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A computational model of gene expression reveals early transcriptional events at the subtelomeric regions of the malaria parasite, Plasmodium falciparum

Matthias Scholz* and Martin J Fraunholz

Author Affiliations

Competence Center for Functional Genomics, Ernst-Moritz-Arndt University, Friedrich-Ludwig-Jahn Strasse, D-17487 Greifswald, Germany

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Genome Biology 2008, 9:R88  doi:10.1186/gb-2008-9-5-r88

Published: 27 May 2008



The malaria parasite, Plasmodium falciparum, replicates asexually in a well-defined infection cycle within human erythrocytes (red blood cells). The intra-erythrocytic developmental cycle (IDC) proceeds with a 48 hour periodicity.


Based on available malaria microarray data, which monitored gene expression over one complete IDC in one-hour time intervals, we built a mathematical model of the IDC using a circular variant of non-linear principal component analysis. This model enables us to identify rates of expression change within the data and reveals early transcriptional events at the subtelomeres of the parasite's nuclear chromosomes.


A delay between subtelomeric and central gene activities suggests that key events of the IDC are initiated at the subtelomeric regions of the P. falciparum nuclear chromosomes.