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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. PubMed PMID: 33975022; PubMed Central PMCID: PMC8205998.
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. PubMed PMID: 33529838; PubMed Central PMCID: PMC7851417.
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). doi: 10.1073/pnas.2023438118. PubMed PMID: 33653959; PubMed Central PMCID: PMC7958459.
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. PubMed PMID: 33303025; PubMed Central 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). doi: 10.1128/mSystems.00116-20. PubMed PMID: 32636334; PubMed Central 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;18(5):e3000711. doi: 10.1371/journal.pbio.3000711. eCollection 2020 May. PubMed PMID: 32365102; PubMed Central 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. PubMed PMID: 32228559; PubMed Central 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. PubMed PMID: 31574253.
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. PubMed PMID: 31541097; PubMed Central 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. PubMed PMID: 31077328; PubMed Central PMCID: PMC6735882.
Kim A, Popovici J, Menard D, Serre D. Plasmodium vivax transcriptomes reveal stage-specific chloroquine response and differential regulation of male and female gametocytes. Nat Commun. 2019 Jan 22;10(1):371. doi: 10.1038/s41467-019-08312-z. PubMed PMID: 30670687; PubMed Central PMCID: PMC6342968.
Popovici J, Pierce-Friedrich L, Kim S, Bin S, Run V, Lek D, Hee KHD, Lee Soon-U L, Cannon MV, Serre D, Menard D. Recrudescence, Reinfection, or Relapse? A More Rigorous Framework to Assess Chloroquine Efficacy for Plasmodium vivax Malaria. J Infect Dis. 2019 Jan 7;219(2):315-322. doi: 10.1093/infdis/jiy484. PubMed PMID: 30102351; PubMed Central PMCID: PMC6306015.
Cannon MV, Bogale H, Rutt L, Humphrys M, Korpe P, Duggal P, Ravel J, Serre D. A high-throughput sequencing assay to comprehensively detect and characterize unicellular eukaryotes and helminths from biological and environmental samples. Microbiome. 2018 Oct 29;6(1):195. doi: 10.1186/s40168-018-0581-6. PubMed PMID: 30373673; PubMed Central PMCID: 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. Genetic diversity in two Plasmodium vivax protein ligands for reticulocyte invasion. PLoS Negl Trop Dis. 2018 Oct;12(10):e0006555. doi: 10.1371/journal.pntd.0006555. eCollection 2018 Oct. PubMed PMID: 30346980; PubMed Central PMCID: PMC6211765.
Bascuñán P, Niño-Garcia JP, Galeano-Castañeda Y, Serre D, Correa MM. Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors. Microbiome. 2018 Aug 27;6(1):148. doi: 10.1186/s40168-018-0528-y. PubMed PMID: 30149801; PubMed Central PMCID: PMC6112144.
Popovici J, Vantaux A, Primault L, Samreth R, Piv EP, Bin S, Kim S, Lek D, Serre D, Menard D. Therapeutic and Transmission-Blocking 
Efficacy of Dihydroartemisinin/Piperaquine and Chloroquine against Plasmodium vivax Malaria, Cambodia. Emerg Infect Dis. 2018 Aug;24(8):1516-1519. doi: 10.3201/eid2408.170768. Epub 2018 Aug 17. PubMed PMID: 29798745; PubMed Central PMCID: 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. 2018 Jan 23;9(1). doi: 10.1128/mBio.01888-17. PubMed PMID: 29362233; PubMed Central PMCID: PMC5784252.
Chung M, Small ST, Serre D, Zimmerman PA, Dunning Hotopp JC. Draft genome sequence of the Wolbachia endosymbiont of Wuchereria bancrofti wWb. Pathog Dis. 2017 Dec 29;75(9). doi: 10.1093/femspd/ftx115. PubMed PMID: 29099918; PubMed Central PMCID: 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. 2017;12(10):e0186290. doi: 10.1371/journal.pone.0186290. eCollection 2017. PubMed PMID: 29049324; PubMed Central PMCID: 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 P. vivax blood stage transcriptomes from field isolates reveals similarities among infections and complex gene isoforms. Sci Rep. 2017 Aug 10;7(1):7761. doi: 10.1038/s41598-017-07275-9. PubMed PMID: 28798400; PubMed Central PMCID: PMC5552866.
Cannon MV, Pilarowski G, Liu X, Serre D. Extensive Epigenetic Changes Accompany Terminal Differentiation of Mouse Hepatocytes After Birth. G3 (Bethesda). 2016 Nov 8;6(11):3701-3709. doi: 10.1534/g3.116.034785. PubMed PMID: 27652892; PubMed Central PMCID: 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. 2016 Oct 15;214(8):1235-42. doi: 10.1093/infdis/jiw323. Epub 2016 Jul 24. PubMed PMID: 27456706; PubMed Central PMCID: PMC5034950.
Small ST, Reimer LJ, Tisch DJ, King CL, Christensen BM, Siba PM, Kazura JW, Serre D, Zimmerman PA. Population genomics of the filarial nematode parasite Wuchereria bancrofti from mosquitoes. Mol Ecol. 2016 Apr;25(7):1465-77. doi: 10.1111/mec.13574. Epub 2016 Mar 15. PubMed PMID: 26850696; PubMed Central PMCID: PMC4808423.
Friedrich LR, Popovici J, Kim S, Dysoley L, Zimmerman PA, Menard D, Serre D. Complexity of Infection and Genetic Diversity in Cambodian Plasmodium vivax. PLoS Negl Trop Dis. 2016 Mar;10(3):e0004526. doi: 10.1371/journal.pntd.0004526. eCollection 2016 Mar. PubMed PMID: 27018585; PubMed Central PMCID: PMC4809505.
Cannon MV, Hester J, Shalkhauser A, Chan ER, Logue K, Small ST, Serre D. In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River. Sci Rep. 2016 Mar 11;6:22908. doi: 10.1038/srep22908. PubMed PMID: 26965911; PubMed Central PMCID: PMC4786790.
Logue K, Keven JB, Cannon MV, Reimer L, Siba P, Walker ED, Zimmerman PA, Serre D. Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing. PLoS Negl Trop Dis. 2016 Mar;10(3):e0004512. doi: 10.1371/journal.pntd.0004512. eCollection 2016 Mar. PubMed PMID: 26963245; PubMed Central PMCID: PMC4786206.
Baniecki ML, Faust AL, Schaffner SF, Park DJ, Galinsky K, Daniels RF, Hamilton E, Ferreira MU, Karunaweera ND, Serre D, Zimmerman PA, Sá JM, Wellems TE, Musset L, Legrand E, Melnikov A, Neafsey DE, Volkman SK, Wirth DF, Sabeti PC. Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections. PLoS Negl Trop Dis. 2015 Mar;9(3):e0003539. doi: 10.1371/journal.pntd.0003539. eCollection 2015 Mar. PubMed PMID: 25781890; PubMed Central PMCID: PMC4362761.
Chan ER, Barnwell JW, Zimmerman PA, Serre D. Comparative analysis of field-isolate and monkey-adapted Plasmodium vivax genomes. PLoS Negl Trop Dis. 2015 Mar;9(3):e0003566. doi: 10.1371/journal.pntd.0003566. eCollection 2015 Mar. PubMed PMID: 25768941; PubMed Central PMCID: PMC4358935.
Kondratova A, Watanabe T, Marotta M, Cannon M, Segall AM, Serre D, Tanaka H. Replication fork integrity and intra-S phase checkpoint suppress gene amplification. Nucleic Acids Res. 2015 Mar 11;43(5):2678-90. doi: 10.1093/nar/gkv084. Epub 2015 Feb 11. PubMed PMID: 25672394; PubMed Central PMCID: PMC4357702.
Logue K, Small ST, Chan ER, Reimer L, Siba PM, Zimmerman PA, Serre D. Whole-genome sequencing reveals absence of recent gene flow and separate demographic histories for Anopheles punctulatus mosquitoes in Papua New Guinea. Mol Ecol. 2015 Mar;24(6):1263-74. doi: 10.1111/mec.13107. Epub 2015 Mar 6. PubMed PMID: 25677924; PubMed Central PMCID: PMC4504211.
Haghiac M, Basu S, Presley L, Serre D, Catalano PM, Hauguel-de Mouzon S. Patterns of adiponectin expression in term pregnancy: impact of obesity. J Clin Endocrinol Metab. 2014 Sep;99(9):3427-34. doi: 10.1210/jc.2013-4074. Epub 2014 May 5. PubMed PMID: 24796925; PubMed Central PMCID: PMC4154091.
Nair S, Nkhoma SC, Serre D, Zimmerman PA, Gorena K, Daniel BJ, Nosten F, Anderson TJ, Cheeseman IH. Single-cell genomics for dissection of complex malaria infections. Genome Res. 2014 Jun;24(6):1028-38. doi: 10.1101/gr.168286.113. Epub 2014 May 8. PubMed PMID: 24812326; PubMed Central PMCID: PMC4032849.
Cheruvu VK, Igo RP Jr, Jurevic RJ, Serre D, Zimmerman PA, Rodriguez B, Mehlotra RK. African ancestry influences CCR5 -2459G>A genotype-associated virologic success of highly active antiretroviral therapy. J Acquir Immune Defic Syndr. 2014 May 1;66(1):102-7. doi: 10.1097/QAI.0000000000000129. PubMed PMID: 24714069; PubMed Central PMCID: PMC3996453.
Cannon MV, Buchner DA, Hester J, Miller H, Sehayek E, Nadeau JH, Serre D. Maternal nutrition induces pervasive gene expression changes but no detectable DNA methylation differences in the liver of adult offspring. PLoS One. 2014;9(3):e90335. doi: 10.1371/journal.pone.0090335. eCollection 2014. PubMed PMID: 24594983; PubMed Central PMCID: PMC3940881.
Hester J, Chan ER, Menard D, Mercereau-Puijalon O, Barnwell J, Zimmerman PA, Serre D. De novo assembly of a field isolate genome reveals novel Plasmodium vivax erythrocyte invasion genes. PLoS Negl Trop Dis. 2013;7(12):e2569. doi: 10.1371/journal.pntd.0002569. eCollection 2013. PubMed PMID: 24340114; PubMed Central PMCID: PMC3854868.
Menard D, Chan ER, Benedet C, Ratsimbasoa A, Kim S, Chim P, Do C, Witkowski B, Durand R, Thellier M, Severini C, Legrand E, Musset L, Nour BY, Mercereau-Puijalon O, Serre D, Zimmerman PA. Whole genome sequencing of field isolates reveals a common duplication of the Duffy binding protein gene in Malagasy Plasmodium vivax strains. PLoS Negl Trop Dis. 2013 Nov;7(11):e2489. doi: 10.1371/journal.pntd.0002489. eCollection 2013 Nov. PubMed PMID: 24278487; PubMed Central PMCID: PMC3836732.
Tan N, Chung MK, Smith JD, Hsu J, Serre D, Newton DW, Castel L, Soltesz E, Pettersson G, Gillinov AM, Van Wagoner DR, Barnard J. Weighted gene coexpression network analysis of human left atrial tissue identifies gene modules associated with atrial fibrillation. Circ Cardiovasc Genet. 2013 Aug;6(4):362-71. doi: 10.1161/CIRCGENETICS.113.000133. Epub 2013 Jul 17. PubMed PMID: 23863953; PubMed Central PMCID: PMC3955718.
Wong WPS, Altemus JB, Hester JF, Chan ER, Côté JF, Serre D, Sehayek E. Cathepsin B is a novel gender-dependent determinant of cholesterol absorption from the intestine. J Lipid Res. 2013 Mar;54(3):816-822. doi: 10.1194/jlr.M034579. Epub 2012 Dec 17. PubMed PMID: 23248330; PubMed Central PMCID: PMC3617955.
Logue K, Chan ER, Phipps T, Small ST, Reimer L, Henry-Halldin C, Sattabongkot J, Siba PM, Zimmerman PA, Serre D. Mitochondrial genome sequences reveal deep divergences among Anopheles punctulatus sibling species in Papua New Guinea. Malar J. 2013 Feb 14;12:64. doi: 10.1186/1475-2875-12-64. PubMed PMID: 23405960; PubMed Central PMCID: PMC3577438.
Chan ER, Menard D, David PH, Ratsimbasoa A, Kim S, Chim P, Do C, Witkowski B, Mercereau-Puijalon O, Zimmerman PA, Serre D. Whole genome sequencing of field isolates provides robust characterization of genetic diversity in Plasmodium vivax. PLoS Negl Trop Dis. 2012;6(9):e1811. doi: 10.1371/journal.pntd.0001811. Epub 2012 Sep 6. PubMed PMID: 22970335; PubMed Central PMCID: PMC3435244.
Hsu J, Hanna P, Van Wagoner DR, Barnard J, Serre D, Chung MK, Smith JD. Whole genome expression differences in human left and right atria ascertained by RNA sequencing. Circ Cardiovasc Genet. 2012 Jun;5(3):327-35. doi: 10.1161/CIRCGENETICS.111.961631. Epub 2012 Apr 3. PubMed PMID: 22474228; PubMed Central PMCID: PMC3380143.
Ramesh A, Small ST, Kloos ZA, Kazura JW, Nutman TB, Serre D, Zimmerman PA. The complete mitochondrial genome sequence of the filarial nematode Wuchereria bancrofti from three geographic isolates provides evidence of complex demographic history. Mol Biochem Parasitol. 2012 May;183(1):32-41. doi: 10.1016/j.molbiopara.2012.01.004. Epub 2012 Feb 1. PubMed PMID: 22326389; PubMed Central PMCID: PMC3725818.
Chan ER, Hester J, Kalady M, Xiao H, Li X, Serre D. A novel method for determining microflora composition using dynamic phylogenetic analysis of 16S ribosomal RNA deep sequencing data. Genomics. 2011 Oct;98(4):253-9. doi: 10.1016/j.ygeno.2011.04.002. Epub 2011 Apr 15. PubMed PMID: 21515358; PubMed Central PMCID: PMC3168955.
Berisha SZ, Serre D, Schauer P, Kashyap SR, Smith JD. Changes in whole blood gene expression in obese subjects with type 2 diabetes following bariatric surgery: a pilot study. PLoS One. 2011 Mar 10;6(3):e16729. doi: 10.1371/journal.pone.0016729. PubMed PMID: 21423737; PubMed Central PMCID: PMC3053356.
Kalhan SC, Uppal SO, Moorman JL, Bennett C, Gruca LL, Parimi PS, Dasarathy S, Serre D, Hanson RW. Metabolic and genomic response to dietary isocaloric protein restriction in the rat. J Biol Chem. 2011 Feb 18;286(7):5266-77. doi: 10.1074/jbc.M110.185991. Epub 2010 Dec 8. PubMed PMID: 21147771; PubMed Central PMCID: PMC3037639.
Serre D, Lee BH, Ting AH. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res. 2010 Jan;38(2):391-9. doi: 10.1093/nar/gkp992. Epub 2009 Nov 11. PubMed PMID: 19906696; PubMed Central PMCID: PMC2811030.
Rung J, Cauchi S, Albrechtsen A, Shen L, Rocheleau G, Cavalcanti-Proença C, Bacot F, Balkau B, Belisle A, Borch-Johnsen K, Charpentier G, Dina C, Durand E, Elliott P, Hadjadj S, Järvelin MR, Laitinen J, Lauritzen T, Marre M, Mazur A, Meyre D, Montpetit A, Pisinger C, Posner B, Poulsen P, Pouta A, Prentki M, Ribel-Madsen R, Ruokonen A, Sandbaek A, Serre D, Tichet J, Vaxillaire M, Wojtaszewski JF, Vaag A, Hansen T, Polychronakos C, Pedersen O, Froguel P, Sladek R. Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia. Nat Genet. 2009 Oct;41(10):1110-5. doi: 10.1038/ng.443. Epub 2009 Sep 6. PubMed PMID: 19734900.
Jacob K, Albrecht S, Sollier C, Faury D, Sader E, Montpetit A, Serre D, Hauser P, Garami M, Bognar L, Hanzely Z, Montes JL, Atkinson J, Farmer JP, Bouffet E, Hawkins C, Tabori U, Jabado N. Duplication of 7q34 is specific to juvenile pilocytic astrocytomas and a hallmark of cerebellar and optic pathway tumours. Br J Cancer. 2009 Aug 18;101(4):722-33. doi: 10.1038/sj.bjc.6605179. Epub 2009 Jul 14. PubMed PMID: 19603027; PubMed Central PMCID: PMC2736806.
Serre D, Gurd S, Ge B, Sladek R, Sinnett D, Harmsen E, Bibikova M, Chudin E, Barker DL, Dickinson T, Fan JB, Hudson TJ. Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet. 2008 Feb 29;4(2):e1000006. doi: 10.1371/journal.pgen.1000006. PubMed PMID: 18454203; PubMed Central PMCID: PMC2265535.
Serre D, Montpetit A, Paré G, Engert JC, Yusuf S, Keavney B, Hudson TJ, Anand S. Correction of population stratification in large multi-ethnic association studies. PLoS One. 2008 Jan 2;3(1):e1382. doi: 10.1371/journal.pone.0001382. PubMed PMID: 18196181; PubMed Central PMCID: PMC2198793.
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