epiforecasts / epiforecasts.github.io

Quarto website for EpiForecasts
https://epiforecasts.io/
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New epiforecasts papers #3

Open Bisaloo opened 2 years ago

Bisaloo commented 2 years ago

This issue will be updated monthly to list new publications from the team (relevant GitHub Actions job).

We then have until the end of the month to decide which ones should be added to the website by checking them. The first day of the next month, another GitHub Actions job will run to submit a pull request adding the selected articles to _data/papers.bib.

github-actions[bot] commented 9 months ago

Papers published last month:

@Article{paranoiac_nabarlek,
  title = {Challenges in specifying parameter values for COVID-19 simulation models},
  journal = {F1000Research},
  author = {Akira Endo and Akihiro Nishi},
  year = {2022},
  doi = {10.12688/f1000research.125531.1},
}
@Article{semiparalysis_olingo,
  title = {Scoring epidemiological forecasts on transformed scales},
  journal = {PLOS Computational Biology},
  author = {Nikos I. Bosse and Sam Abbott and Anne Cori and Edwin {van Leeuwen} and Johannes Bracher and Sebastian Funk},
  year = {2023},
  doi = {10.1371/journal.pcbi.1011393},
}
@Article{manipulative_redheadedwoodpecker,
  title = {Human judgement forecasting of COVID-19 in the UK},
  journal = {Wellcome Open Research},
  author = {Nikos I. Bosse and Sam Abbott and Johannes Bracher and Edwin {van Leeuwen} and Anne Cori and Sebastian Funk},
  year = {2023},
  doi = {10.12688/wellcomeopenres.19380.1},
}
@Article{highspiritedly_glassfrog,
  title = {Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Sang Woo Park and Kaiyuan Sun and Sam Abbott and Ron Sender and Yinon M. Bar-on and Joshua S. Weitz and Sebastian Funk and Bryan T. Grenfell and Jantien A. Backer and Jacco Wallinga and Cecile Viboud and Jonathan Dushoff},
  year = {2023},
  doi = {10.1073/pnas.2221887120},
}
@Article{malevolent_babirusa,
  title = {Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England},
  journal = {PLOS Computational Biology},
  author = {James D. Munday and Sam Abbott and Sophie Meakin and Sebastian Funk},
  year = {2023},
  doi = {10.1371/journal.pcbi.1011453},
}

github-actions[bot] commented 7 months ago

Papers published last month:

@Article{megacephalic_pekingese,
  title = {Modelling outbreak response impact in human vaccine-preventable diseases: A systematic review of differences in practices between collaboration types before COVID-19},
  journal = {Epidemics},
  author = {James M. Azam and Xiaoxi Pang and Elisha B. Are and Juliet R.C. Pulliam and Matthew J. Ferrari},
  year = {2023},
  doi = {10.1016/j.epidem.2023.100720},
}
@Article{depilatory_africanbushviper,
  title = {The importance of investing in data, models, experiments, team science, and public trust to help policymakers prepare for the next pandemic},
  journal = {PLOS Global Public Health},
  author = {Richard Grieve and Youqi Yang and Sam Abbott and Giridhara R. Babu and Malay Bhattacharyya and Natalie Dean and Stephen Evans and Nicholas Jewell and Sinéad M. Langan and Woojoo Lee and Geert Molenberghs and Liam Smeeth and Elizabeth Williamson and Bhramar Mukherjee},
  year = {2023},
  doi = {10.1371/journal.pgph.0002601},
}
@Article{apricot_kakarikis,
  title = {A review and agenda for integrated disease models including social and behavioural factors},
  journal = {Nature Human Behaviour},
  author = {Jamie Bedson and Laura A. Skrip and Danielle Pedi and Sharon Abramowitz and Simone Carter and Mohamed F. Jalloh and Sebastian Funk and Nina Gobat and Tamara Giles-Vernick and Gerardo Chowell and João Rangel {de Almeida} and Rania Elessawi and Samuel V. Scarpino and Ross A. Hammond and Sylvie Briand and Joshua M. Epstein and Laurent Hébert-Dufresne and Benjamin M. Althouse},
  year = {2021},
  doi = {10.1038/s41562-021-01136-2},
}
@Article{unloved_drongo,
  title = {Within and between classroom transmission patterns of seasonal influenza among primary school students in Matsumoto city, Japan},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Akira Endo and Mitsuo Uchida and Naoki Hayashi and Yang Liu and Katherine E. Atkins and Adam J. Kucharski and Sebastian Funk},
  year = {2021},
  doi = {10.1073/pnas.2112605118},
}
@Article{chartreuse_malamute,
  title = {The burden and dynamics of hospital-acquired SARS-CoV-2 in England},
  journal = {Nature},
  author = {Ben S. Cooper and Stephanie Evans and Yalda Jafari and Thi Mui Pham and Yin Mo and Cherry Lim and Mark G. Pritchard and Diane Pople and Victoria Hall and James Stimson and David W. Eyre and Jonathan M. Read and Christl A. Donnelly and Peter Horby and Conall Watson and Sebastian Funk and Julie V. Robotham and Gwenan M. Knight},
  year = {2023},
  doi = {10.1038/s41586-023-06634-z},
}
@Article{chancy_boubou,
  title = {The importance of the generation interval in investigating dynamics and control of new SARS-CoV-2 variants},
  journal = {Journal of The Royal Society Interface},
  author = {Sang Woo Park and Benjamin M. Bolker and Sebastian Funk and C. Jessica E. Metcalf and Joshua S. Weitz and Bryan T. Grenfell and Jonathan Dushoff},
  year = {2022},
  doi = {10.1098/rsif.2022.0173},
}

github-actions[bot] commented 6 months ago

Papers published last month:

@Article{paganist_nauplius,
  title = {Modelling outbreak response impact in human vaccine-preventable diseases: A systematic review of differences in practices between collaboration types before COVID-19},
  journal = {Epidemics},
  author = {James M. Azam and Xiaoxi Pang and Elisha B. Are and Juliet R.C. Pulliam and Matthew J. Ferrari},
  year = {2023},
  doi = {10.1016/j.epidem.2023.100720},
}

github-actions[bot] commented 5 months ago

Papers published last month:

@Article{nonspiny_buffalo,
  title = {Modelling outbreak response impact in human vaccine-preventable diseases: A systematic review of differences in practices between collaboration types before COVID-19},
  journal = {Epidemics},
  author = {James M. Azam and Xiaoxi Pang and Elisha B. Are and Juliet R.C. Pulliam and Matthew J. Ferrari},
  year = {2023},
  doi = {10.1016/j.epidem.2023.100720},
}
@Article{planispherical_pinniped,
  title = {Improving modelling for epidemic responses: reflections from members of the UK infectious disease modelling community on their experiences during the COVID-19 pandemic},
  journal = {Wellcome Open Research},
  author = {Katharine Sherratt and Anna C Carnegie and Adam Kucharski and Anne Cori and Carl A B Pearson and Christopher I Jarvis and Christopher Overton and Dale Weston and Edward M Hill and Edward Knock and Elizabeth Fearon and Emily Nightingale and Joel Hellewell and W John Edmunds and Julián Villabona Arenas and Kiesha Prem and Li Pi and Marc Baguelin and Michelle Kendall and Neil Ferguson and Nicholas Davies and Rosalind M Eggo and Sabine {van Elsland} and Timothy Russell and Sebastian Funk and Yang Liu and Sam Abbott},
  year = {2024},
  doi = {10.12688/wellcomeopenres.19601.1},
}
@Article{subsimian_urutu,
  title = {The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia},
  journal = {Science},
  author = {Martin Pavelka and Kevin Van-Zandvoort and Sam Abbott and Katharine Sherratt and Marek Majdan and Pavol Jarčuška and Marek Krajčí and Stefan Flasche and Sebastian Funk},
  year = {2021},
  doi = {10.1126/science.abf9648},
}
@Article{conceptual_mantid,
  title = {Accumulation of Immunity in Heavy-Tailed Sexual Contact Networks Shapes Mpox Outbreak Sizes},
  journal = {The Journal of Infectious Diseases},
  author = {Hiroaki Murayama and Carl A B Pearson and Sam Abbott and Fuminari Miura and Sung-mok Jung and Elizabeth Fearon and Sebastian Funk and Akira Endo},
  year = {2023},
  doi = {10.1093/infdis/jiad254},
}
@Article{stouthearted_kentrosaurus,
  title = {Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England},
  journal = {Science},
  author = {Nicholas G. Davies and Sam Abbott and Rosanna C. Barnard and Christopher I. Jarvis and Adam J. Kucharski and James D. Munday and Carl A. B. Pearson and Timothy W. Russell and Damien C. Tully and Alex D. Washburne and Tom Wenseleers and Amy Gimma and William Waites and Kerry L. M. Wong and Kevin {van Zandvoort} and Justin D. Silverman and Karla Diaz-Ordaz and Ruth Keogh and Rosalind M. Eggo and Sebastian Funk and Mark Jit and Katherine E. Atkins and W. John Edmunds},
  year = {2021},
  doi = {10.1126/science.abg3055},
}
@Article{deformable_crane,
  title = {Heavy-tailed sexual contact networks and monkeypox epidemiology in the global outbreak, 2022},
  journal = {Science},
  author = {Akira Endo and Hiroaki Murayama and Sam Abbott and Ruwan Ratnayake and Carl A. B. Pearson and W. John Edmunds and Elizabeth Fearon and Sebastian Funk},
  year = {2022},
  doi = {10.1126/science.add4507},
}
@Article{blueribbon_newtnutria,
  title = {Genomic and epidemiological monitoring of yellow fever virus transmission potential},
  journal = {Science},
  author = {N. R. Faria and M. U. G. Kraemer and S. C. Hill and J. Goes {de Jesus} and R. S. Aguiar and F. C. M. Iani and J. Xavier and J. Quick and L. du Plessis and S. Dellicour and J. Thézé and R. D. O. Carvalho and G. Baele and C.-H. Wu and P. P. Silveira and M. B. Arruda and M. A. Pereira and G. C. Pereira and J. Lourenço and U. Obolski and L. Abade and T. I. Vasylyeva and M. Giovanetti and D. Yi and D. J. Weiss and G. R. W. Wint and F. M. Shearer and S. Funk and B. Nikolay and V. Fonseca and T. E. R. Adelino and M. A. A. Oliveira and M. V. F. Silva and L. Sacchetto and P. O. Figueiredo and I. M. Rezende and E. M. Mello and R. F. C. Said and D. A. Santos and M. L. Ferraz and M. G. Brito and L. F. Santana and M. T. Menezes and R. M. Brindeiro and A. Tanuri and F. C. P. dos Santos and M. S. Cunha and J. S. Nogueira and I. M. Rocco and A. C. da Costa and S. C. V. Komninakis and V. Azevedo and A. O. Chieppe and E. S. M. Araujo and M. C. L. Mendonça and C. C. dos Santos and C. D. dos Santos and A. M. Mares-Guia and R. M. R. Nogueira and P. C. Sequeira and R. G. Abreu and M. H. O. Garcia and A. L. Abreu and O. Okumoto and E. G. Kroon and C. F. C. {de Albuquerque} and K. Lewandowski and S. T. Pullan and M. Carroll and T. {de Oliveira} and E. C. Sabino and R. P. Souza and M. A. Suchard and P. Lemey and G. S. Trindade and B. P. Drumond and A. M. B. Filippis and N. J. Loman and S. Cauchemez and L. C. J. Alcantara and O. G. Pybus},
  year = {2018},
  doi = {10.1126/science.aat7115},
}

github-actions[bot] commented 4 months ago

Papers published last month:

@Article{lowish_waterdragons,
  title = {Opening the floor for discussion: A perspective on how scholars perceive attitudes to science in policymaking in South Africa},
  journal = {South African Journal of Science},
  author = {Molly V. Czachur and Melvi Todd and Tainã Gonçalves Loureiro and James M. Azam and Siphokazi Nyeleka and Amanda Alblas and Sarah J. Davies},
  year = {2021},
  doi = {10.17159/sajs.2021/7948},
}
@Article{equiangular_crustacean,
  title = {Human judgement forecasting of COVID-19 in the UK},
  journal = {Wellcome Open Research},
  author = {Nikos I. Bosse and Sam Abbott and Johannes Bracher and Edwin {van Leeuwen} and Anne Cori and Sebastian Funk},
  year = {2023},
  doi = {10.12688/wellcomeopenres.19380.1},
}
@Article{antipestilence_chevrotain,
  title = {Tailoring Immunization Programmes: using patient file data to explore vaccination uptake and associated factors},
  journal = {Human Vaccines & Immunotherapeutics},
  author = {Sanjin Musa and Katrine Bach Habersaat and Cath Jackson and Aida Kulo and Emilija Primorac and Mirsad Smjecanin and Sebastian Funk},
  year = {2020},
  doi = {10.1080/21645515.2020.1769396},
}

github-actions[bot] commented 3 months ago

Papers published last month:

@Article{unequal_scallop,
  title = {Human judgement forecasting of COVID-19 in the UK},
  journal = {Wellcome Open Research},
  author = {Nikos I. Bosse and Sam Abbott and Johannes Bracher and Edwin {van Leeuwen} and Anne Cori and Sebastian Funk},
  year = {2024},
  doi = {10.12688/wellcomeopenres.19380.2},
}
@Article{daemonic_stickleback,
  title = {Tailoring Immunization Programmes: using patient file data to explore vaccination uptake and associated factors},
  journal = {Human Vaccines & Immunotherapeutics},
  author = {Sanjin Musa and Katrine Bach Habersaat and Cath Jackson and Aida Kulo and Emilija Primorac and Mirsad Smjecanin and Sebastian Funk},
  year = {2020},
  doi = {10.1080/21645515.2020.1769396},
}
@Article{oversolemn_chameleon,
  title = {Patient Characteristics and Public Health Office Factors Associated With Long Reporting Delay of COVID-19 Cases in Sapporo City, Japan},
  journal = {Journal of Epidemiology},
  author = {Daichi Watanuki and Akiko Tamakoshi and Takashi Kimura and Toshiaki Asakura and Masayuki Saijo},
  year = {2024},
  doi = {10.2188/jea.je20220359},
}

github-actions[bot] commented 2 months ago

Papers published last month:

@Article{gentlewomanly_bandicoot,
  title = {Human judgement forecasting of COVID-19 in the UK},
  journal = {Wellcome Open Research},
  author = {Nikos I. Bosse and Sam Abbott and Johannes Bracher and Edwin {van Leeuwen} and Anne Cori and Sebastian Funk},
  year = {2024},
  doi = {10.12688/wellcomeopenres.19380.2},
}
@Article{clairvoyant_willet,
  title = {Human judgement forecasting of COVID-19 in the UK},
  journal = {Wellcome Open Research},
  author = {Nikos I. Bosse and Sam Abbott and Johannes Bracher and Edwin {van Leeuwen} and Anne Cori and Sebastian Funk},
  year = {2023},
  doi = {10.12688/wellcomeopenres.19380.1},
}
@Article{phonophobic_galapagossealion,
  title = {Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates},
  journal = {PLOS Computational Biology},
  author = {Adrian Lison and Sam Abbott and Jana Huisman and Tanja Stadler},
  year = {2024},
  doi = {10.1371/journal.pcbi.1012021},
}

github-actions[bot] commented 2 days ago

Papers published last month:

@Article{antipolitics_bandicoot,
  title = {The impact of control strategies and behavioural changes on the elimination of Ebola from Lofa County, Liberia},
  journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
  author = {Sebastian Funk and Iza Ciglenecki and Amanda Tiffany and Etienne Gignoux and Anton Camacho and Rosalind M. Eggo and Adam J. Kucharski and W. John Edmunds and Josephus Bolongei and Phillip Azuma and Peter Clement and Tamba S. Alpha and Esther Sterk and Barbara Telfer and Gregory Engel and Lucy Anne Parker and Motoi Suzuki and Nico Heijenberg and Bruce Reeder},
  year = {2017},
  doi = {10.1098/rstb.2016.0302},
}
@Article{surprised_megalosaurus,
  title = {Comparative analysis of dengue and Zika outbreaks reveals differences by setting and virus},
  journal = {medRxiv},
  author = {Sebastian Funk and Adam J. Kucharski and Anton Camacho and Rosalind M. Eggo and Laith Yakob and Lawrence M. Murray and W. John Edmunds},
  year = {2016},
  doi = {10.1101/043265},
}
@Article{overjoyed_muskox,
  title = {Comparative Analysis of Dengue and Zika Outbreaks Reveals Differences by Setting and Virus},
  journal = {PLOS Neglected Tropical Diseases},
  author = {Sebastian Funk and Adam J. Kucharski and Anton Camacho and Rosalind M. Eggo and Laith Yakob and Lawrence M. Murray and W. John Edmunds},
  year = {2016},
  doi = {10.1371/journal.pntd.0005173},
}