2026

@article{Harris2026,
  title = {Emerging frontiers in infectious disease modelling: reassessing the data-driven feedback loop between human behaviour and disease dynamics},
  volume = {13},
  ISSN = {2054-5703},
  url = {http://dx.doi.org/10.1098/rsos.260369},
  DOI = {10.1098/rsos.260369},
  number = {6},
  journal = {Royal Society Open Science},
  publisher = {The Royal Society},
  author = {Harris,  Mallory J. and Sinclair,  Alyssa H. and Pullano,  Giulia and Beckett,  Stephen J. and LeJeune,  Leah and Agusto,  Folashade B. and Bauch,  Chris T. and Baur,  Cynthia and Berestycki,  Henri and Dushoff,  Jonathan and Griette,  Quentin and Levin,  Simon A. and Velasco-Hernández,  Jorge X. and Wu,  Jianhong and Weitz,  Joshua S.},
  editor = {Rogers,  Tim and Wise,  Sarah},
  year = {2026},
  month = June 
}

@article{Sinclair2026,
  title = {Personalized feedback about immunity corrects risk misestimation and motivates vaccination},
  volume = {5},
  ISSN = {2752-6542},
  url = {http://dx.doi.org/10.1093/pnasnexus/pgag227},
  DOI = {10.1093/pnasnexus/pgag227},
  number = {7},
  journal = {PNAS Nexus},
  publisher = {Oxford University Press (OUP)},
  author = {Sinclair,  Alyssa H and Taylor,  Morgan K and Beckett,  Stephen J and Chande,  Aroon T and Weitz,  Joshua S and Samanez-Larkin,  Gregory R},
  editor = {Van Lange,  Paul},
  year = {2026},
  month = June 
}

@article{Frmont2026,
  title = {Coexistence of Photosynthetic Marine Microorganisms,  Viruses and Grazers: Towards Integration in Ocean Ecosystem Models},
  volume = {28},
  ISSN = {1462-2920},
  url = {http://dx.doi.org/10.1111/1462-2920.70295},
  DOI = {10.1111/1462-2920.70295},
  number = {4},
  journal = {Environmental Microbiology},
  publisher = {Wiley},
  author = {Frémont,  Paul and Beckett,  Stephen J. and Demory,  David and Carr,  Eric and Follett,  Christopher L. and Lindell,  Debbie and Talmy,  David and Dutkiewicz,  Stephanie and Weitz,  Joshua S.},
  year = {2026},
  month = Apr 
}

@article{Dey2026,
  title = {Density-dependent feedback and higher-order interactions enable coexistence in phage–bacteria community dynamics},
  volume = {20},
  ISSN = {1751-7370},
  url = {http://dx.doi.org/10.1093/ismejo/wrag041},
  DOI = {10.1093/ismejo/wrag041},
  number = {1},
  journal = {The ISME Journal},
  publisher = {Oxford University Press (OUP)},
  author = {Dey,  Raunak and Coenen,  Ashley R and Solonenko,  Natalie E and Burris,  Marie N and Mackey,  Anna I and Galasso,  Julia and Sun,  Christine L and Demory,  David and Muratore,  Daniel and Beckett,  Stephen J and Sullivan,  Matthew B and Weitz,  Joshua S},
  year = {2026},
  month = Jan 
}

2025

@article{Cornfeld2025,
  title = {Integrating macroeconomic and public health impacts in social planning policies for pandemic response},
  volume = {53},
  ISSN = {1755-4365},
  url = {http://dx.doi.org/10.1016/j.epidem.2025.100873},
  DOI = {10.1016/j.epidem.2025.100873},
  journal = {Epidemics},
  publisher = {Elsevier BV},
  author = {Cornfeld,  Ofer and Niu,  Kaicheng and Neeman,  Oded and Roswell,  Michael and Steinbach,  Gabi and Beckett,  Stephen J. and Wardi,  Yorai and Weitz,  Joshua S. and Yashiv,  Eran},
  year = {2025},
  month = Dec,
  pages = {100873}
}

@article{Harris2025,
  title = {Infections are not alike: The effects of covariation between individual susceptibility and transmissibility on epidemic dynamics},
  volume = {613},
  ISSN = {0022-5193},
  url = {http://dx.doi.org/10.1016/j.jtbi.2025.112211},
  DOI = {10.1016/j.jtbi.2025.112211},
  journal = {Journal of Theoretical Biology},
  publisher = {Elsevier BV},
  author = {Harris,  Jeremy D. and Gallmeier,  Esther and Dushoff,  Jonathan and Beckett,  Stephen J. and Weitz,  Joshua S.},
  year = {2025},
  month = Oct,
  pages = {112211}
}

@article{Goel2025,
  title = {Eco-evolutionary dynamics of temperate phages in periodic environments},
  volume = {11},
  ISSN = {2057-1577},
  url = {http://dx.doi.org/10.1093/ve/veaf019},
  DOI = {10.1093/ve/veaf019},
  number = {1},
  journal = {Virus Evolution},
  publisher = {Oxford University Press (OUP)},
  author = {Goel,  Tapan and Beckett,  Stephen J and Weitz,  Joshua S},
  year = {2025}
}

2024

@article{Beckett2024,
  title = {Disentangling top-down drivers of mortality underlying diel population dynamics of \textit{Prochlorococcus} in the {North Pacific Subtropical Gyre}},
  volume = {15},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-024-46165-3},
  DOI = {10.1038/s41467-024-46165-3},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Beckett,  Stephen J. and Demory,  David and Coenen,  Ashley R. and Casey,  John R. and Dugenne,  Mathilde and Follett,  Christopher L. and Connell,  Paige and Carlson,  Michael C. G. and Hu,  Sarah K. and Wilson,  Samuel T. and Muratore,  Daniel and Rodriguez-Gonzalez,  Rogelio A. and Peng,  Shengyun and Becker,  Kevin W. and Mende,  Daniel R. and Armbrust,  E. Virginia and Caron,  David A. and Lindell,  Debbie and White,  Angelicque E. and Ribalet,  Fran\c{c}ois and Weitz,  Joshua S.},
  year = {2024},
  month = Mar 
}

@article{Sinclair2024,
  title = {Scenario-based messages on social media motivate {COVID-19} information seeking.},
  volume = {13},
  ISSN = {2211-3681},
  url = {http://dx.doi.org/10.1037/mac0000114},
  DOI = {10.1037/mac0000114},
  number = {1},
  journal = {Journal of Applied Research in Memory and Cognition},
  publisher = {American Psychological Association (APA)},
  author = {Sinclair,  Alyssa H. and Taylor,  Morgan K. and Davidson,  Audra and Weitz,  Joshua S. and Beckett,  Stephen J. and Samanez-Larkin,  Gregory R.},
  year = {2024},
  month = Mar,
  pages = {124–135}
}

2023

@article{Sinclair2023b,
  title = {Communicating {COVID-19} exposure risk with an interactive website counteracts risk misestimation},
  volume = {18},
  ISSN = {1932-6203},
  url = {http://dx.doi.org/10.1371/journal.pone.0290708},
  DOI = {10.1371/journal.pone.0290708},
  number = {10},
  journal = {PLOS ONE},
  publisher = {Public Library of Science (PLoS)},
  author = {Sinclair,  Alyssa H. and Taylor,  Morgan K. and Brandel-Tanis,  Freyja and Davidson,  Audra and Chande,  Aroon T. and Rishishwar,  Lavanya and Andris,  Clio and Adcock,  R. Alison and Weitz,  Joshua S. and Samanez-Larkin,  Gregory R. and Beckett,  Stephen J.},
  editor = {Daoust,  Jean-Fran\c{c}ois},
  year = {2023},
  month = Oct,
  pages = {e0290708}
}

@article{Beckett2023,
  title = {localcovid19now: processing and mapping {COVID-19} case data at subnational scales},
  volume = {8},
  ISSN = {2475-9066},
  url = {http://dx.doi.org/10.21105/joss.04898},
  DOI = {10.21105/joss.04898},
  number = {81},
  journal = {Journal of Open Source Software},
  publisher = {The Open Journal},
  author = {Beckett,  Stephen J. and Brandel-Tanis,  Freyja A. and Nguyen,  Quan and Chande,  Aroon T. and Rishishwar,  Lavanya and Andris,  Clio and Weitz,  Joshua S.},
  year = {2023},
  month = Jan,
  pages = {4898}
}

@article{Sinclair2023a,
  title = {Reasons for Receiving or Not Receiving Bivalent {COVID-19} Booster Vaccinations Among Adults — {United States,  November 1–December 10,  2022}},
  volume = {72},
  ISSN = {1545-861X},
  url = {http://dx.doi.org/10.15585/mmwr.mm7203a5},
  DOI = {10.15585/mmwr.mm7203a5},
  number = {3},
  journal = {MMWR. Morbidity and Mortality Weekly Report},
  publisher = {Centers for Disease Control MMWR Office},
  author = {Sinclair,  Alyssa H. and Taylor,  Morgan K. and Weitz,  Joshua S. and Beckett,  Stephen J. and Samanez-Larkin,  Gregory R.},
  year = {2023},
  month = Jan,
  pages = {73–75}
}

2022

@article{Muratore2022,
  title = {Complex marine microbial communities partition metabolism of scarce resources over the diel cycle},
  volume = {6},
  ISSN = {2397-334X},
  url = {http://dx.doi.org/10.1038/s41559-021-01606-w},
  DOI = {10.1038/s41559-021-01606-w},
  number = {2},
  journal = {Nature Ecology \& Evolution},
  publisher = {Springer Science and Business Media LLC},
  author = {Muratore,  Daniel and Boysen,  Angela K. and Harke,  Matthew J. and Becker,  Kevin W. and Casey,  John R. and Coesel,  Sacha N. and Mende,  Daniel R. and Wilson,  Samuel T. and Aylward,  Frank O. and Eppley,  John M. and Vislova,  Alice and Peng,  Shengyun and Rodriguez-Gonzalez,  Rogelio A. and Beckett,  Stephen J. and Virginia Armbrust,  E. and DeLong,  Edward F. and Karl,  David M. and White,  Angelicque E. and Zehr,  Jonathan P. and Van Mooy,  Benjamin A. S. and Dyhrman,  Sonya T. and Ingalls,  Anitra E. and Weitz,  Joshua S.},
  year = {2022},
  month = Jan,
  pages = {218–229}
}

@article{Gibson2021,
  title = {Surveillance-to-Diagnostic Testing Program for Asymptomatic {SARS-CoV-2} Infections on a Large, Urban Campus in Fall 2020},
  volume = {33},
  ISSN = {1044-3983},
  url = {http://dx.doi.org/10.1097/EDE.0000000000001448},
  DOI = {10.1097/ede.0000000000001448},
  number = {2},
  journal = {Epidemiology},
  publisher = {Ovid Technologies (Wolters Kluwer Health)},
  author = {Gibson,  Greg and Weitz,  Joshua S. and Shannon,  Michael P. and Holton,  Benjamin and Bryksin,  Anton and Liu,  Brian and Sieglinger,  Madeline and Coenen,  Ashley R. and Zhao,  Conan and Beckett,  Stephen J. and Bramblett,  Sandra and Williamson,  JulieAnne and Farrell,  Michael and Ortiz,  Alexander and Abdallah,  Chaouki T. and García,  Andrés J.},
  year = {2021},
  month = Dec,
  pages = {209–216}
}

2021

@article{Lopman2021,
  title = {A framework for monitoring population immunity to {SARS-CoV-2}},
  volume = {63},
  ISSN = {1047-2797},
  url = {http://dx.doi.org/10.1016/j.annepidem.2021.08.013},
  DOI = {10.1016/j.annepidem.2021.08.013},
  journal = {Annals of Epidemiology},
  publisher = {Elsevier BV},
  author = {Lopman,  Benjamin A. and Shioda,  Kayoko and Nguyen,  Quan and Beckett,  Stephen J. and Siegler,  Aaron J. and Sullivan,  Patrick S. and Weitz,  Joshua S.},
  year = {2021},
  month = Nov,
  pages = {75–78}
}

@article{Mruwat2021,
  title = {A single-cell polony method reveals low levels of infected \textit{Prochlorococcus} in oligotrophic waters despite high cyanophage abundances},
  volume = {15},
  ISSN = {1751-7370},
  url = {http://dx.doi.org/10.1038/s41396-020-00752-6},
  DOI = {10.1038/s41396-020-00752-6},
  number = {1},
  journal = {The ISME Journal},
  publisher = {Oxford University Press (OUP)},
  author = {Mruwat,  Noor and Carlson,  Michael C G and Goldin,  Svetlana and Ribalet,  Fran\c{c}ois and Kirzner,  Shay and Hulata,  Yotam and Beckett,  Stephen J and Shitrit,  Dror and Weitz,  Joshua S and Armbrust,  E Virginia and Lindell,  Debbie},
  year = {2021},
  month = Jan,
  pages = {41–54}
}

2020

@article{Chande2020,
  title = {Real-time, interactive website for {US-county-level COVID-19} event risk assessment},
  volume = {4},
  ISSN = {2397-3374},
  url = {http://dx.doi.org/10.1038/s41562-020-01000-9},
  DOI = {10.1038/s41562-020-01000-9},
  number = {12},
  journal = {Nature Human Behaviour},
  publisher = {Springer Science and Business Media LLC},
  author = {Chande,  Aroon and Lee,  Seolha and Harris,  Mallory and Nguyen,  Quan and Beckett,  Stephen J. and Hilley,  Troy and Andris,  Clio and Weitz,  Joshua S.},
  year = {2020},
  month = Nov,
  pages = {1313–1319}
}

@article{Weitz2020,
  title = {Modeling shield immunity to reduce {COVID-19} epidemic spread},
  volume = {26},
  ISSN = {1546-170X},
  url = {http://dx.doi.org/10.1038/s41591-020-0895-3},
  DOI = {10.1038/s41591-020-0895-3},
  number = {6},
  journal = {Nature Medicine},
  publisher = {Springer Science and Business Media LLC},
  author = {Weitz,  Joshua S. and Beckett,  Stephen J. and Coenen,  Ashley R. and Demory,  David and Dominguez-Mirazo,  Marian and Dushoff,  Jonathan and Leung,  Chung-Yin and Li,  Guanlin and Măgălie,  Andreea and Park,  Sang Woo and Rodriguez-Gonzalez,  Rogelio and Shivam,  Shashwat and Zhao,  Conan Y.},
  year = {2020},
  month = May,
  pages = {849–854}
}

2019

@article{Barone2019,
  title = {The ecological and biogeochemical state of the {North Pacific Subtropical Gyre} is linked to sea surface height},
  volume = {77},
  ISSN = {0022-2402},
  url = {https://elischolar.library.yale.edu/journal_of_marine_research/478},
  number = {2},
  journal = {Journal of Marine Research},
  publisher = {Journal of Marine Research/Yale},
  author = {Barone,  Benedetto and Coenen,  Ashley R. and Beckett,  Stephen J. and McGillicuddy,  Dennis J. and Weitz,  Joshua S. and Karl,  David M.},
  year = {2019},
  month = Dec,
  pages = {215–245}
}

@article{Talmy2019b,
  title = {An empirical model of carbon flow through marine viruses and microzooplankton grazers},
  volume = {21},
  ISSN = {1462-2920},
  url = {http://dx.doi.org/10.1111/1462-2920.14626},
  DOI = {10.1111/1462-2920.14626},
  number = {6},
  journal = {Environmental Microbiology},
  publisher = {Wiley},
  author = {Talmy,  David and Beckett,  Stephen J. and Taniguchi,  Darcy A. A. and Brussaard,  Corina P. D. and Weitz,  Joshua S. and Follows,  Michael J.},
  year = {2019},
  month = May,
  pages = {2171–2181}
}

@article{Talmy2019a,
  title = {Contrasting Controls on Microzooplankton Grazing and Viral Infection of Microbial Prey},
  volume = {6},
  ISSN = {2296-7745},
  url = {http://dx.doi.org/10.3389/fmars.2019.00182},
  DOI = {10.3389/fmars.2019.00182},
  journal = {Frontiers in Marine Science},
  publisher = {Frontiers Media SA},
  author = {Talmy,  David and Beckett,  Stephen J. and Zhang,  Adam B. and Taniguchi,  Darcy A. A. and Weitz,  Joshua S. and Follows,  Michael J.},
  year = {2019},
  month = Apr 
}

2018

@article{Beckett2018,
  title = {The Effect of Strain Level Diversity on Robust Inference of Virus-Induced Mortality of Phytoplankton},
  volume = {9},
  ISSN = {1664-302X},
  url = {http://dx.doi.org/10.3389/fmicb.2018.01850},
  DOI = {10.3389/fmicb.2018.01850},
  journal = {Frontiers in Microbiology},
  publisher = {Frontiers Media SA},
  author = {Beckett,  Stephen J. and Weitz,  Joshua S.},
  year = {2018},
  month = Sept 
}

2017

@article{Weitz2017,
  title = {Lysis, lysogeny and virus–microbe ratios},
  volume = {549},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/nature23295},
  DOI = {10.1038/nature23295},
  number = {7672},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {Weitz,  Joshua S. and Beckett,  Stephen J. and Brum,  Jennifer R. and Cael,  B. B. and Dushoff,  Jonathan},
  year = {2017},
  month = Sept,
  pages = {E1–E3}
}

@article{Beckett2017,
  title = {Disentangling niche competition from grazing mortality in phytoplankton dilution experiments},
  volume = {12},
  ISSN = {1932-6203},
  url = {http://dx.doi.org/10.1371/journal.pone.0177517},
  DOI = {10.1371/journal.pone.0177517},
  number = {5},
  journal = {PLOS ONE},
  publisher = {Public Library of Science (PLoS)},
  author = {Beckett,  Stephen J. and Weitz,  Joshua S.},
  editor = {Dam,  Hans G.},
  year = {2017},
  month = May,
  pages = {e0177517}
}

2016

@article{Beckett2016,
  title = {Improved community detection in weighted bipartite networks},
  volume = {3},
  ISSN = {2054-5703},
  url = {http://dx.doi.org/10.1098/rsos.140536},
  DOI = {10.1098/rsos.140536},
  number = {1},
  journal = {Royal Society Open Science},
  publisher = {The Royal Society},
  author = {Beckett,  Stephen J.},
  year = {2016},
  month = Jan,
  pages = {140536}
}

2015

@phdthesis{Beckett2015,
  author = "Stephen J. Beckett",
  title = "Nestedness and Modularity in Bipartite Networks",
  year = "2015",
  month = "5",
  school = "University of Exeter",
  type = "PhD Thesis",
  eprint = {10871/17913},
  archiveprefix = {hdl},
  url = "https://ore.exeter.ac.uk/articles/thesis/Nestedness_and_Modularity_in_Bipartite_Networks/29708327",
}

@article{Cowley2015,
  title = {Analysis of whole genome sequencing for the \textit{Escherichia coli} O157:H7 typing phages},
  volume = {16},
  ISSN = {1471-2164},
  url = {http://dx.doi.org/10.1186/s12864-015-1470-z},
  DOI = {10.1186/s12864-015-1470-z},
  number = {1},
  journal = {BMC Genomics},
  publisher = {Springer Science and Business Media LLC},
  author = {Cowley,  Lauren A and Beckett,  Stephen J and Chase-Topping,  Margo and Perry,  Neil and Dallman,  Tim J and Gally,  David L and Jenkins,  Claire},
  year = {2015},
  month = Apr 
}

2014

@article{Beckett2014,
  title = {{FALCON:} a software package for analysis of nestedness in bipartite networks},
  volume = {3},
  ISSN = {2046-1402},
  url = {http://dx.doi.org/10.12688/f1000research.4831.1},
  DOI = {10.12688/f1000research.4831.1},
  journal = {F1000Research},
  publisher = {F1000 Research Ltd},
  author = {Beckett,  Stephen J. and Boulton,  Chris A. and Williams,  Hywel T. P.},
  year = {2014},
  month = Aug,
  pages = {185}
}

@article{Watts2014,
  title = {Uptake and Retention of Microplastics by the Shore Crab \textit{Carcinus maenas}},
  volume = {48},
  ISSN = {1520-5851},
  url = {http://dx.doi.org/10.1021/es501090e},
  DOI = {10.1021/es501090e},
  number = {15},
  journal = {Environmental Science \& Technology},
  publisher = {American Chemical Society (ACS)},
  author = {Watts,  Andrew J. R. and Lewis,  Ceri and Goodhead,  Rhys M. and Beckett,  Stephen J. and Moger,  Julian and Tyler,  Charles R. and Galloway,  Tamara S.},
  year = {2014},
  month = July,
  pages = {8823–8830}
}

2013

@article{Beckett2013,
  title = {Coevolutionary diversification creates nested-modular structure in phage–bacteria interaction networks},
  volume = {3},
  ISSN = {2042-8901},
  url = {http://dx.doi.org/10.1098/rsfs.2013.0033},
  DOI = {10.1098/rsfs.2013.0033},
  number = {6},
  journal = {Interface Focus},
  publisher = {The Royal Society},
  author = {Beckett,  Stephen J. and Williams,  Hywel T. P.},
  year = {2013},
  month = Dec,
  pages = {20130033}
}