List of works by Marc Lipsitch

A missing dimension in measures of vaccination impacts

scientific article

A modified Janus cassette (Sweet Janus) to improve allelic replacement efficiency by high-stringency negative selection in Streptococcus pneumoniae

scientific article

A new approach to the analysis of antibiotic resistance data from hospitals

scientific article

Absolute Humidity and the Seasonal Onset of Influenza in the Continental US.

scientific article

Absolute humidity and pandemic versus epidemic influenza

scientific article

Absolute humidity and the seasonal onset of influenza in the continental United States

scientific article

Addendum: Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China

scientific article published on 21 May 2020

Age- and serogroup-related differences in observed durations of nasopharyngeal carriage of penicillin-resistant pneumococci

scientific article published on 3 January 2007

Age- and sex-related risk factors for influenza-associated mortality in the United States between 1997-2007.

scientific article

Age-specific immunoglobulin g (IgG) and IgA to pneumococcal protein antigens in a population in coastal kenya

scientific article

Aggregated mobility data could help fight COVID-19

scientific article published on 23 March 2020

Alert threshold algorithms and malaria epidemic detection

scientific article published in July 2004

Analysis of a meningococcal meningitis outbreak in Niger - potential effectiveness of reactive prophylaxis

scientific article published on 11 March 2019

Analysis of multiple bacterial species and antibiotic classes reveals large variation in the association between seasonal antibiotic use and resistance

scientific article published in 2022

Analyzing Vaccine Trials in Epidemics with Mild and Asymptomatic Infection

scientific article published on 01 February 2019

Analyzing Vaccine Trials in Epidemics with Mild and Asymptomatic Infection

scientific article published on 07 April 2018

Antibiotic Consumption and Antibiotic Resistance Across Organisms, Drugs, and Consumer Groups

scientific article published on 4 October 2017

Antibiotic resistance--the interplay between antibiotic use in animals and human beings.

scientific article

Antibiotics in agriculture and the risk to human health: how worried should we be?

scientific article

Antibiotics in agriculture: when is it time to close the barn door?

scientific article

Antibodies to conserved pneumococcal antigens correlate with, but are not required for, protection against pneumococcal colonization induced by prior exposure in a mouse model

scientific article

Antibody testing will enhance the power and accuracy of COVID-19-prevention trials

scientific article published on 27 April 2020

Antibody-independent, CD4+ T-cell-dependent protection against pneumococcal colonization elicited by intranasal immunization with purified pneumococcal proteins

scientific article

Antibody-independent, interleukin-17A-mediated, cross-serotype immunity to pneumococci in mice immunized intranasally with the cell wall polysaccharide

scientific article

Antigenic Variation in Streptococcus pneumoniae PspC Promotes Immune Escape in the Presence of Variant-Specific Immunity.

scientific article published on 13 March 2018

Antimicrobial resistance prevalence, rates of hospitalization with septicemia and rates of mortality with sepsis in adults in different US states

scientific article published on 06 March 2019

Antimicrobial use and antimicrobial resistance: a population perspective

scientific article published on April 2002

Antiviral resistance and the control of pandemic influenza

scientific article

Antiviral usage for H1N1 treatment: pros, cons and an argument for broader prescribing guidelines in the United States.

scientific article

Apparent declining efficacy in randomized trials: examples of the Thai RV144 HIV vaccine and South African CAPRISA 004 microbicide trials

scientific article published in January 2012

Are anticapsular antibodies the primary mechanism of protection against invasive pneumococcal disease?

scientific article

Association of serotype with risk of death due to pneumococcal pneumonia: a meta-analysis

scientific article published on September 2010

Association of the pneumococcal pilus with certain capsular serotypes but not with increased virulence

scientific article published on 28 March 2007

Avian influenza: Ferret H7N9 flu model questioned.

scientific article published in September 2013

Azithromycin Susceptibility Among Neisseria gonorrhoeae Isolates and Seasonal Macrolide Use

scientific article published in 2019

Bacterial vaccines and serotype replacement: lessons from Haemophilus influenzae and prospects for Streptococcus pneumoniae

scientific article published on May 1999

Beneficial and perverse effects of isoniazid preventive therapy for latent tuberculosis infection in HIV-tuberculosis coinfected populations

scholarly article

Broad conditions favor the evolution of phase-variable loci.

scientific article published on 8 January 2013

CD4+ T cells mediate antibody-independent acquired immunity to pneumococcal colonization

scientific article

Calls for caution in genome engineering should be a model for similar dialogue on pandemic pathogen research.

scientific article

Can antibiotic resistance be reduced by vaccinating against respiratory disease?

scientific article published on 31 July 2018

Can limited scientific value of potential pandemic pathogen experiments justify the risks?

scientific article published on 14 October 2014

Can the Heterosexual HIV Epidemic be Eliminated in South Africa Using Combination Prevention? A Modeling Analysis

scientific article published on 13 July 2016

Capsule homology does not increase the frequency of transformation of linked penicillin binding proteins PBP 1a and PBP 2x in Streptococcus pneumoniae

scientific article published on April 2005

Carriage burden, multiple colonization and antibiotic pressure promote emergence of resistant vaccine escape pneumococci

scientific article published on June 2015

Carried pneumococci in Massachusetts children: the contribution of clonal expansion and serotype switching.

scientific article

Case-based surveillance of antimicrobial resistance with full susceptibility profiles

scientific article published on 10 December 2019

Challenges of Vaccine Effectiveness and Waning Studies

scientific article published on 01 May 2019

Changes in severity of 2009 pandemic A/H1N1 influenza in England: a Bayesian evidence synthesis

scientific article

Choices in vaccine trial design in epidemics of emerging infections

scientific article published on 07 August 2018

Cholera modeling: challenges to quantitative analysis and predicting the impact of interventions

scientific article

Clonal replacement among 19A Streptococcus pneumoniae in Massachusetts, prior to 13 valent conjugate vaccination.

scientific article published on 29 September 2011

Colonoscopy and Risk of Infective Endocarditis in the Elderly

scientific article

Comment on "Gain-of-Function Research and the Relevance to Clinical Practice".

scientific article

Comment on "Seroevidence for H5N1 Influenza Infections in Humans: Meta-Analysis"

scientific article published in Science

Comment on: 'Antibiotic footprint' as a communication tool to aid reduction of antibiotic consumption

scientific article published on 01 November 2019

Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen

scientific article

Competing Effects Of Indirect Protection And Clustering On The Power Of Cluster-Randomized Controlled Vaccine Trials.

scientific article

Competing effects of indirect protection and clustering on the power of cluster-randomized controlled vaccine trials

Competition among Streptococcus pneumoniae for intranasal colonization in a mouse model.

scientific article published in June 2000

Concentration-dependent selection of small phenotypic differences in TEM beta-lactamase-mediated antibiotic resistance

scientific article

Construction of otherwise isogenic serotype 6B, 7F, 14, and 19F capsular variants of Streptococcus pneumoniae strain TIGR4

scientific article

Continued impact of pneumococcal conjugate vaccine on carriage in young children.

scientific article published on July 2009

Control-group selection importance in studies of antimicrobial resistance: examples applied to Pseudomonas aeruginosa, Enterococci, and Escherichia coli.

scientific article published on 23 May 2002

Coronavirus: sampling now for future analysis

scientific article published on 01 April 2020

Correction: Absolute Humidity and the Seasonal Onset of Influenza in the Continental United States.

scientific article published on 15 March 2010

Correction: Absolute Humidity and the Seasonal Onset of Influenza in the Continental United States.

scientific article published on 18 March 2010

Cross-reactive memory T cells and herd immunity to SARS-CoV-2

scientific article published on 06 October 2020

Defining the Epidemiology of Covid-19 — Studies Needed

scholarly article by Marc Lipsitch published in 2020

Defusing a Biological Bomb

Depletion-of-susceptibles Bias in Analyses of Intra-season Waning of Influenza Vaccine Effectiveness

scientific article published on 01 March 2020

Depletion-of-susceptibles bias in influenza vaccine waning studies: how to ensure robust results

scientific article published on 27 November 2019

Development, calibration and performance of an HIV transmission model incorporating natural history and behavioral patterns: application in South Africa

scientific article

Displacement of sexual partnerships in trials of sexual behavior interventions: A model-based assessment of consequences

scientific article published on 2 April 2017

Distinct effects on diversifying selection by two mechanisms of immunity against Streptococcus pneumoniae.

scientific article

Distribution of vaccine/antivirals and the 'least spread line' in a stratified population

scientific article

Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening

scientific article published on 04 January 2017

Diversity and Antibiotic Resistance among Nonvaccine Serotypes ofStreptococcus pneumoniaeCarriage Isolates in the Post–Heptavalent Conjugate Vaccine Era

article

Does pneumococcal conjugate vaccine influence Staphylococcus aureus carriage in children?

scientific article published in July 2008

Dual roles for DNA sequence identity and the mismatch repair system in the regulation of mitotic crossing-over in yeast ⬇️

scientific article published on September 2, 1997

Ecological theory suggests that antimicrobial cycling will not reduce antimicrobial resistance in hospitals

scholarly article

Effect of Serotype on Pneumococcal Competition in a Mouse Colonization Model

scientific article

Effect of human leukocyte antigen heterozygosity on infectious disease outcome: the need for allele-specific measures

scientific article

Effects of antiviral usage on transmission dynamics of herpes simplex virus type 1 and on antiviral resistance: predictions of mathematical models

scientific article

Enhancing Situational Awareness to Prevent Infectious Disease Outbreaks from Becoming Catastrophic

scientific article published on 01 January 2019

Enhancing disease surveillance with novel data streams: challenges and opportunities

scientific article

Epidemiologic data and pathogen genome sequences: a powerful synergy for public health

scientific article

Epidemiologic evidence for serotype-specific acquired immunity to pneumococcal carriage

scientific article published in June 2008

Epidemiology and risk factors for Staphylococcus aureus colonization in children in the post-PCV7 era

scientific article

Epidemiology of Covid-19. Reply

scientific article published on 27 March 2020

Erratum for lipsitch and inglesby, moratorium on research intended to create novel potential pandemic pathogens

scientific article published on 10 February 2015

Estimated Demand for US Hospital Inpatient and Intensive Care Unit Beds for Patients With COVID-19 Based on Comparisons With Wuhan and Guangzhou, China

scientific article published on 01 May 2020

Estimates of the prevalence of pandemic (H1N1) 2009, United States, April-July 2009.

scientific article

Estimating case fatality rates of COVID-19

scientific article published on 31 March 2020

Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China

scientific article published on 19 March 2020

Estimating incidence curves of several infections using symptom surveillance data

scientific article

Estimating rates of carriage acquisition and clearance and competitive ability for pneumococcal serotypes in Kenya with a Markov transition model

scientific article published on July 2012

Estimating the Prevalence of COVID-19 in the United States: Three Complementary Approaches

scientific article published on 23 April 2020

Estimating the contribution of different age strata to vaccine serotype pneumococcal transmission in the pre vaccine era: a modelling study

scientific article published on 10 June 2020

Estimating the hospitalization burden associated with influenza and respiratory syncytial virus in New York City, 2003-2011.

scientific article

Estimating the number of undetected COVID-19 cases exported internationally from all of China

scientific article (preprint)

Estimating the per-exposure effect of infectious disease interventions

scientific article published on January 2014

Estimating the proportion of bystander selection for antibiotic resistance among potentially pathogenic bacterial flora

article

Estimating the proportion of bystander selection for antibiotic resistance among potentially pathogenic bacterial flora

scientific article published on 01 December 2018

Estimating variability in the transmission of severe acute respiratory syndrome to household contacts in Hong Kong, China

scientific article published on 10 May 2007

Estimation of the reproductive number and the serial interval in early phase of the 2009 influenza A/H1N1 pandemic in the USA.

scientific article

Ethical alternatives to experiments with novel potential pandemic pathogens.

scientific article

Ethics of rationing the flu vaccine.

scientific article published in January 2005

Evaluating treatment protocols to prevent antibiotic resistance

scientific article published on October 1997

Evaluation of Nowcasting for Real-Time COVID-19 Tracking - New York City, March-May 2020

scientific article published on 20 October 2020

Evolution in health and disease

scientific article published in August 1997

Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage

scientific article published on 17 January 2017

Evolution, safety, and highly pathogenic influenza viruses

scientific article

Examining the role of different age groups, and of vaccination during the 2012 Minnesota pertussis outbreak

scientific article

Exploring the relationship between incidence and the average age of infection during seasonal epidemics

scientific article

Exploring the role of competition induced by non-vaccine serotypes for herd protection following pneumococcal vaccination

scientific article published in November 2017

Factors related to increasing prevalence of resistance to ciprofloxacin and other antimicrobial drugs in Neisseria gonorrhoeae, United States

scientific article

Fractional Dosing of Yellow Fever Vaccine to Extend Supply: A Modeling Study

scholarly article published 14 May 2016

Fractional dosing of yellow fever vaccine to extend supply: a modelling study

scientific article published on 9 November 2016

Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae

scientific article published on 22 October 2020

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.

scientific article published on 16 October 2017

Gain-of-function experiments: time for a real debate

scientific article

Generation interval contraction and epidemic data analysis

scientific article

Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013

scientific article (publication date: 15 November 2016)

Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study

scientific article

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.

scientific article published on 6 February 2012

Geographic and temporal trends in antimicrobial nonsusceptibility in Streptococcus pneumoniae in the post-vaccine era in the United States

scientific article published on 12 July 2013

Geographic diversity and temporal trends of antimicrobial resistance in Streptococcus pneumoniae in the United States.

scientific article

Good science is good science: we need specialists, not sects

scientific article published on 20 June 2020

H1N1 vaccination and adults with underlying health conditions in the US.

scientific article

HOST POPULATION STRUCTURE AND THE EVOLUTION OF VIRULENCE: A "LAW OF DIMINISHING RETURNS"

scientific article published on 01 August 1995

Hedging against antiviral resistance during the next influenza pandemic using small stockpiles of an alternative chemotherapy

scientific article (publication date: 19 May 2009)

Herd immunity alters the conditions for performing dose schedule comparisons: an individual-based model of pneumococcal carriage

scholarly article by Alan Yang et al published 5 March 2019 in BMC Infectious Diseases

Historical intensity of natural selection for resistance to tuberculosis

scientific article

Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae

scientific article published on 20 May 2020

Hospitalizations Associated with Respiratory Syncytial Virus and Influenza in Children, Including Children Diagnosed with Asthma

scientific article published on 01 November 2019

Host Population Structure and the Evolution of Virulence: A "Law of Diminishing Returns"

Host population structure and treatment frequency maintain balancing selection on drug resistance

scientific article

How Can Vaccines Contribute to Solving the Antimicrobial Resistance Problem?

scientific article

How could preventive therapy affect the prevalence of drug resistance? Causes and consequences

scientific article published on June 2015

How generation intervals shape the relationship between growth rates and reproductive numbers.

scientific article published in February 2007

How to maintain surveillance for novel influenza A H1N1 when there are too many cases to count

scientific article published on 11 August 2009

Human challenge studies to accelerate coronavirus vaccine licensure

scientific article published on 31 March 2020

Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity.

scientific article published on 9 May 2015

Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions

scientific article published on 24 March 2020

Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus

scientific article published on 13 February 2016

If a Global Catastrophic Biological Risk Materializes, at What Stage Will We Recognize It?

scientific article published on 26 July 2017

Immunization, Antibiotic Use, and Pneumococcal Colonization Over a 15-Year Period

scientific article published on 4 October 2017

Impact of Antimicrobial Treatment for Acute Otitis Media on Carriage Dynamics of Penicillin-Susceptible and Penicillin-Nonsusceptible Streptococcus pneumoniae

scientific article published in 2018

Impact of Host Heterogeneity on the Efficacy of Interventions to Reduce Staphylococcus aureus Carriage

scientific article published on 24 November 2015

Impact of more than a decade of pneumococcal conjugate vaccine use on carriage and invasive potential in Native American communities ⬇️

scientific article published on 29 November 2011

Impact of stochastically generated heterogeneity in hazard rates on individually randomized vaccine efficacy trials

scientific article published in January 2018

Impaired innate and adaptive immunity to Streptococcus pneumoniae and its effect on colonization in an infant mouse model

scientific article published on 21 January 2009

Improving Control of Antibiotic-Resistant Gonorrhea by Integrating Research Agendas Across Disciplines: Key Questions Arising From Mathematical Modeling

scientific article published on 30 October 2015

Improving pandemic influenza risk assessment

scientific article

Improving the estimation of influenza-related mortality over a seasonal baseline

scientific article

Improving the evidence base for decision making during a pandemic: the example of 2009 influenza A/H1N1.

scientific article

Improving vaccine trials in infectious disease emergencies

scientific article published in July 2017

In Vitro selection of Neisseria gonorrhoeae mutants with elevated MIC values and increased resistance to cephalosporins

scientific article published on 8 September 2014

In vitro bactericidal activity of Streptococcus pneumoniae and bactericidal susceptibility of Staphylococcus aureus strains isolated from cocolonized versus noncocolonized children

scientific article

Incremental Increase in Fitness Cost with Increased β‐Lactam Resistance in Pneumococci Evaluated by Competition in an Infant Rat Nasal Colonization Model

article

Individual quarantine versus active monitoring of contacts for the mitigation of COVID-19: a modelling study

scientific article published on 20 May 2020

Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo

scientific article

Infectious Diseases Society of America and Gain-of-Function Experiments With Pathogens Having Pandemic Potential

scientific article

Infectious disease epidemiology

scholarly article published 15 April 2010

Infective endocarditis and cancer in the elderly

scientific article published on 18 December 2015

Inference of seasonal and pandemic influenza transmission dynamics.

scientific article

Influenza A Hemagglutinin Passage Bias Sites and Host Specificity Mutations

scientific article published on 22 August 2019

Influenza seasonality: lifting the fog

scholarly article

Interaction Patterns of Men Who Have Sex With Men on a Geosocial Networking Mobile App in Seven United States Metropolitan Areas: Observational Study

scientific article published on 12 September 2019

Interference between Streptococcus pneumoniae and Staphylococcus aureus: In vitro hydrogen peroxide-mediated killing by Streptococcus pneumoniae

scientific article

Interleukin-17A mediates acquired immunity to pneumococcal colonization

scientific article

Interpreting results from trials of pneumococcal conjugate vaccines: a statistical test for detecting vaccine-induced increases in carriage of nonvaccine serotypes

scientific article published in July 2001

Intranasal immunization with killed unencapsulated whole cells prevents colonization and invasive disease by capsulated pneumococci

scientific article

Investigate the origins of COVID-19

scientific article

Invited commentary: real-time tracking of control measures for emerging infections

scientific article published in September 2004

Is methicillin-resistant Staphylococcus aureus replacing methicillin-susceptible S. aureus?

scientific article

Levels of outpatient prescribing for four major antibiotic classes and rates of septicemia hospitalization in adults in different US states - a statistical analysis

scientific article published on 19 August 2019

Limited available evidence supports theoretical predictions of reduced vaccine efficacy at higher exposure dose

scientific article published on 01 March 2019

Little evidence for genetic susceptibility to influenza A (H5N1) from family clustering data

scientific article

Lockdown measures and relative changes in the age-specific incidence of SARS-CoV-2 in Spain

scientific article published on 02 July 2020

Lockdown measures and relative changes in the age-specific incidence of SARS-CoV-2 in Spain

scientific article published on 21 October 2020

Macrolide and Nonmacrolide Resistance with Mass Azithromycin Distribution

scientific article published on 01 November 2020

Managing and reducing uncertainty in an emerging influenza pandemic

scientific article

Mathematical modelling for antibiotic resistance control policy: do we know enough?

scientific article published on 29 November 2019

Mathematical models of parasite responses to host immune defences

scientific article published on January 1997

Measurement of Vaccine Direct Effects under the Test-Negative Design

scientific article published on 01 December 2018

Measuring and interpreting associations between antibiotic use and penicillin resistance in Streptococcus pneumoniae

scientific article

Mechanisms by which antibiotics promote dissemination of resistant pneumococci in human populations

scientific article published on 30 November 2005

Microbiology. Bacterial population genetics and disease

scientific article published on 01 April 2001

Microbiome as a tool and a target in the effort to address antimicrobial resistance

article published in the Proceedings of the National Academy of Sciences of the United States of America

Mobile messaging as surveillance tool during pandemic (H1N1) 2009, Mexico

scientific article published on September 2010

Model-informed COVID-19 vaccine prioritization strategies by age and serostatus

scientific article published on 07 December 2020

Modeling Community- and Individual-Level Effects of Child-Care Center Attendance on Pneumococcal Carriage

article

Modeling the Comparative Impact of Individual Quarantine vs. Active Monitoring of Contacts for the Mitigation of COVID-19

scientific article (preprint)

Modelling seasonal variations in the age and incidence of Kawasaki disease to explore possible infectious aetiologies.

scientific article published on 7 March 2012

Modelling the epidemiologic impact of achieving UNAIDS fast-track 90-90-90 and 95-95-95 targets in South Africa

scientific article published on 01 January 2019

Models of immune selection for multi-locus antigenic diversity of pathogens

scientific article published on 01 January 2019

Monitoring the fitness of antiviral-resistant influenza strains during an epidemic: a mathematical modelling study

scientific article

Moratorium on research intended to create novel potential pandemic pathogens

scientific article published on 12 December 2014

Multidrug-resistant Neisseria gonorrhoeae: implications for future treatment strategies

scientific article published on 01 June 2018

Multiple Outbreaks and Flu Containment Plans

scientific article published in Science

Multiple equilibria: tuberculosis transmission require unrealistic assumptions

scientific article published in March 2003

Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis

scientific article published on 09 June 2013

Natural selection, infectious transfer and the existence conditions for bacterial plasmids

scientific article

Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data

scientific article published on 31 March 2022

Negative controls: a tool for detecting confounding and bias in observational studies

scientific article published on May 2010

Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes

scientific article published in March 2012

No coexistence for free: neutral null models for multistrain pathogens

scientific article

Novel methods for the analysis of stepped wedge cluster randomized trials

scientific article published on 26 December 2019

Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking

scientific article published on 06 April 2020

Nuanced risk assessment for emerging infectious diseases

scientific article published on January 2014

Observational studies and the difficult quest for causality: lessons from vaccine effectiveness and impact studies

scientific article

On the Role of Different Age Groups and Pertussis Vaccines During the 2012 Outbreak in Wisconsin.

scientific article

On the evolutionary ecology of multidrug resistance in bacteria

scientific article published on 13 May 2019

On the relative role of different age groups during epidemics associated with respiratory syncytial virus

scientific article published on 3 November 2017

On the relative role of different age groups in influenza epidemics

scientific article

On the role of different age groups during pertussis epidemics in California, 2010 and 2014

scientific article published on 01 January 2019

Opinion: It's ethical to test promising coronavirus vaccines against less-promising ones

scientific article published on 22 July 2020

Opinion: Risk to study nonparticipants: A procedural approach

article published in the Proceedings of the National Academy of Sciences of the United States of America

Optimizing infectious disease interventions during an emerging epidemic

scientific article

Origin and proliferation of multiple-drug resistance in bacterial pathogens

scientific article

Oseltamivir and risk of lower respiratory tract complications in patients with flu symptoms: a meta-analysis of eleven randomized clinical trials

scientific article

Oseltamivir effect on antibiotic-treated lower respiratory tract complications in virologically positive randomized trial participants

scientific article

Oseltamivir for treatment and prevention of pandemic influenza A/H1N1 virus infection in households, Milwaukee, 2009.

scientific article

Pan-serotype reduction in progression of Streptococcus pneumoniae to otitis media after rollout of pneumococcal conjugate vaccines.

scientific article published on 29 July 2017

Pandemic flu: we are not prepared

scientific article published on 15 April 2005

Pandemic influenza: risk of multiple introductions and the need to prepare for them. ⬇️

scientific article

Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination

article

Pathogen diversity and hidden regimes of apparent competition

scientific article

Patient sharing and population genetic structure of methicillin-resistant Staphylococcus aureus

scientific article (publication date: 24 April 2012)

Patterns of antigenic diversity and the mechanisms that maintain them

scientific article published on October 2007

Pneumococcal capsular polysaccharide structure predicts serotype prevalence

scientific article

Pneumococcal carriage and antibiotic resistance in young children before 13-valent conjugate vaccine

scientific article published on March 2012

Pneumococcal sequence type replacement among American Indian children: A comparison of pre- and routine-PCV7 eras

scientific article published in March 2012

Population Biology, Evolution, and Infectious Disease: Convergence and Synthesis

scientific article published in Science

Population dynamics of tuberculosis treatment: mathematical models of the roles of non-compliance and bacterial heterogeneity in the evolution of drug resistance.

scientific article published in March 1998

Population effect of influenza vaccination under co-circulation of non-vaccine variants and the case for a bivalent A/H3N2 vaccine component

scientific article published on 21 February 2017

Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae

scientific article

Population genomics of pneumococcal carriage in Massachusetts children following PCV-13 introduction

Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13

scientific article published in 2019

Population genomics of post-vaccine changes in pneumococcal epidemiology.

scientific article published on 05 May 2013

Population impact of SARS-CoV-2 variants with enhanced transmissibility and/or partial immune escape

scientific article published on 19 November 2021

Postexposure Effects of Vaccines on Infectious Diseases

scientific article published on 04 November 2019

Potential Biases in Estimating Absolute and Relative Case-Fatality Risks during Outbreaks

scientific article

Potential benefits of a serodiagnostic test for herpes simplex virus type 1 (HSV-1) to prevent neonatal HSV-1 infection

scientific article published in July 2002

Potential biases arising from epidemic dynamics in observational seroprotection studies

scientific article published on 06 May 2020

Potential impact of outpatient stewardship interventions on antibiotic exposures of common bacterial pathogens

scientific article published on 05 February 2020

Practical considerations for measuring the effective reproductive number, Rt

scientific article published on 20 June 2020

Practical considerations for measuring the effective reproductive number, Rt

scientific article published on 10 December 2020

Pre-dispensing of antivirals to high-risk individuals in an influenza pandemic.

scientific article

Predicting the epidemic sizes of influenza A/H1N1, A/H3N2, and B: a statistical method

scientific article

Prediction of post-vaccine population structure of Streptococcus pneumoniae using accessory gene frequencies

article

Prediction of serotypes causing invasive pneumococcal disease in unvaccinated and vaccinated populations

scientific article

Predictors of indoor absolute humidity and estimated effects on influenza virus survival in grade schools

scientific article

Predispensing of antivirals to high-risk individuals in an influenza pandemic

scientific article

Preprints: An underutilized mechanism to accelerate outbreak science. ⬇️

scientific article

Projected benefits of active surveillance for vancomycin-resistant enterococci in intensive care units

scientific article published on 5 April 2004

Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period

scientific article (preprint)

Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period

scientific article published on 14 April 2020

Projection of the future dimensions and costs of the genital herpes simplex type 2 epidemic in the United States

scientific article published on October 2002

Proposed Changes to U.S. Policy on Potential Pandemic Pathogen Oversight and Implementation

scientific article published on 22 January 2020

Protection against nasopharyngeal colonization by Streptococcus pneumoniae is mediated by antigen-specific CD4+ T cells.

scientific article

Public health interventions and epidemic intensity during the 1918 influenza pandemic

scientific article

Quantifying bias of COVID-19 prevalence and severity estimates in Wuhan, China that depend on reported cases in international travelers

scientific article

Quantifying child mortality reductions related to measles vaccination

scientific article

Quantifying interhospital patient sharing as a mechanism for infectious disease spread

scientific article

Rates of acquisition and clearance of pneumococcal serotypes in the nasopharynges of children in Kilifi District, Kenya

scientific article

Re-emergence of the type 1 pilus among Streptococcus pneumoniae isolates in Massachusetts, USA.

scientific article

Real-time influenza forecasts during the 2012-2013 season

scientific article published on January 2013

Recognition of pneumolysin by Toll-like receptor 4 confers resistance to pneumococcal infection

scholarly article

Reconstructing influenza incidence by deconvolution of daily mortality time series

scholarly article

Regulating impact on bystanders in clinical trials: An unsettled frontier

scientific article published on 01 August 2019

Reopening Primary Schools during the Pandemic

scientific article published on 29 July 2020

Reply to "Studies on influenza virus transmission between ferrets: the public health risks revisited".

scientific article published on 23 January 2015

Reply to Allan-Blitz and Klausner

scientific article published on 21 December 2016

Reply to Cochrane Neuraminidase Inhibitors Review Team

scientific article published in December 2011

Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany

scientific article

Reply to Hasford and to Spinola et al

scientific article published on 26 August 2020

Reply to ‘Declining adherence as a more likely explanation than frailty of the apparent decline in efficacy in the CAPRISA 004 trial’

Reproductive numbers, epidemic spread and control in a community of households.

scientific article

Resistance diagnostics as a public health tool to combat antibiotic resistance: A model-based evaluation.

scientific article published on 16 May 2019

Resistance to antimicrobial chemotherapy: a prescription for research and action

scientific article published in February 1998

Response to Cioffi

scientific article published on 29 April 2020

Response to Dawson et al

scientific article published on 04 June 2020

Response to comment on 'The distribution of antibiotic use and its association with antibiotic resistance'

scientific article published on 03 May 2019

Rethinking biosafety in research on potential pandemic pathogens

scientific article

Searching for sharp drops in the incidence of pandemic A/H1N1 influenza by single year of age

scientific article

Seasonality of antibiotic-resistant streptococcus pneumoniae that causes acute otitis media: a clue for an antibiotic-restriction policy?

scientific article published on April 2008

Secular trends in Helicobacter pylori seroprevalence in adults in the United States: evidence for sustained race/ethnic disparities

scientific article published on 15 November 2011

Selective and genetic constraints on pneumococcal serotype switching

scientific article published on 31 March 2015

Sequence tag-based analysis of microbial population dynamics

scientific article

Serotype replacement in disease after pneumococcal vaccination

scientific article

Serotype specific invasive capacity and persistent reduction in invasive pneumococcal disease

scientific article published on 26 October 2010

Serotype-specific immune responses to pneumococcal conjugate vaccine among children are significantly correlated by individual: Analysis of randomized controlled trial data

scientific article published on 13 December 2017

Serum antipneumococcal antibodies and pneumococcal colonization in adults with chronic obstructive pulmonary disease.

scientific article published on 7 August 2007

Serum serotype-specific pneumococcal anticapsular immunoglobulin g concentrations after immunization with a 9-valent conjugate pneumococcal vaccine correlate with nasopharyngeal acquisition of pneumococcus

scientific article

Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data

scientific article published in November 2017

Shortcomings of vitamin D-based model simulations of seasonal influenza

scientific article (publication date: 2011)

Simulations for Designing and Interpreting Intervention Trials in Infectious Diseases

Simulations for designing and interpreting intervention trials in infectious diseases

scientific article published on 29 December 2017

Single-step capsular transformation and acquisition of penicillin resistance in Streptococcus pneumoniae

scientific article

Social distancing strategies for curbing the COVID-19 epidemic

scientific article (preprint)

SpxB is a suicide gene of Streptococcus pneumoniae and confers a selective advantage in an in vivo competitive colonization model

scientific article published on 13 July 2007

Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced

scientific article

Statistical Properties of Stepped Wedge Cluster-Randomized Trials in Infectious Disease Outbreaks

scientific article published on 06 May 2020

Statistical Properties of Stepped Wedge Cluster-Randomized Trials in Infectious Disease Outbreaks

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Strain characteristics of Streptococcus pneumoniae carriage and invasive disease isolates during a cluster-randomized clinical trial of the 7-valent pneumococcal conjugate vaccine

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Streptococcus pneumoniae capsular serotype invasiveness correlates with the degree of factor H binding and opsonization with C3b/iC3b ⬇️

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Student behavior during a school closure caused by pandemic influenza A/H1N1

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Studies needed to address public health challenges of the 2009 H1N1 influenza pandemic: insights from modeling

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Surface charge of Streptococcus pneumoniae predicts serotype distribution.

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Surveillance to maintain the sensitivity of genotype-based antibiotic resistance diagnostics

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Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses

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THE AUTHORS REPLY

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THE EVOLUTION OF VIRULENCE IN PATHOGENS WITH VERTICAL AND HORIZONTAL TRANSMISSION.

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TRANSMISSION RATES AND HIV VIRULENCE: COMMENTS TO MASSAD.

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Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants

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Targeting imperfect vaccines against drug-resistance determinants: a strategy for countering the rise of drug resistance

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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?

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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

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Temporally Varying Relative Risks for Infectious Diseases: Implications for Infectious Disease Control

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Testing COVID-19 therapies to prevent progression of mild disease

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The Effect of Parasites on Host Population Density and Extinction: Experimental Epidemiology with Daphnia and Six Microparasites

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The El Nino-Southern Oscillation (ENSO)-pandemic influenza connection: coincident or causal?

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The Relative Impact of Community and Hospital Antibiotic Use on the Selection of Extended-spectrum Beta-lactamase-producing Escherichia coli

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The US 2009 A(H1N1) influenza epidemic: quantifying the impact of school openings on the reproductive number.

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The Use of Test-negative Controls to Monitor Vaccine Effectiveness: A Systematic Review of Methodology

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The analysis of hospital infection data using hidden Markov models

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The association of meningococcal disease with influenza in the United States, 1989-2009.

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The demand for inpatient and ICU beds for COVID-19 in the US: lessons from Chinese cities

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The distribution of antibiotic use and its association with antibiotic resistance

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The distribution of antibiotic use and its association with antibiotic resistance

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The distribution of pairwise genetic distances: a tool for investigating disease transmission

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The effect of antiretroviral therapy on secondary transmission of HIV among men who have sex with men

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The epidemiology of antibiotic resistance in hospitals: paradoxes and prescriptions

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The ethics of biosafety considerations in gain-of-function research resulting in the creation of potential pandemic pathogens.

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The evolution of antibiotic resistance in a structured host population

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The evolution of virulence in sexually transmitted HIV/AIDS.

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The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome.

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The influence of hitchhiking and deleterious mutation upon asexual mutation rates

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The pneumococcal pilus predicts the absence of Staphylococcus aureus co-colonization in pneumococcal carriers

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The population dynamics of antimicrobial chemotherapy.

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The population dynamics of vertically and horizontally transmitted parasites.

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The population genetics of antibiotic resistance

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The population genetics of antibiotic resistance. II: Analytic theory for sustained populations of bacteria in a community of hosts.

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The prevalence and risk factors for pneumococcal colonization of the nasopharynx among children in Kilifi District, Kenya

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The relation between prescribing of different antibiotics and rates of mortality with sepsis in US adults

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The rise and fall of antimicrobial resistance

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The role of absolute humidity on transmission rates of the COVID-19 outbreak

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The role of complement in innate and adaptive immunity to pneumococcal colonization and sepsis in a murine model

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The severity of pandemic H1N1 influenza in the United States, April - July 2009

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The severity of pandemic H1N1 influenza in the United States, from April to July 2009: a Bayesian analysis

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The within-host population dynamics of antibacterial chemotherapy: conditions for the evolution of resistance.

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Time from illness onset to death, 1918 influenza and pneumococcal pneumonia

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Too little of a good thing: a paradox of moderate infection control

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Toward economic evaluation of the value of vaccines and other health technologies in addressing AMR

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Transmissibility of 1918 pandemic influenza

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Transmission dynamics and control of severe acute respiratory syndrome

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Trends in outpatient antibiotic prescribing practice among US older adults, 2011-2015: an observational study

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Underprotection of Unpredictable Statistical Lives Compared to Predictable Ones

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Understanding Australia's influenza pandemic policy on the strategic use of the antiviral drug stockpile.

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Understanding the spread of antibiotic resistant pathogens in hospitals: mathematical models as tools for control

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Upgrading antibiotic use within a class: tradeoff between resistance and treatment success

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Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine

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Use of cumulative incidence of novel influenza A/H1N1 in foreign travelers to estimate lower bounds on cumulative incidence in Mexico

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Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

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Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli

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Using observational data to quantify bias of traveller-derived COVID-19 prevalence estimates in Wuhan, China

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Using pneumococcal carriage data to monitor postvaccination changes in invasive disease

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Using predicted imports of 2019-nCoV cases to determine locations that may not be identifying all imported cases

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Using simulation to aid trial design: Ring-vaccination trials

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Using simulation to aid trial design: ring-vaccination trials

Utilizing syndromic surveillance data for estimating levels of influenza circulation

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Vaccination against colonizing bacteria with multiple serotypes

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Vaccine Effects on Heterogeneity in Susceptibility and Implications for Population Health Management.

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Vaccine allocation in a declining epidemic

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Vaccine production, distribution, access, and uptake

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Vaccine testing for emerging infections: the case for individual randomisation

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Vaccine testing. Ebola and beyond

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Viral factors in influenza pandemic risk assessment.

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Viral shedding and clinical illness in naturally acquired influenza virus infections

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Virulence and transmissibility of pathogens: what is the relationship?

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Visualizing pneumococcal infections in the lungs of live mice using bioluminescent Streptococcus pneumoniae transformed with a novel gram-positive lux transposon

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Weak Epistasis May Drive Adaptation in Recombining Bacteria

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Weather-based prediction of Plasmodium falciparum malaria in epidemic-prone regions of Ethiopia I. Patterns of lagged weather effects reflect biological mechanisms

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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

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What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae?

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Why Do Exceptionally Dangerous Gain-of-Function Experiments in Influenza?

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Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data

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Within-host selection is limited by an effective population of Streptococcus pneumoniae during nasopharyngeal colonization

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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

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Zika vaccine trials

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