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List of works by Caroline Colijn

A curated genome-scale metabolic model of Bordetella pertussis metabolism.

scientific article published on 17 July 2017

A mathematical model of hematopoiesis--I. Periodic chronic myelogenous leukemia

scientific article published on 21 June 2005

A mathematical model of hematopoiesis: II. Cyclical neutropenia

scientific article published on 21 June 2005

A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens.

scientific article

Analysis of complex metabolic behavior through pathway decomposition ⬇️

scientific article published on June 3, 2011

Are survey-based estimates of the burden of drug resistant TB too low? Insight from a simulation study

scientific article

Bayesian inference of infectious disease transmission from whole genome sequence data

article

Bayesian inference of infectious disease transmission from whole-genome sequence data

scientific article

Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions

article

Beyond the SNP threshold: identifying outbreak clusters using inferred transmissions

article

COVID-19 in schools: Mitigating classroom clusters in the context of variable transmission

scientific article published on 08 July 2021

Challenges in estimating the total burden of drug-resistant tuberculosis.

scientific article published on 27 March 2008

ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections

scientific article published in February 2016

Community-wide isoniazid preventive therapy drives drug-resistant tuberculosis: a model-based analysis

scientific article published on April 2013

Comparing phylogenetic trees according to tip label categories

scholarly article published 22 January 2018

Competition, coinfection and strain replacement in models of Bordetella pertussis.

scientific article published on 30 May 2015

Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru.

scientific article

Correction: Evaluating strategies for control of tuberculosis in prisons and prevention of spillover into communities: An observational and modeling study from Brazil

article

Correction: Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models.

scientific article published on 24 August 2012

Declaring a tuberculosis outbreak over with genomic epidemiology

preprint, published 22 February 2016

Designing ecologically optimized pneumococcal vaccines using population genomics

scientific article published on 03 February 2020

Diverse drug-resistant subpopulations of Mycobacterium tuberculosis are sustained in continuous culture

scientific article

Effects of memory on the shapes of simple outbreak trees

scientific article published on 18 February 2016

Effects of smoking and solid-fuel use on COPD, lung cancer, and tuberculosis in China: a time-based, multiple risk factor, modelling study

scientific article

Emergent heterogeneity in declining tuberculosis epidemics

scientific article published on 27 April 2007

Errors in reported degrees and respondent driven sampling: implications for bias

scientific article

Evaluating strategies for control of tuberculosis in prisons and prevention of spillover into communities: An observational and modeling study from Brazil

scientific article published in January 2019

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study.

scientific article

Event-specific interventions to minimize COVID-19 transmission

scientific article published on 19 November 2020

Evidence for transmission of COVID-19 prior to symptom onset

scientific article published on 22 June 2020

Exogenous re-infection and the dynamics of tuberculosis epidemics: local effects in a network model of transmission

scientific article

G-CSF treatment of canine cyclical neutropenia: a comprehensive mathematical model

scientific article published in June 2007

Genome-based transmission modelling separates imported tuberculosis from recent transmission within an immigrant population.

scientific article published on 14 September 2018

Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks

scientific article published on 18 January 2017

Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks

scholarly article published 22 July 2016

Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences

scientific article published on 31 July 2020

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

scientific article published on 18 May 2013

HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences

scientific article published on 25 May 2017

High frequency spikes in long period blood cell oscillations

scientific article published on 2 August 2006

High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain

scientific article published on 31 October 2019

Host population structure and treatment frequency maintain balancing selection on drug resistance

scientific article

How competition governs whether moderate or aggressive treatment minimizes antibiotic resistance

scientific article

How could preventive therapy affect the prevalence of drug resistance? Causes and consequences

scientific article published on June 2015

How the dynamics and structure of sexual contact networks shape pathogen phylogenies

scientific article

Inferring carbon sources from gene expression profiles using metabolic flux models

scientific article

Influenza and RSV make a modest contribution to invasive pneumococcal disease incidence in the UK

scientific article published on 5 March 2013

Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis

article

Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production

scientific article

Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

scientific article

Latent coinfection and the maintenance of strain diversity

scientific article

Magnitude and sources of bias in the detection of mixed strain M. tuberculosis infection

scientific article published on 29 December 2014

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution ⬇️

scientific article published on 24 June 2016

Mathematical models of the epidemiology and control of drug-resistant TB.

scientific article published on February 2009

Mixed-strain mycobacterium tuberculosis infections and the implications for tuberculosis treatment and control

scientific article

Modeling the Dynamic Relationship Between HIV and the Risk of Drug-Resistant Tuberculosis ⬇️

scientific article published on May 23, 2012

Modeling the effects of strain diversity and mechanisms of strain competition on the potential performance of new tuberculosis vaccines

scholarly article

Models to understand the population-level impact of mixed strain M. tuberculosis infections ⬇️

scientific article published on April 16, 2011

No coexistence for free: neutral null models for multistrain pathogens

scientific article

OutbreakTools: a new platform for disease outbreak analysis using the R software

scientific article (publication date: June 2014)

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.

scientific article published on 07 October 2016

Phylogenetic tree shapes resolve disease transmission patterns

article

Phylogenetic tree shapes resolve disease transmission patterns.

scientific article

Phylogenies from dynamic networks

scientific article published on 26 February 2019

Predicting the short-term success of human influenza virus variants with machine learning

scientific article published on 08 April 2020

Quantifying the impact of COVID-19 control measures using a Bayesian model of physical distancing

scientific article published on 03 December 2020

Response to comment on "Community-wide isoniazid preventive therapy drives drug-resistant tuberculosis: a model-based analysis".

scientific article

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

scientific article

Spontaneous Emergence of Multiple Drug Resistance in Tuberculosis before and during Therapy ⬇️

scientific article published on March 30, 2011

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

scientific article

The cost-effectiveness of alternative vaccination strategies for polyvalent meningococcal vaccines in Burkina Faso: A transmission dynamic modeling study.

scientific article published on 24 January 2018

The dynamics of sexual contact networks: Effects on disease spread and control ⬇️

scientific article published on January 8, 2012

Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling

scientific article published on 01 June 2019

Transmission dynamics are crucial to COVID-19 vaccination policy

scientific article published on 6 July 2021

Transmission interval estimates suggest pre-symptomatic spread of COVID-19

scientific article (preprint)

What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae?

scientific article

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe

scientific article

Whole-genome sequencing of Mycobacterium tuberculosis for rapid diagnostics and beyond

scientific article published on 3 December 2015

treespace: Statistical exploration of landscapes of phylogenetic trees

scientific article

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