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Marc Lipsitch

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

Eyal N, Lipsitch M, Smith PG. (2020). Human challenge studies to accelerate coronavirus vaccine licensure. The Journal of infectious diseases

Lipsitch M. (2020). Estimating case fatality rates of COVID-19. The Lancet. Infectious diseases

Hicks AL, Kissler SM, Mortimer TD, Ma KC, Taiaroa G, Ashcroft M, Williamson DA, Lipsitch M, Grad YH. (2020). Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants. eLife, (9)

Levinson M, Cevik M, Lipsitch M. (2020). Reopening Primary Schools during the Pandemic. The New England journal of medicine, 383(10)

Swerdlow DL, Finelli L, Lipsitch M. (2020). Epidemiology of Covid-19. Reply. The New England journal of medicine, (382)

Lipsitch M, Kahn R, Mina MJ. (2020). Antibody testing will enhance the power and accuracy of COVID-19-prevention trials. Nature medicine

Menkir TF, Chin T, Hay JA, Surface E, Martinez de Salazar P, Buckee C, Mina MJ, Khan K, Watts A, Lipsitch M, Niehus R. (2020). Estimating the number of undetected COVID-19 cases exported internationally from all of China. medRxiv : the preprint server for health sciences

De Salazar PM, Niehus R, Taylor A, Buckee CO, Lipsitch M. (2020). Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions. Emerging infectious diseases, 26(7)

Buckee CO, Balsari S, Chan J, Crosas M, Dominici F, Gasser U, Grad YH, Grenfell B, Halloran ME, Kraemer MUG, Lipsitch M, Metcalf CJE, Meyers LA, Perkins TA, Santillana M, Scarpino SV, Viboud C, Wesolowski A, Schroeder A. (2020). Aggregated mobility data could help fight COVID-19. Science (New York, N.Y.)

Goldstein E, Lipsitch M. (2020). The relation between prescribing of different antibiotics and rates of mortality with sepsis in US adults. BMC infectious diseases, 20(1)

Inglesby TV, Lipsitch M. (2020). Proposed Changes to U.S. Policy on Potential Pandemic Pathogen Oversight and Implementation. mSphere, 5(1)

Eyal N, Lipsitch M. (2020). Opinion: It's ethical to test promising coronavirus vaccines against less-promising ones. Proceedings of the National Academy of Sciences of the United States of America

Gostic KM, McGough L, Baskerville E, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday J, Bosse N, Sherratt K, Thompson RM, White LF, Huisman J, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. (2020). Practical considerations for measuring the effective reproductive number, Rt. medRxiv : the preprint server for health sciences

Peak CM, Kahn R, Grad YH, Childs LM, Li R, Lipsitch M, Buckee CO. (2020). Individual quarantine versus active monitoring of contacts for the mitigation of COVID-19: a modelling study. The Lancet. Infectious diseases

Lu FS, Nguyen AT, Link NB, Lipsitch M, Santillana M. (2020). Estimating the Early Outbreak Cumulative Incidence of COVID-19 in the United States: Three Complementary Approaches. medRxiv : the preprint server for health sciences

Li R, Rivers C, Tan Q, Murray MB, Toner E, Lipsitch M. (2020). The demand for inpatient and ICU beds for COVID-19 in the US: lessons from Chinese cities. medRxiv : the preprint server for health sciences

Kissler SM, Tedijanto C, Goldstein E, Grad YH, Lipsitch M. (2020). Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period. Science (New York, N.Y.)

Messinger CJ, Lipsitch M, Bateman BT, He M, Huybrechts KF, MacDonald S, Mogun H, Mott K, Hernández-Díaz S. (2020). Association Between Congenital Cytomegalovirus and the Prevalence at Birth of Microcephaly in the United States. JAMA pediatrics

Goldstein E, Lipsitch M. (2020). Temporal rise in the proportion of both younger adults and older adolescents among COVID-19 cases in Germany: evidence of lesser adherence to social distancing practices?. medRxiv : the preprint server for health sciences

Flasche S, Lipsitch M, Ojal J, Pinsent A. (2020). Estimating the contribution of different age strata to vaccine serotype pneumococcal transmission in the pre vaccine era: a modelling study. BMC medicine, 18(1)

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

Peak CM, Kahn R, Grad YH, Childs LM, Li R, Lipsitch M, Buckee CO. (2020). Comparative Impact of Individual Quarantine vs. Active Monitoring of Contacts for the Mitigation of COVID-19: a modelling study. medRxiv : the preprint server for health sciences

Lipsitch M, Perlman S, Waldor MK. (2020). Testing COVID-19 therapies to prevent progression of mild disease. The Lancet. Infectious diseases

McGough SF, Johansson MA, Lipsitch M, Menzies NA. (2020). Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking. PLoS computational biology, 16(4)

Tedijanto C, Grad YH, Lipsitch M. (2020). Potential impact of outpatient stewardship interventions on antibiotic exposures of common bacterial pathogens. eLife, (9)

Martinez de Salazar P, Gomez-Barroso D, Pampaka D, Gil JM, Penalver B, Fernandez-Escobar C, Lipsitch M, Larrauri A, Goldstein E, Hernan M. (2020). Lockdown measures and relative changes in the age-specific incidence of SARS-CoV-2 in Spain. medRxiv : the preprint server for health sciences

De Salazar Pablo M, Niehus Rene, Taylor Aimee, Buckee Caroline O, Lipsitch Marc. (2020). Using predicted imports of 2019-nCoV cases to determine locations that may not be identifying all imported cases

Niehus R, De Salazar PM, Taylor AR, Lipsitch M. (2020). Using observational data to quantify bias of traveller-derived COVID-19 prevalence estimates in Wuhan, China. The Lancet. Infectious diseases

Goldstein E, Lipsitch M. (2020). Temporal rise in the proportion of younger adults and older adolescents among coronavirus disease (COVID-19) cases following the introduction of physical distancing measures, Germany, March to April 2020. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 25(17)

Niehus Rene, Salazar Pablo M De, Taylor Aimee, Lipsitch Marc. (2020). Quantifying bias of COVID-19 prevalence and severity estimates in Wuhan, China that depend on reported cases in international travelers. Cold Spring Harbor Laboratory Press

Kissler Stephen M, Tedijanto Christine, Goldstein Edward, Grad Yonatan H., Lipsitch Marc. (2020). Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period. Cold Spring Harbor Laboratory Press

Kahn R, Kennedy-Shaffer L, Grad YH, Robins JM, Lipsitch M. (2020). Potential Biases Arising from Epidemic Dynamics in Observational Seroprotection Studies. American journal of epidemiology

Peak Corey M, Kahn Rebecca, Grad Yonatan H, Childs Lauren M, Li Ruoran, Lipsitch Marc, Buckee Caroline O. (2020). Modeling the Comparative Impact of Individual Quarantine vs. Active Monitoring of Contacts for the Mitigation of COVID-19. 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)

Lipsitch M. (2020). Good science is good science: we need specialists, not sects. European journal of epidemiology, 35(6)

Salazar Pablo M De, Niehus Rene, Taylor Aimee, Lipsitch Marc. (2020). Estimating underdetection of internationally imported COVID-19 cases. Cold Spring Harbor Laboratory Press

Wu JT, Leung K, Bushman M, Kishore N, Niehus R, de Salazar PM, Cowling BJ, Lipsitch M, Leung GM. (2020). Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China. Nature medicine, 26(4)

Li R, Rivers C, Tan Q, Murray MB, Toner E, Lipsitch M. (2020). Estimated Demand for US Hospital Inpatient and Intensive Care Unit Beds for Patients With COVID-19 Based on Comparisons With Wuhan and Guangzhou, China. JAMA network open, 3(5)

Thaler DS, Lipsitch M. (2020). Coronavirus: sampling now for future analysis. Nature, 580(7805)

Wu JT, Leung K, Bushman M, Kishore N, Niehus R, de Salazar PM, Cowling BJ, Lipsitch M, Leung GM. (2020). Addendum: Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China. Nature medicine, 26(7)

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)

Goldstein E, Finelli L, O'Halloran A, Liu P, Karaca Z, Steiner CA, Viboud C, Lipsitch M. (2019). Hospitalizations Associated with Respiratory Syncytial Virus and Influenza in Children, Including Children Diagnosed with Asthma. Epidemiology (Cambridge, Mass.), 30(6)

Lewnard JA, Tedijanto C, Cowling BJ, Lipsitch M. (2019). THE AUTHORS REPLY. American journal of epidemiology, 188(4)

Kennedy-Shaffer L, de Gruttola V, Lipsitch M. (2019). Novel methods for the analysis of stepped wedge cluster randomized trials. Statistics in medicine

Lee RTC, Chang HH, Russell CA, Lipsitch M, Maurer-Stroh S. (2019). Influenza A Hemagglutinin Passage Bias Sites and Host Specificity Mutations. Cells, 8(9)

Goldstein E, Olesen SW, Karaca Z, Steiner CA, Viboud C, Lipsitch M. (2019). Levels of outpatient prescribing for four major antibiotic classes and rates of septicemia hospitalization in adults in different US states - a statistical analysis. BMC Public Health, 19(1)

Lipsitch M, Shaman J. (2019). Comment on: 'Antibiotic footprint' as a communication tool to aid reduction of antibiotic consumption. The Journal of antimicrobial chemotherapy, 74(11)

Abuelezam NN, Reshef YA, Novak D, Grad YH, Seage Iii GR, Mayer K, Lipsitch M. (2019). Interaction Patterns of Men Who Have Sex With Men on a Geosocial Networking Mobile App in Seven United States Metropolitan Areas: Observational Study. Journal of medical Internet research, 21(9)

Lipsitch M, Santillana M. (2019). Enhancing Situational Awareness to Prevent Infectious Disease Outbreaks from Becoming Catastrophic. Current topics in microbiology and immunology

Chua H, Feng S, Lewnard JA, Sullivan SG, Blyth CC, Lipsitch M, Cowling BJ. (2019). The use of test-negative controls to monitor vaccine effectiveness: a systematic review of methodology. Epidemiology (Cambridge, Mass.)

Goldstein E, MacFadden DR, Karaca Z, Steiner CA, Viboud C, Lipsitch M. (2019). Antimicrobial resistance prevalence, rates of hospitalization with septicemia and rates of mortality with sepsis in adults in different US states. International journal of antimicrobial agents, 54(1)

Yang A, Cai F, Lipsitch M. (2019). Herd immunity alters the conditions for performing dose schedule comparisons: an individual-based model of pneumococcal carriage. BMC infectious diseases, 19(1)

Gallagher T, Lipsitch M. (2019). Post-Exposure Effects of Vaccines on Infectious Diseases. Epidemiologic reviews

Olesen SW, Lipsitch M, Grad YH. (2019). Response to comment on 'The distribution of antibiotic use and its association with antibiotic resistance'. eLife, (8)

Eyal N, Kimmelman J, Holtzman LG, Lipsitch M. (2019). Regulating impact on bystanders in clinical trials: An unsettled frontier. Clinical trials (London, England), 16(5)

Hicks AL, Kissler SM, Lipsitch M, Grad YH. (2019). Surveillance to maintain the sensitivity of genotype-based antibiotic resistance diagnostics. PLoS biology, 17(11)

McAdams D, Wollein Waldetoft K, Tedijanto C, Lipsitch M, Brown SP. (2019). Resistance diagnostics as a public health tool to combat antibiotic resistance: A model-based evaluation. PLoS biology, 17(5)

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)

Lehtinen S, Blanquart F, Lipsitch M, Fraser C, . (2019). On the evolutionary ecology of multidrug resistance in bacteria. PLoS pathogens, 15(5)

Langwig KE, Gomes MGM, Clark MD, Kwitny M, Yamada S, Wargo AR, Lipsitch M. (2019). Limited available evidence supports theoretical predictions of reduced vaccine efficacy at higher exposure dose. Scientific reports, 9(1)

Ryu S, Cowling BJ, Wu P, Olesen S, Fraser C, Sun DS, Lipsitch M, Grad YH. (2019). Case-based surveillance of antimicrobial resistance with full susceptibility profiles. JAC-antimicrobial resistance, 1(3)

Hitchings MDT, Coldiron ME, Grais RF, Lipsitch M. (2019). Analysis of a meningococcal meningitis outbreak in Niger - potential effectiveness of reactive prophylaxis. PLoS neglected tropical diseases, 13(3)

Kahn R, Hitchings M, Bellan S, Lipsitch M. (2018). Impact of stochastically generated heterogeneity in hazard rates on individually randomized vaccine efficacy trials. Clinical trials (London, England), 15(2)

Georgieva M, Buckee CO, Lipsitch M. (2019). Models of immune selection for multi-locus antigenic diversity of pathogens. Nature reviews. Immunology, 19(1)

Olesen SW, Barnett ML, MacFadden DR, Lipsitch M, Grad YH. (2018). Trends in outpatient antibiotic use and prescribing practice among US older adults, 2011-15: observational study. BMJ (Clinical research ed.), (362)

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)

Olesen SW, Torrone EA, Papp JR, Kirkcaldy RD, Lipsitch M, Grad YH. (2019). Azithromycin Susceptibility Among Neisseria gonorrhoeae Isolates and Seasonal Macrolide Use. The Journal of infectious diseases, 219(4)

Sevilla JP, Bloom DE, Cadarette D, Jit M, Lipsitch M. (2018). Toward economic evaluation of the value of vaccines and other health technologies in addressing AMR. Proceedings of the National Academy of Sciences of the United States of America, 115(51)

Olesen SW, Barnett ML, MacFadden DR, Brownstein JS, Hernández-Díaz S, Lipsitch M, Grad YH. (2018). The distribution of antibiotic use and its association with antibiotic resistance. eLife, (7)

Relman DA, Lipsitch M. (2018). Microbiome as a tool and a target in the effort to address antimicrobial resistance. Proceedings of the National Academy of Sciences of the United States of America, 115(51)

Tedijanto C, Olesen SW, Grad YH, Lipsitch M. (2018). Estimating the proportion of bystander selection for antibiotic resistance among potentially pathogenic bacterial flora. Proceedings of the National Academy of Sciences of the United States of America, 115(51)

Kahn R, Hitchings M, Wang R, Bellan SE, Lipsitch M. (2019). Analyzing Vaccine Trials in Epidemics With Mild and Asymptomatic Infection. American journal of epidemiology, 188(2)

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)

Lewnard JA, Tedijanto C, Cowling BJ, Lipsitch M. (2018). Measurement of Vaccine Direct Effects Under the Test-Negative Design. American journal of epidemiology, 187(12)

Lipsitch M. (2019). Challenges of Vaccine Effectiveness and Waning Studies. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 68(10)

Hitchings MDT, Lipsitch M, Wang R, Bellan SE. (2018). Competing Effects of Indirect Protection and Clustering on the Power of Cluster-Randomized Controlled Vaccine Trials. American journal of epidemiology, 187(8)

Lewnard JA, Tähtinen PA, Laine MK, Lindholm L, Jalava J, Huovinen P, Lipsitch M, Ruohola A. (2018). Impact of Antimicrobial Treatment for Acute Otitis Media on Carriage Dynamics of Penicillin-Susceptible and Penicillin-Nonsusceptible Streptococcus pneumoniae. The Journal of infectious diseases, 218(9)

Atkins KE, Lipsitch M. (2018). Can antibiotic resistance be reduced by vaccinating against respiratory disease?. The Lancet. Respiratory medicine, 6(11)

Lipsitch M. (2018). Why Do Exceptionally Dangerous Gain-of-Function Experiments in Influenza?. Methods in molecular biology (Clifton, N.J.), (1836)

Cai FY, Fussell T, Cobey S, Lipsitch M. (2018). Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine. PLoS computational biology, 14(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)

Blanquart F, Lehtinen S, Lipsitch M, Fraser C. (2018). The evolution of antibiotic resistance in a structured host population. Journal of the Royal Society, Interface, 15(143)

Johansson MA, Reich NG, Meyers LA, Lipsitch M. (2018). Preprints: An underutilized mechanism to accelerate outbreak science. PLoS medicine, 15(4)

Goldstein E, Worby CJ, Lipsitch M. (2018). On the Role of Different Age Groups and Pertussis Vaccines During the 2012 Outbreak in Wisconsin. Open forum infectious diseases, 5(5)

Kahn R, Rid A, Smith PG, Eyal N, Lipsitch M. (2018). Choices in vaccine trial design in epidemics of emerging infections. PLoS medicine, 15(8)

Halloran ME, Auranen K, Baird S, Basta NE, Bellan SE, Brookmeyer R, Cooper BS, DeGruttola V, Hughes JP, Lessler J, Lofgren ET, Longini IM, Onnela JP, Özler B, Seage GR, Smith TA, Vespignani A, Vynnycky E, Lipsitch M. (2017). Simulations for designing and interpreting intervention trials in infectious diseases. BMC medicine, 15(1)

Lipsitch M. (2017). If a Global Catastrophic Biological Risk Materializes, at What Stage Will We Recognize It?. Health security, 15(4)

Langwig KE, Wargo AR, Jones DR, Viss JR, Rutan BJ, Egan NA, Sá-Guimarães P, Kim MS, Kurath G, Gomes MGM, Lipsitch M. (2017). Vaccine Effects on Heterogeneity in Susceptibility and Implications for Population Health Management. MBio, 8(6)

Lipsitch M, Li LM, Patterson S, Trammel J, Juergens C, Gruber WC, Scott DA, Dagan R. (2018). Serotype-specific immune responses to pneumococcal conjugate vaccine among children are significantly correlated by individual: Analysis of randomized controlled trial data. Vaccine, 36(4)

McCormick AW, Abuelezam NN, Fussell T, Seage GR 3rd., Lipsitch M. (2017). Displacement of sexual partnerships in trials of sexual behavior interventions: A model-based assessment of consequences. Epidemics, (20)

Lehtinen S, Blanquart F, Croucher NJ, Turner P, Lipsitch M, Fraser C. (2017). Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage. 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)

Lipsitch M, Eyal N. (2017). Improving vaccine trials in infectious disease emergencies. Science (New York, N.Y.), 357(6347)

Eyal N, Lipsitch M. (2017). Vaccine testing for emerging infections: the case for individual randomisation. Journal of medical ethics, 43(9)

Lewnard JA, Givon-Lavi N, Weinberger DM, Lipsitch M, Dagan R. (2017). Pan-serotype Reduction in Progression of Streptococcus pneumoniae to Otitis Media After Rollout of Pneumococcal Conjugate Vaccines. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 65(11)

Goldstein E, Nguyen HH, Liu P, Viboud C, Steiner CA, Worby CJ, Lipsitch M. (2018). On the Relative Role of Different Age Groups During Epidemics Associated With Respiratory Syncytial Virus. The Journal of infectious diseases, 217(2)

Worby CJ, Wallinga J, Lipsitch M, Goldstein E. (2017). Population effect of influenza vaccination under co-circulation of non-vaccine variants and the case for a bivalent A/H3N2 vaccine component. Epidemics, (19)

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)

Hitchings MD, Grais RF, Lipsitch M. (2017). Using simulation to aid trial design: Ring-vaccination trials. PLoS neglected tropical diseases, 11(3)

Chang HH, Huber RG, Bond PJ, Grad YH, Camerini D, Maurer-Stroh S, Lipsitch M. (2017). Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses. Bulletin of the World Health Organization, 95(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)

Grad YH, Harris SR, Kirkcaldy RD, Green AG, Marks DS, Bentley SD, Trees D, Lipsitch M. (2016). Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013. The Journal of infectious diseases, 214(10)

Lipsitch M, Jha A, Simonsen L. (2016). Observational studies and the difficult quest for causality: lessons from vaccine effectiveness and impact studies. International journal of epidemiology, 45(6)

Grad YH, Lipsitch M. (2017). Reply to Allan-Blitz and Klausner. The Journal of infectious diseases, 215(3)

Goldstein E, Pitzer VE, O'Hagan JJ, Lipsitch M. (2017). Temporally Varying Relative Risks for Infectious Diseases: Implications for Infectious Disease Control. Epidemiology (Cambridge, Mass.), 28(1)

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)

Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA. (2016). Viral factors in influenza pandemic risk assessment. Elife, (5)

Lipsitch M, Evans NG, Cotton-Barratt O. (2017). Underprotection of Unpredictable Statistical Lives Compared to Predictable Ones. Risk analysis : an official publication of the Society for Risk Analysis, 37(5)

Lipsitch M. (2016). Comment on "Gain-of-Function Research and the Relevance to Clinical Practice". The Journal of infectious diseases, 214(8)

Lipsitch M, Cowling BJ. (2016). Zika vaccine trials. Science (New York, N.Y.), 353(6304)

Lipsitch M, Siber GR. (2016). How Can Vaccines Contribute to Solving the Antimicrobial Resistance Problem?. MBio, 7(3)

Leung K, Lipsitch M, Yuen KY, Wu JT. (2017). Monitoring the fitness of antiviral-resistant influenza strains during an epidemic: a mathematical modelling study. The Lancet. Infectious diseases, 17(3)

Kunkel A, Colijn C, Lipsitch M, Cohen T. (2015). How could preventive therapy affect the prevalence of drug resistance? Causes and consequences. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 370(1670)

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)

Lipsitch M, Inglesby TV. (2015). Reply to "Studies on influenza virus transmission between ferrets: the public health risks revisited". MBio, 6(1)

Worby CJ, Chaves SS, Wallinga J, Lipsitch M, Finelli L, Goldstein E. (2015). On the relative role of different age groups in influenza epidemics. Epidemics, (13)

Abel S, Abel zur Wiesch P, Chang HH, Davis BM, Lipsitch M, Waldor MK. (2015). Sequence tag-based analysis of microbial population dynamics. Nature methods, 12(3)

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)

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)

Worby CJ, Kenyon C, Lynfield R, Lipsitch M, Goldstein E. (2015). Examining the role of different age groups, and of vaccination during the 2012 Minnesota pertussis outbreak. Scientific reports, (5)

Lipsitch M, Donnelly CA, Fraser C, Blake IM, Cori A, Dorigatti I, Ferguson NM, Garske T, Mills HL, Riley S, Van Kerkhove MD, Hernán MA. (2015). Potential Biases in Estimating Absolute and Relative Case-Fatality Risks during Outbreaks. PLoS neglected tropical diseases, 9(7)

Trzciński K, Li Y, Weinberger DM, Thompson CM, Cordy D, Bessolo A, Malley R, Lipsitch M. (2015). Effect of Serotype on Pneumococcal Competition in a Mouse Colonization Model. MBio, 6(5)

Lipsitch M, Inglesby TV. (2015). Erratum for lipsitch and inglesby, moratorium on research intended to create novel potential pandemic pathogens. MBio, 6(1)

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)

Lipsitch M, Esvelt K, Inglesby T. (2015). Calls for caution in genome engineering should be a model for similar dialogue on pandemic pathogen research. Annals of internal medicine, 163(10)

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)

Lipsitch M, Eyal N, Halloran ME, Hernán MA, Longini IM, Perencevich EN, Grais RF. (2015). Vaccine testing. Ebola and beyond. Science (New York, N.Y.), 348(6230)

Yang W, Lipsitch M, Shaman J. (2015). Inference of seasonal and pandemic influenza transmission dynamics. Proceedings of the National Academy of Sciences of the United States of America, 112(9)

Evans NG, Lipsitch M, Levinson M. (2015). The ethics of biosafety considerations in gain-of-function research resulting in the creation of potential pandemic pathogens. Journal of medical ethics, 41(11)

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)

Grad YH, Goldstein E, Lipsitch M, White PJ. (2016). Improving Control of Antibiotic-Resistant Gonorrhea by Integrating Research Agendas Across Disciplines: Key Questions Arising From Mathematical Modeling. The Journal of infectious diseases, 213(6)

Althouse BM, Scarpino SV, Meyers LA, Ayers JW, Bargsten M, Baumbach J, Brownstein JS, Castro L, Clapham H, Cummings DA, Del Valle S, Eubank S, Fairchild G, Finelli L, Generous N, George D, Harper DR, Hébert-Dufresne L, Johansson MA, Konty K, Lipsitch M, Milinovich G, Miller JD, Nsoesie EO, Olson DR, Paul M, Polgreen PM, Priedhorsky R, Read JM, Rodriguez-Barraquer I, Smith DJ, Stefansen C, Swerdlow DL, Thompson D, Vespignani A, Wesolowski A. (2015). Enhancing disease surveillance with novel data streams: challenges and opportunities. EPJ data science, (4)

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)

Jacobs JH, Viboud C, Tchetgen ET, Schwartz J, Steiner C, Simonsen L, Lipsitch M. (2014). The association of meningococcal disease with influenza in the United States, 1989-2009. PLoS One, 9(9)

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)

Ascioglu S, Samore MH, Lipsitch M. (2014). A new approach to the analysis of antibiotic resistance data from hospitals. Microbial drug resistance (Larchmont, N.Y.), 20(6)

Li Y, Thompson CM, Lipsitch M. (2014). A modified Janus cassette (Sweet Janus) to improve allelic replacement efficiency by high-stringency negative selection in Streptococcus pneumoniae. PLoS One, 9(6)

Patterson-Lomba O, Van Noort S, Cowling BJ, Wallinga J, Gomes MG, Lipsitch M, Goldstein E. (2014). Utilizing syndromic surveillance data for estimating levels of influenza circulation. American journal of epidemiology, 179(11)

Huang KE, Lipsitch M, Shaman J, Goldstein E. (2014). The US 2009 A(H1N1) influenza epidemic: quantifying the impact of school openings on the reproductive number. Epidemiology (Cambridge, Mass.), 25(2)

Fisman DN, Leung GM, Lipsitch M. (2014). Nuanced risk assessment for emerging infectious diseases. Lancet, 383(9913)

Grad YH, Lipsitch M. (2014). Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome biology, 15(11)

Russell CA, Kasson PM, Donis RO, Riley S, Dunbar J, Rambaut A, Asher J, Burke S, Davis CT, Garten RJ, Gnanakaran S, Hay SI, Herfst S, Lewis NS, Lloyd-Smith JO, Macken CA, Maurer-Stroh S, Neuhaus E, Parrish CR, Pepin KM, Shepard SS, Smith DL, Suarez DL, Trock SC, Widdowson MA, George DB, Lipsitch M, Bloom JD. (2014). Improving pandemic influenza risk assessment. eLife, (3)

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

Lipsitch M. (2014). Can limited scientific value of potential pandemic pathogen experiments justify the risks?. MBio, 5(5)

Lipsitch M, Inglesby TV. (2014). Moratorium on research intended to create novel potential pandemic pathogens. MBio, 5(6)

Johnson SR, Grad Y, Ganakammal SR, Burroughs M, Frace M, Lipsitch M, Weil R, Trees D. (2014). In Vitro selection of Neisseria gonorrhoeae mutants with elevated MIC values and increased resistance to cephalosporins. Antimicrobial agents and chemotherapy, 58(11)

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)

Lipsitch M, Galvani AP. (2014). Ethical alternatives to experiments with novel potential pandemic pathogens. PLoS medicine, 11(5)

Gomes MG, Lipsitch M, Wargo AR, Kurath G, Rebelo C, Medley GF, Coutinho A. (2014). A missing dimension in measures of vaccination impacts. PLoS pathogens, 10(3)

Lipsitch M, Hernán MA. (2013). Oseltamivir effect on antibiotic-treated lower respiratory tract complications in virologically positive randomized trial participants. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 57(9)

Joice R, Lipsitch M. (2013). Targeting imperfect vaccines against drug-resistance determinants: a strategy for countering the rise of drug resistance. PLoS One, 8(7)

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)

O'Hagan JJ, Lipsitch M, Hernán MA. (2014). Estimating the per-exposure effect of infectious disease interventions. Epidemiology (Cambridge, Mass.), 25(1)

Link-Gelles R, Thomas A, Lynfield R, Petit S, Schaffner W, Harrison L, Farley MM, Aragon D, Nicols M, Kirley PD, Zansky S, Jorgensen J, Juni BA, Jackson D, Moore MR, Lipsitch M. (2013). Geographic and temporal trends in antimicrobial nonsusceptibility in Streptococcus pneumoniae in the post-vaccine era in the United States. The Journal of infectious diseases, 208(8)

Ford CB, Shah RR, Maeda MK, Gagneux S, Murray MB, Cohen T, Johnston JC, Gardy J, Lipsitch M, Fortune SM. (2013). Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nature genetics, 45(7)

Weinberger DM, Bruden DT, Grant LR, Lipsitch M, O'Brien KL, Pelton SI, Sanders EA, Feikin DR. (2013). Using pneumococcal carriage data to monitor postvaccination changes in invasive disease. American journal of epidemiology, 178(9)

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)

Quandelacy TM, Viboud C, Charu V, Lipsitch M, Goldstein E. (2014). Age- and sex-related risk factors for influenza-associated mortality in the United States between 1997-2007. American journal of epidemiology, 179(2)

Koep TH, Enders FT, Pierret C, Ekker SC, Krageschmidt D, Neff KL, Lipsitch M, Shaman J, Huskins WC. (2013). Predictors of indoor absolute humidity and estimated effects on influenza virus survival in grade schools. BMC infectious diseases, (13)

Lipsitch M. (2013). Avian influenza: Ferret H7N9 flu model questioned. Nature, 501(7465)

Li Y, Thompson CM, Trzcinski K, Lipsitch M. (2013). Within-host selection is limited by an effective population of Streptococcus pneumoniae during nasopharyngeal colonization. Infection and immunity, 81(12)

Li Y, Weinberger DM, Thompson CM, Trzcinski K, Lipsitch M. (2013). Surface charge of Streptococcus pneumoniae predicts serotype distribution. Infection and immunity, 81(12)

Shaman J, Karspeck A, Yang W, Tamerius J, Lipsitch M. (2013). Real-time influenza forecasts during the 2012-2013 season. Nature communications, (4)

Goldstein E, Kirkcaldy RD, Reshef D, Berman S, Weinstock H, Sabeti P, Del Rio C, Hall G, Hook EW, Lipsitch M. (2012). Factors related to increasing prevalence of resistance to ciprofloxacin and other antimicrobial drugs in Neisseria gonorrhoeae, United States. Emerging infectious diseases, 18(8)

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)

Lipsitch M, Abdullahi O, DʼAmour A, Xie W, Weinberger DM, Tchetgen Tchetgen E, Scott JA. (2012). Estimating rates of carriage acquisition and clearance and competitive ability for pneumococcal serotypes in Kenya with a Markov transition model. Epidemiology (Cambridge, Mass.), 23(4)

Lipsitch M, Plotkin JB, Simonsen L, Bloom B. (2012). Evolution, safety, and highly pathogenic influenza viruses. Science (New York, N.Y.), 336(6088)

Van Kerkhove MD, Riley S, Lipsitch M, Guan Y, Monto AS, Webster RG, Zambon M, Nicoll A, Peiris JS, Ferguson NM. (2012). Comment on "Seroevidence for H5N1 influenza infections in humans: meta-analysis". Science (New York, N.Y.), 336(6088)

Ke W, Huang SS, Hudson LO, Elkins KR, Nguyen CC, Spratt BG, Murphy CR, Avery TR, Lipsitch M. (2012). Patient sharing and population genetic structure of methicillin-resistant Staphylococcus aureus. Proceedings of the National Academy of Sciences of the United States of America, 109(17)

Goldstein E, Viboud C, Charu V, Lipsitch M. (2012). Improving the estimation of influenza-related mortality over a seasonal baseline. Epidemiology (Cambridge, Mass.), 23(6)

Cobey S, Lipsitch M. (2013). Pathogen diversity and hidden regimes of apparent competition. The American naturalist, 181(1)

Lipsitch M, Bloom BR. (2012). Rethinking biosafety in research on potential pandemic pathogens. MBio, 3(5)

Pitzer VE, Burgner D, Viboud C, Simonsen L, Andreasen V, Steiner CA, Lipsitch M. (2012). Modelling seasonal variations in the age and incidence of Kawasaki disease to explore possible infectious aetiologies. Proceedings. Biological sciences, 279(1739)

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)

Li Y, Gierahn T, Thompson CM, Trzcinski K, Ford CB, Croucher N, Gouveia P, Flechtner JB, Malley R, Lipsitch M. (2012). Distinct effects on diversifying selection by two mechanisms of immunity against Streptococcus pneumoniae. PLoS pathogens, 8(11)

Shaman J, Lipsitch M. (2013). The El Nino-Southern Oscillation (ENSO)-pandemic influenza connection: coincident or causal?. Proceedings of the National Academy of Sciences of the United States of America, (110 Suppl 1)

Grad YH, Miller JC, Lipsitch M. (2012). Cholera modeling: challenges to quantitative analysis and predicting the impact of interventions. Epidemiology (Cambridge, Mass.), 23(4)

Cobey S, Lipsitch M. (2012). Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes. Science (New York, N.Y.), 335(6074)

Jacobs JH, Archer BN, Baker MG, Cowling BJ, Heffernan RT, Mercer G, Uez O, Hanshaoworakul W, Viboud C, Schwartz J, Tchetgen Tchetgen E, Lipsitch M. (2012). Searching for sharp drops in the incidence of pandemic A/H1N1 influenza by single year of age. PLoS One, 7(8)

Lipsitch M, Finelli L, Heffernan RT, Leung GM, Redd SC, . (2011). Improving the evidence base for decision making during a pandemic: the example of 2009 influenza A/H1N1. Biosecurity and bioterrorism : biodefense strategy, practice, and science, 9(2)

Ford CB, Lin PL, Chase MR, Shah RR, Iartchouk O, Galagan J, Mohaideen N, Ioerger TR, Sacchettini JC, Lipsitch M, Flynn JL, Fortune SM. (2011). Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nature genetics, 43(5)

Goldstein E, Cowling BJ, Aiello AE, Takahashi S, King G, Lu Y, Lipsitch M. (2011). Estimating incidence curves of several infections using symptom surveillance data. PLoS One, 6(8)

Grad YH, Lipsitch M, Aiello AE. (2012). Secular trends in Helicobacter pylori seroprevalence in adults in the United States: evidence for sustained race/ethnic disparities. American journal of epidemiology, 175(1)

Hernán MA, Lipsitch M. (2011). Oseltamivir and risk of lower respiratory tract complications in patients with flu symptoms: a meta-analysis of eleven randomized clinical trials. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 53(3)

Weinberger DM, Malley R, Lipsitch M. (2011). Serotype replacement in disease after pneumococcal vaccination. Lancet, 378(9807)

Smith J, Lipsitch M, Almond JW. (2011). Vaccine production, distribution, access, and uptake. Lancet, 378(9789)

Mostofsky E, Lipsitch M, Regev-Yochay G. (2011). Is methicillin-resistant Staphylococcus aureus replacing methicillin-susceptible S. aureus?. The Journal of antimicrobial chemotherapy, 66(10)

Shaman J, Jeon CY, Giovannucci E, Lipsitch M. (2011). Shortcomings of vitamin D-based model simulations of seasonal influenza. PLoS One, 6(6)

O'Hagan JJ, Hernán MA, Walensky RP, Lipsitch M. (2012). Apparent declining efficacy in randomized trials: examples of the Thai RV144 HIV vaccine and South African CAPRISA 004 microbicide trials. AIDS (London, England), 26(2)

Weinberger DM, Harboe ZB, Flasche S, Scott JA, Lipsitch M. (2011). Prediction of serotypes causing invasive pneumococcal disease in unvaccinated and vaccinated populations. Epidemiology (Cambridge, Mass.), 22(2)

Goldstein E, Cobey S, Takahashi S, Miller JC, Lipsitch M. (2011). Predicting the epidemic sizes of influenza A/H1N1, A/H3N2, and B: a statistical method. PLoS medicine, 8(7)

Huang SS, Avery TR, Song Y, Elkins KR, Nguyen CC, Nutter SK, Nafday AA, Condon CJ, Chang MT, Chrest D, Boos J, Bobashev G, Wheaton W, Frank SA, Platt R, Lipsitch M, Bush RM, Eubank S, Burke DS, Lee BY. (2010). Quantifying interhospital patient sharing as a mechanism for infectious disease spread. Infection control and hospital epidemiology, 31(11)

Lipsitch M, Tchetgen Tchetgen E, Cohen T. (2010). Negative controls: a tool for detecting confounding and bias in observational studies. Epidemiology (Cambridge, Mass.), 21(3)

Lajous M, Danon L, López-Ridaura R, Astley CM, Miller JC, Dowell SF, O'Hagan JJ, Goldstein E, Lipsitch M. (2010). Mobile messaging as surveillance tool during pandemic (H1N1) 2009, Mexico. Emerging infectious diseases, 16(9)

Shaman J, Pitzer VE, Viboud C, Grenfell BT, Lipsitch M. (2010). Absolute humidity and the seasonal onset of influenza in the continental United States. PLoS biology, 8(2)

Goldstein E, Miller JC, O'Hagan JJ, Lipsitch M. (2010). Pre-dispensing of antivirals to high-risk individuals in an influenza pandemic. Influenza and other respiratory viruses, 4(2)

Goldstein E, Cowling BJ, O'Hagan JJ, Danon L, Fang VJ, Hagy A, Miller JC, Reshef D, Robins J, Biedrzycki P, Lipsitch M. (2010). Oseltamivir for treatment and prevention of pandemic influenza A/H1N1 virus infection in households, Milwaukee, 2009. BMC infectious diseases, (10)

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)

Weinberger DM, Harboe ZB, Sanders EA, Ndiritu M, Klugman KP, Rückinger S, Dagan R, Adegbola R, Cutts F, Johnson HL, O'Brien KL, Scott JA, Lipsitch M. (2010). Association of serotype with risk of death due to pneumococcal pneumonia: a meta-analysis. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 51(6)

Shaman J, Goldstein E, Lipsitch M. (2011). Absolute humidity and pandemic versus epidemic influenza. American journal of epidemiology, 173(2)

Wallinga J, van Boven M, Lipsitch M. (2010). Optimizing infectious disease interventions during an emerging epidemic. Proceedings of the National Academy of Sciences of the United States of America, 107(2)

Lau LL, Cowling BJ, Fang VJ, Chan KH, Lau EH, Lipsitch M, Cheng CK, Houck PM, Uyeki TM, Peiris JS, Leung GM. (2010). Viral shedding and clinical illness in naturally acquired influenza virus infections. The Journal of infectious diseases, 201(10)

Miller JC, Danon L, O'Hagan JJ, Goldstein E, Lajous M, Lipsitch M. (2010). Student behavior during a school closure caused by pandemic influenza A/H1N1. PLoS One, 5(5)

Van Kerkhove MD, Asikainen T, Becker NG, Bjorge S, Desenclos JC, dos Santos T, Fraser C, Leung GM, Lipsitch M, Longini IM Jr., McBryde ES, Roth CE, Shay DK, Smith DJ, Wallinga J, White PJ, Ferguson NM, Riley S, . (2010). Studies needed to address public health challenges of the 2009 H1N1 influenza pandemic: insights from modeling. PLoS medicine, 7(6)

Lipsitch M, Riley S, Cauchemez S, Ghani AC, Ferguson NM. (2009). Managing and reducing uncertainty in an emerging influenza pandemic. The New England journal of medicine, 361(2)

Goldstein E, Lipsitch M. (2009). Antiviral usage for H1N1 treatment: pros, cons and an argument for broader prescribing guidelines in the United States. PLoS currents, (1)

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)

Presanis AM, Lipsitch M, Daniela De Angelis, , Hagy A, Reed C, Riley S, Cooper B, Biedrzycki P, Finelli L, B J. (2009). The severity of pandemic H1N1 influenza in the United States, April - July 2009. PLoS currents, (1)

Goldstein E, Lipsitch M. (2009). H1N1 vaccination and adults with underlying health conditions in the US. PLoS currents, (1)

Goldstein E, Dushoff J, Ma J, Plotkin JB, Earn DJ, Lipsitch M. (2009). Reconstructing influenza incidence by deconvolution of daily mortality time series. Proceedings of the National Academy of Sciences of the United States of America, 106(51)

Goldstein E, Miller JC, O'Hagan J, Lipsitch M. (2009). Predispensing of antivirals to high-risk individuals in an influenza pandemic. PLoS currents, (1)

Shaman J, Pitzer V, Viboud C, Lipsitch M, Grenfell B. (2009). Absolute Humidity and the Seasonal Onset of Influenza in the Continental US. PLoS currents, (2)

Pitzer VE, Lipsitch M. (2009). Exploring the relationship between incidence and the average age of infection during seasonal epidemics. Journal of theoretical biology, 260(2)

Lipsitch M, Hayden FG, Cowling BJ, Leung GM. (2009). How to maintain surveillance for novel influenza A H1N1 when there are too many cases to count. Lancet, 374(9696)

Wu JT, Leung GM, Lipsitch M, Cooper BS, Riley S. (2009). Hedging against antiviral resistance during the next influenza pandemic using small stockpiles of an alternative chemotherapy. PLoS medicine, 6(5)

Lipsitch M, Viboud C. (2009). Influenza seasonality: lifting the fog. Proceedings of the National Academy of Sciences of the United States of America, 106(10)

Lipsitch M, Lajous M, O'Hagan JJ, Cohen T, Miller JC, Goldstein E, Danon L, Wallinga J, Riley S, Dowell SF, Reed C, McCarron M. (2009). Use of cumulative incidence of novel influenza A/H1N1 in foreign travelers to estimate lower bounds on cumulative incidence in Mexico. PLoS One, 4(9)

McCaw JM, Wood JG, McBryde ES, Nolan TM, Wu JT, Lipsitch M, McVernon J. (2009). Understanding Australia's influenza pandemic policy on the strategic use of the antiviral drug stockpile. The Medical journal of Australia, 191(3)

Klugman KP, Astley CM, Lipsitch M. (2009). Time from illness onset to death, 1918 influenza and pneumococcal pneumonia. Emerging infectious diseases, 15(2)

Presanis AM, De Angelis D, , Hagy A, Reed C, Riley S, Cooper BS, Finelli L, Biedrzycki P, Lipsitch M. (2009). The severity of pandemic H1N1 influenza in the United States, from April to July 2009: a Bayesian analysis. PLoS medicine, 6(12)

Weinberger DM, Trzcinski K, Lu YJ, Bogaert D, Brandes A, Galagan J, Anderson PW, Malley R, Lipsitch M. (2009). Pneumococcal capsular polysaccharide structure predicts serotype prevalence. PLoS pathogens, 5(6)

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

White LF, Wallinga J, Finelli L, Reed C, Riley S, Lipsitch M, Pagano M. (2009). Estimation of the reproductive number and the serial interval in early phase of the 2009 influenza A/H1N1 pandemic in the USA. Influenza and other respiratory viruses, 3(6)

Reed C, Angulo FJ, Swerdlow DL, Lipsitch M, Meltzer MI, Jernigan D, Finelli L. (2009). Estimates of the prevalence of pandemic (H1N1) 2009, United States, April-July 2009. Emerging infectious diseases, 15(12)

Cohen T, Lipsitch M. (2008). Too little of a good thing: a paradox of moderate infection control. Epidemiology (Cambridge, Mass.), 19(4)

Dagan R, Barkai G, Givon-Lavi N, Sharf AZ, Vardy D, Cohen T, Lipsitch M, Greenberg D. (2008). Seasonality of antibiotic-resistant streptococcus pneumoniae that causes acute otitis media: a clue for an antibiotic-restriction policy?. The Journal of infectious diseases, 197(8)

Weinberger DM, Dagan R, Givon-Lavi N, Regev-Yochay G, Malley R, Lipsitch M. (2008). Epidemiologic evidence for serotype-specific acquired immunity to pneumococcal carriage. The Journal of infectious diseases, 197(11)

Trzciński K, Thompson CM, Srivastava A, Basset A, Malley R, Lipsitch M. (2008). Protection against nasopharyngeal colonization by Streptococcus pneumoniae is mediated by antigen-specific CD4+ T cells. Infection and immunity, 76(6)

Kenah E, Lipsitch M, Robins JM. (2008). Generation interval contraction and epidemic data analysis. Mathematical biosciences, 213(1)

Regev-Yochay G, Malley R, Rubinstein E, Raz M, Dagan R, Lipsitch M. (2008). In vitro bactericidal activity of Streptococcus pneumoniae and bactericidal susceptibility of Staphylococcus aureus strains isolated from cocolonized versus noncocolonized children. Journal of clinical microbiology, 46(2)

Lipsitch M, O'Neill K, Cordy D, Bugalter B, Trzcinski K, Thompson CM, Goldstein R, Pelton S, Huot H, Bouchet V, Reid R, Santosham M, O'Brien KL. (2007). Strain characteristics of Streptococcus pneumoniae carriage and invasive disease isolates during a cluster-randomized clinical trial of the 7-valent pneumococcal conjugate vaccine. The Journal of infectious diseases, 196(8)

Lipsitch M, O'Hagan JJ. (2007). Patterns of antigenic diversity and the mechanisms that maintain them. Journal of the Royal Society, Interface, 4(16)

Pitzer VE, Leung GM, Lipsitch M. (2007). Estimating variability in the transmission of severe acute respiratory syndrome to household contacts in Hong Kong, China. American journal of epidemiology, 166(3)

Hatchett RJ, Mecher CE, Lipsitch M. (2007). Public health interventions and epidemic intensity during the 1918 influenza pandemic. Proceedings of the National Academy of Sciences of the United States of America, 104(18)

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)

Pitzer VE, Olsen SJ, Bergstrom CT, Dowell SF, Lipsitch M. (2007). Little evidence for genetic susceptibility to influenza A (H5N1) from family clustering data. Emerging infectious diseases, 13(7)

Lipsitch M, Cohen T, Murray M, Levin BR. (2007). Antiviral resistance and the control of pandemic influenza. PLoS medicine, 4(1)

Cohen T, Lipsitch M, Walensky RP, Murray M. (2006). Beneficial and perverse effects of isoniazid preventive therapy for latent tuberculosis infection in HIV-tuberculosis coinfected populations. Proceedings of the National Academy of Sciences of the United States of America, 103(18)

Regev-Yochay G, Trzcinski K, Thompson CM, Malley R, Lipsitch M. (2006). Interference between Streptococcus pneumoniae and Staphylococcus aureus: In vitro hydrogen peroxide-mediated killing by Streptococcus pneumoniae. Journal of bacteriology, 188(13)

Palmer ME, Lipsitch M. (2006). The influence of hitchhiking and deleterious mutation upon asexual mutation rates. Genetics, 173(1)

Wang YC, Lipsitch M. (2006). Upgrading antibiotic use within a class: tradeoff between resistance and treatment success. Proceedings of the National Academy of Sciences of the United States of America, 103(25)

Lipsitch M, Robins JM, Mills CE, Bergstrom CT. (2006). Multiple outbreaks and flu containment plans. Science (New York, N.Y.), 312(5775)

Trzcinski K, Thompson CM, Gilbey AM, Dowson CG, Lipsitch M. (2006). Incremental increase in fitness cost with increased beta -lactam resistance in pneumococci evaluated by competition in an infant rat nasal colonization model. The Journal of infectious diseases, 193(9)

Mills CE, Robins JM, Bergstrom CT, Lipsitch M. (2006). Pandemic influenza: risk of multiple introductions and the need to prepare for them. PLoS medicine, 3(6)

Trzciński K, MacNeil A, Klugman KP, Lipsitch M. (2005). Capsule homology does not increase the frequency of transformation of linked penicillin binding proteins PBP 1a and PBP 2x in Streptococcus pneumoniae. Antimicrobial agents and chemotherapy, 49(4)

Trzcinski K, Thompson C, Malley R, Lipsitch M. (2005). Antibodies to conserved pneumococcal antigens correlate with, but are not required for, protection against pneumococcal colonization induced by prior exposure in a mouse model. Infection and immunity, 73(10)

Malley R, Trzcinski K, Srivastava A, Thompson CM, Anderson PW, Lipsitch M. (2005). CD4+ T cells mediate antibody-independent acquired immunity to pneumococcal colonization. Proceedings of the National Academy of Sciences of the United States of America, 102(13)

Lipsitch M. (2005). Pandemic flu: we are not prepared. MedGenMed : Medscape general medicine, 7(2)

Huang SS, Finkelstein JA, Lipsitch M. (2005). Modeling community- and individual-level effects of child-care center attendance on pneumococcal carriage. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 40(9)

Lipsitch M. (2005). Ethics of rationing the flu vaccine. Science (New York, N.Y.), 307(5706)

Lipsitch M, Whitney CG, Zell E, Kaijalainen T, Dagan R, Malley R. (2005). Are anticapsular antibodies the primary mechanism of protection against invasive pneumococcal disease?. PLoS medicine, 2(1)

Trzcinski K, Thompson CM, Lipsitch M. (2004). Single-step capsular transformation and acquisition of penicillin resistance in Streptococcus pneumoniae. Journal of bacteriology, 186(11)

Teklehaimanot HD, Schwartz J, Teklehaimanot A, Lipsitch M. (2004). Weather-based prediction of Plasmodium falciparum malaria in epidemic-prone regions of Ethiopia II. Weather-based prediction systems perform comparably to early detection systems in identifying times for interventions. Malaria journal, (3)

Bergstrom CT, Lo M, Lipsitch M. (2004). Ecological theory suggests that antimicrobial cycling will not reduce antimicrobial resistance in hospitals. Proceedings of the National Academy of Sciences of the United States of America, 101(36)

Mills CE, Robins JM, Lipsitch M. (2004). Transmissibility of 1918 pandemic influenza. Nature, 432(7019)

Lipsitch M, Bergstrom CT. (2004). Invited commentary: real-time tracking of control measures for emerging infections. American journal of epidemiology, 160(6)

Cooper B, Lipsitch M. (2004). The analysis of hospital infection data using hidden Markov models. Biostatistics (Oxford, England), 5(2)

Teklehaimanot HD, Schwatrz J, Teklehaimanot A, Lipsitch M. (2004). Alert threshold algorithms and malaria epidemic detection. Emerging infectious diseases, 10(7)

Lipsitch M, Cohen T, Cooper B, Robins JM, Ma S, James L, Gopalakrishna G, Chew SK, Tan CC, Samore MH, Fisman D, Murray M. (2003). Transmission dynamics and control of severe acute respiratory syndrome. Science (New York, N.Y.), 300(5627)

Lipsitch M, Bergstrom CT, Antia R. (2003). Effect of human leukocyte antigen heterozygosity on infectious disease outcome: the need for allele-specific measures. BMC medical genetics, (4)

McCormick AW, Whitney CG, Farley MM, Lynfield R, Harrison LH, Bennett NM, Schaffner W, Reingold A, Hadler J, Cieslak P, Samore MH, Lipsitch M. (2003). Geographic diversity and temporal trends of antimicrobial resistance in Streptococcus pneumoniae in the United States. Nature medicine, 9(4)

Lipsitch M, Murray MB. (2003). Multiple equilibria: tuberculosis transmission require unrealistic assumptions. Theoretical population biology, 63(2)

Trzcinski K, Thompson CM, Lipsitch M. (2003). Construction of otherwise isogenic serotype 6B, 7F, 14, and 19F capsular variants of Streptococcus pneumoniae strain TIGR4. Applied and environmental microbiology, 69(12)

Singer RS, Finch R, Wegener HC, Bywater R, Walters J, Lipsitch M. (2003). Antibiotic resistance--the interplay between antibiotic use in animals and human beings. The Lancet. Infectious diseases, 3(1)

Lipsitch M, Singer RS, Levin BR. (2002). Antibiotics in agriculture: when is it time to close the barn door?. Proceedings of the National Academy of Sciences of the United States of America, 99(9)

Lipsitch M, Davis G, Corey L. (2002). Potential benefits of a serodiagnostic test for herpes simplex virus type 1 (HSV-1) to prevent neonatal HSV-1 infection. Sexually transmitted diseases, 29(7)

Lipsitch M, Sousa AO. (2002). Historical intensity of natural selection for resistance to tuberculosis. Genetics, 161(4)

Lipsitch M, Samore MH. (2002). Antimicrobial use and antimicrobial resistance: a population perspective. Emerging infectious diseases, 8(4)

Lipsitch M. (1997). TRANSMISSION RATES AND HIV VIRULENCE: COMMENTS TO MASSAD. Evolution; international journal of organic evolution, 51(1)

Lipsitch M, Siller S, Nowak MA. (1996). THE EVOLUTION OF VIRULENCE IN PATHOGENS WITH VERTICAL AND HORIZONTAL TRANSMISSION. Evolution; international journal of organic evolution, 50(5)

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