Imperial College London

DrCarolineColijn

Faculty of Natural SciencesDepartment of Mathematics

Visiting Professor
 
 
 
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Contact

 

+44 (0)20 7594 2647c.colijn Website

 
 
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Location

 

626Huxley BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

84 results found

Kendall M, Colijn C, 2015, A tree metric using structure and length to capture distinct phylogenetic signals

Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources (e.g. several genes from the same organisms) and different inference methods. We propose a new metric for robust, quantitative comparison of rooted, labeled trees. It enables clear visualizations of tree space, gives meaningful comparisons between trees, and can detect distinct islands of tree topologies in posterior distributions of trees. This makes it possible to select well-supported summary trees. We demonstrate our approach on Dengue fever phylogenies.

WORKING PAPER

Kendall M, Colijn C, 2015, A tree metric using structure and length to capture distinct phylogenetic signals

Phylogenetic trees are a central tool in understanding evolution. They aretypically inferred from sequence data, and capture evolutionary relationshipsthrough time. It is essential to be able to compare trees from different datasources (e.g. several genes from the same organisms) and different inferencemethods. We propose a new metric for robust, quantitative comparison of rooted,labeled trees. It enables clear visualizations of tree space, gives meaningfulcomparisons between trees, and can detect distinct islands of tree topologiesin posterior distributions of trees. This makes it possible to selectwell-supported summary trees. We demonstrate our approach on Dengue feverphylogenies.

WORKING PAPER

Knight GM, Colijn C, Shrestha S, Fofana M, Cobelens F, White RG, Dowdy DW, Cohen Tet al., 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, CLINICAL INFECTIOUS DISEASES, Vol: 61, Pages: S147-S154, ISSN: 1058-4838

JOURNAL ARTICLE

Kunkel A, Colijn C, Lipsitch M, Cohen Tet al., 2015, How could preventive therapy affect the prevalence of drug resistance? Causes and consequences, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 370, ISSN: 0962-8436

JOURNAL ARTICLE

Nicoli EJ, Ayabina D, Trotter CL, Turner KME, Colijn Cet al., 2015, Competition, coinfection and strain replacement in models of Bordetella pertussis!, THEORETICAL POPULATION BIOLOGY, Vol: 103, Pages: 84-92, ISSN: 0040-5809

JOURNAL ARTICLE

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, Vol: 368, Pages: 67-73, ISSN: 0022-5193

JOURNAL ARTICLE

Colijn C, Gardy J, 2014, Phylogenetic tree shapes resolve disease transmission patterns., Evol Med Public Health, Vol: 2014, Pages: 96-108, ISSN: 2050-6201

BACKGROUND AND OBJECTIVES: Whole-genome sequencing is becoming popular as a tool for understanding outbreaks of communicable diseases, with phylogenetic trees being used to identify individual transmission events or to characterize outbreak-level overall transmission dynamics. Existing methods to infer transmission dynamics from sequence data rely on well-characterized infectious periods, epidemiological and clinical metadata which may not always be available, and typically require computationally intensive analysis focusing on the branch lengths in phylogenetic trees. We sought to determine whether the topological structures of phylogenetic trees contain signatures of the transmission patterns underlying an outbreak. METHODOLOGY: We use simulated outbreaks to train and then test computational classifiers. We test the method on data from two real-world outbreaks. RESULTS: We show that different transmission patterns result in quantitatively different phylogenetic tree shapes. We describe topological features that summarize a phylogeny's structure and find that computational classifiers based on these are capable of predicting an outbreak's transmission dynamics. The method is robust to variations in the transmission parameters and network types, and recapitulates known epidemiology of previously characterized real-world outbreaks. CONCLUSIONS AND IMPLICATIONS: There are simple structural properties of phylogenetic trees which, when combined, can distinguish communicable disease outbreaks with a super-spreader, homogeneous transmission and chains of transmission. This is possible using genome data alone, and can be done during an outbreak. We discuss the implications for management of outbreaks.

JOURNAL ARTICLE

Didelot X, Gardy J, Colijn C, 2014, Bayesian Inference of Infectious Disease Transmission from Whole-Genome Sequence Data, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 31, Pages: 1869-1879, ISSN: 0737-4038

JOURNAL ARTICLE

Farhat MR, Shapiro BJ, Sheppard SK, Colijn C, Murray Met al., 2014, A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens, GENOME MEDICINE, Vol: 6, ISSN: 1756-994X

JOURNAL ARTICLE

Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X, Fraser C, Frost S, Hens N, Hugues J, Hohle M, Opatowski L, Rambautm A, Ratmann O, Soubeyrand S, Suchard MA, Wallinga J, Ypma R, Ferguso Net al., 2014, OutbreakTools: A new platform for disease outbreak analysis using the R software, EPIDEMICS, Vol: 7, Pages: 28-34, ISSN: 1755-4365

JOURNAL ARTICLE

Mills HL, Johnson S, Hickman M, Jones NS, Colijn Cet al., 2014, Errors in reported degrees and respondent driven sampling: Implications for bias, DRUG AND ALCOHOL DEPENDENCE, Vol: 142, Pages: 120-126, ISSN: 0376-8716

JOURNAL ARTICLE

Mills HL, Cohen T, Colijn C, 2013, Community-Wide Isoniazid Preventive Therapy Drives Drug-Resistant Tuberculosis: A Model-Based Analysis, SCIENCE TRANSLATIONAL MEDICINE, Vol: 5, ISSN: 1946-6234

JOURNAL ARTICLE

Mills HL, Cohen T, Colijn C, 2013, Response to Comment on "Community-Wide Isoniazid Preventive Therapy Drives Drug-Resistant Tuberculosis: A Model-Based Analysis", SCIENCE TRANSLATIONAL MEDICINE, Vol: 5, ISSN: 1946-6234

JOURNAL ARTICLE

Mills HL, Ganesh A, Colljn C, 2013, Pathogen spread on coupled networks: Effect of host and network properties on transmission thresholds, JOURNAL OF THEORETICAL BIOLOGY, Vol: 320, Pages: 47-57, ISSN: 0022-5193

JOURNAL ARTICLE

Mills HL, White E, Colijn C, Vickerman P, Heimer Ret al., 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, Vol: 133, Pages: 242-247, ISSN: 0376-8716

JOURNAL ARTICLE

Nicoli EJ, Trotter CL, Turner KME, Colijn C, Waight P, Miller Eet al., 2013, Influenza and RSV make a modest contribution to invasive pneumococcal disease incidence in the UK, JOURNAL OF INFECTION, Vol: 66, Pages: 512-520, ISSN: 0163-4453

JOURNAL ARTICLE

Robinson K, Fyson N, Cohen T, Fraser C, Colijn Cet al., 2013, How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies, PLOS COMPUTATIONAL BIOLOGY, Vol: 9, ISSN: 1553-7358

JOURNAL ARTICLE

Brandes A, Lun DS, Ip K, Zucker J, Colijn C, Weiner B, Galagan JEet al., 2012, Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models, PLOS ONE, Vol: 7, ISSN: 1932-6203

JOURNAL ARTICLE

Brandes A, Lun DS, Ip K, Zucker J, Colijn C, Weiner B, Galagan JEet al., 2012, Correction: Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models., PLoS One, Vol: 7

[This corrects the article on p. e36947 in vol. 7.].

JOURNAL ARTICLE

Cohen T, van Helden PD, Wilson D, Colijn C, McLaughlin MM, Abubakar I, Warren RMet al., 2012, Mixed-Strain Mycobacterium tuberculosis Infections and the Implications for Tuberculosis Treatment and Control, CLINICAL MICROBIOLOGY REVIEWS, Vol: 25, Pages: 708-+, ISSN: 0893-8512

JOURNAL ARTICLE

Irving TJ, Blyuss KB, Colijn C, Trotter CLet al., 2012, Modelling meningococcal meningitis in the African meningitis belt, EPIDEMIOLOGY AND INFECTION, Vol: 140, Pages: 897-905, ISSN: 0950-2688

JOURNAL ARTICLE

Mills HL, Colijn C, Vickerman P, Leslie D, Hope V, Hickman Met al., 2012, Respondent driven sampling and community structure in a population of injecting drug users, Bristol, UK, DRUG AND ALCOHOL DEPENDENCE, Vol: 126, Pages: 324-332, ISSN: 0376-8716

JOURNAL ARTICLE

Robinson K, Cohen T, Colijn C, 2012, The dynamics of sexual contact networks: Effects on disease spread and control, THEORETICAL POPULATION BIOLOGY, Vol: 81, Pages: 89-96, ISSN: 0040-5809

JOURNAL ARTICLE

Sergeev R, Colijn C, Murray M, Cohen Tet al., 2012, Modeling the Dynamic Relationship Between HIV and the Risk of Drug-Resistant Tuberculosis, SCIENCE TRANSLATIONAL MEDICINE, Vol: 4, ISSN: 1946-6234

JOURNAL ARTICLE

Sergeev R, Colijn C, Murray M, Cohen Tet al., 2012, Only Time Will Tell, SCIENCE TRANSLATIONAL MEDICINE, Vol: 4, ISSN: 1946-6234

JOURNAL ARTICLE

Colijn C, Cohen T, Ganesh A, Murray Met al., 2011, Spontaneous Emergence of Multiple Drug Resistance in Tuberculosis before and during Therapy, PLOS ONE, Vol: 6, ISSN: 1932-6203

JOURNAL ARTICLE

Ip K, Colijn C, Lun DS, 2011, Analysis of complex metabolic behavior through pathway decomposition, BMC SYSTEMS BIOLOGY, Vol: 5, ISSN: 1752-0509

JOURNAL ARTICLE

Mills HL, 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, Vol: 8, Pages: 1510-1520, ISSN: 1742-5689

JOURNAL ARTICLE

Sergeev R, Colijn C, Cohen T, 2011, Models to understand the population-level impact of mixed strain M. tuberculosis infections, JOURNAL OF THEORETICAL BIOLOGY, Vol: 280, Pages: 88-100, ISSN: 0022-5193

JOURNAL ARTICLE

Colijn C, Cohen T, Fraser C, Hanage W, Goldstein E, Givon-Lavi N, Dagan R, Lipsitch Met al., 2010, What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae?, JOURNAL OF THE ROYAL SOCIETY INTERFACE, Vol: 7, Pages: 905-919, ISSN: 1742-5689

JOURNAL ARTICLE

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