PUBLICATIONS
Peer-reviewed articles
Chang N, Tsai Y, Chen WJ, Lo CC#, Chang HH#. COVID-19 control measures unexpectedly increased the duration of stay at High Speed Rail stations during the first community outbreak in Taiwan. BMC Public Health, 2024. 24(1):551.
Cheng C, Jiang WM, Fan B, Cheng YC, Hsu YT, Wu HY, Chang HH, Tsou HH#. Real-time forecasting of COVID-19 spread according to protective behavior and vaccination: autoregressive integrated moving average models. 2023. BMC Public Health. 23(1):1500.
Li HH*, Su MP*, Wu SC*, Tsou HH, Chang MC, Cheng YC, Tsai KN, Wang HW, Chen GH, Tang CK, Chung PJ, Tsai, WT, Huang, LR, Yueh, YA, Chen HW, Pan CY, Akbari, Omar S., Chang HH, Yu GY, Marshall, John M., Chen CH#. Mechanical transmission of dengue virus by Aedes aegypti may influence disease transmission dynamics during outbreaks. 2023. eBioMedicine. 94.
傅涵#、詹大千、伍倢瑩、溫在弘、藍之辰、周玫芳、林征發、李維森、陳為堅、劉宇倫、鄭皓元、林柏丞、郭飛鷹、林雨宣、蔡懿晨、張寧、林先和、張筱涵# (2023) 。人潮流動資料於傳染病防治決策之應用：以新冠肺炎為例。臺灣公共衛生雜誌，42卷2期，頁148-152。
Pan CT, Lin CC, Lin IJ, Chien KY, Lin YS#, Chang HH#, Wu WG#. The evolution and structure of snake venom phosphodiesterase (svPDE) highlight its importance in venom actions. 2023. eLife. 12: p. ae83966.
Li NK, Corander J, Grad YH, Chang HH#. Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales. 2022. Virus Evolution, veac108. doi: 10.1093/ve/veac108
Brown TS#, Taylor AR, Arogbokun O, Buckee CO, Chang HH#. Distinguishing gene flow between malaria parasite populations. 2021. PLoS Genetics 17(12): e1009335. doi: 10.1371/journal.pgen.1009335
Tran LK*, Huang DW*, Li NK, Li LM#, Palacios JA#, Chang HH#. The impact of COVID-19 pandemic on influenza transmission: molecular and epidemiological evidence. 2021. International Journal of Infectious Diseases. doi: 10.1016/j.ijid.2021.12.323
Chang HH#, Chang MC, Kiang M, Mahmud AS, Ekapirat N, Engø-Monsen K, Sudathip P, Buckee CO, Maude RJ#. Low parasite connectivity among three malaria hotspots in Thailand. 2021. Scientific Reports 11, 23348. doi: 10.1038/s41598-021-02746-6.
Bushman M, Worby CJ, Chang HH, Kraemer MUG, Hanage WP. Transmission of SARS-CoV-2 before and after symptom onset: impact of nonpharmaceutical interventions in China. 2021. Eur J Epidemiol. 36(4):429-439. doi: 10.1007/s10654-021-00746-4
Ng TC*, Cheng HY*, Chang HH, Liu CC, Yang CC, Jian SW, Liu DP, Cohen T, Lin HH. Comparison of Estimated Effectiveness of Case-Based and Population-Based Interventions on COVID-19 Containment in Taiwan. 2021. JAMA Internal Medicine. doi:10.1001/jamainternmed.2021.1644
Watson OJ, Okell LC, Hellewell J, Slater HC, Unwin HJT, Omedo I, Bejon P, Snow RW, Noor AM, Rockett K, Hubbart C, Nankabirwa JI, Greenhouse B, Chang HH, Ghani AC, Verity R. Evaluating the performance of malaria genomics for inferring changes in transmission intensity using transmission modelling. 2021. Mol Biol Evol 38(1):274-289. doi: 10.1093/molbev/msaa225
Chang MC*, Kahn R*, Li YA, Lee CS, Buckee CO, Chang HH#. Variation in human mobility and its impact on the risk of future COVID-19 outbreaks in Taiwan. 2021. BMC Public Health 21, 226. doi: 10.1186/s12889-021-10260-7
CJ Worby#, Chang HH#. Face mask use in the general population and optimal resource allocation during the COVID-19 pandemic. 2020. Nat Commun 11, 4049. doi: 10.1038/s41467-020-17922-x
Sinha I#, Sayeed AA, Uddin D, Wesolowski A, Zaman SI, Faiz MA, Ghose A, Rahman MR, Islam A, Karim MJ, Saha A, Rezwan MK, Shamsuzzaman AKN, Jhora ST, Aktaruzzaman MM, Chang HH, Miotto O, Kwiatkowski D, Dondorp AM, Day NPJ, Hossain MA, Buckee CO, Maude RJ. 2020. Mapping the travel patterns of people with malaria in Bangladesh. BMC Med 18, 45. doi: 10.1186/s12916-020-1512-5
Lee RTC, Chang HH, Russell CA, Lipsitch M, Maurer-Stroh S#. 2019. Influenza A Hemagglutinin Passage Bias Sites and Host Specificity Mutations. Cells 8. doi: 10.3390/cells8090958
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 CO 2019. Mapping imported malaria in Bangladesh using parasite genetic and human mobility data. eLife 8:e43481. doi: 10.7554/eLife.43481
Wesolowski A, Taylor AR, Chang HH, Verity R, Tessema S, Bailey JA, Alex Perkins T, Neafsey DE, Greenhouse B, Buckee CO 2018. Mapping malaria by combining parasite genomic and epidemiologic data. BMC Med 16:190. doi: 10.1186/s12916-018-1181-9
Chang HH, Huber RG, Bond PJ, Grad YH, Camerini D, Maurer-Stroh S, Lipsitch M 2017. Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses. Bulletin of the World Health Organization 95: 517-525I. doi: 10.2471/BLT.16.182105
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 C, Greenhouse B 2017. THE REAL McCOIL: A Method for the Concurrent Estimation of the Complexity of Infection and SNP Allele Frequency for Malaria Parasites. PLoS computational biology 13(1): e1005348. doi: 10.1371/journal.pcbi.1005348
Chang HH, Childs LM, Buckee CO 2016. Variation in infection length and superinfection enhance selection efficiency in the human malaria parasite. Sci Rep 6: 26370. doi: 10.1038/srep26370
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 2016. Persistence of Plasmodium falciparum parasitemia after artemisinin combination therapy: evidence from a randomized trial in Uganda. Sci Rep 6: 26330. doi: 10.1038/srep26330
Chang HH, Dordel J, Donker T, Worby CJ, Feil EJ, Hanage WP, Bentley SD, Huang SS, Lipsitch M 2016. Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus. Genome Med 8: 18. doi: 10.1186/s13073-016-0274-3
Lee CS, Wang RW, Chang HH, Capurso D, Segal MR, Haber JE 2016. Chromosome position determines the success of double-strand break repair. Proc Natl Acad Sci U S A 113: E146-154. doi: 10.1073/pnas.1523660113
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 2015. Clonal outbreak of Plasmodium falciparum infection in eastern Panama. J Infect Dis 211: 1087-1096. doi: 10.1093/infdis/jiu575
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 2015. Modeling malaria genomics reveals transmission decline and rebound in Senegal. Proc Natl Acad Sci U S A 112: 7067-7072. doi: 10.1073/pnas.1505691112
Chang HH, Cohen T, Grad YH, Hanage WP, O'Brien TF, Lipsitch M# 2015. Origin and proliferation of multiple-drug resistance in bacterial pathogens. Microbiol Mol Biol Rev 79: 101-116. doi: 10.1128/MMBR.00039-14
Abel S, Abel zur Wiesch P, Chang HH, Davis BM, Lipsitch M, Waldor MK 2015. Sequence tag-based analysis of microbial population dynamics. Nat Methods 12: 223-226, 223 p following 226. doi: 10.1038/nmeth.3253
Chang HH, Hartl DL 2015. Recurrent bottlenecks in the malaria life cycle obscure signals of positive selection. Parasitology 142 Suppl 1: S98-S107. doi: 10.1017/S0031182014000067
Worby CJ, Chang HH, Hanage WP, Lipsitch M 2014. The distribution of pairwise genetic distances: a tool for investigating disease transmission. Genetics 198: 1395-1404. doi: 10.1534/genetics.114.171538
Chang HH, Moss EL, Park DJ, Ndiaye D, Mboup S, Volkman SK, Sabeti PC, Wirth DF, Neafsey DE, Hartl DL 2013. Malaria life cycle intensifies both natural selection and random genetic drift. Proc Natl Acad Sci U S A 110: 20129-20134. doi: 10.1073/pnas.1319857110
Lee YC*, Chang HH* 2013. The evolution and functional significance of nested gene structures in Drosophila melanogaster. Genome Biol Evol 5: 1978-1985. doi: 10.1093/gbe/evt149
Daniels R*, Chang HH*, Sene 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* 2013. Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal. PLoS One 8: e60780. doi: 10.1371/journal.pone.0060780
Park DJ, Lukens AK, Neafsey DE, Schaffner SF, Chang HH, Valim C, Ribacke U, Van Tyne D, Galinsky K, Galligan M, Becker JS, Ndiaye D, Mboup S, Wiegand RC, Hartl DL*, Sabeti PC*, Wirth DF*, Volkman SK* 2012. Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite. Proc Natl Acad Sci U S A 109: 13052-13057. doi: 10.1073/pnas.1210585109
Chang HH, Park DJ, Galinsky KJ, Schaffner SF, Ndiaye D, Ndir O, Mboup S, Wiegand RC, Volkman SK, Sabeti PC, Wirth DF, Neafsey DE, Hartl DL 2012. Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population. Mol Biol Evol 29: 3427-3439. doi: 10.1093/molbev/mss161
Book chapter
Chang HH, Daniels RF, Hartl DL. Evolution of Virulence in Eukaryotic Microbes: Wiley-Blackwell; 2012. Chapter 1, Population genetics and parasite diversity; p. 1-19.