Comparison of genomic signatures of selection on Plasmodium falciparum between different regions of a country with high malaria endemicity

by Duffy, Craig W., Assefa, Samuel A., Abugri, James, Amoako, Nicholas, Owusu-Agyei, Seth, Anyorigiya, Thomas, MacInnis, Bronwyn, Kwiatkowski, Dominic P., Conway, David J., Awandare, Gordon A.
Published 2015

Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation

by Clarkson, Chris S., Weetman, David, Essandoh, John, Yawson, Alexander E., Maslen, Gareth, Manske, Magnus, Field, Stuart G., Webster, Mark, Antão, Tiago, MacInnis, Bronwyn, Kwiatkowski, Dominic, Donnelly, Martin J.
Published 2014

Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data

by Auburn, Sarah, Campino, Susana, Miotto, Olivo, Djimde, Abdoulaye A., Zongo, Issaka, Manske, Magnus, Maslen, Gareth, Mangano, Valentina, Alcock, Daniel, MacInnis, Bronwyn, Rockett, Kirk A., Clark, Taane G., Doumbo, Ogobara K., Ouédraogo, Jean Bosco, Kwiatkowski, Dominic P.
Published 2012

Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

by Oyola, Samuel O, Otto, Thomas D, Gu, Yong, Maslen, Gareth, Manske, Magnus, Campino, Susana, Turner, Daniel J, MacInnis, Bronwyn, Kwiatkowski, Dominic P, Swerdlow, Harold P, Quail, Michael A
Published 2012

Genome-Wide Analysis of Selection on the Malaria Parasite Plasmodium falciparum in West African Populations of Differing Infection Endemicity

by Mobegi, Victor A., Duffy, Craig W., Amambua-Ngwa, Alfred, Loua, Kovana M., Laman, Eugene, Nwakanma, Davis C., MacInnis, Bronwyn, Aspeling-Jones, Harvey, Murray, Lee, Clark, Taane G., Kwiatkowski, Dominic P., Conway, David J.
Published 2014

Optimized Whole-Genome Amplification Strategy for Extremely AT-Biased Template

by Oyola, Samuel O., Manske, Magnus, Campino, Susana, Claessens, Antoine, Hamilton, William L., Kekre, Mihir, Drury, Eleanor, Mead, Daniel, Gu, Yong, Miles, Alistair, MacInnis, Bronwyn, Newbold, Chris, Berriman, Matthew, Kwiatkowski, Dominic P.
Published 2014

Drug-Resistant Genotypes and Multi-Clonality in Plasmodium falciparum Analysed by Direct Genome Sequencing from Peripheral Blood of Malaria Patients

by Robinson, Timothy, Campino, Susana G., Auburn, Sarah, Assefa, Samuel A., Polley, Spencer D., Manske, Magnus, MacInnis, Bronwyn, Rockett, Kirk A., Maslen, Gareth L., Sanders, Mandy, Quail, Michael A., Chiodini, Peter L., Kwiatkowski, Dominic P., Clark, Taane G., Sutherland, Colin J.
Published 2011

An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing

by Auburn, Sarah, Campino, Susana, Clark, Taane G., Djimde, Abdoulaye A., Zongo, Issaka, Pinches, Robert, Manske, Magnus, Mangano, Valentina, Alcock, Daniel, Anastasi, Elisa, Maslen, Gareth, MacInnis, Bronwyn, Rockett, Kirk, Modiano, David, Newbold, Christopher I., Doumbo, Ogobara K., Ouédraogo, Jean Bosco, Kwiatkowski, Dominic P.
Published 2011

Effective Preparation of Plasmodium vivax Field Isolates for High-Throughput Whole Genome Sequencing

by Auburn, Sarah, Marfurt, Jutta, Maslen, Gareth, Campino, Susana, Ruano Rubio, Valentin, Manske, Magnus, MacHunter, Barbara, Kenangalem, Enny, Noviyanti, Rintis, Trianty, Leily, Sebayang, Boni, Wirjanata, Grennady, Sriprawat, Kanlaya, Alcock, Daniel, MacInnis, Bronwyn, Miotto, Olivo, Clark, Taane G., Russell, Bruce, Anstey, Nicholas M., Nosten, François, Kwiatkowski, Dominic P., Price, Ric N.
Published 2013

Population Genomic Scan for Candidate Signatures of Balancing Selection to Guide Antigen Characterization in Malaria Parasites

by Amambua-Ngwa, Alfred, Tetteh, Kevin K. A., Manske, Magnus, Gomez-Escobar, Natalia, Stewart, Lindsay B., Deerhake, M. Elizabeth, Cheeseman, Ian H., Newbold, Christopher I., Holder, Anthony A., Knuepfer, Ellen, Janha, Omar, Jallow, Muminatou, Campino, Susana, MacInnis, Bronwyn, Kwiatkowski, Dominic P., Conway, David J.
Published 2012

A Genome Wide Association Study of Plasmodium falciparum Susceptibility to 22 Antimalarial Drugs in Kenya

by Wendler, Jason P., Okombo, John, Amato, Roberto, Miotto, Olivo, Kiara, Steven M., Mwai, Leah, Pole, Lewa, O'Brien, John, Manske, Magnus, Alcock, Dan, Drury, Eleanor, Sanders, Mandy, Oyola, Samuel O., Malangone, Cinzia, Jyothi, Dushyanth, Miles, Alistair, Rockett, Kirk A., MacInnis, Bronwyn L., Marsh, Kevin, Bejon, Philip, Nzila, Alexis, Kwiatkowski, Dominic P.
Published 2014

Changes in Malaria Parasite Drug Resistance in an Endemic Population Over a 25-Year Period With Resulting Genomic Evidence of Selection

by Nwakanma, Davis C., Duffy, Craig W., Amambua-Ngwa, Alfred, Oriero, Eniyou C., Bojang, Kalifa A., Pinder, Margaret, Drakeley, Chris J., Sutherland, Colin J., Milligan, Paul J., MacInnis, Bronwyn, Kwiatkowski, Dominic P., Clark, Taane G., Greenwood, Brian M., Conway, David J.
Published 2014

Whole-Genome Scans Provide Evidence of Adaptive Evolution in Malawian Plasmodium falciparum Isolates

by Ocholla, Harold, Preston, Mark D., Mipando, Mwapatsa, Jensen, Anja T. R., Campino, Susana, MacInnis, Bronwyn, Alcock, Daniel, Terlouw, Anja, Zongo, Issaka, Oudraogo, Jean-Bosco, Djimde, Abdoulaye A., Assefa, Samuel, Doumbo, Ogobara K., Borrmann, Steffen, Nzila, Alexis, Marsh, Kevin, Fairhurst, Rick M., Nosten, Francois, Anderson, Tim J. C., Kwiatkowski, Dominic P., Craig, Alister, Clark, Taane G., Montgomery, Jacqui
Published 2014

Population Genetic Analysis of Plasmodium falciparum Parasites Using a Customized Illumina GoldenGate Genotyping Assay

by Campino, Susana, Auburn, Sarah, Kivinen, Katja, Zongo, Issaka, Ouedraogo, Jean-Bosco, Mangano, Valentina, Djimde, Abdoulaye, Doumbo, Ogobara K., Kiara, Steven M., Nzila, Alexis, Borrmann, Steffen, Marsh, Kevin, Michon, Pascal, Mueller, Ivo, Siba, Peter, Jiang, Hongying, Su, Xin-Zhuan, Amaratunga, Chanaki, Socheat, Duong, Fairhurst, Rick M., Imwong, Mallika, Anderson, Timothy, Nosten, François, White, Nicholas J., Gwilliam, Rhian, Deloukas, Panos, MacInnis, Bronwyn, Newbold, Christopher I., Rockett, Kirk, Clark, Taane G., Kwiatkowski, Dominic P.
Published 2011

Genomic analysis of local variation and recent evolution in Plasmodium vivax

by Pearson, Richard D, Amato, Roberto, Auburn, Sarah, Miotto, Olivo, Almagro-Garcia, Jacob, Amaratunga, Chanaki, Suon, Seila, Mao, Sivanna, Noviyanti, Rintis, Trimarsanto, Hidayat, Marfurt, Jutta, Anstey, Nicholas M, William, Timothy, Boni, Maciej F, Dolecek, Christiane, Hien, Tinh Tran, White, Nicholas J, Michon, Pascal, Siba, Peter, Tavul, Livingstone, Harrison, Gabrielle, Barry, Alyssa, Mueller, Ivo, Ferreira, Marcelo U, Karunaweera, Nadira, Randrianarivelojosia, Milijaona, Gao, Qi, Hubbart, Christina, Hart, Lee, Jeffery, Ben, Drury, Eleanor, Mead, Daniel, Kekre, Mihir, Campino, Susana, Manske, Magnus, Cornelius, Victoria J, MacInnis, Bronwyn, Rockett, Kirk A, Miles, Alistair, Rayner, Julian C, Fairhurst, Rick M, Nosten, Francois, Price, Ric N, Kwiatkowski, Dominic P
Published 2016

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

by Manske, Magnus, Miotto, Olivo, Campino, Susana, Auburn, Sarah, Almagro-Garcia, Jacob, Maslen, Gareth, O’Brien, Jack, Djimde, Abdoulaye, Doumbo, Ogobara, Zongo, Issaka, Ouedraogo, Jean-Bosco, Michon, Pascal, Mueller, Ivo, Siba, Peter, Nzila, Alexis, Borrmann, Steffen, Kiara, Steven M., Marsh, Kevin, Jiang, Hongying, Su, Xin-Zhuan, Amaratunga, Chanaki, Fairhurst, Rick, Socheat, Duong, Nosten, Francois, Imwong, Mallika, White, Nicholas J., Sanders, Mandy, Anastasi, Elisa, Alcock, Dan, Drury, Eleanor, Oyola, Samuel, Quail, Michael A., Turner, Daniel J., Rubio, Valentin Ruano, Jyothi, Dushyanth, Amenga-Etego, Lucas, Hubbart, Christina, Jeffreys, Anna, Rowlands, Kate, Sutherland, Colin, Roper, Cally, Mangano, Valentina, Modiano, David, Tan, John C., Ferdig, Michael T., Amambua-Ngwa, Alfred, Conway, David J., Takala-Harrison, Shannon, Plowe, Christopher V., Rayner, Julian C., Rockett, Kirk A., Clark, Taane G., Newbold, Chris I., Berriman, Matthew, MacInnis, Bronwyn, Kwiatkowski, Dominic P.
Published 2012

Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia

by Miotto, Olivo, Almagro-Garcia, Jacob, Manske, Magnus, MacInnis, Bronwyn, Campino, Susana, Rockett, Kirk A, Amaratunga, Chanaki, Lim, Pharath, Suon, Seila, Sreng, Sokunthea, Anderson, Jennifer M, Duong, Socheat, Nguon, Chea, Chuor, Char Meng, Saunders, David, Se, Youry, Lon, Chantap, Fukuda, Mark M, Amenga-Etego, Lucas, Hodgson, Abraham VO, Asoala, Victor, Imwong, Mallika, Takala-Harrison, Shannon, Nosten, Francois, Su, Xin-zhuan, Ringwald, Pascal, Ariey, Frédéric, Dolecek, Christiane, Hien, Tran Tinh, Boni, Maciej F, Thai, Cao Quang, Amambua-Ngwa, Alfred, Conway, David J, Djimdé, Abdoulaye A, Doumbo, Ogobara K, Zongo, Issaka, Ouedraogo, Jean-Bosco, Alcock, Daniel, Drury, Eleanor, Auburn, Sarah, Koch, Oliver, Sanders, Mandy, Hubbart, Christina, Maslen, Gareth, Ruano-Rubio, Valentin, Jyothi, Dushyanth, Miles, Alistair, O’Brien, John, Gamble, Chris, Oyola, Samuel O, Rayner, Julian C, Newbold, Chris I, Berriman, Matthew, Spencer, Chris CA, McVean, Gilean, Day, Nicholas P, White, Nicholas J, Bethell, Delia, Dondorp, Arjen M, Plowe, Christopher V, Fairhurst, Rick M, Kwiatkowski, Dominic P
Published 2013

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

by Park, Daniel J., Dudas, Gytis, Wohl, Shirlee, Goba, Augustine, Whitmer, Shannon L.M., Andersen, Kristian G., Sealfon, Rachel S., Ladner, Jason T., Kugelman, Jeffrey R., Matranga, Christian B., Winnicki, Sarah M., Qu, James, Gire, Stephen K., Gladden-Young, Adrianne, Jalloh, Simbirie, Nosamiefan, Dolo, Yozwiak, Nathan L., Moses, Lina M., Jiang, Pan-Pan, Lin, Aaron E., Schaffner, Stephen F., Bird, Brian, Towner, Jonathan, Mamoh, Mambu, Gbakie, Michael, Kanneh, Lansana, Kargbo, David, Massally, James L.B., Kamara, Fatima K., Konuwa, Edwin, Sellu, Josephine, Jalloh, Abdul A., Mustapha, Ibrahim, Foday, Momoh, Yillah, Mohamed, Erickson, Bobbie R., Sealy, Tara, Blau, Dianna, Paddock, Christopher, Brault, Aaron, Amman, Brian, Basile, Jane, Bearden, Scott, Belser, Jessica, Bergeron, Eric, Campbell, Shelley, Chakrabarti, Ayan, Dodd, Kimberly, Flint, Mike, Gibbons, Aridth, Goodman, Christin, Klena, John, McMullan, Laura, Morgan, Laura, Russell, Brandy, Salzer, Johanna, Sanchez, Angela, Wang, David, Jungreis, Irwin, Tomkins-Tinch, Christopher, Kislyuk, Andrey, Lin, Michael F., Chapman, Sinead, MacInnis, Bronwyn, Matthews, Ashley, Bochicchio, James, Hensley, Lisa E., Kuhn, Jens H., Nusbaum, Chad, Schieffelin, John S., Birren, Bruce W., Forget, Marc, Nichol, Stuart T., Palacios, Gustavo F., Ndiaye, Daouda, Happi, Christian, Gevao, Sahr M., Vandi, Mohamed A., Kargbo, Brima, Holmes, Edward C., Bedford, Trevor, Gnirke, Andreas, Ströher, Ute, Rambaut, Andrew, Garry, Robert F., Sabeti, Pardis C.
Published 2015