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Method: Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum
- Heather J. Painter,
- Manuela Carrasquilla,
- and Manuel Llinás
Genome Res. June 2017 27: 1074-1086; Published in Advance April 17, 2017, doi:10.1101/gr.217356.116
..., the human malaria parasite, Plasmodium falciparum, is incapable of pyrimidine salvage for mRNA biogenesis. To capture cellular mRNA dynamics during Plasmodium development, we engineered parasites that can salvage pyrimidines through the expression of a single bifunctional yeast fusion gene, cytosine...
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Research: Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum
- Junya Yamagishi,
- Anna Natori,
- Mohammed E.M. Tolba,
- Arthur E. Mongan,
- Chihiro Sugimoto,
- Toshiaki Katayama,
- Shuichi Kawashima,
- Wojciech Makalowski,
- Ryuichiro Maeda,
- Yuki Eshita,
- Josef Tuda,
- and Yutaka Suzuki
Genome Res. September 2014 24: 1433-1444; Published in Advance August 4, 2014, doi:10.1101/gr.158980.113
...the transcriptomes of the human hosts and the infecting parasites affect one another. Here we report the RNA-seq analysis of 116 Indonesian patients infected with the malaria parasite Plasmodium falciparum (Pf). We extracted RNAs from their peripheral blood as a mixture of host and parasite transcripts and mapped...
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Resource: Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
- Alistair Miles,
- Zamin Iqbal,
- Paul Vauterin,
- Richard Pearson,
- Susana Campino,
- Michel Theron,
- Kelda Gould,
- Daniel Mead,
- Eleanor Drury,
- John O'Brien,
- Valentin Ruano Rubio,
- Bronwyn MacInnis,
- Jonathan Mwangi,
- Upeka Samarakoon,
- Lisa Ranford-Cartwright,
- Michael Ferdig,
- Karen Hayton,
- Xin-zhuan Su,
- Thomas Wellems,
- Julian Rayner,
- Gil McVean,
- and Dominic Kwiatkowski
Genome Res. September 2016 26: 1288-1299; Published in Advance August 16, 2016, doi:10.1101/gr.203711.115
...-9806, USA; 10Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom Corresponding author: alistair.miles@well.ox.ac.uk Abstract The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity...
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Research: Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals
- Ulrike Böhme,
- Thomas D. Otto,
- James A. Cotton,
- Sascha Steinbiss,
- Mandy Sanders,
- Samuel O. Oyola,
- Antoine Nicot,
- Sylvain Gandon,
- Kailash P. Patra,
- Colin Herd,
- Ellen Bushell,
- Katarzyna K. Modrzynska,
- Oliver Billker,
- Joseph M. Vinetz,
- Ana Rivero,
- Chris I. Newbold,
- and Matthew Berriman
Genome Res. April 2018 28: 547-560; Published in Advance March 2, 2018, doi:10.1101/gr.218123.116
...orthologs of genes that had previously appeared to be restricted to the clades of parasites containing Plasmodium falciparum and Plasmodium vivax, the species with the greatest impact on human health. From these orthologs, we explore differential diversifying selection across the genus and show...
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Resource: Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
- The Anopheles gambiae 1000 Genomes Consortium
Genome Res. October 2020 30: 1533-1546; Published in Advance September 28, 2020, doi:10.1101/gr.262790.120
..., making a valuable comparison. Among other eukaryotes, comparable data resources exist only for humans (The 1000 Genomes Project Consortium 2015) and malaria parasites (MalariaGEN Plasmodium falciparum Community Project 2019), and thus, there remains an absence of open genomic data for studying...
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Resource: Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii
- Carlos Vargas-Chavez,
- Neil Michel Longo Pendy,
- Sandrine E. Nsango,
- Laura Aguilera,
- Diego Ayala,
- and Josefa González
Genome Res. January 2022 32: 189-202; Published in Advance December 29, 2021, doi:10.1101/gr.275761.121
...of genes containing insertions -wide (χ2 test P-value = 0.7788). Eleven of the 148 genes containing TE insertions are differentially expressed in response to a Plasmodium invasion (Supplemental Table S12). These 11 genes participate in several pathways of the immune response including the small regulatory...
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LETTER: Comparative Genomics of Transcriptional Control in the Human Malaria Parasite Plasmodium falciparum
- Richard M.R. Coulson,
- Neil Hall,
- and Christos A. Ouzounis
Genome Res. August 2004 14: 1548-1554; Published in Advance July 15, 2004, doi:10.1101/gr.2218604
...Comparative Genomics of Transcriptional Control in the Human Malaria Parasite Plasmodium falciparum Richard M.R. Coulson 1 , 3 , Neil Hall 2 , and Christos A. Ouzounis 1 1 Computational Genomics Group, The European Bioinformatics Institute...
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Research: Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes
- Francesco Papa,
- Nikolai Windbichler,
- Robert M. Waterhouse,
- Alessia Cagnetti,
- Rocco D'Amato,
- Tania Persampieri,
- Mara K.N. Lawniczak,
- Tony Nolan,
- and Philippos Aris Papathanos
Genome Res. September 2017 27: 1536-1548; Published in Advance July 26, 2017, doi:10.1101/gr.217216.116
...increases both bacterial and parasite numbers (Dong et al. 2006), and AGAP000570 (AgSGU), which is one of themost abundant peritrophic matrix proteins (Dinglasan et al. 2009) and has important roles in ookinete attachment of Plasmodium falciparum (Mathias et al. 2014), were also identified. Of the remaining...
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Research: Genome scanning of Amazonian Plasmodium falciparum shows subtelomeric instability and clindamycin-resistant parasites
- Neekesh V. Dharia,
- David Plouffe,
- Selina E.R. Bopp,
- Gonzalo E. González-Páez,
- Carmen Lucas,
- Carola Salas,
- Valeria Soberon,
- Badry Bursulaya,
- Tadeusz J. Kochel,
- David J. Bacon,
- and Elizabeth A. Winzeler
Genome Res. November 2010 20: 1534-1544; Published in Advance September 9, 2010, doi:10.1101/gr.105163.110
...increase in the parasite clearance times in ACT-treated Plasmodium falciparum malaria cases from near the Thai–Cambodian border, suggesting that case numbers may soon begin increasing (Dondorp et al. 2009). Remarkably, although artemisinin is used on tens of millions of individuals annually, we have little...
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Letter: Nucleosome landscape and control of transcription in the human malaria parasite
- Nadia Ponts,
- Elena Y. Harris,
- Jacques Prudhomme,
- Ivan Wick,
- Colleen Eckhardt-Ludka,
- Glenn R. Hicks,
- Gary Hardiman,
- Stefano Lonardi,
- and Karine G. Le Roch
Genome Res. February 2010 20: 228-238; Published in Advance January 6, 2010, doi:10.1101/gr.101063.109
...factors to access DNA. In this model, promoter-specific transcription factors bind DNA to initiate the production of mRNA in a tightly regulated manner. In the case of the human malaria parasite, Plasmodium falciparum , specific transcription factors are apparently underrepresented with regards...

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