Caroline Colijn

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 32

Top Topics

Electronic Health Record

Acinetobacter Baumannii

Mycobacterium Tuberculosis

Top Venues

PLoS computational biology

medRxiv : the preprint server for health sciences

This page only lists publications with an associated author ORCID identifier.

Publications

Peiyu Xu, Shenni Liang, Andrew Hahn, Vivian Zhao, Wai Tung 'Jack' Lo, Benjamin C Haller, Benjamin Sobkowiak, Melanie H Chitwood, Caroline Colijn, Ted Cohen, Kyu Y Rhee, Philipp W Messer, Martin T Wells, Andrew G Clark, Jaehee Kim
e3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology. bioRxiv : the preprint server for biology (2024)
Peiyu Xu, Shenni Liang, Andrew Hahn, Vivian Zhao, Wai Tung 'Jack' Lo, Benjamin C Haller, Benjamin Sobkowiak, Melanie H Chitwood, Caroline Colijn, Ted Cohen, Kyu Y Rhee, Philipp W Messer, Martin T Wells, Andrew G Clark, Jaehee Kim
e3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology. bioRxiv : the preprint server for biology (2024)
Amber J Barton, Caroline Colijn
Genomic, clinical and immunity data join forces for public health. Nature reviews. Microbiology (2023)
Katharine S Walter, Ted Cohen, Barun Mathema, Caroline Colijn, Benjamin Sobkowiak, Iñaki Comas, Galo A Goig, Julio Henrique da Rosa Croda, Jason R Andrews
Signatures of transmission in within-host M. tuberculosis variation. medRxiv : the preprint server for health sciences (2023)
Katharine S Walter, Ted Cohen, Barun Mathema, Caroline Colijn, Benjamin Sobkowiak, Iñaki Comas, Galo A Goig, Julio Henrique da Rosa Croda, Jason R Andrews
Signatures of transmission in within-host M. tuberculosis variation. medRxiv : the preprint server for health sciences (2023)
Maryam Hayati, Benjamin Sobkowiak, Jessica E Stockdale, Caroline Colijn
Phylogenetic identification of influenza virus candidates for seasonal vaccines. Science advances 9 (44) (2023)
Katharine S Walter, Ted Cohen, Barun Mathema, Caroline Colijn, Benjamin Sobkowiak, Iñaki Comas, Galo A Goig, Julio Henrique da Rosa Croda, Jason R Andrews
Signatures of transmission in within-host M. tuberculosis variation. medRxiv : the preprint server for health sciences (2023)
Katharine S Walter, Ted Cohen, Barun Mathema, Caroline Colijn, Benjamin Sobkowiak, Iñaki Comas, Galo A Goig, Julio Henrique da Rosa Croda, Jason R Andrews
Signatures of transmission in within-host M. tuberculosis variation. medRxiv : the preprint server for health sciences (2023)
Katharine S Walter, Ted Cohen, Barun Mathema, Caroline Colijn, Benjamin Sobkowiak, Iñaki Comas, Galo A Goig, Julio Henrique da Rosa Croda, Jason R Andrews
Signatures of transmission in within-host M. tuberculosis variation. medRxiv : the preprint server for health sciences (2023)
Madi Yerlanov, Piyush Agarwal, Caroline Colijn, Jessica E Stockdale
Effective population size in simple infectious disease models. Journal of mathematical biology 87 (6) (2023)
Irving Cancino-Muñoz, Mariana G López, Manuela Torres-Puente, Luis M Villamayor, Rafael Borrás, María Borrás-Máñez, Montserrat Bosque, Juan J Camarena, Caroline Colijn, Ester Colomer-Roig, Javier Colomina, Isabel Escribano, Oscar Esparcia-Rodríguez, Francisco García-García, Ana Gil-Brusola, Concepción Gimeno, Adelina Gimeno, Bárbara Gomila-Sard, Damiana Gónzales-Granda, Nieves Gonzalo-Jiménez, María Remedios Guna-Serrano, Jose Luis Lopez-Hontangas, Coral Martín-González, Rosario Moreno-Muñoz, David Navarro, María Navarro, Nieves Orta, Elvira Pérez, Josep Prat, Juan Carlos Rodríguez, Ma Montserrat Ruiz-García, Hermelinda Vanaclocha, null null, Iñaki Comas
Population-based sequencing of Mycobacterium tuberculosis reveals how current population dynamics are shaped by past epidemics. eLife 11 (2022)
Jessica E Stockdale, Sean C Anderson, Andrew M Edwards, Sarafa A Iyaniwura, Nicola Mulberry, Michael C Otterstatter, Naveed Z Janjua, Daniel Coombs, Caroline Colijn, Michael A Irvine
Quantifying transmissibility of SARS-CoV-2 and impact of intervention within long-term healthcare facilities. Royal Society open science 9 (1) (2022)
Maryam Hayati, Leonid Chindelevitch, David M Aanensen, Caroline Colijn
Deep clustering of bacterial tree images. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 377 (1861) (2022)
Paul Tupper, Shraddha Pai, null null, Caroline Colijn
COVID-19 cluster size and transmission rates in schools from crowdsourced case reports. eLife 11 (2022)
Jessica E Stockdale, Pengyu Liu, Caroline Colijn
The potential of genomics for infectious disease forecasting. Nature microbiology 7 (11) (2022)
Chongguang Yang, Benjamin Sobkowiak, Vijay Naidu, Alexandru Codreanu, Nelly Ciobanu, Kenneth S Gunasekera, Melanie H Chitwood, Sofia Alexandru, Stela Bivol, Marcus Russi, Joshua Havumaki, Patrick George Tobias Cudahy, Heather Fosburgh, Christopher J Allender, Heather Centner, David M Engelthaler, Nicolas A Menzies, Joshua L Warren, Valeriu Crudu, Caroline Colijn, Ted Cohen
Phylogeography and transmission of M. tuberculosis in Moldova: A prospective genomic analysis. PLoS medicine 19 (2) (2022)
Liangliang Wang, Joosung Min, Renny Doig, Lloyd T Elliott, Caroline Colijn
Estimation of SARS-CoV-2 antibody prevalence through serological uncertainty and daily incidence. The Canadian journal of statistics = Revue canadienne de statistique 50 (3) (2022)
Jonathan Dushoff, Caroline Colijn, David J D Earn, Benjamin M Bolker
Transmission dynamics are crucial to COVID-19 vaccination policy. Proceedings of the National Academy of Sciences of the United States of America 118 (29) (2021)
Nicola Mulberry, Paul Tupper, Erin Kirwin, Christopher McCabe, Caroline Colijn
Vaccine rollout strategies: The case for vaccinating essential workers early. PLOS global public health 1 (10) (2021)
Paul Tupper, Caroline Colijn
COVID-19 in schools: Mitigating classroom clusters in the context of variable transmission. PLoS computational biology 17 (7) (2021)
Sean C Anderson, Andrew M Edwards, Madi Yerlanov, Nicola Mulberry, Jessica E Stockdale, Sarafa A Iyaniwura, Rebeca C Falcao, Michael C Otterstatter, Michael A Irvine, Naveed Z Janjua, Daniel Coombs, Caroline Colijn
Quantifying the impact of COVID-19 control measures using a Bayesian model of physical distancing. PLoS computational biology 16 (12) (2020)
Paul Tupper, Himani Boury, Madi Yerlanov, Caroline Colijn
Event-specific interventions to minimize COVID-19 transmission. Proceedings of the National Academy of Sciences of the United States of America 117 (50) (2020)
Lauren C Tindale, Jessica E Stockdale, Michelle Coombe, Emma S Garlock, Wing Yin Venus Lau, Manu Saraswat, Louxin Zhang, Dongxuan Chen, Jacco Wallinga, Caroline Colijn
Evidence for transmission of COVID-19 prior to symptom onset. eLife 9 (2020)
Caroline Colijn, Jukka Corander, Nicholas J Croucher
Designing ecologically optimized pneumococcal vaccines using population genomics. Nature microbiology 5 (3) (2020)
Cornelia Metzig, Oliver Ratmann, Daniela Bezemer, Caroline Colijn
Phylogenies from dynamic networks. PLoS computational biology 15 (2) (2019)
Tarub S Mabud, Maria de Lourdes Delgado Alves, Albert I Ko, Sanjay Basu, Katharine S Walter, Ted Cohen, Barun Mathema, Caroline Colijn, Everton Lemos, Julio Henrique da Rosa Croda, Jason R Andrews
Evaluating strategies for control of tuberculosis in prisons and prevention of spillover into communities: An observational and modeling study from Brazil. PLoS medicine 16 (1) (2019)
Yuanwei Xu, Irving Cancino-Muñoz, Manuela Torres-Puente, Luis M Villamayor, Rafael Borrás, María Borrás-Máñez, Montserrat Bosque, Juan José Camarena-Miñana, Ester Colomer-Roig, Javier Colomina, Isabel Escribano, Oscar Esparcia-Rodríguez, Ana Gil-Brusola, Concepción Gimeno, Adelina Gimeno, Bárbara Gomila-Sard, Damiana González-Granda, Nieves Gonzalo-Jiménez, María Remedio Guna-Serrano, José Luis López-Hontangas, Coral Martín-González, Rosario Moreno-Muñoz, Víctor Vinuesa, María Navarro, Nieves Orta, Elvira Pérez, Josep Prat, Juan Carlos Rodríguez-Diaz, María Montserrat Ruiz-García, Herme Vanaclocha, Caroline Colijn, Iñaki Comas
High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain. PLoS medicine 16 (10) (2019)
John A Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D Bentley, Simon R Harris
Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study. Wellcome open research 3 (2018)
Reza Yaesoubi, Caroline Trotter, Caroline Colijn, Maziar Yaesoubi, Anaïs Colombini, Stephen Charles Resch, Paul A Kristiansen, F Marc LaForce, Ted Cohen
The cost-effectiveness of alternative vaccination strategies for polyvalent meningococcal vaccines in Burkina Faso: A transmission dynamic modeling study. PLoS medicine 15 (1) (2018)
Don Klinkenberg, Jantien A Backer, Xavier Didelot, Caroline Colijn, Jacco Wallinga
Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS computational biology 13 (5) (2017)
Nick Fyson, Jerry King, Thomas Belcher, Andrew Preston, Caroline Colijn
A curated genome-scale metabolic model of Bordetella pertussis metabolism. PLoS computational biology 13 (7) (2017)
Louis Grandjean, Robert H Gilman, Tomatada Iwamoto, Claudio Umberto Köser, Jorge Coronel, Mirko Zimic, Michelle S Toleman, Diepreye Ayabina, Michelle Kendall, Christophe Fraser, Simon R Harris, Julian Parkhill, Sharon J Peacock, David A J Moore, Caroline Colijn
Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru. PloS one 12 (12) (2017)
Caroline Colijn, Ted Cohen
How competition governs whether moderate or aggressive treatment minimizes antibiotic resistance. eLife 4 (2015)