## Covasim papers -- see papers.md for a human-readable format.

# Covasim methods papers

@article{kerr2021covasim,
  title={Covasim: an agent-based model of COVID-19 dynamics and interventions},
  author={Kerr, Cliff C and Stuart, Robyn M and Mistry, Dina and Abeysuriya, Romesh G and Rosenfeld, Katherine and Hart, Gregory R and N{\'u}{\~n}ez, Rafael C and Cohen, Jamie A and Selvaraj, Prashanth and Hagedorn, Brittany and others},
  journal={PLOS Computational Biology},
  volume={17},
  number={7},
  pages={e1009149},
  year={2021},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article {cohen2021mechanistic,
    author = {Cohen, Jamie A. and Stuart, Robyn M. and Rosenfeld, Katherine and Lyons, Hil and White, Michael and Kerr, Cliff C. and Klein, Daniel J. and Famulare, Michael},
    title = {Quantifying the role of naturally- and vaccine-derived neutralizing antibodies as a correlate of protection against COVID-19 variants},
    elocation-id = {2021.05.31.21258018},
    year = {2021},
    doi = {10.1101/2021.05.31.21258018},
    publisher = {Cold Spring Harbor Laboratory Press},
    URL = {https://www.medrxiv.org/content/early/2021/09/28/2021.05.31.21258018},
    eprint = {https://www.medrxiv.org/content/early/2021/09/28/2021.05.31.21258018.full.pdf},
    journal = {medRxiv}
}


# Scientific papers from the Covasim development team

@article{panovska2020determining,
  title={Determining the optimal strategy for reopening schools, the impact of test and trace interventions, and the risk of occurrence of a second COVID-19 epidemic wave in the UK: a modelling study},
  author={Panovska-Griffiths, Jasmina and Kerr, Cliff C and Stuart, Robyn M and Mistry, Dina and Klein, Daniel J and Viner, Russell M and Bonell, Chris},
  journal={The Lancet Child \& Adolescent Health},
  volume={4},
  number={11},
  pages={817--827},
  year={2020},
  publisher={Elsevier}
}

@article{kerr2021controlling,
  title={Controlling COVID-19 via test-trace-quarantine},
  author={Kerr, Cliff C and Mistry, Dina and Stuart, Robyn M and Rosenfeld, Katherine and Hart, Gregory R and N{\'u}{\~n}ez, Rafael C and Cohen, Jamie A and Selvaraj, Prashanth and Abeysuriya, Romesh G and Jastrz{\k{e}}bski, Micha{\l} and others},
  journal={Nature Communications},
  volume={12},
  number={1},
  pages={1--12},
  year={2021},
  publisher={Nature Publishing Group}
}

@article{pham2021estimating,
  title={Estimating and mitigating the risk of COVID-19 epidemic rebound associated with reopening of international borders in Vietnam: a modelling study},
  author={Pham, Quang D and Stuart, Robyn M and Nguyen, Thuong V and Luong, Quang C and Tran, Quang D and Pham, Thai Q and Phan, Lan T and Dang, Tan Q and Tran, Duong N and Do, Hung T and others},
  journal={The Lancet Global Health},
  volume={9},
  number={7},
  pages={e916--e924},
  year={2021},
  publisher={Elsevier}
}

@article{scott2020modelling,
  title={Modelling the impact of reducing control measures on the COVID-19 pandemic in a low transmission setting},
  author={Scott, Nick and Palmer, Anna and Delport, Dominic and Abeysuriya, Romesh and Stuart, Robyn and Kerr, Cliff C and Mistry, Dina and Klein, Daniel J and Sacks-Davis, Rachel and Heath, Katie and others},
  journal={Med J Aust},
  volume={214},
  number={2},
  pages={79--83},
  year={2020}
}

@article{stuart2021role,
  title={Role of masks, testing and contact tracing in preventing COVID-19 resurgences: a case study from New South Wales, Australia},
  author={Stuart, Robyn M and Abeysuriya, Romesh G and Kerr, Cliff C and Mistry, Dina and Klein, Dan J and Gray, Richard T and Hellard, Margaret and Scott, Nick},
  journal={BMJ open},
  volume={11},
  number={4},
  pages={e045941},
  year={2021},
  publisher={British Medical Journal Publishing Group}
}

@article{panovska2021modelling,
  title={Modelling the potential impact of mask use in schools and society on COVID-19 control in the UK},
  author={Panovska-Griffiths, J and Kerr, CC and Waites, W and Stuart, RM and Mistry, D and Foster, D and Klein, DJ and Viner, RM and Bonell, C},
  journal={Scientific reports},
  volume={11},
  number={1},
  pages={1--12},
  year={2021},
  publisher={Nature Publishing Group}
}

@article{cohen2020schools,
  title={Schools are not islands: Balancing COVID-19 risk and educational benefits using structural and temporal countermeasures},
  author={Cohen, Jamie A and Mistry, Dina and Kerr, Cliff C and Klein, Daniel J},
  journal={MedRxiv},
  year={2020},
  publisher={Cold Spring Harbor Laboratory Press}
}

@article{shea2020covid,
  title={COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support},
  author={Shea, Katriona and Borchering, Rebecca K and Probert, William JM and Howerton, Emily and Bogich, Tiffany L and Li, Shouli and van Panhuis, Willem G and Viboud, Cecile and Agu{\'a}s, Ricardo and Belov, Artur and others},
  journal={MedRxiv},
  year={2020},
  publisher={Cold Spring Harbor Laboratory Preprints}
}

@article{abeysuriya2022preventing,
  title={Preventing a cluster from becoming a new wave in settings with zero community COVID-19 cases},
  author={Abeysuriya, Romesh G and Delport, Dominic and Stuart, Robyn M and Sacks-Davis, Rachel and Kerr, Cliff C and Mistry, Dina and Klein, Daniel J and Hellard, Margaret and Scott, Nick},
  journal={BMC infectious diseases},
  volume={22},
  number={1},
  pages={1--15},
  year={2022},
  publisher={BioMed Central}
}

@article {panovska2021modelling,
    author = {Panovska-Griffiths, J. and Stuart, R.M. and Kerr, C.C. and Rosenfield, K. and Mistry, D. and Waites, W. and Klein, D.J. and Bonell, C. and Viner, R.M.},
    title = {Modelling the impact of reopening schools in the UK in early 2021 in the presence of the alpha variant and with roll-out of vaccination against SARS-CoV-2},
    elocation-id = {2021.02.07.21251287},
    year = {2021},
    doi = {10.1101/2021.02.07.21251287},
    publisher = {Cold Spring Harbor Laboratory Press},
    URL = {https://www.medrxiv.org/content/early/2021/07/22/2021.02.07.21251287},
    eprint = {https://www.medrxiv.org/content/early/2021/07/22/2021.02.07.21251287.full.pdf},
    journal = {medRxiv}
}


# Scientific papers from external authors

@article{krebs2021partial,
  title={Partial lockdown on unvaccinated individuals promises breaking of fourth COVID-19 wave in Bavaria},
  author={Krebs, Tobias and Moeckel, Michael J},
  journal={medRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory Press}
}

@article{li2021returning,
  title={Returning to a normal life via COVID-19 vaccines in the United States: a large-scale Agent-Based simulation study},
  author={Li, Junjiang and Giabbanelli, Philippe and others},
  journal={JMIR Medical Informatics},
  volume={9},
  number={4},
  pages={e27419},
  year={2021},
  publisher={JMIR Publications Inc., Toronto, Canada}
}

@article{cattaneo2022agent,
  title={An agent-based model to assess large-scale COVID-19 vaccination campaigns for the Italian territory: The case study of Lombardy region},
  author={Cattaneo, Andrea and Vitali, Andrea and Mazzoleni, Mirko and Previdi, Fabio},
  journal={Computer Methods and Programs in Biomedicine},
  volume={224},
  pages={107029},
  year={2022},
  publisher={Elsevier}
}

@article{li2022estimation,
  title={Estimation of local time-varying reproduction numbers in noisy surveillance data},
  author={Li, Wenrui and Bulekova, Katia and Gregor, Brian and White, Laura F and Kolaczyk, Eric D},
  journal={Philosophical Transactions of the Royal Society A},
  volume={380},
  number={2233},
  pages={20210303},
  year={2022},
  publisher={The Royal Society}
}

@article{bushaj2022simulation,
  title={A simulation-deep reinforcement learning (SiRL) approach for epidemic control optimization},
  author={Bushaj, Sabah and Yin, Xuecheng and Beqiri, Arjeta and Andrews, Donald and B{\"u}y{\"u}ktahtak{\i}n, {\.I} Esra},
  journal={Annals of Operations Research},
  pages={1--33},
  year={2022},
  publisher={Springer}
}