Genomic architecture and introgression shape a butterfly radiation von Edelman, Nathaniel B., Frandsen, Paul B., Miyagi, Michael, Clavijo, Bernardo, Davey, John, Dikow, Rebecca B., García-Accinelli, Gonzalo, Van Belleghem, Steven M., Patterson, Nick, Neafsey, Daniel E., Challis, Richard, Kumar, Sujai, Moreira, Gilson R. P., Salazar, Camilo, Chouteau, Mathieu, Counterman, Brian A., Papa, Riccardo, Blaxter, Mark, Reed, Robert D., Dasmahapatra, Kanchon K., Kronforst, Marcus, Joron, Mathieu, Jiggins, Chris D., McMillan, W. Owen, Di Palma, Federica, Blumberg, Andrew J., Wakeley, John, Jaffe, David, Mallet, James

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hmmIBD: software to infer pairwise identity by descent between haploid genotypes von Schaffner, Stephen F, Taylor, Aimee R, Wong, Wesley, Wirth, Dyann F, Neafsey, Daniel E

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Extensive introgression in a malaria vector species complex revealed by phylogenomics von Fontaine, Michael C., Pease, James B., Steele, Aaron, Waterhouse, Robert M., Neafsey, Daniel E., Sharakhov, Igor V., Jiang, Xiaofang, Hall, Andrew B., Catteruccia, Flaminia, Kakani, Evdoxia, Mitchell, Sara N., Wu, Yi-Chieh, Smith, Hilary A., Love, R. Rebecca, Lawniczak, Mara K., Slotman, Michel A., Emrich, Scott J., Hahn, Matthew W., Besansky, Nora J.

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Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent von Taylor, Aimee R, Schaffner, Stephen F, Cerqueira, Gustavo C, Nkhoma, Standwell C, Anderson, Timothy J C, Sriprawat, Kanlaya, Pyae Phyo, Aung, Nosten, François, Neafsey, Daniel E, Buckee, Caroline O

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Resolving the cause of recurrent Plasmodium vivax malaria probabilistically von Taylor, Aimee R., Watson, James A., Chu, Cindy S., Puaprasert, Kanokpich, Duanguppama, Jureeporn, Day, Nicholas P. J., Nosten, Francois, Neafsey, Daniel E., Buckee, Caroline O., Imwong, Mallika, White, Nicholas J.

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Local emergence in Amazonia of Plasmodium falciparum k13 C580Y mutants associated with in vitro artemisinin resistance von Mathieu, Luana C, Cox, Horace, Early, Angela M, Mok, Sachel, Lazrek, Yassamine, Paquet, Jeanne-Celeste, Ade, Maria-Paz, Lucchi, Naomi W, Grant, Quacy, Udhayakumar, Venkatachalam, Alexandre, Jean Sf, Demar, Magalie, Ringwald, Pascal, Neafsey, Daniel E, Fidock, David A, Musset, Lise

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A novel CSP C-terminal epitope targeted by an antibody with protective activity against Plasmodium falciparum von Beutler, Nathan, Pholcharee, Tossapol, Oyen, David, Flores-Garcia, Yevel, MacGill, Randall S, Garcia, Elijah, Calla, Jaeson, Parren, Mara, Yang, Linlin, Volkmuth, Wayne, Locke, Emily, Regules, Jason A, Dutta, Sheetij, Emerling, Daniel, Early, Angela M, Neafsey, Daniel E, Winzeler, Elizabeth A, King, C Richter, Zavala, Fidel, Burton, Dennis R, Wilson, Ian A, Rogers, Thomas F

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Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance von Cerqueira, Gustavo C, Cheeseman, Ian H, Schaffner, Steve F, Nair, Shalini, McDew-White, Marina, Phyo, Aung Pyae, Ashley, Elizabeth A, Melnikov, Alexandre, Rogov, Peter, Birren, Bruce W, Nosten, François, Anderson, Timothy J C, Neafsey, Daniel E

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Modeling malaria genomics reveals transmission decline and rebound in Senegal von Daniels, Rachel F., Schaffner, Stephen F., Wenger, Edward A., Proctor, Joshua L., Chang, Hsiao-Han, Wong, Wesley, Baro, Nicholas, Ndiaye, Daouda, Fall, Fatou Ba, Ndiop, Medoune, Ba, Mady, Milner, Danny A., Taylor, Terrie E., Neafsey, Daniel E., Volkman, Sarah K., Eckhoff, Philip A., Hartl, Daniel L., Wirth, Dyann F.

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THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites von Chang, Hsiao-Han, Worby, Colin J, Yeka, Adoke, Nankabirwa, Joaniter, Kamya, Moses R, Staedke, Sarah G, Dorsey, Grant, Murphy, Maxwell, Neafsey, Daniel E, Jeffreys, Anna E, Hubbart, Christina, Rockett, Kirk A, Amato, Roberto, Kwiatkowski, Dominic P, Buckee, Caroline O, Greenhouse, Bryan

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Adaptive evolution of malaria parasites in French Guiana: Reversal of chloroquine resistance by acquisition of a mutation in pfcrt von Pelleau, Stéphane, Moss, Eli L., Dhingra, Satish K., Volney, Béatrice, Casteras, Jessica, Gabryszewski, Stanislaw J., Volkman, Sarah K., Wirth, Dyann F., Legrand, Eric, Fidock, David A., Neafsey, Daniel E., Musset, Lise

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Genetic dissection of Anopheles gambiae gut epithelial responses to Serratia marcescens von Stathopoulos, Stavros, Neafsey, Daniel E, Lawniczak, Mara K N, Muskavitch, Marc A T, Christophides, George K

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Temporal and spatial dynamics of Plasmodium falciparum clonal lineages in Guyana von Vanhove, Mathieu, Schwabl, Philipp, Clementson, Collette, Early, Angela M, Laws, Margaret, Anthony, Frank, Florimond, Célia, Mathieu, Luana, James, Kashana, Knox, Cheyenne, Singh, Narine, Buckee, Caroline O, Musset, Lise, Cox, Horace, Niles-Robin, Reza, Neafsey, Daniel E

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The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum von Neafsey, Daniel E, Galinsky, Kevin, Jiang, Rays H Y, Young, Lauren, Sykes, Sean M, Saif, Sakina, Gujja, Sharvari, Goldberg, Jonathan M, Young, Sarah, Zeng, Qiandong, Chapman, Sinéad B, Dash, Aditya P, Anvikar, Anupkumar R, Sutton, Patrick L, Birren, Bruce W, Escalante, Ananias A, Barnwell, John W, Carlton, Jane M

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Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis von Carrasquilla, Manuela, Early, Angela M, Taylor, Aimee R, Knudson Ospina, Angélica, Echeverry, Diego F, Anderson, Timothy J C, Mancilla, Elvira, Aponte, Samanda, Cárdenas, Pablo, Buckee, Caroline O, Rayner, Julian C, Sáenz, Fabián E, Neafsey, Daniel E, Corredor, Vladimir

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Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast von Taylor, Aimee R, Echeverry, Diego F, Anderson, Timothy J C, Neafsey, Daniel E, Buckee, Caroline O

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Stepwise acquisition of pyrimethamine resistance in the malaria parasite von Lozovsky, Elena R, Chookajorn, Thanat, Brown, Kyle M, Imwong, Mallika, Shaw, Philip J, Kamchonwongpaisan, Sumalee, Neafsey, Daniel E, Weinreich, Daniel M, Hartl, Daniel L

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Mapping malaria by combining parasite genomic and epidemiologic data von Wesolowski, Amy, Taylor, Aimee R, Chang, Hsiao-Han, Verity, Robert, Tessema, Sofonias, Bailey, Jeffrey A, Alex Perkins, T, Neafsey, Daniel E, Greenhouse, Bryan, Buckee, Caroline O

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Integration of whole genome sequencing and transcriptomics reveals a complex picture of the reestablishment of insecticide resistance in the major malaria vector Anopheles coluzzii von Ingham, Victoria A, Tennessen, Jacob A, Lucas, Eric R, Elg, Sara, Yates, Henrietta Carrington, Carson, Jessica, Guelbeogo, Wamdaogo Moussa, Sagnon, N'Fale, Hughes, Grant L, Heinz, Eva, Neafsey, Daniel E, Ranson, Hilary

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Genomic Sequencing of Plasmodium falciparum Malaria Parasites from Senegal Reveals the Demographic History of the Population von Chang, Hsiao-Han, Park, Daniel J., Galinsky, Kevin J., Schaffner, Stephen F., Ndiaye, Daouda, Ndir, Omar, Mboup, Souleymane, Wiegand, Roger C., Volkman, Sarah K., Sabeti, Pardis C., Wirth, Dyann F., Neafsey, Daniel E., Hartl, Daniel L.

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