Claessens, Antoine; Affara, Muna; Assefa, Samuel A; Kwiatkowski, Dominic P; Conway, David J; (2017) Culture adaptation of malaria parasites selects for convergent loss-of-function mutants. Scientific reports, 7 (1). 41303-. ISSN 2045-2322 DOI: https://doi.org/10.1038/srep41303

Duffy, Craig W; Ba, Hampate; Assefa, Samuel; Ahouidi, Ambroise D; Deh, Yacine B; Tandia, Abderahmane; Kirsebom, Freja CM; Kwiatkowski, Dominic P; Conway, David J; (2017) Population genetic structure and adaptation of malaria parasites on the edge of endemic distribution. Molecular ecology, 26 (11). pp. 2880-2894. ISSN 0962-1083 DOI: https://doi.org/10.1111/mec.14066

Ba, H; Ahouidi, AD; Duffy, CW; Deh, YB; Diedhiou, C; Tandia, A; Diallo, MY; Assefa, S; Lô, BB; Elkory, MB; +1 more... Conway, DJ; (2016) [Evaluation of malaria rapid diagnostic test Optimal-IT® pLDH along the Plasmodium falciparum distribution limit in Mauritania]. Bulletin de la Societe de pathologie exotique (1990), 110 (1). pp. 31-37. ISSN 0037-9085 DOI: https://doi.org/10.1007/s13149-017-0541-y

Campino, Susana; Benavente, Ernest Diez; Assefa, Samuel; Thompson, Eloise; Drought, Laura G; Taylor, Catherine J; Gorvett, Zaria; Carret, Celine K; Flueck, Christian; Ivens, Al C; +4 more... Kwiatkowski, Dominic P; Alano, Pietro; Baker, David A; Clark, Taane G; (2016) Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines. Malaria journal, 15 (1). 229-. ISSN 1475-2875 DOI: https://doi.org/10.1186/s12936-016-1254-1

Murray, Lee; Mobegi, Victor A; Duffy, Craig W; Assefa, Samuel A; Kwiatkowski, Dominic P; Laman, Eugene; Loua, Kovana M; Conway, David J; (2016) Microsatellite genotyping and genome-wide single nucleotide polymorphism-based indices of Plasmodium falciparum diversity within clinical infections. Malaria journal, 15 (1). 275-. ISSN 1475-2875 DOI: https://doi.org/10.1186/s12936-016-1324-4

Assefa, Samuel; Lim, Caeul; Preston, Mark D; Duffy, Craig W; Nair, Mridul B; Adroub, Sabir A; Kadir, Khamisah A; Goldberg, Jonathan M; Neafsey, Daniel E; Divis, Paul; +5 more... Clark, Taane G; Duraisingh, Manoj T; Conway, David J; Pain, Arnab; Singh, Balbir; (2015) Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi. Proceedings of the National Academy of Sciences of the United States of America, 112 (42). pp. 13027-13032. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.1509534112

Divis, Paul CS; Singh, Balbir; Anderios, Fread; Hisam, Shamilah; Matusop, Asmad; Kocken, Clemens H; Assefa, Samuel A; Duffy, Craig W; Conway, David J; (2015) Admixture in Humans of Two Divergent Plasmodium knowlesi Populations Associated with Different Macaque Host Species. PLoS pathogens, 11 (5). e1004888-. ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1004888

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; (2015) Comparison of genomic signatures of selection on Plasmodium falciparum between different regions of a country with high malaria endemicity. BMC genomics, 16 (1). 527-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-015-1746-3

Assefa, Samuel A; Preston, Mark D; Campino, Susana; Ocholla, Harold; Sutherland, Colin J; Clark, Taane G; (2014) estMOI: estimating multiplicity of infection using parasite deep sequencing data. Bioinformatics (Oxford, England), 30 (9). pp. 1292-1294. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/btu005

Ocholla, Harold; Preston, Mark D; Mipando, Mwapatsa; Jensen, Anja TR; Campino, Susana; MacInnis, Bronwyn; Alcock, Daniel; Terlouw, Anja; Zongo, Issaka; Oudraogo, Jean-Bosco; +13 more... Djimde, Abdoulaye A; Assefa, Samuel; Doumbo, Ogobara K; Borrmann, Steffen; Nzila, Alexis; Marsh, Kevin; Fairhurst, Rick M; Nosten, Francois; Anderson, Tim JC; Kwiatkowski, Dominic P; Craig, Alister; Clark, Taane G; Montgomery, Jacqui; (2014) Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates. The Journal of infectious diseases, 210 (12). pp. 1991-2000. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiu349

Preston, Mark D; Campino, Susana; Assefa, Samuel A; Echeverry, Diego F; Ocholla, Harold; Amambua-Ngwa, Alfred; Stewart, Lindsay B; Conway, David J; Borrmann, Steffen; Michon, Pascal; +12 more... Zongo, Issaka; Ouédraogo, Jean-Bosco; Djimde, Abdoulaye A; Doumbo, Ogobara K; Nosten, Francois; Pain, Arnab; Bousema, Teun; Drakeley, Chris J; Fairhurst, Rick M; Sutherland, Colin J; Roper, Cally; Clark, Taane G; (2014) A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains. Nature communications, 5 (1). 4052-. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms5052

Clark, Taane G; Mallard, Kim; Coll, Francesc; Preston, Mark; Assefa, Samuel; Harris, David; Ogwang, Sam; Mumbowa, Francis; Kirenga, Bruce; O'Sullivan, Denise M; +8 more... Okwera, Alphonse; Eisenach, Kathleen D; Joloba, Moses; Bentley, Stephen D; Ellner, Jerrold J; Parkhill, Julian; Jones-López, Edward C; McNerney, Ruth; (2013) Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. PloS one, 8 (12). e83012-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0083012

Preston, Mark D; Assefa, Samuel A; Ocholla, Harold; Sutherland, Colin J; Borrmann, Steffen; Nzila, Alexis; Michon, Pascal; Hien, Tran Tinh; Bousema, Teun; Drakeley, Christopher J; +9 more... Zongo, Issaka; Ouédraogo, Jean-Bosco; Djimde, Abdoulaye A; Doumbo, Ogobara K; Nosten, Francois; Fairhurst, Rick M; Conway, David J; Roper, Cally; Clark, Taane G; (2013) PlasmoView: a web-based resource to visualise global Plasmodium falciparum genomic variation. The Journal of infectious diseases, 209 (11). pp. 1808-1815. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jit812

Sepúlveda, Nuno; Campino, Susana G; Assefa, Samuel A; Sutherland, Colin J; Pain, Arnab; Clark, Taane G; (2013) A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data. BMC genomics, 14 (1). 128-. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-14-128