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William Hanage

Associate Professor

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Pathogens/Diseases of Main Interest/Expertise

COVID-19

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Papers

Reichert E, Schaeffer B, Gantt S, Rumpler E, Govender N, Welch R, Shonhiwa AM, Iwu CD, Lamola TM, Moema-Matiea I, Muganhiri D, Hanage W, Santillana M, Jassat W, Cohen C, Swerdlow D. (2022). Methods for early characterisation of the severity and dynamics of SARS-CoV-2 variants: a population-based time series analysis in South Africa. The Lancet. Microbe

Wikle NB, Tran TN, Gentilesco B, Leighow SM, Albert E, Strong ER, Brinda K, Inam H, Yang F, Hossain S, Chan P, Hanage WP, Messick M, Pritchard JR, Hanks EM, Boni MF. (2022). SARS-CoV-2 epidemic after social and economic reopening in three U.S. states reveals shifts in age structure and clinical characteristics. Science advances, 8(4)

Che Y, Xu X, Yang Y, Břinda K, Hanage W, Yang C, Zhang T. (2022). High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteria. Microbiome, 10(1)

Petros BA, Turcinovic J, Welch NL, White LF, Kolaczyk ED, Bauer MR, Cleary M, Dobbins ST, Doucette-Stamm L, Gore M, Nair P, Nguyen TG, Rose S, Taylor BP, Tsang D, Wendlandt E, Hope M, Platt JT, Jacobson KR, Bouton T, Yune S, Auclair JR, Landaverde L, Klapperich CM, Hamer DH, Hanage WP, MacInnis BL, Sabeti PC, Connor JH, Springer M. (2022). Early introduction and rise of the Omicron SARS-CoV-2 variant in highly vaccinated university populations. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Turcinovic J, Schaeffer B, Taylor BP, Bouton TC, Odom-Mabey AR, Weber SE, Lodi S, Ragan EJ, Connor JH, Jacobson KR, Hanage WP. (2022). Understanding early pandemic SARS-CoV-2 transmission in a medical center by incorporating public sequencing databases to mitigate bias. The Journal of infectious diseases

Dennehy JJ, Gupta RK, Hanage WP, Johnson MC, Peacock TP. (2022). Where is the next SARS-CoV-2 variant of concern?. Lancet, 399(10339)

Corander J, Hanage WP, Pensar J. (2022). Causal discovery for the microbiome. The Lancet. Microbe

Bhattacharyya RP, Hanage WP. (2022). Intrinsic Severity of the SARS-CoV-2 Omicron Variant. Reply. The New England journal of medicine

Xiao A, Wu F, Bushman M, Zhang J, Imakaev M, Chai PR, Duvallet C, Endo N, Erickson TB, Armas F, Arnold B, Chen H, Chandra F, Ghaeli N, Gu X, Hanage WP, Lee WL, Matus M, McElroy KA, Moniz K, Rhode SF, Thompson J, Alm EJ. (2022). Metrics to relate COVID-19 wastewater data to clinical testing dynamics. Water research, (212)

Turcinovic J, Kuhfeldt K, Sullivan M, Landaverde L, Platt JT, Doucette-Stamm L, Hanage WP, Hamer DH, Klapperich C, Landsberg HE, Connor JH. (2022). Linking contact tracing with genomic surveillance to deconvolute SARS-CoV-2 transmission on a university campus. iScience

Specht I, Sani K, Loftness BC, Hoffman C, Gionet G, Bronson A, Marshall J, Decker C, Bailey L, Siyanbade T, Kemball M, Pickett BE, Hanage WP, Brown T, Sabeti PC, Colubri A. (2022). Analyzing the impact of a real-life outbreak simulator on pandemic mitigation: An epidemiological modeling study. Patterns (New York, N.Y.), 3(8)

Petrone ME, Rothman JE, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Badr H, Kelly K, Omerza G, Renzette N, Watkins AE, Kalinich CC, Alpert T, Brito AF, Earnest R, Tikhonova IR, Castaldi C, Kelly JP, Shudt M, Plitnick J, Schneider E, Murphy S, Neal C, Laszlo E, Altajar A, Pearson C, Muyombwe A, Downing R, Razeq J, Niccolai L, Wilson MS, Anderson ML, Wang J, Liu C, Hui P, Mane S, Taylor BP, Hanage WP, Landry ML, Peaper DR, Bilguvar K, Fauver JR, Vogels CBF, Gardner LM, Pitzer VE, St George K, Adams MD, Grubaugh ND. (2022). Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota. Communications biology, 5(1)

Tran TN, Wikle NB, Yang F, Inam H, Leighow S, Gentilesco B, Chan P, Albert E, Strong ER, Pritchard JR, Hanage WP, Hanks EM, Crawford FW, Boni MF. (2022). SARS-CoV-2 Attack Rate and Population Immunity in Southern New England, March 2020 to May 2021. JAMA network open, 5(5)

Bhattacharyya RP, Hanage WP. (2022). Challenges in Inferring Intrinsic Severity of the SARS-CoV-2 Omicron Variant. The New England journal of medicine

Senghore M, Chaguza C, Bojang E, Tientcheu PE, Bancroft RE, Lo SW, Gladstone RA, McGee L, Worwui A, Foster-Nyarko E, Ceesay F, Okoi CB, Klugman KP, Breiman RF, Bentley SD, Adegbola R, Antonio M, Hanage WP, Kwambana-Adams BA. (2022). Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints. Microbial genomics, 8(2)

Che Y, Yang Y, Xu X, Břinda K, Polz MF, Hanage WP, Zhang T. (2021). Reply to Partridge et al.: Complementary bioinformatics and experimental approaches to investigate the transfer of AMR genes. Proceedings of the National Academy of Sciences of the United States of America, 118(35)

Choudhary MC, Crain CR, Qiu X, Hanage W, Li JZ. (2021). SARS-CoV-2 Sequence Characteristics of COVID-19 Persistence and Reinfection. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Wikle N, Tran TN, Gentilesco B, Leighow SM, Albert J, Strong ER, Břinda K, Inam H, Yang F, Hossain S, Chan P, Hanage WP, Messick M, Pritchard JR, Hanks EM, Boni MF. (2021). SARS-CoV-2 epidemic after social and economic reopening in three US states reveals shifts in age structure and clinical characteristics. medRxiv : the preprint server for health sciences

Siddle KJ, Krasilnikova LA, Moreno GK, Schaffner SF, Vostok J, Fitzgerald NA, Lemieux JE, Barkas N, Loreth C, Specht I, Tomkins-Tinch CH, Paull JS, Schaeffer B, Taylor BP, Loftness B, Johnson H, Schubert PL, Shephard HM, Doucette M, Fink T, Lang AS, Baez S, Beauchamp J, Hennigan S, Buzby E, Ash S, Brown J, Clancy S, Cofsky S, Gagne L, Hall J, Harrington R, Gionet GL, DeRuff KC, Vodzak ME, Adams GC, Dobbins ST, Slack SD, Reilly SK, Anderson LM, Cipicchio MC, DeFelice MT, Grimsby JL, Anderson SE, Blumenstiel BS, Meldrim JC, Rooke HM, Vicente G, Smith NL, Messer KS, Reagan FL, Mandese ZM, Lee MD, Ray MC, Fisher ME, Ulcena MA, Nolet CM, English SE, Larkin KL, Vernest K, Chaluvadi S, Arvidson D, Melchiono M, Covell T, Harik V, Brock-Fisher T, Dunn M, Kearns A, Hanage WP, Bernard C, Philippakis A, Lennon NJ, Gabriel SB, Gallagher GR, Smole S, Madoff LC, Brown CM, Park DJ, MacInnis BL, Sabeti PC. (2021). Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak. Cell

Hanage WP, Russell CA. (2021). Partial immunity and SARS-CoV-2 mutations. Science (New York, N.Y.), 372(6540)

Bushman M, Worby C, Chang HH, Kraemer MUG, Hanage WP. (2021). Transmission of SARS-CoV-2 before and after symptom onset: impact of nonpharmaceutical interventions in China. European journal of epidemiology

Bushman M, Kahn R, Taylor BP, Lipsitch M, Hanage WP. (2021). Population impact of SARS-CoV-2 variants with enhanced transmissibility and/or partial immune escape. Cell

Krieger N, Waterman PD, Chen JT, Testa C, Hanage WP. (2021). Missing again: US racial and ethnic data for COVID-19 vaccination. Lancet

Xiao A, Wu F, Bushman M, Zhang J, Imakaev M, Chai PR, Duvallet C, Endo N, Erickson TB, Armas F, Arnold B, Chen H, Chandra F, Ghaeli N, Gu X, Hanage WP, Lee WL, Matus M, McElroy KA, Moniz K, Rhode SF, Thompson J, Alm EJ. (2021). Metrics to relate COVID-19 wastewater data to clinical testing dynamics. medRxiv : the preprint server for health sciences

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. (2021). Optimal SARS-CoV-2 vaccine allocation using real-time seroprevalence estimates in Rhode Island and Massachusetts. medRxiv : the preprint server for health sciences

Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, Hanage WP, Huang KH, Lee WL, Matus M, McElroy KA, Rhode SF, Wuertz S, Thompson J, Alm EJ. (2021). Wastewater Surveillance of SARS-CoV-2 across 40 U.S. states. medRxiv : the preprint server for health sciences

D'Aeth JC, van der Linden MPG, McGee L, De Lencastre H, Turner P, Song JH, Lo SW, Gladstone RA, Sa-Leao R, Ko KS, Hanage WP, Breiman RF, Beall B, Bentley SD, Croucher NJ, . (2021). The role of interspecies recombinations in the evolution of antibiotic resistant pneumococci. eLife, (10)

Schaeffer B, Taylor B, Bushman M, Hanage WP. (2021). The devil in the details: Herd immunity and pandemic response. Cell host & microbe, 29(7)

Che Y, Yang Y, Xu X, Břinda K, Polz MF, Hanage WP, Zhang T. (2021). Reply to Shaw: Challenges for enrichment analysis of AMR gene-bearing plasmids. Proceedings of the National Academy of Sciences of the United States of America, 118(21)

Tran TN, Wikle NB, Albert E, Inam H, Strong E, Brinda K, Leighow SM, Yang F, Hossain S, Pritchard JR, Chan P, Hanage WP, Hanks EM, Boni MF. (2021). Optimal SARS-CoV-2 vaccine allocation using real-time attack-rate estimates in Rhode Island and Massachusetts. BMC medicine, 19(1)

Qiu X, Hanage WP, Taylor BP. (2021). Coming to America: Genomic surveillance and how B.1.1.7 arrived in the US. Cell, 184(10)

Kennedy-Shaffer L, Baym M, Hanage WP. (2021). Perfect as the enemy of good: tracing transmissions with low-sensitivity tests to mitigate SARS-CoV-2 outbreaks. The Lancet. Microbe

Arnold BJ, Huang IT, Hanage WP. (2021). Horizontal gene transfer and adaptive evolution in bacteria. Nature reviews. Microbiology

Ung L, Stothard JR, Phalkey R, Azman AS, Chodosh J, Hanage WP, Standley CJ. (2021). Towards global control of parasitic diseases in the Covid-19 era: One Health and the future of multisectoral global health governance. Advances in parasitology, (114)

Kennedy-Shaffer L, Qiu X, Hanage WP. (2021). Snowball Sampling Study Design for Serosurveys Early in Disease Outbreaks. American journal of epidemiology

Tran TN, Wikle NB, Yang F, Inam H, Leighow S, Gentilesco B, Chan P, Albert E, Strong ER, Pritchard JR, Hanage WP, Hanks EM, Crawford FW, Boni MF. (2021). SARS-CoV-2 attack rate and population immunity in southern New England, March 2020 - May 2021. medRxiv : the preprint server for health sciences

Harrow GL, Lees JA, Hanage WP, Lipsitch M, Corander J, Colijn C, Croucher NJ. (2021). Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. The ISME journal

Zhang AN, Gaston JM, Dai CL, Zhao S, Poyet M, Groussin M, Yin X, Li LG, van Loosdrecht MCM, Topp E, Gillings MR, Hanage WP, Tiedje JM, Moniz K, Alm EJ, Zhang T. (2021). An omics-based framework for assessing the health risk of antimicrobial resistance genes. Nature communications, 12(1)

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. (2021). SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases. The Science of the total environment, (805)

Che Y, Yang Y, Xu X, Břinda K, Polz MF, Hanage WP, Zhang T. (2021). Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes. Proceedings of the National Academy of Sciences of the United States of America, 118(6)

Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, Hanage WP, Huang KH, Lee WL, McElroy KA, Rhode SF, Matus M, Wuertz S, Thompson J, Alm EJ. (2021). Wastewater surveillance of SARS-CoV-2 across 40 U.S. states from February to June 2020. Water research, (202)

Qiu X, Miller JC, MacFadden DR, Hanage WP. (2021). Evaluating the contributions of strategies to prevent SARS-CoV-2 transmission in the healthcare setting: a modelling study. BMJ open, 11(3)

Bouton TC, Lodi S, Turcinovic J, Schaeffer B, Weber SE, Quinn E, Korn C, Steiner J, Schechter-Perkins EM, Duffy E, Ragan EJ, Taylor BP, Miller N, Davidoff R, Hanage WP, Connor J, Pierre C, Jacobson KR. (2021). Coronavirus Disease 2019 Vaccine Impact on Rates of Severe Acute Respiratory Syndrome Coronavirus 2 Cases and Postvaccination Strain Sequences Among Health Care Workers at an Urban Academic Medical Center: A Prospective Cohort Study. Open forum infectious diseases, 8(10)

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. (2021). An early warning approach to monitor COVID-19 activity with multiple digital traces in near real time. Science advances, 7(10)

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.)

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. (2020). Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events. medRxiv : the preprint server for health sciences

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

Grubaugh ND, Hanage WP, Rasmussen AL. (2020). Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. Cell, 182(4)

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. (2020). SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases. mSystems, 5(4)

Villabona-Arenas CJ, Hanage WP, Tully DC. (2020). Phylogenetic interpretation during outbreaks requires caution. Nature microbiology, 5(7)

Senghore M, Savi MK, Gnangnon B, Hanage WP, Okeke IN. (2020). Leveraging Africa's preparedness towards the next phase of the COVID-19 pandemic. The Lancet. Global health, 8(7)

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

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. (2020). Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host. The New England journal of medicine, 383(23)

Břinda 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

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. (2020). Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science (New York, N.Y.)

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

Krieger N, Testa C, Hanage WP, Chen JT. (2020). US racial and ethnic data for COVID-19 cases: still missing in action. Lancet, 396(10261)

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

Hanage WP, Vincent VI, Low NM. (2020). Seroprevalence of SARS-CoV-2 in Hong Kong returnees. The Lancet. Microbe, 1(4)

Lee RS, Hanage WP. (2020). Reproducibility in science: important or incremental?. The Lancet. Microbe, 1(2)

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)

Levin AT, Hanage WP, Owusu-Boaitey N, Cochran KB, Walsh SP, Meyerowitz-Katz G. (2020). Assessing the age specificity of infection fatality rates for COVID-19: systematic review, meta-analysis, and public policy implications. European journal of epidemiology, 35(12)

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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