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Influenza

Free Subscription Articles published in PLoS Comput Biol Retrieve available abstracts of 255 articles: HTML format

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March 2024
1. 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
   
   
   
2. 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
   
   
   
3. 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
   
   
   
4. 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
   
   
   
5. 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
6. 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
   
   
   
7. 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
   
   
   
8. 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
   
   
   
9. 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
   
   
   
10. 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
    
    
    
11. 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
    
    
    
12. 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
13. 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
    
    
    
14. 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
    
    
    
15. 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
16. 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
    
    
    
17. 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
    
    
    
18. 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
    
    
    
19. 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
    
    
    
20. 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
    
    
    
21. 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
22. 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
23. 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
    
    
    
24. 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
    
    
    
25. 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
    
    
    
26. 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
    
    
    
27. 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
28. 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
    
    
    
29. 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
    
    
    
30. 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
    
    
    
31. 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
    
    
    
32. 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
    
    
    
33. 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
    
    
    
34. 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
    
    
    
35. 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
36. 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
    
    
    
37. 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
    
    
    
38. 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
    
    
    
39. PARAG KV, Obolski U
    Risk averse reproduction numbers improve resurgence detection.
    PLoS Comput Biol. 2023;19:e1011332.
    PubMed     Abstract available
    
    
    
40. YANG W, Shaman J
    Development of Accurate Long-lead COVID-19 Forecast.
    PLoS Comput Biol. 2023;19:e1011278.
    PubMed     Abstract available
    
    
    June 2023
41. 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
    
    
    
42. 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
    
    
    
43. 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
    
    
    
44. 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
    
    
    
45. 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
46. MICHALSKI M, Setny P
    Two modes of fusogenic action for influenza virus fusion peptide.
    PLoS Comput Biol. 2023;19:e1011174.
    PubMed     Abstract available
    
    
    
47. 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
    
    
    
48. 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
    
    
    
49. 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
    
    
    
50. 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
    
    
    
51. 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
52. 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
53. 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
    
    
    
54. 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
    
    
    
55. 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
    
    
    
56. 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
    
    
    
57. 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
58. 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
    
    
    
59. 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
    
    
    
60. 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
    
    
    
61. 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
62. 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
    
    
    
63. 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
    
    
    
64. 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
    
    
    
65. 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
    
    
    
66. 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
    
    
    
67. 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
68. 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
    
    
    
69. 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
    
    
    
70. RUMACK A, Tibshirani RJ, Rosenfeld R
    Recalibrating probabilistic forecasts of epidemics.
    PLoS Comput Biol. 2022;18:e1010771.
    PubMed     Abstract available
    
    
    November 2022
71. 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
    
    
    
72. 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
73. 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
    
    
    
74. 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
    
    
    
75. 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
    
    
    
76. 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
    
    
    
77. 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
    
    
    
78. 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
    
    
    
79. 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
    
    
    
80. 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
81. 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
    
    
    
82. 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
    
    
    
83. 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
    
    
    
84. 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
    
    
    
85. 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
    
    
    
86. KREFL D, Bergmann S
    Cross-GWAS coherence test at the gene and pathway level.
    PLoS Comput Biol. 2022;18:e1010517.
    PubMed     Abstract available
    
    
    
87. 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
    
    
    
88. 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
    
    
    
89. 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
    
    
    
90. 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
91. BARRAT-CHARLAIX P, Vaughan TG, Neher RA
    TreeKnit: Inferring ancestral reassortment graphs of influenza viruses.
    PLoS Comput Biol. 2022;18:e1010394.
    PubMed     Abstract available
    
    
    
92. 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
    
    
    
93. 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
    
    
    
94. 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
    
    
    
95. 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
    
    
    
96. 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
    
    
    
97. 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
    
    
    
98. 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
    
    
    
99. 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
    
    
    
100. 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
101. 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
     
     
     
102. 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
     
     
     
103. 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
     
     
     
104. 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
     
     
     
105. 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
     
     
     
106. 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
107. 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
     
     
     
108. 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
     
     
     
109. 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
     
     
     
110. 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
     
     
     
111. 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
     
     
     
112. 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
113. 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
     
     
     
114. RAHMANDAD H, Xu R, Ghaffarzadegan N
     Enhancing long-term forecasting: Learning from COVID-19 models.
     PLoS Comput Biol. 2022;18:e1010100.
     PubMed     Abstract available
     
     
     
115. 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
     
     
     
116. 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
     
     
     
117. 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
     
     
     
118. 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
     
     
     
119. 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
120. 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
     
     
     
121. 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
     
     
     
122. 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
     
     
     
123. 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
     
     
     
124. 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
125. 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
     
     
     
126. 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
     
     
     
127. 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
     
     
     
128. 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
     
     
     
129. 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
     
     
     
130. 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
     
     
     
131. 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
     
     
     
132. 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
133. 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
     
     
     
134. 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
     
     
     
135. 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
     
     
     
136. 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
     
     
     
137. 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
     
     
     
138. 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
     
     
     
139. 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
140. OSTHUS D
     Fast and accurate influenza forecasting in the United States with Inferno.
     PLoS Comput Biol. 2022;18:e1008651.
     PubMed     Abstract available
     
     
     
141. 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
     
     
     
142. 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
     
     
     
143. 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
     
     
     
144. 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
145. AMITAI A
     Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure.
     PLoS Comput Biol. 2021;17:e1009664.
     PubMed     Abstract available
     
     
     
146. 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
     
     
     
147. 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
     
     
     
148. 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
     
     
     
149. 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
     
     
     
150. 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
     
     
     
151. 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
     
     
     
152. 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
153. 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
     
     
     
154. 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
     
     
     
155. 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
156. 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
     
     
     
157. 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
     
     
     
158. 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
     
     
     
159. 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
     
     
     
160. CHEN D, Xue Y, Xiao Y
     Determining travel fluxes in epidemic areas.
     PLoS Comput Biol. 2021;17:e1009473.
     PubMed     Abstract available
     
     
     
161. 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
     
     
     
162. 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
     
     
     
163. 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
164. 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
     
     
     
165. 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
     
     
     
166. 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
     
     
     
167. 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
     
     
     
168. 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
     
     
     
169. 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
     
     
     
170. 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
     
     
     
171. 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
     
     
     
172. 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
173. 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
     
     
     
174. 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
     
     
     
175. 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
     
     
     
176. 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
     
     
     
177. 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
     
     
     
178. 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
     
     
     
179. 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
180. 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
     
     
     
181. 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
     
     
     
182. 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
     
     
     
183. 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
     
     
     
184. CHERIAN P, Krishna S, Menon GI
     Optimizing testing for COVID-19 in India.
     PLoS Comput Biol. 2021;17:e1009126.
     PubMed     Abstract available
     
     
     
185. 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
     
     
     
186. 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
     
     
     
187. 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
     
     
     
188. 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
     
     
     
189. 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
     
     
     
190. 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
     
     
     
191. 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
     
     
     
192. 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
193. 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
     
     
     
194. 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
     
     
     
195. 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
     
     
     
196. 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
     
     
     
197. GARDNER BJ, Kilpatrick AM
     Contact tracing efficiency, transmission heterogeneity, and accelerating COVID-19 epidemics.
     PLoS Comput Biol. 2021;17:e1009122.
     PubMed     Abstract available
     
     
     
198. 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
199. 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
     
     
     
200. 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
     
     
     
201. 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
     
     
     
202. 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
203. 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
     
     
     
204. 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
205. ZIPFEL CM, Colizza V, Bansal S
     Health inequities in influenza transmission and surveillance.
     PLoS Comput Biol. 2021;17:e1008642.
     PubMed     Abstract available
     
     
     
206. 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
     
     
     
207. 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
     
     
     
208. 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
     
     
     
209. 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
     
     
     
210. 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
     
     
     
211. 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
     
     
     
212. 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
     
     
     
213. 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
     
     
     
214. 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
     
     
     
215. 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
     
     
     
216. 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
217. 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
     
     
     
218. 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
     
     
     
219. 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
     
     
     
220. 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
     
     
     
221. 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
     
     
     
222. 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
     
     
     
223. 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
224. 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
     
     
     
225. 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
     
     
     
226. 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
     
     
     
227. 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
     
     
     
228. 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
     
     
     
229. 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
     
     
     
230. SHARKER Y, Kenah E
     Estimating and interpreting secondary attack risk: Binomial considered biased.
     PLoS Comput Biol. 2021;17:e1008601.
     PubMed     Abstract available
     
     
     
231. 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
232. 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
     
     
     
233. 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
     
     
     
234. 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
     
     
     
235. 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
     
     
     
236. 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
     
     
     
237. 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
     
     
     
238. 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
     
     
     
239. 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
     
     
     
240. 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
     
     
     
241. 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
242. 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
     
     
     
243. 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
     
     
     
244. 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
245. 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
     
     
     
246. 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
     
     
     
247. 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
     
     
     
248. 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
     
     
     
249. 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
     
     
     
250. 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
     
     
     
251. 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
     
     
     
252. 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    
     
     
     
253. 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
254. 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
     
     
     
255. 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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