Publications

"Renal outcomes in adults with HBV, HIV and HBV/HIV coinfection after 3 years of antiviral therapy in urban Tanzania." Wu EL, Christian B, Rivera AS, Fabian E, Macha I, Aris E, Mpangala S, Ulenga N, Mugusi F, Murphy RL, Hawkins CA. J Antimicrob Chemother (2024)

"Effect of high-dose multivitamin supplements on alanine aminotransferase elevations among adults living with HIV on antiretroviral therapy in Tanzania." Mugusi SF, Sando DM, Mugusi FM, Hawkins CA, Aboud SS, Fawzi WW, Sudfeld CR. BMC Nutr (2024).

"A multiplexed real-time PCR assay for simultaneous quantification of human immunodeficiency virus and Hepatitis B virus for low-and-middle- income countries." Fofana DB, Coulibaly TA, Maiga M, Nguyen T, Gozlan J, Diarra Z, Koné A, Cissoko Y, Maiga AI, Hawkins CA, Murphy RL, Morand-Joubert L, Diakité M, Holl JL, McFall SM. J Virol Methods (2024).

"Design, creation, and use of the Test Us Bank (TUB) COVID-19 sample biorepository." Broach J, Achenbach C, Behar S, O'Connor L, Tarrant S, Ferranto J, Wright C, Hartin P, Orwig T, Nanavati J, Kalibala B, Woods K, Shaw B, Flahive J, Barton B, Hafer N, Herbert C, Fahey N, Gibson L, Simin K, Kowalik T, Ward DV, Mirza AW, Murphy RL, Caputo M, Buchholz B, Fantasia H, Koren A, Marchand L, Oludare S, Sogade F, Ritland D, Davis C, Grenier A, Baron C, Brent E, McKenney JB, Elder N, Michaels L, Ferrara L, Theron G, Palmer Z, Levy B, Daly J, Parang K, Schmidt M, Buxton D, Heetderks W, Manabe YC, Soni A, McManus D. BMC Infect Dis (2024)

"Surveillance Metrics and History of the COVID-19 Pandemic in Central Asia: Updated Epidemiological Assessment." Lundberg AL, Ozer EA, Wu SA, Soetikno AG, Welch SB, Liu Y, Havey RJ, Murphy RL, Hawkins C, Mason M, Achenbach CJ, Post LA. JMIR Public Health Surveill (2024).

"South Asia's COVID-19 History and Surveillance: Updated Epidemiological Assessment." Post LA, Soetikno AG, Wu SA, Hawkins C, Mason M, Ozer EA, Murphy RL, Welch SB, Liu Y, Havey RJ, Moss CB, Achenbach CJ, Lundberg AL. JMIR Public Health Surveill (2024).

"Updated Surveillance Metrics and History of the COVID-19 Pandemic (2020-2023) in Canada: Longitudinal Trend Analysis." Wu SA, Soetikno AG, Ozer EA, Welch SB, Liu Y, Havey RJ, Murphy RL, Hawkins C, Mason M, Post LA, Achenbach CJ, Lundberg AL. JMIR Public Health Surveill (2024).

"Updated Surveillance Metrics and History of the COVID-19 Pandemic (2020-2023) in Sub-Saharan Africa: Longitudinal Trend Analysis." Lundberg AL, Soetikno AG, Wu SA, Ozer EA, Welch SB, Mason M, Murphy RL, Hawkins C, Liu Y, Moss CB, Havey RJ, Achenbach CJ, Post LA. JMIR Public Health Surveill (2024).

"Integration of individualized and population-level molecular epidemiology data to model COVID-19 outcomes." Ling-Hu T, Simons LM, Dean TJ, Rios-Guzman E, Caputo MT, Alisoltani A, Qi C, Malczynski M, Blanke T, Jennings LJ, Ison MG, Achenbach CJ, Larkin PM, Kaul KL, Lorenzo-Redondo R, Ozer EA, Hultquist JF. Cell Rep Med (2024).

"Hepatocellular carcinoma presentation and prognosis among Nigerian adults with and without HIV." Davwar PM, Okeke E, Duguru M, Nyam D, Bell K, Odeghe EA, Oyeleke G, Lesi OA, Singh R, Kim KY, Imade G, Akanmu AS, Sagay AS, Ogunsola FT, Peters MG, Roberts LR, Hou L, Murphy RL, Hawkins CA. PLoS One (2023).

"Hepatitis B Virus in West African Children: Systematic Review and Meta-Analysis of HIV and Other Factors Associated with Hepatitis B Infection." Fofana DB, Somboro AM, Maiga M, Kampo MI, Diakité B, Cissoko Y, McFall SM, Hawkins CA, Maiga AI, Sylla M, Gozlan J, El-Sayed MH, Morand-Joubert L, Murphy RL, Diakité M, Holl JL. Int J Environ Res Public Health (2023).

"Prevalence of HIV-1 Natural Polymorphisms and Integrase-Resistance-Associated Mutations in African Children." Fofana DB, Diarra H, Guindo I, Savadogo MK, d'Almeida M, Diallo FI, Baldé A, Soulié C, Kone A, Marcelin AG, Maiga AI, Lambert-Niclot S, Maiga M, McFall S, Hawkins CA, Murphy RL, Sylla M, Katlama C, Holl JL, Calvez V, Morand-Joubert L. Viruses (2023).

"Incident Kaposi sarcoma during the expansion of antiretroviral therapy eligibility in Nigeria: a retrospective cohort study." Akanbi MO, Bilaver LA, Achenbach C, Hirschhorn LR, Rivera AS, Adekolujo OS, Adekola KUA, Silas OA, Agaba PA, Agbaji O, Shehu NY, Sagay SA, Hou L, Murphy RL. BMC Cancer (2023).

"Relationship between patient sex and anatomical sites of extrapulmonary tuberculosis in Mali." Baya B, Sanogo I, Kone M, Soumare D, Ouattara K, Somboro A, Wague M, Coulibaly N, Koloma I, Coulibaly M, Nantoume M, Perou M, Kone K, Coulibaly D, Boukary Diarra H, Kone B, Diarra A, Coulibaly MD, Sanogo M, Diarra B, Diakite M, Achenbach CJ, Doumbia S, Bishai WR, Klein SL, Holl JL, Diallo S, Murphy RL, Toloba Y, Dabitao D. J Clin Tuberc Other Mycobact Dis (2023).

"Epidemiology and survival outcomes of HIV-associated cervical cancer in Nigeria." Musa J, Kocherginsky M, Magaji FA, Maryam AJ, Asufi J, Nenrot D, Burdett K, Katam N, Christian EN, Palanisamy N, Odukoya O, Silas OA, Abdulkareem F, Akpa P, Badmos K, Imade GE, Akanmu AS, Gursel DB, Zheng Y, Joyce BT, Achenbach CJ, Sagay AS, Anorlu R, Wei JJ, Ogunsola F, Murphy RL, Hou L, Simon MA. Infect Agent Cancer (2023).

"Vaginal microbiome community state types and high-risk human papillomaviruses in cervical precancer and cancer in North-central Nigeria." Musa J, Maiga M, Green SJ, Magaji FA, Maryam AJ, Okolo M, Nyam CJ, Cosmas NT, Silas OA, Imade GE, Zheng Y, Joyce BT, Diakite B, Morhason-Bello I, Achenbach CJ, Sagay AS, Ujah IAO, Murphy RL, Hou L, Mehta SD. BMC Cancer (2023).

"Clinical evaluation of the Diagnostic Analyzer for Selective Hybridization (DASH): A point-of-care PCR test for rapid detection of SARS-CoV-2 infection." Achenbach CJ, Caputo M, Hawkins C, Balmert LC, Qi C, Odorisio J, Dembele E, Jackson A, Abbas H, Frediani JK, Levy JM, Rebolledo PA, Kempker RR, Esper AM, Lam WA, Martin GS, Murphy RL. PLoS One (2022).

"Overlapping Delta and Omicron Outbreaks During the COVID-19 Pandemic: Dynamic Panel Data Estimates." Lundberg AL, Lorenzo-Redondo R, Hultquist JF, Hawkins CA, Ozer EA, Welch SB, Prasad PVV, Achenbach CJ, White JI, Oehmke JF, Murphy RL, Havey RJ, Post LA. JMIR Public Health Surveill (2022).

"Has Omicron changed the evolution of the pandemic?" Lundberg AL, Lorenzo-Redondo R, Ozer EA, Hawkins CA, Hultquist JF, Welch SB, Prasad PVV, Oehmke JF, Achenbach CJ, Murphy RL, White JI, Havey RJ, Post LA. JMIR Public Health Surveil (2022).

"Multiple expansions of globally uncommon SARS-CoV-2 lineages in Nigeria." Ozer, E.A., Simons, L.M., Adewumi, O.M. et al. Nat Commun (2022).

"High SARS-CoV-2 Seroprevalence among Healthcare Workers in Bamako, Mali." Somboro AM, Cissoko Y, Camara I, Kodio O, Tolofoudie M, Dembele E, Togo ACG, Ba DM, Sarro YDS, Baya B, Samake S, Diallo IB, Kumar A, Traore M, Kone B, Kone A, Diarra B, Dabitao DK, Wague M, Dabo G, Doumbia S, Holl JL, Murphy RL, Diallo S, Maiga AI, Maiga M, Dao S. Viruses (2022).

"Sex Differences in Active Pulmonary Tuberculosis Outcomes in Mali, West Africa." Dabitao D, Somboro A, Sanogo I, Diarra B, Achenbach CJ, Holl JL, Baya B, Sanogo M, Wague M, Coulibaly N, Kone M, Drame HB, Tolofoudie M, Kone B, Diarra A, Coulibaly MD, Saliba-Shaw K, Toloba Y, Diakite M, Doumbia S, Klein SL, Bishai WR, Diallo S, Murphy RL. Am J Trop Med Hyg (2022).

"Modeling robust COVID-19 intensive care unit occupancy thresholds for imposing mitigation to prevent exceeding capacities." Runge M., Richardson R.A.K., Clay P., Eagan A., Holden T.M., Singam M., Tsuboyama N., Arevalo P., Fornoff J., Patrick S., Ezike N.O., Gerardin J. PLOS Global Public Health (in press 2022).

"Socioeconomic, demographic and environmental factors inform intervention prioritization in urban Nigeria." Chiziba C., Diallo O., Bertozzi-Villa A., Weiss D., Mercer L., Gerardin J., Ozodiegwu I.D. medRxiv (2022).

"Modeling impact and cost‐effectiveness of driving‐Y gene drives for malaria elimination in the Democratic Republic of the Congo." Metchanun N., Borgemeister C., Amzati G., von Braun J., Nikolov M., Selvaraj P., Gerardin J. Evolutionary Applications (2022).

"Long-term effects of increased adoption of artemisinin combination therapies in Burkina Faso." Zupko R., Nguyen T.D., Some A.F., Tran T.N., Gerardin J., Dudas P., Giang D.D., Wesolowski A., Ouedraogo J.B., Boni M.F. PLoS Global Public Health (2022).

"Accelerated Epigenetic Age Among Women with Invasive Cervical Cancer and HIV-Infection in Nigeria." Musa J, Kim K, Zheng Y, Qu Y, Joyce BT, Wang J, Nannini DR, Gursel DB, Silas O, Abdulkareem FB, Imade G, Akanmu AS, Wei JJ, Kocherginsky M, Kim KA, Wehbe F, Achenbach CJ, Anorlu R, Simon MA, Sagay A, Ogunsola FT, Murphy RL, Hou L. Front Public Health (2022).

"The Clinical Review Committee: Impact of the Development of In Vitro Diagnostic Tests for SARS-CoV-2 Within RADx Tech." Robinson M, Gaydos C, Van Der Pol B, McFall S, Hsieh YH, Clarke W, Murphy RL, Widdice LE, Hirschhorn LR, Rothman R, Achenbach C, Hawkins C, Samuta A, Gibson L, McManus D, Manabe YC. IEEE Open J Eng Med Biol (2021). *GH Technologies, Primary Care

"Geographic and demographic heterogeneity of SARS-CoV-2 diagnostic testing in Illinois, USA, March to December 2020." Holden T.M.*, Richardson R.A.K.*, Arevalo P., Duffus W.A., Runge M., Whitney E., Wise L., Ezike N.O., Patrick S., Cobey S., Gerardin J. BMC Public Health (2021).

"Mobility network modeling explains higher SARS-CoV-2 infection rates among disadvantaged groups and informs reopening strategies." Chang S.Y.*, Pierson E.*, Koh P.W.*, Gerardin J., Redbird B., Grusky D., Leskovec J. Nature (2021).

"Identifying the measurements required to estimate rates of COVID-19 transmission, infection, and detection, using variational data assimilation." Armstrong E., Runge M., Gerardin J. Infectious Disease Modelling (2021).

"A method to detect and quantify SARS-CoV-2 in nasal exhaled breath." Lane, G.; Zhou, G.; McCarthy, D.; Noto, T.; Yang, Q.; Zelano, C. Chemical Senses (2021).

"Accelerating adolescent HIV research in low-income and middle-income countries: evidence from a research consortium." Tucker JD, Iwelunmor J, Abrams E, Donenberg G, Wilson EC, Blachman-Demner D, Laimon L, Taiwo BO, Kuhns LM, John-Stewart GC, Kohler P, Subramanian S, Ayieko J, Gbaja-Biamila T, Oladele D, Obiezu-Umeh C, Chima KP, Jalil EM, Falcao J, Ezechi OC, Kapogiannis BG. AIDS (2021).

Mechanistic within-host models of the asexual Plasmodium falciparum infection: a review and analytical assessment. Camponovo F., Lee, T.E., Russell, J.R., Burgert L., Gerardin J., and Penny M.A. Malaria Journal 20:309 (2021).

"Beyond national indicators: adapting the Demographic and Health Surveys’ sampling strategies and questions to better inform subnational malaria intervention policy." Ozodiegwu I.D., Ambrose M., Battle K.E., Bever C.A., Diallo O., Galatas B., Runge M., and Gerardin J. Malaria Journal 20:122 (2021).

"Prevalence of cervical HPV infection, sexually transmitted infections and associated antimicrobial resistance in women attending cervical cancer screening in Mali." Jary A, Teguete I, Sidibé Y, Kodio A, Dolo O, Burrel S, Boutolleau D, Beauvais-Remigereau L, Sayon S, Kampo M, Traoré FT, Sylla M, Achenbach C, Murphy R, Berçot B, Bébéar C, Calvez V, Marcelin AG, Maiga AI. Int J Infect Dis (2021).

"The Interplay Between Policy and COVID-19 Outbreaks in South Asia: Longitudinal Trend Analysis of Surveillance Data." Welch SB, Kulasekere DA, Prasad PVV, Moss CB, Murphy RL, Achenbach CJ, Ison MG, Resnick D, Singh L, White J, Issa TZ, Culler K, Boctor MJ, Mason M, Oehmke JF, Faber JMM, Post LA. JMIR Public Health Surveill (2021).

"SARS-CoV-2 Surveillance in the Middle East and North Africa: Longitudinal Trend Analysis." Post L, Marogi E, Moss CB, Murphy RL, Ison MG, Achenbach CJ, Resnick D, Singh L, White J, Boctor MJ, Welch SB, Oehmke JF. J Med Internet Res (2021).