Selected publications
publications
2022
Carpi G, Gorenstein L, Harkins TT, Samadi M, Vats P. A GPU-accelerated compute framework for pathogen genomic variant identification to aid genomic epidemiology of infectious disease: a malaria case study. Briefings in Bioinformatics, 2022; bbac314, https://doi.org/10.1093/bib/bbac314
Ciubotari II, Dorman J, Perry NM, Gorenstein L, Kattoor JJ, Fola AA, Zine A, Hendrix GK, Wilkes RP, Kitchen A, Carpi G, Genomic Surveillance of SARS-CoV-2 in a University Community: Insights Into Tracking Variants, Transmission, and Spread of Gamma (P.1) Variant. Open Forum Infectious Diseases, Volume 9, Issue 7, July 2022, ofac268. https://doi.org/10.1093/ofid/ofac268.
Preprint on medRxiv: doi: https://doi.org/10.1101/2022.02.25.22271521.
2021
Molina-Cruz A, Raytselis N, Withers R, Dwivedi A, Crompton PD, Traore B, Carpi G, Silva JC, Barillas-Mury C. A genotyping assay to determine geographic origin and transmission potential of Plasmodium falciparum malaria cases. Communications Biology. 2021, 4(1):1145. doi: 10.1038/s42003-021-02667-0.
Mwenda MC*, Fola AA*, Ciubotariu II*, Mulube C, Mambwe B, Kasaro R, Hawela MB, Hamainza B, Miller JM, Carpi G, Bridges DJ. Performance evaluation of RDT, light microscopy, and PET-PCR for detecting Plasmodium falciparum malaria infections in the 2018 Zambia National Malaria Indicator Survey. Malaria Journal 2021, 20(1):386. doi: 10.1186/s12936-021-03917-6.
Ramirez E, Wilkes RP, Carpi G, Dorman J, Bowen C, Smith S. SARS-CoV-2 Breakthrough Infections in Fully Vaccinated Individuals in a University Setting. Journal of Infectious Diseases and Therapy 2021, 9, 4.
Preprint on medRxiv: doi: https://doi.org/10.1101/2021.06.21.21258990.
Hoffman JE, Ciubotariu II, Simubali L, Mudenda T, Moss WJ, Carpi G, Norris DE, Stevenson JC, on behalf of Southern and Central Africa International Centers of Excellence for Malaria Research. Phylogenetic Complexity of Morphologically Identified Anopheles squamosus in Southern Zambia. Insects 2021, 12, 146. https://doi.org/10.3390/insects12020146.
2020
Ciubotariu II, Jones CM, Kobayashi T, Bobanga T, Muleba M, Pringle JC, Stevenson JC, Carpi G*, Norris DE* (2020). Genetic diversity of Anopheles coustani in malaria transmission foci in southern and central Africa. Journal of Medical Entomology. 2020, 1-11, https://doi.org/10.1093/jme/tjaa132.
Preprint on bioRxiv: doi: https://doi.org/10.1101/2020.04.04.020537.
Drummond C, Gebhardt ME, Sáenz Robles MT, Carpi G, Hoyer I, Pastusiak A, Reddy MR, Norris DE, Pipas JM, Jackson EK (2020). Stability and detection of nucleic acid from viruses and hosts in controlled mosquito blood feeds. PLoS One. 15(6): e0231061. https://doi.org/10.1371/journal.pone.0231061.
Preprint on bioRxiv: doi: https://doi.org/10.1101/2020.03.17.995126.
2019
Pringle JC, Wesolowski A, Berube S, Kobayashi T, Gebhardt ME, Mulenga M, Chaponda M, Bobanga T, Juliano JJ, Meshnick S, Moss WJ, Carpi G, and Norris DE. (2019). High Plasmodium falciparum genetic diversity and temporal stability despite control efforts in high transmission settings along the international border between Zambia and the Democratic Republic of the Congo. Malaria Journal. 18, 400. doi:10.1186/s12936-019-3023-4.
Bloch EM, Mrango Z, Kasubi M, Weaver J, Mihailovic A, Munoz B, Weimer A, Levin A, Tonnetti L, Linnen JM, Brès V, Norris DE, Carpi G, and West SK. (2019). The Babesia observational antibody (BAOBAB) study: A cross-sectional evaluation of Babesia in two communities in Kilosa district, Tanzania. PLOS Neglected Tropical Diseases. 13: e0007632. doi 10.1371/journal.pntd.0007632.
2018
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, and Norris DE. (2018). Genetic Evidence of Focal Plasmodium falciparum Transmission in a Pre-elimination Setting in Southern Province, Zambia. The Journal of Infectious Diseases. 219:1254-1263. doi.org/10.1093/infdis/jiy64.
Jones CM, Lee Y, Kitchen A, Collier T, Pringle JC, Muleba M, Irish S, Stevenson JC, Coetzee M, Cornel AJ, Norris DE, and Carpi G. (2018). Complete Anopheles funestus mitogenomes reveal an ancient history of mitochondrial lineages and their distribution in southern and central Africa. Scientific Reports. 13;8(1):9054. doi: 10.1038/s41598-018-27092-y.
News article: Sequencing a malaria mosquito's motherline. EurekAlert, AAAS, July 30, 2018.
Popular press: ScienceDaily, Newswise.
Pringle JC, Carpi G, Almagro-Garcia J, Zhu SJ, Kobayashi T, Mulenga M, Bobanga T, Chaponda M, Moss WJ, and Norris DE. (2018). RTS,S/AS01 malaria vaccine mismatch observed among Plasmodium falciparum isolates from southern and central Africa and globally. Scientific Reports. 8(1):6622. doi: 10.1038/s41598-018-24585-8.
Tokarz R, Smeroff S, Tagliafierro T, Jain K, Williams SH, Cucura DM, Rochlin I, Monzon J, Carpi G, Tufts D, Diuk-Wasser M, Brinkerhoff J, and Lipkin WI. (2018). Identification of novel viruses in Amblyomma americanum, Dermacentor variabilis and Ixodes scapularis ticks. mSphere. 3(2), e00614-17. doi:0.1128/mSphere.00614-17.
2017
Walter KS, Carpi G, Caccone A, and Diuk-Wasser MA. (2017). Genomic insights into the ancient spread of Lyme disease across North America. Nature Ecology & Evolution. 1(10):1569-1576. doi:10.1038/s41559-017-0282-8.
Insight article: The ancient history of Lyme disease. Nature Ecology & Evolution, Behind the paper.
News article: Lyme Disease History, Future Explored With North American Borrelia Genome Set. GenomeWeb article.
Searle KM, Katowa B, Kobayashi T, Siame MNS, Mharakurwa S, Carpi G, Norris DE, Stevenson JC, Thuma PE, Moss WJ; Southern Africa International Centers of Excellence for Malaria Research. (2017). Distinct parasite populations infect individuals identified through passive and active case detection in a region of declining malaria transmission in southern Zambia. Malaria Journal. 16(1):154. doi: 10.1186/s12936-017-1810-3.
2016
Carpi G, Walter KS, Mamoun CB, Krause PJ, Kitchen A, Lepore TJ, Dwivedi A, Cornillot E, Caccone A, and Diuk-Wasser MA. (2016). Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States. BMC Genomics. 7;17(1):888.
Walter KS, Carpi G, Evans BR, Caccone A, and Diuk-Wasser MA. (2016). Vectors as Epidemiological Sentinels: Patterns of Within-Tick Borrelia burgdorferi Diversity. PLoS Pathogens. 12(7):e1005759. doi: 10.1371/journal.ppat.1005759.
Carpi G, Kitchen A, Kim HL, Ratan A, Drautz-Moses DI, McGraw JJ, Kazimirova M, Rizzoli A, and Schuster SC. (2016). Mitogenomes reveal diversity of the European Lyme borreliosis vector Ixodes ricinus in Italy. Molecular Phylogenetics and Evolution. 101:194-202. doi: 10.1016/j.ympev.2016.05.009.
2015
Carpi G*, Walter SK*, Bent SJ, Hoen AG, Diuk-Wasser M, and Caccone A. (2015). Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi. BMC Genomics. 16:434 DOI:10.1186/s12864-015-1634-x.
2014
States SL, Brinkerhoff RJ, Carpi G, Steeves TK, Folsom-O'keefe C, Deveaux M, and Diuk-Wasser MA. (2014). Lyme disease risk not amplified in a species-poor vertebrate community: Similar Borrelia burgdorferi tick infection prevalence and OspC genotype frequencies. Infection, Genetics and Evolution. 27, 566-575. doi: 10.1016/j.meegid.2014.04.014.
Barakova I, Derdakova M, Carpi G, Rosso F, Collini M, Tagliapietra V, Ramponi C, Hauffe HC, and Rizzoli A. (2014). Genetic and ecologic variability among Anaplasma phagocytophilum strains, northern Italy. Emerging Infectious Diseases. 20, 1082-1085. doi: 10.1016/j.ttbdis.2014.07.012.
Blanarova L, Stanko M, Carpi G, Miklisova D, Vichova B, Mosansky L, Bona M, and Derdakova M. (2014). Distinct Anaplasma phagocytophilum genotypes associated with Ixodes trianguliceps ticks and rodents in Central Europe. Ticks and Tick-Borne Diseases. 5, 928-938. doi: 10.3201/eid2006.131023.
2012
Cagnacci F, Bolzoni L, Rosa R, Carpi G, Hauffe HC, Valent M, Tagliapietra V, Kazimirova M, Koci J, Stanko M, Lukan M, Henttonen H, and Rizzoli A. (2012). Effects of deer density on tick infestation of rodents and the hazard of tick-borne encephalitis. I: empirical assessment. International Journal for Parasitology. 42, 365-372. doi: 10.1016/j.ijpara.2012.02.012.
2011
Carpi G, Cagnacci F, Wittekindt NE, Zhao F, Qi J, Tomsho LP, Drautz DI, Rizzoli A, and Schuster SC. (2011). Metagenomic profile of the bacterial communities associated with Ixodes ricinus ticks. PLoS One. 6, e25604. doi: 10.1371/journal.pone.0025604.
Rizzoli A, Hauffe H, Carpi G, Vourc HG, Neteler M, and Rosa R. (2011). Lyme borreliosis in Europe. EuroSurveillance. 16(27). pii: 19906.
2010
Carpi G, Holmes EC, and Kitchen A. (2010). The evolutionary dynamics of bluetongue virus. Journal of Molecular Evolution. 70, 583-592. doi: 10.1007/s00239-010-9354-y.
2009
Carpi G, Bertolotti L, Pecchioli E, Cagnacci F, and Rizzoli A. (2009). Anaplasma phagocytophilum groEL gene heterogeneity in Ixodes ricinus larvae feeding on roe deer in Northeastern Italy. Vector-Borne and Zoonotic Diseases. 9, 179-184. doi: 10.1089/vbz.2008.0068.
Carpi G, Bertolotti L, Rosati S, and Rizzoli A. (2009). Prevalence and genetic variability of tick-borne encephalitis virus in host-seeking Ixodes ricinus in northern Italy. Journal of General Virology. 90, 2877-2883. doi: 10.1099/vir.0.013367-0.
2008
Carpi G, Cagnacci F, Neteler M, and Rizzoli A. (2008). Tick infestation on roe deer in relation to geographic and remotely sensed climatic variables in a tick-borne encephalitis endemic area. Epidemiology and Infection. 136, 1416-1424.
* Authors contributed equally