Publications

(2020). Migration Interacts with the Local Transmission of HIV in Developed Trade Areas: A Molecular Transmission Network Analysis in China. Infection, Genetics and Evolution.

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(2020). Characterizing Norovirus Transmission from Outbreak Data, United States. Emerging Infectious Diseases.

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(2020). A Cluster of Novel Coronavirus Disease 2019 Infections Indicating Person-to-Person Transmission Among Casual Contacts From Social Gatherings: An Outbreak Case-Contact Investigation. Open Forum Infectious Diseases.

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(2020). Virulence-Mediated Infectiousness and Activity Trade-Offs and Their Impact on Transmission Potential of Influenza Patients. Proceedings of the Royal Society B: Biological Sciences.

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(2020). Varying Inoculum Dose to Assess the Roles of the Immune Response and Target Cell Depletion by the Pathogen in Control of Acute Viral Infections. Bulletin of Mathematical Biology.

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(2020). Simulation Modelling for Immunologists. Nature Reviews Immunology.

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(2020). A Bayesian Approach to Estimate Parameters of Ordinary Differential Equation. Computational Statistics.

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(2020). SARS-CoV-2 Viral and Serological Testing When College Campuses Reopen: Some Practical Considerations. Disaster Medicine and Public Health Preparedness.

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(2019). Evidence for supercoughers in an analysis of six tuberculosis cohorts from China, Peru, The Gambia and Uganda.

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(2019). A Risk Classification Model to Predict Mortality Among Laboratory-Confirmed Avian Influenza A H7N9 Patients: A Population-Based Observational Cohort Study. The Journal of Infectious Diseases.

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(2019). Impact of a Rapid Point of Care Test for Influenza on Guideline Consistent Care and Antibiotic Use.. Journal of the American Board of Family Medicine : JABFM.

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(2019). Validation of a Pictorial Survey Tool to Measure Time Use in an African Urban Setting. Sociological Methods & Research.

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(2019). Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTL responses. Nature Communications.

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(2018). Progress and trends in mathematical modelling of influenza A virus infections. Current Opinion in Systems Biology.

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(2018). Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design.. PLoS Comput Biol.

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(2018). Performance of the QuantiFERON®-TB Gold In-Tube assay in tuberculin skin test converters: a prospective cohort study.. Int J Tuberc Lung Dis.

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(2018). Heterogeneity and longevity of antibody memory to viruses and vaccines.. PLoS Biol.

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(2018). Intermediate levels of vaccination coverage may minimize seasonal influenza outbreaks. PLOS ONE.

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(2018). Applying functional data analysis to assess tele-interpersonal psychotherapy's efficacy to reduce depression. Journal of Applied Statistics.

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(2018). A Prospective Validation of a Clinical Algorithm to Detect Tuberculosis in Child Contacts. American Journal of Respiratory and Critical Care Medicine.

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(2018). Effectiveness of WHO's pragmatic screening algorithm for child contacts of tuberculosis cases in resource-constrained settings: a prospective cohort study in Uganda. The Lancet Respiratory Medicine.

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(2017). Cell Biology by the Numbers by Ron Milo and Rob Phillips. The Quarterly Review of Biology.

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(2017). Learning infectious disease epidemiology in a modern framework. PLOS Computational Biology.

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(2017). Dominant protection from HLA-linked autoimmunity by antigen-specific regulatory T cells. NATURE.

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(2017). Is IPT more effective in high-burden settings? Modelling the effect of tuberculosis incidence on IPT impact. The International Journal of Tuberculosis and Lung Disease.

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(2016). Targeting pediatric versus elderly populations for norovirus vaccines: a model-based analysis of mass vaccination options. Epidemics.

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(2016). Viral factors in influenza pandemic risk assessment. ELIFE.

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(2016). Feasibility of achieving the 2025 WHO global tuberculosis targets in South Africa, China, and India: a combined analysis of 11 mathematical models. LANCET GLOBAL HEALTH.

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(2016). Cost-effectiveness and resource implications of aggressive action on tuberculosis in China, India, and South Africa: a combined analysis of nine models. LANCET GLOBAL HEALTH.

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(2016). Mathematical Model Reveals the Role of Memory CD8 T Cell Populations in Recall Responses to Influenza. FRONTIERS IN IMMUNOLOGY.

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(2016). Heightened self-reactivity associated with selective survival, but not expansion, of naive virus-specific CD8(+) T cells in aged mice. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA.

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(2015). Four Degrees of Separation: Social Contacts and Health Providers Influence the Steps to Final Diagnosis of Active Tuberculosis Patients in Urban Uganda. BMC INFECTIOUS DISEASES.

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(2015). Crossing the scale from within-host infection dynamics to between-host transmission fitness: a discussion of current assumptions and knowledge. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES.

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(2015). Oseltamivir Prophylaxis Reduces Inflammation and Facilitates Establishment of Cross-Strain Protective T Cell Memory to Influenza Viruses. PLOS ONE.

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(2015). Neuraminidase inhibitors for influenza: fully evaluating benefits and harms. The Lancet Respiratory Medicine.

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(2014). Trade-offs between and within scales: environmental persistence and within-host fitness of avian influenza viruses. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES.

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(2014). Recognition of Distinct Cross-Reactive Virus-Specific CD8(+) T Cells Reveals a Unique TCR Signature in a Clinical Setting. JOURNAL OF IMMUNOLOGY.

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(2014). Modeling inoculum dose dependent patterns of acute virus infections. JOURNAL OF THEORETICAL BIOLOGY.

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(2014). How sticky should a virus be? The impact of virus binding and release on transmission fitness using influenza as an example. JOURNAL OF THE ROYAL SOCIETY INTERFACE.

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(2014). Reproducible selection of high avidity CD8(+) T-cell clones following secondary acute virus infection. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA.

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(2013). A Multi-scale Analysis of Influenza A Virus Fitness Trade-offs due to Temperature-dependent Virus Persistence. PLOS COMPUTATIONAL BIOLOGY.

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(2013). Ecological analysis of antigen-specific CTL repertoires defines the relationship between naive and immune T-cell populations. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA.

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(2012). Molecular evolution and emergence of avian gammacoronaviruses. INFECTION GENETICS AND EVOLUTION.

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(2012). Severe Outcomes Are Associated With Genogroup 2 Genotype 4 Norovirus Outbreaks: A Systematic Literature Review. CLINICAL INFECTIOUS DISEASES.

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(2010). Influenza Epitope-Specific CD8(+) T Cell Avidity, but Not Cytokine Polyfunctionality, Can Be Determined by TCR beta Clonotype. JOURNAL OF IMMUNOLOGY.

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(2010). Towards a quantitative understanding of the within-host dynamics of influenza A infections. JOURNAL OF THE ROYAL SOCIETY INTERFACE.

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(2009). Sharing the burden: antigen transport and firebreaks in immune responses. Journal of The Royal Society Interface.

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(2009). Exploring the role of the immune response in preventing antibiotic resistance. JOURNAL OF THEORETICAL BIOLOGY.

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(2008). Heterogeneous Adaptive Trajectories of Small Populations on Complex Fitness Landscapes. PLoS ONE.

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(2007). Gap junction-mediated antigen transport in immune responses. Trends in Immunology.

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(2007). What is the best control strategy for multiple infectious disease outbreaks?. Proceedings of the Royal Society B: Biological Sciences.

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(2007). Neuraminidase Inhibitor Resistance in Influenza: Assessing the Danger of Its Generation and Spread. PLoS Computational Biology.

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(2006). Transient dynamics and nonlinear stability of spatially extended systems. PHYSICAL REVIEW E.

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(2006). The Role of Compensatory Mutations in the Emergence of Drug Resistance. PLoS Computational Biology.

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(2005). Pattern selection and control via localized feedback. PHYSICAL REVIEW E.

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(2002). Non-normality and the localized control of extended systems. PHYSICAL REVIEW E.

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