Publications | Caroline Colijn

2024

Abhari, N., Colijn, C., Mooers, A., & Tupper, P. (2024). Capturing Diversity: Split Systems and Circular Approximations for Conservation. Journal of Theoretical Biology, 578:111689 https://doi.org/10.1016/j.jtbi.2023.111689
Are, E.B., Card, K.G. & Colijn, C. (2024). The role of vaccine status homophily in the COVID-19 pandemic: a cross-sectional survey with modelling, BMC Public Health, 24(1), 472. https://doi.org/10.1186/s12889-024-17957-5
Otto, S.P., MacPherson, A., & Colijn, C. (2024) Endemic does not mean constant as SARS-CoV-2 continues to evolve. Evolution,; qpae041, https://doi.org/10.1093/evolut/qpae041

2023

Mulberry N, Rutherford AR, Colijn C. (2023). Pneumococcal population dynamics: Investigating vaccine-induced changes through multiscale modelling. PLOS Computational Biology. 2023;19: e1011755 doi:10.1371/journal.pcbi.1011755
Are EB, Stockdale J, Colijn C. (2023) Long-Term Dynamics of COVID-19 in a Multi-strain Model. Book Chapter: David, J., Wu, J. (eds) Mathematics of Public Health. Fields Institute Communications, vol 88. Springer, Cham. 295-317. https://doi.org/10.1007/978-3-031-40805-2_11
Walter KS, Cohen T, Mathema B, Colijn C, Sobkowiak B, Comas I, Goig GA, Croda J, Andrews JR. (2023). Signatures of transmission in within-hose M. tuberculosis variation [Preprint]. medRxiv. 2023(12), 28.23300451
Are, E. B., Song, Y., Stockdale, J. E., Tupper, P., & Colijn, C. (2023). COVID-19 endgame: From pandemic to endemic? Vaccination, reopening and evolution in low- and high-vaccinated populations. Journal of Theoretical Biology, 559, 111368. https://doi.org/10.1016/j.jtbi.2022.111368
Barton, A., & Colijn, C. (2023). Genomic, clinical and immunity data join forces for public health. Nature Reviews. Microbiology, 21(10), 639–639. https://doi.org/10.1038/s41579-023-00965-4
Chitwood, M. H., Colijn, C., Yang, C., Crudu, V., Ciobanu, N., Codreanu, A., Kim, J., Rancu, I., Rhee, K., Cohen, T., & Sobkowiak, B. (2023). The recent rapid expansion of multidrug resistant strains of Mycobacterium tuberculosis Ural lineage 4.2 in the Republic of Moldova [Preprint]. Epidemiology. https://doi.org/10.1101/2023.11.10.23298377
Colijn, C., Halloran, M. E., O’Neill, P., & Trapman, P. (2023). Design and Analysis of Infectious Disease Studies. Oberwolfach Reports, 20(1), 487–435. https://doi.org/10.4171/OWR/2023/8
Hayati, M., Sobkowiak, B., Stockdale, J. E., & Colijn, C. (2023). Phylogenetic identification of influenza virus candidates for seasonal vaccines. Science Advances, 9(44), eabp9185. https://doi.org/10.1126/sciadv.abp9185
Lewis, M. A., Brown, P., Colijn, C., Cowen, L., Cotton, C., Day, T., Deardon, R., Earn, D., Haskell, D., Heffernan, J., Leighton, P., Murty, K., Otto, S., Rafferty, E., Tuohy, C. H., Wu, J., & Zhu, H. (2023). Charting a future for emerging infectious disease modelling in Canada. University of Victoria. http://hdl.handle.net/1828/15042
Otto, S. P., MacPherson, A., & Colijn, C. (2023). Endemic means change as SARS-CoV-2 evolves [Preprint]. Epidemiology. https://doi.org/10.1101/2023.09.28.23296264
Shaver, N., Katz, M., Darko Asamoah, G., Linkins, L.-A., Abdelkader, W., Beck, A., Bennett, A., Hughes, S. E., Smith, M., Begin, M., Coyle, D., Piggott, T., Kagina, B. M., Welch, V., Colijn, C., Earn, D. J. D., El Emam, K., Heffernan, J., O’Brien, S. F., … Little, J. (2023). Protocol for a living evidence synthesis on variants of concern and COVID-19 vaccine effectiveness. Vaccine, 41(43), 6411–6418. https://doi.org/10.1016/j.vaccine.2023.09.012
Sobkowiak, B., Haghmaram, P., Prystajecky, N., Zlosnik, J. E. A., Tyson, J., Hoang, L. M. N., & Colijn, C. (2023). The utility of SARS-CoV-2 genomic data for informative clustering under different epidemiological scenarios and sampling. Infection Genetics and Evolution, 113, 105484.
Stockdale, J. E., Susvitasari, K., Tupper, P., Sobkowiak, B., Mulberry, N., Gonçalves Da Silva, A., Watt, A. E., Sherry, N. L., Minko, C., Howden, B. P., Lane, C. R., & Colijn, C. (2023). Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19. Nature Communications, 14(1), 4830. https://doi.org/10.1038/s41467-023-40544-y
Susvitasari, K., Tupper, P. F., Cancino-Muños, I., Lòpez, M. G., Comas, I., & Colijn, C. (2023). Epidemiological cluster identification using multiple data sources: An approach using logistic regression. Microbial Genomics, 9(3). https://doi.org/10.1099/mgen.0.000929
Susvitasari, K., Tupper, P., Stockdale, J. E., & Colijn, C. (2023). A method to estimate the serial interval distribution under partially-sampled data. Epidemics, 45, 100733. https://doi.org/10.1016/j.epidem.2023.100733
Wang, S., Ge, S., Sobkowiak, B., Wang, L., Grandjean, L., Colijn, C., & Elliott, L. T. (2023). Genome-Wide Association with Uncertainty in the Genetic Similarity Matrix. Journal of Computational Biology, 30(2), 189–203.
Warren, J. L., Chitwood, M. H., Sobkowiak, B., Colijn, C., & Cohen, T. (2023). Spatial modeling of Mycobacterium tuberculosis transmission with dyadic genetic relatedness data. Biometrics. Journal of the International Biometric Society, biom.13836. https://doi.org/10.1111/biom.13836
Yerlanov, M., Agarwal, P., Colijn, C., & Stockdale, J. E. (2023). Effective population size in simple infectious disease models. Journal of Mathematical Biology, 87(6), 80. https://doi.org/10.1007/s00285-023-02016-1
Zhang, L., Abhari, N., Colijn, C., & Wu, Y. (2023). A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings. Genome Research, 33(7), 1053–1060.

2022

Cancino-Muñoz, I., López, M. G., Torres-Puente, M., Villamayor, L. M., Borrás, R., Borrás-Máñez, M., Bosque, M., Camarena, J. J., Colijn, C., Colomer-Roig, E., Colomina, J., Escribano, I., Esparcia-Rodríguez, O., García-García, F., Gil-Brusola, A., Gimeno, C., Gimeno-Gascón, A., Gomila-Sard, B., Gónzales-Granda, D., … Comas, I. (2022). Population-based sequencing of Mycobacterium tuberculosis reveals how current population dynamics are shaped by past epidemics. eLife, 11, e76605. https://doi.org/10.7554/eLife.76605
Colijn, C., Earn, D. J., Dushoff, J., Ogden, N. H., Li, M., Knox, N., Van Domselaar, G., Franklin, K., Jolly, G., & Otto, S. P. (2022). La nécessité d’une surveillance génomique liée du SRAS-CoV-2. RMTC, 48(4), 147–155. https://doi.org/10.14745/ccdr.v48i04a03f
Colijn, C., Earn, D. J., Dushoff, J., Ogden, N. H., Li, M., Knox, N., Van Domselaar, G., Franklin, K., Jolly, G., & Otto, S. P. (2022). The need for linked genomic surveillance of SARS-CoV-2. Canada Communicable Disease Report, 48(4), 131–139.
Fibke, C. D., Joffres, Y., Tyson, J. R., Colijn, C., Janjua, N. Z., Fjell, C., Prystajecky, N., Jassem, A., & Sbihi, H. (2022). Spike Mutation Profiles Associated With SARS-CoV-2 Breakthrough Infections in Delta Emerging and Predominant Time Periods in British Columbia, Canada. Frontiers in Public Health, 10, 915363. https://doi.org/10.3389/fpubh.2022.915363
Grandjean, L., Saso, A., Torres Ortiz, A., Lam, T., Hatcher, J., Thistlethwayte, R., Harris, M., Best, T., Johnson, M., Wagstaffe, H., Ralph, E., Mai, A., Colijn, C., Breuer, J., Buckland, M., Gilmour, K., Goldblatt, D., & COVID-19 Staff Testing of Antibody Responses Study (Co-Stars) team. (2022). Long-Term Persistence of Spike Protein Antibody and Predictive Modeling of Antibody Dynamics After Infection With Severe Acute Respiratory Syndrome Coronavirus 2. Clinical Infectious Diseases, 74(7), 1220–1229.
Hayati, M., Chindelevitch, L., Aanensen, D., & Colijn, C. (2022). Deep clustering of bacterial tree images. Philosophical Transactions of the Royal Society B: Biological Sciences, 377(1861), 20210231. https://doi.org/10.1098/rstb.2021.0231
Iyaniwura, S. A., Falcão, R. C., Ringa, N., Adu, P. A., Spencer, M., Taylor, M., Colijn, C., Coombs, D., Janjua, N. Z., Irvine, M. A., & Otterstatter, M. (2022). Mathematical modeling of COVID-19 in British Columbia: An age-structured model with time-dependent contact rates. Epidemics, 39, 100559. https://doi.org/10.1016/j.epidem.2022.100559
Liu, P., Biller, P., Gould, M., & Colijn, C. (2022). Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial. Systematic Biology, 71(6), 1378–1390. https://doi.org/10.1093/sysbio/syac008
Liu, P., Song, Y., Colijn, C., & MacPherson, A. (2022). The impact of sampling bias on viral phylogeographic reconstruction. PLOS Glob Public Health, 2(9), e0000577. https://doi.org/10.1371/journal.pgph.0000577
Sobkowiak, B., & Colijn, C. (2022). Characterising indel diversity in a large Mycobacterium tuberculosis outbreak – implications for transmission reconstruction [Preprint]. Genomics. https://doi.org/10.1101/2022.10.26.513840
Sobkowiak, B., Kamelian, K., Zlosnik, J. E. A., Tyson, J., Silva, A. G. D., Hoang, L. M. N., Prystajecky, N., & Colijn, C. (2022). Cov2clusters: Genomic clustering of SARS-CoV-2 sequences. BMC Genomics, 23(1), 710. https://doi.org/10.1186/s12864-022-08936-4
Stockdale, J. E., Anderson, S. C., Edwards, A. M., Iyaniwura, S. A., Mulberry, N., Otterstatter, M. C., Janjua, N. Z., Coombs, D., Colijn, C., & Irvine, M. A. (2022). Quantifying transmissibility of SARS-CoV-2 and impact of intervention within long-term healthcare facilities. Royal Society Open Science, 9(1), 211710.
Stockdale, J. E., Liu, P., & Colijn, C. (2022). The potential of genomics for infectious disease forecasting. Nature Microbiology, 7(11), 1736–1743. https://doi.org/10.1038/s41564-022-01233-6
Tupper, P., Pai, S., COVID Schools Canada, & Colijn, C. (2022). COVID-19 cluster size and transmission rates in schools from crowdsourced case reports. eLife, 11, e76174. https://doi.org/10.7554/eLife.76174
Walter, K. S., Pereira Dos Santos, P. C., Gonçalves, T. O., Da Silva, B. O., Santos, A. D. S., Leite, A. D. C., Da Silva, A. M., Moreira, F. M. F., De Oliveira, R. D., Lemos, E. F., Cunha, E., Liu, Y. E., Ko, A. I., Colijn, C., Cohen, T., Mathema, B., Croda, J., & Andrews, J. R. (2022). The role of prisons in disseminating tuberculosis in Brazil: A genomic epidemiology study. The Lancet Regional Health - Americas, 9, 100186. https://doi.org/10.1016/j.lana.2022.100186
Wang, L., Min, J., Doig, R., Elliott, L. T., & Colijn, C. (2022). Estimation of SARS‐CoV‐2 antibody prevalence through serological uncertainty and daily incidence. Can J Statistics, 50(3), 734–750. https://doi.org/10.1002/cjs.11722
Yang, C., Sobkowiak, B., Naidu, V., Codreanu, A., Ciobanu, N., Gunasekera, K. S., Chitwood, M. H., Alexandru, S., Bivol, S., Russi, M., Havumaki, J., Cudahy, P., Fosburgh, H., Allender, C. J., Centner, H., Engelthaler, D. M., Menzies, N. A., Warren, J. L., Crudu, V., … Cohen, T. (2022). Phylogeography and transmission of M. tuberculosis in Moldova: A prospective genomic analysis. PLoS Medicine, 19(2), e1003933. https://doi.org/10.1371/journal.pmed.1003933

2021

Anderson, S. C., Mulberry, N., Edwards, A. M., Stockdale, J. E., Iyaniwura, S. A., Falcao, R. C., Otterstatter, M. C., Janjua, N. Z., Coombs, D., & Colijn, C. (2021). How much leeway is there to relax COVID-19 control measures? Epidemics, 35, 100453. https://doi.org/10.1016/j.epidem.2021.100453
Are, E. B., & Colijn, C. (2021). Projected spread of COVID-19’s second wave in South Africa under different levels of lockdown [Preprint]. Epidemiology. https://doi.org/10.1101/2021.01.22.21250308
Brown, T. S., Eldholm, V., Brynildsrud, O., Osnes, M., Levy, N., Stimson, J., Colijn, C., Alexandru, S., Noroc, E., Ciobanu, N., Crudu, V., Cohen, T., & Mathema, B. (2021). Evolution and emergence of multidrug-resistant Mycobacterium tuberculosis in Chisinau, Moldova. Microbial Genomics, 7(8). https://doi.org/10.1099/mgen.0.000620
Chindelevitch, L., Hayati, M., Poon, A. F. Y., & Colijn, C. (2021). Network science inspires novel tree shape statistics. PLoS ONE, 16(12), e0259877. https://doi.org/10.1371/journal.pone.0259877
Dushoff, J., Colijn, C., Earn, D. J. D., & Bolker, B. M. (2021). Transmission dynamics are crucial to COVID-19 vaccination policy. Proceedings of the National Academy of Sciences of the United States of America, 118(29), e2105878118. https://doi.org/10.1073/pnas.2105878118
Harrow, G. L., Lees, J. A., Hanage, W. P., Lipsitch, M., Corander, J., Colijn, C., & Croucher, N. J. (2021). Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. The ISME Journal, 15(5), 1523–1538. https://doi.org/10.1038/s41396-020-00867-w
Liu, P., McQuarrie, L., Song, Y., & Colijn, C. (2021). Modelling the impact of household size distribution on the transmission dynamics of COVID-19. Journal of The Royal Society Interface, 18(177), rsif.2021.0036, 20210036. https://doi.org/10.1098/rsif.2021.0036
Mulberry, N., Tupper, P., Kirwin, E., McCabe, C., & Colijn, C. (2021). Vaccine rollout strategies: The case for vaccinating essential workers early. PLOS Glob Public Health, 1(10), e0000020. https://doi.org/10.1371/journal.pgph.0000020
Otto, S. P., Day, T., Arino, J., Colijn, C., Dushoff, J., Li, M., Mechai, S., Van Domselaar, G., Wu, J., Earn, D. J. D., & Ogden, N. H. (2021). The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic. Current Biology, 31(14), R918–R929. https://doi.org/10.1016/j.cub.2021.06.049
Quan, A. M. L., Mah, C., Krebs, E., Zang, X., Chen, S., Althoff, K., Armstrong, W., Behrends, C. N., Dombrowski, J. C., Enns, E., Feaster, D. J., Gebo, K. A., Goedel, W. C., Golden, M., Marshall, B. D. L., Mehta, S. H., Pandya, A., Schackman, B. R., Strathdee, S. A., … Weiner, J. (2021). Improving health equity and ending the HIV epidemic in the USA: A distributional cost-effectiveness analysis in six cities. The Lancet HIV, 8(9), e581–e590. https://doi.org/10.1016/S2352-3018(21)00147-8
Sadarangani, M., Abu Raya, B., Conway, J. M., Iyaniwura, S. A., Falcao, R. C., Colijn, C., Coombs, D., & Gantt, S. (2021). Importance of COVID-19 vaccine efficacy in older age groups. Vaccine, 39(15), 2020–2023. https://doi.org/10.1016/j.vaccine.2021.03.020
Stockdale, J. E., Doig, R., Min, J., Mulberry, N., Wang, L., Elliott, L. T., & Colijn, C. (2021). Long time frames to detect the impact of changing COVID-19 measures, Canada, March to July 2020. Eurosurveillance, 26(40). https://doi.org/10.2807/1560-7917.ES.2021.26.40.2001204
Tupper, P., & Colijn, C. (2021). COVID-19 in schools: Mitigating classroom clusters in the context of variable transmission. PLoS Computational Biology, 17(7), e1009120. https://doi.org/10.1371/journal.pcbi.1009120
Tupper, P., Otto, S. P., & Colijn, C. (2021). Fundamental limitations of contact tracing for COVID-19. FACETS, 6, 1993–2001. https://doi.org/10.1139/facets-2021-0016
Wang, S., Ge, S., Colijn, C., Biller, P., Wang, L., & Elliott, L. T. (2021). Estimating Genetic Similarity Matrices Using Phylogenies. Journal of Computational Biology, 28(6), 587–600. https://doi.org/10.1089/cmb.2020.0375
Warren, J. L., Chitwood, M. H., Sobkowiak, B., Crudu, V., Colijn, C., & Cohen, T. (2021). Spatial modeling of dyadic genetic relatedness data: Identifying factors associated with M. tuberculosis transmission in Moldova. https://doi.org/10.48550/arXiv.2109.14003

2020

Anderson, S. C., Edwards, A. M., Yerlanov, M., Mulberry, N., Stockdale, J. E., Iyaniwura, S. A., Falcao, R. C., Otterstatter, M. C., Irvine, M. A., Janjua, N. Z., Coombs, D., & Colijn, C. (2020). Quantifying the impact of COVID-19 control measures using a Bayesian model of physical distancing. PLoS Computational Biology, 16(12), e1008274. https://doi.org/10.1371/journal.pcbi.1008274
Colijn, C., Corander, J., & Croucher, N. J. (2020). Designing ecologically optimized pneumococcal vaccines using population genomics. Nature Microbiology, 5(3), 473–485. https://doi.org/10.1038/s41564-019-0651-y
Hayati, M., Biller, P., & Colijn, C. (2020). Predicting the short-term success of human influenza virus variants with machine learning. Proceedings of the Royal Society Biology, 287(1924), 20200319. https://doi.org/10.1098/rspb.2020.0319
Metzig, C., & Colijn, C. (2020). A Maximum Entropy Method for the Prediction of Size Distributions. Entropy. An International and Interdisciplinary Journal of Entropy and Information Studies, 22(3).
Metzig, C., Gould, M., Noronha, R., Abbey, R., Sandler, M., & Colijn, C. (2020). Classification of origin with feature selection and network construction for folk tunes. Pattern Recognition Letters, 133, 356–364. https://doi.org/10.1016/j.patrec.2020.03.023
Tindale, L. C., Stockdale, J. E., Coombe, M., Garlock, E. S., Lau, W. Y. V., Saraswat, M., Zhang, L., Chen, D., Wallinga, J., & Colijn, C. (2020). Evidence for transmission of COVID-19 prior to symptom onset. eLife, 9, e57149. https://doi.org/10.7554/eLife.57149
Tupper, P., Boury, H., Yerlanov, M., & Colijn, C. (2020). Event-specific interventions to minimize COVID-19 transmission. Proceedings of the National Academy of Sciences of the United States of America, 117(50), 32038–32045. https://doi.org/10.1073/pnas.2019324117
Walter, K. S., Colijn, C., Cohen, T., Mathema, B., Liu, Q., Bowers, J., Engelthaler, D. M., Narechania, A., Lemmer, D., Croda, J., & Andrews, J. R. (2020). Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences. Microbial Genomics, 6(8). https://doi.org/10.1099/mgen.0.000418
Xu, Y., Stockdale, J. E., Naidu, V., Hatherell, H., Stimson, J., Stagg, H. R., Abubakar, I., & Colijn, C. (2020). Transmission analysis of a large tuberculosis outbreak in London: A mathematical modelling study using genomic data. Microbial Genomics, 6(11). https://doi.org/10.1099/mgen.0.000450
Mulberry, N., Rutherford, A., & Colijn, C. (2020). Systematic comparison of coexistence in models of drug-sensitive and drug-resistant pathogen strains. Theoretical Population Biology, 202(133), 150–158. https://doi.org/10.1016/j.tpb.2019.12.001

2019

Hall, M. D., & Colijn, C. (2019). Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling. Molecular Biology and Evolution, 36(6), 1333–1343. https://doi.org/10.1093/molbev/msz058
Knight, G. M., Davies, N. G., Colijn, C., Coll, F., Donker, T., Gifford, D. R., Glover, R. E., Jit, M., Klemm, E., Lehtinen, S., Lindsay, J. A., Lipsitch, M., Llewelyn, M. J., Mateus, A. L. P., Robotham, J. V., Sharland, M., Stekel, D., Yakob, L., & Atkins, K. E. (2019). Mathematical modelling for antibiotic resistance control policy: Do we know enough? BMC Infectious Diseases, 19(1), 1011. https://doi.org/10.1186/s12879-019-4630-y
Mabud, T. S., De Lourdes Delgado Alves, M., Ko, A. I., Basu, S., Walter, K. S., Cohen, T., Mathema, B., Colijn, C., Lemos, E., Croda, J., & Andrews, J. R. (2019). Correction: Evaluating strategies for control of tuberculosis in prisons and prevention of spillover into communities: An observational and modeling study from Brazil. PLoS Medicine, 16(3), e1002764. https://doi.org/10.1371/journal.pmed.1002764
Mabud, T. S., De Lourdes Delgado Alves, M., Ko, A. I., Basu, S., Walter, K. S., Cohen, T., Mathema, B., Colijn, C., Lemos, E., Croda, J., & Andrews, J. R. (2019). 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), e1002737. https://doi.org/10.1371/journal.pmed.1002737
Metzig, C., Ratmann, O., Bezemer, D., & Colijn, C. (2019). Phylogenies from dynamic networks. PLoS Computational Biology, 15(2), e1006761. https://doi.org/10.1371/journal.pcbi.1006761
Stimson, J., Gardy, J., Mathema, B., Crudu, V., Cohen, T., & Colijn, C. (2019). Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions. Molecular Biology and Evolution, 36(3), 587–603. https://doi.org/10.1093/molbev/msy242
Xu, Y., Cancino-Muñoz, I., Torres-Puente, M., Villamayor, L. M., Borrás, R., Borrás-Máñez, M., Bosque, M., Camarena, J. J., Colomer-Roig, E., Colomina, J., Escribano, I., Esparcia-Rodríguez, O., Gil-Brusola, A., Gimeno, C., Gimeno-Gascón, A., Gomila-Sard, B., González-Granda, D., Gonzalo-Jiménez, N., Guna-Serrano, M. R., … Comas, I. (2019). High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain. PLoS Medicine, 16(10), e1002961. https://doi.org/10.1371/journal.pmed.1002961
Xu, Y., Topliffe, H., Stimson, J., Stagg, H.R., Abubakar, I., & Colijn, C. (2019) Transmission analysis of a large TB outbreak in London: mathematical modelling study using genomic data. bioRxiv. 761411. doi: 10.1101/761411

2018

Ayabina, D., Ronning, J. O., Alfsnes, K., Debech, N., Brynildsrud, O. B., Arnesen, T., Norheim, G., Mengshoel, A.-T., Rykkvin, R., Dahle, U. R., Colijn, C., & Eldholm, V. (2018). Genome-based transmission modelling separates imported tuberculosis from recent transmission within an immigrant population. Microbial Genomics, 4(10). https://doi.org/10.1099/mgen.0.000219
Colijn, C., & Plazzotta, G. (2018). A Metric on Phylogenetic Tree Shapes. Systematic Biology, 67(1), 113–126. https://doi.org/10.1093/sysbio/syx046
Kendall, M., Ayabina, D., & Colijn, C. (2018). Estimating transmission from genetic and epidemiological data: A metric to compare transmission trees. Statistical Science, 33(1), 70–85. https://doi.org/10.1214/17-STS637
Kendall, M., Eldholm, V., & Colijn, C. (2018). Comparing phylogenetic trees according to tip label categories [Preprint]. Evolutionary Biology. https://doi.org/10.1101/251710
Lees, J. A., Kendall, M., Parkhill, J., Colijn, C., Bentley, S. D., & Harris, S. R. (2018). Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: A simulation based study. Wellcome Open Research, 3, 33. https://doi.org/10.12688/wellcomeopenres.14265.1
Ratmann, O., Camacho, A., Hu, S., & Colijn, C. (2018). Informed choices: How to calibrate ABC with hypothesis testing. In Handbook of approximate bayesian computation (1st ed.). Chapman and Hall. https://www.routledgehandbooks.com/doi/10.1201/9781315117195-11
Yaesoubi, R., Trotter, C., Colijn, C., Yaesoubi, M., Colombini, A., Resch, S., Kristiansen, P. A., LaForce, F. M., & Cohen, T. (2018). The cost-effectiveness of alternative vaccination strategies for polyvalent meningococcal vaccines in Burkina Faso: A transmission dynamic modeling study. PLoS Medicine, 15(1), e1002495. https://doi.org/10.1371/journal.pmed.1002495
Yang, C., Lu, L., Warren, J. L., Wu, J., Jiang, Q., Zuo, T., Gan, M., Liu, M., Liu, Q., DeRiemer, K., Hong, J., Shen, X., Colijn, C., Guo, X., Gao, Q., & Cohen, T. (2018). Internal migration and transmission dynamics of tuberculosis in Shanghai, China: An epidemiological, spatial, genomic analysis. The Lancet Infectious Diseases, 18(7), 788–795. https://doi.org/10.1016/S1473-3099(18)30218-4
Metzig, C., & Colijn, C. (2018) Preferential attachment in systems and networks of constant size [Preprint]. arXiv. 10:e22030312.

2017

Cobey, S., Baskerville, E. B., Colijn, C., Hanage, W., Fraser, C., & Lipsitch, M. (2017). Host population structure and treatment frequency maintain balancing selection on drug resistance. Journal of The Royal Society Interface, 14(133), 20170295. https://doi.org/10.1098/rsif.2017.0295
Colijn, C., Jones, N., Johnston, I. G., Yaliraki, S., & Barahona, M. (2017). Toward Precision Healthcare: Context and Mathematical Challenges. Frontiers in Physiology, 8. https://doi.org/10.3389/fphys.2017.00136
Didelot, X., Fraser, C., Gardy, J., & Colijn, C. (2017). Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks. Molecular Biology and Evolution, msw075. https://doi.org/10.1093/molbev/msw275
Fyson, N., Kim, M. K., Lun, D. S., & Colijn, C. (2017). Gene-centric constraint of metabolic models [Preprint]. Biochemistry. https://doi.org/10.1101/116558
Fyson, N., King, J., Belcher, T., Preston, A., & Colijn, C. (2017). A curated genome-scale metabolic model of Bordetella pertussis metabolism. Plos Computational Biology, 13(7), e1005639.
Grandjean, L., Gilman, R. H., Iwamoto, T., Köser, C. U., Coronel, J., Zimic, M., Török, M. E., Ayabina, D., Kendall, M., Fraser, C., Harris, S., Parkhill, J., Peacock, S. J., Moore, D. A. J., & Colijn, C. (2017). Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru. PLoS ONE, 12(12), e0189838. https://doi.org/10.1371/journal.pone.0189838
Jombart, T., Kendall, M., Almagro‐Garcia, J., & Colijn, C. (2017). treespace: Statistical exploration of landscapes of phylogenetic trees. Molecular Ecology Resources, 17(6), 1385–1392. https://doi.org/10.1111/1755-0998.12676
Klinkenberg, D., Backer, J. A., Didelot, X., Colijn, C., & Wallinga, J. (2017). Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Computational Biology, 13(5), e1005495. https://doi.org/10.1371/journal.pcbi.1005495
Ratmann, O., Hodcroft, E. B., Pickles, M., Cori, A., Hall, M., Lycett, S., Colijn, C., Dearlove, B., Didelot, X., Frost, S., Hossain, A. S. M. M., Joy, J. B., Kendall, M., Kühnert, D., Leventhal, G. E., Liang, R., Plazzotta, G., Poon, A. F. Y., Rasmussen, D. A., … on behalf of the PANGEA-HIV Consortium. (2017). Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison. Molecular Biology and Evolution, 34(1), 185–203. https://doi.org/10.1093/molbev/msw217
Ratmann, O., Wymant, C., Colijn, C., Danaviah, S., Essex, M., Frost, S., Gall, A., Gaseitsiwe, S., Grabowski, M. K., Gray, R., Guindon, S., Von Haeseler, A., Kaleebu, P., Kendall, M., Kozlov, A., Manasa, J., Minh, B. Q., Moyo, S., Novitsky, V., … On Behalf Of The Pangea-Hiv Consort. (2017). HIV-1 Full-Genome Phylogenetics of Generalized Epidemics in Sub-Saharan Africa: Impact of Missing Nucleotide Characters in Next-Generation Sequences. AIDS Research and Human Retroviruses, 33(11), 1083–1098. https://doi.org/10.1089/aid.2017.0061
Plazzotta, G., & Colijn, C. (2017). Phylodynamics without trees: estimating R0 directly from pathogen sequences [Preprint]. bioRxiv. 102061. doi:10.1101/1020612017

2016

Aanensen, D. M., Feil, E. J., Holden, M. T. G., Dordel, J., Yeats, C. A., Fedosejev, A., Goater, R., Castillo-Ramírez, S., Corander, J., Colijn, C., Chlebowicz, M. A., Schouls, L., Heck, M., Pluister, G., Ruimy, R., Kahlmeter, G., Åhman, J., Matuschek, E., Friedrich, A. W., … Kearns, A. (2016). Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: A Population Snapshot of Invasive Staphylococcus aureus in Europe. American Society for Microbiology, 7(3), e00444-16.
Ayabina, D., Hendon-Dunn, C., Bacon, J., & Colijn, C. (2016). Diverse drug-resistant subpopulations of Mycobacterium tuberculosis are sustained in continuous culture. Journal of The Royal Society Interface, 13(124), 20160745. https://doi.org/10.1098/rsif.2016.0745
Chindelevitch, L., Colijn, C., Moodley, P., Wilson, D., & Cohen, T. (2016). ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections. PLoS Computational Biology, 12(2), e1004475. https://doi.org/10.1371/journal.pcbi.1004475
Colijn, C., & Cohen, T. (2016). Whole-genome sequencing of Mycobacterium tuberculosis for rapid diagnostics and beyond. The Lancet Respiratory Medicine, 4(1), 6–8. https://doi.org/10.1016/S2213-2600(15)00510-X
Hatherell, H. A., Colijn, C., Stagg, H. R., Jackson, C., Winter, J. R., & Abubakar, I. (2016). Interpreting whole genome sequencing for investigating tuberculosis transmission: A systematic review. BMC Medicine, 14(1), 21. https://doi.org/10.1186/s12916-016-0566-x
Hatherell, H.A., Didelot, X., Pollock, S. L., Tang, P., Crisan, A., Johnston, J. C., Colijn, C., & Gardy, J. L. (2016). Declaring a tuberculosis outbreak over with genomic epidemiology. Microbial Genomics, 2(5). https://doi.org/10.1099/mgen.0.000060
Kendall, M., & Colijn, C. (2016). Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution. Molecular Biology and Evolution, 33(10), 2735–2743. https://doi.org/10.1093/molbev/msw124
Klinkenberg, D., Backer, J., Didelot, X., Colijn, C., & Wallinga, J. (2016). New method to reconstruct phylogenetic and transmission trees with sequence data from infectious disease outbreaks [Preprint]. Epidemiology. https://doi.org/10.1101/069195
Plazzotta, G., & Colijn, C. (2016). Asymptotic frequency of shapes in supercritical branching trees. Journal of Applied Probability, 53(4), 1143–1155. https://doi.org/10.1017/jpr.2016.70
Plazzotta, G., Kwan, C., Boyd, M., & Colijn, C. (2016). Effects of memory on the shapes of simple outbreak trees. Scientific Reports, 6(1), 21159. https://doi.org/10.1038/srep21159
Sartelli, M., Weber, D. G., Ruppé, E., Bassetti, M., Wright, B. J., Ansaloni, L., Catena, F., Coccolini, F., Abu-Zidan, F. M., Coimbra, R., Moore, E. E., Moore, F. A., Maier, R. V., De Waele, J. J., Kirkpatrick, A. W., Griffiths, E. A., Eckmann, C., Brink, A. J., Mazuski, J. E., … Viale, P. (2016). Antimicrobials: A global alliance for optimizing their rational use in intra-abdominal infections (AGORA). World Journal of Emergency Surgery : WJES, 11(1), 33. https://doi.org/10.1186/s13017-016-0089-y

2015

Colijn, C., & Cohen, T. (2015). How competition governs whether moderate or aggressive treatment minimizes antibiotic resistance. eLife, 4, e10559. https://doi.org/10.7554/eLife.10559
Crisan, A., Wong, H. Y., Johnston, J. C., Tang, P., Colijn, C., Otterstatter, M., Hiscoe, L., Parker, R., Pollock, S. L., & Gardy, J. L. (2015). Spatio-temporal analysis of tuberculous infection risk among clients of a homeless shelter during an outbreak. The International Journal of Tuberculosis and Lung Disease : The Official Journal of the International Union against Tuberculosis and Lung Disease, 19(9), 1033–1038. https://doi.org/10.5588/ijtld.14.0957
Knight, G. M., Colijn, C., Shrestha, S., Fofana, M., Cobelens, F., White, R. G., Dowdy, D. W., & Cohen, T. (2015). The Distribution of Fitness Costs of Resistance-Conferring Mutations Is a Key Determinant for the Future Burden of Drug-Resistant Tuberculosis: A Model-Based Analysis. Clin Infect Dis., 61(suppl 3), S147–S154. https://doi.org/10.1093/cid/civ579
Kunkel, A., Colijn, C., Lipsitch, M., & Cohen, T. (2015). How could preventive therapy affect the prevalence of drug resistance? Causes and consequences. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1670), 20140306. https://doi.org/10.1098/rstb.2014.0306
Nicoli, E. J., Ayabina, D., Trotter, C. L., Turner, K. M. E., & Colijn, C. (2015). Competition, coinfection and strain replacement in models of Bordetella pertussis. Theoretical Population Biology, 103, 84–92. https://doi.org/10.1016/j.tpb.2015.05.003
Plazzotta, G., Cohen, T., & Colijn, C. (2015). Magnitude and sources of bias in the detection of mixed strain M. tuberculosis infection. Journal of Theoretical Biology, 368, 67–73. https://doi.org/10.1016/j.jtbi.2014.12.009
Kendall, M., & Colijn, C. (2015). A tree metric using structure and length to capture distinct phylogenetic signals. arXiv:1507.05211v3 [q-bio.PE].

2014

Didelot, X., Gardy, J., & Colijn, C. (2014). Bayesian Inference of Infectious Disease Transmission from Whole-Genome Sequence Data. Molecular Biology and Evolution, 31(7), 1869–1879. https://doi.org/10.1093/molbev/msu121
Farhat, M. R., Shapiro, B. J., Sheppard, S. K., Colijn, C., & Murray, M. (2014). A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens. Genome Medicine, 6(11), 101. https://doi.org/10.1186/s13073-014-0101-7
Jombart, T., Aanensen, D. M., Baguelin, M., Birrell, P., Cauchemez, S., Camacho, A., Colijn, C., Collins, C., Cori, A., Didelot, X., Fraser, C., Frost, S., Hens, N., Hugues, J., Höhle, M., Opatowski, L., Rambaut, A., Ratmann, O., Soubeyrand, S., … Ferguson, N. (2014). OutbreakTools: A new platform for disease outbreak analysis using the R software. Epidemics, 7, 28–34. https://doi.org/10.1016/j.epidem.2014.04.003
Mills, H. L., Johnson, S., Hickman, M., Jones, N. S., & Colijn, C. (2014). Errors in reported degrees and respondent driven sampling: Implications for bias. Drug and Alcohol Dependence, 142, 120–126. https://doi.org/10.1016/j.drugalcdep.2014.06.015
Colijn, C., & Gardy, J. (2014). Phylogenetic tree shapes resolve disease transmission patterns. Evol Med Public Health, 2014(1), 96–108. doi:10.1093/emph/eou018
Aanensen, D.M., Baguelin, M., Birrell, P., Cauchemez, S., Camacho, A., Colijn, C., et al. (2014). OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics, 7, 28-34. doi:10.1016/j.epidem.2014.04.003

2013

Mills, H. L., Cohen, T., & Colijn, C. (2013). Community-wide isoniazid preventive therapy drives drug-resistant tuberculosis: A model-based analysis. Science Translational Medicine, 5(180), 180ra49. https://doi.org/10.1126/scitranslmed.3005260
Mills, H. L., Ganesh, A., & Colijn, C. (2013). Pathogen spread on coupled networks: Effect of host and network properties on transmission thresholds. Journal of Theoretical Biology, 320, 47–57. https://doi.org/10.1016/j.jtbi.2012.12.006
Mills, H. L., White, E., Colijn, C., Vickerman, P., & Heimer, R. (2013). HIV transmission from drug injectors to partners who do not inject, and beyond: Modelling the potential for a generalized heterosexual epidemic in St. Petersburg, Russia. Drug and Alcohol Dependence, 133(1), 242–247. https://doi.org/10.1016/j.drugalcdep.2013.04.028
Nicoli, E. J., Trotter, C. L., Turner, K. M. E., Colijn, C., Waight, P., & Miller, E. (2013). Influenza and RSV make a modest contribution to invasive pneumococcal disease incidence in the UK. Journal of Infection, 66(6), 512–520. https://doi.org/10.1016/j.jinf.2013.02.007
Robinson, K., Fyson, N., Cohen, T., Fraser, C., & Colijn, C. (2013). How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies. PLoS Computational Biology, 9(6), e1003105. https://doi.org/10.1371/journal.pcbi.1003105

2012

Brandes, A., Lun, D. S., Ip, K., Zucker, J., Colijn, C., Weiner, B., & Galagan, J. E. (2012). Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models. PLoS ONE, 7(5), e36947. https://doi.org/10.1371/journal.pone.0036947
Cohen, T., Van Helden, P. D., Wilson, D., Colijn, C., McLaughlin, M. M., Abubakar, I., & Warren, R. M. (2012). Mixed-Strain Mycobacterium tuberculosis Infections and the Implications for Tuberculosis Treatment and Control. Clinical Microbiology Reviews, 25(4), 708–719. https://doi.org/10.1128/CMR.00021-12
Irving, T. J., Blyuss, K. B., Colijn, C., & Trotter, C. L. (2012). Modelling meningococcal meningitis in the African meningitis belt. Epidemiology and Infection, 140(5), 897–905. https://doi.org/10.1017/S0950268811001385
Mills, H. L., Colijn, C., Vickerman, P., Leslie, D., Hope, V., & Hickman, M. (2012). Respondent driven sampling and community structure in a population of injecting drug users, Bristol, UK. Drug and Alcohol Dependence, 126(3), 324–332. https://doi.org/10.1016/j.drugalcdep.2012.05.036
Robinson, K., Cohen, T., & Colijn, C. (2012). The dynamics of sexual contact networks: Effects on disease spread and control. Theoretical Population Biology, 81(2), 89–96. https://doi.org/10.1016/j.tpb.2011.12.009
Sergeev, R., Colijn, C., Murray, M., & Cohen, T. (2012). Modeling the Dynamic Relationship Between HIV and the Risk of Drug-Resistant Tuberculosis. Science Translational Medicine, 4(135), 135ra67. https://doi.org/10.1126/scitranslmed.3003815

2011

Colijn, C., Cohen, T., Ganesh, A., & Murray, M. (2011). Spontaneous Emergence of Multiple Drug Resistance in Tuberculosis before and during Therapy. PLoS ONE, 6(3), e18327. https://doi.org/10.1371/journal.pone.0018327
Ip, K., Colijn, C., & Lun, D. S. (2011). Analysis of complex metabolic behavior through pathway decomposition. BMC Systems Biology, 5(1), 91. https://doi.org/10.1186/1752-0509-5-91
Mills, H. L., Cohen, T., & Colijn, C. (2011). Modelling the performance of isoniazid preventive therapy for reducing tuberculosis in HIV endemic settings: The effects of network structure. Journal of The Royal Society Interface, 8(63), 1510–1520. https://doi.org/10.1098/rsif.2011.0160
Sergeev, R., Colijn, C., & Cohen, T. (2011). Models to understand the population-level impact of mixed strain M. tuberculosis infections. Journal of Theoretical Biology, 280(1), 88–100. https://doi.org/10.1016/j.jtbi.2011.04.011

2010

Colijn, C., Cohen, T., Fraser, C., Hanage, W., Goldstein, E., Givon-Lavi, N., Dagan, R., & Lipsitch, M. (2010). What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae ? Journal of The Royal Society Interface, 7(47), 905–919. https://doi.org/10.1098/rsif.2009.0400

2009

Cohen, T., Colijn, C., Wright, A., Zignol, M., Pym, A., & Murray, M. (2009). Does Current Drug Resistance Surveillance Provide Useful Information in Tuberculosis? American Journal of Respiratory and Critical Care Medicine, 179(1), 82–83. https://doi.org/10.1164/ajrccm.179.1.82a
Cohen, T., Dye, C., Colijn, C., Williams, B., & Murray, M. (2009). Mathematical models of the epidemiology and control of drug-resistant TB. Expert Review of Respiratory Medicine, 3(1), 67–79. https://doi.org/10.1586/17476348.3.1.67
Colijn, C. (2009). Propagation through dynamic networks: Degree distribution and the spread of disease. 2009 IEEE Information Theory Workshop, 594–598. https://doi.org/10.1109/ITW.2009.5351503
Colijn, C., Brandes, A., Zucker, J., Lun, D. S., Weiner, B., Farhat, M. R., Cheng, T.-Y., Moody, D. B., Murray, M., & Galagan, J. E. (2009). Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production. PLoS Computational Biology, 5(8), e1000489. https://doi.org/10.1371/journal.pcbi.1000489
Colijn, C., Cohen, T., & Murray, M. (2009). Latent Coinfection and the Maintenance of Strain Diversity. Bulletin of Mathematical Biology, 71(1), 247–263. https://doi.org/10.1007/s11538-008-9361-y
Lipsitch, M., Colijn, C., Cohen, T., Hanage, W. P., & Fraser, C. (2009). No coexistence for free: Neutral null models for multistrain pathogens. Epidemics, 1(1), 2–13. https://doi.org/10.1016/j.epidem.2008.07.001 Cohen T, Colijn C, Wright A, Zignol M, Pym A, Murray M. (2009). Reply-Does Current Drug Resistance Surveillance Provide Useful Information in Tuberculosis?. American Journal of Respiratory and Critical Care Medicine, 179(1), 80.

2008

Cohen, T., Colijn, C., Finklea, B., Wright, A., Zignol, M., Pym, A., & Murray, M. (2008). Are survey-based estimates of the burden of drug resistant TB too low? Insight from a simulation study. PLoS One, 3(6), e2363.
Cohen, T., Colijn, C., & Murray, M. (2008). Mathematical Modeling of Tuberculosis Transmission Dynamics. In S. H. E. Kaufmann, E. Rubin, W. J. Britton, & P. Helden (Eds.), Handbook of Tuberculosis (1st ed., pp. 227–243). Wiley. https://doi.org/10.1002/9783527611614.ch44
Cohen, T., Colijn, C., & Murray, M. (2008). Modeling the effects of strain diversity and mechanisms of strain competition on the potential performance of new tuberculosis vaccines. Proceedings of the National Academy of Sciences of the United States of America, 105(42), 16302–16307. https://doi.org/10.1073/pnas.0808746105
Cohen, T., Colijn, C., Wright, A., Zignol, M., Pym, A., & Murray, M. (2008). Challenges in Estimating the Total Burden of Drug-resistant Tuberculosis. American Journal of Respiratory and Critical Care Medicine, 177(12), 1302–1306. https://doi.org/10.1164/rccm.200801-175PP
Lin, H.-H., Murray, M., Cohen, T., Colijn, C., & Ezzati, M. (2008). Effects of smoking and solid-fuel use on COPD, lung cancer, and tuberculosis in China: A time-based, multiple risk factor, modelling study. The Lancet, 372(9648), 1473–1483. https://doi.org/10.1016/S0140-6736(08)61345-8
Yang, G.H., Zhong, N.S., Lin, H.H., Murray, M., Cohen, T., Colijn, C., & Ezzati, M. (2008). Effects of smoking and solid-fuel use on COPD, lung cancer, and tuberculosis in China: A time-based, multiple risk factor, modelling study. Commentary. Lancet, London, 372(9648), 445–1446, 1473-1483 [13 p.].

2007

Cohen, T., Colijn, C., Finklea, B., & Murray, M. (2007). Exogenous re-infection and the dynamics of tuberculosis epidemics: Local effects in a network model of transmission. Journal of The Royal Society Interface, 4(14), 523–531. https://doi.org/10.1098/rsif.2006.0193
Colijn, C., Cohen, T., & Murray, M. (2007). Emergent heterogeneity in declining tuberculosis epidemics. Journal of Theoretical Biology, 247(4), 765–774. https://doi.org/10.1016/j.jtbi.2007.04.015
Colijn, C., Cohen, T., & Murray, M. (2007). Mathematical Models of Tuberculosis: Accomplishments and future challenges. BIOMAT 2006, 123–148. https://doi.org/10.1142/9789812708779_0008
Colijn, C., Foley, C., & Mackey, M. C. (2007). G-CSF treatment of canine cyclical neutropenia: A comprehensive mathematical model. Experimental Hematology, 35(6), 898–907. https://doi.org/10.1016/j.exphem.2007.02.015
Colijn, C., & Mackey, M. C. (2007). Bifurcation and Bistability in a Model of Hematopoietic Regulation. Siam Journal On Applied Dynamical Systems, 6(2), 378–394. https://doi.org/10.1137/050640072

2006

Colijn, C., Dale, D. C., Foley, C., & Mackey, M. C. (2006). Observations on the Pathophysiology and Mechanisms for Cyclic Neutropenia. Mathematical Modelling of Natural Phenomena, 1(2), 45–69. https://doi.org/10.1051/mmnp:2008004
Colijn, C., Fowler, A. C., & Mackey, M. C. (2006). High frequency spikes in long period blood cell oscillations. Journal of Mathematical Biology, 53(4), 499–519. https://doi.org/10.1007/s00285-006-0027-9

2005

Colijn, C., & Mackey, M. C. (2005). A mathematical model of hematopoiesis: II. Cyclical neutropenia. Journal of Theoretical Biology, 237(2), 133–146. https://doi.org/10.1016/j.jtbi.2005.03.034
Colijn, C., & Mackey, M. C. (2005). A mathematical model of hematopoiesis—I. Periodic chronic myelogenous leukemia. Journal of Theoretical Biology, 237(2), 117–132. https://doi.org/10.1016/j.jtbi.2005.03.033

2004

Colijn, C., & Vrscay, E. R. (2004). Quantum relaxation in hydrogen eigenstates and two-state transitions. Physics Letters A, 327(2–3), 113–122. https://doi.org/10.1016/j.physleta.2004.05.020

2003

Colijn, C. (2003). The de Broglie-Bohm Causal Interpretation of Quantum Mechanics and its Application to some Simple Systems [Phd]. University of Waterloo.
Colijn, C., & Vrscay, E. R. (2003). Erratum to: “Spin-dependent Bohm trajectories for hydrogen eigenstates”. Physics Letters A, 316(6), 424. https://doi.org/10.1016/S0375-9601(03)01032-6
Colijn, C., & Vrscay, E. R. (2003). Spin-dependent Bohm trajectories associated with an electronic transition in hydrogen. Journal of Physics A: Mathematical and General, 36(16), 4689–4702. https://doi.org/10.1088/0305-4470/36/16/317
Colijn, C., & Vrscay, E. R. (2003). Spin-Dependent Bohm Trajectories for Pauli and Dirac Eigenstates of Hydrogen. Foundations of Physics Letters, 16(4), 303–323. https://doi.org/10.1023/A:1025344924499

2002

Colijn, C., & Vrscay, E. R. (2002). Spin-dependent Bohm trajectories for hydrogen eigenstates. Physics Letters A, 300(4–5), 334–340. https://doi.org/10.1016/S0375-9601(02)00824-1

1999

Colijn, C. (1999). Addressing Complexity: Exploring Social Change Through Chaos and Complexity Theory. York University.