National Institutes of Health, National Institute of General Medical Sciences
People: Katia Koelle, Jon Zelner, Ben Lopman, Andreas Handel, Kristin Nelson
2018 – 2023
Drake JM, Dahlin K, Rohani P, Handel A. (2021). Five approaches to the suppression of SARS-CoV-2 without intensive social distancing. Proceedings. Biological sciences, 288(1949)
Ge Y, Martinez L, Sun S, Chen Z, Zhang F, Li F, Sun W, Chen E, Pan J, Li C, Sun J, Handel A, Ling F, Shen Y. (2021). COVID-19 Transmission Dynamics Among Close Contacts of Index Patients With COVID-19: A Population-Based Cohort Study in Zhejiang Province, China. JAMA internal medicine
Lopman B, Liu CY, Le Guillou A, Handel A, Lash TL, Isakov AP, Jenness SM. (2021). A modeling study to inform screening and testing interventions for the control of SARS-CoV-2 on university campuses. Scientific reports, 11(1)
Ge Y, Chen Z, Handel A, Martinez L, Xiao Q, Li C, Chen E, Pan J, Li Y, Ling F, Shen Y. (2021). The impact of social distancing, contact tracing, and case isolation interventions to suppress the COVID-19 epidemic: A modeling study. Epidemics, (36)
Mercaldo R, Whalen C, Kakaire R, Nakkonde D, Handel A, Sekandi JN. (2021). Community drivers of tuberculosis diagnostic delay in Kampala, Uganda: a retrospective cohort study. BMC infectious diseases, 21(1)
Sung MH, Shen Y, Handel A, Bahl J, Ross TM. (2021). Longitudinal Assessment of Immune Responses to Repeated Annual Influenza Vaccination in a Human Cohort of Adults and Teenagers. Frontiers in immunology, (12)
Drake J, Rohani P, Dahlin K, Handel A. (2020). Five approaches to the suppression of SARS-CoV-2 without intensive social distancing. medRxiv : the preprint server for health sciences
Shen Y, Li C, Dong H, Wang Z, Martinez L, Sun Z, Handel A, Chen Z, Chen E, Ebell MH, Wang F, Yi B, Wang H, Wang X, Wang A, Chen B, Qi Y, Liang L, Li Y, Ling F, Chen J, Xu G. (2020). Community Outbreak Investigation of SARS-CoV-2 Transmission Among Bus Riders in Eastern China. JAMA internal medicine
McKay B, Ebell M, Billings WZ, Dale AP, Shen Y, Handel A. (2020). Associations Between Relative Viral Load at Diagnosis and Influenza A Symptoms and Recovery. Open forum infectious diseases, 7(11)
Shen Y, Xu W, Li C, Handel A, Martinez L, Ling F, Ebell M, Fu X, Pan J, Ren J, Gu W, Chen E. (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, 7(6)
Fung IC, Cheung CN, Handel A. (2020). SARS-CoV-2 Viral and Serological Testing When College Campuses Reopen: Some Practical Considerations. Disaster medicine and public health preparedness
Zhang J, Yao J, Jiang J, Pan X, Luo M, Xia Y, Fan Q, Ding X, Ruan J, Handel A, Bahl J, Chen W, Zha L, Fu T. (2020). Migration interacts with the local transmission of HIV in developed trade areas: A molecular transmission network analysis in China. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
Gallagher ME, Sieben AJ, Nelson KN, Kraay ANM, Orenstein WA, Lopman B, Handel A, Koelle K. (2020). Indirect benefits are a crucial consideration when evaluating SARS-CoV-2 vaccine candidates. Nature medicine
Steele MK, Wikswo ME, Hall AJ, Koelle K, Handel A, Levy K, Waller LA, Lopman BA. (2020). Characterizing Norovirus Transmission from Outbreak Data, United States. Emerging infectious diseases, 26(8)
Skarlupka AL, Handel A, Ross TM. (2020). Influenza hemagglutinin antigenic distance measures capture trends in HAI differences and infection outcomes, but are not suitable predictive tools. Vaccine, 38(36)
Skarlupka AL, Handel A, Ross TM. (2020). Dataset of antigenic distance measures, hemagglutination inhibition, viral lung titers, and weight loss in mice and ferrets when exposed to HA-based vaccination or sub-lethal A(H1) influenza infection. Data in brief, (32)
Cheng W, Pan A, Rathbun SL, Ge Y, Xiao Q, Martinez L, Ling F, Liu S, Wang X, Yu Z, Ebell MH, Li C, Handel A, Chen E, Shen Y. (2020). Effectiveness of Neuraminidase Inhibitors to Prevent Mortality in Laboratory-Confirmed Avian Influenza A H7N9 Patients. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases
McKay B, Ebell M, Dale AP, Shen Y, Handel A. (2020). Virulence-mediated infectiousness and activity trade-offs and their impact on transmission potential of influenza patients. Proceedings. Biological sciences, 287(1927)
Gallagher ME, Sieben AJ, Nelson KN, Kraay ANM, Lopman B, Handel A, Koelle K. (2020). Considering indirect benefits is critical when evaluating SARS-CoV-2 vaccine candidates. medRxiv : the preprint server for health sciences
Moore JR, Ahmed H, Manicassamy B, Garcia-Sastre A, Handel A, Antia R. (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, 82(3)
Handel A. (2020). A software package for immunologists to learn simulation modeling. BMC immunology, 21(1)
Wu T, Guan J, Handel A, Tscharke DC, Sidney J, Sette A, Wakim LM, Sng XYX, Thomas PG, Croft NP, Purcell AW, La Gruta NL. (2019). Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTL responses. Nature communications, 10(1)
McKay B, Castellanos M, Ebell M, Whalen CC, Handel A. (2019). An attempt to reproduce a previous meta-analysis and a new analysis regarding the impact of directly observed therapy on tuberculosis treatment outcomes. PloS one, 14(5)
Martinez L, Cheng W, Wang X, Ling F, Mu L, Li C, Huo X, Ebell MH, Huang H, Zhu L, Li C, Chen E, Handel A, Shen Y. (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, 220(11)
Pawelek KA, Dor D Jr., Salmeron C, Handel A. (2019). Correction: Within-Host Models of High and Low Pathogenic Influenza Virus Infections: The Role of Macrophages. PloS one, 14(4)
Dale AP, Ebell M, McKay B, Handel A, Forehand R, Dobbin K. 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, 32(2)
Handel A, La Gruta NL, Thomas PG. (2019). Simulation modelling for immunologists. Nature reviews. Immunology
Antia A, Ahmed H, Handel A, Carlson NE, Amanna IJ, Antia R, Slifka M. (2018). Heterogeneity and longevity of antibody memory to viruses and vaccines. PLoS biology, 16(8)
Handel A, Li Y, McKay B, Pawelek KA, Zarnitsyna V, Antia R. (2018). Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design. PLoS computational biology, 14(10)
Zarnitsyna VI, Bulusheva I, Handel A, Longini IM, Halloran ME, Antia R. (2018). Intermediate levels of vaccination coverage may minimize seasonal influenza outbreaks. PloS one, 13(6)
Woldu H, Heckman TG, Handel A, Shen Y. (2018). Applying Functional Data Analysis to Assess Tele-Interpersonal Psychotherapy's Efficacy to Reduce Depression. Journal of applied statistics, 46(2)
Handel A. (2017). Learning infectious disease epidemiology in a modern framework. PLoS computational biology, 13(10)
Martinez L, Shen Y, Handel A, Chakraburty S, Stein CM, Malone LL, Boom WH, Quinn FD, Joloba ML, Whalen CC, Zalwango S. (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, 6(4)
Martinez L, Handel A, Shen Y, Chakraburty S, Quinn FD, Stein CM, Malone LL, Zalwango S, Whalen CC. (2018). A Prospective Validation of a Clinical Algorithm to Detect Tuberculosis in Child Contacts. American journal of respiratory and critical care medicine, 197(9)
Ooi JD, Petersen J, Tan YH, Huynh M, Willett ZJ, Ramarathinam SH, Eggenhuizen PJ, Loh KL, Watson KA, Gan PY, Alikhan MA, Dudek NL, Handel A, Hudson BG, Fugger L, Power DA, Holt SG, Coates PT, Gregersen JW, Purcell AW, Holdsworth SR, La Gruta NL, Reid HH, Rossjohn J, Kitching AR. (2017). Dominant protection from HLA-linked autoimmunity by antigen-specific regulatory T cells. Nature, 545(7653)
Pawelek KA, Dor D Jr., Salmeron C, Handel A. (2016). Within-Host Models of High and Low Pathogenic Influenza Virus Infections: The Role of Macrophages. PloS one, 11(2)
Houben RMGJ, Menzies NA, Sumner T, Huynh GH, Arinaminpathy N, Goldhaber-Fiebert JD, Lin HH, Wu CY, Mandal S, Pandey S, Suen SC, Bendavid E, Azman AS, Dowdy DW, Bacaër N, Rhines AS, Feldman MW, Handel A, Whalen CC, Chang ST, Wagner BG, Eckhoff PA, Trauer JM, Denholm JT, McBryde ES, Cohen T, Salomon JA, Pretorius C, Lalli M, Eaton JW, Boccia D, Hosseini M, Gomez GB, Sahu S, Daniels C, Ditiu L, Chin DP, Wang L, Chadha VK, Rade K, Dewan P, Hippner P, Charalambous S, Grant AD, Churchyard G, Pillay Y, Mametja LD, Kimerling ME, Vassall A, White RG. (2016). Feasibility of achieving the 2025 WHO global tuberculosis targets in South Africa, China, and India: a combined analysis of 11 mathematical models. The Lancet. Global health, 4(11)
Menzies NA, Gomez GB, Bozzani F, Chatterjee S, Foster N, Baena IG, Laurence YV, Qiang S, Siroka A, Sweeney S, Verguet S, Arinaminpathy N, Azman AS, Bendavid E, Chang ST, Cohen T, Denholm JT, Dowdy DW, Eckhoff PA, Goldhaber-Fiebert JD, Handel A, Huynh GH, Lalli M, Lin HH, Mandal S, McBryde ES, Pandey S, Salomon JA, Suen SC, Sumner T, Trauer JM, Wagner BG, Whalen CC, Wu CY, Boccia D, Chadha VK, Charalambous S, Chin DP, Churchyard G, Daniels C, Dewan P, Ditiu L, Eaton JW, Grant AD, Hippner P, Hosseini M, Mametja D, Pretorius C, Pillay Y, Rade K, Sahu S, Wang L, Houben RMGJ, Kimerling ME, White RG, Vassall A. (2016). Cost-effectiveness and resource implications of aggressive action on tuberculosis in China, India, and South Africa: a combined analysis of nine models. The Lancet. Global health, 4(11)
Quinn KM, Zaloumis SG, Cukalac T, Kan WT, Sng XY, Mirams M, Watson KA, McCaw JM, Doherty PC, Thomas PG, Handel A, La Gruta NL. (2016). Heightened self-reactivity associated with selective survival, but not expansion, of naïve virus-specific CD8+ T cells in aged mice. Proceedings of the National Academy of Sciences of the United States of America, 113(5)
Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA. (2016). Viral factors in influenza pandemic risk assessment. Elife, (5)
Steele MK, Remais JV, Gambhir M, Glasser JW, Handel A, Parashar UD, Lopman BA. (2016). Targeting pediatric versus elderly populations for norovirus vaccines: a model-based analysis of mass vaccination options. Epidemics, (17)
Zarnitsyna VI, Handel A, McMaster SR, Hayward SL, Kohlmeier JE, Antia R. (2016). Mathematical Model Reveals the Role of Memory CD8 T Cell Populations in Recall Responses to Influenza. Frontiers in immunology, (7)
Handel A, Ebell MH. (2015). Neuraminidase inhibitors for influenza: fully evaluating benefits and harms. The Lancet. Respiratory medicine, 3(3)
Sekandi JN, Zalwango S, Martinez L, Handel A, Kakaire R, Nkwata AK, Ezeamama AE, Kiwanuka N, Whalen CC. (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, (15)
Bird NL, Olson MR, Hurt AC, Oshansky CM, Oh DY, Reading PC, Chua BY, Sun Y, Tang L, Handel A, Jackson DC, Turner SJ, Thomas PG, Kedzierska K. (2015). Oseltamivir Prophylaxis Reduces Inflammation and Facilitates Establishment of Cross-Strain Protective T Cell Memory to Influenza Viruses. PloS one, 10(6)
Handel A, Rohani P. (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 of London. Series B, Biological sciences, 370(1675)
Nguyen TH, Rowntree LC, Pellicci DG, Bird NL, Handel A, Kjer-Nielsen L, Kedzierska K, Kotsimbos TC, Mifsud NA. (2014). Recognition of distinct cross-reactive virus-specific CD8+ T cells reveals a unique TCR signature in a clinical setting. Journal of immunology (Baltimore, Md. : 1950), 192(11)
Cukalac T, Chadderton J, Handel A, Doherty PC, Turner SJ, Thomas PG, La Gruta NL. (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, 111(4)
Zheng N, Whalen CC, Handel A. (2014). Modeling the potential impact of host population survival on the evolution of M. tuberculosis latency. PloS one, 9(8)
Li Y, Handel A. (2014). Modeling inoculum dose dependent patterns of acute virus infections. Journal of theoretical biology, (347)
Handel A, Lebarbenchon C, Stallknecht D, Rohani P. (2015). Correction to: Trade-offs between and within scales: environmental persistence and within-host fitness of avian influenza viruses. Proceedings. Biological sciences, 282(1800)
Handel A, Akin V, Pilyugin SS, Zarnitsyna V, Antia R. (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, 11(92)
Handel A, Lebarbenchon C, Stallknecht D, Rohani P. (2014). Trade-offs between and within scales: environmental persistence and within-host fitness of avian influenza viruses. Proceedings. Biological sciences, 281(1787)
Handel A, Brown J, Stallknecht D, Rohani P. (2013). A multi-scale analysis of influenza A virus fitness trade-offs due to temperature-dependent virus persistence. PLoS computational biology, 9(3)
Thomas PG, Handel A, Doherty PC, La Gruta NL. (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, 110(5)
Jackwood MW, Hall D, Handel A. (2012). Molecular evolution and emergence of avian gammacoronaviruses. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 12(6)
Desai R, Hembree CD, Handel A, Matthews JE, Dickey BW, McDonald S, Hall AJ, Parashar UD, Leon JS, Lopman B. (2012). Severe outcomes are associated with genogroup 2 genotype 4 norovirus outbreaks: a systematic literature review. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 55(2)
Fung IC, Antia R, Handel A. (2012). How to minimize the attack rate during multiple influenza outbreaks in a heterogeneous population. PloS one, 7(6)
Beauchemin CA, Handel A. (2011). A review of mathematical models of influenza A infections within a host or cell culture: lessons learned and challenges ahead. BMC public health, (11 Suppl 1)
Moffat JM, Handel A, Doherty PC, Turner SJ, Thomas PG, La Gruta NL. (2010). Influenza epitope-specific CD8+ T cell avidity, but not cytokine polyfunctionality, can be determined by TCRβ clonotype. Journal of immunology (Baltimore, Md. : 1950), 185(11)
Handel A, Longini IM Jr., Antia R. (2009). Intervention strategies for an influenza pandemic taking into account secondary bacterial infections. Epidemics, 1(3)
Handel A, Longini IM Jr., Antia R. (2010). Towards a quantitative understanding of the within-host dynamics of influenza A infections. Journal of the Royal Society, Interface, 7(42)
Handel A, Rozen DE. (2009). The impact of population size on the evolution of asexual microbes on smooth versus rugged fitness landscapes. BMC evolutionary biology, (9)
Handel A, Longini IM Jr., Antia R. (2009). Antiviral resistance and the control of pandemic influenza: the roles of stochasticity, evolution and model details. Journal of theoretical biology, 256(1)
Handel A, Yates A, Pilyugin SS, Antia R. (2009). Sharing the burden: antigen transport and firebreaks in immune responses. Journal of the Royal Society, Interface, 6(34)
Handel A, Bennett MR. (2008). Surviving the bottleneck: transmission mutants and the evolution of microbial populations. Genetics, 180(4)
Handel A, Antia R. (2008). A simple mathematical model helps to explain the immunodominance of CD8 T cells in influenza A virus infections. Journal of virology, 82(16)
Handel A, Margolis E, Levin BR. (2009). Exploring the role of the immune response in preventing antibiotic resistance. Journal of theoretical biology, 256(4)
Rozen DE, Habets MG, Handel A, de Visser JA. (2008). Heterogeneous adaptive trajectories of small populations on complex fitness landscapes. PloS one, 3(3)
Handel A, Longini IM Jr., Antia R. (2007). Neuraminidase inhibitor resistance in influenza: assessing the danger of its generation and spread. PLoS computational biology, 3(12)
Handel A, Longini IM Jr., Antia R. (2007). What is the best control strategy for multiple infectious disease outbreaks?. Proceedings. Biological sciences, 274(1611)
Handel A, Yates A, Pilyugin SS, Antia R. (2007). Gap junction-mediated antigen transport in immune responses. Trends in immunology, 28(11)
Handel A, Grigoriev RO. (2006). Transient dynamics and nonlinear stability of spatially extended systems. Physical review. E, Statistical, nonlinear, and soft matter physics, 74(3 Pt 2)
Handel A, Regoes RR, Antia R. (2006). The role of compensatory mutations in the emergence of drug resistance. PLoS computational biology, 2(10)
Viboud C, Tam T, Fleming D, Handel A, Miller MA, Simonsen L. (2006). Transmissibility and mortality impact of epidemic and pandemic influenza, with emphasis on the unusually deadly 1951 epidemic. Vaccine, 24(44-46)
Handel A, Grigoriev RO. (2005). Pattern selection and control via localized feedback. Physical review. E, Statistical, nonlinear, and soft matter physics, 72(6 Pt 2)
Grigoriev RO, Handel A. (2002). Spectral theory for the failure of linear control in a nonlinear stochastic system. Physical review. E, Statistical, nonlinear, and soft matter physics, 66(6 Pt 2)
Grigoriev RO, Handel A. (2002). Non-normality and the localized control of extended systems. Physical review. E, Statistical, nonlinear, and soft matter physics, 66(6 Pt 2)
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Thank you to NIGMS Grant U24GM132013 for supporting the work at the Coordination Center.
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