Marc Lipsitch

Education and Career

Lipsitch received his Bachelor of Arts degree in Philosophy from Yale University in 1991. He earned his Dphil in Zoology from Oxford University, graduating in 1995.

From 1995 to 1999, Mark completed a postdoctoral fellowship on bacterial population biology at Emory University. During this time, from 1997 to 1999, Lipsitch worked as a visiting scientist at the Centers for Disease Control and Prevention, studying Streptococcus pneumoniae serotype interactions.

Since 1999, Dr. Lipsitch has worked as a professor with a primary appointment in the Department of Epidemiology, and a joint appointment in the Department of Immunology and Infectious Diseases at Harvard University T. H. Chan School of Public Health. In 2021, Mark began working as a director for science in the Center for Forecasting and Outbreak Analytics at the Centers for Disease Control and Prevention.

Awards and Recognition

• 2020 — Elected Fellow, National Academy of Medicine
• 2015 — Elected Fellow, American Academy of Microbiology
• 2011 — Kenneth Rothman Epidemiology Prize
• 1995 — Rhodes Scholarship

Research

Dr. Lipsitch’s research focuses on understanding the triggers and mechanisms of disease immunity, the evolution of infectious diseases, and their effect on humans.

Streptococcus pneumoniae: population biology and immune responses

Lipsitch’s studies of Streptococcus pneumoniae combine population-biological and practical questions with quantitative and experimental approaches. The research focuses on Streptococcus pneumoniae, which causes pneumonia, meningitis, septicemia, and otitis media.

For over a decade, Dr. Lipstitch has worked to find out how various pathogen serotypes coexist regardless of significant fitness differences between serotypes by modeling the effect of existing conjugate vaccines and other proposed vaccines.

Pneumococcal population genomics and protein diversity

Another of Dr. Lipsitch’s studies investigates the genomic diversity of pneumococci protein antigens. A question of particular interest includes the role of immune selection in diversifying antigens. Findings show that signals of diversifying selection are apparent in proteins targeted by antibodies, specifically in epitope regions, reflecting the ability of these cells to prevent immune escape.

Antimicrobial resistance in S. pneumoniae

Dr. Lipsitch’s research on antimicrobial resistance focused on measuring the cost of resistance and documenting the cotransfer of capsular and resistance loci in the lab. With colleagues, he assessed trends in resistance and partitioned these into the effects of changing serotype distribution and resistance within a serotype before and after the introduction of conjugate vaccines.

Applied pneumococcal epidemiology

In addition to projects in population biology, Mark Lipsitch has a continuing interest in the applied epidemiology of pneumococcal carriage and disease. Collaborating with other researchers, he provided a unique view of the pneumococcal carriage epidemiology by introducing two vaccines: PCV7 and PCV13.

These studies have focused on the dynamics of serotypes and drug resistance, clonal dynamics, and their invasiveness. They also work on estimating serotype differences in disease severity, documenting serotype replacement in invasive pneumococcal disease globally, and investigating how carriage data can predict invasive disease trends.

Pandemic preparedness and response

Dr. Lispsitch, along with collaborators, made one of the earliest estimates of the spreading of the SARS virus. Other works focused on predicting the potential risks for drug resistance following massive antiviral use in a pandemic. Another focus of the research was on defining the optimal targeting of scarce pandemic control measures by taking advantage of the data available early in a pandemic or during the epidemic’s declining phase.

Response to the 2009 influenza A/H1N1 pandemic

Along with his collaborators, Dr. Lipsitch was involved in data analysis and advising public health authorities during the 2009 A/H1N1 pandemic. They published articles on decision-making and maintaining surveillance under uncertainty during the pandemic.

Antimicrobial resistance

Dr. Mark Lipsitch has written about various topics regarding drug resistance. His research aims to explain the effects of antimicrobial use on the pathogen population and resistance to hospital-acquired infections. The findings show the ineffectiveness of cycling antibiotics to control resistance. Other research interests include the coexistence of drug-susceptible and drug-resistant organisms, antimicrobial resistance data analysis, and the impact of veterinary antimicrobial use in promoting resistance in human medicine.

Seasonal influenza: mechanisms, forecasting, the burden of disease estimation

Lipsitch’s collaboration with other researchers has developed into systematic efforts at influenza forecasting. They have worked on predicting subtype abundance based on incorporating inter-subtype competitive inhibition. The research applies an improved regression framework to estimate the seasonal influenza mortality burden.

HIV transmission modeling and behavioral aspects of STI transmission

Other Lipsitch research focuses on studying the potential transmission effects of HIV prevention interventions. His work also models how the number and makeup of sexual partnerships change following behavioral interventions.

Vaccine action mechanisms

With other researchers, Lipsitch has been exploring the consequences of modeling vaccines. Together, they examine this question experimentally using two vaccines against the diseases of salmon. Lipsitch’s research interest also lies in the statistical problems of incorporating vaccines into transmission dynamics models and estimating vaccine effects in trials.

Publications

• Pannu J, Palmer MJ, Cicero A, Relman DA, Lipsitch M, Inglesby T. Strengthen oversight of risky research on pathogens. Science. 2022 12 16; 378(6625):1170-1172. PMID: 36480598.
• Kahn R, Eyal N, Sow SO, Lipsitch M. Mass drug administration of azithromycin: an analysis. Clin Microbiol Infect. 2022 Oct 27. PMID: 36309328.
• Goldstein E, Fireman BH, Klein NP, Lipsitch M, Ray GT. Prescribing for different antibiotic classes across age groups in the Kaiser Permanente Northern California population in association with influenza incidence, 2010-2018. Epidemiol Infect. 2022 10 26; 150:e180. PMID: 36285506.
• Kogan NE, Gantt S, Swerdlow D, Viboud C, Semakula M, Lipsitch M, Santillana M. Leveraging Serosurveillance and Postmortem Surveillance to Quantify the Impact of COVID-19 in Africa. Clin Infect Dis. 2022 Oct 05. PMID: 36196586; PMCID: PMC9619616.
• Boyer CB, Rumpler E, Kissler SM, Lipsitch M. Infectious disease dynamics and restrictions on social gathering size. Epidemics. 2022 09; 40:100620. PMID: 36058184; PMCID: PMC9384337.
• Joshi K, Rumpler E, Kennedy-Shaffer L, Bosan R, Lipsitch M. Comparative performance of between-population vaccine allocation strategies with applications for emerging pandemics. medRxiv. 2022 Jul 13. PMID: 34212161; PMCID: PMC8246345.
• Boyer CB, Rumpler E, Kissler SM, Lipsitch M. Infectious disease dynamics and restrictions on social gathering size. medRxiv. 2022 Jul 12. PMID: 35860220; PMCID: PMC9298137.
• Cohen-Stavi CJ, Magen O, Barda N, Yaron S, Peretz A, Netzer D, Giaquinto C, Judd A, Leibovici L, Hernán MA, Lipsitch M, Reis BY, Balicer RD, Dagan N. BNT162b2 Vaccine Effectiveness against Omicron in Children 5 to 11 Years of Age. N Engl J Med. 2022 07 21; 387(3):227-236. PMID: 35767475; PMCID: PMC9258754.
• Malden DE, Hong V, Lewin BJ, Ackerson BK, Lipsitch M, Lewnard JA, Tartof SY. Hospitalization and Emergency Department Encounters for COVID-19 After Paxlovid Treatment – California, December 2021-May 2022. MMWR Morb Mortal Wkly Rep. 2022 Jun 24; 71(25):830-833. PMID: 35737591.
• Lewnard JA, Hong VX, Patel MM, Kahn R, Lipsitch M, Tartof SY. Clinical outcomes associated with SARS-CoV-2 Omicron (B.1.1.529) variant and BA.1/BA.1.1 or BA.2 subvariant infection in Southern California. Nat Med. 2022 09; 28(9):1933-1943. PMID: 35675841.
• Rubin EJ, Baden LR, Lipsitch M, Morrissey S. Audio Interview: Forecasting the Future of Covid. N Engl J Med. 2022 05 12; 386(19):e58. PMID: 35544392.
• Figueiredo JC, Hirsch FR, Kushi LH, Nembhard WN, Crawford JM, Mantis N, Finster L, Merin NM, Merchant A, Reckamp KL, Melmed GY, Braun J, McGovern D, Parekh S, Corley DA, Zohoori N, Amick BC, Du R, Gregersen PK, Diamond B, Taioli E, Sariol C, Espino A, Weiskopf D, Gifoni A, Brien J, Hanege W, Lipsitch M, Zidar DA, Scheck McAlearney A, Wajnberg A, LaBaer J, Yvonne Lewis E, Binder RA, Moormann AM, Forconi C, Forrester S, Batista J, Schieffelin J, Kim D, Biancon G, VanOudenhove J, Halene S, Fan R, Barouch DH, Alter G, Pinninti S, Boppana SB, Pati SK, Latting M, Karaba AH, Roback J, Sekaly R, Neish A, Brincks AM, Granger DA, Karger AB, Thyagarajan B, Thomas SN, Klein SL, Cox AL, Lucas T, Furr-Holden D, Key K, Jones N, Wrammerr J, Suthar M, Yu Wong S, Bowman NM, Simon V, Richardson LD, McBride R, Krammer F, Rana M, Kennedy J, Boehme K, Forrest C, Granger SW, Heaney CD, Knight Lapinski M, Wallet S, Baric RS, Schifanella L, Lopez M, Fernández S, Kenah E, Panchal AR, Britt WJ, Sanz I, Dhodapkar M, Ahmed R, Bartelt LA, Markmann AJ, Lin JT, Hagan RS, Wolfgang MC, Skarbinski J. Mission, Organization, and Future Direction of the Serological Sciences Network for COVID-19 (SeroNet) Epidemiologic Cohort Studies. Open Forum Infect Dis. 2022 Jun; 9(6):ofac171. PMID: 35765315; PMCID: PMC9129196.
• Lipsitch M. Wrong question and the wrong standard of proof. J Med Ethics. 2022 06; 48(6):378-379. PMID: 35444009.
• Magen O, Waxman JG, Makov-Assif M, Vered R, Dicker D, Hernán MA, Lipsitch M, Reis BY, Balicer RD, Dagan N. Fourth Dose of BNT162b2 mRNA Covid-19 Vaccine in a Nationwide Setting. N Engl J Med. 2022 04 28; 386(17):1603-1614. PMID: 35417631; PMCID: PMC9020581.
• De Salazar PM, Lu F, Hay JA, Gómez-Barroso D, Fernández-Navarro P, Martínez EV, Astray-Mochales J, Amillategui R, García-Fulgueiras A, Chirlaque MD, Sánchez-Migallón A, Larrauri A, Sierra MJ, Lipsitch M, Simón F, Santillana M, Hernán MA. Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data. PLoS Comput Biol. 2022 03; 18(3):e1009964. PMID: 35358171; PMCID: PMC9004750.
• Kahn R, Schrag SJ, Verani JR, Lipsitch M. Identifying and Alleviating Bias Due to Differential Depletion of Susceptible People in Postmarketing Evaluations of COVID-19 Vaccines. Am J Epidemiol. 2022 03 24; 191(5):800-811. PMID: 35081612; PMCID: PMC8807238.
• Sun DS, Kissler SM, Kanjilal S, Olesen SW, Lipsitch M, Grad YH. Analysis of multiple bacterial species and antibiotic classes reveals large variation in the association between seasonal antibiotic use and resistance. PLoS Biol. 2022 03; 20(3):e3001579. PMID: 35263322; PMCID: PMC8936496.
• Magosi LE, Zhang Y, Golubchik T, DeGruttola V, Tchetgen Tchetgen E, Novitsky V, Moore J, Bachanas P, Segolodi T, Lebelonyane R, Pretorius Holme M, Moyo S, Makhema J, Lockman S, Fraser C, Essex MM, Lipsitch M. Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/Ya Tsie trial. Elife. 2022 03 01; 11. PMID: 35229714; PMCID: PMC8912920.
• Goldstein E, Fireman BH, Klein NP, Lipsitch M, Ray GT. Antibiotic prescribing across age groups in the Kaiser Permanente Northern California population in association with different diagnoses, and with influenza incidence, 2010-2018. Epidemiol Infect. 2022 02 24; 150:e85. PMID: 35506177; PMCID: PMC9074113.
• Cohen K, Ren S, Heath K, Dasmariñas MC, Jubilo KG, Guo Y, Lipsitch M, Daugherty SE. Risk of persistent and new clinical sequelae among adults aged 65 years and older during the post-acute phase of SARS-CoV-2 infection: retrospective cohort study. BMJ. 2022 02 09; 376:e068414. PMID: 35140117; PMCID: PMC8828141.
• Hayek S, Shaham G, Ben-Shlomo Y, Kepten E, Dagan N, Nevo D, Lipsitch M, Reis BY, Balicer RD, Barda N. Indirect protection of children from SARS-CoV-2 infection through parental vaccination. Science. 2022 03 11; 375(6585):1155-1159. PMID: 35084938.
• de Kraker MEA, Lipsitch M. Burden of Antimicrobial Resistance: Compared to What? Epidemiol Rev. 2022 01 14; 43(1):53-64. PMID: 33710259; PMCID: PMC8763122.
• Tedijanto C, Nevers M, Samore MH, Lipsitch M. Antibiotic Use and Presumptive Pathogens in the Veterans Affairs Healthcare System. Clin Infect Dis. 2022 01 07; 74(1):105-112. PMID: 33621326; PMCID: PMC8752245.
• Eyal N, Lipsitch M. How to Test Severe Acute Respiratory Syndrome Coronavirus 2 Vaccines Ethically Even After One Is Available. Clin Infect Dis. 2021 12 16; 73(12):2332-2334. PMID: 33639622; PMCID: PMC7989578.
• Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Correction: Practical considerations for measuring the effective reproductive number, Rt. PLoS Comput Biol. 2021 Dec; 17(12):e1009679. PMID: 34879070.
• Lipsitch M, Krammer F, Regev-Yochay G, Lustig Y, Balicer RD. SARS-CoV-2 breakthrough infections in vaccinated individuals: measurement, causes and impact. Nat Rev Immunol. 2022 01; 22(1):57-65. PMID: 34876702; PMCID: PMC8649989.
• Singer SR, Angulo FJ, Swerdlow DL, McLaughlin JM, Hazan I, Ginish N, Anis E, Mendelson E, Mor O, Zuckerman NS, Erster O, Southern J, Pan K, Mircus G, Lipsitch M, Haas EJ, Jodar L, Levy Y, Alroy-Preis S. Effectiveness of BNT162b2 mRNA COVID-19 vaccine against SARS-CoV-2 variant Beta (B.1.351) among persons identified through contact tracing in Israel: A prospective cohort study. EClinicalMedicine. 2021 Dec; 42:101190. PMID: 34870134; PMCID: PMC8628463.
• Bushman M, Kahn R, Taylor BP, Lipsitch M, Hanage WP. Population impact of SARS-CoV-2 variants with enhanced transmissibility and/or partial immune escape. Cell. 2021 12 22; 184(26):6229-6242.e18. PMID: 34910927; PMCID: PMC8603072.
• Kennedy-Shaffer L, Kahn R, Lipsitch M. Estimating Vaccine Efficacy Against Transmission via Effect on Viral Load. Epidemiology. 2021 11 01; 32(6):820-828. PMID: 34469363.
• Barda N, Dagan N, Cohen C, Hernán MA, Lipsitch M, Kohane IS, Reis BY, Balicer RD. Effectiveness of a third dose of the BNT162b2 mRNA COVID-19 vaccine for preventing severe outcomes in Israel: an observational study. Lancet. 2021 12 04; 398(10316):2093-2100. PMID: 34756184; PMCID: PMC8555967.
• Reis BY, Barda N, Leshchinsky M, Kepten E, Hernán MA, Lipsitch M, Dagan N, Balicer RD. Effectiveness of BNT162b2 Vaccine against Delta Variant in Adolescents. N Engl J Med. 2021 11 25; 385(22):2101-2103. PMID: 34670036.
• Haas EJ, McLaughlin JM, Khan F, Angulo FJ, Anis E, Lipsitch M, Singer SR, Mircus G, Brooks N, Smaja M, Pan K, Southern J, Swerdlow DL, Jodar L, Levy Y, Alroy-Preis S. Infections, hospitalisations, and deaths averted via a nationwide vaccination campaign using the Pfizer-BioNTech BNT162b2 mRNA COVID-19 vaccine in Israel: a retrospective surveillance study. Lancet Infect Dis. 2022 03; 22(3):357-366. PMID: 34562375; PMCID: PMC8457761.
• Dagan N, Barda N, Biron-Shental T, Makov-Assif M, Key C, Kohane IS, Hernán MA, Lipsitch M, Hernandez-Diaz S, Reis BY, Balicer RD. Effectiveness of the BNT162b2 mRNA COVID-19 vaccine in pregnancy. Nat Med. 2021 10; 27(10):1693-1695. PMID: 34493859.
• Kahn R, Wang R, Leavitt SV, Hanage WP, Lipsitch M. Leveraging Pathogen Sequence and Contact Tracing Data to Enhance Vaccine Trials in Emerging Epidemics. Epidemiology. 2021 09 01; 32(5):698-704. PMID: 34039898; PMCID: PMC8338748.
• Barda N, Dagan N, Ben-Shlomo Y, Kepten E, Waxman J, Ohana R, Hernán MA, Lipsitch M, Kohane I, Netzer D, Reis BY, Balicer RD. Safety of the BNT162b2 mRNA Covid-19 Vaccine in a Nationwide Setting. N Engl J Med. 2021 09 16; 385(12):1078-1090. PMID: 34432976; PMCID: PMC8427535.
• Nikolay B, Ribeiro Dos Santos G, Lipsitch M, Rahman M, Luby SP, Salje H, Gurley ES, Cauchemez S. Assessing the feasibility of Nipah vaccine efficacy trials based on previous outbreaks in Bangladesh. Vaccine. 2021 09 15; 39(39):5600-5606. PMID: 34426025.
• Vekemans J, Hasso-Agopsowicz M, Kang G, Hausdorff WP, Fiore A, Tayler E, Klemm EJ, Laxminarayan R, Srikantiah P, Friede M, Lipsitch M. Leveraging Vaccines to Reduce Antibiotic Use and Prevent Antimicrobial Resistance: A World Health Organization Action Framework. Clin Infect Dis. 2021 08 16; 73(4):e1011-e1017. PMID: 33493317.
• Bergwerk M, Gonen T, Lustig Y, Amit S, Lipsitch M, Cohen C, Mandelboim M, Levin EG, Rubin C, Indenbaum V, Tal I, Zavitan M, Zuckerman N, Bar-Chaim A, Kreiss Y, Regev-Yochay G. Covid-19 Breakthrough Infections in Vaccinated Health Care Workers. N Engl J Med. 2021 10 14; 385(16):1474-1484. PMID: 34320281; PMCID: PMC8362591.
• Regev-Yochay G, Amit S, Bergwerk M, Lipsitch M, Leshem E, Kahn R, Lustig Y, Cohen C, Doolman R, Ziv A, Novikov I, Rubin C, Gimpelevich I, Huppert A, Rahav G, Afek A, Kreiss Y. Decreased infectivity following BNT162b2 vaccination: A prospective cohort study in Israel. Lancet Reg Health Eur. 2021 Aug; 7:100150. PMID: 34250518; PMCID: PMC8261633.
• Lu FS, Nguyen AT, Link NB, Molina M, Davis JT, Chinazzi M, Xiong X, Vespignani A, Lipsitch M, Santillana M. Estimating the cumulative incidence of COVID-19 in the United States using influenza surveillance, virologic testing, and mortality data: Four complementary approaches. PLoS Comput Biol. 2021 06; 17(6):e1008994. PMID: 34138845; PMCID: PMC8241061.
• Lipsitch M, Kahn R. Interpreting vaccine efficacy trial results for infection and transmission. Vaccine. 2021 07 05; 39(30):4082-4088. PMID: 34130883; PMCID: PMC8197448.
• Hay JA, Kennedy-Shaffer L, Kanjilal S, Lennon NJ, Gabriel SB, Lipsitch M, Mina MJ. Estimating epidemiologic dynamics from cross-sectional viral load distributions. Science. 2021 07 16; 373(6552). PMID: 34083451; PMCID: PMC8527857.
• Patel MK, Bergeri I, Bresee JS, Cowling BJ, Crowcroft NS, Fahmy K, Hirve S, Kang G, Katz MA, Lanata CF, L’Azou Jackson M, Joshi S, Lipsitch M, Mwenda JM, Nogareda F, Orenstein WA, Ortiz JR, Pebody R, Schrag SJ, Smith PG, Srikantiah P, Subissi L, Valenciano M, Vaughn DW, Verani JR, Wilder-Smith A, Feikin DR. Evaluation of post-introduction COVID-19 vaccine effectiveness: Summary of interim guidance of the World Health Organization. Vaccine. 2021 07 05; 39(30):4013-4024. PMID: 34119350; PMCID: PMC8166525.
• Lipsitch M, Kahn R. Interpreting vaccine efficacy trial results for infection and transmission. medRxiv. 2021 May 27. PMID: 33655276; PMCID: PMC7924301.
• Daugherty SE, Guo Y, Heath K, Dasmariñas MC, Jubilo KG, Samranvedhya J, Lipsitch M, Cohen K. Risk of clinical sequelae after the acute phase of SARS-CoV-2 infection: retrospective cohort study. BMJ. 2021 05 19; 373:n1098. PMID: 34011492; PMCID: PMC8132065.
• Ma KC, Menkir TF, Kissler S, Grad YH, Lipsitch M. Modeling the impact of racial and ethnic disparities on COVID-19 epidemic dynamics. Elife. 2021 05 18; 10. PMID: 34003112.
• Bloom JD, Chan YA, Baric RS, Bjorkman PJ, Cobey S, Deverman BE, Fisman DN, Gupta R, Iwasaki A, Lipsitch M, Medzhitov R, Neher RA, Nielsen R, Patterson N, Stearns T, van Nimwegen E, Worobey M, Relman DA. Investigate the origins of COVID-19. Science. 2021 05 14; 372(6543):694. PMID: 33986172; PMCID: PMC9520851.
• Cobey S, Larremore DB, Grad YH, Lipsitch M. Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination. Nat Rev Immunol. 2021 05; 21(5):330-335. PMID: 33795856; PMCID: PMC8014893.
• Accorsi EK, Qiu X, Rumpler E, Kennedy-Shaffer L, Kahn R, Joshi K, Goldstein E, Stensrud MJ, Niehus R, Cevik M, Lipsitch M. How to detect and reduce potential sources of biases in studies of SARS-CoV-2 and COVID-19. Eur J Epidemiol. 2021 Feb; 36(2):179-196. PMID: 33634345.
• Dagan N, Barda N, Kepten E, Miron O, Perchik S, Katz MA, Hernán MA, Lipsitch M, Reis B, Balicer RD. BNT162b2 mRNA Covid-19 Vaccine in a Nationwide Mass Vaccination Setting. N Engl J Med. 2021 04 15; 384(15):1412-1423. PMID: 33626250; PMCID: PMC7944975.
• Hay JA, Kennedy-Shaffer L, Kanjilal S, Lennon NJ, Gabriel SB, Lipsitch M, Mina MJ. Estimating epidemiologic dynamics from cross-sectional viral load distributions. medRxiv. 2021 Feb 13. PMID: 33594381.
• Goldstein E, Lipsitch M, Cevik M. On the Effect of Age on the Transmission of SARS-CoV-2 in Households, Schools, and the Community. J Infect Dis. 2021 02 13; 223(3):362-369. PMID: 33119738; PMCID: PMC7665686.
• Kahn R, Kennedy-Shaffer L, Grad YH, Robins JM, Lipsitch M. Potential Biases Arising From Epidemic Dynamics in Observational Seroprotection Studies. Am J Epidemiol. 2021 02 01; 190(2):328-335. PMID: 32870977; PMCID: PMC7499481.
• De Salazar PM, Lu F, Hay JA, Gómez-Barroso D, Fernández-Navarro P, Martínez E, Astray-Mochales J, Amillategui R, García-Fulgueiras A, Chirlaque MD, Sánchez-Migallón A, Larrauri A, Sierra MJ, Lipsitch M, Simón F, Santillana M, Hernán MA. Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data. medRxiv. 2021 Jan 26. PMID: 33532788; PMCID: PMC7852239.
• Bubar KM, Reinholt K, Kissler SM, Lipsitch M, Cobey S, Grad YH, Larremore DB. Model-informed COVID-19 vaccine prioritization strategies by age and serostatus. Science. 2021 02 26; 371(6532):916-921. PMID: 33479118.
• Rid A, Lipsitch M, Miller FG. The Ethics of Continuing Placebo in SARS-CoV-2 Vaccine Trials. JAMA. 2021 01 19; 325(3):219-220. PMID: 33315080.
• Greene SK, McGough SF, Culp GM, Graf LE, Lipsitch M, Menzies NA, Kahn R. Nowcasting for Real-Time COVID-19 Tracking in New York City: An Evaluation Using Reportable Disease Data From Early in the Pandemic. JMIR Public Health Surveill. 2021 01 15; 7(1):e25538. PMID: 33406053; PMCID: PMC7812916.
• Menkir TF, Chin T, Hay JA, Surface ED, De Salazar PM, Buckee CO, Watts A, Khan K, Sherbo R, Yan AWC, Mina MJ, Lipsitch M, Niehus R. Estimating internationally imported cases during the early COVID-19 pandemic. Nat Commun. 2021 01 12; 12(1):311. PMID: 33436574.
• Bubar KM, Reinholt K, Kissler SM, Lipsitch M, Cobey S, Grad YH, Larremore DB. Model-informed COVID-19 vaccine prioritization strategies by age and serostatus. medRxiv. 2021 Jan 08. PMID: 33330882; PMCID: PMC7743091.
• Eyal N, Lipsitch M. Testing SARS-CoV-2 vaccine efficacy through deliberate natural viral exposure. Clin Microbiol Infect. 2021 Mar; 27(3):372-377. PMID: 33421580; PMCID: PMC7787506.
• Harrow GL, Lees JA, Hanage WP, Lipsitch M, Corander J, Colijn C, Croucher NJ. Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. ISME J. 2021 05; 15(5):1523-1538. PMID: 33408365; PMCID: PMC8115253.
• Ma KC, Lipsitch M. Big data and simple models used to track the spread of COVID-19 in cities. Nature. 2021 01; 589(7840):26-28. PMID: 33173216.
• Accorsi EK, Franzosa EA, Hsu T, Joice Cordy R, Maayan-Metzger A, Jaber H, Reiss-Mandel A, Kline M, DuLong C, Lipsitch M, Regev-Yochay G, Huttenhower C. Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome. Genome Biol. 2020 12 11; 21(1):301. PMID: 33308267.
• Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Practical considerations for measuring the effective reproductive number, Rt. PLoS Comput Biol. 2020 12; 16(12):e1008409. PMID: 33301457.
• Messinger CJ, Lipsitch M, Bateman BT, He M, Huybrechts KF, MacDonald S, Mogun H, Mott K, Hernández-Díaz S. Association Between Congenital Cytomegalovirus and the Prevalence at Birth of Microcephaly in the United States. JAMA Pediatr. 2020 12 01; 174(12):1159-1167. PMID: 32926077; PMCID: PMC7490747.
• Doan T, Worden L, Hinterwirth A, Arzika AM, Maliki R, Abdou A, Zhong L, Chen C, Cook C, Lebas E, O’Brien KS, Oldenburg CE, Chow ED, Porco TC, Lipsitch M, Keenan JD, Lietman TM. Macrolide and Nonmacrolide Resistance with Mass Azithromycin Distribution. N Engl J Med. 2020 11 12; 383(20):1941-1950. PMID: 33176084; PMCID: PMC7492079.
• Olesen SW, Lipsitch M, Grad YH. The role of “spillover” in antibiotic resistance. Proc Natl Acad Sci U S A. 2020 11 17; 117(46):29063-29068. PMID: 33139558.
• Kennedy-Shaffer L, Lipsitch M. Statistical Properties of Stepped Wedge Cluster-Randomized Trials in Infectious Disease Outbreaks. Am J Epidemiol. 2020 11 02; 189(11):1324-1332. PMID: 32648891.
• 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. Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae. PLoS Biol. 2020 10; 18(10):e3000878. PMID: 33091022.
• Lipsitch M, Dean NE. Understanding COVID-19 vaccine efficacy. Science. 2020 11 13; 370(6518):763-765. PMID: 33087460.
• De Salazar PM, Gómez-Barroso D, Pampaka D, Gil JM, Peñalver B, Fernández-Escobar C, Lipsitch M, Larrauri A, Goldstein E, Hernán MA. Lockdown measures and relative changes in the age-specific incidence of SARS-CoV-2 in Spain. Epidemiol Infect. 2020 10 21; 148:e268. PMID: 33081851.
• Greene SK, McGough SF, Culp GM, Graf LE, Lipsitch M, Menzies NA, Kahn R. Evaluation of Nowcasting for Real-Time COVID-19 Tracking – New York City, March-May 2020. medRxiv. 2020 Oct 20. PMID: 33106814.
• 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. Scientific consensus on the COVID-19 pandemic: we need to act now. Lancet. 2020 10 31; 396(10260):e71-e72. PMID: 33069277; PMCID: PMC7557300.
• Lipsitch M, Grad YH, Sette A, Crotty S. Cross-reactive memory T cells and herd immunity to SARS-CoV-2. Nat Rev Immunol. 2020 11; 20(11):709-713. PMID: 33024281; PMCID: PMC7537578.
• Eyal N, Lipsitch M, Smith PG. Reply to Hasford and to Spinola et al. J Infect Dis. 2020 10 01; 222(9):1574-1575. PMID: 32845306; PMCID: PMC7529012.
• Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay J, De Salazar PM, Hellewell J, Meakin S, Munday J, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Practical considerations for measuring the effective reproductive number, Rt. medRxiv. 2020 Aug 28. PMID: 32607522; PMCID: PMC7325187.
• Lu FS, Nguyen AT, Link NB, Davis JT, Chinazzi M, Xiong X, Vespignani A, Lipsitch M, Santillana M. Estimating the Cumulative Incidence of COVID-19 in the United States Using Four Complementary Approaches. medRxiv. 2020 Aug 07. PMID: 32587997; PMCID: PMC7310656.
• Levinson M, Cevik M, Lipsitch M. Reopening Primary Schools during the Pandemic. N Engl J Med. 2020 09 03; 383(10):981-985. PMID: 32726550.
• Goldstein E, Lipsitch M, Cevik M. On the effect of age on the transmission of SARS-CoV-2 in households, schools and the community. medRxiv. 2020 Jul 28. PMID: 32743609; PMCID: PMC7386533.
• Eyal N, Lipsitch M. Opinion: It’s ethical to test promising coronavirus vaccines against less-promising ones. Proc Natl Acad Sci U S A. 2020 08 11; 117(32):18898-18901. PMID: 32699147.
• Menkir TF, Chin T, Hay J, Surface ED, De Salazar PM, Buckee CO, Watts A, Khan K, Sherbo R, Yan AWC, Mina M, Lipsitch M, Niehus R. Estimating internationally imported cases during the early COVID-19 pandemic. medRxiv. 2020 Jul 17. PMID: 32511613; PMCID: PMC7276040.
• Eyal N, Lipsitch M, Smith PG. Response to Dawson et al. J Infect Dis. 2020 07 06; 222(3):516-517. PMID: 32495823; PMCID: PMC8494001.
• D GB, D P, Jm G, B P, C FE, M L, A L, E G, Ma H. Lockdown measures and relative changes in the age-specific incidence of SARS-CoV-2 in Spain. medRxiv. 2020 Jul 02. PMID: 32637975.
• Wu JT, Leung K, Bushman M, Kishore N, Niehus R, de Salazar PM, Cowling BJ, Lipsitch M, Leung GM. Addendum: Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China. Nat Med. 2020 07; 26(7):1149-1150. PMID: 32661399.
• Hicks AL, Kissler SM, Mortimer TD, Ma KC, Taiaroa G, Ashcroft M, Williamson DA, Lipsitch M, Grad YH. Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants. Elife. 2020 06 30; 9. PMID: 32602459.
• De Salazar PM, Niehus R, Taylor A, Buckee CO, Lipsitch M. Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions. Emerg Infect Dis. 2020 07; 26(7):1465-1469. PMID: 32207679; PMCID: PMC7323530.
• Lipsitch M. Good science is good science: we need specialists, not sects. Eur J Epidemiol. 2020 Jun; 35(6):519-522. PMID: 32564181.
• Eyal N, Lipsitch M, Smith PG. Response to Cioffi. J Infect Dis. 2020 06 16; 222(1):169-170. PMID: 32348499.
• Flasche S, Lipsitch M, Ojal J, Pinsent A. Estimating the contribution of different age strata to vaccine serotype pneumococcal transmission in the pre vaccine era: a modelling study. BMC Med. 2020 06 10; 18(1):129. PMID: 32517683; PMCID: PMC7285529.
• Lipsitch M, Kahn R, Mina MJ. Antibody testing will enhance the power and accuracy of COVID-19-prevention trials. Nat Med. 2020 06; 26(6):818-819. PMID: 32341581.
• Lehtinen S, Chewapreecha C, Lees J, Hanage WP, Lipsitch M, Croucher NJ, Bentley SD, Turner P, Fraser C, Mostowy RJ. Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae. Sci Adv. 2020 05; 6(21):eaaz6137. PMID: 32671212; PMCID: PMC7314567.
• Peak CM, Kahn R, Grad YH, Childs LM, Li R, Lipsitch M, Buckee CO. Individual quarantine versus active monitoring of contacts for the mitigation of COVID-19: a modelling study. Lancet Infect Dis. 2020 09; 20(9):1025-1033. PMID: 32445710.
• Eyal N, Lipsitch M, Smith PG. Human Challenge Studies to Accelerate Coronavirus Vaccine Licensure. J Infect Dis. 2020 05 11; 221(11):1752-1756. PMID: 32232474; PMCID: PMC7184325.
• Lipsitch M, Perlman S, Waldor MK. Testing COVID-19 therapies to prevent progression of mild disease. Lancet Infect Dis. 2020 12; 20(12):1367. PMID: 32618282.
• Kahn R, Kennedy-Shaffer L, Grad YH, Robins JM, Lipsitch M. Potential biases arising from epidemic dynamics in observational seroprotection studies. medRxiv. 2020 May 06. PMID: 32511485.
• Kennedy-Shaffer L, Lipsitch M. Statistical Properties of Stepped Wedge Cluster-Randomized Trials in Infectious Disease Outbreaks. medRxiv. 2020 May 06. PMID: 32511544.
• Li R, Rivers C, Tan Q, Murray MB, Toner E, Lipsitch M. 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 Netw Open. 2020 05 01; 3(5):e208297. PMID: 32374400.
• MacFadden DR, Coburn B, Brinda K, Corbeil A, Daneman N, Fisman D, Lee RS, Lipsitch M, McGeer A, Melano RG, Mubareka S, Hanage WP. Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli. Antimicrob Agents Chemother. 2020 04 21; 64(5). PMID: 32152083.
• Kissler SM, Tedijanto C, Goldstein E, Grad YH, Lipsitch M. Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period. Science. 2020 05 22; 368(6493):860-868. PMID: 32291278.
• Goldstein E, Lipsitch M. 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. 2020 Apr 11. PMID: 32511603; PMCID: PMC7276030.
• McGough SF, Johansson MA, Lipsitch M, Menzies NA. Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking. PLoS Comput Biol. 2020 04; 16(4):e1007735. PMID: 32251464.
• Thaler DS, Lipsitch M. Coronavirus: sampling now for future analysis. Nature. 2020 04; 580(7805):590. PMID: 32346142.
• Goldstein E, Lipsitch M. 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 Surveill. 2020 04; 25(17). PMID: 32372753; PMCID: PMC7201953.
• Niehus R, De Salazar PM, Taylor AR, Lipsitch M. Using observational data to quantify bias of traveller-derived COVID-19 prevalence estimates in Wuhan, China. Lancet Infect Dis. 2020 07; 20(7):803-808. PMID: 32246905.
• Lipsitch M. Estimating case fatality rates of COVID-19. Lancet Infect Dis. 2020 07; 20(7):775. PMID: 32243813.
• Swerdlow DL, Finelli L, Lipsitch M. Epidemiology of Covid-19. Reply. N Engl J Med. 2020 05 07; 382(19):1869-1870. PMID: 32220201.
• 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. Aggregated mobility data could help fight COVID-19. Science. 2020 04 10; 368(6487):145-146. PMID: 32205458.
• Wu JT, Leung K, Bushman M, Kishore N, Niehus R, de Salazar PM, Cowling BJ, Lipsitch M, Leung GM. Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China. Nat Med. 2020 04; 26(4):506-510. PMID: 32284616; PMCID: PMC7094929.
• Ray GT, Lewis N, Klein NP, Daley MF, Lipsitch M, Fireman B. Depletion-of-susceptibles Bias in Analyses of Intra-season Waning of Influenza Vaccine Effectiveness. Clin Infect Dis. 2020 03 17; 70(7):1484-1486. PMID: 31351439.
• Li R, Rivers C, Tan Q, Murray MB, Toner E, Lipsitch M. The demand for inpatient and ICU beds for COVID-19 in the US: lessons from Chinese cities. medRxiv. 2020 Mar 16. PMID: 32511447; PMCID: PMC7239072.
• Peak CM, Kahn R, Grad YH, Childs LM, Li R, Lipsitch M, Buckee CO. Comparative Impact of Individual Quarantine vs. Active Monitoring of Contacts for the Mitigation of COVID-19: a modelling study. medRxiv. 2020 Mar 08. PMID: 32511440; PMCID: PMC7239061.
• Goldstein E, Lipsitch M. The relation between prescribing of different antibiotics and rates of mortality with sepsis in US adults. BMC Infect Dis. 2020 Feb 22; 20(1):169. PMID: 32087679.
• Lipsitch M, Swerdlow DL, Finelli L. Defining the Epidemiology of Covid-19 – Studies Needed. N Engl J Med. 2020 Mar 26; 382(13):1194-1196. PMID: 32074416.
• Niehus R, De Salazar PM, Taylor AR, Lipsitch M. Quantifying bias of COVID-19 prevalence and severity estimates in Wuhan, China that depend on reported cases in international travelers. medRxiv. 2020 Feb 18. PMID: 32511442; PMCID: PMC7239063.
• De Salazar PM, Niehus R, Taylor A, Buckee C, Lipsitch M. Using predicted imports of 2019-nCoV cases to determine locations that may not be identifying all imported cases. medRxiv. 2020 Feb 11. PMID: 32511458; PMCID: PMC7239086.
• Tedijanto C, Grad YH, Lipsitch M. Potential impact of outpatient stewardship interventions on antibiotic exposures of common bacterial pathogens. Elife. 2020 02 05; 9. PMID: 32022685.
• Inglesby TV, Lipsitch M. Proposed Changes to U.S. Policy on Potential Pandemic Pathogen Oversight and Implementation. mSphere. 2020 01 22; 5(1). PMID: 31969482.
• Chua H, Feng S, Lewnard JA, Sullivan SG, Blyth CC, Lipsitch M, Cowling BJ. The Use of Test-negative Controls to Monitor Vaccine Effectiveness: A Systematic Review of Methodology. Epidemiology. 2020 01; 31(1):43-64. PMID: 31609860.
• Kennedy-Shaffer L, de Gruttola V, Lipsitch M. Novel methods for the analysis of stepped wedge cluster randomized trials. Stat Med. 2020 03 30; 39(7):815-844. PMID: 31876979.
• Ryu S, Cowling BJ, Wu P, Olesen S, Fraser C, Sun DS, Lipsitch M, Grad YH. Case-based surveillance of antimicrobial resistance with full susceptibility profiles. JAC Antimicrob Resist. 2019 Dec; 1(3):dlz070. PMID: 32280945.
• Knight GM, Davies NG, Colijn C, Coll F, Donker T, Gifford DR, Glover RE, Jit M, Klemm E, Lehtinen S, Lindsay JA, Lipsitch M, Llewelyn MJ, Mateus ALP, Robotham JV, Sharland M, Stekel D, Yakob L, Atkins KE. Mathematical modelling for antibiotic resistance control policy: do we know enough? BMC Infect Dis. 2019 Nov 29; 19(1):1011. PMID: 31783803; PMCID: PMC6884858.
• Lipsitch M, Goldstein E, Ray GT, Fireman B. Depletion-of-susceptibles bias in influenza vaccine waning studies: how to ensure robust results. Epidemiol Infect. 2019 11 27; 147:e306. PMID: 31774051.
• Hicks AL, Kissler SM, Lipsitch M, Grad YH. Surveillance to maintain the sensitivity of genotype-based antibiotic resistance diagnostics. PLoS Biol. 2019 11; 17(11):e3000547. PMID: 31714937.
• Lipsitch M, Shaman J. Comment on: ‘Antibiotic footprint’ as a communication tool to aid reduction of antibiotic consumption. J Antimicrob Chemother. 2019 11 01; 74(11):3404-3406. PMID: 31314102.
• Goldstein E, Finelli L, O’Halloran A, Liu P, Karaca Z, Steiner CA, Viboud C, Lipsitch M. Hospitalizations Associated with Respiratory Syncytial Virus and Influenza in Children, Including Children Diagnosed with Asthma. Epidemiology. 2019 11; 30(6):918-926. PMID: 31469696.
• Abuelezam NN, Reshef YA, Novak D, Grad YH, Seage Iii GR, Mayer K, Lipsitch M. Interaction Patterns of Men Who Have Sex With Men on a Geosocial Networking Mobile App in Seven United States Metropolitan Areas: Observational Study. J Med Internet Res. 2019 09 12; 21(9):e13766. PMID: 31516124.
• Lee RTC, Chang HH, Russell CA, Lipsitch M, Maurer-Stroh S. Influenza A Hemagglutinin Passage Bias Sites and Host Specificity Mutations. Cells. 2019 08 22; 8(9). PMID: 31443542; PMCID: PMC6770435.
• Goldstein E, Olesen SW, Karaca Z, Steiner CA, Viboud C, Lipsitch M. 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. 2019 Aug 19; 19(1):1138. PMID: 31426780; PMCID: PMC6701127.
• Eyal N, Kimmelman J, Holtzman LG, Lipsitch M. Regulating impact on bystanders in clinical trials: An unsettled frontier. Clin Trials. 2019 10; 16(5):450-454. PMID: 31368813.
• MacFadden DR, Fisman DN, Hanage WP, Lipsitch M. The Relative Impact of Community and Hospital Antibiotic Use on the Selection of Extended-spectrum Beta-lactamase-producing Escherichia coli. Clin Infect Dis. 2019 06 18; 69(1):182-188. PMID: 30462185; PMCID: PMC6771767.
• McAdams D, Wollein Waldetoft K, Tedijanto C, Lipsitch M, Brown SP. Resistance diagnostics as a public health tool to combat antibiotic resistance: A model-based evaluation. PLoS Biol. 2019 05; 17(5):e3000250. PMID: 31095567; PMCID: PMC6522007.
• Lehtinen S, Blanquart F, Lipsitch M, Fraser C. On the evolutionary ecology of multidrug resistance in bacteria. PLoS Pathog. 2019 05; 15(5):e1007763. PMID: 31083687; PMCID: PMC6532944.
• Olesen SW, Lipsitch M, Grad YH. Response to comment on ‘The distribution of antibiotic use and its association with antibiotic resistance’. Elife. 2019 05 03; 8. PMID: 31050649; PMCID: PMC6499536.
• Lipsitch M. Challenges of Vaccine Effectiveness and Waning Studies. Clin Infect Dis. 2019 05 02; 68(10):1631-1633. PMID: 30204853; PMCID: PMC6495011.
• Lewnard JA, Tedijanto C, Cowling BJ, Lipsitch M. THE AUTHORS REPLY. Am J Epidemiol. 2019 04 01; 188(4):807-808. PMID: 30689694.
• Hitchings MDT, Coldiron ME, Grais RF, Lipsitch M. Analysis of a meningococcal meningitis outbreak in Niger – potential effectiveness of reactive prophylaxis. PLoS Negl Trop Dis. 2019 03; 13(3):e0007077. PMID: 30856166.
• Goldstein E, MacFadden DR, Karaca Z, Steiner CA, Viboud C, Lipsitch M. Antimicrobial resistance prevalence, rates of hospitalization with septicemia and rates of mortality with sepsis in adults in different US states. Int J Antimicrob Agents. 2019 Jul; 54(1):23-34. PMID: 30851403; PMCID: PMC6571064.
• Yang A, Cai F, Lipsitch M. Herd immunity alters the conditions for performing dose schedule comparisons: an individual-based model of pneumococcal carriage. BMC Infect Dis. 2019 Mar 05; 19(1):227. PMID: 30836941; PMCID: PMC6402138.
• Langwig KE, Gomes MGM, Clark MD, Kwitny M, Yamada S, Wargo AR, Lipsitch M. Limited available evidence supports theoretical predictions of reduced vaccine efficacy at higher exposure dose. Sci Rep. 2019 03 01; 9(1):3203. PMID: 30824732; PMCID: PMC6397254.
• Mitchell PK, Azarian T, Croucher NJ, Callendrello A, Thompson CM, Pelton SI, Lipsitch M, Hanage WP. Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13. Microb Genom. 2019 02; 5(2). PMID: 30777813.
• Kahn R, Hitchings M, Wang R, Bellan SE, Lipsitch M. Analyzing Vaccine Trials in Epidemics With Mild and Asymptomatic Infection. Am J Epidemiol. 2019 02 01; 188(2):467-474. PMID: 30329134; PMCID: PMC6357804.
• Gallagher T, Lipsitch M. Postexposure Effects of Vaccines on Infectious Diseases. Epidemiol Rev. 2019 01 31; 41(1):13-27. PMID: 31680134.
• Olesen SW, Torrone EA, Papp JR, Kirkcaldy RD, Lipsitch M, Grad YH. Azithromycin Susceptibility Among Neisseria gonorrhoeae Isolates and Seasonal Macrolide Use. J Infect Dis. 2019 01 29; 219(4):619-623. PMID: 30239814; PMCID: PMC6350947.
• Lipsitch M, Santillana M. Enhancing Situational Awareness to Prevent Infectious Disease Outbreaks from Becoming Catastrophic. Curr Top Microbiol Immunol. 2019; 424:59-74. PMID: 31292726.
• Mahmud AS, Lipsitch M, Goldstein E. On the role of different age groups during pertussis epidemics in California, 2010 and 2014. Epidemiol Infect. 2019 01; 147:e184. PMID: 31063110; PMCID: PMC6518560.
• Abuelezam NN, McCormick AW, Surface ED, Fussell T, Freedberg KA, Lipsitch M, Seage GR. Modelling the epidemiologic impact of achieving UNAIDS fast-track 90-90-90 and 95-95-95 targets in South Africa. Epidemiol Infect. 2019 01; 147:e122. PMID: 30869008; PMCID: PMC6452860.
• Georgieva M, Buckee CO, Lipsitch M. Models of immune selection for multi-locus antigenic diversity of pathogens. Nat Rev Immunol. 2019 01; 19(1):55-62. PMID: 30479379; PMCID: PMC6352731.
• Campo JJ, Le TQ, Pablo JV, Hung C, Teng AA, Tettelin H, Tate A, Hanage WP, Alderson MR, Liang X, Malley R, Lipsitch M, Croucher NJ. Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination. Elife. 2018 12 28; 7. PMID: 30592459; PMCID: PMC6344088.
• Relman DA, Lipsitch M. Microbiome as a tool and a target in the effort to address antimicrobial resistance. Proc Natl Acad Sci U S A. 2018 12 18; 115(51):12902-12910. PMID: 30559176; PMCID: PMC6304941.
• Olesen SW, Barnett ML, MacFadden DR, Brownstein JS, Hernández-Díaz S, Lipsitch M, Grad YH. The distribution of antibiotic use and its association with antibiotic resistance. Elife. 2018 12 18; 7. PMID: 30560781; PMCID: PMC6307856.
• Sevilla JP, Bloom DE, Cadarette D, Jit M, Lipsitch M. Toward economic evaluation of the value of vaccines and other health technologies in addressing AMR. Proc Natl Acad Sci U S A. 2018 12 18; 115(51):12911-12919. PMID: 30559203; PMCID: PMC6305008.
• Tedijanto C, Olesen SW, Grad YH, Lipsitch M. Estimating the proportion of bystander selection for antibiotic resistance among potentially pathogenic bacterial flora. Proc Natl Acad Sci U S A. 2018 12 18; 115(51):E11988-E11995. PMID: 30559213; PMCID: PMC6304942.
• Lewnard JA, Tedijanto C, Cowling BJ, Lipsitch M. Measurement of Vaccine Direct Effects Under the Test-Negative Design. Am J Epidemiol. 2018 12 01; 187(12):2686-2697. PMID: 30099505; PMCID: PMC6269249.
• Cai FY, Fussell T, Cobey S, Lipsitch M. Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine. PLoS Comput Biol. 2018 10; 14(10):e1006333. PMID: 30273332; PMCID: PMC6181404.
• Lewnard JA, Tähtinen PA, Laine MK, Lindholm L, Jalava J, Huovinen P, Lipsitch M, Ruohola A. Impact of Antimicrobial Treatment for Acute Otitis Media on Carriage Dynamics of Penicillin-Susceptible and Penicillin-Nonsusceptible Streptococcus pneumoniae. J Infect Dis. 2018 09 22; 218(9):1356-1366. PMID: 29873739; PMCID: PMC6151080.
• Kahn R, Rid A, Smith PG, Eyal N, Lipsitch M. Choices in vaccine trial design in epidemics of emerging infections. PLoS Med. 2018 08; 15(8):e1002632. PMID: 30086139; PMCID: PMC6080746.
• Eyal N, Lipsitch M, Bärnighausen T, Wikler D. Opinion: Risk to study nonparticipants: A procedural approach. Proc Natl Acad Sci U S A. 2018 08 07; 115(32):8051-8053. PMID: 30087210; PMCID: PMC6094093.
• Hitchings MDT, Lipsitch M, Wang R, Bellan SE. Competing Effects of Indirect Protection and Clustering on the Power of Cluster-Randomized Controlled Vaccine Trials. Am J Epidemiol. 2018 08 01; 187(8):1763-1771. PMID: 29522080; PMCID: PMC6070038.
• Atkins KE, Lipsitch M. Can antibiotic resistance be reduced by vaccinating against respiratory disease? Lancet Respir Med. 2018 11; 6(11):820-821. PMID: 30076121.
• Olesen SW, Barnett ML, MacFadden DR, Lipsitch M, Grad YH. Trends in outpatient antibiotic use and prescribing practice among US older adults, 2011-15: observational study. BMJ. 2018 07 27; 362:k3155. PMID: 30054353; PMCID: PMC6062849.
• Blanquart F, Lehtinen S, Lipsitch M, Fraser C. The evolution of antibiotic resistance in a structured host population. J R Soc Interface. 2018 06; 15(143). PMID: 29925579.
• MacFadden DR, Lipsitch M, Olesen SW, Grad Y. Multidrug-resistant Neisseria gonorrhoeae: implications for future treatment strategies. Lancet Infect Dis. 2018 06; 18(6):599. PMID: 29856349.
• Goldstein E, Worby CJ, Lipsitch M. On the Role of Different Age Groups and Pertussis Vaccines During the 2012 Outbreak in Wisconsin. Open Forum Infect Dis. 2018 May; 5(5):ofy082. PMID: 29942818; PMCID: PMC5961225.
• 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. The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome. PLoS Pathog. 2018 04; 14(4):e1006966. PMID: 29617440.
• Johansson MA, Reich NG, Meyers LA, Lipsitch M. Preprints: An underutilized mechanism to accelerate outbreak science. PLoS Med. 2018 04; 15(4):e1002549. PMID: 29614073; PMCID: PMC5882117.
• Georgieva M, Kagedan L, Lu YJ, Thompson CM, Lipsitch M. Antigenic Variation in Streptococcus pneumoniae PspC Promotes Immune Escape in the Presence of Variant-Specific Immunity. mBio. 2018 03 13; 9(2). PMID: 29535198.
• Kahn R, Hitchings M, Bellan S, Lipsitch M. Impact of stochastically generated heterogeneity in hazard rates on individually randomized vaccine efficacy trials. Clin Trials. 2018 04; 15(2):207-211. PMID: 29374974.
• Arnold BJ, Gutmann MU, Grad YH, Sheppard SK, Corander J, Lipsitch M, Hanage WP. Weak Epistasis May Drive Adaptation in Recombining Bacteria. Genetics. 2018 03; 208(3):1247-1260. PMID: 29330348.
• Goldstein E, Nguyen HH, Liu P, Viboud C, Steiner CA, Worby CJ, Lipsitch M. On the Relative Role of Different Age Groups During Epidemics Associated With Respiratory Syncytial Virus. J Infect Dis. 2018 01 04; 217(2):238-244. PMID: 29112722; PMCID: PMC5853559.
• Lipsitch M. Why Do Exceptionally Dangerous Gain-of-Function Experiments in Influenza? Methods Mol Biol. 2018; 1836:589-608. PMID: 30151594; PMCID: PMC7119956.
• 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. Simulations for designing and interpreting intervention trials in infectious diseases. BMC Med. 2017 12 29; 15(1):223. PMID: 29287587; PMCID: PMC5747936.
• Lipsitch M, Li LM, Patterson S, Trammel J, Juergens C, Gruber WC, Scott DA, Dagan R. Serotype-specific immune responses to pneumococcal conjugate vaccine among children are significantly correlated by individual: Analysis of randomized controlled trial data. Vaccine. 2018 01 25; 36(4):473-478. PMID: 29248266.
• Langwig KE, Wargo AR, Jones DR, Viss JR, Rutan BJ, Egan NA, Sá-Guimarães P, Kim MS, Kurath G, Gomes MGM, Lipsitch M. Vaccine Effects on Heterogeneity in Susceptibility and Implications for Population Health Management. mBio. 2017 11 21; 8(6). PMID: 29162706.
• Worby CJ, Lipsitch M, Hanage WP. Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data. Am J Epidemiol. 2017 Nov 15; 186(10):1209-1216. PMID: 29149252; PMCID: PMC5860558.
• Lewnard JA, Givon-Lavi N, Weinberger DM, Lipsitch M, Dagan R. Pan-serotype Reduction in Progression of Streptococcus pneumoniae to Otitis Media After Rollout of Pneumococcal Conjugate Vaccines. Clin Infect Dis. 2017 Nov 13; 65(11):1853-1861. PMID: 29020218; PMCID: PMC6248775.
• Masala GL, Lipsitch M, Bottomley C, Flasche S. Exploring the role of competition induced by non-vaccine serotypes for herd protection following pneumococcal vaccination. J R Soc Interface. 2017 11; 14(136). PMID: 29093131; PMCID: PMC5721164.
• Corander J, Fraser C, Gutmann MU, Arnold B, Hanage WP, Bentley SD, Lipsitch M, Croucher NJ. Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. Nat Ecol Evol. 2017 Dec; 1(12):1950-1960. PMID: 29038424.
• Lee GM, Kleinman K, Pelton S, Lipsitch M, Huang SS, Lakoma M, Dutta-Linn M, Rett M, Hanage WP, Finkelstein JA. Immunization, Antibiotic Use, and Pneumococcal Colonization Over a 15-Year Period. Pediatrics. 2017 Nov; 140(5). PMID: 28978716; PMCID: PMC5654389.
• Cobey S, Baskerville EB, Colijn C, Hanage W, Fraser C, Lipsitch M. Host population structure and treatment frequency maintain balancing selection on drug resistance. J R Soc Interface. 2017 08; 14(133). PMID: 28835542.
• Lipsitch M. If a Global Catastrophic Biological Risk Materializes, at What Stage Will We Recognize It? Health Secur. 2017 Jul/Aug; 15(4):331-334. PMID: 28745911.
• Lipsitch M, Eyal N. Improving vaccine trials in infectious disease emergencies. Science. 2017 07 14; 357(6347):153-156. PMID: 28706038.
• Eyal N, Lipsitch M. Vaccine testing for emerging infections: the case for individual randomisation. J Med Ethics. 2017 09; 43(9):625-631. PMID: 28396558; PMCID: PMC5577361.
• McCormick AW, Abuelezam NN, Fussell T, Seage GR, Lipsitch M. Displacement of sexual partnerships in trials of sexual behavior interventions: A model-based assessment of consequences. Epidemics. 2017 09; 20:94-101. PMID: 28416219.
• Hitchings MD, Grais RF, Lipsitch M. Using simulation to aid trial design: Ring-vaccination trials. PLoS Negl Trop Dis. 2017 03; 11(3):e0005470. PMID: 28328984.
• 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. Association of Pneumococcal Protein Antigen Serology With Age and Antigenic Profile of Colonizing Isolates. J Infect Dis. 2017 03 01; 215(5):713-722. PMID: 28035010; PMCID: PMC6005115.
• Worby CJ, Wallinga J, Lipsitch M, Goldstein E. Population effect of influenza vaccination under co-circulation of non-vaccine variants and the case for a bivalent A/H3N2 vaccine component. Epidemics. 2017 06; 19:74-82. PMID: 28262588.
• Grad YH, Lipsitch M. Reply to Allan-Blitz and Klausner. J Infect Dis. 2017 02 01; 215(3):491-492. PMID: 28003355; PMCID: PMC5873214.
• Lehtinen S, Blanquart F, Croucher NJ, Turner P, Lipsitch M, Fraser C. Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage. Proc Natl Acad Sci U S A. 2017 01 31; 114(5):1075-1080. PMID: 28096340; PMCID: PMC5293062.
• Croucher NJ, Campo JJ, Le TQ, Liang X, Bentley SD, Hanage WP, Lipsitch M. Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening. Proc Natl Acad Sci U S A. 2017 01 17; 114(3):E357-E366. PMID: 28053228; PMCID: PMC5255586.
• Goldstein E, Pitzer VE, O’Hagan JJ, Lipsitch M. Temporally Varying Relative Risks for Infectious Diseases: Implications for Infectious Disease Control. Epidemiology. 2017 01; 28(1):136-144. PMID: 27748685.
• Lipsitch M, Jha A, Simonsen L. Observational studies and the difficult quest for causality: lessons from vaccine effectiveness and impact studies. Int J Epidemiol. 2016 12 01; 45(6):2060-2074. PMID: 27453361.
• Leung K, Lipsitch M, Yuen KY, Wu JT. Monitoring the fitness of antiviral-resistant influenza strains during an epidemic: a mathematical modelling study. Lancet Infect Dis. 2017 03; 17(3):339-347. PMID: 27914853.
• 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. Viral factors in influenza pandemic risk assessment. Elife. 2016 11 11; 5. PMID: 27834632.
• Wu JT, Peak CM, Leung GM, Lipsitch M. Fractional dosing of yellow fever vaccine to extend supply: a modelling study. Lancet. 2016 12 10; 388(10062):2904-2911. PMID: 27837923; PMCID: PMC5161610.
• Grad YH, Harris SR, Kirkcaldy RD, Green AG, Marks DS, Bentley SD, Trees D, Lipsitch M. Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013. J Infect Dis. 2016 11 15; 214(10):1579-1587. PMID: 27638945; PMCID: PMC5091375.
• Lipsitch M, Cowling BJ. Zika vaccine trials. Science. 2016 09 09; 353(6304):1094-5. PMID: 27609872.
• Lipsitch M. Comment on “Gain-of-Function Research and the Relevance to Clinical Practice”. J Infect Dis. 2016 10 15; 214(8):1284-5. PMID: 27503367; PMCID: PMC7107370.
• García-Albéniz X, Hsu J, Lipsitch M, Bretthauer M, Logan RW, Hernández-Díaz S, Hernán MA. Colonoscopy and Risk of Infective Endocarditis in the Elderly. J Am Coll Cardiol. 2016 08 02; 68(5):570-571. PMID: 27470461; PMCID: PMC5287292.
• Chang HH, Huber RG, Bond PJ, Grad YH, Camerini D, Maurer-Stroh S, Lipsitch M. Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses. Bull World Health Organ. 2017 Jul 01; 95(7):517-525I. PMID: 28670016; PMCID: PMC5487971.
• Abuelezam NN, McCormick AW, Fussell T, Afriyie AN, Wood R, DeGruttola V, Freedberg KA, Lipsitch M, Seage GR. Can the Heterosexual HIV Epidemic be Eliminated in South Africa Using Combination Prevention? A Modeling Analysis. Am J Epidemiol. 2016 08 01; 184(3):239-48. PMID: 27416841; PMCID: PMC4967594.
• Lipsitch M, Evans NG, Cotton-Barratt O. Underprotection of Unpredictable Statistical Lives Compared to Predictable Ones. Risk Anal. 2017 05; 37(5):893-904. PMID: 27393181; PMCID: PMC5222861.
• Lipsitch M, Siber GR. How Can Vaccines Contribute to Solving the Antimicrobial Resistance Problem? mBio. 2016 06 07; 7(3). PMID: 27273824; PMCID: PMC4959668.
• Chang HH, Dordel J, Donker T, Worby CJ, Feil EJ, Hanage WP, Bentley SD, Huang SS, Lipsitch M. Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus. Genome Med. 2016 Feb 13; 8(1):18. PMID: 26873713; PMCID: PMC4752745.
• García-Albéniz X, Hsu J, Lipsitch M, Logan RW, Hernández-Díaz S, Hernán MA. Infective endocarditis and cancer in the elderly. Eur J Epidemiol. 2016 Jan; 31(1):41-9. PMID: 26683995; PMCID: PMC5354127.
• Worby CJ, Chaves SS, Wallinga J, Lipsitch M, Finelli L, Goldstein E. On the relative role of different age groups in influenza epidemics. Epidemics. 2015 Dec; 13:10-16. PMID: 26097505.
• Chang Q, Lipsitch M, Hanage WP. Impact of Host Heterogeneity on the Efficacy of Interventions to Reduce Staphylococcus aureus Carriage. Infect Control Hosp Epidemiol. 2016 Feb; 37(2):197-204. PMID: 26598029; PMCID: PMC4760641.
• Grad YH, Goldstein E, Lipsitch M, White PJ. Improving Control of Antibiotic-Resistant Gonorrhea by Integrating Research Agendas Across Disciplines: Key Questions Arising From Mathematical Modeling. J Infect Dis. 2016 Mar 15; 213(6):883-90. PMID: 26518045; PMCID: PMC4760416.
• Croucher NJ, Finkelstein JA, Pelton SI, Parkhill J, Bentley SD, Lipsitch M, Hanage WP. Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae. Sci Data. 2015; 2:150058. PMID: 26528397; PMCID: PMC4622223.
• 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, Rodríguez-Barraquer I, Smith DJ, Stefansen C, Swerdlow DL, Thompson D, Vespignani A, Wesolowski A. Enhancing disease surveillance with novel data streams: challenges and opportunities. EPJ Data Sci. 2015; 4. PMID: 27990325; PMCID: PMC5156315.
• Frank GM, Adalja A, Barbour A, Casadevall A, Dormitzer PR, Duchin J, Hayden FG, Hirsch MS, Hynes NA, Lipsitch M, Pavia AT, Relman DA. Infectious Diseases Society of America and Gain-of-Function Experiments With Pathogens Having Pandemic Potential. J Infect Dis. 2016 May 01; 213(9):1359-61. PMID: 26416656; PMCID: PMC7313907.
• Trzcinski K, Li Y, Weinberger DM, Thompson CM, Cordy D, Bessolo A, Malley R, Lipsitch M. Effect of Serotype on Pneumococcal Competition in a Mouse Colonization Model. mBio. 2015 Sep 15; 6(5):e00902-15. PMID: 26374118.
• Lipsitch M, Esvelt K, Inglesby T. Calls for caution in genome engineering should be a model for similar dialogue on pandemic pathogen research. Ann Intern Med. 2015 Nov 17; 163(10):790-1. PMID: 26344802.
• Goldstein E, Greene SK, Olson DR, Hanage WP, Lipsitch M. Estimating the hospitalization burden associated with influenza and respiratory syncytial virus in New York City, 2003-2011. Influenza Other Respir Viruses. 2015 Sep; 9(5):225-33. PMID: 25980600.
• Evans NG, Lipsitch M, Levinson M. The ethics of biosafety considerations in gain-of-function research resulting in the creation of potential pandemic pathogens. J Med Ethics. 2015 Nov; 41(11):901-8. PMID: 26320212; PMCID: PMC4623968.
• Worby CJ, Kenyon C, Lynfield R, Lipsitch M, Goldstein E. Examining the role of different age groups, and of vaccination during the 2012 Minnesota pertussis outbreak. Sci Rep. 2015 Aug 17; 5:13182. PMID: 26278132.
• 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. Potential Biases in Estimating Absolute and Relative Case-Fatality Risks during Outbreaks. PLoS Negl Trop Dis. 2015; 9(7):e0003846. PMID: 26181387; PMCID: PMC4504518.
• Kunkel A, Colijn C, Lipsitch M, Cohen T. How could preventive therapy affect the prevalence of drug resistance? Causes and consequences. Philos Trans R Soc Lond B Biol Sci. 2015 Jun 05; 370(1670):20140306. PMID: 25918446; PMCID: PMC4424438.
• Mitchell PK, Lipsitch M, Hanage WP. Carriage burden, multiple colonization and antibiotic pressure promote emergence of resistant vaccine escape pneumococci. Philos Trans R Soc Lond B Biol Sci. 2015 Jun 05; 370(1670):20140342. PMID: 25918447; PMCID: PMC4424439.
• Li Y, Croucher NJ, Thompson CM, Trzcinski K, Hanage WP, Lipsitch M. Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity. BMC Genomics. 2015 May 09; 16:369. PMID: 25956132; PMCID: PMC4424882.
• Lipsitch M, Eyal N, Halloran ME, Hernán MA, Longini IM, Perencevich EN, Grais RF. Vaccine testing. Ebola and beyond. Science. 2015 Apr 03; 348(6230):46-8. PMID: 25838371.
• Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M, Hanage WP. Selective and genetic constraints on pneumococcal serotype switching. PLoS Genet. 2015 Mar; 11(3):e1005095. PMID: 25826208; PMCID: PMC4380333.
• Chang HH, Cohen T, Grad YH, Hanage WP, O’Brien TF, Lipsitch M. Origin and proliferation of multiple-drug resistance in bacterial pathogens. Microbiol Mol Biol Rev. 2015 Mar; 79(1):101-16. PMID: 25652543; PMCID: PMC4402963.
• Chang Q, Stevenson AE, Croucher NJ, Lee GM, Pelton SI, Lipsitch M, Finkelstein JA, Hanage WP. Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced. BMC Infect Dis. 2015 Feb 18; 15:68. PMID: 25887323; PMCID: PMC4336693.
• Yang W, Lipsitch M, Shaman J. Inference of seasonal and pandemic influenza transmission dynamics. Proc Natl Acad Sci U S A. 2015 Mar 03; 112(9):2723-8. PMID: 25730851; PMCID: PMC4352784.
• Lipsitch M, Inglesby TV. Erratum for lipsitch and inglesby, moratorium on research intended to create novel potential pandemic pathogens. mBio. 2015 Feb 10; 6(1). PMID: 25670775.
• Lipsitch M, Inglesby TV. Reply to “Studies on influenza virus transmission between ferrets: the public health risks revisited”. mBio. 2015 Jan 23; 6(1). PMID: 25616376; PMCID: PMC4323416.
• Abel S, Abel zur Wiesch P, Chang HH, Davis BM, Lipsitch M, Waldor MK. Sequence tag-based analysis of microbial population dynamics. Nat Methods. 2015 Mar; 12(3):223-6, 3 p following 226. PMID: 25599549; PMCID: PMC4344388.
• Lipsitch M, Inglesby TV. Moratorium on research intended to create novel potential pandemic pathogens. mBio. 2014 Dec 12; 5(6). PMID: 25505122.
• Duprex WP, Fouchier RA, Imperiale MJ, Lipsitch M, Relman DA. Gain-of-function experiments: time for a real debate. Nat Rev Microbiol. 2015 01; 13(1):58-64. PMID: 25482289; PMCID: PMC7097416.
• Ascioglu S, Samore MH, Lipsitch M. A new approach to the analysis of antibiotic resistance data from hospitals. Microb Drug Resist. 2014 Dec; 20(6):583-90. PMID: 25055133.
• Grad YH, Lipsitch M. Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol. 2014 Nov 18; 15(11):538. PMID: 25418119; PMCID: PMC4282151.
• 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. Improving pandemic influenza risk assessment. Elife. 2014 Oct 16; 3:e03883. PMID: 25321142; PMCID: PMC4199076.
• Lipsitch M. Can limited scientific value of potential pandemic pathogen experiments justify the risks? mBio. 2014 Oct 14; 5(5):e02008-14. PMID: 25316701; PMCID: PMC4205796.
• Worby CJ, Chang HH, Hanage WP, Lipsitch M. The distribution of pairwise genetic distances: a tool for investigating disease transmission. Genetics. 2014 Dec; 198(4):1395-404. PMID: 25313129.
• Jacobs JH, Viboud C, Tchetgen ET, Schwartz J, Steiner C, Simonsen L, Lipsitch M. The association of meningococcal disease with influenza in the United States, 1989-2009. PLoS One. 2014; 9(9):e107486. PMID: 25265409; PMCID: PMC4180274.
• Johnson SR, Grad Y, Ganakammal SR, Burroughs M, Frace M, Lipsitch M, Weil R, Trees D. In Vitro selection of Neisseria gonorrhoeae mutants with elevated MIC values and increased resistance to cephalosporins. Antimicrob Agents Chemother. 2014 Nov; 58(11):6986-9. PMID: 25199775.
• Chang Q, Wang W, Regev-Yochay G, Lipsitch M, Hanage WP. Antibiotics in agriculture and the risk to human health: how worried should we be? Evol Appl. 2015 Mar; 8(3):240-7. PMID: 25861382; PMCID: PMC4380918.
• Li Y, Thompson CM, Lipsitch M. A modified Janus cassette (Sweet Janus) to improve allelic replacement efficiency by high-stringency negative selection in Streptococcus pneumoniae. PLoS One. 2014; 9(6):e100510. PMID: 24959661.
• McCormick AW, Abuelezam NN, Rhode ER, Hou T, Walensky RP, Pei PP, Becker JE, DiLorenzo MA, Losina E, Freedberg KA, Lipsitch M, Seage GR. Development, calibration and performance of an HIV transmission model incorporating natural history and behavioral patterns: application in South Africa. PLoS One. 2014; 9(5):e98272. PMID: 24867402.
• Lipsitch M, Galvani AP. Ethical alternatives to experiments with novel potential pandemic pathogens. PLoS Med. 2014 May; 11(5):e1001646. PMID: 24844931; PMCID: PMC4028196.
• Patterson-Lomba O, Van Noort S, Cowling BJ, Wallinga J, Gomes MG, Lipsitch M, Goldstein E. Utilizing syndromic surveillance data for estimating levels of influenza circulation. Am J Epidemiol. 2014 Jun 01; 179(11):1394-401. PMID: 24748609.
• Grad YH, Newman R, Zody M, Yang X, Murphy R, Qu J, Malboeuf CM, Levin JZ, Lipsitch M, DeVincenzo J. Within-host whole-genome deep sequencing and diversity analysis of human respiratory syncytial virus infection reveals dynamics of genomic diversity in the absence and presence of immune pressure. J Virol. 2014 Jul; 88(13):7286-93. PMID: 24741088.
• Worby CJ, Lipsitch M, Hanage WP. Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data. PLoS Comput Biol. 2014 Mar; 10(3):e1003549. PMID: 24675511.
• Gomes MG, Lipsitch M, Wargo AR, Kurath G, Rebelo C, Medley GF, Coutinho A. A missing dimension in measures of vaccination impacts. PLoS Pathog. 2014 Mar; 10(3):e1003849. PMID: 24603721.
• Huang KE, Lipsitch M, Shaman J, Goldstein E. The US 2009 A(H1N1) influenza epidemic: quantifying the impact of school openings on the reproductive number. Epidemiology. 2014 Mar; 25(2):203-6. PMID: 24434751.
• Grad YH, Kirkcaldy RD, Trees D, Dordel J, Harris SR, Goldstein E, Weinstock H, Parkhill J, Hanage WP, Bentley S, Lipsitch M. Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study. Lancet Infect Dis. 2014 Mar; 14(3):220-6. PMID: 24462211.
• Fisman DN, Leung GM, Lipsitch M. Nuanced risk assessment for emerging infectious diseases. Lancet. 2014 Jan 18; 383(9913):189-90. PMID: 24439726; PMCID: PMC7137147.
• O’Hagan JJ, Lipsitch M, Hernán MA. Estimating the per-exposure effect of infectious disease interventions. Epidemiology. 2014 Jan; 25(1):134-8. PMID: 24240656.
• Quandelacy TM, Viboud C, Charu V, Lipsitch M, Goldstein E. Age- and sex-related risk factors for influenza-associated mortality in the United States between 1997-2007. Am J Epidemiol. 2014 Jan 15; 179(2):156-67. PMID: 24190951.
• Li Y, Thompson CM, Trzcinski K, Lipsitch M. Within-host selection is limited by an effective population of Streptococcus pneumoniae during nasopharyngeal colonization. Infect Immun. 2013 Dec; 81(12):4534-43. PMID: 24082074.
• Li Y, Weinberger DM, Thompson CM, Trzcinski K, Lipsitch M. Surface charge of Streptococcus pneumoniae predicts serotype distribution. Infect Immun. 2013 Dec; 81(12):4519-24. PMID: 24082068.
• Weinberger DM, Bruden DT, Grant LR, Lipsitch M, O’Brien KL, Pelton SI, Sanders EA, Feikin DR. Using pneumococcal carriage data to monitor postvaccination changes in invasive disease. Am J Epidemiol. 2013 Nov 01; 178(9):1488-95. PMID: 24013204.
• Lipsitch M. Avian influenza: Ferret H7N9 flu model questioned. Nature. 2013 Sep 05; 501(7465):33. PMID: 24005404.
• Joice R, Lipsitch M. Targeting imperfect vaccines against drug-resistance determinants: a strategy for countering the rise of drug resistance. PLoS One. 2013; 8(7):e68940. PMID: 23935910.
• Lipsitch M, Hernán MA. Oseltamivir effect on antibiotic-treated lower respiratory tract complications in virologically positive randomized trial participants. Clin Infect Dis. 2013 Nov; 57(9):1368-9. PMID: 23883518.
• 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. Geographic and temporal trends in antimicrobial nonsusceptibility in Streptococcus pneumoniae in the post-vaccine era in the United States. J Infect Dis. 2013 Oct 15; 208(8):1266-73. PMID: 23852588; PMCID: PMC3778966.
• Ford CB, Shah RR, Maeda MK, Gagneux S, Murray MB, Cohen T, Johnston JC, Gardy J, Lipsitch M, Fortune SM. Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat Genet. 2013 Jul; 45(7):784-90. PMID: 23749189.
• Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM, Parkhill J, Bentley SD, Hanage WP, Lipsitch M. Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet. 2013 Jun; 45(6):656-63. PMID: 23644493.
• Koep TH, Enders FT, Pierret C, Ekker SC, Krageschmidt D, Neff KL, Lipsitch M, Shaman J, Huskins WC. Predictors of indoor absolute humidity and estimated effects on influenza virus survival in grade schools. BMC Infect Dis. 2013 Feb 05; 13:71. PMID: 23383620.
• 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. Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen. mBio. 2013 Jan 22; 4(1):e00452-12. PMID: 23341549.
• Palmer ME, Lipsitch M, Moxon ER, Bayliss CD. Broad conditions favor the evolution of phase-variable loci. mBio. 2013 Jan 08; 4(1):e00430-12. PMID: 23300246.
• Shaman J, Karspeck A, Yang W, Tamerius J, Lipsitch M. Real-time influenza forecasts during the 2012-2013 season. Nat Commun. 2013; 4:2837. PMID: 24302074.
• 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. Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany. Proc Natl Acad Sci U S A. 2012 Dec 26; 109(52):E3629-30. PMID: 23479789.
• Cobey S, Lipsitch M. Pathogen diversity and hidden regimes of apparent competition. Am Nat. 2013 Jan; 181(1):12-24. PMID: 23234842.
• Hyams C, Trzcinski K, Camberlein E, Weinberger DM, Chimalapati S, Noursadeghi M, Lipsitch M, Brown JS. Streptococcus pneumoniae capsular serotype invasiveness correlates with the degree of factor H binding and opsonization with C3b/iC3b. Infect Immun. 2013 Jan; 81(1):354-63. PMID: 23147038; PMCID: PMC3536142.
• Li Y, Gierahn T, Thompson CM, Trzcinski K, Ford CB, Croucher N, Gouveia P, Flechtner JB, Malley R, Lipsitch M. Distinct effects on diversifying selection by two mechanisms of immunity against Streptococcus pneumoniae. PLoS Pathog. 2012; 8(11):e1002989. PMID: 23144610.
• Goldstein E, Viboud C, Charu V, Lipsitch M. Improving the estimation of influenza-related mortality over a seasonal baseline. Epidemiology. 2012 Nov; 23(6):829-38. PMID: 22992574.
• Lipsitch M, Bloom BR. Rethinking biosafety in research on potential pandemic pathogens. mBio. 2012 Oct 09; 3(5). PMID: 23047752.
• 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. Searching for sharp drops in the incidence of pandemic A/H1N1 influenza by single year of age. PLoS One. 2012; 7(8):e42328. PMID: 22876316.
• Goldstein E, Kirkcaldy RD, Reshef D, Berman S, Weinstock H, Sabeti P, Del Rio C, Hall G, Hook EW, Lipsitch M. Factors related to increasing prevalence of resistance to ciprofloxacin and other antimicrobial drugs in Neisseria gonorrhoeae, United States. Emerg Infect Dis. 2012 Aug; 18(8):1290-7. PMID: 22840274.
• Abdullahi O, Karani A, Tigoi CC, Mugo D, Kungu S, Wanjiru E, Jomo J, Musyimi R, Lipsitch M, Scott JA. Rates of acquisition and clearance of pneumococcal serotypes in the nasopharynges of children in Kilifi District, Kenya. J Infect Dis. 2012 Oct 01; 206(7):1020-9. PMID: 22829650; PMCID: PMC3433858.
• Goldstein E, Wallinga J, Lipsitch M. Vaccine allocation in a declining epidemic. J R Soc Interface. 2012 Nov 07; 9(76):2798-803. PMID: 22772378.
• Lipsitch M, Abdullahi O, D’Amour A, Xie W, Weinberger DM, Tchetgen Tchetgen E, Scott JA. Estimating rates of carriage acquisition and clearance and competitive ability for pneumococcal serotypes in Kenya with a Markov transition model. Epidemiology. 2012 Jul; 23(4):510-9. PMID: 22441543.
• Grad YH, Miller JC, Lipsitch M. Cholera modeling: challenges to quantitative analysis and predicting the impact of interventions. Epidemiology. 2012 Jul; 23(4):523-30. PMID: 22659546.
• Lipsitch M, Plotkin JB, Simonsen L, Bloom B. Evolution, safety, and highly pathogenic influenza viruses. Science. 2012 Jun 22; 336(6088):1529-31. PMID: 22723411.
• Van Kerkhove MD, Riley S, Lipsitch M, Guan Y, Monto AS, Webster RG, Zambon M, Nicoll A, Peiris JS, Ferguson NM. Comment on “Seroevidence for H5N1 influenza infections in humans: meta-analysis”. Science. 2012 Jun 22; 336(6088):1506; author reply 1506. PMID: 22723396.
• Ke W, Huang SS, Hudson LO, Elkins KR, Nguyen CC, Spratt BG, Murphy CR, Avery TR, Lipsitch M. Patient sharing and population genetic structure of methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci U S A. 2012 Apr 24; 109(17):6763-8. PMID: 22431601.
• Pitzer VE, Burgner D, Viboud C, Simonsen L, Andreasen V, Steiner CA, Lipsitch M. Modelling seasonal variations in the age and incidence of Kawasaki disease to explore possible infectious aetiologies. Proc Biol Sci. 2012 Jul 22; 279(1739):2736-43. PMID: 22398170.
• Cobey S, Lipsitch M. Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes. Science. 2012 Mar 16; 335(6074):1376-80. PMID: 22383809.
• Wroe PC, Lee GM, Finkelstein JA, Pelton SI, Hanage WP, Lipsitch M, Stevenson AE, Rifas-Shiman SL, Kleinman K, Dutta-Linn MM, Hinrichsen VL, Lakoma M, Huang SS. Pneumococcal carriage and antibiotic resistance in young children before 13-valent conjugate vaccine. Pediatr Infect Dis J. 2012 Mar; 31(3):249-54. PMID: 22173142.
• Abdullahi O, Karani A, Tigoi CC, Mugo D, Kungu S, Wanjiru E, Jomo J, Musyimi R, Lipsitch M, Scott JA. The prevalence and risk factors for pneumococcal colonization of the nasopharynx among children in Kilifi District, Kenya. PLoS One. 2012; 7(2):e30787. PMID: 22363489.
• 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. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci U S A. 2012 Feb 21; 109(8):3065-70. PMID: 22315421.
• Shaman J, Lipsitch M. The El Nino-Southern Oscillation (ENSO)-pandemic influenza connection: coincident or causal? Proc Natl Acad Sci U S A. 2013 Feb 26; 110 Suppl 1:3689-91. PMID: 22308322.
• O’Hagan JJ, Hernán MA, Walensky RP, Lipsitch M. Apparent declining efficacy in randomized trials: examples of the Thai RV144 HIV vaccine and South African CAPRISA 004 microbicide trials. AIDS. 2012 Jan 14; 26(2):123-6. PMID: 22045345; PMCID: PMC3319457.
• Scott JR, Millar EV, Lipsitch M, Moulton LH, Weatherholtz R, Perilla MJ, Jackson DM, Beall B, Craig MJ, Reid R, Santosham M, O’Brien KL. Impact of more than a decade of pneumococcal conjugate vaccine use on carriage and invasive potential in Native American communities. J Infect Dis. 2012 Jan 15; 205(2):280-8. PMID: 22128315; PMCID: PMC3244367.
• Grad YH, Lipsitch M, Aiello AE. Secular trends in Helicobacter pylori seroprevalence in adults in the United States: evidence for sustained race/ethnic disparities. Am J Epidemiol. 2012 Jan 01; 175(1):54-9. PMID: 22085628; PMCID: PMC3244610.
• Scott JR, Hanage WP, Lipsitch M, Millar EV, Moulton LH, Hinds J, Reid R, Santosham M, O’Brien KL. Pneumococcal sequence type replacement among American Indian children: a comparison of pre- and routine-PCV7 eras. Vaccine. 2012 Mar 16; 30(13):2376-81. PMID: 22094283.
• Hanage WP, Bishop CJ, Lee GM, Lipsitch M, Stevenson A, Rifas-Shiman SL, Pelton SI, Huang SS, Finkelstein JA. Clonal replacement among 19A Streptococcus pneumoniae in Massachusetts, prior to 13 valent conjugate vaccination. Vaccine. 2011 Nov 08; 29(48):8877-81. PMID: 21964059.
• Presanis AM, Pebody RG, Paterson BJ, Tom BD, Birrell PJ, Charlett A, Lipsitch M, De Angelis D. Changes in severity of 2009 pandemic A/H1N1 influenza in England: a Bayesian evidence synthesis. BMJ. 2011 Sep 08; 343:d5408. PMID: 21903689; PMCID: PMC3168935.
• Goldstein E, Cowling BJ, Aiello AE, Takahashi S, King G, Lu Y, Lipsitch M. Estimating incidence curves of several infections using symptom surveillance data. PLoS One. 2011; 6(8):e23380. PMID: 21887246.
• Mostofsky E, Lipsitch M, Regev-Yochay G. Is methicillin-resistant Staphylococcus aureus replacing methicillin-susceptible S. aureus? J Antimicrob Chemother. 2011 Oct; 66(10):2199-214. PMID: 21737459.
• Goldstein E, Cobey S, Takahashi S, Miller JC, Lipsitch M. Predicting the epidemic sizes of influenza A/H1N1, A/H3N2, and B: a statistical method. PLoS Med. 2011 Jul; 8(7):e1001051. PMID: 21750666.
• Hernán MA, Lipsitch M. Oseltamivir and risk of lower respiratory tract complications in patients with flu symptoms: a meta-analysis of eleven randomized clinical trials. Clin Infect Dis. 2011 Aug 01; 53(3):277-9. PMID: 21677258.
• Smith J, Lipsitch M, Almond JW. Vaccine production, distribution, access, and uptake. Lancet. 2011 Jul 30; 378(9789):428-38. PMID: 21664680; PMCID: PMC3164579.
• Shaman J, Jeon CY, Giovannucci E, Lipsitch M. Shortcomings of vitamin D-based model simulations of seasonal influenza. PLoS One. 2011; 6(6):e20743. PMID: 21677774.
• Lipsitch M, Finelli L, Heffernan RT, Leung GM, Redd SC. Improving the evidence base for decision making during a pandemic: the example of 2009 influenza A/H1N1. Biosecur Bioterror. 2011 Jun; 9(2):89-115. PMID: 21612363.
• Ford CB, Lin PL, Chase MR, Shah RR, Iartchouk O, Galagan J, Mohaideen N, Ioerger TR, Sacchettini JC, Lipsitch M, Flynn JL, Fortune SM. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat Genet. 2011 May; 43(5):482-6. PMID: 21516081.
• Weinberger DM, Malley R, Lipsitch M. Serotype replacement in disease after pneumococcal vaccination. Lancet. 2011 Dec 03; 378(9807):1962-73. PMID: 21492929; PMCID: PMC3256741.
• Hanage WP, Bishop CJ, Huang SS, Stevenson AE, Pelton SI, Lipsitch M, Finkelstein JA. Carried pneumococci in Massachusetts children: the contribution of clonal expansion and serotype switching. Pediatr Infect Dis J. 2011 Apr; 30(4):302-8. PMID: 21085049.
• Weinberger DM, Harboe ZB, Flasche S, Scott JA, Lipsitch M. Prediction of serotypes causing invasive pneumococcal disease in unvaccinated and vaccinated populations. Epidemiology. 2011 Mar; 22(2):199-207. PMID: 21646962.
• Shaman J, Goldstein E, Lipsitch M. Absolute humidity and pandemic versus epidemic influenza. Am J Epidemiol. 2011 Jan 15; 173(2):127-35. PMID: 21081646.
• Goldhaber-Fiebert JD, Lipsitch M, Mahal A, Zaslavsky AM, Salomon JA. Quantifying child mortality reductions related to measles vaccination. PLoS One. 2010 Nov 04; 5(11):e13842. PMID: 21079809.
• 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. Quantifying interhospital patient sharing as a mechanism for infectious disease spread. Infect Control Hosp Epidemiol. 2010 Nov; 31(11):1160-9. PMID: 20874503; PMCID: PMC3064463.
• Yildirim I, Hanage WP, Lipsitch M, Shea KM, Stevenson A, Finkelstein J, Huang SS, Lee GM, Kleinman K, Pelton SI. Serotype specific invasive capacity and persistent reduction in invasive pneumococcal disease. Vaccine. 2010 Dec 16; 29(2):283-8. PMID: 21029807.
• 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. Association of serotype with risk of death due to pneumococcal pneumonia: a meta-analysis. Clin Infect Dis. 2010 Sep 15; 51(6):692-9. PMID: 20715907.
• Lajous M, Danon L, López-Ridaura R, Astley CM, Miller JC, Dowell SF, O’Hagan JJ, Goldstein E, Lipsitch M. Mobile messaging as surveillance tool during pandemic (H1N1) 2009, Mexico. Emerg Infect Dis. 2010 Sep; 16(9):1488-9. PMID: 20735942.
• Goldstein E, Cowling BJ, O’Hagan JJ, Danon L, Fang VJ, Hagy A, Miller JC, Reshef D, Robins J, Biedrzycki P, Lipsitch M. Oseltamivir for treatment and prevention of pandemic influenza A/H1N1 virus infection in households, Milwaukee, 2009. BMC Infect Dis. 2010 Jul 20; 10:211. PMID: 20642862.
• Van Kerkhove MD, Asikainen T, Becker NG, Bjorge S, Desenclos JC, dos Santos T, Fraser C, Leung GM, Lipsitch M, Longini IM, McBryde ES, Roth CE, Shay DK, Smith DJ, Wallinga J, White PJ, Ferguson NM, Riley S. Studies needed to address public health challenges of the 2009 H1N1 influenza pandemic: insights from modeling. PLoS Med. 2010 Jun 01; 7(6):e1000275. PMID: 20532237.
• Lau LL, Cowling BJ, Fang VJ, Chan KH, Lau EH, Lipsitch M, Cheng CK, Houck PM, Uyeki TM, Peiris JS, Leung GM. Viral shedding and clinical illness in naturally acquired influenza virus infections. J Infect Dis. 2010 May 15; 201(10):1509-16. PMID: 20377412; PMCID: PMC3060408.
• Miller JC, Danon L, O’Hagan JJ, Goldstein E, Lajous M, Lipsitch M. Student behavior during a school closure caused by pandemic influenza A/H1N1. PLoS One. 2010 May 05; 5(5):e10425. PMID: 20463960.
• Lipsitch M, Tchetgen Tchetgen E, Cohen T. Negative controls: a tool for detecting confounding and bias in observational studies. Epidemiology. 2010 May; 21(3):383-8. PMID: 20335814.
• Regev-Yochay G, Hanage WP, Trzcinski K, Rifas-Shiman SL, Lee G, Bessolo A, Huang SS, Pelton SI, McAdam AJ, Finkelstein JA, Lipsitch M, Malley R. Re-emergence of the type 1 pilus among Streptococcus pneumoniae isolates in Massachusetts, USA. Vaccine. 2010 Jul 05; 28(30):4842-6. PMID: 20434550.
• Goldstein E, Miller JC, O’Hagan JJ, Lipsitch M. Pre-dispensing of antivirals to high-risk individuals in an influenza pandemic. Influenza Other Respir Viruses. 2010 Mar; 4(2):101-12. PMID: 20167050.
• Shaman J, Pitzer VE, Viboud C, Grenfell BT, Lipsitch M. Absolute humidity and the seasonal onset of influenza in the continental United States. PLoS Biol. 2010 Feb 23; 8(2):e1000316. PMID: 20186267.
• Wallinga J, van Boven M, Lipsitch M. Optimizing infectious disease interventions during an emerging epidemic. Proc Natl Acad Sci U S A. 2010 Jan 12; 107(2):923-8. PMID: 20080777.
• Shaman J, Pitzer V, Viboud C, Lipsitch M, Grenfell B. Absolute Humidity and the Seasonal Onset of Influenza in the Continental US. PLoS Curr. 2009 Dec 18; 2:RRN1138. PMID: 20066155.
• Goldstein E, Dushoff J, Ma J, Plotkin JB, Earn DJ, Lipsitch M. Reconstructing influenza incidence by deconvolution of daily mortality time series. Proc Natl Acad Sci U S A. 2009 Dec 22; 106(51):21825-9. PMID: 20080801.
• Presanis AM, De Angelis D, Hagy A, Reed C, Riley S, Cooper BS, Finelli L, Biedrzycki P, Lipsitch M. The severity of pandemic H1N1 influenza in the United States, from April to July 2009: a Bayesian analysis. PLoS Med. 2009 Dec; 6(12):e1000207. PMID: 19997612.
• Reed C, Angulo FJ, Swerdlow DL, Lipsitch M, Meltzer MI, Jernigan D, Finelli L. Estimates of the prevalence of pandemic (H1N1) 2009, United States, April-July 2009. Emerg Infect Dis. 2009 Dec; 15(12):2004-7. PMID: 19961687; PMCID: PMC3375879.
• Colijn C, Cohen T, Fraser C, Hanage W, Goldstein E, Givon-Lavi N, Dagan R, Lipsitch M. What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae? J R Soc Interface. 2010 Jun 06; 7(47):905-19. PMID: 19940002.
• Goldstein E, Lipsitch M. H1N1 vaccination and adults with underlying health conditions in the US. PLoS Curr. 2009 Nov 23; 1:RRN1132. PMID: 20029669.
• Bogaert D, Thompson CM, Trzcinski K, Malley R, Lipsitch M. The role of complement in innate and adaptive immunity to pneumococcal colonization and sepsis in a murine model. Vaccine. 2010 Jan 08; 28(3):681-5. PMID: 19892042.
• White LF, Wallinga J, Finelli L, Reed C, Riley S, Lipsitch M, Pagano M. Estimation of the reproductive number and the serial interval in early phase of the 2009 influenza A/H1N1 pandemic in the USA. Influenza Other Respir Viruses. 2009 Nov; 3(6):267-76. PMID: 19903209.
• Goldstein E, Lipsitch M. Antiviral usage for H1N1 treatment: pros, cons and an argument for broader prescribing guidelines in the United States. PLoS Curr. 2009 Oct 29; 1:RRN1122. PMID: 20029660.
• Goldstein E, Apolloni A, Lewis B, Miller JC, Macauley M, Eubank S, Lipsitch M, Wallinga J. Distribution of vaccine/antivirals and the ‘least spread line’ in a stratified population. J R Soc Interface. 2010 May 06; 7(46):755-64. PMID: 19828505.
• Presanis AM, Lipsitch M, Hagy A, Reed C, Riley S, Cooper B. The severity of pandemic H1N1 influenza in the United States, April — July 2009. PLoS Curr. 2009 Sep 25; 1:RRN1042. PMID: 20029614; PMCID: PMC2762775.1.
• 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. Use of cumulative incidence of novel influenza A/H1N1 in foreign travelers to estimate lower bounds on cumulative incidence in Mexico. PLoS One. 2009 Sep 09; 4(9):e6895. PMID: 19742302.
• Goldstein E, Miller JC, O’Hagan J, Lipsitch M. Conditions Under Which Predispensing of Antiviral Drugs to Individuals at High Risk of Death from Pandemic Influenza Is Expected to Save Lives: Predispensing of Antiviral Drugs to Individuals at High Risk of Severe Outcomes of H1N1 Influenza. PLoS Curr. 2009 Aug 21; 1:RRN1007. PMID: 20029604.
• Lipsitch M, Hayden FG, Cowling BJ, Leung GM. How to maintain surveillance for novel influenza A H1N1 when there are too many cases to count. Lancet. 2009 Oct 03; 374(9696):1209-11. PMID: 19679345.
• McCaw JM, Wood JG, McBryde ES, Nolan TM, Wu JT, Lipsitch M, McVernon J. Understanding Australia’s influenza pandemic policy on the strategic use of the antiviral drug stockpile. Med J Aust. 2009 Aug 03; 191(3):136-7. PMID: 19645639.
• Lee GM, Huang SS, Rifas-Shiman SL, Hinrichsen VL, Pelton SI, Kleinman K, Hanage WP, Lipsitch M, McAdam AJ, Finkelstein JA. Epidemiology and risk factors for Staphylococcus aureus colonization in children in the post-PCV7 era. BMC Infect Dis. 2009 Jul 11; 9:110. PMID: 19594890.
• Huang SS, Hinrichsen VL, Stevenson AE, Rifas-Shiman SL, Kleinman K, Pelton SI, Lipsitch M, Hanage WP, Lee GM, Finkelstein JA. Continued impact of pneumococcal conjugate vaccine on carriage in young children. Pediatrics. 2009 Jul; 124(1):e1-11. PMID: 19564254; PMCID: PMC2782668.
• Goldstein E, Paur K, Fraser C, Kenah E, Wallinga J, Lipsitch M. Reproductive numbers, epidemic spread and control in a community of households. Math Biosci. 2009 Sep; 221(1):11-25. PMID: 19559715.
• Pitzer VE, Lipsitch M. Exploring the relationship between incidence and the average age of infection during seasonal epidemics. J Theor Biol. 2009 Sep 21; 260(2):175-85. PMID: 19527734.
• Weinberger DM, Trzcinski K, Lu YJ, Bogaert D, Brandes A, Galagan J, Anderson PW, Malley R, Lipsitch M. Pneumococcal capsular polysaccharide structure predicts serotype prevalence. PLoS Pathog. 2009 Jun; 5(6):e1000476. PMID: 19521509.
• Lipsitch M, Riley S, Cauchemez S, Ghani AC, Ferguson NM. Managing and reducing uncertainty in an emerging influenza pandemic. N Engl J Med. 2009 Jul 09; 361(2):112-5. PMID: 19474417; PMCID: PMC3066026.
• Wu JT, Leung GM, Lipsitch M, Cooper BS, Riley S. Hedging against antiviral resistance during the next influenza pandemic using small stockpiles of an alternative chemotherapy. PLoS Med. 2009 May 19; 6(5):e1000085. PMID: 19440354.
• Regev-Yochay G, Lipsitch M, Basset A, Rubinstein E, Dagan R, Raz M, Malley R. The pneumococcal pilus predicts the absence of Staphylococcus aureus co-colonization in pneumococcal carriers. Clin Infect Dis. 2009 Mar 15; 48(6):760-3. PMID: 19207082.
• Lipsitch M, Viboud C. Influenza seasonality: lifting the fog. Proc Natl Acad Sci U S A. 2009 Mar 10; 106(10):3645-6. PMID: 19276125.
• Klugman KP, Astley CM, Lipsitch M. Time from illness onset to death, 1918 influenza and pneumococcal pneumonia. Emerg Infect Dis. 2009 Feb; 15(2):346-7. PMID: 19193293.
• Bogaert D, Weinberger D, Thompson C, Lipsitch M, Malley R. Impaired innate and adaptive immunity to Streptococcus pneumoniae and its effect on colonization in an infant mouse model. Infect Immun. 2009 Apr; 77(4):1613-22. PMID: 19168741.
• Lipsitch M, Colijn C, Cohen T, Hanage WP, Fraser C. No coexistence for free: neutral null models for multistrain pathogens. Epidemics. 2009 Mar; 1(1):2-13. PMID: 21352747.
• Lu YJ, Gross J, Bogaert D, Finn A, Bagrade L, Zhang Q, Kolls JK, Srivastava A, Lundgren A, Forte S, Thompson CM, Harney KF, Anderson PW, Lipsitch M, Malley R. Interleukin-17A mediates acquired immunity to pneumococcal colonization. PLoS Pathog. 2008 Sep 19; 4(9):e1000159. PMID: 18802458; PMCID: PMC2528945.
• Regev-Yochay G, Bogaert D, Malley R, Hermans PW, Veenhoven RH, Sanders EA, Lipsitch M, Rubinstein E. Does pneumococcal conjugate vaccine influence Staphylococcus aureus carriage in children? Clin Infect Dis. 2008 Jul 15; 47(2):289-91; author reply 291-2. PMID: 18564933.
• Cohen T, Lipsitch M. Too little of a good thing: a paradox of moderate infection control. Epidemiology. 2008 Jul; 19(4):588-9. PMID: 18552592.
• Weinberger DM, Dagan R, Givon-Lavi N, Regev-Yochay G, Malley R, Lipsitch M. Epidemiologic evidence for serotype-specific acquired immunity to pneumococcal carriage. J Infect Dis. 2008 Jun 01; 197(11):1511-8. PMID: 18471062.
• Dagan R, Barkai G, Givon-Lavi N, Sharf AZ, Vardy D, Cohen T, Lipsitch M, Greenberg D. Seasonality of antibiotic-resistant streptococcus pneumoniae that causes acute otitis media: a clue for an antibiotic-restriction policy? J Infect Dis. 2008 Apr 15; 197(8):1094-102. PMID: 18419528; PMCID: PMC2652754.
• Trzcinski K, Thompson CM, Srivastava A, Basset A, Malley R, Lipsitch M. Protection against nasopharyngeal colonization by Streptococcus pneumoniae is mediated by antigen-specific CD4+ T cells. Infect Immun. 2008 Jun; 76(6):2678-84. PMID: 18391006.
• Kenah E, Lipsitch M, Robins JM. Generation interval contraction and epidemic data analysis. Math Biosci. 2008 May; 213(1):71-9. PMID: 18394654.
• Regev-Yochay G, Malley R, Rubinstein E, Raz M, Dagan R, Lipsitch M. In vitro bactericidal activity of Streptococcus pneumoniae and bactericidal susceptibility of Staphylococcus aureus strains isolated from cocolonized versus noncocolonized children. J Clin Microbiol. 2008 Feb; 46(2):747-9. PMID: 18039795.
• Lipsitch M, O’Hagan JJ. Patterns of antigenic diversity and the mechanisms that maintain them. J R Soc Interface. 2007 Oct 22; 4(16):787-802. PMID: 17426010.
• 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. Strain characteristics of Streptococcus pneumoniae carriage and invasive disease isolates during a cluster-randomized clinical trial of the 7-valent pneumococcal conjugate vaccine. J Infect Dis. 2007 Oct 15; 196(8):1221-7. PMID: 17955441; PMCID: PMC3350793.
• Basset A, Thompson CM, Hollingshead SK, Briles DE, Ades EW, Lipsitch M, Malley R. Antibody-independent, CD4+ T-cell-dependent protection against pneumococcal colonization elicited by intranasal immunization with purified pneumococcal proteins. Infect Immun. 2007 Nov; 75(11):5460-4. PMID: 17698570; PMCID: PMC2168310.
• Malley R, Lipsitch M, Bogaert D, Thompson CM, Hermans P, Watkins AC, Sethi S, Murphy TF. Serum antipneumococcal antibodies and pneumococcal colonization in adults with chronic obstructive pulmonary disease. J Infect Dis. 2007 Sep 15; 196(6):928-35. PMID: 17703425.
• Regev-Yochay G, Trzcinski K, Thompson CM, Lipsitch M, Malley R. SpxB is a suicide gene of Streptococcus pneumoniae and confers a selective advantage in an in vivo competitive colonization model. J Bacteriol. 2007 Sep; 189(18):6532-9. PMID: 17631628; PMCID: PMC2045178.
• Pitzer VE, Olsen SJ, Bergstrom CT, Dowell SF, Lipsitch M. Little evidence for genetic susceptibility to influenza A (H5N1) from family clustering data. Emerg Infect Dis. 2007 Jul; 13(7):1074-6. PMID: 18214184.
• Pitzer VE, Leung GM, Lipsitch M. Estimating variability in the transmission of severe acute respiratory syndrome to household contacts in Hong Kong, China. Am J Epidemiol. 2007 Aug 01; 166(3):355-63. PMID: 17493952; PMCID: PMC7110150.
• Hatchett RJ, Mecher CE, Lipsitch M. Public health interventions and epidemic intensity during the 1918 influenza pandemic. Proc Natl Acad Sci U S A. 2007 May 01; 104(18):7582-7. PMID: 17416679; PMCID: PMC1849867.
• Basset A, Trzcinski K, Hermos C, O’Brien KL, Reid R, Santosham M, McAdam AJ, Lipsitch M, Malley R. Association of the pneumococcal pilus with certain capsular serotypes but not with increased virulence. J Clin Microbiol. 2007 Jun; 45(6):1684-9. PMID: 17392439; PMCID: PMC1933072.
• McCormick AW, Walensky RP, Lipsitch M, Losina E, Hsu H, Weinstein MC, Paltiel AD, Freedberg KA, Seage GR. The effect of antiretroviral therapy on secondary transmission of HIV among men who have sex with men. Clin Infect Dis. 2007 Apr 15; 44(8):1115-22. PMID: 17366461; PMCID: PMC2365722.
• Wallinga J, Lipsitch M. How generation intervals shape the relationship between growth rates and reproductive numbers. Proc Biol Sci. 2007 Feb 22; 274(1609):599-604. PMID: 17476782; PMCID: PMC1766383.
• Högberg L, Geli P, Ringberg H, Melander E, Lipsitch M, Ekdahl K. Age- and serogroup-related differences in observed durations of nasopharyngeal carriage of penicillin-resistant pneumococci. J Clin Microbiol. 2007 Mar; 45(3):948-52. PMID: 17202280; PMCID: PMC1829115.
• Lipsitch M, Cohen T, Murray M, Levin BR. Antiviral resistance and the control of pandemic influenza. PLoS Med. 2007 Jan; 4(1):e15. PMID: 17253900; PMCID: PMC1779817.
• Hanage WP, Huang SS, Lipsitch M, Bishop CJ, Godoy D, Pelton SI, Goldstein R, Huot H, Finkelstein JA. Diversity and antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae carriage isolates in the post-heptavalent conjugate vaccine era. J Infect Dis. 2007 Feb 01; 195(3):347-52. PMID: 17205472.
• Regev-Yochay G, Trzcinski K, Thompson CM, Malley R, Lipsitch M. Interference between Streptococcus pneumoniae and Staphylococcus aureus: In vitro hydrogen peroxide-mediated killing by Streptococcus pneumoniae. J Bacteriol. 2006 Jul; 188(13):4996-5001. PMID: 16788209; PMCID: PMC1482988.
• Wang YC, Lipsitch M. Upgrading antibiotic use within a class: tradeoff between resistance and treatment success. Proc Natl Acad Sci U S A. 2006 Jun 20; 103(25):9655-60. PMID: 16772381; PMCID: PMC1480462.
• Mills CE, Robins JM, Bergstrom CT, Lipsitch M. Pandemic influenza: risk of multiple introductions and the need to prepare for them. PLoS Med. 2006 Jun; 3(6):e135. PMID: 17214503; PMCID: PMC1370924.
• Lipsitch M, Robins JM, Mills CE, Bergstrom CT. Multiple outbreaks and flu containment plans. Science. 2006 May 12; 312(5775):845. PMID: 16690840.
• Cohen T, Lipsitch M, Walensky RP, Murray M. Beneficial and perverse effects of isoniazid preventive therapy for latent tuberculosis infection in HIV-tuberculosis coinfected populations. Proc Natl Acad Sci U S A. 2006 May 02; 103(18):7042-7. PMID: 16632605.
• Malley R, Srivastava A, Lipsitch M, Thompson CM, Watkins C, Tzianabos A, Anderson PW. Antibody-independent, interleukin-17A-mediated, cross-serotype immunity to pneumococci in mice immunized intranasally with the cell wall polysaccharide. Infect Immun. 2006 Apr; 74(4):2187-95. PMID: 16552049; PMCID: PMC1418935.
• Trzcinski K, Thompson CM, Gilbey AM, Dowson CG, Lipsitch M. Incremental increase in fitness cost with increased beta -lactam resistance in pneumococci evaluated by competition in an infant rat nasal colonization model. J Infect Dis. 2006 May 01; 193(9):1296-303. PMID: 16586368.
• Asquith B, Edwards CT, Lipsitch M, McLean AR. Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo. PLoS Biol. 2006 Apr; 4(4):e90. PMID: 16515366; PMCID: PMC1395353.
• Palmer ME, Lipsitch M. The influence of hitchhiking and deleterious mutation upon asexual mutation rates. Genetics. 2006 May; 173(1):461-72. PMID: 16489233; PMCID: PMC1461451.
• Samore MH, Lipsitch M, Alder SC, Haddadin B, Stoddard G, Williamson J, Sebastian K, Carroll K, Ergonul O, Carmeli Y, Sande MA. Mechanisms by which antibiotics promote dissemination of resistant pneumococci in human populations. Am J Epidemiol. 2006 Jan 15; 163(2):160-70. PMID: 16319292.
• Trzcinski K, Thompson C, Malley R, Lipsitch M. Antibodies to conserved pneumococcal antigens correlate with, but are not required for, protection against pneumococcal colonization induced by prior exposure in a mouse model. Infect Immun. 2005 Oct; 73(10):7043-6. PMID: 16177389; PMCID: PMC1230924.
• Dagan R, Givon-Lavi N, Fraser D, Lipsitch M, Siber GR, Kohberger R. Serum serotype-specific pneumococcal anticapsular immunoglobulin g concentrations after immunization with a 9-valent conjugate pneumococcal vaccine correlate with nasopharyngeal acquisition of pneumococcus. J Infect Dis. 2005 Aug 01; 192(3):367-76. PMID: 15995949.
• Lipsitch M. Pandemic flu: we are not prepared. MedGenMed. 2005 Apr 15; 7(2):56. PMID: 16369434.
• Trzcinski K, MacNeil A, Klugman KP, Lipsitch M. Capsule homology does not increase the frequency of transformation of linked penicillin binding proteins PBP 1a and PBP 2x in Streptococcus pneumoniae. Antimicrob Agents Chemother. 2005 Apr; 49(4):1591-2. PMID: 15793147; PMCID: PMC1068637.
• Huang SS, Finkelstein JA, Lipsitch M. Modeling community- and individual-level effects of child-care center attendance on pneumococcal carriage. Clin Infect Dis. 2005 May 01; 40(9):1215-22. PMID: 15825020.
• Malley R, Trzcinski K, Srivastava A, Thompson CM, Anderson PW, Lipsitch M. CD4+ T cells mediate antibody-independent acquired immunity to pneumococcal colonization. Proc Natl Acad Sci U S A. 2005 Mar 29; 102(13):4848-53. PMID: 15781870; PMCID: PMC555733.
• Lipsitch M, Whitney CG, Zell E, Kaijalainen T, Dagan R, Malley R. Are anticapsular antibodies the primary mechanism of protection against invasive pneumococcal disease? PLoS Med. 2005 Jan; 2(1):e15. PMID: 15696204; PMCID: PMC545206.
• Lipsitch M. Ethics of rationing the flu vaccine. Science. 2005 Jan 07; 307(5706):41. PMID: 15637252.
• Mills CE, Robins JM, Lipsitch M. Transmissibility of 1918 pandemic influenza. Nature. 2004 Dec 16; 432(7019):904-6. PMID: 15602562; PMCID: PMC7095078.
• Teklehaimanot HD, Schwartz J, Teklehaimanot A, Lipsitch M. 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. Malar J. 2004 Nov 19; 3:44. PMID: 15555061; PMCID: PMC535541.
• Teklehaimanot HD, Lipsitch M, Teklehaimanot A, Schwartz J. Weather-based prediction of Plasmodium falciparum malaria in epidemic-prone regions of Ethiopia I. Patterns of lagged weather effects reflect biological mechanisms. Malar J. 2004 Nov 12; 3:41. PMID: 15541174; PMCID: PMC535540.
• Lipsitch M, Bergstrom CT. Invited commentary: real-time tracking of control measures for emerging infections. Am J Epidemiol. 2004 Sep 15; 160(6):517-9; discussion 520. PMID: 15353410.
• Bergstrom CT, Lo M, Lipsitch M. Ecological theory suggests that antimicrobial cycling will not reduce antimicrobial resistance in hospitals. Proc Natl Acad Sci U S A. 2004 Sep 07; 101(36):13285-90. PMID: 15308772; PMCID: PMC516561.
• Teklehaimanot HD, Schwatrz J, Teklehaimanot A, Lipsitch M. Alert threshold algorithms and malaria epidemic detection. Emerg Infect Dis. 2004 Jul; 10(7):1220-6. PMID: 15324541; PMCID: PMC3323320.
• Trzcinski K, Thompson CM, Lipsitch M. Single-step capsular transformation and acquisition of penicillin resistance in Streptococcus pneumoniae. J Bacteriol. 2004 Jun; 186(11):3447-52. PMID: 15150231; PMCID: PMC415782.
• Laine C, Mwangi T, Thompson CM, Obiero J, Lipsitch M, Scott JA. Age-specific immunoglobulin g (IgG) and IgA to pneumococcal protein antigens in a population in coastal kenya. Infect Immun. 2004 Jun; 72(6):3331-5. PMID: 15155637; PMCID: PMC415695.
• Perencevich EN, Fisman DN, Lipsitch M, Harris AD, Morris JG, Smith DL. Projected benefits of active surveillance for vancomycin-resistant enterococci in intensive care units. Clin Infect Dis. 2004 Apr 15; 38(8):1108-15. PMID: 15095215.
• Cooper B, Lipsitch M. The analysis of hospital infection data using hidden Markov models. Biostatistics. 2004 Apr; 5(2):223-37. PMID: 15054027.
• Trzcinski K, Thompson CM, Lipsitch M. Construction of otherwise isogenic serotype 6B, 7F, 14, and 19F capsular variants of Streptococcus pneumoniae strain TIGR4. Appl Environ Microbiol. 2003 Dec; 69(12):7364-70. PMID: 14660386.
• Lipsitch M, Cohen T, Cooper B, Robins JM, Ma S, James L, Gopalakrishna G, Chew SK, Tan CC, Samore MH, Fisman D, Murray M. Transmission dynamics and control of severe acute respiratory syndrome. Science. 2003 Jun 20; 300(5627):1966-70. PMID: 12766207.
• McCormick AW, Whitney CG, Farley MM, Lynfield R, Harrison LH, Bennett NM, Schaffner W, Reingold A, Hadler J, Cieslak P, Samore MH, Lipsitch M. Geographic diversity and temporal trends of antimicrobial resistance in Streptococcus pneumoniae in the United States. Nat Med. 2003 Apr; 9(4):424-30. PMID: 12627227.
• Lipsitch M, Murray MB. Multiple equilibria: tuberculosis transmission require unrealistic assumptions. Theor Popul Biol. 2003 Mar; 63(2):169-70. PMID: 12615499.
• Malley R, Henneke P, Morse SC, Cieslewicz MJ, Lipsitch M, Thompson CM, Kurt-Jones E, Paton JC, Wessels MR, Golenbock DT. Recognition of pneumolysin by Toll-like receptor 4 confers resistance to pneumococcal infection. Proc Natl Acad Sci U S A. 2003 Feb 18; 100(4):1966-71. PMID: 12569171; PMCID: PMC149942.
• Lipsitch M, Bergstrom CT, Antia R. Effect of human leukocyte antigen heterozygosity on infectious disease outcome: the need for allele-specific measures. BMC Med Genet. 2003 Jan 24; 4:2. PMID: 12542841; PMCID: PMC149356.
• Singer RS, Finch R, Wegener HC, Bywater R, Walters J, Lipsitch M. Antibiotic resistance–the interplay between antibiotic use in animals and human beings. Lancet Infect Dis. 2003 Jan; 3(1):47-51. PMID: 12505035.
• Fisman DN, Lipsitch M, Hook EW, Goldie SJ. Projection of the future dimensions and costs of the genital herpes simplex type 2 epidemic in the United States. Sex Transm Dis. 2002 Oct; 29(10):608-22. PMID: 12370529.
• Lipsitch M, Sousa AO. Historical intensity of natural selection for resistance to tuberculosis. Genetics. 2002 Aug; 161(4):1599-607. PMID: 12196403.
• Lipsitch M, Davis G, Corey L. Potential benefits of a serodiagnostic test for herpes simplex virus type 1 (HSV-1) to prevent neonatal HSV-1 infection. Sex Transm Dis. 2002 Jul; 29(7):399-405. PMID: 12170129.
• Harris AD, Samore MH, Lipsitch M, Kaye KS, Perencevich E, Carmeli Y. Control-group selection importance in studies of antimicrobial resistance: examples applied to Pseudomonas aeruginosa, Enterococci, and Escherichia coli. Clin Infect Dis. 2002 Jun 15; 34(12):1558-63. PMID: 12032889.
• Lipsitch M, Singer RS, Levin BR. Antibiotics in agriculture: when is it time to close the barn door? Proc Natl Acad Sci U S A. 2002 Apr 30; 99(9):5752-4. PMID: 11983874; PMCID: PMC122845.
• Lipsitch M, Samore MH. Antimicrobial use and antimicrobial resistance: a population perspective. Emerg Infect Dis. 2002 Apr; 8(4):347-54. PMID: 11971765; PMCID: PMC2730242.
• Bonten MJ, Austin DJ, Lipsitch M. Understanding the spread of antibiotic resistant pathogens in hospitals: mathematical models as tools for control. Clin Infect Dis. 2001 Nov 15; 33(10):1739-46. PMID: 11595995.
• Lipsitch M. The rise and fall of antimicrobial resistance. Trends Microbiol. 2001 Sep; 9(9):438-44. PMID: 11553456.
• Malley R, Lipsitch M, Stack A, Saladino R, Fleisher G, Pelton S, Thompson C, Briles D, Anderson P. Intranasal immunization with killed unencapsulated whole cells prevents colonization and invasive disease by capsulated pneumococci. Infect Immun. 2001 Aug; 69(8):4870-3. PMID: 11447162; PMCID: PMC98576.
• Lipsitch M. Interpreting results from trials of pneumococcal conjugate vaccines: a statistical test for detecting vaccine-induced increases in carriage of nonvaccine serotypes. Am J Epidemiol. 2001 Jul 01; 154(1):85-92. PMID: 11427408.
• Francis KP, Yu J, Bellinger-Kawahara C, Joh D, Hawkinson MJ, Xiao G, Purchio TF, Caparon MG, Lipsitch M, Contag PR. Visualizing pneumococcal infections in the lungs of live mice using bioluminescent Streptococcus pneumoniae transformed with a novel gram-positive lux transposon. Infect Immun. 2001 May; 69(5):3350-8. PMID: 11292758; PMCID: PMC98294.
• Lipsitch M. Microbiology. Bacterial population genetics and disease. Science. 2001 Apr 06; 292(5514):59-60. PMID: 11294216.
• Lipsitch M. Measuring and interpreting associations between antibiotic use and penicillin resistance in Streptococcus pneumoniae. Clin Infect Dis. 2001 Apr 01; 32(7):1044-54. PMID: 11264033.
• Ebert D, Lipsitch M, Mangin KL. The Effect of Parasites on Host Population Density and Extinction: Experimental Epidemiology with Daphnia and Six Microparasites. Am Nat. 2000 Nov; 156(5):459-477. PMID: 29587512.
• Lipsitch M, Bacon TH, Leary JJ, Antia R, Levin BR. Effects of antiviral usage on transmission dynamics of herpes simplex virus type 1 and on antiviral resistance: predictions of mathematical models. Antimicrob Agents Chemother. 2000 Oct; 44(10):2824-35. PMID: 10991866.
• Negri MC, Lipsitch M, Blázquez J, Levin BR, Baquero F. Concentration-dependent selection of small phenotypic differences in TEM beta-lactamase-mediated antibiotic resistance. Antimicrob Agents Chemother. 2000 Sep; 44(9):2485-91. PMID: 10952599.
• Bergstrom CT, Lipsitch M, Levin BR. Natural selection, infectious transfer and the existence conditions for bacterial plasmids. Genetics. 2000 Aug; 155(4):1505-19. PMID: 10924453; PMCID: PMC1461221.
• Lipsitch M, Dykes JK, Johnson SE, Ades EW, King J, Briles DE, Carlone GM. Competition among Streptococcus pneumoniae for intranasal colonization in a mouse model. Vaccine. 2000 Jun 15; 18(25):2895-901. PMID: 10812233.
• Lipsitch M, Bergstrom CT, Levin BR. The epidemiology of antibiotic resistance in hospitals: paradoxes and prescriptions. Proc Natl Acad Sci U S A. 2000 Feb 15; 97(4):1938-43. PMID: 10677558; PMCID: PMC26540.
• Lipsitch M. Bacterial vaccines and serotype replacement: lessons from Haemophilus influenzae and prospects for Streptococcus pneumoniae. Emerg Infect Dis. 1999 May-Jun; 5(3):336-45. PMID: 10341170; PMCID: PMC2640786.
• Levin BR, Lipsitch M, Bonhoeffer S. Population biology, evolution, and infectious disease: convergence and synthesis. Science. 1999 Feb 05; 283(5403):806-9. PMID: 9933155.
• Stewart FM, Antia R, Levin BR, Lipsitch M, Mittler JE. The population genetics of antibiotic resistance. II: Analytic theory for sustained populations of bacteria in a community of hosts. Theor Popul Biol. 1998 Apr; 53(2):152-65. PMID: 9615474.
• Lipsitch M, Levin BR. Population dynamics of tuberculosis treatment: mathematical models of the roles of non-compliance and bacterial heterogeneity in the evolution of drug resistance. Int J Tuberc Lung Dis. 1998 Mar; 2(3):187-99. PMID: 9526190.
• Levin BR, Antia R, Berliner E, Bloland P, Bonhoeffer S, Cohen M, DeRouin T, Fields PI, Jafari H, Jernigan D, Lipsitch M, McGowan JE, Mead P, Nowak M, Porco T, Sykora P, Simonsen L, Spitznagel J, Tauxe R, Tenover F. Resistance to antimicrobial chemotherapy: a prescription for research and action. Am J Med Sci. 1998 Feb; 315(2):87-94. PMID: 9472907.
• Bonhoeffer S, Lipsitch M, Levin BR. Evaluating treatment protocols to prevent antibiotic resistance. Proc Natl Acad Sci U S A. 1997 Oct 28; 94(22):12106-11. PMID: 9342370; PMCID: PMC23718.
• Datta A, Hendrix M, Lipsitch M, Jinks-Robertson S. Dual roles for DNA sequence identity and the mismatch repair system in the regulation of mitotic crossing-over in yeast. Proc Natl Acad Sci U S A. 1997 Sep 02; 94(18):9757-62. PMID: 9275197; PMCID: PMC23263.
• Lipsitch M. Evolution in health and disease. Trends Microbiol. 1997 Aug; 5(8):303-5. PMID: 9263405.
• Lipsitch M. Vaccination against colonizing bacteria with multiple serotypes. Proc Natl Acad Sci U S A. 1997 Jun 10; 94(12):6571-6. PMID: 9177259; PMCID: PMC21091.
• Lipsitch M, Levin BR. The population dynamics of antimicrobial chemotherapy. Antimicrob Agents Chemother. 1997 Feb; 41(2):363-73. PMID: 9021193; PMCID: PMC163715.
• Lipsitch M. TRANSMISSION RATES AND HIV VIRULENCE: COMMENTS TO MASSAD. Evolution. 1997 Feb; 51(1):319-320. PMID: 28568797.
• Lipsitch M, Moxon ER. Virulence and transmissibility of pathogens: what is the relationship? Trends Microbiol. 1997 Jan; 5(1):31-7. PMID: 9025233.
• Lipsitch M, Levin BR. The within-host population dynamics of antibacterial chemotherapy: conditions for the
• Levin BR, Lipsitch M, Perrot V, Schrag S, Antia R, Simonsen L, Walker NM, Stewart FM. The population genetics of antibiotic resistance. Clin Infect Dis. 1997 Jan; 24 Suppl 1:S9-16. PMID: 8994776.
• Antia R, Lipsitch M. Mathematical models of parasite responses to host immune defences. Parasitology. 1997; 115 Suppl:S155-67. PMID: 9571700.
• Lipsitch M, Siller S, Nowak MA. THE EVOLUTION OF VIRULENCE IN PATHOGENS WITH VERTICAL AND HORIZONTAL TRANSMISSION. Evolution. 1996 Oct; 50(5):1729-1741. PMID: 28565576.
• Lipsitch M, Herre EA, Nowak MA. HOST POPULATION STRUCTURE AND THE EVOLUTION OF VIRULENCE: A “LAW OF DIMINISHING RETURNS”. Evolution. 1995 Aug; 49(4):743-748. PMID: 28565133.
• Lipsitch M, Nowak MA, Ebert D, May RM. The population dynamics of vertically and horizontally transmitted parasites. Proc Biol Sci. 1995 Jun 22; 260(1359):321-7. PMID: 7630898.
• Lipsitch M, Nowak MA. The evolution of virulence in sexually transmitted HIV/AIDS. J Theor Biol. 1995 Jun 21; 174(4):427-40. PMID: 7666673.