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COVID-19: Daily Top 10 Papers

  Bacterial Infections and Mycoses

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Articles published in PLoS Comput Biol

Retrieve available abstracts of 64 articles:
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    June 2021
  1. 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.
    PubMed     Abstract available

  2. 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.
    PubMed     Abstract available

    March 2021
  3. 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.
    PubMed     Abstract available

  4. 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.
    PubMed     Abstract available

    February 2021
  5. 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.
    PubMed     Abstract available

    Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection.
    PLoS Comput Biol. 2021;17:e1008782.
    PubMed     Abstract available

    January 2021
  7. 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.
    PubMed     Abstract available

  8. 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.
    PubMed     Abstract available

  9. 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.
    PubMed     Abstract available

  10. 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.
    PubMed     Abstract available

    December 2020
  11. 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.
    PubMed     Abstract available

  12. 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.
    PubMed     Abstract available

    October 2020
  13. 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.
    PubMed     Abstract available

  14. 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.
    PubMed     Abstract available

    August 2020
  15. 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.
    PubMed     Abstract available

  16. 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.
    PubMed     Abstract available

  17. 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.
    PubMed     Abstract available

    July 2020
  18. 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.
    PubMed     Abstract available

    June 2020
  19. 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.
    PubMed     Abstract available

  20. 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.
    PubMed     Abstract available

  21. 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.
    PubMed     Abstract available

    May 2020
  22. 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.
    PubMed     Abstract available

  23. 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.
    PubMed     Abstract available

  24. 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.
    PubMed     Abstract available

  25. 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.
    PubMed     Abstract available

    March 2020
  26. 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.
    PubMed     Abstract available

    December 2019
  27. 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.
    PubMed     Abstract available

  28. 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.
    PubMed     Abstract available

    September 2019
  29. 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.
    PubMed     Abstract available

  30. 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.
    PubMed     Abstract available

    August 2019
  31. 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.
    PubMed     Abstract available

    July 2019
  32. 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.
    PubMed     Abstract available

  33. 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.
    PubMed     Abstract available

  34. MIKKAICHI T, Yeaman MR, Hoffmann A
    Identifying determinants of persistent MRSA bacteremia using mathematical modeling.
    PLoS Comput Biol. 2019;15:e1007087.
    PubMed     Abstract available

    June 2019
  35. 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.
    PubMed     Abstract available

    May 2019
  36. 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.
    PubMed     Abstract available

  37. 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.
    PubMed     Abstract available

  38. 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.
    PubMed     Abstract available

    April 2019
  39. NICHOLSON MD, Antal T
    Competing evolutionary paths in growing populations with applications to multidrug resistance.
    PLoS Comput Biol. 2019;15:e1006866.
    PubMed     Abstract available

    March 2019
  40. 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.
    PubMed     Abstract available

  41. WHITTLES LK, White PJ, Didelot X
    A dynamic power-law sexual network model of gonorrhoea outbreaks.
    PLoS Comput Biol. 2019;15:e1006748.
    PubMed     Abstract available

  42. 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.
    PubMed     Abstract available

  43. 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.
    PubMed     Abstract available

    January 2019
  44. 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.
    PubMed     Abstract available

  45. MURALL CL, Jackson R, Zehbe I, Boulle N, et al
    Epithelial stratification shapes infection dynamics.
    PLoS Comput Biol. 2019;15:e1006646.
    PubMed     Abstract available

    December 2018
  46. 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.
    PubMed     Abstract available

  47. 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.
    PubMed     Abstract available

  48. 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.
    PubMed     Abstract available

    October 2018
  49. 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.
    PubMed     Abstract available

    June 2018
  50. 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.
    PubMed     Abstract available

  51. ESTRELA S, Brown SP
    Community interactions and spatial structure shape selection on antibiotic resistant lineages.
    PLoS Comput Biol. 2018;14:e1006179.
    PubMed     Abstract available

    May 2018
  52. 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.
    PubMed     Abstract available

  53. HOZE N, Bonhoeffer S, Regoes R
    Assessing the public health impact of tolerance-based therapies with mathematical models.
    PLoS Comput Biol. 2018;14:e1006119.
    PubMed     Abstract available

  54. 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.
    PubMed     Abstract available

    April 2018
  55. 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.
    PubMed     Abstract available

    March 2018
  56. 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.
    PubMed     Abstract available

    February 2018
  57. 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.
    PubMed     Abstract available

  58. JONES EW, Carlson JM
    In silico analysis of antibiotic-induced Clostridium difficile infection: Remediation techniques and biological adaptations.
    PLoS Comput Biol. 2018;14:e1006001.
    PubMed     Abstract available

    November 2017
    A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation.
    PLoS Comput Biol. 2017;13:e1005868.
    PubMed     Abstract available

  60. 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.
    PubMed     Abstract available

    September 2017
  61. HOLME P, Litvak N
    Cost-efficient vaccination protocols for network epidemiology.
    PLoS Comput Biol. 2017;13:e1005696.
    PubMed     Abstract available

  62. 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.
    PubMed     Abstract available

  63. 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.
    PubMed     Abstract available

  64. 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.
    PubMed     Abstract available

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