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COVID-19: Daily Top 10 Papers


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Articles published in PLoS Comput Biol

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    September 2021
  1. RUDIGER D, Pelz L, Hein MD, Kupke SY, et al
    Multiscale model of defective interfering particle replication for influenza A virus infection in animal cell culture.
    PLoS Comput Biol. 2021;17:e1009357.
    PubMed     Abstract available


  2. BAUER S, Contreras S, Dehning J, Linden M, et al
    Relaxing restrictions at the pace of vaccination increases freedom and guards against further COVID-19 waves.
    PLoS Comput Biol. 2021;17:e1009288.
    PubMed     Abstract available


    August 2021
  3. PINKY L, Burke CW, Russell CJ, Smith AM, et al
    Quantifying dose-, strain-, and tissue-specific kinetics of parainfluenza virus infection.
    PLoS Comput Biol. 2021;17:e1009299.
    PubMed     Abstract available


  4. DUTTA R, Gomes SN, Kalise D, Pacchiardi L, et al
    Using mobility data in the design of optimal lockdown strategies for the COVID-19 pandemic.
    PLoS Comput Biol. 2021;17:e1009236.
    PubMed     Abstract available


  5. MAURAS S, Cohen-Addad V, Duboc G, Dupre la Tour M, et al
    Mitigating COVID-19 outbreaks in workplaces and schools by hybrid telecommuting.
    PLoS Comput Biol. 2021;17:e1009264.
    PubMed     Abstract available


  6. TERUEL N, Mailhot O, Najmanovich RJ
    Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants.
    PLoS Comput Biol. 2021;17:e1009286.
    PubMed     Abstract available


  7. YANG S, Senapati P, Wang D, Bauch CT, et al
    Targeted pandemic containment through identifying local contact network bottlenecks.
    PLoS Comput Biol. 2021;17:e1009351.
    PubMed     Abstract available


    July 2021
  8. TURTLE J, Riley P, Ben-Nun M, Riley S, et al
    Accurate influenza forecasts using type-specific incidence data for small geographic units.
    PLoS Comput Biol. 2021;17:e1009230.
    PubMed     Abstract available


  9. MILIOU I, Xiong X, Rinzivillo S, Zhang Q, et al
    Predicting seasonal influenza using supermarket retail records.
    PLoS Comput Biol. 2021;17:e1009087.
    PubMed     Abstract available


  10. JANG H, Polgreen PM, Segre AM, Pemmaraju SV, et al
    COVID-19 modeling and non-pharmaceutical interventions in an outpatient dialysis unit.
    PLoS Comput Biol. 2021;17:e1009177.
    PubMed     Abstract available


  11. TUPPER P, Colijn C
    COVID-19 in schools: Mitigating classroom clusters in the context of variable transmission.
    PLoS Comput Biol. 2021;17:e1009120.
    PubMed     Abstract available


  12. CHERIAN P, Krishna S, Menon GI
    Optimizing testing for COVID-19 in India.
    PLoS Comput Biol. 2021;17:e1009126.
    PubMed     Abstract available


  13. NAUMOV V, Putin E, Pushkov S, Kozlova E, et al
    COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity.
    PLoS Comput Biol. 2021;17:e1009183.
    PubMed     Abstract available


  14. GIBBS H, Nightingale E, Liu Y, Cheshire J, et al
    Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19.
    PLoS Comput Biol. 2021;17:e1009162.
    PubMed     Abstract available


  15. LI T, White LF
    Bayesian back-calculation and nowcasting for line list data during the COVID-19 pandemic.
    PLoS Comput Biol. 2021;17:e1009210.
    PubMed     Abstract available


  16. CAZELLES B, Champagne C, Nguyen-Van-Yen B, Comiskey C, et al
    A mechanistic and data-driven reconstruction of the time-varying reproduction number: Application to the COVID-19 epidemic.
    PLoS Comput Biol. 2021;17:e1009211.
    PubMed     Abstract available


  17. KERR CC, Stuart RM, Mistry D, Abeysuriya RG, et al
    Covasim: An agent-based model of COVID-19 dynamics and interventions.
    PLoS Comput Biol. 2021;17:e1009149.
    PubMed     Abstract available


  18. PARISI A, Brand SPC, Hilton J, Aziza R, et al
    Spatially resolved simulations of the spread of COVID-19 in three European countries.
    PLoS Comput Biol. 2021;17:e1009090.
    PubMed     Abstract available


  19. HINCH R, Probert WJM, Nurtay A, Kendall M, et al
    OpenABM-Covid19-An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing.
    PLoS Comput Biol. 2021;17:e1009146.
    PubMed     Abstract available


  20. PREM K, Zandvoort KV, Klepac P, Eggo RM, et al
    Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era.
    PLoS Comput Biol. 2021;17:e1009098.
    PubMed     Abstract available


    June 2021
  21. LU FS, Nguyen AT, Link NB, Molina M, et al
    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;17:e1008994.
    PubMed     Abstract available


  22. YUAN H, Kramer SC, Lau EHY, Cowling BJ, et al
    Modeling influenza seasonality in the tropics and subtropics.
    PLoS Comput Biol. 2021;17:e1009050.
    PubMed     Abstract available


  23. HILL EM, Atkins BD, Keeling MJ, Dyson L, et al
    A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2.
    PLoS Comput Biol. 2021;17:e1009058.
    PubMed     Abstract available


  24. DILLON MR, Bolyen E, Adamov A, Belk A, et al
    Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.
    PLoS Comput Biol. 2021;17:e1009056.
    PubMed     Abstract available


  25. GARDNER BJ, Kilpatrick AM
    Contact tracing efficiency, transmission heterogeneity, and accelerating COVID-19 epidemics.
    PLoS Comput Biol. 2021;17:e1009122.
    PubMed     Abstract available


  26. CAVALLARO M, Moiz H, Keeling MJ, McCarthy ND, et al
    Contrasting factors associated with COVID-19-related ICU admission and death outcomes in hospitalised patients by means of Shapley values.
    PLoS Comput Biol. 2021;17:e1009121.
    PubMed     Abstract available


    May 2021
  27. MOORE S, Hill EM, Dyson L, Tildesley MJ, et al
    Modelling optimal vaccination strategy for SARS-CoV-2 in the UK.
    PLoS Comput Biol. 2021;17:e1008849.
    PubMed     Abstract available


  28. SERRANO-SOLANO B, Foll MC, Gallardo-Alba C, Erxleben A, et al
    Fostering accessible online education using Galaxy as an e-learning platform.
    PLoS Comput Biol. 2021;17:e1008923.
    PubMed     Abstract available


  29. GALLARDO-ALBA C, Gruning B, Serrano-Solano B
    A constructivist-based proposal for bioinformatics teaching practices during lockdown.
    PLoS Comput Biol. 2021;17:e1008922.
    PubMed     Abstract available


  30. LIM JT, Maung K, Tan ST, Ong SE, et al
    Estimating direct and spill-over impacts of political elections on COVID-19 transmission using synthetic control methods.
    PLoS Comput Biol. 2021;17:e1008959.
    PubMed     Abstract available


    April 2021
  31. SIKORA M, von Bulow S, Blanc FEC, Gecht M, et al
    Computational epitope map of SARS-CoV-2 spike protein.
    PLoS Comput Biol. 2021;17:e1008790.
    PubMed     Abstract available


  32. NANDA P, Ghosh A
    Genome Scale-Differential Flux Analysis reveals deregulation of lung cell metabolism on SARS-CoV-2 infection.
    PLoS Comput Biol. 2021;17:e1008860.
    PubMed     Abstract available


    March 2021
  33. ZIPFEL CM, Colizza V, Bansal S
    Health inequities in influenza transmission and surveillance.
    PLoS Comput Biol. 2021;17:e1008642.
    PubMed     Abstract available


  34. BRAULT V, Mallein B, Rupprecht JF
    Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance.
    PLoS Comput Biol. 2021;17:e1008726.
    PubMed     Abstract available


  35. LIBIN PJK, Willem L, Verstraeten T, Torneri A, et al
    Assessing the feasibility and effectiveness of household-pooled universal testing to control COVID-19 epidemics.
    PLoS Comput Biol. 2021;17:e1008688.
    PubMed     Abstract available


  36. CZUPPON P, Debarre F, Goncalves A, Tenaillon O, et al
    Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action.
    PLoS Comput Biol. 2021;17:e1008752.
    PubMed     Abstract available


  37. DING J, Hostallero DE, El Khili MR, Fonseca GJ, et al
    A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes' interactions points to Neutrophil extracellular traps as mediators of thrombosis in COVID-19.
    PLoS Comput Biol. 2021;17:e1008810.
    PubMed     Abstract available


  38. RICHARD Q, Alizon S, Choisy M, Sofonea MT, et al
    Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic.
    PLoS Comput Biol. 2021;17:e1008776.
    PubMed     Abstract available


  39. STURNIOLO S, Waites W, Colbourn T, Manheim D, et al
    Testing, tracing and isolation in compartmental models.
    PLoS Comput Biol. 2021;17:e1008633.
    PubMed     Abstract available


  40. DI LAURO F, Kiss IZ, Miller JC
    Optimal timing of one-shot interventions for epidemic control.
    PLoS Comput Biol. 2021;17:e1008763.
    PubMed     Abstract available


  41. GONCALVES A, Maisonnasse P, Donati F, Albert M, et al
    SARS-CoV-2 viral dynamics in non-human primates.
    PLoS Comput Biol. 2021;17:e1008785.
    PubMed     Abstract available


  42. HOLCOMB D, Alexaki A, Hernandez N, Hunt R, et al
    Gene variants of coagulation related proteins that interact with SARS-CoV-2.
    PLoS Comput Biol. 2021;17:e1008805.
    PubMed     Abstract available


  43. WATSON GL, Xiong D, Zhang L, Zoller JA, et al
    Pandemic velocity: Forecasting COVID-19 in the US with a machine learning & Bayesian time series compartmental model.
    PLoS Comput Biol. 2021;17:e1008837.
    PubMed     Abstract available


  44. TORNERI A, Libin P, Scalia Tomba G, Faes C, et al
    On realized serial and generation intervals given control measures: The COVID-19 pandemic case.
    PLoS Comput Biol. 2021;17:e1008892.
    PubMed     Abstract available


    February 2021
  45. FISCON G, Conte F, Farina L, Paci P, et al
    SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19.
    PLoS Comput Biol. 2021;17:e1008686.
    PubMed     Abstract available


  46. BRACHER J, Ray EL, Gneiting T, Reich NG, et al
    Evaluating epidemic forecasts in an interval format.
    PLoS Comput Biol. 2021;17:e1008618.
    PubMed     Abstract available


  47. DATTNER I, Goldberg Y, Katriel G, Yaari R, et al
    The role of children in the spread of COVID-19: Using household data from Bnei Brak, Israel, to estimate the relative susceptibility and infectivity of children.
    PLoS Comput Biol. 2021;17:e1008559.
    PubMed     Abstract available


  48. NANDE A, Adlam B, Sheen J, Levy MZ, et al
    Dynamics of COVID-19 under social distancing measures are driven by transmission network structure.
    PLoS Comput Biol. 2021;17:e1008684.
    PubMed     Abstract available


  49. TREVEIL A, Bohar B, Sudhakar P, Gul L, et al
    ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways.
    PLoS Comput Biol. 2021;17:e1008685.
    PubMed     Abstract available


  50. BOUMAN JA, Riou J, Bonhoeffer S, Regoes RR, et al
    Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches.
    PLoS Comput Biol. 2021;17:e1008728.
    PubMed     Abstract available


  51. ARTHUR RF, Jones JH, Bonds MH, Ram Y, et al
    Adaptive social contact rates induce complex dynamics during epidemics.
    PLoS Comput Biol. 2021;17:e1008639.
    PubMed     Abstract available


    January 2021
  52. LEE BY, Bartsch SM, Ferguson MC, Wedlock PT, et al
    The value of decreasing the duration of the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.
    PLoS Comput Biol. 2021;17:e1008470.
    PubMed     Abstract available


  53. KEELING MJ, Hill EM, Gorsich EE, Penman B, et al
    Predictions of COVID-19 dynamics in the UK: Short-term forecasting and analysis of potential exit strategies.
    PLoS Comput Biol. 2021;17:e1008619.
    PubMed     Abstract available


  54. TEPEKULE B, Hauser A, Kachalov VN, Andresen S, et al
    Assessing the potential impact of transmission during prolonged viral shedding on the effect of lockdown relaxation on COVID-19.
    PLoS Comput Biol. 2021;17:e1008609.
    PubMed     Abstract available


  55. KOYAMA S, Horie T, Shinomoto S
    Estimating the time-varying reproduction number of COVID-19 with a state-space method.
    PLoS Comput Biol. 2021;17:e1008679.
    PubMed     Abstract available


  56. BIN M, Cheung PYK, Crisostomi E, Ferraro P, et al
    Post-lockdown abatement of COVID-19 by fast periodic switching.
    PLoS Comput Biol. 2021;17:e1008604.
    PubMed     Abstract available


  57. OMAR SI, Zhao M, Sekar RV, Moghadam SA, et al
    Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers.
    PLoS Comput Biol. 2021;17:e1008603.
    PubMed     Abstract available


  58. SHARKER Y, Kenah E
    Estimating and interpreting secondary attack risk: Binomial considered biased.
    PLoS Comput Biol. 2021;17:e1008601.
    PubMed     Abstract available


  59. GIBSON GC, Moran KR, Reich NG, Osthus D, et al
    Improving probabilistic infectious disease forecasting through coherence.
    PLoS Comput Biol. 2021;17:e1007623.
    PubMed     Abstract available


    December 2020
  60. GOSTIC KM, McGough L, Baskerville EB, Abbott S, et al
    Practical considerations for measuring the effective reproductive number, Rt.
    PLoS Comput Biol. 2020;16:e1008409.
    PubMed     Abstract available


  61. CATALA M, Alonso S, Alvarez-Lacalle E, Lopez D, et al
    Empirical model for short-time prediction of COVID-19 spreading.
    PLoS Comput Biol. 2020;16:e1008431.
    PubMed     Abstract available


  62. RODRIGUES JPGLM, Barrera-Vilarmau S, M C Teixeira J, Sorokina M, et al
    Insights on cross-species transmission of SARS-CoV-2 from structural modeling.
    PLoS Comput Biol. 2020;16:e1008449.
    PubMed     Abstract available


  63. ANDERSON SC, Edwards AM, Yerlanov M, Mulberry N, et al
    Quantifying the impact of COVID-19 control measures using a Bayesian model of physical distancing.
    PLoS Comput Biol. 2020;16:e1008274.
    PubMed     Abstract available


  64. ZHANG H, Yang Y, Li J, Wang M, et al
    A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro.
    PLoS Comput Biol. 2020;16:e1008489.
    PubMed     Abstract available


  65. RICH S, Diaconescu AO, Griffiths JD, Lankarany M, et al
    Ten simple rules for creating a brand-new virtual academic meeting (even amid a pandemic).
    PLoS Comput Biol. 2020;16:e1008485.
    PubMed     Abstract available


  66. PADMANABHAN P, Desikan R, Dixit NM
    Targeting TMPRSS2 and Cathepsin B/L together may be synergistic against SARS-CoV-2 infection.
    PLoS Comput Biol. 2020;16:e1008461.
    PubMed     Abstract available


  67. DELGADO BLANCO J, Hernandez-Alias X, Cianferoni D, Serrano L, et al
    In silico mutagenesis of human ACE2 with S protein and translational efficiency explain SARS-CoV-2 infectivity in different species.
    PLoS Comput Biol. 2020;16:e1008450.
    PubMed     Abstract available


  68. SEGO TJ, Aponte-Serrano JO, Ferrari Gianlupi J, Heaps SR, et al
    A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness.
    PLoS Comput Biol. 2020;16:e1008451.
    PubMed     Abstract available


  69. LIU QH, Bento AI, Yang K, Zhang H, et al
    The COVID-19 outbreak in Sichuan, China: Epidemiology and impact of interventions.
    PLoS Comput Biol. 2020;16:e1008467.
    PubMed     Abstract available


    November 2020
  70. LEUBA SI, Yaesoubi R, Antillon M, Cohen T, et al
    Tracking and predicting U.S. influenza activity with a real-time surveillance network.
    PLoS Comput Biol. 2020;16:e1008180.
    PubMed     Abstract available


  71. QUIROUETTE C, Younis NP, Reddy MB, Beauchemin CAA, et al
    Correction: A mathematical model describing the localization and spread of influenza A virus infection within the human respiratory tract.
    PLoS Comput Biol. 2020;16:e1008424.
    PubMed     Abstract available


  72. RILLIG MC, Bielcik M, Chaudhary VB, Grunfeld L, et al
    Ten simple rules for increased lab resilience.
    PLoS Comput Biol. 2020;16:e1008313.
    PubMed     Abstract available


    October 2020
  73. PEI S, Shaman J
    Aggregating forecasts of multiple respiratory pathogens supports more accurate forecasting of influenza-like illness.
    PLoS Comput Biol. 2020;16:e1008301.
    PubMed     Abstract available


  74. KRAMER SC, Pei S, Shaman J
    Forecasting influenza in Europe using a metapopulation model incorporating cross-border commuting and air travel.
    PLoS Comput Biol. 2020;16:e1008233.
    PubMed     Abstract available


  75. HILL EM, Petrou S, Forster H, de Lusignan S, et al
    Optimising age coverage of seasonal influenza vaccination in England: A mathematical and health economic evaluation.
    PLoS Comput Biol. 2020;16:e1008278.
    PubMed     Abstract available


  76. NORDMANN E, Horlin C, Hutchison J, Murray JA, et al
    Ten simple rules for supporting a temporary online pivot in higher education.
    PLoS Comput Biol. 2020;16:e1008242.
    PubMed     Abstract available


  77. SADRIA M, Layton AT
    Use of Angiotensin-Converting Enzyme Inhibitors and Angiotensin II Receptor Blockers During the COVID-19 Pandemic: A Modeling Analysis.
    PLoS Comput Biol. 2020;16:e1008235.
    PubMed     Abstract available


  78. HOLLINGSWORTH B, Okamoto KW, Lloyd AL
    After the honeymoon, the divorce: Unexpected outcomes of disease control measures against endemic infections.
    PLoS Comput Biol. 2020;16:e1008292.
    PubMed     Abstract available


  79. MCCOMBS A, Kadelka C
    A model-based evaluation of the efficacy of COVID-19 social distancing, testing and hospital triage policies.
    PLoS Comput Biol. 2020;16:e1008388.
    PubMed     Abstract available


  80. KREEGER PK, Brock A, Gibbs HC, Grande-Allen KJ, et al
    Ten simple rules for women principal investigators during a pandemic.
    PLoS Comput Biol. 2020;16:e1008370.
    PubMed    


  81. KARCHER MD, Carvalho LM, Suchard MA, Dudas G, et al
    Estimating effective population size changes from preferentially sampled genetic sequences.
    PLoS Comput Biol. 2020;16:e1007774.
    PubMed     Abstract available


    September 2020
  82. ZHAO Z, Sokhansanj BA, Malhotra C, Zheng K, et al
    Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization.
    PLoS Comput Biol. 2020;16:e1008269.
    PubMed     Abstract available


  83. POLITANO G, Benso A
    IL6-mediated HCoV-host interactome regulatory network and GO/Pathway enrichment analysis.
    PLoS Comput Biol. 2020;16:e1008238.
    PubMed     Abstract available


    July 2020
  84. SCARPINO SV, Scott JG, Eggo RM, Clements B, et al
    Socioeconomic bias in influenza surveillance.
    PLoS Comput Biol. 2020;16:e1007941.
    PubMed     Abstract available


  85. HILTON J, Keeling MJ
    Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices.
    PLoS Comput Biol. 2020;16:e1008031.
    PubMed     Abstract available


  86. PARAG KV, Donnelly CA
    Using information theory to optimise epidemic models for real-time prediction and estimation.
    PLoS Comput Biol. 2020;16:e1007990.
    PubMed     Abstract available


  87. BUCUR D, Holme P
    Beyond ranking nodes: Predicting epidemic outbreak sizes by network centralities.
    PLoS Comput Biol. 2020;16:e1008052.
    PubMed     Abstract available


    June 2020
  88. YANG W, Lau EHY, Cowling BJ
    Dynamic interactions of influenza viruses in Hong Kong during 1998-2018.
    PLoS Comput Biol. 2020;16:e1007989.
    PubMed     Abstract available


  89. SAAD-ROY CM, Arinaminpathy N, Wingreen NS, Levin SA, et al
    Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans.
    PLoS Comput Biol. 2020;16:e1007892.
    PubMed     Abstract available


  90. DUVIGNEAU S, Durr R, Laske T, Bachmann M, et al
    Model-based approach for predicting the impact of genetic modifications on product yield in biopharmaceutical manufacturing-Application to influenza vaccine production.
    PLoS Comput Biol. 2020;16:e1007810.
    PubMed     Abstract available


    May 2020
  91. WANG TE, Chao TL, Tsai HT, Lin PH, et al
    Differentiation of Cytopathic Effects (CPE) induced by influenza virus infection using deep Convolutional Neural Networks (CNN).
    PLoS Comput Biol. 2020;16:e1007883.
    PubMed     Abstract available


  92. GOZZI N, Perrotta D, Paolotti D, Perra N, et al
    Towards a data-driven characterization of behavioral changes induced by the seasonal flu.
    PLoS Comput Biol. 2020;16:e1007879.
    PubMed     Abstract available


    April 2020
  93. QUIROUETTE C, Younis NP, Reddy MB, Beauchemin CAA, et al
    A mathematical model describing the localization and spread of influenza A virus infection within the human respiratory tract.
    PLoS Comput Biol. 2020;16:e1007705.
    PubMed     Abstract available


  94. MCGOUGH SF, Johansson MA, Lipsitch M, Menzies NA, et al
    Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking.
    PLoS Comput Biol. 2020;16:e1007735.
    PubMed     Abstract available


    February 2020
  95. CASTRO LA, Bedford T, Ancel Meyers L
    Early prediction of antigenic transitions for influenza A/H3N2.
    PLoS Comput Biol. 2020;16:e1007683.
    PubMed     Abstract available


  96. REIMERING S, Munoz S, McHardy AC
    Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic.
    PLoS Comput Biol. 2020;16:e1007101.
    PubMed     Abstract available


    December 2019
  97. ENDO A, Uchida M, Kucharski AJ, Funk S, et al
    Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15.
    PLoS Comput Biol. 2019;15:e1007589.
    PubMed     Abstract available


    November 2019
  98. REICH NG, McGowan CJ, Yamana TK, Tushar A, et al
    Accuracy of real-time multi-model ensemble forecasts for seasonal influenza in the U.S.
    PLoS Comput Biol. 2019;15:e1007486.
    PubMed     Abstract available


  99. RANGARAJAN P, Mody SK, Marathe M
    Forecasting dengue and influenza incidences using a sparse representation of Google trends, electronic health records, and time series data.
    PLoS Comput Biol. 2019;15:e1007518.
    PubMed     Abstract available


    October 2019
  100. HILL EM, Petrou S, de Lusignan S, Yonova I, et al
    Seasonal influenza: Modelling approaches to capture immunity propagation.
    PLoS Comput Biol. 2019;15:e1007096.
    PubMed     Abstract available


  101. PRIEDHORSKY R, Daughton AR, Barnard M, O'Connell F, et al
    Estimating influenza incidence using search query deceptiveness and generalized ridge regression.
    PLoS Comput Biol. 2019;15:e1007165.
    PubMed     Abstract available


    September 2019
  102. VENKATRAMANAN S, Chen J, Fadikar A, Gupta S, et al
    Optimizing spatial allocation of seasonal influenza vaccine under temporal constraints.
    PLoS Comput Biol. 2019;15:e1007111.
    PubMed     Abstract available


  103. BECKER AD, Wesolowski A, Bjornstad ON, Grenfell BT, et al
    Long-term dynamics of measles in London: Titrating the impact of wars, the 1918 pandemic, and vaccination.
    PLoS Comput Biol. 2019;15:e1007305.
    PubMed     Abstract available


    August 2019
  104. HAY JA, Laurie K, White M, Riley S, et al
    Characterising antibody kinetics from multiple influenza infection and vaccination events in ferrets.
    PLoS Comput Biol. 2019;15:e1007294.
    PubMed     Abstract available


  105. YANG J, Muller NF, Bouckaert R, Xu B, et al
    Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration.
    PLoS Comput Biol. 2019;15:e1007189.
    PubMed     Abstract available


  106. KANDULA S, Shaman J
    Reappraising the utility of Google Flu Trends.
    PLoS Comput Biol. 2019;15:e1007258.
    PubMed     Abstract available


    May 2019
  107. BEN-NUN M, Riley P, Turtle J, Bacon DP, et al
    Forecasting national and regional influenza-like illness for the USA.
    PLoS Comput Biol. 2019;15:e1007013.
    PubMed     Abstract available


    April 2019
  108. LASKE T, Bachmann M, Dostert M, Karlas A, et al
    Model-based analysis of influenza A virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth.
    PLoS Comput Biol. 2019;15:e1006944.
    PubMed     Abstract available


  109. KALIMERI K, Delfino M, Cattuto C, Perrotta D, et al
    Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms.
    PLoS Comput Biol. 2019;15:e1006173.
    PubMed     Abstract available


  110. MENG H, Yaari G, Bolen CR, Avey S, et al
    Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE).
    PLoS Comput Biol. 2019;15:e1006899.
    PubMed     Abstract available


    February 2019
  111. KRAMER SC, Shaman J
    Development and validation of influenza forecasting for 64 temperate and tropical countries.
    PLoS Comput Biol. 2019;15:e1006742.
    PubMed     Abstract available


  112. RUDIGER D, Kupke SY, Laske T, Zmora P, et al
    Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions.
    PLoS Comput Biol. 2019;15:e1006819.
    PubMed     Abstract available


  113. OSTHUS D, Daughton AR, Priedhorsky R
    Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited.
    PLoS Comput Biol. 2019;15:e1006599.
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  114. PEI S, Cane MA, Shaman J
    Predictability in process-based ensemble forecast of influenza.
    PLoS Comput Biol. 2019;15:e1006783.
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    January 2019
  115. MAJARIAN TD, Murphy RF, Lakdawala SS
    Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization.
    PLoS Comput Biol. 2019;15:e1006199.
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  116. YAN AWC, Zaloumis SG, Simpson JA, McCaw JM, et al
    Sequential infection experiments for quantifying innate and adaptive immunity during influenza infection.
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  117. HAW DJ, Cummings DAT, Lessler J, Salje H, et al
    Differential mobility and local variation in infection attack rate.
    PLoS Comput Biol. 2019;15:e1006600.
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    November 2018
  118. VOLZ EM, Siveroni I
    Bayesian phylodynamic inference with complex models.
    PLoS Comput Biol. 2018;14:e1006546.
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    October 2018
  119. CHAKRABORTY P, Lewis B, Eubank S, Brownstein JS, et al
    What to know before forecasting the flu.
    PLoS Comput Biol. 2018;14:e1005964.
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    September 2018
  120. HILL EM, House T, Dhingra MS, Kalpravidh W, et al
    The impact of surveillance and control on highly pathogenic avian influenza outbreaks in poultry in Dhaka division, Bangladesh.
    PLoS Comput Biol. 2018;14:e1006439.
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  121. ERTEM Z, Raymond D, Meyers LA
    Optimal multi-source forecasting of seasonal influenza.
    PLoS Comput Biol. 2018;14:e1006236.
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    August 2018
  122. COPE RC, Ross JV, Chilver M, Stocks NP, et al
    Characterising seasonal influenza epidemiology using primary care surveillance data.
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    June 2018
  123. BROOKS LC, Farrow DC, Hyun S, Tibshirani RJ, et al
    Nonmechanistic forecasts of seasonal influenza with iterative one-week-ahead distributions.
    PLoS Comput Biol. 2018;14:e1006134.
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    March 2018
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    Role of genetic heterogeneity in determining the epidemiological severity of H1N1 influenza.
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  125. LEE EC, Arab A, Goldlust SM, Viboud C, et al
    Deploying digital health data to optimize influenza surveillance at national and local scales.
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    February 2018
  126. THOMPSON RN, Gilligan CA, Cunniffe NJ
    Control fast or control smart: When should invading pathogens be controlled?
    PLoS Comput Biol. 2018;14:e1006014.
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  127. RAY EL, Reich NG
    Prediction of infectious disease epidemics via weighted density ensembles.
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    November 2017
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    The use of ambient humidity conditions to improve influenza forecast.
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  129. YAMANA TK, Kandula S, Shaman J
    Individual versus superensemble forecasts of seasonal influenza outbreaks in the United States.
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    fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks.
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    October 2017
  131. FOX SJ, Miller JC, Meyers LA
    Seasonality in risk of pandemic influenza emergence.
    PLoS Comput Biol. 2017;13:e1005749.
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    June 2017
  132. DORRATOLTAJ N, Marathe A, Lewis BL, Swarup S, et al
    Epidemiological and economic impact of pandemic influenza in Chicago: Priorities for vaccine interventions.
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    February 2017
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    Human mobility and the spatial transmission of influenza in the United States.
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  134. MAGEE D, Suchard MA, Scotch M
    Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction.
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  135. WON M, Marques-Pita M, Louro C, Goncalves-Sa J, et al
    Early and Real-Time Detection of Seasonal Influenza Onset.
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    December 2016
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    Universal or Specific? A Modeling-Based Comparison of Broad-Spectrum Influenza Vaccines against Conventional, Strain-Matched Vaccines.
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    November 2016
  137. YANG W, Olson DR, Shaman J
    Forecasting Influenza Outbreaks in Boroughs and Neighborhoods of New York City.
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    October 2016
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