

Lehtinen S, Chewapreecha C, Lees J, Hanage WP, Lipsitch M, Croucher NJ, Bentley SD, Turner P, Fraser C, Mostowy RJ. (2020). Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae. Science advances, 6(21)

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. (2020). Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae. PLoS biology, 18(10)

Lehtinen S, Chewapreecha C, Lees J, Hanage WP, Lipsitch M, Croucher NJ, Bentley SD, Turner P, Fraser C, Mostowy RJ. (2020). . Science advances, 6(21)

Hanage WP. (2019). Two Health or Not Two Health? That Is the Question. MBio, 10(2)

MacFadden DR, Hanage WP. (2019). Potential for Erosion of Efficacy in Noninferiority Trials of Decreasing Duration of Antibiotic Therapy. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 69(7)

Lewnard JA, Hanage WP. (2019). Making sense of differences in pneumococcal serotype replacement. The Lancet. Infectious diseases, 19(6)

Mitchell PK, Azarian T, Croucher NJ, Callendrello A, Thompson CM, Pelton SI, Lipsitch M, Hanage WP. (2019). Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13. Microbial genomics, 5(2)

MacFadden DR, Fisman DN, Hanage WP, Lipsitch M. (2019). The Relative Impact of Community and Hospital Antibiotic Use on the Selection of Extended-spectrum Beta-lactamase-producing Escherichia coli. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 69(1)

MacFadden DR, McGeer A, Athey T, Perusini S, Olsha R, Li A, Eshaghi A, Gubbay JB, Hanage WP. (2018). Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15. Emerging infectious diseases, 24(3)

Arnold BJ, Gutmann MU, Grad YH, Sheppard SK, Corander J, Lipsitch M, Hanage WP. (2018). Weak Epistasis May Drive Adaptation in Recombining Bacteria. Genetics, 208(3)

Martin MA, Lee RS, Cowley LA, Gardy JL, Hanage WP. (2018). Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission. Microbial genomics, 4(10)

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. (2018). The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome. PLoS pathogens, 14(4)

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. (2018). Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci. PLoS pathogens, 14(11)

Hanage WP. (2018). From bacterial genomics to clinical epidemiology: an interview with Bill Hanage. BMC biology, 16(1)

Cowley LA, Petersen FC, Junges R, Jimson D Jimenez M, Morrison DA, Hanage WP. (2018). Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae. PLoS genetics, 14(6)

Chang Q, Abuelaish I, Biber A, Jaber H, Callendrello A, Andam CP, Regev-Yochay G, Hanage WP, On Behalf Of The Picr Study Group. (2018). ST22 widespread in communities of the Gaza Strip, 2009. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 23(34)

Andam CP, Mitchell PK, Callendrello A, Chang Q, Corander J, Chaguza C, McGee L, Beall BW, Hanage WP. (2017). Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States. Journal of clinical microbiology, 55(4)

Andam CP, Worby CJ, Gierke R, McGee L, Pilishvili T, Hanage WP. (2017). Penicillin Resistance of Nonvaccine Type Pneumococcus before and after PCV13 Introduction, United States. Emerging infectious diseases, 23(6)

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. (2017). Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks. Proceedings of the National Academy of Sciences of the United States of America, 114(5)

Worby CJ, Lipsitch M, Hanage WP. (2017). Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data. American journal of epidemiology, 186(10)

Croucher NJ, Campo JJ, Le TQ, Liang X, Bentley SD, Hanage WP, Lipsitch M. (2017). Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening. Proceedings of the National Academy of Sciences of the United States of America, 114(3)

Marttinen P, Hanage WP. (2017). Speciation trajectories in recombining bacterial species. PLoS computational biology, 13(7)

Cobey S, Baskerville EB, Colijn C, Hanage W, Fraser C, Lipsitch M. (2017). Host population structure and treatment frequency maintain balancing selection on drug resistance. Journal of the Royal Society, Interface, 14(133)

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. (2017). Association of Pneumococcal Protein Antigen Serology With Age and Antigenic Profile of Colonizing Isolates. The Journal of infectious diseases, 215(5)

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. (2016). Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule. MBio, 7(5)

Hanage WP. (2016). Not So Simple After All: Bacteria, Their Population Genetics, and Recombination. Cold Spring Harbor perspectives in biology, 8(7)

Chang HH, Dordel J, Donker T, Worby CJ, Feil EJ, Hanage WP, Bentley SD, Huang SS, Lipsitch M. (2016). Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus. Genome medicine, 8(1)

Hausdorff WP, Hanage WP. (2016). Interim results of an ecological experiment - Conjugate vaccination against the pneumococcus and serotype replacement. Human vaccines & immunotherapeutics, 12(2)

Mitchell PK, Lipsitch M, Hanage WP. (2015). Carriage burden, multiple colonization and antibiotic pressure promote emergence of resistant vaccine escape pneumococci. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 370(1670)

Croucher NJ, Finkelstein JA, Pelton SI, Parkhill J, Bentley SD, Lipsitch M, Hanage WP. (2015). Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae. Scientific data, (2)

Chang Q, Lipsitch M, Hanage WP. (2016). Impact of Host Heterogeneity on the Efficacy of Interventions to Reduce Staphylococcus aureus Carriage. Infection control and hospital epidemiology, 37(2)

Goldstein E, Greene SK, Olson DR, Hanage WP, Lipsitch M. (2015). Estimating the hospitalization burden associated with influenza and respiratory syncytial virus in New York City, 2003-2011. Influenza and other respiratory viruses, 9(5)

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. (2015). Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 61(3)

Chang Q, Stevenson AE, Croucher NJ, Lee GM, Pelton SI, Lipsitch M, Finkelstein JA, Hanage WP. (2015). Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced. BMC infectious diseases, (15)

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. (2015). Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis. Genome biology and evolution, 7(5)

Li Y, Croucher NJ, Thompson CM, Trzciński K, Hanage WP, Lipsitch M. (2015). Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity. BMC Genomics, (16)

Chang HH, Cohen T, Grad YH, Hanage WP, O'Brien TF, Lipsitch M. (2015). Origin and proliferation of multiple-drug resistance in bacterial pathogens. Microbiology and molecular biology reviews : MMBR, 79(1)

Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M, Hanage WP. (2015). Selective and genetic constraints on pneumococcal serotype switching. PLoS genetics, 11(3)

Marttinen P, Croucher NJ, Gutmann MU, Corander J, Hanage WP. (2015). Recombination produces coherent bacterial species clusters in both core and accessory genomes. Microbial genomics, 1(5)

Chang Q, Wang W, Regev-Yochay G, Lipsitch M, Hanage WP. (2015). Antibiotics in agriculture and the risk to human health: how worried should we be?. Evolutionary applications, 8(3)

Grad YH, Kirkcaldy RD, Trees D, Dordel J, Harris SR, Goldstein E, Weinstock H, Parkhill J, Hanage WP, Bentley S, Lipsitch M. (2014). Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study. The Lancet. Infectious diseases, 14(3)

Hanage WP. (2014). Microbiology: Microbiome science needs a healthy dose of scepticism. Nature, 512(7514)

Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD, Hanage WP. (2014). Diversification of bacterial genome content through distinct mechanisms over different timescales. Nature communications, (5)

Worby CJ, Chang HH, Hanage WP, Lipsitch M. (2014). The distribution of pairwise genetic distances: a tool for investigating disease transmission. Genetics, 198(4)

Andam CP, Hanage WP. (2015). Mechanisms of genome evolution of Streptococcus. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, (33)

Worby CJ, Lipsitch M, Hanage WP. (2014). Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data. PLoS computational biology, 10(3)

Mostowy R, Croucher NJ, Hanage WP, Harris SR, Bentley S, Fraser C. (2014). Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution. PLoS genetics, 10(5)

Polz MF, Alm EJ, Hanage WP. (2013). Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends in genetics : TIG, 29(3)

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. (2013). Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen. MBio, 4(1)

Hanage WP. (2013). Fuzzy species revisited. BMC biology, (11)

Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM, Parkhill J, Bentley SD, Hanage WP, Lipsitch M. (2013). Population genomics of post-vaccine changes in pneumococcal epidemiology. Nature genetics, 45(6)

Shepheard MA, Fleming VM, Connor TR, Corander J, Feil EJ, Fraser C, Hanage WP. (2013). Historical zoonoses and other changes in host tropism of Staphylococcus aureus, identified by phylogenetic analysis of a population dataset. PLoS One, 8(5)

Croucher NJ, Harris SR, Grad YH, Hanage WP. (2013). Bacterial genomes in epidemiology--present and future. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 368(1614)

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. (2013). Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. mBio, 4(4)

Scott JR, Hinds J, Gould KA, Millar EV, Reid R, Santosham M, O'Brien KL, Hanage WP. (2012). Nontypeable pneumococcal isolates among navajo and white mountain apache communities: are these really a cause of invasive disease?. The Journal of infectious diseases, 206(1)

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. (2012). 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, 109(52)

Sirén J, Hanage WP, Corander J. (2013). Inference on population histories by approximating infinite alleles diffusion. Molecular biology and evolution, 30(2)

Willems RJ, Top J, van Schaik W, Leavis H, Bonten M, Sirén J, Hanage WP, Corander J. (2012). Restricted gene flow among hospital subpopulations of Enterococcus faecium. mBio, 3(4)

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. (2012). Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proceedings of the National Academy of Sciences of the United States of America, 109(8)

Connor TR, Corander J, Hanage WP. (2012). Population subdivision and the detection of recombination in non-typable Haemophilus influenzae. Microbiology (Reading, England), 158(Pt 12)

Corander J, Connor TR, O'Dwyer CA, Kroll JS, Hanage WP. (2012). Population structure in the Neisseria, and the biological significance of fuzzy species. Journal of the Royal Society, Interface, 9(71)

Willems RJ, Hanage WP, Bessen DE, Feil EJ. (2011). Population biology of Gram-positive pathogens: high-risk clones for dissemination of antibiotic resistance. FEMS microbiology reviews, 35(5)

Marttinen P, Hanage WP, Croucher NJ, Connor TR, Harris SR, Bentley SD, Corander J. (2012). Detection of recombination events in bacterial genomes from large population samples. Nucleic acids research, 40(1)

Hanage WP, Bishop CJ, Huang SS, Stevenson AE, Pelton SI, Lipsitch M, Finkelstein JA. (2011). Carried pneumococci in Massachusetts children: the contribution of clonal expansion and serotype switching. The Pediatric infectious disease journal, 30(4)

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. (2010). HIV-1 transmitting couples have similar viral load set-points in Rakai, Uganda. PLoS pathogens, 6(5)

Hanage WP, Finkelstein JA, Huang SS, Pelton SI, Stevenson AE, Kleinman K, Hinrichsen VL, Fraser C. (2010). Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete. Epidemics, 2(2)

Colijn C, Cohen T, Fraser C, Hanage W, Goldstein E, Givon-Lavi N, Dagan R, Lipsitch M. (2010). What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae?. Journal of the Royal Society, Interface, 7(47)

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, . (2009). Pandemic potential of a strain of influenza A (H1N1): early findings. Science (New York, N.Y.), 324(5934)

Hanage WP, Fraser C, Tang J, Connor TR, Corander J. (2009). Hyper-recombination, diversity, and antibiotic resistance in pneumococcus. Science (New York, N.Y.), 324(5933)

Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP. (2009). The bacterial species challenge: making sense of genetic and ecological diversity. Science (New York, N.Y.), 323(5915)

Lipsitch M, Colijn C, Cohen T, Hanage WP, Fraser C. (2009). No coexistence for free: neutral null models for multistrain pathogens. Epidemics, 1(1)

Hanage WP, Aanensen DM. (2009). Methods for data analysis. Methods in molecular biology (Clifton, N.J.), (551)

Hanage WP. (2008). Serotype-specific problems associated with pneumococcal conjugate vaccination. Future microbiology, 3(1)

Pelton SI, Huot H, Finkelstein JA, Bishop CJ, Hsu KK, Kellenberg J, Huang SS, Goldstein R, Hanage WP. (2007). 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, 26(6)

Fraser C, Hanage WP, Spratt BG. (2007). Recombination and the nature of bacterial speciation. Science (New York, N.Y.), 315(5811)

Fraser C, Hollingsworth TD, Chapman R, de Wolf F, Hanage WP. (2007). 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, 104(44)

Hanage WP, Huang SS, Lipsitch M, Bishop CJ, Godoy D, Pelton SI, Goldstein R, Huot H, Finkelstein JA. (2007). Diversity and antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae carriage isolates in the post-heptavalent conjugate vaccine era. The Journal of infectious diseases, 195(3)

Hanage WP, Fraser C, Spratt BG. (2006). Sequences, sequence clusters and bacterial species. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 361(1475)

Hanage WP, Spratt BG, Turner KM, Fraser C. (2006). Modelling bacterial speciation. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 361(1475)

Hanage WP, Fraser C, Spratt BG. (2006). The impact of homologous recombination on the generation of diversity in bacteria. Journal of theoretical biology, 239(2)

Hanage WP, Kaijalainen T, Herva E, Saukkoriipi A, Syrjänen R, Spratt BG. (2005). Using multilocus sequence data to define the pneumococcus. Journal of bacteriology, 187(17)

Hanage WP, Fraser C, Spratt BG. (2005). Fuzzy species among recombinogenic bacteria. BMC biology, (3)

Fraser C, Hanage WP, Spratt BG. (2005). Neutral microepidemic evolution of bacterial pathogens. Proceedings of the National Academy of Sciences of the United States of America, 102(6)

Hanage WP, Kaijalainen TH, Syrjänen RK, Auranen K, Leinonen M, Mäkelä PH, Spratt BG. (2005). Invasiveness of serotypes and clones of Streptococcus pneumoniae among children in Finland. Infection and immunity, 73(1)

Hanage WP, Auranen K, Syrjänen R, Herva E, Mäkelä PH, Kilpi T, Spratt BG. (2004). Ability of pneumococcal serotypes and clones to cause acute otitis media: implications for the prevention of otitis media by conjugate vaccines. Infection and immunity, 72(1)

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