Bifurcation and Bistability in a Model of Hematopoietic Regulation. - Caroline Colijn; Michael C. Mackey (SIAM J. Appl. Dyn. Syst., 2007)

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production. - Caroline Colijn; Aaron Brandes; Jeremy Zucker; Desmond S. Lun; Brian Weiner; Maha R. Farhat; Tan-Yun Cheng; D. Branch Moody; Megan Murray; James E. Galagan (PLoS Comput. Biol., 2009)

Analysis of complex metabolic behavior through pathway decomposition. - Kuhn Ip; Caroline Colijn; Desmond S. Lun (BMC Syst. Biol., 2011)

How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies. - Katy Robinson; Nick Fyson; Ted Cohen; Christophe Fraser; Caroline Colijn (PLoS Comput. Biol., 2013)

Asymptotic frequency of shapes in supercritical branching trees. - Giacomo Plazzotta; Caroline Colijn (J. Appl. Probab., 2016)

ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections. - Leonid Chindelevitch; Caroline Colijn; Prashini Moodley; Douglas Wilson; Ted Cohen (PLoS Comput. Biol., 2016)

A curated genome-scale metabolic model of Bordetella pertussis metabolism. - Nick Fyson; Jerry King; Thomas Belcher; Andrew Preston; Caroline Colijn (PLoS Comput. Biol., 2017)

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. - Don Klinkenberg; Jantien A. Backer; Xavier Didelot; Caroline Colijn; Jacco Wallinga (PLoS Comput. Biol., 2017)

Phylogenies from dynamic networks. - Cornelia Metzig; Oliver Ratmann; Daniela Bezemer; Caroline Colijn (PLoS Comput. Biol., 2019)

A Maximum Entropy Method for the Prediction of Size Distributions. - Cornelia Metzig; Caroline Colijn (Entropy, 2020)

Quantifying the impact of COVID-19 control measures using a Bayesian model of physical distancing. - 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 (PLoS Comput. Biol., 2020)

Classification of origin with feature selection and network construction for folk tunes. - Cornelia Metzig; Matthew Gould; Roshan Noronha; Roshani Abbey; Mark Sandler 001; Caroline Colijn (Pattern Recognit. Lett., 2020)

Estimating Genetic Similarity Matrices Using Phylogenies. - Shijia Wang; Shufei Ge; Caroline Colijn; Priscila Biller; Liangliang Wang; Lloyd T. Elliott (J. Comput. Biol., 2021)

COVID-19 in schools: Mitigating classroom clusters in the context of variable transmission. - Paul F. Tupper; Caroline Colijn (PLoS Comput. Biol., 2021)

Genome-Wide Association with Uncertainty in the Genetic Similarity Matrix. - Shijia Wang; Shufei Ge; Benjamin Sobkowiak; Liangliang Wang; Louis Grandjean; Caroline Colijn; Lloyd T. Elliott (J. Comput. Biol., 2023)

Pneumococcal population dynamics: Investigating vaccine-induced changes through multiscale modelling. - Nicola Mulberry; Alexander R. Rutherford; Caroline Colijn (PLoS Comput. Biol., 2023)

A Vector Representation for Phylogenetic Trees. - Cédric Chauve; Caroline Colijn; Louxin Zhang (CoRR, 2024)

Measuring genetic diversity across populations. - Niloufar Abhari; Caroline Colijn; Arne Mooers; Paul F. Tupper (PLoS Comput. Biol., 2024)