Caroline Colijn

Caroline Colijn

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Caroline Colijn

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Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling.

Mol Biol Evol 2019 06;36(6):1333-1343

Department of Mathematics, Simon Fraser University, Burnaby, Canada.

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http://dx.doi.org/10.1093/molbev/msz058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6526902PMC
June 2019

Phylogenies from dynamic networks.

PLoS Comput Biol 2019 02 26;15(2):e1006761. Epub 2019 Feb 26.

Dept of Mathematics, Simon Fraser University, Burnaby, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1006761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420041PMC
February 2019

Antimicrobials: a global alliance for optimizing their rational use in intra-abdominal infections (AGORA).

Authors:
Massimo Sartelli Dieter G Weber Etienne Ruppé Matteo Bassetti Brian J Wright Luca Ansaloni Fausto Catena Federico Coccolini Fikri M Abu-Zidan Raul Coimbra Ernest E Moore Frederick A Moore Ronald V Maier Jan J De Waele Andrew W Kirkpatrick Ewen A Griffiths Christian Eckmann Adrian J Brink John E Mazuski Addison K May Rob G Sawyer Dominik Mertz Philippe Montravers Anand Kumar Jason A Roberts Jean-Louis Vincent Richard R Watkins Warren Lowman Brad Spellberg Iain J Abbott Abdulrashid Kayode Adesunkanmi Sara Al-Dahir Majdi N Al-Hasan Ferdinando Agresta Asma A Althani Shamshul Ansari Rashid Ansumana Goran Augustin Miklosh Bala Zsolt J Balogh Oussama Baraket Aneel Bhangu Marcelo A Beltrán Michael Bernhard Walter L Biffl Marja A Boermeester Stephen M Brecher Jill R Cherry-Bukowiec Otmar R Buyne Miguel A Cainzos Kelly A Cairns Adrian Camacho-Ortiz Sujith J Chandy Asri Che Jusoh Alain Chichom-Mefire Caroline Colijn Francesco Corcione Yunfeng Cui Daniel Curcio Samir Delibegovic Zaza Demetrashvili Belinda De Simone Sameer Dhingra José J Diaz Isidoro Di Carlo Angel Dillip Salomone Di Saverio Michael P Doyle Gereltuya Dorj Agron Dogjani Hervé Dupont Soumitra R Eachempati Mushira Abdulaziz Enani Valery N Egiev Mutasim M Elmangory Paula Ferrada Joseph R Fitchett Gustavo P Fraga Nathalie Guessennd Helen Giamarellou Wagih Ghnnam George Gkiokas Staphanie R Goldberg Carlos Augusto Gomes Harumi Gomi Manuel Guzmán-Blanco Mainul Haque Sonja Hansen Andreas Hecker Wolfgang R Heizmann Torsten Herzog Adrien Montcho Hodonou Suk-Kyung Hong Reinhold Kafka-Ritsch Lewis J Kaplan Garima Kapoor Aleksandar Karamarkovic Martin G Kees Jakub Kenig Ronald Kiguba Peter K Kim Yoram Kluger Vladimir Khokha Kaoru Koike Kenneth Y Y Kok Victory Kong Matthew C Knox Kenji Inaba Arda Isik Katia Iskandar Rao R Ivatury Maurizio Labbate Francesco M Labricciosa Pierre-François Laterre Rifat Latifi Jae Gil Lee Young Ran Lee Marc Leone Ari Leppaniemi Yousheng Li Stephen Y Liang Tonny Loho Marc Maegele Sydney Malama Hany E Marei Ignacio Martin-Loeches Sanjay Marwah Amos Massele Michael McFarlane Renato Bessa Melo Ionut Negoi David P Nicolau Carl Erik Nord Richard Ofori-Asenso AbdelKarim H Omari Carlos A Ordonez Mouaqit Ouadii Gerson Alves Pereira Júnior Diego Piazza Guntars Pupelis Timothy Miles Rawson Miran Rems Sandro Rizoli Claudio Rocha Boris Sakakushev Miguel Sanchez-Garcia Norio Sato Helmut A Segovia Lohse Gabriele Sganga Boonying Siribumrungwong Vishal G Shelat Kjetil Soreide Rodolfo Soto Peep Talving Jonathan V Tilsed Jean-Francois Timsit Gabriel Trueba Ngo Tat Trung Jan Ulrych Harry van Goor Andras Vereczkei Ravinder S Vohra Imtiaz Wani Waldemar Uhl Yonghong Xiao Kuo-Ching Yuan Sanoop K Zachariah Jean-Ralph Zahar Tanya L Zakrison Antonio Corcione Rita M Melotti Claudio Viscoli Perluigi Viale

World J Emerg Surg 2016 15;11:33. Epub 2016 Jul 15.

Infectious Diseases Unit, Department of Medical and Surgical Sciences, Sant' Orsola Hospital, University of Bologna, Bologna, Italy.

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http://dx.doi.org/10.1186/s13017-016-0089-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4946132PMC
May 2018

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

Wellcome Open Res 2018 23;3:33. Epub 2018 Mar 23.

Infection Genomics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.

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http://dx.doi.org/10.12688/wellcomeopenres.14265.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930550PMC
March 2018

treespace: Statistical exploration of landscapes of phylogenetic trees.

Mol Ecol Resour 2017 Nov 15;17(6):1385-1392. Epub 2017 May 15.

Department of Mathematics, Imperial College London, London, UK.

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http://dx.doi.org/10.1111/1755-0998.12676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5724650PMC
November 2017

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

J R Soc Interface 2017 08;14(133)

Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1098/rsif.2017.0295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5582124PMC
August 2017

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

PLoS Comput Biol 2017 Jul 17;13(7):e1005639. Epub 2017 Jul 17.

Department of Mathematics, Imperial College, London, UK.

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http://dx.doi.org/10.1371/journal.pcbi.1005639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5553986PMC
July 2017

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks.

PLoS Comput Biol 2017 05 18;13(5):e1005495. Epub 2017 May 18.

Department of Epidemiology and Surveillance, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1005495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5436636PMC
May 2017

Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks.

Mol Biol Evol 2017 04;34(4):997-1007

Department of Mathematics, Imperial College, London, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msw275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850352PMC
April 2017

Toward Precision Healthcare: Context and Mathematical Challenges.

Front Physiol 2017 21;8:136. Epub 2017 Mar 21.

Department of Mathematics, Imperial College LondonLondon, UK; EPSRC Centre for Mathematics of Precision Healthcare, Imperial College LondonLondon, UK.

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http://dx.doi.org/10.3389/fphys.2017.00136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5359292PMC
March 2017

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

J R Soc Interface 2016 11;13(124)

Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.

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http://dx.doi.org/10.1098/rsif.2016.0745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134024PMC
November 2016

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution.

Mol Biol Evol 2016 10 24;33(10):2735-43. Epub 2016 Jun 24.

Department of Mathematics, Imperial College London, London, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msw124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026250PMC
October 2016

Declaring a tuberculosis outbreak over with genomic epidemiology.

Microb Genom 2016 05 31;2(5):e000060. Epub 2016 May 31.

5​Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, and School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1099/mgen.0.000060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320671PMC
May 2016

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

BMC Med 2016 Mar 23;14:21. Epub 2016 Mar 23.

Centre for Infectious Disease Epidemiology, Infection and Population Health, University College London, London, WC1E 6JB, UK.

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http://dx.doi.org/10.1186/s12916-016-0566-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804562PMC
March 2016

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

PLoS Comput Biol 2016 Feb 1;12(2):e1004475. Epub 2016 Feb 1.

Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4734664PMC
February 2016

Effects of memory on the shapes of simple outbreak trees.

Sci Rep 2016 Feb 18;6:21159. Epub 2016 Feb 18.

Department of Mathematics, Imperial College London, London, UK.

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http://www.nature.com/articles/srep21159
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http://dx.doi.org/10.1038/srep21159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758066PMC
February 2016

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

Lancet Respir Med 2016 Jan 4;4(1):6-8. Epub 2015 Dec 4.

Yale School of Public Health, Laboratory of Epidemiology and Public Health, New Haven, CT, USA.

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http://dx.doi.org/10.1016/S2213-2600(15)00510-XDOI Listing
January 2016

How competition governs whether moderate or aggressive treatment minimizes antibiotic resistance.

Elife 2015 Sep 22;4. Epub 2015 Sep 22.

School of Public Health, Yale University, New Haven, United States.

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http://dx.doi.org/10.7554/eLife.10559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4641510PMC
September 2015

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

Theor Popul Biol 2015 Aug 30;103:84-92. Epub 2015 May 30.

Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.tpb.2015.05.003DOI Listing
August 2015

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

Philos Trans R Soc Lond B Biol Sci 2015 Jun;370(1670):20140306

Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1098/rstb.2014.0306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424438PMC
June 2015

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

J Theor Biol 2015 Mar 29;368:67-73. Epub 2014 Dec 29.

Imperial College London, United Kingdom.

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http://dx.doi.org/10.1016/j.jtbi.2014.12.009DOI Listing
March 2015

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

Genome Med 2014 15;6(11):101. Epub 2014 Nov 15.

Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Avenue Suite 4A, Boston, MA 02115 USA ; Department of Epidemiology, Harvard School of Public Health, Boston, MA USA.

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http://dx.doi.org/10.1186/s13073-014-0101-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256898PMC
December 2014

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

Drug Alcohol Depend 2014 Sep 21;142:120-6. Epub 2014 Jun 21.

Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.

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http://dx.doi.org/10.1016/j.drugalcdep.2014.06.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150985PMC
September 2014

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

Mol Biol Evol 2014 Jul 8;31(7):1869-79. Epub 2014 Apr 8.

Department of Mathematics, Imperial College London, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msu121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4069612PMC
July 2014

Phylogenetic tree shapes resolve disease transmission patterns.

Evol Med Public Health 2014 Jun 9;2014(1):96-108. Epub 2014 Jun 9.

Department of Mathematics, Imperial College London, 180 Queen's Gate London SW7 2AZ, UK and Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, 655 West 12th Avenue, Vancouver, BC, Canada V5Z 4R4.

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http://dx.doi.org/10.1093/emph/eou018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097963PMC
June 2014

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

PLoS Comput Biol 2013 20;9(6):e1003105. Epub 2013 Jun 20.

University of Bristol, Bristol, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1003105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3688487PMC
January 2014

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 Alcohol Depend 2013 Nov 18;133(1):242-7. Epub 2013 May 18.

Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.drugalcdep.2013.04.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113725PMC
November 2013

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

Sci Transl Med 2013 Sep;5(204):204lr4

Bristol Centre for Complexity Sciences, University of Bristol, Bristol BS8 1TR, UK.

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http://dx.doi.org/10.1126/scitranslmed.3007442DOI Listing
September 2013

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

J Infect 2013 Jun 5;66(6):512-20. Epub 2013 Mar 5.

School of Social and Community Medicine, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol BS8 2PS, UK.

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http://dx.doi.org/10.1016/j.jinf.2013.02.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650581PMC
June 2013

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

Sci Transl Med 2013 Apr;5(180):180ra49

Bristol Centre for Complexity Sciences, University of Bristol, Bristol BS8 1TR, UK.

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http://dx.doi.org/10.1126/scitranslmed.3005260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3714172PMC
April 2013

Inferring carbon sources from gene expression profiles using metabolic flux models.

PLoS One 2012 14;7(5):e36947. Epub 2012 May 14.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0036947PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351459PMC
October 2012

Modeling the dynamic relationship between HIV and the risk of drug-resistant tuberculosis.

Sci Transl Med 2012 May;4(135):135ra67

Department of Medicine, Brigham and Women's Hospital, 641 Huntington Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1126/scitranslmed.3003815DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3387814PMC
May 2012

The dynamics of sexual contact networks: effects on disease spread and control.

Theor Popul Biol 2012 Mar 8;81(2):89-96. Epub 2012 Jan 8.

Bristol Centre for Complexity Sciences, Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom.

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http://dx.doi.org/10.1016/j.tpb.2011.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328800PMC
March 2012

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

J Theor Biol 2011 Jul 16;280(1):88-100. Epub 2011 Apr 16.

Division of Global Health Equity, Brigham and Women's Hospital, 641 Huntington Ave, 02115 Boston, MA, USA.

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http://dx.doi.org/10.1016/j.jtbi.2011.04.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111980PMC
July 2011

Analysis of complex metabolic behavior through pathway decomposition.

BMC Syst Biol 2011 Jun 3;5:91. Epub 2011 Jun 3.

Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes, SA 5095, Australia.

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http://dx.doi.org/10.1186/1752-0509-5-91DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135541PMC
June 2011

Spontaneous emergence of multiple drug resistance in tuberculosis before and during therapy.

PLoS One 2011 Mar 30;6(3):e18327. Epub 2011 Mar 30.

Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018327PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068161PMC
March 2011

No coexistence for free: neutral null models for multistrain pathogens.

Epidemics 2009 Mar 4;1(1):2-13. Epub 2008 Nov 4.

Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.epidem.2008.07.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3099423PMC
March 2009

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

Expert Rev Respir Med 2009 Feb;3(1):67-79

Division of Global Health Equity, Brigham and Women's Hospital, Boston, MA, USA and Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1586/17476348.3.1.67DOI Listing
February 2009

Latent coinfection and the maintenance of strain diversity.

Bull Math Biol 2009 Jan 10;71(1):247-63. Epub 2008 Dec 10.

Department of Engineering Mathematics, University of Bristol, Bristol, UK.

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http://dx.doi.org/10.1007/s11538-008-9361-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652765PMC
January 2009

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

Proc Natl Acad Sci U S A 2008 Oct 10;105(42):16302-7. Epub 2008 Oct 10.

Division of Global Health Equity, Brigham and Women's Hospital, Boston MA 02115, USA.

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http://dx.doi.org/10.1073/pnas.0808746105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570977PMC
October 2008

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

Am J Respir Crit Care Med 2008 Jun 27;177(12):1302-6. Epub 2008 Mar 27.

Division of Social Medicine and Health Inequalities, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1164/rccm.200801-175PPDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720088PMC
June 2008

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

PLoS One 2008 Jun 4;3(6):e2363. Epub 2008 Jun 4.

Division of Social Medicine and Health Inequalities, Brigham and Women's Hospital, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002363PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408555PMC
June 2008

Emergent heterogeneity in declining tuberculosis epidemics.

J Theor Biol 2007 Aug 27;247(4):765-74. Epub 2007 Apr 27.

Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1016/j.jtbi.2007.04.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652758PMC
August 2007

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

J R Soc Interface 2007 Jun;4(14):523-31

Division of Social Medicine and Health Inequalities, Brigham and Women's Hospital, One Brigham Circle, Boston, MA 02120, USA

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http://dx.doi.org/10.1098/rsif.2006.0193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373405PMC
June 2007

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

Exp Hematol 2007 Jun;35(6):898-907

Department of Mathematics, Center for Nonlinear Dynamics in Physiology and Medicine, McGill University, Montreal, QC, Canada.

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http://dx.doi.org/10.1016/j.exphem.2007.02.015DOI Listing
June 2007

High frequency spikes in long period blood cell oscillations.

J Math Biol 2006 Oct 2;53(4):499-519. Epub 2006 Aug 2.

Department of Mathematics and Centre for Nonlinear Dynamics, McGill University, 3655 Promenade Sir William Osler, Montreal, QC, Canada, H3G 1Y6.

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http://dx.doi.org/10.1007/s00285-006-0027-9DOI Listing
October 2006

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

J Theor Biol 2005 Nov 21;237(2):117-32. Epub 2005 Jun 21.

Department of Mathematics and Centre for Nonlinear Dynamics, McGill University, 3655 Promenade Sir William Osler, Montreal, Que., Canada H3G 1Y6.

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http://dx.doi.org/10.1016/j.jtbi.2005.03.033DOI Listing
November 2005

A mathematical model of hematopoiesis: II. Cyclical neutropenia.

J Theor Biol 2005 Nov 21;237(2):133-46. Epub 2005 Jun 21.

Department of Mathematics and Centre for Nonlinear Dynamics, McGill University, 3655 Promenade Sir William Osler, Montreal, QC, Canada H3G 1Y6.

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http://dx.doi.org/10.1016/j.jtbi.2005.03.034DOI Listing
November 2005