Lista de obras - Caroline Colijn - Dominio Público Uruguay

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

artículo científico publicado en 2017

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

artículo científico publicado en 2005

A mathematical model of hematopoiesis: II. Cyclical neutropenia

artículo científico publicado en 2005

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

artículo científico publicado en 2014

Analysis of complex metabolic behavior through pathway decomposition ⬇️

artículo científico publicado el 3 de junio de 2011

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

artículo científico publicado en 2008

Bayesian inference of infectious disease transmission from whole genome sequence data

article

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

artículo científico publicado en 2014

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

artículo científico publicado en 2021

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

artículo científico publicado en 2008

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

artículo científico publicado en 2016

Community-Wide Isoniazid Preventive Therapy Drives Drug-Resistant Tuberculosis: A Model-Based Analysis ⬇️

artículo científico publicado el 10 de abril de 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.

artículo científico publicado en 2015

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

artículo científico publicado en 2017

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.

artículo científico publicado en 2012

Declaring a tuberculosis outbreak over with genomic epidemiology

preprint, published 22 February 2016

Designing ecologically optimized pneumococcal vaccines using population genomics

artículo científico publicado en 2020

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

artículo científico publicado en 2016

Effects of memory on the shapes of simple outbreak trees

artículo científico

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

artículo científico publicado en 2008

Emergent heterogeneity in declining tuberculosis epidemics

artículo científico publicado en 2007

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

artículo científico publicado en 2014

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

artículo científico publicado en 2019

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

artículo científico publicado en 2018

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

artículo científico publicado en 2007

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

artículo científico publicado en 2007

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

artículo científico publicado en 2018

Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2013

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

artículo científico publicado en 2017

High frequency spikes in long period blood cell oscillations

artículo científico publicado en 2006

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

artículo científico publicado en 2019

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

artículo científico publicado en 2017

How competition governs whether moderate or aggressive treatment minimizes antibiotic resistance

artículo científico publicado en 2015

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

artículo científico publicado en 2015

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

artículo científico publicado en 2013

Inferring carbon sources from gene expression profiles using metabolic flux models

artículo científico publicado en 2012

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

artículo científico publicado en 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

artículo científico publicado en 2009

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

artículo científico publicado en 2016

Latent coinfection and the maintenance of strain diversity

artículo científico publicado en 2008

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

artículo científico publicado en 2014

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution ⬇️

artículo científico publicado en 2016

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

artículo científico publicado en 2009

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

artículo científico publicado en 2012

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

artículo científico publicado el 23 de mayo de 2012

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

artículo científico publicado en 2008

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

artículo científico publicado el 16 de abril de 2011

No coexistence for free: neutral null models for multistrain pathogens

artículo científico publicado en 2008

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

artículo científico publicado en 2014

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

artículo científico publicado en 2016

Phylogenetic tree shapes resolve disease transmission patterns

article

Phylogenetic tree shapes resolve disease transmission patterns.

artículo científico publicado en 2014

Phylogenies from dynamic networks

artículo científico publicado en 2019

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

artículo científico publicado en 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".

artículo científico publicado en 2013

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

artículo científico publicado en 2017

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

artículo científico publicado el 30 de marzo de 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

artículo científico publicado en 2015

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

artículo científico publicado en 2018

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

artículo científico publicado el 8 de enero de 2012

Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling

artículo científico publicado en 2019

Transmission dynamics are crucial to COVID-19 vaccination policy

artículo científico publicado en 2021

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

artículo científico publicado en 2020

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

artículo científico publicado en 2009

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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

treespace: Statistical exploration of landscapes of phylogenetic trees

artículo científico publicado en 2017

Lista de obras de Caroline Colijn

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

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

A mathematical model of hematopoiesis: II. Cyclical neutropenia

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

Analysis of complex metabolic behavior through pathway decomposition ⬇️

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

Bayesian inference of infectious disease transmission from whole genome sequence data

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

Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions

Beyond the SNP threshold: identifying outbreak clusters using inferred transmissions

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

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

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

Community-Wide Isoniazid Preventive Therapy Drives Drug-Resistant Tuberculosis: A Model-Based Analysis ⬇️

Comparing phylogenetic trees according to tip label categories

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

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

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

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

Declaring a tuberculosis outbreak over with genomic epidemiology

Designing ecologically optimized pneumococcal vaccines using population genomics

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

Effects of memory on the shapes of simple outbreak trees

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

Emergent heterogeneity in declining tuberculosis epidemics

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

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

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

Event-specific interventions to minimize COVID-19 transmission

Evidence for transmission of COVID-19 prior to symptom onset

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

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

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

Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks

Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks

Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences

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

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

High frequency spikes in long period blood cell oscillations

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

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

How competition governs whether moderate or aggressive treatment minimizes antibiotic resistance

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

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

Inferring carbon sources from gene expression profiles using metabolic flux models

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

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

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

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

Latent coinfection and the maintenance of strain diversity

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

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution ⬇️

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

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

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

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

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

No coexistence for free: neutral null models for multistrain pathogens

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

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

Phylogenetic tree shapes resolve disease transmission patterns

Phylogenetic tree shapes resolve disease transmission patterns.

Phylogenies from dynamic networks

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

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

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

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

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

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

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

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

Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling

Transmission dynamics are crucial to COVID-19 vaccination policy

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

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

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

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

treespace: Statistical exploration of landscapes of phylogenetic trees