Items where the Publication is PLoS computational biology
Number of items: 47.
2025
Why the growth of arboviral diseases necessitates a new generation of global risk maps and future projections. (2025)
Brady, Oliver J; Bastos, Leonardo S; Caldwell, Jamie M; Cauchemez, Simon; Clapham, Hannah E; Dorigatti, Illaria; Gaythorpe, Katy AM; Hu, Wenbiao; Hussain-Alkhateeb, Laith; Johansson, Michael A; Lim, Ahyoung; Lopez, Velma K; Maude, Richard James; Messina, Jane P; Mordecai, Erin A; Peterson, Andrew Townsend; Rodriquez-Barraquer, Isabel; Rabe, Ingrid B; Rojas, Diana P; Ryan, Sadie J; Salje, Henrik; Semenza, Jan C; Tran, Quan Minh
2024
EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering. (2024)
Judge, Ciara; Vaughan, Timothy; Russell, Timothy; Abbott, Sam; du Plessis, Louis; Stadler, Tanja; Brady, Oliver; Hill, Sarah
A new approach to Health Benefits Package design: an application of the Thanzi La Onse model in Malawi. (2024)
Molaro, Margherita; Mohan, Sakshi; She, Bingling; Chalkley, Martin; Colbourn, Tim; Collins, Joseph H; Connolly, Emilia; Graham, Matthew M; Janoušková, Eva; Li Lin, Ines; Manthalu, Gerald; Mnjowe, Emmanuel; Nkhoma, Dominic; Twea, Pakwanja D; Phillips, Andrew N; Revill, Paul; Tamuri, Asif U; Mfutso-Bengo, Joseph; Mangal, Tara D; Hallett, Timothy B
2023
Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany. (2023)
Brockhaus, Elisabeth K; Wolffram, Daniel; Stadler, Tanja; Osthege, Michael; Mitra, Tanmay; Littek, Jonas M; Krymova, Ekaterina; Klesen, Anna J; Huisman, Jana S; Heyder, Stefan; Helleckes, Laura M; An der Heiden, Matthias; Funk, Sebastian; Abbott, Sam; Bracher, Johannes
Optimizing COVID-19 testing strategies on college campuses: Evaluation of the health and economic costs. (2023)
Johnson, Kaitlyn E; Pasco, Remy; Woody, Spencer; Lachmann, Michael; Johnson-Leon, Maureen; Bhavnani, Darlene; Klima, Jessica; Paltiel, A David; Fox, Spencer J; Meyers, Lauren Ancel
2022
Unsupervised machine learning predicts future sexual behaviour and sexually transmitted infections among HIV-positive men who have sex with men. (2022)
Andresen, Sara; Balakrishna, Suraj; Mugglin, Catrina; Schmidt, Axel J; Braun, Dominique L; Marzel, Alex; Doco Lecompte, Thanh; Darling, Katharine Ea; Roth, Jan A; Schmid, Patrick; Bernasconi, Enos; Günthard, Huldrych F; Rauch, Andri; Kouyos, Roger D; Salazar-Vizcaya, Luisa; Swiss HIV Cohort Study
Comparing human and model-based forecasts of COVID-19 in Germany and Poland. (2022)
Bosse, Nikos I; Abbott, Sam; Bracher, Johannes; Hain, Habakuk; Quilty, Billy J; Jit, Mark; Centre for the Mathematical Modelling of Infectious Diseases COV; van Leeuwen, Edwin; Cori, Anne; Funk, Sebastian
Modelling the synergistic effect of bacteriophage and antibiotics on bacteria: Killers and drivers of resistance evolution. (2022)
Leclerc, Quentin J; Lindsay, Jodi A; Knight, Gwenan M
Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches. (2022)
Papadopoulos, Timos; Vynnycky, Emilia
Polypolish: Short-read polishing of long-read bacterial genome assemblies. (2022)
Wick, Ryan R; Holt, Kathryn E
2021
Operational response simulation tool for epidemics within refugee and IDP settlements: A scenario-based case study of the Cox's Bazar settlement. (2021)
Aylett-Bullock, Joseph; Cuesta-Lazaro, Carolina; Quera-Bofarull, Arnau; Katta, Anjali; Hoffmann Pham, Katherine; Hoover, Benjamin; Strobelt, Hendrik; Moreno Jimenez, Rebeca; Sedgewick, Aidan; Samir Evers, Egmond; Kennedy, David; Harlass, Sandra; Gidraf Kahindo Maina, Allen; Hussien, Ahmad; Luengo-Oroz, Miguel
Assessing the drivers of syphilis among men who have sex with men in Switzerland reveals a key impact of screening frequency: A modelling study. (2021)
Balakrishna, Suraj; Salazar-Vizcaya, Luisa; Schmidt, Axel J; Kachalov, Viacheslav; Kusejko, Katharina; Thurnheer, Maria Christine; Roth, Jan A; Nicca, Dunja; Cavassini, Matthias; Battegay, Manuel; Schmid, Patrick; Bernasconi, Enos; Günthard, Huldrych F; Rauch, Andri; Kouyos, Roger D; Swiss HIV Cohort Study (SHCS)
Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19. (2021)
Gibbs, Hamish; Nightingale, Emily; Liu, Yang; Cheshire, James; Danon, Leon; Smeeth, Liam; Pearson, Carl AB; Grundy, Chris; LSHTM CMMID COVID-19 working group; Kucharski, Adam J; Eggo, Rosalind M
Estimation of country-level incidence of early-onset invasive Group B Streptococcus disease in infants using Bayesian methods. (2021)
Gonçalves, Bronner P; Procter, Simon R; Clifford, Sam; Koukounari, Artemis; Paul, Proma; Lewin, Alexandra; Jit, Mark; Lawn, Joy
Optima TB: A tool to help optimally allocate tuberculosis spending. (2021)
Goscé, Lara; Abou Jaoude, Gerard J; Kedziora, David J; Benedikt, Clemens; Hussain, Azfar; Jarvis, Sarah; Skrahina, Alena; Klimuk, Dzmitry; Hurevich, Henadz; Zhao, Feng; Fraser-Hurt, Nicole; Cheikh, Nejma; Gorgens, Marelize; Wilson, David J; Abeysuriya, Romesh; Martin-Hughes, Rowan; Kelly, Sherrie L; Roberts, Anna; Stuart, Robyn M; Palmer, Tom; Panovska-Griffiths, Jasmina; Kerr, Cliff C; Wilson, David P; Haghparast-Bidgoli, Hassan; Skordis, Jolene; Abubakar, Ibrahim
PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial. (2021)
Pickles, Michael; Cori, Anne; Probert, William JM; Sauter, Rafael; Hinch, Robert; Fidler, Sarah; Ayles, Helen; Bock, Peter; Donnell, Deborah; Wilson, Ethan; Piwowar-Manning, Estelle; Floyd, Sian; Hayes, Richard J; Fraser, Christophe; HPTN 071 (PopART) Study Team
Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era. (2021)
Prem, Kiesha; Zandvoort, Kevin van; Klepac, Petra; Eggo, Rosalind M; Davies, Nicholas G; Centre for the Mathematical Modelling of Infectious Diseases COV; Cook, Alex R; Jit, Mark
Testing, tracing and isolation in compartmental models. (2021)
Sturniolo, Simone; Waites, William; Colbourn, Tim; Manheim, David; Panovska-Griffiths, Jasmina
2020
A model of tuberculosis clustering in low incidence countries reveals more transmission in the United Kingdom than the Netherlands between 2010 and 2015. (2020)
Brooks-Pollock, Ellen; Danon, Leon; Korthals Altes, Hester; Davidson, Jennifer A; Pollock, Andrew MT; van Soolingen, Dick; Campbell, Colin; Lalor, Maeve K
An open source tool to infer epidemiological and immunological dynamics from serological data: serosolver. (2020)
Hay, James A; Minter, Amanda; Ainslie, Kylie EC; Lessler, Justin; Yang, Bingyi; Cummings, Derek AT; Kucharski, Adam J; Riley, Steven
2019
Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15. (2019)
Endo, Akira; Uchida, Mitsuo; Kucharski, Adam J; Funk, Sebastian
Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15. (2019)
Funk, Sebastian; Camacho, Anton; Kucharski, Adam J; Lowe, Rachel; Eggo, Rosalind M; Edmunds, W John
A population of bang-bang switches of defective interfering particles makes within-host dynamics of dengue virus controllable. (2019)
Mapder, Tarunendu; Clifford, Sam; Aaskov, John; Burrage, Kevin
2018
Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents. (2018)
Giuliani, Sandra; Silva, Arthur C; Borba, Joyce VVB; Ramos, Pablo IP; Paveley, Ross A; Muratov, Eugene N; Andrade, Carolina Horta; Furnham, Nicholas
Ten simple rules for writing a popular science book. (2018)
Kucharski, Adam J
Near real-time forecasting for cholera decision making in Haiti after Hurricane Matthew. (2018)
Pasetto, Damiano; Finger, Flavio; Camacho, Anton; Grandesso, Francesco; Cohuet, Sandra; Lemaitre, Joseph C; Azman, Andrew S; Luquero, Francisco J; Bertuzzo, Enrico; Rinaldo, Andrea
Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. (2018)
Wick, Ryan R; Judd, Louise M; Holt, Kathryn E
2017
THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites. (2017)
Chang, Hsiao-Han; Worby, Colin J; Yeka, Adoke; Nankabirwa, Joaniter; Kamya, Moses R; Staedke, Sarah G; Dorsey, Grant; Murphy, Maxwell; Neafsey, Daniel E; Jeffreys, Anna E; Hubbart, Christina; Rockett, Kirk A; Amato, Roberto; Kwiatkowski, Dominic P; Buckee, Caroline O; Greenhouse, Bryan
Epidemiological and economic impact of pandemic influenza in Chicago: Priorities for vaccine interventions. (2017)
Dorratoltaj, Nargesalsadat; Marathe, Achla; Lewis, Bryan L; Swarup, Samarth; Eubank, Stephen G; Abbas, Kaja M
A mechanistic spatio-temporal framework for modelling individual-to-individual transmission-With an application to the 2014-2015 West Africa Ebola outbreak. (2017)
Lau, Max SY; Gibson, Gavin J; Adrakey, Hola; McClelland, Amanda; Riley, Steven; Zelner, Jon; Streftaris, George; Funk, Sebastian; Metcalf, Jessica; Dalziel, Benjamin D; Grenfell, Bryan T
Spatial dynamics and control of a crop pathogen with mixed-mode transmission. (2017)
McQuaid, Christopher Finn; van den Bosch, Frank; Szyniszewska, Anna; Alicai, Titus; Pariyo, Anthony; Chikoti, Patrick Chiza; Gilligan, Christopher Aidan
Projecting social contact matrices in 152 countries using contact surveys and demographic data. (2017)
Prem, Kiesha; Cook, Alex R; Jit, Mark
fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks. (2017)
van Leeuwen, Edwin; Klepac, Petra; Thorrington, Dominic; Pebody, Richard; Baguelin, Marc
2015
Bayesian history matching of complex infectious disease models using emulation: a tutorial and a case study on HIV in Uganda. (2015)
Andrianakis, Ioannis; Vernon, Ian R; McCreesh, Nicky; McKinley, Trevelyan J; Oakley, Jeremy E; Nsubuga, Rebecca N; Goldstein, Michael; White, Richard G
The serotype distribution among healthy carriers before vaccination is essential for predicting the impact of pneumococcal conjugate vaccine on invasive disease. (2015)
Flasche, Stefan; Le Polain de Waroux, Olivier; O'Brien, Katherine L; Edmunds, W John
Characterizing the transmission potential of zoonotic infections from minor outbreaks. (2015)
Kucharski, Adam J; Edmunds, W John
Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity. (2015)
Tyagi, Nidhi; Farnell, Edward J; Fitzsimmons, Colin M; Ryan, Stephanie; Tukahebwa, Edridah; Maizels, Rick M; Dunne, David W; Thornton, Janet M; Furnham, Nicholas
2013
Identifying transmission cycles at the human-animal interface: the role of animal reservoirs in maintaining gambiense human african trypanosomiasis. (2013)
Funk, Sebastian; Nishiura, Hiroshi; Heesterbeek, Hans; Edmunds, W John; Checchi, Francesco
A latent Markov modelling approach to the evaluation of circulating cathodic antigen strips for schistosomiasis diagnosis pre- and post-praziquantel treatment in Uganda. (2013)
Koukounari, Artemis; Donnelly, Christl A; Moustaki, Irini; Tukahebwa, Edridah M; Kabatereine, Narcis B; Wilson, Shona; Webster, Joanne P; Deelder, André M; Vennervald, Birgitte J; van Dam, Govert J
2012
Measured dynamic social contact patterns explain the spread of H1N1v influenza. (2012)
Eames, Ken TD; Tilston, Natasha L; Brooks-Pollock, Ellen; Edmunds, W John
Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies. (2012)
Furnham, Nicholas; Sillitoe, Ian; Holliday, Gemma L; Cuff, Alison L; Laskowski, Roman A; Orengo, Christine A; Thornton, Janet M
The role of social contacts and original antigenic sin in shaping the age pattern of immunity to seasonal influenza. (2012)
Kucharski, Adam J; Gog, Julia R
2010
Forcing versus feedback: epidemic malaria and monsoon rains in northwest India. (2010)
Laneri, Karina; Bhadra, Anindya; Ionides, Edward L; Bouma, Menno; Dhiman, Ramesh C; Yadav, Rajpal S; Pascual, Mercedes
A Bayesian approach to quantifying the effects of mass poultry vaccination upon the spatial and temporal dynamics of H5N1 in Northern Vietnam. (2010)
Walker, Patrick GT; Cauchemez, Simon; Métras, Raphaëlle; Dung, Do Huu; Pfeiffer, Dirk; Ghani, Azra C
