WestConn Vector-Borne Disease Genomics Lab

Popkin-Hall Research Laboratory at WCSU

Publications

Published Research Papers

Publications appear in reverse chronological order. Student/mentee co-authors are underlined. Publications marked with an asterisk indicate joint first-authorship.

  1. Wiener, D., M. D. Seth, C. I. Mandara, R. A. Madebe, Z. R. Popkin-Hall, D. Giesbrecht, C. Bakari, B. Lyimo, D. Pereus, F. Francis, D. Mbwambo, S. Aaron, A. Lusasi, S. Lazaro, T. P. Sheahan, J.B. Parr, D. S. Ishengoma, and J. J. Juliano. Varying Malaria Rapid Diagnostic Test Accuracy by Regional Transmission Level and Demographics in Tanzania. American Journal of Tropical Medicine and Hygiene. https://doi.org/10.4269/ajtmh.25-0460
  2. White, S. J., V. P. K. Tchuenkam, M. Mbouh, C. F. Gaither, A. G. Bouopda-Tuedom, B. Kiam, Z. R. Popkin-Hall, E. Hand, J. M. Sadler, K. Carey-Ewend, M. N. Ngum, Y. N. Ngomsi, J. B. Parr, J. A. Bailey, D. B. Nguene, L. Kamg, L. G. Nino, V. Goel, I. Ibrahima, J. C. Onguene, J. T. Lin, R. R. Dinglasan, S. E. Nsango, J. J. Juliano, and I. M. Ali. Epidemiology of Relapsing and Falciparum Malaria in the Highlands of Cameroon: An Integrated Community Survey of Human Infection and Vector Abundance. PLoS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0013549
  3. Carey-Ewend, K., A. Marten, J. Muller, E. E. Peter, M. Odas, M. C. Dominick, M. Muller, S. Chhetri, K. Amagai, I. Rutha, F. Kisandu, L. Beka, O. Kharabora, Z. R. Popkin-Hall, J. A. Bailey, J. Edwards, E. W. Gower, J. J. Juliano, B. E. Ngasala, and J. T. Lin. Seasonal variation and interspecies dynamics among Plasmodium falciparum and ovale species in Bagamoyo, Tanzania. Journal of Infectious Diseases. https://doi.org/10.1093/infdis/jiaf498
  4. Kiam, B., A. G. Bouopda Tuedom, I. Ibrahima, S. J. White, P. Tchuenkam, Z. R. Popkin-Hall, M. Mbouh, J. A. Mbida Mbida, C. T. Nanssong, L. M. Abate, C. J. Onguene, B. Fotso Tumamo, J. M. Sadler, J. B. Parr, J. T. Lin, J. J. Juliano, I. M. Ali, R. Dinglasan, and S. E. Nsango. Diversity, abundance of anopheline species, and malaria transmission dynamics in high-altitude areas of western Cameroon. Malaria Journal. https://doi.org/10.1186/s12936-025-05480-w
  5. Seth, M. D., Z. R. Popkin-Hall, R. A. Madebe, R. Budodo, C. Bakari, B. M. Lyimo, D. Giesbrecht, R. Moshi, R. B. Mbwambo, F. Francis, D. Pereus, D. Mbata, D. P. Challe, S. S. Mandai, G. A. Chacha, A. J. Kisambale, D. Mbwambo, S. Aaron, A. Lusasi, S. Lazaro, C. I. Mandara, J. A. Bailey, J. J. Juliano, J. R. Gutman, and D. S. Ishengoma. Prevalence of subpatent Plasmodium falciparum infections in regions with varying transmission intensities and implications for malaria transmission in Mainland Tanzania. 2025. Malaria Journal. https://doi.org/10.1186/s12936-025-05341-6
  6. Popkin-Hall, Z. R. and M.A. Slotman. Selection on Gustatory Receptor Genes in the Anopheles gambiae Species Complex. 2025. BMC Ecology and Evolution. https://doi.org/10.1186/s12862-025-02359-x
  7. Carey-Ewend, K., Z. R. Popkin-Hall, A. Simkin, M. Muller, C. Hennelly, W. He, K. Moser, C. Gaither, K. Niaré, F. Aghakhanian, S. Feleke, B. G. Brhane, F. Phanzu, K. Mwandagalirwa, Ö. Aydemir, C. Sutherland, D. Ishengoma, I. M. Ali, B. Ngasala, A. Kalonji, A. Tshefu, J. Parr, J. A. Bailey, J. J. Juliano, and J. T. Lin. Population Genomics of Plasmodium ovale Species in sub-Saharan Africa. 2024. Nature Communications. https://doi.org/10.1038/s41467-024-54667-3
  8. Popkin-Hall, Z. R., K. Niaré, R. Crudale, A. Simkin, A. A. Fola, J. F. Sanchez, D. L. Pannebaker, D. J. Giesbrecht, I. E. Kim, Jr., Ö. Aydemir, J. A. Bailey, H. O. Valdivia, and J. J. Juliano.High-Throughput Genotyping of Plasmodium vivax in the Peruvian Amazon via Molecular Inversion Probes. 2024. Nature Communications. https://doi.org/10.1038/s41467-024-54731-y
  9. Juliano, J. J., D. J. Giesbrecht, A. Simkin, A. A. Fola,  B. M. Lyimo, D. Pereus, C. Bakari, R. A. Madebe, M. D. Seth, C. I. Mandara, Z. R. Popkin-Hall, R. Moshi, R. B. Mbwambo, K. Niaré, B. MacInnis, F. Francis, D. Mbwambo, I. Garimo, F. Chacky, S. Aaron, A. Lusasi, F. Molteni, R. Njau, S. Lazaro, A. Mohamed, J. A. Bailey, and D. S. Ishengoma. Prevalence of mutations associated with artemisinin partial resistance and sulfadoxine-pyrimethamine resistance in 13 regions in Tanzania in 2021: a cross-sectional survey 2024. The Lancet Microbe. https://doi.org/10.1016/S2666-5247(24)00160-5
  10. Connelly, S.V., N.F. Brazeau, M. Msellem, B. E. Ngasala, O. Aydemir, V. Goel, K. Niaré, D. J. Giesbrecht, Z. R. Popkin-Hall, C. M. Hennelly, Z. Park, A. M. Moormann, J. M. Ong’echa, R. Verity, S. Mohammed, S. J. Shija, L. E. Mhamilawa, U. Morris, A. Mårtensson, J. T. Lin, A. Björkman, J. J. Juliano, and J. A. Bailey. Strong isolation by distance and evidence of population microstructure reflect ongoing Plasmodium falciparum transmission in Zanzibar. 2024. eLife. https://doi.org/10.7554/eLife.90173.3
  11. Popkin-Hall, Z. R. and M. A. Slotman. The Role of the Major Chemosensory Organs in the Host-Seeking Activity of Anopheles coluzzii. 2024. Journal of Medical Entomology. https://doi.org/10.1093/jme/tjae062
  12. Lyimo, B. M., C. Bakari, Z. R. Popkin-Hall, D. J. Giesbrecht, M. D. Seth, D. Pereus, R. Moshi, R. Boniface, C. I. Mandara, R. Madebe, J. J. Juliano, J. A. Bailey, and D. S. Ishengoma. Genetic polymorphism and evidence of signatures of selection in the Plasmodium falciparum circumsporozoite protein gene in Tanzanian regions with different malaria endemicity. 2024. Malaria Journal. https://doi.org/10.1186/s12936-024-04974-3
  13. Rogier, E., N. Battle, C. Bakari, M. D. Seth, D. Nace, C. Herman, R. A. Madebe, C. I. Mandara, B. M. Lyimo, D. J. Giesbrecht, Z. R. Popkin-Hall, F. Francis, D. Mbwambo, I. Garimo, S. Aaron, A. Lusasi, F. Molteni, R. Njau, J. A. Cunningham, S. Lazaro, A. Mohamed, J. J. Juliano, J. A. Bailey, V. Udhayaumar, and D. S. Ishengoma. Plasmodium falciparum hrp2 and hrp3 gene deletions among patients enrolled at 100 health facilities throughout Tanzania: February to July 2021. 2024. Scientific Reports. https://doi.org/10.1038/s41598-024-58455-3
  14. Popkin-Hall, Z. R., M. D. Seth, R. A. Madebe, R. Budodo, C. Bakari, F. Francis, D. Pereus, D. J. Giesbrecht, C. I. Mandara, D. Mbwambo, S. Aaron, A. Lusasi, S. Lazaro, J. A. Bailey, J. J. Juliano, J. R. Gutman, and D. S. Ishengoma. Malaria species prevalence among asymptomatic individuals in four regions of Mainland Tanzania. 2024. Parasites and Vectors https://doi.org/10.1186/s13071-024-06242-4
  15. Ngasala, B., F. Chacky, A. Mohamed, F. Molteni, S. Nyinondi, B. Kabula, H. Mkali, K. Thwai, Z. R. Popkin-Hall, C. Mitchell, J. B. Parr, J. J. Juliano, and J. T. Lin. Evaluation of malaria rapid diagnostic test performance and HRP2 deletions in Tanzania school surveys, 2017. 2024. The American Journal of Tropical Medicine and Hygiene. https://doi.org/10.4269/ajtmh.23-0771
  16. Popkin-Hall, Z. R., M. D. Seth, R. A. Madebe, R. Budodo, C. Bakari, F. Francis, D. Pereus, D. J. Giesbrecht, C. I. Mandara, D. Mbwambo, S. Aaron, A. Lusasi, S. Lazaro, J. A. Bailey, J. J. Juliano, and D. S. Ishengoma. Malaria species positivity rates among symptomatic individuals across regions of differing transmission intensities in Mainland Tanzania. 2023. The Journal of Infectious Diseases. https://doi.org/10.1093/infdis/jiad522
  17. Lyimo, B. M.*, Z. R. Popkin-Hall*, D. J. Giesbrecht, R. A. Madebe, C. I. Mandara, C. Bakari, M. D. Seth, D. Pereus, R. M. Ngamba, R. B. Mbwambo, B. MacInnis, D. Mbwambo, I. Garimo, S. Aaron, F. Chacky, A. Lusasi, F. Molteni, R. Njau, J. A. Cunningham, S. Lazaro, A. Mohamed, J. J. Juliano, J. A. Bailey, and D. S. Ishengoma. Potential opportunities and challenges for the Application of Next Generation Sequencing and CRISPR-Cas systems to support diagnostics and surveillance towards malaria control and elimination in Tanzania. 2022. Frontiers in Cellular and Infection Microbiology. https://www.frontiersin.org/articles/10.3389/fcimb.2022.757844/full
  18. Cerami, C., Z. R. Popkin-Hall, T. Rapp, K. Tompkins, H. Zhang, M. S. Muller, C. Basham, M. Whittelsey, S. B. Chhetri, J. Smith, C. Litel, K. D. Lin, M. Churiwal, S. Khan, R. Rubinstein, F. Claman, K. Mollan, D. Wohl, L. Premkumar, K. A. Powers, J. J. Juliano, F-C. Lin, and J.T. Lin. Household transmission of SARS-CoV-2 in the United States: living density, viral load, and disproportionate impact on communities of color. 2021. Clinical Infectious Diseases. https://doi.org/10.1093/cid/ciab701
  19. Athrey, G.*, Z. R. Popkin-Hall*, W. Takken, and M. A. Slotman. The Expression of Chemosensory Genes in Male Maxillary Palps of Anopheles coluzzii (Diptera: Culicidae) and An. quadriannulatus. 2021. Journal of Medical Entomology. 58:3. https://doi.org/10.1093/jme/tjaa290
  20. Athrey, G., Z. R. Popkin-Hall, L. V. Cosme, W. Takken, and M. A. Slotman. Species and sex-specific chemosensory gene expression in An. coluzzii and An. quadriannulatus antennae. 2020. Parasites & Vectors. 13:212. https://doi.org/10.1186/s13071-020-04085-3  
  21. Athrey, G., L.V. Cosme, Z. R. Popkin-Hall, S. Pathikonda, W. Takken, and M.A. Slotman. Chemosensory gene expression in olfactory organs of the Anthropophilic Anopheles coluzzii and the zoophilic Anopheles quadriannulatus. 2017. BMC Genomics. 18: 751. https://doi.org/10.1186/s12864-017-4122-7  
  22. Jay, K. R, Z. R. Popkin-Hall, M. J. Coblens, J. T. Oberski, P. P. Sharma, and S.L. Boyer. New species of Austropurcellia, cryptic short-range endemic mite harvestmen (Arachnida, Opiliones, Cyphophthalmi) from Australia’s Wet Tropics biodiversity hotspot. 2016. Zookeys 586:37-93. http://dx.doi.org/10.3897/zookeys.586.6774
  23. Meyers, J.I., S. Pathikonda, Z.R. Popkin-Hall, MC. Medeiros, G. Fuseini, A. Matias, G. Garcia, H.J. Overgaard, V. Kulkarni, V.P. Reddy, C. Schwabe, J. Lines, I. Kleinschmidt, and M.A. Slotman. Increasing outdoor host-seeking in Anopheles gambiae over 6 years of vector control on Bioko Island. 2016. Malaria Journal 15:239. http://dx.doi.org10.1186/s12936-016-1286-6  
  24. Boyer, S.L., C.M. Baker, Z.R. Popkin-Hall, D.I. Laukó, H.W. Wiesner, and R.M. Quay. Phylogeny and biogeography of the mite harvestmen (Arachnida, Opiliones, Cyphophthalmi) of Queensland, Australia, with a description of six new species from the rainforests of the Wet Tropics. 2015. Invertebrate Systematics 29: 37-70.  http://dx.doi.org/10.1071/IS14025
  25. Popkin-Hall, Z.R. and S.L. Boyer. New species of mite harvestmen from southeast Queensland, Australia greatly extend the known range of the genus Austropurcellia (Arachnida, Opiliones, Cyphophthalmi). 2014. Zootaxa 3827(4): 517-541. http://dx.doi.org/10.11646/zootaxa.3827.4.5

Preprints

These publications have not yet been peer-reviewed.

  1. Wernsman Young, N., C. P. G. Meier-Scherling, G. Cuomo-Dannenburg, G. A. Tollefson, S. V. Connelly, J. Marglous, I. G. Gyuricza, K. Carey-Ewend, R. Kyong-Shin, Z. R. Popkin-Hall, A. J. Zeleke, D. S. Ishengoma, A. A. Fola, A. Simkin, K. Niaré, J. B. Parr, M. Conrad, L. C. Okell, S. Ruybal-Pesántez, O. J. Watson, J. J. Juliano, J. A. Bailey, and R. Verity. Mapping the prevalence of molecular markers in Plasmodium falciparum artemisinin partial resistance in Africa: a spatial-temporal modelling study. medRxiv. https://doi.org/10.64898/2025.12.22.25342873
  2. Pereus, D., A. A. Fola, C. Bakari, M. D. Seth, R. DeFeo, B. Lyimo, C. I. Mandara, R. A. Madebe, D. M. Mbata, Z. R. Popkin-Hall, R. Moshi, R. B. Mbwambo, S. Aaron, A. Lusasi, S. Lazaro, D. J. Giesbrecht, B. Kulohoma, J. J. Juliano, J. A. Bailey, G. Juma, V. A. Mobegi, and D. S. Ishengoma. Genetic Metrics Decodes Plasmodium falciparum Diversity: Complexity of Infections, Parasite Connectivity, and Transmission Intensity in Mainland Tanzania’s Diverse Regions. medRxiv. https://doi.org/10.1101/2025.04.18.25326063
  3. He, W., T. Bobanga, A. Piantodosi, Z. R. Popkin-Hall, F. Vulu, M. H. Collins, M. M. Kashamuka, A. K. Tshefu, J. J. Juliano, and J. B. Parr. Evidence of dengue virus transmission and a diverse Aedes mosquito virome on the Democratic Republic of Congo-Angola border. bioRxiv. https://doi.org/10.1101/2025.01.16.633031
  4. Popkin-Hall, Z. R.*, K. Carey-Ewend*, F. Aghakhanian, E. C. Oriero, M. D. Seth, M. M. Kashamuka, B. Ngasala, I. M. Ali, E. S. Mukomena, C. I. Mandara, R. Sendor, A. Simkin, A. Amambua-Ngwa, A. Tshefu, A. A. Fola, J. A. Bailey, D. S. Ishengoma, J. B. Parr, J. T. Lin, and J. J. Juliano. Population Genomics of Plasmodium malariae from Four African Countries. medRxiv. https://doi.org/10.1101/2024.09.07.24313132

Manuscripts in Review/Revision

  1. Wernsman Young, N., C. P. G. Meier-Scherling, G. Cuomo-Dannenburg, G. A. Tollefson, S. V. Connelly, J. Marglous, I. G. Gyuricza, K. Carey-Ewend, R. Kyong-Shin, Z. R. Popkin-Hall, A. J. Zeleke, D. S. Ishengoma, A. A. Fola, A. Simkin, K. Niaré, J. B. Parr, M. Conrad, L. C. Okell, S. Ruybal-Pesántez, O. J. Watson, J. J. Juliano, J. A. Bailey, and R. Verity. Mapping the prevalence of molecular markers in Plasmodium falciparum artemisinin partial resistance in Africa: a spatial-temporal modelling study. Submitted, The Lancet Infectious Diseases.
  2. Pereus, D., A. A. Fola, C. Bakari, M. D. Seth, R. Crudale, B. M. Lyimo, C. I. Mandara, R. A. Madebe, D. Mbata, Z. R. Popkin-Hall, R. Moshi, R. B. Mbwambo, D. Mbwambo, S. Aaron, A. Lusasi, S. Lazaro, D. J. Giesbrecht, B. Kulohoma, J. J. Juliano, J. A. Bailey, G. Juma, V. A. Mobegi, and D. S. Ishengoma. Genetic Metrics Decode Plasmodium falciparum Diversity: Complexity of Infections, Parasite Connectivity, and Transmission Intensity in Mainland Tanzania’s Diverse Regions. Submitted, PLoS Pathogens.
  3. Popkin-Hall, Z. R.*, K. Carey-Ewend*, F. Aghakhanian, E. C. Oriero, M. D. Seth, M. M. Kashamuka, B. Ngasala, I. M. Ali, E. S. Mukomena, C. I. Mandara, R. Sendor, A. Simkin, A. Amambua-Ngwa, A. Tshefu, A. A. Fola, J. A. Bailey, D. S. Ishengoma, J. B. Parr, J. T. Lin, and J. J. Juliano. Population Genomics of Plasmodium malariae from Four African Countries. In revision, JCI Insight.
  4. He, W., T. Bobanga, A. Piantodosi, Z. R. Popkin-Hall, F. Vulu, M. H. Collins, M. M. Kashamuka, A. K. Tshefu, J. J. Juliano, and J. B. Parr. Evidence of endemic dengue virus transmission and a highly diverse virome in wild-caught Aedes mosquitoes from Kimpese, Democratic Republic of the Congo. In revision, Nature Communications.

Conference Proceedings and Abstracts

  1. Popkin-Hall, Z. R., K. Niaré, R. Crudale, A. Simkin, A. A. Fola, J. F. Sanchez, D. L. Pannebaker, D. J. Giesbrecht, I. E. Kim, Jr., Ö. Aydemir, J. A. Bailey, H. O. Valdivia, and J. J. Juliano. High-Throughput genotyping of Plasmodium vivax in the Peruvian Amazon via molecular inversion probes. 2025. Malaria Journal, 24(Suppl 1): T1-O10. https://doi.org/10.1186/s12936-025-05498-0

Manuscripts in Preparation

  1. Popkin-Hall, Z. R., B. Rajasekar, Z. Park, M. Spring, M. Wojnarski, D. Saunders, C. Lon, J. J. Juliano, and J. T. Lin. Genomic Variation of Relapsing Plasmodium vivax in Cambodia. In preparation for submission to PLoS Neglected Tropical Diseases.
  2. Popkin-Hall, Z.R., X. Huang, and M. A. Slotman. Species and Sex-Biased Expression of Chemosensory Genes in the Labella of Sister Species Anopheles coluzzii and Anopheles quadriannulatus. In preparation for submission to BMC Genomics.
  3. Geospatial And Temporal Emergence of Resistance in Africa (GATER-Africa)- A Report from an Informal Convening, London, September 2024. Mapping the prevalence of molecular markers of artemisinin partial and partner drug antimalarial resistance in Africa: a spatial and temporal modelling study.

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