Publications

Recent publications from the lab

A list of all publications can be found here.

2023

Tebben K, Yirampo S, Coulibaly D, Koné AK, Laurens MB, Stucke EM, Dembélé A, Tolo Y, Traoré K, Niangaly A, Berry AA, Kouriba B, Plowe CV, Doumbo OK, Lyke KE, Takala-Harrison S, Thera MA, Travassos MA, Serre D. Malian children infected with Plasmodium ovale and Plasmodium falciparum display very similar gene expression profiles. PLoS Negl Trop Dis. 2023 Jan 25;17(1):e0010802. doi: 10.1371/journal.pntd.0010802. PMID: 36696438; PMCID: PMC9901758.

2022

Hazzard B, Sá JM, Ellis AC, Pascini TV, Amin S, Wellems TE, Serre D. Long read single cell RNA sequencing reveals the isoform diversity of Plasmodium vivax transcripts. PLoS Negl Trop Dis. 2022 Dec 16;16(12):e0010991. doi: 10.1371/journal.pntd.0010991. PMID: 36525464; PMCID: PMC9803293.

Tebben K, Dia A, Serre D. Determination of the Stage Composition of Plasmodium Infections from Bulk Gene Expression Data. mSystems. 2022 Aug 30;7(4):e0025822. doi: 10.1128/msystems.00258-22. Epub 2022 Jul 5. PMID: 35862820; PMCID: PMC9426464.

Zhou AE, Shah ZV, Bradwell KR, Munro JB, Berry AA, Serre D, Takala-Harrison S, O’Connor TD, Silva JC, Travassos MA. STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families. BMC Bioinformatics. 2022 Jan 6;23(1):15. doi: 10.1186/s12859-021-04515-8. PMID: 34991452; PMCID: PMC8733436.

2021

Stucke EM, Dara A, Dwivedi A, Hodges TK, Ott S, Coulibaly D, Koné AK, Traoré K, Guindo B, Tangara BM, Niangaly A, Daou M, Diarra I, Tolo Y, Sissoko M, Tallon LJ, Sadzewicz L, Zhou AE, Laurens MB, Ouattara A, Kouriba B, Doumbo OK, Takala-Harrison S, Serre D, Plowe CV, Thera MA, Travassos MA, Silva JC. Successful Profiling of Plasmodium falciparum var Gene Expression in Clinical Samples via a Custom Capture Array. mSystems. 2021 Dec 21;6(6):e0022621. doi: 10.1128/mSystems.00226-21. Epub 2021 Nov 30. PMID: 34846163; PMCID: PMC8631312.

Cannon MV, Bogale HN, Bhalerao D, Keita K, Camara D, Barry Y, Keita M, Coulibaly D, Kone AK, Doumbo OK, Thera MA, Plowe CV, Travassos MA, Irish SR, Yeroshefsky J, Dorothy J, Prendergast B, St Laurent B, Fritz ML, Serre D. High-throughput detection of eukaryotic parasites and arboviruses in mosquitoes. Biol Open. 2021 Jul 15;10(7):bio058855. doi: 10.1242/bio.058855. Epub 2021 Jul 19. PMID: 34156069; PMCID: PMC8325944.

Shah Z, Naung MT, Moser KA, Adams M, Buchwald AG, Dwivedi A, Ouattara A, Seydel KB, Mathanga DP, Barry AE, Serre D, Laufer MK, Silva JC, Takala-Harrison S. Whole-genome analysis of Malawian Plasmodium falciparum isolates identifies possible targets of allele-specific immunity to clinical malaria. PLoS Genet. 2021 May 25;17(5):e1009576. doi: 10.1371/journal.pgen.1009576. PMID: 34033654; PMCID: PMC8184011.

Tebben K, Bradwell K, Serre D. Variation in selective constraints along the Plasmodium life cycle. Infect Genet Evol. 2021 Aug;92:104908. doi: 10.1016/j.meegid.2021.104908. Epub 2021 May 8. PMID: 33975022; PMCID: PMC8205998.

Bogale HN, Pascini TV, Kanatani S, Sá JM, Wellems TE, Sinnis P, Vega-Rodríguez J, Serre D. Transcriptional heterogeneity and tightly regulated changes in gene expression during Plasmodium berghei sporozoite development. Proc Natl Acad Sci U S A. 2021 Mar 9;118(10):e2023438118. doi: 10.1073/pnas.2023438118. PMID: 33653959; PMCID: PMC7958459.

Popovici J, Tebben K, Witkowski B, Serre D. Primaquine for Plasmodium vivax radical cure: What we do not know and why it matters. Int J Parasitol Drugs Drug Resist. 2021 Apr;15:36-42. doi: 10.1016/j.ijpddr.2020.12.004. Epub 2021 Jan 24. PMID: 33529838; PMCID: PMC7851417.

2020

Bogale HN, Cannon MV, Keita K, Camara D, Barry Y, Keita M, Coulibaly D, Kone AK, Doumbo OK, Thera MA, Plowe CV, Travassos M, Irish S, Serre D. Relative contributions of various endogenous and exogenous factors to the mosquito microbiota. Parasit Vectors. 2020 Dec 10;13(1):619. doi: 10.1186/s13071-020-04491-7. PMID: 33303025; PMCID: PMC7726613.

Bradwell KR, Coulibaly D, Koné AK, Laurens MB, Dembélé A, Tolo Y, Traoré K, Niangaly A, Berry AA, Kouriba B, Plowe CV, Doumbo OK, Lyke KE, Takala-Harrison S, Thera MA, Travassos MA, Serre D. Host and Parasite Transcriptomic Changes upon Successive Plasmodium falciparum Infections in Early Childhood. mSystems. 2020 Jul 7;5(4):e00116-20. doi: 10.1128/mSystems.00116-20. PMID: 32636334; PMCID: PMC7343306.

Sà JM, Cannon MV, Caleon RL, Wellems TE, Serre D. Single-cell transcription analysis of Plasmodium vivax blood-stage parasites identifies stage- and species-specific profiles of expression. PLoS Biol. 2020 May 4;18(5):e3000711. doi: 10.1371/journal.pbio.3000711. PMID: 32365102; PMCID: PMC7224573.

Shah Z, Adams M, Moser KA, Shrestha B, Stucke EM, Laufer MK, Serre D, Silva JC, Takala-Harrison S. Optimization of parasite DNA enrichment approaches to generate whole genome sequencing data for Plasmodium falciparum from low parasitaemia samples. Malar J. 2020 Mar 30;19(1):135. doi: 10.1186/s12936-020-03195-8. PMID: 32228559; PMCID: PMC7106660.

Galeano-Castañeda Y, Bascuñán P, Serre D, Correa MM. Trans-stadial fate of the gut bacterial microbiota in Anopheles albimanus. Acta Trop. 2020 Jan;201:105204. doi: 10.1016/j.actatropica.2019.105204. Epub 2019 Sep 28. PMID: 31574253.

2019

Sá JM, Kaslow SR, Moraes Barros RR, Brazeau NF, Parobek CM, Tao D, Salzman RE, Gibson TJ, Velmurugan S, Krause MA, Melendez-Muniz V, Kite WA, Han PK, Eastman RT, Kim A, Kessler EG, Abebe Y, James ER, Chakravarty S, Orr-Gonzalez S, Lambert LE, Engels T, Thomas ML, Fasinu PS, Serre D, Gwadz RW, Walker L, DeConti DK, Mu J, Bailey JA, Sim BKL, Hoffman SL, Fay MP, Dinglasan RR, Juliano JJ, Wellems TE. Plasmodium vivax chloroquine resistance links to pvcrt transcription in a genetic cross. Nat Commun. 2019 Sep 20;10(1):4300. doi: 10.1038/s41467-019-12256-9. PMID: 31541097; PMCID: PMC6754410.

Small ST, Labbé F, Coulibaly YI, Nutman TB, King CL, Serre D, Zimmerman PA. Human Migration and the Spread of the Nematode Parasite Wuchereria bancrofti. Mol Biol Evol. 2019 Sep 1;36(9):1931-1941. doi: 10.1093/molbev/msz116. PMID: 31077328; PMCID: PMC6735882.

Kim A, Popovici J, Menard D, Serre D (2019) Plasmodium vivax transcriptomes reveal stage-specific chloroquine response and differential regulation of male and female gametocytes. Nature Communications. 10(1): 371.

2018

Cannon MV, Bogale H, Rutt L, Humphrys M, Korpe P, Duggal P, Ravel J, Serre D (2018) A high-throughput sequencing assay to comprehensively detect and characterize unicellular eukaryotes and helminths from biological and environmental samples. Microbiome. 6(1):195. doi: 10.1186/s40168-018-0581-6. PMC6206884.

Roesch C, Popovici J, Bin S, Run V, Kim S, Ramboarina S, Rakotomalala E, Rakotoarison RL, Rasoloharimanana T, Andriamanantena Z, Kumar A, Guillotte-Blisnick M, Huon C, Serre D, Chitnis CE, Vigan-Womas I, Menard D (2018) Genetic diversity in two Plasmodium vivax protein ligands for reticulocyte invasion. PLoS Negl Trop Dis. 12(10):e0006555. PMC6211765.

Bascuñán P, Niño-Garcia JP, Galeano-Castañeda Y, Serre D, Correa MM (2018) Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors. Microbiome. 6(1):148.

Popovici J, Pierce-Friedrich L, Kim S, Bin S, Run V, Lek D, Hor Daryl HK, Lee Soon-U L, Cannon MV, Serre D, Menard D (2018) Recrudescence, reinfection or relapse? A more rigorous framework to assess chloroquine efficacy for vivax malaria. J Infect Dis.

Popovici J, Vantaux A, Primault L, Samreth R, Piv EP, Bin S, Kim S, Lek D, Serre D, Menard D (2018) Therapeutic and Transmission-Blocking Efficacy of Dihydroartemisinin-Piperaquine and Chloroquine against Plasmodium vivax Malaria, Cambodia. Emerg Infect Dis. 24(8):1516-1519. PMC6056113.

Popovici J, Friedrich LR, Kim S, Bin S, Run V, Lek D, Cannon MV, Menard D, Serre D. Genomic Analyses Reveal the Common Occurrence and Complexity of Plasmodium vivax Relapses in Cambodia. MBio. 9(1). pii: e01888-17. PMC5784252.

2017

Chung M, Small ST, Serre D, Zimmerman PA, Dunning Hotopp JC. Draft genome sequence of the Wolbachia endosymbiont of Wuchereria bancrofti wWb. Pathog Dis. 75(9). PMC5827699

Cannon MV, Craine J, Hester J, Shalkhauser A, Chan ER, Logue K, Small S, Serre D. Dynamic microbial populations along the Cuyahoga River. PLoS One 12(10):e0186290. PMC5648161

Kim A, Popovici J, Vantaux A, Samreth R, Bin S, Kim S, Roesch C, Liang L, Davies H, Felgner P, Herrera S, Arévalo-Herrera M, Ménard D, Serre D. Characterization of vivax blood stage transcriptomes from field isolates reveals similarities among infections and complex gene isoforms. Sci Rep. 7(1):7761. PMC5552866

2016

Cannon MV, Pilarowski G, Liu X, Serre D. Extensive Epigenetic Changes Accompany Terminal Differentiation of Mouse Hepatocytes After Birth. G3 (Bethesda). g3.116.034785. PMC5100869

Auburn S, Serre D, Pearson RD, Amato R, Sriprawat K, To S, Handayuni I, Suwanarusk R, Russell B, Drury E, Stalker J, Miotto O, Kwiatkowski DP, Nosten F, Price RN. Genomic Analysis Reveals a Common Breakpoint in Amplifications of the Plasmodium vivax Multidrug Resistance 1 Locus in Thailand. J Infect Dis. 214(8):1235-42. PMC5034950.

Cannon MV, Hester J, Shalkhauser A, Chan ER, Logue K, Small ST and Serre D. In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River. Sci Rep. 6:22908. PMC4786790.

Small ST, Reimer LJ, Tisch DJ, King CL, Christensen BM, Siba PM, Kazura JW, Serre D and Zimmerman PA. Population genomics of the filarial nematode parasite Wuchereria bancrofti from mosquitoes. Mol Ecol. 25(7):1465-77. PMC4808423.

Friedrich LR, Popovici J, Kim S, Dysoley L, Zimmerman PA, Menard D and Serre D. Complexity of infection and genetic diversity in Cambodian Plasmodium vivax. PLoS Negl Trop Dis. 10(3):e0004526. PMC4809505.

Logue K, Keven JB, Cannon MV, Reimer L, Siba P, Walker ED, Zimmerman PA and Serre D. Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing. PLoS Negl Trop Dis. 10(3):e0004512. PMC4786206.