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Influenza A Hemagglutinin Passage Bias Sites and Host Specificity Mutations.

Lee RTC, Chang HH, Russell CA, Lipsitch M, Maurer-Stroh S.

Cells. 2019 Aug 22;8(9). pii: E958. doi: 10.3390/cells8090958.


Mapping imported malaria in Bangladesh using parasite genetic and human mobility data.

Chang HH, Wesolowski A, Sinha I, Jacob CG, Mahmud A, Uddin D, Zaman SI, Hossain MA, Faiz MA, Ghose A, Sayeed AA, Rahman MR, Islam A, Karim MJ, Rezwan MK, Shamsuzzaman AKM, Jhora ST, Aktaruzzaman MM, Drury E, Gonçalves S, Kekre M, Dhorda M, Vongpromek R, Miotto O, Engø-Monsen K, Kwiatkowski D, Maude RJ, Buckee C.

Elife. 2019 Apr 2;8. pii: e43481. doi: 10.7554/eLife.43481.


Correction to: Mapping malaria by combining parasite genomic and epidemiologic data.

Wesolowski A, Taylor AR, Chang HH, Verity R, Tessema S, Bailey JA, Alex Perkins T, Neafsey DE, Greenhouse B, Buckee CO.

BMC Med. 2018 Dec 28;16(1):241. doi: 10.1186/s12916-018-1232-2.


Mapping malaria by combining parasite genomic and epidemiologic data.

Wesolowski A, Taylor AR, Chang HH, Verity R, Tessema S, Bailey JA, Alex Perkins T, Neafsey DE, Greenhouse B, Buckee CO.

BMC Med. 2018 Oct 18;16(1):190. doi: 10.1186/s12916-018-1181-9. Erratum in: BMC Med. 2018 Dec 28;16(1):241.


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

Chang HH, Huber RG, Bond PJ, Grad YH, Camerini D, Maurer-Stroh S, Lipsitch M.

Bull World Health Organ. 2017 Jul 1;95(7):517-525I. doi: 10.2471/BLT.16.182105. Epub 2016 Jul 18.


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

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.

PLoS Comput Biol. 2017 Jan 26;13(1):e1005348. doi: 10.1371/journal.pcbi.1005348. eCollection 2017 Jan.


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

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.

Sci Rep. 2016 May 20;6:26330. doi: 10.1038/srep26330.


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

Chang HH, Childs LM, Buckee CO.

Sci Rep. 2016 May 19;6:26370. doi: 10.1038/srep26370.


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

Chang HH, Dordel J, Donker T, Worby CJ, Feil EJ, Hanage WP, Bentley SD, Huang SS, Lipsitch M.

Genome Med. 2016 Feb 13;8(1):18. doi: 10.1186/s13073-016-0274-3.


Chromosome position determines the success of double-strand break repair.

Lee CS, Wang RW, Chang HH, Capurso D, Segal MR, Haber JE.

Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):E146-54. doi: 10.1073/pnas.1523660113. Epub 2015 Dec 29.


Modeling malaria genomics reveals transmission decline and rebound in Senegal.

Daniels RF, Schaffner SF, Wenger EA, Proctor JL, Chang HH, Wong W, Baro N, Ndiaye D, Fall FB, Ndiop M, Ba M, Milner DA Jr, Taylor TE, Neafsey DE, Volkman SK, Eckhoff PA, Hartl DL, Wirth DF.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):7067-72. doi: 10.1073/pnas.1505691112. Epub 2015 May 4.


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

Chang HH, Cohen T, Grad YH, Hanage WP, O'Brien TF, Lipsitch M.

Microbiol Mol Biol Rev. 2015 Mar;79(1):101-16. doi: 10.1128/MMBR.00039-14. Review.


Sequence tag-based analysis of microbial population dynamics.

Abel S, Abel zur Wiesch P, Chang HH, Davis BM, Lipsitch M, Waldor MK.

Nat Methods. 2015 Mar;12(3):223-6, 3 p following 226. doi: 10.1038/nmeth.3253. Epub 2015 Jan 19.


Clonal outbreak of Plasmodium falciparum infection in eastern Panama.

Obaldia N 3rd, Baro NK, Calzada JE, Santamaria AM, Daniels R, Wong W, Chang HH, Hamilton EJ, Arevalo-Herrera M, Herrera S, Wirth DF, Hartl DL, Marti M, Volkman SK.

J Infect Dis. 2015 Apr 1;211(7):1087-96. doi: 10.1093/infdis/jiu575. Epub 2014 Oct 21.


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

Worby CJ, Chang HH, Hanage WP, Lipsitch M.

Genetics. 2014 Dec;198(4):1395-404. doi: 10.1534/genetics.114.171538. Epub 2014 Oct 13.


Recurrent bottlenecks in the malaria life cycle obscure signals of positive selection.

Chang HH, Hartl DL.

Parasitology. 2015 Feb;142 Suppl 1:S98-S107. doi: 10.1017/S0031182014000067. Epub 2014 Feb 20.


Malaria life cycle intensifies both natural selection and random genetic drift.

Chang HH, Moss EL, Park DJ, Ndiaye D, Mboup S, Volkman SK, Sabeti PC, Wirth DF, Neafsey DE, Hartl DL.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20129-34. doi: 10.1073/pnas.1319857110. Epub 2013 Nov 20.


The evolution and functional significance of nested gene structures in Drosophila melanogaster.

Lee YC, Chang HH.

Genome Biol Evol. 2013;5(10):1978-85. doi: 10.1093/gbe/evt149. Erratum in: Genome Biol Evol. 2013;5(11):2072. Genome Biol Evol. 2013;5(11):2188.


Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal.

Daniels R, Chang HH, Séne PD, Park DC, Neafsey DE, Schaffner SF, Hamilton EJ, Lukens AK, Van Tyne D, Mboup S, Sabeti PC, Ndiaye D, Wirth DF, Hartl DL, Volkman SK.

PLoS One. 2013 Apr 4;8(4):e60780. doi: 10.1371/journal.pone.0060780. Print 2013.

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