The present invention provides molecular methods for efficiently transforming the genome of common disease-transmitting parasites, such as Plasmodium falciparum. The transformation efficiencies are improved up to 100 times over those conventionally known. The methods provide high saturation of the target parasite genome, of 50% or greater, and target non-specifically TTAA-rich sites in the parasite genome. The invention also discloses a model that may be used to functionally annotate the genome of the Plasmodium falciparum, thus permitting the design and screening of compounds that may be useful in the control and inhibiting of diseases caused and transmitted by these parasites, including malaria. Highly efficient and multi-site integrating transposons, particularly piggyBac transposons, which provide for random and multi-site integration into parasite genomes in the presence of a helper plasmid, are also presented.