Publications

graph of gametocyte density

Sources of persistent malaria transmission in a setting with effective malaria control in eastern Uganda: a longitudinal, observational cohort study

Chiara Andolina, John C Rek, Jessica Briggs, Joseph Okoth, Alex Musiime, Jordache Ramjith, Noam Teyssier, Melissa Conrad, Joaniter INankabirwa, Kjerstin Lanke, Isabel Rodriguez-Barraquer, Lisette Meerstein-Kessel, Emmanuel Arinaitwe, Peter Olwoch, Philip J Rosenthal, Moses Kamya, Grant Dorsey, Bryan Greenhouse, Chris Drakeley, Sarah Staedke, Teun Bousema. Lancet Infectious Disease Nov 2021

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DOI: ​​​​​

10.1016/S1473-3099(21)00072-4

 

map of San Francisco showing infection and vaccination rates by zip code

Using sero-epidemiology to monitor disparities in vaccination and infection with SARS-CoV-2

Isobel Routledge, Saki Takahashi, Adrienne Epstein, Jill Hakim, Owen Janson, Keirstinne Turcios, Jo Vinden, John Tomas Risos, Margaret Rose Baniqued, Lori Pham, Clara Di Germanio, Michael Busch, Margot Kushel, Bryan Greenhouse, Isabel Rodríguez-Barraquer medrxiv Oct 2021

 

DOI: ​​​​​

doi.org/10.1101/2021.10.06.21264573

GitHub Scale-It

 

adjusted seroprevalence by survey maps of italy, US and Spain

SARS-CoV-2 serology across scales: a framework for unbiased seroprevalence estimation incorporating antibody kinetics and epidemic recency

Saki Takahashi, Michael J. Peluso, Jill Hakim, Keirstinne Turcios, Owen Janson, Isobel Routledge, Michael P. Busch, Rebecca Hoh, Viva Tai, J. Daniel Kelly, Jeffrey N. Martin, Steven G. Deeks, Timothy J. Henrich, Bryan Greenhouse, Isabel Rodríguez-Barraquer. MedXiv Sept 14, 2021

 

Spearman correlation of random intercepts derived from a mixed-effects model,

SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay

Michael Peluso, Saki Takahashi, Jill Hakim, J. Daniel Kelly, Leonel Torres, Nikita Iyer, Keirstinne Turcios, Owen Janson, Sadie Munter, Cassandra Thanh, Christopher Nixon, Rebecca Hoh, Viva Tai, Emily Fehrman, Yanel Hernandez, Matthew Spinelli, Monica Gandhi, Mary-Ann Palafox, Ana Vallari, Mary Rodgers, John Prostko, John Hackett Jr., Lan Trinh, Terri Wrin, Christos Petropoulos, Charles Chiu, Philip Norris, Clara DiGermanio, Mars Stone, Michael Busch, Susanna Elledge, Xin X. Zhou, James Wells, Albert Shu, Theodore Kurtz, John Pak, Wesley Wu, Peter Burbelo, Jeffrey Cohen, Rachel Rutishauser, Jeffrey Martin, Steven Deeks, Timothy Henrich, Isabel Rodriguez-Barraquer, Bryan Greenhouse. Science Advances July 30, 2021

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DOI: ​​​​​

10.1101/2021.03.03.21251639

GitHub liinc-Ab-dynamics

 

 

EPPIcenter logo

SARS-CoV-2 PCR and antibody testing for an entire rural community: methods and feasibility of high-throughput testing procedures

Ayesha Appa, Gabriel Chamie, Aenor Sawyer, Kimberly Baltzell, Kathryn Dippel, Salu Ribeiro, Elias Duarte, Joanna Vinden, Cliahub Consortium, Jonathan Kramer-Feldman, Shahryar Rahdari, Doug MacIntosh, Katherine Nicholson, Jonathan Im, Diane Havlir, Bryan Greenhouse: Archives of Public Health volume 2021 July 7 Article 125 

 

Map of the study area

Effectiveness and safety of reactive focal mass drug administration (rfMDA) using dihydroartemisinin-piperaquine to reduce malaria transmission in very low-endemic setting of Eswatini: a pragmatic cluster randomised controlled trial

Sibonakaliso Vilakati, Nontokozo Mngadi, Jade Benjamin-Chung, Nomcebo Dlamini, Mi-Suk Kang Dufour, Brooke Whittemore, Khayelihle Bhangu, Lisa M. Prach, Kimberly Baltzell, Nomcebo Nhlabathi, Calisile Malambe, Bongani Dlamini, Danica Helb, Bryan Greenhouse, Gugu Maphalala, Deepa Pindolia, Muhindo Kalungero, Getahun Tesfa, Roly Gosling, Nyasatu Ntshalintshali, Simon Kunene, Michelle Hsiang.BMJ Global Health 2021;6:e005021. June 30, 2021

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DOI: ​​​​​

10.1136/bmjgh-2021-005021

 

maps showing seroprevelence

Citywide serosurveillance of the initial SARS-CoV-2 outbreak in San Francisco

Isobel Routledge, Adrienne Epstein, Saki Takahashi, Jill Hakim, Own Janson, Elias Duarte, Keirstinne Turcios, Joanna Vinden, Kirk Sujishi, Jesus Rangel, Marcelina Coh, Lee Besana, Wai-Kit Ho, Ching-Ying Oon, Chui Mei Ong, Cassandra Yun, Kara Lynch, Alan Wu, Wesley Wu, William Karlon, Edward Thornborrow, Michael Peluso, Timothy Henrich, John Pak, Jessica Briggs, Bryan Greenhouse, Isabel Rodriguez-Barraquer. Nature Communications 12, Article number: 3566 (2021) June 11, 2021

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    ​​​​​DOI: ​​​​​

    10.1038/s41467-021-23651-6

    GitHub ScaleIT       FlexFit

     

    Predicted number of SARS-CoV-2 infections

    Comparison of infection control strategies to reduce COVID-19 outbreaks in homeless shelters in the United States: a simulation study

    Lloyd A.C. Chapman, Margot Kushel, Sarah N. Cox, Ashley Scarborough, Caroline Cawley, Trang Nguyen, Isabel Rodriguez-Barraquer, Bryan Greenhouse, Elizabeth Imbert, Nathan C. Lo. BMC Med. 2021 May 7;19(1):116.

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    DOI: ​​​​​

    10.1186/s12916-021-01965-y

     

    graphic illustration of sample pipeline

    multiSero: open multiplex-ELISA platform for analyzing antibody responses to SARS-CoV-2 infection

    Janie Byrum, Eric Waltari, Owen Janson, Syuan-Ming Guo, Jenny Folkesson, Bryant Chhun, Joanna Vinden, Ivan Ivanov, Marcus Forst, Hongquan Li, Adam Larson, Wesley Wu, Cristina Tato, Krista McCutcheon, Michael Peluso, Timothy Henrich, Steven Deeks, Manu Prakash, Bryan Greenhouse, John Pak, Shalin Mehta MedRXiv May 11 2021
    doi: https://doi.org/10.1101/2021.05.07.21249238

    PDF (19M)

    DOI: ​​​​​

    10.1101/2021.05.07.21249238

     

    Schematic of the solution-based serology assay.

    Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection

    Susanna K. Elledge, Xin X. Zhou, James R. Byrnes, Alexander J. Martinko, Irene Lui, Katarina Pance, Shion A. Lim, Jeff E. Glasgow, Anum A. Glasgow, Keirstinne Turcios, Nikita S. Iyer, Leonel Torres, Michael J. Peluso, Timothy J. Henrich, Taia T. Wang, Cristina M. Tato, Kevin K. Leung, Bryan Greenhouse & James A. Wells. Nature Biotech March 25, 2021

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    DOI: ​​​​​

    10.1101/2020.08.17.20176925

     

    Ratio of false positive to true positive test results for test-and-travel strategies

    Routine asymptomatic testing strategies for airline travel during the COVID-19 pandemic: a simulation analysis

    Mathew Kiang, Elizabeth Chin, Benjamin Huynh, Lloyd Chapman, Isabel Rodriguez-Barraquer, Bryan& Greenhouse, George Rutherford, Kirsten Bibbins-Domingo, Diane Havlir, Sanjay Basu, Nathan Lo. Lancet, March 22, 2021

     

    Cumulative incidence of confirmed COVID-19 cases (left column) and deaths (right column) in California up to December 30, 2020,

    Comparison of COVID-19 vaccine prioritization strategies in the United States

    Lloyd A C Chapman, Poojan Shukla, Isabel Rodríguez-Barraquer, Priya B. Shete, Tomás M. León, Kirsten Bibbins-Domingo, George W Rutherford, Robert Schechter, Nathan C Lo preprint 2021 March 8.

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    DOI: ​​​​​

    10.1101/2021.03.04.21251264

     

    eppi logo

    Validation of Pooled SARS-CoV-2 Testing in the Outbreak Setting

    Jessica Briggs. Am J Trop Med Hyg. 2021 March 8 ;99(5):1120-1127.

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    DOI: ​​​​​

    10.4269/ajtmh.21-0202

     

    Maximum a posteriori transmission networks in Eswatini

    Inferring person-to-person networks of Plasmodium falciparum transmission: is routine surveillance data up to the task?

    John Huber, Michelle Hsiang, Nomcebo Dlamini, Maxwell Murphy, Sibonakaliso Vilakati, Nomcebo Nhlabathi, Anita Lerch, Rasmus Nielsen, Nyasatu Ntshalintshali, Bryan Greenhouse, T. Alex Perkins. preprint Feb 18, 2021

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    DOI: ​​​​​

    10.1101/2020.08.24.20180844

     

    Comparisons of genome coverage and dropout rate

    Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples

    Noam Teyssier, Anna Chen, Elias Duarte, Rene Sit, Bryan Greenhouse & Sofonias Tessema. Malaria Journal 2021 Feb 26; 20(1):116.

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    DOI: ​​​​​

    10.1186/s12936-021-03630-4

     

    catterplot of DAPC in genetic clusters of P. falciparum

    Parasite genetic diversity reflects continued residual malaria transmission in Vhembe District, a hotspot in the Limpopo Province of South Africa

    Hazel Gwarinda, Sofonias Tessema, Jaishree Raman, Bryan Greenhouse, Lyn-Marié Birkholtz. Malar J. 2021 Feb 16;20(1):96

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    ​​​​​DOI: ​​​​​

    10.1186/s12936-021-03635-z

     

     

     individual malaria status over 160 study sampling time points

    Impact of a Rapid Decline in Malaria Transmission on Antimalarial IgG Subclasses and Avidity

    Isaac Ssewanyana, John Rek, Isabel Rodriguez-Barraquer, Lindsey Wu, Emmanuel Arinaitwe, Joaniter Nankabirwa, James Beeson, Harriet Mayanja-Kizza, Philip J. Rosenthal, Grant Dorsey, Moses Kamya, Chris Drakeley, Bryan Greenhouse, Kevin Tetteh. Frontiers in Immunology. 2021 Jan 27;11:576663

     

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    ​​​​​DOI: ​​​​​

    10.3389/fimmu.2020.576663

     

    map of malaria reference centers

    Relationships between test positivity rate, total laboratory confirmed cases of malaria, and malaria incidence in high burden settings of Uganda: an ecological analysis

    Jaffer Okiring, Adrienne Epstein, Jane Namuganga, Victor Kamya, Asadu Sserwanga, James Kapisi, Chris Ebong, Simon P. Kigozi, Arthur Mpimbaza, Humphrey Wanzira, Jessica Briggs, Moses Kamya, Joaniter, Nankabirwa & Grant Dorsey. Malar J. 2021 Jan 13;20(1):42

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    ​​​​​DOI: ​​​​​

    10.1186/s12936-021-03584-7​​​​​​

     

    Bolinas testing site

    Universal PCR and antibody testing demonstrate little to no transmission of SARS-CoV-2 in a rural community

    Ayesha Appa, Saki Takahashi, Isabel Rodriguez-Barraquer, Gabriel Chamie, Aenor Sawyer, Elias Duarte, Jill Hakim, Keirstinne Turcios, Joanna Vinden, Owen Janson, Aashish Manglik, Michael J Peluso, Steven Deeks, Timothy J Henrich, Leonel Torres, Mary Rodgers, John Hackett, Charles Chiu, Diane Havlir, Bryan Greenhouse: Open Forum Infectious Diseases, Volume 8, Issue 1, January 2021, ofaa531,

     

    Adjusted IRR and predicted case counts from multilevel negative binomial model 153

    The impact of stopping and starting indoor residual spraying on malaria burden in 14 districts of Uganda

    Jane Frances Namuganga, Adrienne Epstein, Joaniter Nankabirwa, Arthur Mpimbaza, Moses Kiggundu, Asadu Sserwanga, James Kapisi, Emmanuel Arinaitwe, Samuel Gonahasa, Jimmy Opigo, Sarah Staedke, Josephat Shililu, Michael Okia, Damian Amanya Rutazaana, Catherine Maiteki-Ssebuguzi, Kassahun Belay, Moses Kamya, Grant Dorsey, Isabel Rodriguez Barraquer; Nat Commun 12, 2635 (2021)

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    DOI: ​​​​​

    10.21203/rs.3.rs-126095/v1

     

    travel time to the health facility and probability of attending

    Estimating malaria incidence from routine health facility-based surveillance data in Uganda

    Adrienne Epstein, Jane Frances Namuganga, Emmanuel Victor Kamya, Joaniter I. Nankabirwa, Samir Bhatt, Isabel Rodriguez-Barraquer, Sarah G. Staedke, Moses R. Kamya, Grant Dorsey & Bryan Greenhouse . Malaria Journal 2020 Dec 2; volume 19: 445 

     

    Genetic complexity and diversity of infections

    Spatial and genetic clustering of Plasmodium falciparum and Plasmodium vivax infections in a low-transmission area of Ethiopia

    Sofonias Tessema, Mulualem Belachew, Cristian Koepfli, Kjerstin Lanke, Tiffany Huwe, Wakweya Chali, Girma Shumie, Elias Mekuria, Chris Drakeley, Endalamaw Gadisa, Bryan Greenhouse, Teun Bousema, Fitsum Tadesse. Sci Rep. 2020 Nov 17;10(1):19975

     

    Timeline of  influenza, varicella, and mumps cases were identified among migrants in 17 centers

    Influenza, Varicella, and Mumps Outbreaks in US Migrant Detention Centers

    Nathan Lo, Sindiso Nyathi, Lloyd Chapman, Isabel Rodriguez-Barraquer, Margot Kushel, Kirsten Bibbins-Domingo, Joseph Lewnard. JAMA. 2020 Oct 29; e2020539.

     

    estimated duration of infection

    Sex-based differences in clearance of chronic Plasmodium falciparum infection

    Jessica Briggs, Noam Teyssier, Joaniter Nankabirwa, John Rek, Prasanna Jagannathan, Emmanuel Arinaitwe, Teun Bousema, Chris Drakeley, Margaret Murray, Emily Crawford, Nicholas Hathaway, Sarah Staedke, David Smith, Phillip J Rosenthal, Moses Kamya, Grant Dorsey, Isabel Rodriguez-Barraquer, Bryan Greenhouse. Elife. 2020 Oct 27;9:e59872.

     

    Projected impact of routine PCR testing frequency on the mean effective reproduction number under different testing scenarios

    Frequency of Routine Testing for Coronavirus Disease
    2019 (COVID-19) in High-risk Healthcare Environments
    to Reduce Outbreaks

    Elizabeth T Chin, Benjamin Huynh, Lloyd Chapman, Matthew Murrill, Sanjay Basu, Nathan Lo. Clinical Infectious Diseases, ciaa1383. 2020 Oct 26

     

     Location of enrolled households in Piedecuesta, Colombia

    Heterogeneity of dengue transmission in an endemic area of Colombia

    María Isabel Estupiñán Cárdenas, Víctor Mauricio Herrera, María Consuelo Miranda Montoya, Anyela Lozano Parra, Zuly Milena Zaraza Moncayo, Janeth Patricia Flórez García, Isabel Rodríguez Barraquer, Luis Ángel Villar Centeno PLoS Negl Trop Dis. 2020 Sep 14; 14(9):e0008122

     

     

    Results of the model fit, graph

    Evaluating the performance of malaria genetics for inferring changes in transmission intensity using transmission modelling

    Oliver Watson, Lucy Okell, Joel Hellewell, Hannah Slater, H Juliette Unwin, Irene Omedo, Philip Bejon, Robert Snow, Abdisalan Noor, Kirk Rockett, Christina Hubbart, Joaniter Nankabirwa, Bryan Greenhouse, Hsiao-Han Chang, Azra Ghani, Robert Verity: Mol Biol Evol 2020 Sep 8; msaa225

     

    Time Since In infection graphs

    Are SARS-CoV-2 seroprevalence estimates biased?

    Saki Takahashi, Bryan Greenhouse, Isabel Rodríguez-Barraquer:  J Infect Dis. 2020 Aug 28

     

    Coverage of multiplexing assay on selected microhaplotypes

    Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome

    Sofonias Tessema, Nicholas Hathaway, Noam Teyssier, Maxwell Murphy, Anna Chen, Ozkan Aydemirz, Elias Duarte, Wilson Simone, James Colborn, Francisco Saute, Emily Crawford, Pedro Aide, Jeffrey Bailey, Bryan Greenhouse: J Infect Dis. 2020 Aug 25;jiaa527

     

    Origins of imported malaria

    Confirmation of the absence of local transmission and geographic assignment of imported falciparum malaria cases to China using microsatellite panel
    ​​​

    Yaobao Liu, Sofonias K. Tessema, Maxwell Murphy, Sui Xu, Alanna Schwartz, Weiming Wang, Yuanyuan Cao, Feng Lu, Jianxia Tang, Yaping Gu, Guoding Zhu, Huayun Zhou, Qi Gao, Rui Huang, Jun Cao & Bryan Greenhouse: Malar J. 2020 Jul 13;19(1):244.

     

    age-specific burden of malaria

    Rapid shifts in the age-specific burden of malaria following successful control interventions in four regions of Uganda

    Simon Kigozi, Ruth Kigozi, Adrienne Epstein, Arthur Mpimbaza, Asadu Sserwanga, Adoke Yeka, Joaniter Nankabirwa, Katherine Halliday, Rachel Pullan, Damian Rutazaana, Catherine Sebuguzi, Jimmy Opigo, Moses Kamya, Sarah Staedke, Grant Dorsey, Bryan Greenhouse & Isabel Rodriguez-Barraquer. Malar J. 2020 Mar 30;19(1):128

     

    Geographic variation in the predicted impact of a transmission-reduction intervention.

    Mapping global variation in dengue transmission intensity

    Lorenzo Cattarino, Isabel Rodriguez-Barraquer, Natsuko Imai, Derek Cummings, Neil Ferguson.Sci Transl Med. 2020 Jan 29;12(528):eaax4144

     

    Flow diagram of participants included in the analyses

    Associations between red blood cell variants and malaria among children and adults from three areas of Uganda: a prospective cohort study

    Elijah Kakande, Bryan Greenhouse, Francis Bajunirwe, Chris Drakeley, Joaniter I. Nankabirwa, Andrew Walakira, Samuel L. Nsobya, Agaba Katureebe, John Rek, Emmanuel Arinaitwe, Philip J. Rosenthal, Moses R. Kamya, Grant Dorsey & Isabel Rodriguez-Barraquer. Malar J
    . 2020 Jan 15;19(1):21.

     

    Weekly overall incidence rate

    The Impact of Multiple Rounds of Indoor Residual Spraying on Malaria Incidence and Hemoglobin Levels in a High-Transmission Setting

    Kate Zinszer, Katia Charland, Sarah Vahey, Deepa Jahagirdar, John Rek, Emmanuel Arinaitwe, Joaniter Nankabirwa, Kathryn Morrison, Margaux Sadoine, Marc-Antoine Tutt-Guérette, Sarah Staedke, Moses R Kamya, Bryan Greenhouse, Isabel Rodriguez-Barraquer, Grant Dorsey J Infect Dis. 2020 Jan 2;221(2):304-312

     

    Graphical abstract

    Heterogeneous local dynamics revealed by classification analysis of spatially disaggregated time series data

    T Alex Perkins, Isabel Rodriguez-Barraquer, Carrie Manore, Amir Siraj, Guido España, Christopher Barker, Michael Johansson, Robert Reiner Jr.Epidemics. 2019 Dec;29:100357.

     

    Cases in Namibia

    Active case-finding for malaria: A three-year national evaluation of optimal approaches to detect infections and hotspots through reactive case detection in the low transmission setting of Eswatini

    Michelle Hsiang, Nyasatu Ntshalintshali, Mi-Suk Kang Dufour, Nomcebo Dlamini, Nomcebo Nhlabathi, Sibonakaliso Vilakati, Calsile Malambe, Zulisile Zulu, Gugu Maphalala, Joseph Novotny, Maxwell Murphy, Alanna Schwartz, Hugh Sturrock, Roly Gosling, Grant Dorsey, Simon Kunene, Bryan Greenhouse.Clin Infect Dis. 2020 Mar 17;70(7):1316-1325.

     

    2

    High Genetic Diversity of Plasmodium falciparum in the Low-Transmission Setting of the Kingdom of Eswatini

    Roh ME, Tessema SK, Murphy M, Nhlabathi N, Mkhonta N, Vilakati S, Ntshalintshali N, Saini M, Maphalala G, Chen A, Wilheim J, Prach L, Gosling R, Kunene S, S Hsiang M, Greenhouse B. J Infect Dis. 2019 Sep 13;220(8):1346-1354

     

    Proportion of women with placental malaria

    Impact of Microscopic and Submicroscopic Parasitemia During Pregnancy on Placental Malaria in a High-Transmission Setting in Uganda

    Jessica Briggs, John Ategeka, Richard Kajubi, Teddy Ochieng, Abel Kakuru, Cephus Ssemanda, Razack Wasswa, Prasanna Jagannathan, Bryan Greenhouse, Isabel Rodriguez-Barraquer, Moses Kamya, Grant Dorsey. J Infect Dis. 2019 Jul 2;220(3):457-466.

     

    Challenges and key priorities of genomic epidemiology in sub-Saharan Africa

    Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa

    Tessema SK, Raman J, Duffy CW, Ishengoma DS, Amambua-Ngwa A, Greenhouse B. Malar J. 2019 Sep 3;18(1):268

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    DOI:

    10.1186/s12936-019-2880-1
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    flash method cartoon

    FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences

    Jenai Quan, Charles Langelier, Alison Kuchta, Joshua Batson, Noam Teyssier, Amy Lyden, Saharai Caldera, Aaron McGeever, Boris Dimitrov, Ryan King, Jordan Wilheim, Maxwell Murphy, Lara Pesce Ares, Katherine Travisano, Rene Sit, Roberto Amato, Davis R Mumbengegwi, Jennifer L Smith, Adam Bennett, Roly Gosling, Peter Mourani, Carolyn Calfee, Norma Neff, Eric Chow, Peter Kim, Bryan Greenhouse, Joseph DeRisi, Emily Crawford. Nucleic Acids Res. 2019 Aug 22;47(14):e83.

     

    Priority applications of exposure markers

    Priority use cases for antibody-detecting assays of recent malaria exposure as tools to achieve and sustain malaria elimination

    Greenhouse B, Daily J, Guinovart C, Goncalves B, Beeson J, Bell D, Chang MA, ;Cohen JM, Ding X, Domingo G, Eisele TP, Lammie PJ, Mayor A, Merienne N, Monteiro W, Painter J, Rodriguez I, White M, Drakeley C, Mueller I; Malaria Serology Convening. Gates Open Res. 2019 Feb 12;3:131. 

     

    estimating FOI

    Opportunities for improved surveillance and control of dengue from age-specific case data

    Rodriguez-Barraquer I, Salje H, Cummings DA. Elife. 2019 May 23;8. 

     

    Local genetic connectivity in northeastern Namibia.

    Using parasite genetic and human mobility data to infer local and cross-border malaria connectivity in Southern Africa

    Tessema S, Wesolowski A, Chen A, Murphy M, Wilheim J, Mupiri AR, Ruktanonchai NW, Alegana VA, Tatem AJ, Tambo M, Didier B, Cohen JM, Bennett A, Sturrock HJ, Gosling R, Hsiang MS, Smith DL, Mumbengegwi DR, Smith JL, Greenhouse B. Elife. 2019 Apr 2;8.

     

    Dengue Pre vaccination supplement figure

    Dengue pre-vaccination screening and positive predictive values

    Rodríguez-Barraquer I, Salje H, Cummings DA. Lancet Infect Dis. 2019 Feb;19(2):132-134

     

    ZIKV infection as a function of age and prior DENV exposure

    Impact of preexisting dengue immunity on Zika virus emergence in a dengue endemic region

    Isabel Rodriguez-Barraquer, Federico Costa, Eduardo Nascimento, Nivison Nery Jr, Priscila Castanha, Gielson Almeida Sacramento, Jaqueline Cruz, Mayara Carvalho, Daiana De Olivera, José Hagan, Haritha Adhikarla, Elsio Wunder Jr, Danilo F. Coêlho, Sasha Azar, Shannan Rossi, Nikos Vasilakis, Scott Weaver, Guilherme Ribeiro, Angel Balmaseda, Eva Harris, Maurício Nogueira, Mitermayer Reis, Ernesto Marques, Derek Cummings, Albert I. Ko. Science. 2019 Feb 8;363(6427):607-610.

     

    Map of study area overlaid with observed vs expected counts

    Genetic Evidence of Focal Plasmodium falciparum Transmission in a Pre-elimination Setting in Southern Province, Zambia

    Pringle JC, Tessema S, Wesolowski A, Chen A, Murphy M, Carpi G, Shields TM, Hamapumbu H, Searle KM, Kobayashi T, Katowa B, Musonda M, Stevenson JC, Thuma PE, Greenhouse B, Moss WJ, Norris DE. J Infect Dis. 2019 Apr 8;219(8):1254-1263.

     

    temporal changes in malaria

    Persistent Parasitemia Despite Dramatic Reduction in Malaria Incidence After 3 Rounds of Indoor Residual Spraying in Tororo, Uganda

    Nankabirwa JI, Briggs J, Rek J, Arinaitwe E, Nayebare P, Katrak S, Staedke SG, Rosenthal PJ, Rodriguez-Barraquer I, Kamya MR, Dorsey G, Greenhouse B. J Infect Dis. 2019 Mar 15;219(7):1104-1111.

     

    malaria transmission

    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.

     

    designing combined antibodies to measure exposure recency assays (CAMERAs)

    Taking Sharper Pictures of Malaria with CAMERAs: Combined Antibodies to Measure Exposure Recency Assays

    Greenhouse B, Smith DL, Rodríguez-Barraquer I, Mueller I, Drakeley CJ. Am J Trop Med Hyg. 2018 Nov;99(5):1120-1127.

     

    Anti parasite

    Quantification of anti-parasite and anti-disease immunity to malaria as a function of age and exposure

    Isabel Rodriguez-Barraquer, Emmanuel Arinaitwe, Prasanna Jagannathan, Moses R Kamya, Phillip J Rosenthal, John Rek, Grant Dorsey, Joaniter Nankabirwa, Sarah G Staedke, Maxwell Kilama, Chris Drakeley, Isaac Ssewanyana, David L Smith, Bryan Greenhouse. Elife. 2018 Jul 25

     

    Proportion of study population with microscopic and submicroscopic parasitaemia

    Clinical consequences of submicroscopic malaria parasitaemia in Uganda

    Shereen Katrak, Patience Nayebare, John Rek, Emmanuel Arinaitwe, Joaniter I. Nankabirwa, Moses Kamya, Grant Dorsey, Philip J. Rosenthal & Bryan Greenhouse.  Malar J. 2018 Feb 5;17(1):67.

     

    Estimates of COI in Nagongera, Walukuba, and Kihihi

    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.

     

    Vaccine Groups

    The Long-Term Safety, Public Health Impact, and Cost-Effectiveness of Routine Vaccination with a Recombinant, Live-Attenuated Dengue Vaccine (Dengyaxia): A Model Comparison Study

    Stefan Flasche, Mark Jit, Isabel Rodríguez-Barraquer, Laurent Coudeville, Mario Recker, Katia Koelle, George Milne, Thomas Hladish, T. Alex Perkins, Derek Cummings, Ilaria Dorigatti, Daniel Laydon, Guido España, Joel Kelso, Ira Longini, Jose Lourenco, Carl Pearson, Robert Reiner, Luis Mier-y-Terán-Romero, Kirsten Vannice, Neil Ferguson. PLoS Med. 2016 Nov 29;13(11):e1002181.

     

    Vaccine Science

    Benefits and risks of the Sanofi-Pasteur dengue vaccine: Modeling optimal deployment

    Neil M. Ferguson, Isabel Rodríguez-Barraquer, Ilaria Dorigatti, Luis Mier-y-Teran-Romero, Daniel Laydon, Derek Cummings. Science. 2016 Sep 2;353(6303):1033-1036.

     

    Elements of the falciparum malaria transmission cycle

    Quantitative, model-based estimates of variability in the generation and serial intervals of Plasmodium falciparum malaria

    Huber JH, Johnston GL, Greenhouse B, Smith DL, Perkins TA. Malar J. 2016 Sep 22;15(1):490.

     

    TCC Exposure

    Quantifying Heterogeneous Malaria Exposure and Clinical Protection in a Cohort of Ugandan Children

    Isabel Rodriguez-Barraquer, Emmanuel Arinaitwe, Prasanna Jagannathan, Michelle J. Boyle, Jordan Tappero, Mary Muhindo, Moses R. Kamya, Grant Dorsey, Chris Drakeley, Isaac Ssewanyana, David L. Smith, Bryan Greenhouse. J Infect Dis. 2016 Oct 1;214(7):1072-80.

     

    Zika Global

    Assessing the global threat from Zika virus

    Lessler J, Chaisson LH, Kucirka LM, Bi Q, Grantz K, Salje H, Carcelen AC, Ott CT, Sheffield JS, Ferguson NM, Cummings DA, Metcalf CJ, Rodriguez-Barraquer I. Science. 2016 Aug 12;353(6300):aaf8160.

     

    B cell kinetics following acute malaria.

    B cell sub-types following acute malaria and associations with clinical immunity

    Richard T. Sullivan, Isaac Ssewanyana, Samuel Wamala, Felistas Nankya, Prasanna Jagannathan, Jordan W. Tappero, Harriet Mayanja-Kizza, Mary K. Muhindo, Emmanuel Arinaitwe, Moses Kamya, Grant Dorsey, Margaret E. Feeney, Eleanor M. Riley, Chris J. Drakeley & Bryan Greenhouse. Malar J. 2016 Mar 3;15:139.

     

    Geographic heterogeneity in Pf exposure

    Novel serologic biomarkers provide accurate estimates of recent Plasmodium falciparum exposure for individuals and communities

    Danica A. Helb, Kevin K. A. Tetteh, Philip L. Felgner, Jeff Skinner, Alan Hubbard, Emmanuel Arinaitwe, Harriet Mayanja-Kizza, Isaac Ssewanyana, Moses R. Kamya, James G. Beeson, Jordan Tappero, David L. Smith, Peter D. Crompton, Philip J. Rosenthal, Grant Dorsey, Christopher J. Drakeley, and Bryan Greenhouse. PNAS August 11, 2015 112 (32) E4438-E4447.

     

    Chennai

    The Hidden Burden of Dengue and Chikungunya in Chennai, India

    Isabel Rodríguez-Barraquer ,Sunil Solomon, Periaswamy Kuganantham, Aylur Kailasom Srikrishnan, Canjeevaram Vasudevan, Syed Iqbal, Pachamuthu Balakrishnan, Suniti Solomon, Shruti Mehta, Derek Cummings. PLoS Negl Trop Dis. 2015 Jul 16;9(7):e0003906.

     

    Whole-transcriptome analysis of atypical and classical MBCs from parasitemic, but asymptomatic, subjects.

    FCRL5 Delineates Functionally Impaired memory B Cells Associated with Plasmodium falciparum Exposure

    Richard Sullivan ,Charles Kim, Mary Fontana, Margaret Feeney, Prasanna Jagannathan, Michelle Boyle, Chris Drakeley, Isaac Ssewanyana, Felistas Nankya, Harriet Mayanja-Kizza, Grant Dorsey, Bryan Greenhouse . PLoS Pathog. 2015 May 19;11(5):e1004894.

     

    Vaccine Perils

    Potential opportunities and perils of imperfect dengue vaccines

    Rodriguez-Barraquer I, Mier-y-Teran-Romero L, Schwartz IB, Burke DS, Cummings DA. Vaccine. 2014 Jan 16;32(4):514-20.

     

    Rayong

    Revisiting Rayong: shifting seroprofiles of dengue in Thailand and their implications for transmission and control

    Isabel Rodríguez-Barraquer, Rome Buathong, Sopon Iamsirithaworn, Ananda Nisalak, Justin Lessler, Richard G. Jarman, Robert V. Gibbons, Derek A.T. Cummings. Am J Epidemiol. 2014 Feb 1;179(3):353-60

     

    Vaccine Challenges

    Challenges in the interpretation of dengue vaccine trial results

    Isabel Rodriguez-Barraquer, Luis Mier-y-Teran-Romero, Donald Burke, Derek Cummings. PLoS Negl Trop Dis. 2013 Aug 29;7(8):e2126.

     

    Age specific seroprevalence of dengue in Recife, 2006.

    From re-emergence to hyperendemicity: the natural history of the dengue epidemic in Brazil

    Isabel Rodriguez-Barraquer, Marli Cordeiro,Cynthia Braga, Wayner de Souza, Ernesto Marques, Derek Cummings. PLoS Negl Trop Dis. 2011 Jan 4;5(1):e935.

     

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