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Articles published in PLoS Comput Biol

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    September 2023
  1. 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

  2. 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

  3. 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

    August 2023
  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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
  12. 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

  13. 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

  14. 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

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

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

    June 2023
  17. 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

  18. 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

  19. 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

  20. 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

  21. 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
  22. MICHALSKI M, Setny P
    Two modes of fusogenic action for influenza virus fusion peptide.
    PLoS Comput Biol. 2023;19:e1011174.
    PubMed     Abstract available

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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
  28. 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
  29. 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

  30. 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

  31. 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

  32. 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

  33. 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
  34. 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

  35. 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

  36. 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

  37. 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
  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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
  44. 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

  45. 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

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

    November 2022
  47. 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

  48. 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
  49. 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

  50. 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

  51. 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

  52. 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

  53. 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

  54. 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

  55. 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

  56. 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
  57. 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

  58. 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

  59. 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

  60. 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

  61. 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

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

  63. 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

  64. 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

  65. 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

  66. 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
  67. BARRAT-CHARLAIX P, Vaughan TG, Neher RA
    TreeKnit: Inferring ancestral reassortment graphs of influenza viruses.
    PLoS Comput Biol. 2022;18:e1010394.
    PubMed     Abstract available

  68. 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

  69. 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

    Modeling within-host and aerosol dynamics of SARS-CoV-2: The relationship with infectiousness.
    PLoS Comput Biol. 2022;18:e1009997.
    PubMed     Abstract available

  71. 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

  72. 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

  73. 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

  74. 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

  75. 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

  76. 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
  77. 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

  78. 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

  79. 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

  80. 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

  81. 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

  82. 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
  83. 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

  84. 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

  85. 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

  86. 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

  87. 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

  88. 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
  89. 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

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

  91. 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

  92. 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

  93. 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

  94. 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

  95. 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
  96. 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

  97. 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

  98. 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

  99. 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

  100. 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
  101. 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

  102. 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

  103. 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

  104. 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

  105. 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

  106. 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

  107. 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

  108. 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
  109. 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

  110. KLINK GV, Kalinina OV, Bazykin GA
    Phylogenetic inference of changes in amino acid propensities with single-position resolution.
    PLoS Comput Biol. 2022;18:e1009878.
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    Use of Angiotensin-Converting Enzyme Inhibitors and Angiotensin II Receptor Blockers During the COVID-19 Pandemic: A Modeling Analysis.
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  226. HOLLINGSWORTH B, Okamoto KW, Lloyd AL
    After the honeymoon, the divorce: Unexpected outcomes of disease control measures against endemic infections.
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    A model-based evaluation of the efficacy of COVID-19 social distancing, testing and hospital triage policies.
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    Ten simple rules for women principal investigators during a pandemic.
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    Estimating effective population size changes from preferentially sampled genetic sequences.
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    IL6-mediated HCoV-host interactome regulatory network and GO/Pathway enrichment analysis.
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