Funk, Sebastian; Camacho, Anton; Kucharski, Adam J; Lowe, Rachel; Eggo, Rosalind M; Edmunds, W John; (2019) Assessing the performance of real-time epidemic forecasts: a case study of Ebola in the Western Area region of Sierra Leone, 2014-15. PLoS computational biology, 15 (2). ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1006785

Giuliani, S; Silva, AC; Borba, JVVB; Ramos, PIP; Paveley, RA; Muratov, EN; Andrade, CH; Furnham, N; (2018) Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents. PLoS computational biology, 14 (10). e1006515. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1006515

Kucharski, AJ; (2018) Ten simple rules for writing a popular science book. PLoS computational biology, 14 (2). e1005808. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1005808

Pasetto, D; Finger, F; Camacho, A; Grandesso, F; Cohuet, S; Lemaitre, JC; Azman, AS; Luquero, FJ; Bertuzzo, E; Rinaldo, A; (2018) Near real-time forecasting for cholera decision making in Haiti after Hurricane Matthew. PLoS computational biology, 14 (5). e1006127. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1006127

Wick, Ryan R; Judd, Louise M; Holt, Kathryn E; (2018) Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. PLoS computational biology, 14 (11). e1006583. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1006583

Chang, HH; Worby, CJ; Yeka, A; Nankabirwa, J; Kamya, MR; Staedke, SG; Dorsey, G; Murphy, M; Neafsey, DE; Jeffreys, AE; +6 more... Hubbart, C; Rockett, KA; Amato, R; Kwiatkowski, DP; Buckee, C; Greenhouse, B; (2017) THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites. PLoS computational biology, 13 (1). e1005348. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1005348

Dorratoltaj, N; Marathe, A; Lewis, BL; Swarup, S; Eubank, SG; Abbas, KM; (2017) Epidemiological and economic impact of pandemic influenza in Chicago: Priorities for vaccine interventions. PLoS computational biology, 13 (6). e1005521. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1005521

Lau, MSY; Gibson, GJ; Adrakey, H; McClelland, A; Riley, S; Zelner, J; Streftaris, G; Funk, S; Metcalf, J; Dalziel, BD; +1 more... Grenfell, BT; (2017) A mechanistic spatio-temporal framework for modelling individual-to-individual transmission-With an application to the 2014-2015 West Africa Ebola outbreak. PLoS computational biology, 13 (10). e1005798. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1005798

McQuaid, CF; van den Bosch, F; Szyniszewska, A; Alicai, T; Pariyo, A; Chikoti, PC; Gilligan, CA; (2017) Spatial dynamics and control of a crop pathogen with mixed-mode transmission. PLoS computational biology, 13 (7). e1005654. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1005654

Prem, K; Cook, AR; Jit, M; (2017) Projecting social contact matrices in 152 countries using contact surveys and demographic data. PLoS computational biology, 13 (9). e1005697. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1005697

van Leeuwen, E; Klepac, P; Thorrington, D; Pebody, R; Baguelin, M; (2017) fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks. PLoS computational biology, 13 (11). e1005838. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1005838

Andrianakis, I; Vernon, IR; McCreesh, N; McKinley, TJ; Oakley, JE; Nsubuga, RN; Goldstein, M; White, RG; (2015) Bayesian History Matching of Complex Infectious Disease Models Using Emulation: A Tutorial and a Case Study on HIV in Uganda. PLoS computational biology, 11 (1). e1003968. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1003968

Flasche, S; Le Polain de Waroux, O; OBrien, KL; Edmunds, WJ; (2015) The Serotype Distribution among Healthy Carriers before Vaccination Is Essential for Predicting the Impact of Pneumococcal Conjugate Vaccine on Invasive Disease. PLoS computational biology, 11 (4). e1004173. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1004173

Kucharski, AJ; Edmunds, WJ; (2015) Characterizing the Transmission Potential of Zoonotic Infections from Minor Outbreaks. PLoS computational biology, 11 (4). e1004154. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1004154

Tyagi, N; Farnell, EJ; Fitzsimmons, CM; Ryan, S; Tukahebwa, E; Maizels, RM; Dunne, DW; Thornton, JM; Furnham, N; (2015) Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity. PLoS computational biology, 11 (10). e1004546. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1004546

Seoane, JA; Campbell, C; Day, IN; Casas, JP; Gaunt, TR; (2014) Canonical correlation analysis for gene-based pleiotropy discovery. PLoS computational biology, 10 (10). e1003876. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1003876

Funk, S; Nishiura, H; Heesterbeek, H; Edmunds, WJ; Checchi, F; (2013) Identifying transmission cycles at the human-animal interface: the role of animal reservoirs in maintaining gambiense human african trypanosomiasis. PLoS computational biology, 9 (1). e1002855. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1002855

Koukounari, A; Donnelly, CA; Moustaki, I; Tukahebwa, EM; Kabatereine, NB; Wilson, S; Webster, JP; Deelder, AM; Vennervald, BJ; van Dam, GJ; (2013) A latent Markov modelling approach to the evaluation of circulating cathodic antigen strips for schistosomiasis diagnosis pre- and post-praziquantel treatment in Uganda. PLoS computational biology, 9 (12). e1003402. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1003402

Eames, KT; Tilston, NL; Brooks-Pollock, E; Edmunds, WJ; (2012) Measured Dynamic Social Contact Patterns Explain the Spread of H1N1v Influenza. PLoS computational biology, 8 (3). e1002425. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1002425

Furnham, N; Sillitoe, I; Holliday, GL; Cuff, AL; Laskowski, RA; Orengo, CA; Thornton, JM; (2012) Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies. PLoS computational biology, 8 (3). e1002403. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1002403

Kucharski, AJ; Gog, JR; (2012) The role of social contacts and original antigenic sin in shaping the age pattern of immunity to seasonal influenza. PLoS computational biology, 8 (10). e1002741. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1002741

Mitchell, KM; Mutapi, F; Savill, NJ; Woolhouse, ME; (2011) Explaining observed infection and antibody age-profiles in populations with urogenital schistosomiasis. PLoS computational biology, 7 (10). e1002237. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1002237

Laneri, K; Bhadra, A; Ionides, EL; Bouma, M; Dhiman, RC; Yadav, RS; Pascual, M; (2010) Forcing Versus Feedback: Epidemic Malaria and Monsoon Rains in Northwest India. PLoS computational biology, 6 (9). ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1000898

Walker, PG; Cauchemez, S; Metras, R; Dung, doH; Pfeiffer, D; Ghani, AC; (2010) A Bayesian approach to quantifying the effects of mass poultry vaccination upon the spatial and temporal dynamics of H5N1 in Northern Vietnam. PLoS computational biology, 6 (2). e1000683. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1000683

Filipe, JA; Riley, EM; Drakeley, CJ; Sutherland, CJ; Ghani, AC; (2007) Determination of the processes driving the acquisition of immunity to malaria using a mathematical transmission model. PLoS computational biology, 3 (12). e255. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.0030255