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Articles published in
PLoS Comput Biol
    July 2021
  1. LLOYD T, Steigler P, Mpande CAM, Rozot V, et al
    Multidimensional analysis of immune responses identified biomarkers of recent Mycobacterium tuberculosis infection.
    PLoS Comput Biol. 2021;17:e1009197.
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    June 2021
  2. ESENER N, Guerra AM, Giebel K, Lea D, et al
    Mass spectrometry and machine learning for the accurate diagnosis of benzylpenicillin and multidrug resistance of Staphylococcus aureus in bovine mastitis.
    PLoS Comput Biol. 2021;17:e1009108.
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  3. GONCALVES BP, Procter SR, Clifford S, Koukounari A, et al
    Estimation of country-level incidence of early-onset invasive Group B Streptococcus disease in infants using Bayesian methods.
    PLoS Comput Biol. 2021;17:e1009001.
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    March 2021
  4. WOOTEN DJ, Zanudo JGT, Murrugarra D, Perry AM, et al
    Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies.
    PLoS Comput Biol. 2021;17:e1008690.
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  5. GUYEUX C, Sola C, Nous C, Refregier G, et al
    CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.
    PLoS Comput Biol. 2021;17:e1008500.
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    February 2021
  6. HAVUMAKI J, Cohen T, Zhai C, Miller JC, et al
    Protective impacts of household-based tuberculosis contact tracing are robust across endemic incidence levels and community contact patterns.
    PLoS Comput Biol. 2021;17:e1008713.
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  7. HENSON MA
    Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection.
    PLoS Comput Biol. 2021;17:e1008782.
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    January 2021
  8. KHAKZAD H, Happonen L, Karami Y, Chowdhury S, et al
    Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology.
    PLoS Comput Biol. 2021;17:e1008169.
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  9. KACHALOV VN, Nguyen H, Balakrishna S, Salazar-Vizcaya L, et al
    Identifying the drivers of multidrug-resistant Klebsiella pneumoniae at a European level.
    PLoS Comput Biol. 2021;17:e1008446.
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  10. LI J, Manitz J, Bertuzzo E, Kolaczyk ED, et al
    Sensor-based localization of epidemic sources on human mobility networks.
    PLoS Comput Biol. 2021;17:e1008545.
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  11. EYRE DW, Laager M, Walker AS, Cooper BS, et al
    Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission.
    PLoS Comput Biol. 2021;17:e1008417.
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    December 2020
  12. EVANS S, Butler JR, Mattila JT, Kirschner DE, et al
    Systems biology predicts that fibrosis in tuberculous granulomas may arise through macrophage-to-myofibroblast transformation.
    PLoS Comput Biol. 2020;16:e1008520.
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  13. LIBISELLER-EGGER J, Phelan J, Campino S, Mohareb F, et al
    Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers.
    PLoS Comput Biol. 2020;16:e1008518.
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    October 2020
  14. CLIFF OM, McLean N, Sintchenko V, Fair KM, et al
    Inferring evolutionary pathways and directed genotype networks of foodborne pathogens.
    PLoS Comput Biol. 2020;16:e1008401.
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  15. LYDEAMORE MJ, Campbell PT, Price DJ, Wu Y, et al
    Estimation of the force of infection and infectious period of skin sores in remote Australian communities using interval-censored data.
    PLoS Comput Biol. 2020;16:e1007838.
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    August 2020
  16. FORS J, Strydom N, Fox WS, Keizer RJ, et al
    Mathematical model and tool to explore shorter multi-drug therapy options for active pulmonary tuberculosis.
    PLoS Comput Biol. 2020;16:e1008107.
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  17. CLARELLI F, Palmer A, Singh B, Storflor M, et al
    Drug-target binding quantitatively predicts optimal antibiotic dose levels in quinolones.
    PLoS Comput Biol. 2020;16:e1008106.
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  18. HOYLE A, Cairns D, Paterson I, McMillan S, et al
    Optimising efficacy of antibiotics against systemic infection by varying dosage quantities and times.
    PLoS Comput Biol. 2020;16:e1008037.
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    July 2020
  19. KRIEGER MS, Denison CE, Anderson TL, Nowak MA, et al
    Population structure across scales facilitates coexistence and spatial heterogeneity of antibiotic-resistant infections.
    PLoS Comput Biol. 2020;16:e1008010.
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    June 2020
  20. LOPEZ-AGUDELO VA, Mendum TA, Laing E, Wu H, et al
    A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks.
    PLoS Comput Biol. 2020;16:e1007533.
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  21. CHISHOLM RH, Sonenberg N, Lacey JA, McDonald MI, et al
    Epidemiological consequences of enduring strain-specific immunity requiring repeated episodes of infection.
    PLoS Comput Biol. 2020;16:e1007182.
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  22. CARRUTHERS J, Lythe G, Lopez-Garcia M, Gillard J, et al
    Stochastic dynamics of Francisella tularensis infection and replication.
    PLoS Comput Biol. 2020;16:e1007752.
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    May 2020
  23. HAZELBAG CM, Dushoff J, Dominic EM, Mthombothi ZE, et al
    Calibration of individual-based models to epidemiological data: A systematic review.
    PLoS Comput Biol. 2020;16:e1007893.
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  24. WESSLER T, Joslyn LR, Borish HJ, Gideon HP, et al
    A computational model tracks whole-lung Mycobacterium tuberculosis infection and predicts factors that inhibit dissemination.
    PLoS Comput Biol. 2020;16:e1007280.
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  25. CATALA M, Bechini J, Tenesa M, Perez R, et al
    Modelling the dynamics of tuberculosis lesions in a virtual lung: Role of the bronchial tree in endogenous reinfection.
    PLoS Comput Biol. 2020;16:e1007772.
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  26. BERNOFF AJ, Culshaw-Maurer M, Everett RA, Hohn ME, et al
    Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometry.
    PLoS Comput Biol. 2020;16:e1007820.
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    March 2020
  27. BROOKS-POLLOCK E, Danon L, Korthals Altes H, Davidson JA, et al
    A model of tuberculosis clustering in low incidence countries reveals more transmission in the United Kingdom than the Netherlands between 2010 and 2015.
    PLoS Comput Biol. 2020;16:e1007687.
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    December 2019
  28. JANDRASITS C, Kroger S, Haas W, Renard BY, et al
    Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters.
    PLoS Comput Biol. 2019;15:e1007527.
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  29. YAN J, Estanbouli H, Liao C, Kim W, et al
    Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection.
    PLoS Comput Biol. 2019;15:e1007562.
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    September 2019
  30. ADHIKARI B, Lewis B, Vullikanti A, Jimenez JM, et al
    Fast and near-optimal monitoring for healthcare acquired infection outbreaks.
    PLoS Comput Biol. 2019;15:e1007284.
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  31. HICKS AL, Wheeler N, Sanchez-Buso L, Rakeman JL, et al
    Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data.
    PLoS Comput Biol. 2019;15:e1007349.
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    August 2019
  32. PHAM TM, Kretzschmar M, Bertrand X, Bootsma M, et al
    Tracking Pseudomonas aeruginosa transmissions due to environmental contamination after discharge in ICUs using mathematical models.
    PLoS Comput Biol. 2019;15:e1006697.
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    July 2019
  33. SEILER E, Trappe K, Renard BY
    Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation.
    PLoS Comput Biol. 2019;15:e1007208.
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  34. ROBERTS PA, Huebinger RM, Keen E, Krachler AM, et al
    Mathematical model predicts anti-adhesion-antibiotic-debridement combination therapies can clear an antibiotic resistant infection.
    PLoS Comput Biol. 2019;15:e1007211.
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  35. MIKKAICHI T, Yeaman MR, Hoffmann A
    Identifying determinants of persistent MRSA bacteremia using mathematical modeling.
    PLoS Comput Biol. 2019;15:e1007087.
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    June 2019
  36. VERSCHEIJDEN LFM, Koenderink JB, de Wildt SN, Russel FGM, et al
    Development of a physiologically-based pharmacokinetic pediatric brain model for prediction of cerebrospinal fluid drug concentrations and the influence of meningitis.
    PLoS Comput Biol. 2019;15:e1007117.
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    May 2019
  37. DUVAL A, Obadia T, Boelle PY, Fleury E, et al
    Close proximity interactions support transmission of ESBL-K. pneumoniae but not ESBL-E. coli in healthcare settings.
    PLoS Comput Biol. 2019;15:e1006496.
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  38. SHARMA A, Menon SN, Sasidevan V, Sinha S, et al
    Epidemic prevalence information on social networks can mediate emergent collective outcomes in voluntary vaccine schemes.
    PLoS Comput Biol. 2019;15:e1006977.
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  39. PINOTTI F, Fleury E, Guillemot D, Boelle PY, et al
    Host contact dynamics shapes richness and dominance of pathogen strains.
    PLoS Comput Biol. 2019;15:e1006530.
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    April 2019
  40. NICHOLSON MD, Antal T
    Competing evolutionary paths in growing populations with applications to multidrug resistance.
    PLoS Comput Biol. 2019;15:e1006866.
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    March 2019
  41. MOON SA, Cohnstaedt LW, McVey DS, Scoglio CM, et al
    A spatio-temporal individual-based network framework for West Nile virus in the USA: Spreading pattern of West Nile virus.
    PLoS Comput Biol. 2019;15:e1006875.
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  42. WHITTLES LK, White PJ, Didelot X
    A dynamic power-law sexual network model of gonorrhoea outbreaks.
    PLoS Comput Biol. 2019;15:e1006748.
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  43. ENGEBRETSEN S, Engo-Monsen K, Frigessi A, Freiesleben de Blasio B, et al
    A theoretical single-parameter model for urbanisation to study infectious disease spread and interventions.
    PLoS Comput Biol. 2019;15:e1006879.
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  44. CAMPBELL F, Cori A, Ferguson N, Jombart T, et al
    Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data.
    PLoS Comput Biol. 2019;15:e1006930.
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    January 2019
  45. SEIF Y, Monk JM, Mih N, Tsunemoto H, et al
    A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.
    PLoS Comput Biol. 2019;15:e1006644.
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  46. MURALL CL, Jackson R, Zehbe I, Boulle N, et al
    Epithelial stratification shapes infection dynamics.
    PLoS Comput Biol. 2019;15:e1006646.
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    December 2018
  47. CORI A, Nouvellet P, Garske T, Bourhy H, et al
    A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies.
    PLoS Comput Biol. 2018;14:e1006554.
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  48. MORADIGARAVAND D, Palm M, Farewell A, Mustonen V, et al
    Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data.
    PLoS Comput Biol. 2018;14:e1006258.
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  49. POLO G, Mera Acosta C, Labruna MB, Ferreira F, et al
    Hosts mobility and spatial spread of Rickettsia rickettsii.
    PLoS Comput Biol. 2018;14:e1006636.
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    October 2018
  50. CAI FY, Fussell T, Cobey S, Lipsitch M, et al
    Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine.
    PLoS Comput Biol. 2018;14:e1006333.
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    June 2018
  51. BROOKS LC, Farrow DC, Hyun S, Tibshirani RJ, et al
    Nonmechanistic forecasts of seasonal influenza with iterative one-week-ahead distributions.
    PLoS Comput Biol. 2018;14:e1006134.
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  52. ESTRELA S, Brown SP
    Community interactions and spatial structure shape selection on antibiotic resistant lineages.
    PLoS Comput Biol. 2018;14:e1006179.
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    May 2018
  53. PASETTO D, Finger F, Camacho A, Grandesso F, et al
    Near real-time forecasting for cholera decision making in Haiti after Hurricane Matthew.
    PLoS Comput Biol. 2018;14:e1006127.
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  54. HOZE N, Bonhoeffer S, Regoes R
    Assessing the public health impact of tolerance-based therapies with mathematical models.
    PLoS Comput Biol. 2018;14:e1006119.
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  55. ROBERTS PA, Huebinger RM, Keen E, Krachler AM, et al
    Predictive modelling of a novel anti-adhesion therapy to combat bacterial colonisation of burn wounds.
    PLoS Comput Biol. 2018;14:e1006071.
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    April 2018
  56. DE MAIO N, Worby CJ, Wilson DJ, Stoesser N, et al
    Bayesian reconstruction of transmission within outbreaks using genomic variants.
    PLoS Comput Biol. 2018;14:e1006117.
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    March 2018
  57. KINYANJUI T, Middleton J, Guttel S, Cassell J, et al
    Scabies in residential care homes: Modelling, inference and interventions for well-connected population sub-units.
    PLoS Comput Biol. 2018;14:e1006046.
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    February 2018
  58. SPALDING C, Keen E, Smith DJ, Krachler AM, et al
    Mathematical modelling of the antibiotic-induced morphological transition of Pseudomonas aeruginosa.
    PLoS Comput Biol. 2018;14:e1006012.
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  59. JONES EW, Carlson JM
    In silico analysis of antibiotic-induced Clostridium difficile infection: Remediation techniques and biological adaptations.
    PLoS Comput Biol. 2018;14:e1006001.
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    November 2017
  60. MCCLOSKEY RM, Poon AFY
    A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation.
    PLoS Comput Biol. 2017;13:e1005868.
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  61. PRICE DJ, Breuze A, Dybowski R, Mastroeni P, et al
    An efficient moments-based inference method for within-host bacterial infection dynamics.
    PLoS Comput Biol. 2017;13:e1005841.
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    September 2017
  62. HOLME P, Litvak N
    Cost-efficient vaccination protocols for network epidemiology.
    PLoS Comput Biol. 2017;13:e1005696.
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  63. TEPEKULE B, Uecker H, Derungs I, Frenoy A, et al
    Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies.
    PLoS Comput Biol. 2017;13:e1005745.
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  64. PREM K, Cook AR, Jit M
    Projecting social contact matrices in 152 countries using contact surveys and demographic data.
    PLoS Comput Biol. 2017;13:e1005697.
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  65. BAUER M, Graf IR, Ngampruetikorn V, Stephens GJ, et al
    Exploiting ecology in drug pulse sequences in favour of population reduction.
    PLoS Comput Biol. 2017;13:e1005747.
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