Publications

Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses.

Author(s): Chang HH, Huber RG, Bond PJ, Grad YH, Camerini D, Maurer-Stroh S, Lipsitch M|Journal: Bull World Health Organ|PMID: 28670016| July 2017

To analyse the proportions of protein identity between Zika virus and dengue, Japanese encephalitis, yellow fever, West Nile and chikungunya…

THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites.

Author(s): Chang HH, Worby CJ, Yeka A, Nankabirwa J, Kamya MR, Staedke SG, Dorsey G, Murphy M, Neafsey DE, Jeffreys AE, Hubbart C, Rockett KA, Amato R, Kwiatkowski DP, Buckee CO, Greenhouse B|Journal: PLoS Comput Biol|PMID: 28125584| January 2017

As many malaria-endemic countries move towards elimination of Plasmodium falciparum, the most virulent human malaria parasite, effective tools for monitoring…

Persistence of Plasmodium falciparum parasitemia after artemisinin combination therapy: evidence from a randomized trial in Uganda.

Author(s): Chang HH, Meibalan E, Zelin J, Daniels R, Eziefula AC, Meyer EC, Tadesse F, Grignard L, Joice RC, Drakeley C, Wirth DF, Volkman SK, Buckee C, Bousema T, Marti M|Journal: Sci Rep|PMID: 27197604| May 2016

Artemisinin resistance is rapidly spreading in Southeast Asia. The efficacy of artemisinin-combination therapy (ACT) continues to be excellent across Africa.…

Variation in infection length and superinfection enhance selection efficiency in the human malaria parasite.

Author(s): Chang HH, Childs LM, Buckee CO|Journal: Sci Rep|PMID: 27193195| May 2016

The capacity for adaptation is central to the evolutionary success of the human malaria parasite Plasmodium falciparum. Malaria epidemiology is…

Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus.

Author(s): Chang HH, Dordel J, Donker T, Worby CJ, Feil EJ, Hanage WP, Bentley SD, Huang SS, Lipsitch M|Journal: Genome Med|PMID: 26873713| February 2016

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common healthcare-associated pathogens. To examine the role of inter-hospital patient sharing…

Sequence tag-based analysis of microbial population dynamics.

Author(s): Abel S, Abel zur Wiesch P, Chang HH, Davis BM, Lipsitch M, Waldor MK|Journal: Nat Methods|PMID: 25599549| March 2015

We describe sequence tag-based analysis of microbial populations (STAMP) for characterization of pathogen population dynamics during infection. STAMP analyzes the…

Origin and proliferation of multiple-drug resistance in bacterial pathogens.

Author(s): Chang HH, Cohen T, Grad YH, Hanage WP, O'Brien TF, Lipsitch M|Journal: Microbiol Mol Biol Rev|PMID: 25652543| March 2015

Many studies report the high prevalence of multiply drug-resistant (MDR) strains. Because MDR infections are often significantly harder and more…

The distribution of pairwise genetic distances: a tool for investigating disease transmission.

Author(s): Worby CJ, Chang HH, Hanage WP, Lipsitch M|Journal: Genetics|PMID: 25313129| December 2014

Whole-genome sequencing of pathogens has recently been used to investigate disease outbreaks and is likely to play a growing role…