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2049 Chinese

The 20K Word Road to Mandarin Proficiency

By B. S. Kamps et al.


  Influenza

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Articles published in PLoS Comput Biol

Retrieve available abstracts of 269 articles:
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Single Articles


    June 2024
  1. HILL EM, Petrou S, de Lusignan S, Yonova I, et al
    Correction: Seasonal influenza: Modelling approaches to capture immunity propagation.
    PLoS Comput Biol. 2024;20:e1012213.
    PubMed     Abstract available


  2. ROJAS CHAVEZ RA, Fili M, Han C, Rahman SA, et al
    Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics.
    PLoS Comput Biol. 2024;20:e1012215.
    PubMed     Abstract available


  3. SHUBIN M, Brustad HK, Midtbo JE, Gunther F, et al
    The influence of cross-border mobility on the COVID-19 epidemic in Nordic countries.
    PLoS Comput Biol. 2024;20:e1012182.
    PubMed     Abstract available


  4. SALWIG S, Drefs J, Lucke J
    Zero-shot denoising of microscopy images recorded at high-resolution limits.
    PLoS Comput Biol. 2024;20:e1012192.
    PubMed     Abstract available


    May 2024
  5. HLADISH TJ, Pillai AN, Pearson CAB, Toh KB, et al
    Evaluating targeted COVID-19 vaccination strategies with agent-based modeling.
    PLoS Comput Biol. 2024;20:e1012128.
    PubMed     Abstract available


  6. LOPEZ VK, Cramer EY, Pagano R, Drake JM, et al
    Challenges of COVID-19 Case Forecasting in the US, 2020-2021.
    PLoS Comput Biol. 2024;20:e1011200.
    PubMed     Abstract available


  7. ASPLIN P, Keeling MJ, Mancy R, Hill EM, et al
    Epidemiological and health economic implications of symptom propagation in respiratory pathogens: A mathematical modelling investigation.
    PLoS Comput Biol. 2024;20:e1012096.
    PubMed     Abstract available


  8. TRINITY L, Stege U, Jabbari H
    Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot.
    PLoS Comput Biol. 2024;20:e1011787.
    PubMed     Abstract available


  9. FOSTER ZSL, Tupper AS, Press CM, Grunwald NJ, et al
    Krisp: A Python package to aid in the design of CRISPR and amplification-based diagnostic assays from whole genome sequencing data.
    PLoS Comput Biol. 2024;20:e1012139.
    PubMed     Abstract available


  10. MASSEY A, Boennec C, Restrepo-Ortiz CX, Blanchet C, et al
    Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model.
    PLoS Comput Biol. 2024;20:e1012124.
    PubMed     Abstract available


  11. RAWSON T, Hinsley W, Sonabend R, Semenova E, et al
    The impact of health inequity on spatial variation of COVID-19 transmission in England.
    PLoS Comput Biol. 2024;20:e1012141.
    PubMed     Abstract available


    April 2024
  12. BENISTON E, Skittrall JP
    Locations and structures of influenza A virus packaging-associated signals and other functional elements via an in silico pipeline for predicting constrained features in RNA viruses.
    PLoS Comput Biol. 2024;20:e1012009.
    PubMed     Abstract available


  13. LISON A, Abbott S, Huisman J, Stadler T, et al
    Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates.
    PLoS Comput Biol. 2024;20:e1012021.
    PubMed     Abstract available


  14. BOUMAN JA, Hauser A, Grimm SL, Wohlfender M, et al
    Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models.
    PLoS Comput Biol. 2024;20:e1011575.
    PubMed     Abstract available


    March 2024
  15. SHAO Y, Magee AF, Vasylyeva TI, Suchard MA, et al
    Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.
    PLoS Comput Biol. 2024;20:e1011640.
    PubMed     Abstract available


  16. JIJON S, Czuppon P, Blanquart F, Debarre F, et al
    Using early detection data to estimate the date of emergence of an epidemic outbreak.
    PLoS Comput Biol. 2024;20:e1011934.
    PubMed     Abstract available


  17. HASSE T, Mantei E, Shahoei R, Pawnikar S, et al
    Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein.
    PLoS Comput Biol. 2024;20:e1011955.
    PubMed     Abstract available


  18. PUNG R, Russell TW, Kucharski AJ
    Detecting changes in generation and serial intervals under varying pathogen biology, contact patterns and outbreak response.
    PLoS Comput Biol. 2024;20:e1011967.
    PubMed     Abstract available


  19. ATAMER BALKAN B, Chang Y, Sparnaaij M, Wouda B, et al
    The multi-dimensional challenges of controlling respiratory virus transmission in indoor spaces: Insights from the linkage of a microscopic pedestrian simulation and SARS-CoV-2 transmission model.
    PLoS Comput Biol. 2024;20:e1011956.
    PubMed     Abstract available


    January 2024
  20. CHAN LYH, Ro G, Midtbo JE, Di Ruscio F, et al
    Modeling geographic vaccination strategies for COVID-19 in Norway.
    PLoS Comput Biol. 2024;20:e1011426.
    PubMed     Abstract available


  21. SHIN B, An G, Cockrell RC
    Examining B-cell dynamics and responsiveness in different inflammatory milieus using an agent-based model.
    PLoS Comput Biol. 2024;20:e1011776.
    PubMed     Abstract available


  22. GRUNNILL M, Arino J, McCarthy Z, Bragazzi NL, et al
    Modelling disease mitigation at mass gatherings: A case study of COVID-19 at the 2022 FIFA World Cup.
    PLoS Comput Biol. 2024;20:e1011018.
    PubMed     Abstract available


  23. PLANK MJ, Watson L, Maclaren OJ
    Near-term forecasting of Covid-19 cases and hospitalisations in Aotearoa New Zealand.
    PLoS Comput Biol. 2024;20:e1011752.
    PubMed     Abstract available


  24. RAMACHANDRAN A, Lumetta SS, Chen D
    PandoGen: Generating complete instances of future SARS-CoV-2 sequences using Deep Learning.
    PLoS Comput Biol. 2024;20:e1011790.
    PubMed     Abstract available


  25. VAN BOVEN M, van Dorp CH, Westerhof I, Jaddoe V, et al
    Estimation of introduction and transmission rates of SARS-CoV-2 in a prospective household study.
    PLoS Comput Biol. 2024;20:e1011832.
    PubMed     Abstract available


  26. LAMB KD, Luka MM, Saathoff M, Orton RJ, et al
    Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules.
    PLoS Comput Biol. 2024;20:e1011795.
    PubMed     Abstract available


    December 2023
  27. MOREL JD, Morel JM, Alvarez L
    Time warping between main epidemic time series in epidemiological surveillance.
    PLoS Comput Biol. 2023;19:e1011757.
    PubMed     Abstract available


  28. JOHNSON KE, Pasco R, Woody S, Lachmann M, et al
    Optimizing COVID-19 testing strategies on college campuses: Evaluation of the health and economic costs.
    PLoS Comput Biol. 2023;19:e1011715.
    PubMed     Abstract available


  29. ISLAM MA, Getz M, Macklin P, Ford Versypt AN, et al
    An agent-based modeling approach for lung fibrosis in response to COVID-19.
    PLoS Comput Biol. 2023;19:e1011741.
    PubMed     Abstract available


    November 2023
  30. ALAHAKOON P, Taylor PG, McCaw JM
    How effective were Australian Quarantine Stations in mitigating transmission aboard ships during the influenza pandemic of 1918-19?
    PLoS Comput Biol. 2023;19:e1011656.
    PubMed     Abstract available


  31. DRAKE JM, Handel A, Marty E, O'Dea EB, et al
    A data-driven semi-parametric model of SARS-CoV-2 transmission in the United States.
    PLoS Comput Biol. 2023;19:e1011610.
    PubMed     Abstract available


  32. WOOD AJ, Sanchez AR, Bessell PR, Wightman R, et al
    Assessing the importance of demographic risk factors across two waves of SARS-CoV-2 using fine-scale case data.
    PLoS Comput Biol. 2023;19:e1011611.
    PubMed     Abstract available


  33. BROCKHAUS EK, Wolffram D, Stadler T, Osthege M, et al
    Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany.
    PLoS Comput Biol. 2023;19:e1011653.
    PubMed     Abstract available


  34. VAN DER ROEST BR, Bootsma MCJ, Fischer EAJ, Klinkenberg D, et al
    A Bayesian inference method to estimate transmission trees with multiple introductions; applied to SARS-CoV-2 in Dutch mink farms.
    PLoS Comput Biol. 2023;19:e1010928.
    PubMed     Abstract available


  35. WARD T, Morris M, Gelman A, Carpenter B, et al
    Bayesian spatial modelling of localised SARS-CoV-2 transmission through mobility networks across England.
    PLoS Comput Biol. 2023;19:e1011580.
    PubMed     Abstract available


    October 2023
  36. HE M, Tang S, Xiao Y
    Combining the dynamic model and deep neural networks to identify the intensity of interventions during COVID-19 pandemic.
    PLoS Comput Biol. 2023;19:e1011535.
    PubMed     Abstract available


    September 2023
  37. ZHOU Z, Li D, Zhao Z, Shi S, et al
    Dynamical modelling of viral infection and cooperative immune protection in COVID-19 patients.
    PLoS Comput Biol. 2023;19:e1011383.
    PubMed     Abstract available


  38. ZHANG K, Xia Z, Huang S, Sun GQ, et al
    Evaluating the impact of test-trace-isolate for COVID-19 management and alternative strategies.
    PLoS Comput Biol. 2023;19:e1011423.
    PubMed     Abstract available


  39. MUNDAY JD, Abbott S, Meakin S, Funk S, et al
    Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England.
    PLoS Comput Biol. 2023;19:e1011453.
    PubMed     Abstract available


  40. OVERTON CE, Abbott S, Christie R, Cumming F, et al
    Nowcasting the 2022 mpox outbreak in England.
    PLoS Comput Biol. 2023;19:e1011463.
    PubMed     Abstract available


  41. WANG Z, Wu P, Wang L, Li B, et al
    Marginal effects of public health measures and COVID-19 disease burden in China: A large-scale modelling study.
    PLoS Comput Biol. 2023;19:e1011492.
    PubMed     Abstract available


    August 2023
  42. MORRIS M, Hayes P, Cox IJ, Lampos V, et al
    Neural network models for influenza forecasting with associated uncertainty using Web search activity trends.
    PLoS Comput Biol. 2023;19:e1011392.
    PubMed     Abstract available


  43. CLAIRON Q, Prague M, Planas D, Bruel T, et al
    Modeling the kinetics of the neutralizing antibody response against SARS-CoV-2 variants after several administrations of Bnt162b2.
    PLoS Comput Biol. 2023;19:e1011282.
    PubMed     Abstract available


  44. WOLFFRAM D, Abbott S, An der Heiden M, Funk S, et al
    Collaborative nowcasting of COVID-19 hospitalization incidences in Germany.
    PLoS Comput Biol. 2023;19:e1011394.
    PubMed     Abstract available


  45. RAACH B, Bundgaard N, Haase MJ, Starruss J, et al
    Influence of cell type specific infectivity and tissue composition on SARS-CoV-2 infection dynamics within human airway epithelium.
    PLoS Comput Biol. 2023;19:e1011356.
    PubMed     Abstract available


  46. YEDIDYA Y, Davis D, Drier Y
    SARS-CoV-2 infection perturbs enhancer mediated transcriptional regulation of key pathways.
    PLoS Comput Biol. 2023;19:e1011397.
    PubMed     Abstract available


  47. MARC A, Marlin R, Donati F, Prague M, et al
    Impact of variants of concern on SARS-CoV-2 viral dynamics in non-human primates.
    PLoS Comput Biol. 2023;19:e1010721.
    PubMed     Abstract available


  48. BOSSE NI, Abbott S, Cori A, van Leeuwen E, et al
    Scoring epidemiological forecasts on transformed scales.
    PLoS Comput Biol. 2023;19:e1011393.
    PubMed     Abstract available


  49. NASH RK, Bhatt S, Cori A, Nouvellet P, et al
    Estimating the epidemic reproduction number from temporally aggregated incidence data: A statistical modelling approach and software tool.
    PLoS Comput Biol. 2023;19:e1011439.
    PubMed     Abstract available


    July 2023
  50. SERVADIO JL, Thai PQ, Choisy M, Boni MF, et al
    Repeatability and timing of tropical influenza epidemics.
    PLoS Comput Biol. 2023;19:e1011317.
    PubMed     Abstract available


  51. LOU S, Yang M, Li T, Zhao W, et al
    Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes.
    PLoS Comput Biol. 2023;19:e1011222.
    PubMed     Abstract available


  52. ANDRESS C, Kappel K, Villena ME, Cuperlovic-Culf M, et al
    DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design.
    PLoS Comput Biol. 2023;19:e1010774.
    PubMed     Abstract available


  53. PARAG KV, Obolski U
    Risk averse reproduction numbers improve resurgence detection.
    PLoS Comput Biol. 2023;19:e1011332.
    PubMed     Abstract available


  54. YANG W, Shaman J
    Development of Accurate Long-lead COVID-19 Forecast.
    PLoS Comput Biol. 2023;19:e1011278.
    PubMed     Abstract available


    June 2023
  55. FOX SJ, Javan E, Pasco R, Gibson GC, et al
    Disproportionate impacts of COVID-19 in a large US city.
    PLoS Comput Biol. 2023;19:e1011149.
    PubMed     Abstract available


  56. DAN S, Chen Y, Chen Y, Monod M, et al
    Estimating fine age structure and time trends in human contact patterns from coarse contact data: The Bayesian rate consistency model.
    PLoS Comput Biol. 2023;19:e1011191.
    PubMed     Abstract available


  57. MOREL JD, Morel JM, Alvarez L
    Learning from the past: A short term forecast method for the COVID-19 incidence curve.
    PLoS Comput Biol. 2023;19:e1010790.
    PubMed     Abstract available


  58. XIONG YX, Wang MG, Chen L, Zhang XF, et al
    Cell-type annotation with accurate unseen cell-type identification using multiple references.
    PLoS Comput Biol. 2023;19:e1011261.
    PubMed     Abstract available


  59. BRETT TS, Bansal S, Rohani P
    Charting the spatial dynamics of early SARS-CoV-2 transmission in Washington state.
    PLoS Comput Biol. 2023;19:e1011263.
    PubMed     Abstract available


    May 2023
  60. MICHALSKI M, Setny P
    Two modes of fusogenic action for influenza virus fusion peptide.
    PLoS Comput Biol. 2023;19:e1011174.
    PubMed     Abstract available


  61. SPERRY MM, Oskotsky TT, Maric I, Kaushal S, et al
    Target-agnostic drug prediction integrated with medical record analysis uncovers differential associations of statins with increased survival in COVID-19 patients.
    PLoS Comput Biol. 2023;19:e1011050.
    PubMed     Abstract available


  62. IYANIWURA SA, Ringa N, Adu PA, Mak S, et al
    Understanding the impact of mobility on COVID-19 spread: A hybrid gravity-metapopulation model of COVID-19.
    PLoS Comput Biol. 2023;19:e1011123.
    PubMed     Abstract available


  63. GHOSH S, Birrell PJ, De Angelis D
    An approximate diffusion process for environmental stochasticity in infectious disease transmission modelling.
    PLoS Comput Biol. 2023;19:e1011088.
    PubMed     Abstract available


  64. SEKAR RV, Oliva PJ, Woodside MT
    Modelling the structures of frameshift-stimulatory pseudoknots from representative bat coronaviruses.
    PLoS Comput Biol. 2023;19:e1011124.
    PubMed     Abstract available


  65. SUNAGAWA J, Komorizono R, Park H, Hart WS, et al
    Contact-number-driven virus evolution: A multi-level modeling framework for the evolution of acute or persistent RNA virus infection.
    PLoS Comput Biol. 2023;19:e1011173.
    PubMed     Abstract available


    April 2023
  66. ZHAO C, Zhang J, Hou X, Yeung CH, et al
    A high-frequency mobility big-data reveals how COVID-19 spread across professions, locations and age groups.
    PLoS Comput Biol. 2023;19:e1011083.
    PubMed     Abstract available


    March 2023
  67. HARVEY WT, Davies V, Daniels RS, Whittaker L, et al
    A Bayesian approach to incorporate structural data into the mapping of genotype to antigenic phenotype of influenza A(H3N2) viruses.
    PLoS Comput Biol. 2023;19:e1010885.
    PubMed     Abstract available


  68. MURGA A, Bale R, Li CG, Ito K, et al
    Large eddy simulation of droplet transport and deposition in the human respiratory tract to evaluate inhalation risk.
    PLoS Comput Biol. 2023;19:e1010972.
    PubMed     Abstract available


  69. DAUTEL KA, Agyingi E, Pathmanathan P
    Validation framework for epidemiological models with application to COVID-19 models.
    PLoS Comput Biol. 2023;19:e1010968.
    PubMed     Abstract available


  70. LEONIDOU N, Renz A, Mostolizadeh R, Drager A, et al
    New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells.
    PLoS Comput Biol. 2023;19:e1010903.
    PubMed     Abstract available


  71. CAPPELLO L, Kim J, Palacios JA
    adaPop: Bayesian inference of dependent population dynamics in coalescent models.
    PLoS Comput Biol. 2023;19:e1010897.
    PubMed     Abstract available


    February 2023
  72. HAW DJ, Biggerstaff M, Prasad P, Walker J, et al
    Using real-time data to guide decision-making during an influenza pandemic: A modelling analysis.
    PLoS Comput Biol. 2023;19:e1010893.
    PubMed     Abstract available


  73. LI K, McCaw JM, Cao P
    Enhanced viral infectivity and reduced interferon production are associated with high pathogenicity for influenza viruses.
    PLoS Comput Biol. 2023;19:e1010886.
    PubMed     Abstract available


  74. NIELSEN BF, Saad-Roy CM, Li Y, Sneppen K, et al
    Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2.
    PLoS Comput Biol. 2023;19:e1010896.
    PubMed     Abstract available


  75. TRINITY L, Wark I, Lansing L, Jabbari H, et al
    Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot.
    PLoS Comput Biol. 2023;19:e1010922.
    PubMed     Abstract available


    January 2023
  76. ASHER J, Lemenuel-Diot A, Clay M, Durham DP, et al
    Novel modelling approaches to predict the role of antivirals in reducing influenza transmission.
    PLoS Comput Biol. 2023;19:e1010797.
    PubMed     Abstract available


  77. CHEN J, Tan S, Avadhanula V, Moise L, et al
    Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus.
    PLoS Comput Biol. 2023;19:e1010360.
    PubMed     Abstract available


  78. MA M, Lei X
    A dual graph neural network for drug-drug interactions prediction based on molecular structure and interactions.
    PLoS Comput Biol. 2023;19:e1010812.
    PubMed     Abstract available


  79. VON BULOW S, Sikora M, Blanc FEC, Covino R, et al
    Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants.
    PLoS Comput Biol. 2023;19:e1010822.
    PubMed     Abstract available


  80. ENGEBRETSEN S, Diz-Lois Palomares A, Ro G, Kristoffersen AB, et al
    A real-time regional model for COVID-19: Probabilistic situational awareness and forecasting.
    PLoS Comput Biol. 2023;19:e1010860.
    PubMed     Abstract available


  81. MEHRJOU A, Soleymani A, Abyaneh A, Bhatt S, et al
    Pyfectious: An individual-level simulator to discover optimal containment policies for epidemic diseases.
    PLoS Comput Biol. 2023;19:e1010799.
    PubMed     Abstract available


    December 2022
  82. BREEN CF, Mahmud AS, Feehan DM
    Novel estimates reveal subnational heterogeneities in disease-relevant contact patterns in the United States.
    PLoS Comput Biol. 2022;18:e1010742.
    PubMed     Abstract available


  83. BERGSTROM F, Gunther F, Hohle M, Britton T, et al
    Bayesian nowcasting with leading indicators applied to COVID-19 fatalities in Sweden.
    PLoS Comput Biol. 2022;18:e1010767.
    PubMed     Abstract available


  84. RUMACK A, Tibshirani RJ, Rosenfeld R
    Recalibrating probabilistic forecasts of epidemics.
    PLoS Comput Biol. 2022;18:e1010771.
    PubMed     Abstract available


    November 2022
  85. PERLINSKA AP, Stasiulewicz A, Nguyen ML, Swiderska K, et al
    Amino acid variants of SARS-CoV-2 papain-like protease have impact on drug binding.
    PLoS Comput Biol. 2022;18:e1010667.
    PubMed     Abstract available


  86. EALES O, Wang H, Haw D, Ainslie KEC, et al
    Trends in SARS-CoV-2 infection prevalence during England's roadmap out of lockdown, January to July 2021.
    PLoS Comput Biol. 2022;18:e1010724.
    PubMed     Abstract available


    October 2022
  87. LIN Y, Loo L, Tran A, Lin DM, et al
    Scalable workflow for characterization of cell-cell communication in COVID-19 patients.
    PLoS Comput Biol. 2022;18:e1010495.
    PubMed     Abstract available


  88. PEREZ-LOPEZ E, Gavrilova L, Disla J, Goodlad M, et al
    Ten simple rules for creating and sustaining antiracist graduate programs.
    PLoS Comput Biol. 2022;18:e1010516.
    PubMed     Abstract available


  89. ESPANA G, Perkins TA, Pollett SD, Smith ME, et al
    Prioritizing interventions for preventing COVID-19 outbreaks in military basic training.
    PLoS Comput Biol. 2022;18:e1010489.
    PubMed     Abstract available


  90. CHOWELL G, Dahal S, Tariq A, Roosa K, et al
    An ensemble n-sub-epidemic modeling framework for short-term forecasting epidemic trajectories: Application to the COVID-19 pandemic in the USA.
    PLoS Comput Biol. 2022;18:e1010602.
    PubMed     Abstract available


  91. GRESSANI O, Wallinga J, Althaus CL, Hens N, et al
    EpiLPS: A fast and flexible Bayesian tool for estimation of the time-varying reproduction number.
    PLoS Comput Biol. 2022;18:e1010618.
    PubMed     Abstract available


  92. HAZRA DK, Pujari BS, Shekatkar SM, Mozaffer F, et al
    Modelling the first wave of COVID-19 in India.
    PLoS Comput Biol. 2022;18:e1010632.
    PubMed     Abstract available


  93. WALDSTEIN KA, Yi J, Cho M, Mudumbai R, et al
    Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond.
    PLoS Comput Biol. 2022;18:e1010629.
    PubMed     Abstract available


  94. OVERTON CE, Webb L, Datta U, Fursman M, et al
    Novel methods for estimating the instantaneous and overall COVID-19 case fatality risk among care home residents in England.
    PLoS Comput Biol. 2022;18:e1010554.
    PubMed     Abstract available


    September 2022
  95. WALTARI E, Nafees S, McCutcheon KM, Wong J, et al
    AIRRscape: An interactive tool for exploring B-cell receptor repertoires and antibody responses.
    PLoS Comput Biol. 2022;18:e1010052.
    PubMed     Abstract available


  96. LI Q, Huang Y
    Optimizing global COVID-19 vaccine allocation: An agent-based computational model of 148 countries.
    PLoS Comput Biol. 2022;18:e1010463.
    PubMed     Abstract available


  97. ZHOU Z, Kolaczyk ED, Thompson RN, White LF, et al
    Estimation of heterogeneous instantaneous reproduction numbers with application to characterize SARS-CoV-2 transmission in Massachusetts counties.
    PLoS Comput Biol. 2022;18:e1010434.
    PubMed     Abstract available


  98. OVERTON CE, Pellis L, Stage HB, Scarabel F, et al
    EpiBeds: Data informed modelling of the COVID-19 hospital burden in England.
    PLoS Comput Biol. 2022;18:e1010406.
    PubMed     Abstract available


  99. HILTON J, Riley H, Pellis L, Aziza R, et al
    A computational framework for modelling infectious disease policy based on age and household structure with applications to the COVID-19 pandemic.
    PLoS Comput Biol. 2022;18:e1010390.
    PubMed     Abstract available


  100. KREFL D, Bergmann S
    Cross-GWAS coherence test at the gene and pathway level.
    PLoS Comput Biol. 2022;18:e1010517.
    PubMed     Abstract available


  101. WANG E, Chakraborty AK
    Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants.
    PLoS Comput Biol. 2022;18:e1010563.
    PubMed     Abstract available


  102. MCANDREW T, Reich NG
    An expert judgment model to predict early stages of the COVID-19 pandemic in the United States.
    PLoS Comput Biol. 2022;18:e1010485.
    PubMed     Abstract available


  103. ZHANG L, Chen L, Yu XA, Duvallet C, et al
    MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes.
    PLoS Comput Biol. 2022;18:e1010472.
    PubMed     Abstract available


  104. BOSSE NI, Abbott S, Bracher J, Hain H, et al
    Comparing human and model-based forecasts of COVID-19 in Germany and Poland.
    PLoS Comput Biol. 2022;18:e1010405.
    PubMed     Abstract available


    August 2022
  105. BARRAT-CHARLAIX P, Vaughan TG, Neher RA
    TreeKnit: Inferring ancestral reassortment graphs of influenza viruses.
    PLoS Comput Biol. 2022;18:e1010394.
    PubMed     Abstract available


  106. YIN S, Xu Y, Xu M, de Jong MCM, et al
    Habitat loss exacerbates pathogen spread: An Agent-based model of avian influenza infection in migratory waterfowl.
    PLoS Comput Biol. 2022;18:e1009577.
    PubMed     Abstract available


  107. ZHANG X, Lobinska G, Feldman M, Dekel E, et al
    A spatial vaccination strategy to reduce the risk of vaccine-resistant variants.
    PLoS Comput Biol. 2022;18:e1010391.
    PubMed     Abstract available


  108. HEITZMAN-BREEN N, Ciupe SM
    Modeling within-host and aerosol dynamics of SARS-CoV-2: The relationship with infectiousness.
    PLoS Comput Biol. 2022;18:e1009997.
    PubMed     Abstract available


  109. BEN-NUN M, Riley P, Turtle J, Riley S, et al
    Consistent pattern of epidemic slowing across many geographies led to longer, flatter initial waves of the COVID-19 pandemic.
    PLoS Comput Biol. 2022;18:e1010375.
    PubMed     Abstract available


  110. SHCHUR V, Spirin V, Sirotkin D, Burovski E, et al
    VGsim: Scalable viral genealogy simulator for global pandemic.
    PLoS Comput Biol. 2022;18:e1010409.
    PubMed     Abstract available


  111. KUYLEN EJ, Torneri A, Willem L, Libin PJK, et al
    Different forms of superspreading lead to different outcomes: Heterogeneity in infectiousness and contact behavior relevant for the case of SARS-CoV-2.
    PLoS Comput Biol. 2022;18:e1009980.
    PubMed     Abstract available


  112. CHITWOOD MH, Russi M, Gunasekera K, Havumaki J, et al
    Reconstructing the course of the COVID-19 epidemic over 2020 for US states and counties: Results of a Bayesian evidence synthesis model.
    PLoS Comput Biol. 2022;18:e1010465.
    PubMed     Abstract available


  113. PIRETTO E, Selvaggio G, Bragantini D, Domenici E, et al
    A novel logical model of COVID-19 intracellular infection to support therapies development.
    PLoS Comput Biol. 2022;18:e1010443.
    PubMed     Abstract available


  114. GAVENCIAK T, Monrad JT, Leech G, Sharma M, et al
    Seasonal variation in SARS-CoV-2 transmission in temperate climates: A Bayesian modelling study in 143 European regions.
    PLoS Comput Biol. 2022;18:e1010435.
    PubMed     Abstract available


    July 2022
  115. TAO J, Wang H, Wang W, Mi N, et al
    Binding mechanism of oseltamivir and influenza neuraminidase suggests perspectives for the design of new anti-influenza drugs.
    PLoS Comput Biol. 2022;18:e1010343.
    PubMed     Abstract available


  116. LEMAITRE JC, Pasetto D, Zanon M, Bertuzzo E, et al
    Optimal control of the spatial allocation of COVID-19 vaccines: Italy as a case study.
    PLoS Comput Biol. 2022;18:e1010237.
    PubMed     Abstract available


  117. JOO R, Sanchez-Tapia A, Mortara S, Bellini Saibene Y, et al
    Ten simple rules to host an inclusive conference.
    PLoS Comput Biol. 2022;18:e1010164.
    PubMed     Abstract available


  118. PAIK H, Kim J, Seo S
    Analysis of the docking property of host variants of hACE2 for SARS-CoV-2 in a large cohort.
    PLoS Comput Biol. 2022;18:e1009834.
    PubMed     Abstract available


  119. BLUMBERG S, Lu P, Kwan AT, Hoover CM, et al
    Modeling scenarios for mitigating outbreaks in congregate settings.
    PLoS Comput Biol. 2022;18:e1010308.
    PubMed     Abstract available


  120. JIMENEZ-GUARDENO JM, Ortega-Prieto AM, Menendez Moreno B, Maguire TJA, et al
    Drug repurposing based on a quantum-inspired method versus classical fingerprinting uncovers potential antivirals against SARS-CoV-2.
    PLoS Comput Biol. 2022;18:e1010330.
    PubMed     Abstract available


    June 2022
  121. WATERLOW NR, Toizumi M, van Leeuwen E, Thi Nguyen HA, et al
    Evidence for influenza and RSV interaction from 10 years of enhanced surveillance in Nha Trang, Vietnam, a modelling study.
    PLoS Comput Biol. 2022;18:e1010234.
    PubMed     Abstract available


  122. BEESLEY LJ, Osthus D, Del Valle SY
    Addressing delayed case reporting in infectious disease forecast modeling.
    PLoS Comput Biol. 2022;18:e1010115.
    PubMed     Abstract available


  123. SCHNEIDER T, Dunbar ORA, Wu J, Bottcher L, et al
    Epidemic management and control through risk-dependent individual contact interventions.
    PLoS Comput Biol. 2022;18:e1010171.
    PubMed     Abstract available


  124. EGUCHI RR, Choe CA, Huang PS
    Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation.
    PLoS Comput Biol. 2022;18:e1010271.
    PubMed     Abstract available


  125. ZHAO S, Chong MKC, Ryu S, Guo Z, et al
    Characterizing superspreading potential of infectious disease: Decomposition of individual transmissibility.
    PLoS Comput Biol. 2022;18:e1010281.
    PubMed     Abstract available


  126. ANDRADE J, Duggan J
    Inferring the effective reproductive number from deterministic and semi-deterministic compartmental models using incidence and mobility data.
    PLoS Comput Biol. 2022;18:e1010206.
    PubMed     Abstract available


    May 2022
  127. GOZZI N, Chinazzi M, Davis JT, Mu K, et al
    Anatomy of the first six months of COVID-19 vaccination campaign in Italy.
    PLoS Comput Biol. 2022;18:e1010146.
    PubMed     Abstract available


  128. RAHMANDAD H, Xu R, Ghaffarzadegan N
    Enhancing long-term forecasting: Learning from COVID-19 models.
    PLoS Comput Biol. 2022;18:e1010100.
    PubMed     Abstract available


  129. RIBEIRO-FILHO HV, Jara GE, Batista FAH, Schleder GR, et al
    Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding.
    PLoS Comput Biol. 2022;18:e1010121.
    PubMed     Abstract available


  130. KOSLOW W, Kuhn MJ, Binder S, Klitz M, et al
    Appropriate relaxation of non-pharmaceutical interventions minimizes the risk of a resurgence in SARS-CoV-2 infections in spite of the Delta variant.
    PLoS Comput Biol. 2022;18:e1010054.
    PubMed     Abstract available


  131. LENG T, Hill EM, Thompson RN, Tildesley MJ, et al
    Assessing the impact of lateral flow testing strategies on within-school SARS-CoV-2 transmission and absences: A modelling study.
    PLoS Comput Biol. 2022;18:e1010158.
    PubMed     Abstract available


  132. MAKOWSKI EK, Schardt JS, Smith MD, Tessier PM, et al
    Mutational analysis of SARS-CoV-2 variants of concern reveals key tradeoffs between receptor affinity and antibody escape.
    PLoS Comput Biol. 2022;18:e1010160.
    PubMed     Abstract available


  133. VALLES TE, Shoenhard H, Zinski J, Trick S, et al
    Networks of necessity: Simulating COVID-19 mitigation strategies for disabled people and their caregivers.
    PLoS Comput Biol. 2022;18:e1010042.
    PubMed     Abstract available


    April 2022
  134. MOLLA J, Ponce de Leon Chavez A, Hiraoka T, Ala-Nissila T, et al
    Adaptive and optimized COVID-19 vaccination strategies across geographical regions and age groups.
    PLoS Comput Biol. 2022;18:e1009974.
    PubMed     Abstract available


  135. LEDEBUR K, Kaleta M, Chen J, Lindner SD, et al
    Meteorological factors and non-pharmaceutical interventions explain local differences in the spread of SARS-CoV-2 in Austria.
    PLoS Comput Biol. 2022;18:e1009973.
    PubMed     Abstract available


  136. BARSI S, Papp H, Valdeolivas A, Toth DJ, et al
    Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity.
    PLoS Comput Biol. 2022;18:e1010021.
    PubMed     Abstract available


  137. SERAFINO M, Monteiro HS, Luo S, Reis SDS, et al
    Digital contact tracing and network theory to stop the spread of COVID-19 using big-data on human mobility geolocalization.
    PLoS Comput Biol. 2022;18:e1009865.
    PubMed     Abstract available


  138. DE MAIO N, Boulton W, Weilguny L, Walker CR, et al
    phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets.
    PLoS Comput Biol. 2022;18:e1010056.
    PubMed     Abstract available


    March 2022
  139. SOUTO FERREIRA L, Canton O, da Silva RLP, Poloni S, et al
    Assessing the best time interval between doses in a two-dose vaccination regimen to reduce the number of deaths in an ongoing epidemic of SARS-CoV-2.
    PLoS Comput Biol. 2022;18:e1009978.
    PubMed     Abstract available


  140. LI H, Deng Y, Li Z, Dorken Gallastegi A, et al
    Multiphysics and multiscale modeling of microthrombosis in COVID-19.
    PLoS Comput Biol. 2022;18:e1009892.
    PubMed     Abstract available


  141. MACGOWAN SA, Barton MI, Kutuzov M, Dushek O, et al
    Missense variants in human ACE2 strongly affect binding to SARS-CoV-2 Spike providing a mechanism for ACE2 mediated genetic risk in Covid-19: A case study in affinity predictions of interface variants.
    PLoS Comput Biol. 2022;18:e1009922.
    PubMed     Abstract available


  142. DE SALAZAR PM, Lu F, Hay JA, Gomez-Barroso D, et al
    Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data.
    PLoS Comput Biol. 2022;18:e1009964.
    PubMed     Abstract available


  143. FRANCO N, Coletti P, Willem L, Angeli L, et al
    Inferring age-specific differences in susceptibility to and infectiousness upon SARS-CoV-2 infection based on Belgian social contact data.
    PLoS Comput Biol. 2022;18:e1009965.
    PubMed     Abstract available


  144. PROVERBIO D, Kemp F, Magni S, Goncalves J, et al
    Performance of early warning signals for disease re-emergence: A case study on COVID-19 data.
    PLoS Comput Biol. 2022;18:e1009958.
    PubMed     Abstract available


  145. TSIRTSIS S, De A, Lorch L, Gomez-Rodriguez M, et al
    Pooled testing of traced contacts under superspreading dynamics.
    PLoS Comput Biol. 2022;18:e1010008.
    PubMed     Abstract available


  146. MUKHERJEE S, Wethington D, Dey TK, Das J, et al
    Determining clinically relevant features in cytometry data using persistent homology.
    PLoS Comput Biol. 2022;18:e1009931.
    PubMed     Abstract available


    February 2022
  147. GAVISH N, Katriel G
    The role of childrens' vaccination for COVID-19-Pareto-optimal allocations of vaccines.
    PLoS Comput Biol. 2022;18:e1009872.
    PubMed     Abstract available


  148. KLINK GV, Kalinina OV, Bazykin GA
    Phylogenetic inference of changes in amino acid propensities with single-position resolution.
    PLoS Comput Biol. 2022;18:e1009878.
    PubMed     Abstract available


  149. 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. 2022;18:e1009851.
    PubMed     Abstract available


  150. ZELNER J, Masters NB, Naraharisetti R, Mojola SA, et al
    There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk.
    PLoS Comput Biol. 2022;18:e1009795.
    PubMed     Abstract available


  151. D'ANDREA V, Gallotti R, Castaldo N, De Domenico M, et al
    Individual risk perception and empirical social structures shape the dynamics of infectious disease outbreaks.
    PLoS Comput Biol. 2022;18:e1009760.
    PubMed     Abstract available


  152. FOIX A, Lopez D, Diez-Fuertes F, McConnell MJ, et al
    Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2.
    PLoS Comput Biol. 2022;18:e1009726.
    PubMed     Abstract available


  153. YANG X, Wang S, Xing Y, Li L, et al
    Bayesian data assimilation for estimating instantaneous reproduction numbers during epidemics: Applications to COVID-19.
    PLoS Comput Biol. 2022;18:e1009807.
    PubMed     Abstract available


    January 2022
  154. OSTHUS D
    Fast and accurate influenza forecasting in the United States with Inferno.
    PLoS Comput Biol. 2022;18:e1008651.
    PubMed     Abstract available


  155. REGULY IZ, Csercsik D, Juhasz J, Tornai K, et al
    Microsimulation based quantitative analysis of COVID-19 management strategies.
    PLoS Comput Biol. 2022;18:e1009693.
    PubMed     Abstract available


  156. NGUYEN LKN, Megiddo I, Howick S
    Hybrid simulation modelling of networks of heterogeneous care homes and the inter-facility spread of Covid-19 by sharing staff.
    PLoS Comput Biol. 2022;18:e1009780.
    PubMed     Abstract available


  157. SAKURABA S, Xie Q, Kasahara K, Iwakiri J, et al
    Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex.
    PLoS Comput Biol. 2022;18:e1009804.
    PubMed     Abstract available


  158. LASSO G, Khan S, Allen SA, Mariano M, et al
    Longitudinally monitored immune biomarkers predict the timing of COVID-19 outcomes.
    PLoS Comput Biol. 2022;18:e1009778.
    PubMed     Abstract available


    December 2021
  159. AMITAI A
    Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure.
    PLoS Comput Biol. 2021;17:e1009664.
    PubMed     Abstract available


  160. LARSEN JR, Martin MR, Martin JD, Hicks JB, et al
    Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant.
    PLoS Comput Biol. 2021;17:e1009629.
    PubMed     Abstract available


  161. MIURA F, Leung KY, Klinkenberg D, Ainslie KEC, et al
    Optimal vaccine allocation for COVID-19 in the Netherlands: A data-driven prioritization.
    PLoS Comput Biol. 2021;17:e1009697.
    PubMed     Abstract available


  162. ROBINSON SA, Raybould MIJ, Schneider C, Wong WK, et al
    Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies.
    PLoS Comput Biol. 2021;17:e1009675.
    PubMed     Abstract available


  163. MOSES ME, Hofmeyr S, Cannon JL, Andrews A, et al
    Spatially distributed infection increases viral load in a computational model of SARS-CoV-2 lung infection.
    PLoS Comput Biol. 2021;17:e1009735.
    PubMed     Abstract available


  164. ANNAPRAGADA AV, Greenstein JL, Bose SN, Winters BD, et al
    SWIFT: A deep learning approach to prediction of hypoxemic events in critically-Ill patients using SpO2 waveform prediction.
    PLoS Comput Biol. 2021;17:e1009712.
    PubMed     Abstract available


  165. MCCALL MN, Chu CY, Wang L, Benoodt L, et al
    A systems genomics approach uncovers molecular associates of RSV severity.
    PLoS Comput Biol. 2021;17:e1009617.
    PubMed     Abstract available


  166. BAKER JJ, Mathy CJP, Schaletzky J
    A proposed workflow for proactive virus surveillance and prediction of variants for vaccine design.
    PLoS Comput Biol. 2021;17:e1009624.
    PubMed    


    November 2021
  167. KING SB, Singh M
    Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections.
    PLoS Comput Biol. 2021;17:e1009560.
    PubMed     Abstract available


  168. ZUVANOV L, Basso Garcia AL, Correr FH, Bizarria R Jr, et al
    The experience of teaching introductory programming skills to bioscientists in Brazil.
    PLoS Comput Biol. 2021;17:e1009534.
    PubMed     Abstract available


  169. WANG S, Hao M, Pan Z, Lei J, et al
    Data-driven multi-scale mathematical modeling of SARS-CoV-2 infection reveals heterogeneity among COVID-19 patients.
    PLoS Comput Biol. 2021;17:e1009587.
    PubMed     Abstract available


    October 2021
  170. MAZZOLI M, Pepe E, Mateo D, Cattuto C, et al
    Interplay between mobility, multi-seeding and lockdowns shapes COVID-19 local impact.
    PLoS Comput Biol. 2021;17:e1009326.
    PubMed     Abstract available


  171. HUANG Y, Chattopadhyay I
    Universal risk phenotype of US counties for flu-like transmission to improve county-specific COVID-19 incidence forecasts.
    PLoS Comput Biol. 2021;17:e1009363.
    PubMed     Abstract available


  172. HOWERTON E, Ferrari MJ, Bjornstad ON, Bogich TL, et al
    Synergistic interventions to control COVID-19: Mass testing and isolation mitigates reliance on distancing.
    PLoS Comput Biol. 2021;17:e1009518.
    PubMed     Abstract available


  173. AYLETT-BULLOCK J, Cuesta-Lazaro C, Quera-Bofarull A, Katta A, et al
    Operational response simulation tool for epidemics within refugee and IDP settlements: A scenario-based case study of the Cox's Bazar settlement.
    PLoS Comput Biol. 2021;17:e1009360.
    PubMed     Abstract available


  174. CHEN D, Xue Y, Xiao Y
    Determining travel fluxes in epidemic areas.
    PLoS Comput Biol. 2021;17:e1009473.
    PubMed     Abstract available


  175. COTMAN ZJ, Bowden MJ, Richter BP, Phelps JH, et al
    Factors affecting aerosol SARS-CoV-2 transmission via HVAC systems; a modeling study.
    PLoS Comput Biol. 2021;17:e1009474.
    PubMed     Abstract available


  176. GUIGNON V, Breton C, Mariette J, Sabot F, et al
    Ten simple rules for switching from face-to-face to remote conference: An opportunity to estimate the reduction in GHG emissions.
    PLoS Comput Biol. 2021;17:e1009321.
    PubMed     Abstract available


  177. RADEV ST, Graw F, Chen S, Mutters NT, et al
    OutbreakFlow: Model-based Bayesian inference of disease outbreak dynamics with invertible neural networks and its application to the COVID-19 pandemics in Germany.
    PLoS Comput Biol. 2021;17:e1009472.
    PubMed     Abstract available


    September 2021
  178. GOZZI N, Bajardi P, Perra N
    The importance of non-pharmaceutical interventions during the COVID-19 vaccine rollout.
    PLoS Comput Biol. 2021;17:e1009346.
    PubMed     Abstract available


  179. 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


  180. 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


  181. ZHANG S, Ponce J, Zhang Z, Lin G, et al
    An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City.
    PLoS Comput Biol. 2021;17:e1009334.
    PubMed     Abstract available


  182. CHIU WA, Ndeffo-Mbah ML
    Using test positivity and reported case rates to estimate state-level COVID-19 prevalence and seroprevalence in the United States.
    PLoS Comput Biol. 2021;17:e1009374.
    PubMed     Abstract available


  183. YIN R, Guest JD, Taherzadeh G, Gowthaman R, et al
    Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants.
    PLoS Comput Biol. 2021;17:e1009380.
    PubMed     Abstract available


  184. CHEN S, Flegg JA, White LJ, Aguas R, et al
    Levels of SARS-CoV-2 population exposure are considerably higher than suggested by seroprevalence surveys.
    PLoS Comput Biol. 2021;17:e1009436.
    PubMed     Abstract available


  185. GUGOLE F, Coffeng LE, Edeling W, Sanderse B, et al
    Uncertainty quantification and sensitivity analysis of COVID-19 exit strategies in an individual-based transmission model.
    PLoS Comput Biol. 2021;17:e1009355.
    PubMed     Abstract available


  186. PARAG KV
    Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves.
    PLoS Comput Biol. 2021;17:e1009347.
    PubMed     Abstract available


    August 2021
  187. GUERSTEIN S, Romeo-Aznar V, Dekel M, Miron O, et al
    The interplay between vaccination and social distancing strategies affects COVID19 population-level outcomes.
    PLoS Comput Biol. 2021;17:e1009319.
    PubMed     Abstract available


  188. 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


  189. 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


  190. 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


  191. 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


  192. 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


  193. WERTHEIM KY, Puniya BL, La Fleur A, Shah AR, et al
    A multi-approach and multi-scale platform to model CD4+ T cells responding to infections.
    PLoS Comput Biol. 2021;17:e1009209.
    PubMed     Abstract available


    July 2021
  194. 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


  195. 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


  196. 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


  197. 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


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


  199. 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


  200. 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


  201. 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


  202. 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


  203. 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


  204. 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


  205. 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


  206. 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
  207. 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


  208. 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


  209. 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


  210. 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


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


  212. 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
  213. 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


  214. 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


  215. 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


  216. 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
  217. 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


  218. 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
  219. ZIPFEL CM, Colizza V, Bansal S
    Health inequities in influenza transmission and surveillance.
    PLoS Comput Biol. 2021;17:e1008642.
    PubMed     Abstract available


  220. 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


  221. 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


  222. 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


  223. 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


  224. 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


  225. 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


  226. 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


  227. 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


  228. 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


  229. 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


  230. 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
  231. 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


  232. 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


  233. 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


  234. 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


  235. 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


  236. 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


  237. 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
  238. 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


  239. 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


  240. 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


  241. 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


  242. 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


  243. 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


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


  245. 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
  246. 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


  247. 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


  248. 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


  249. 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


  250. 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


  251. 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


  252. 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


  253. 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


  254. 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


  255. 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
  256. 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


  257. 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


  258. 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
  259. 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


  260. 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


  261. 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


  262. 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


  263. 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


  264. 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


  265. 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


  266. 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    


  267. 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
  268. 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


  269. 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


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