von der Heyden S, Lipinski MR, Matthee CA. Remarkably low mtDNA control region diversity in an abundant demersal fish. Molecular Phylogenetics and Evolution, doi: 10.1016/j.ympev. 2009.09.018
von der Heyden S, Barendse J, Seebregts AJ, Matthee CA (2009) Misleading the masses: detection of mislabeled and substituted frozen fish products in South Africa. ICES Journal of Marine Science 67: 176-185
von der Heyden S (2009) Why do we need to integrate population genetics into South African Marine Protected Area planning? African Journal of Marine Science 31: 263-269
Neethling M, Matthee CA, Bowie RCK, von der Heyden S (2008) Evidence of successful dispersal across a major oceanographic barrier in the southern African endemic, Caffrogobius caffer (Teleostei: Gobiidae). BMC Evolutionary Biology 8: 325
von der Heyden S, Prochazka K, Bowie RCK (2008) Significant population structure amidst expanding populations of Clinus cottoides (Perciformes, Clinidae): application of molecular tools to marine conservation planning in South Africa. Molecular Ecology 17: 4812-4826
von der Heyden S, Matthee CA (2008) Towards resolving familial relationships within the Gadiformes and the resurrection of the Lyconidae. Molecular Phylogenetics and Evolution 48: 764-769
von der Heyden S, Groeneveld JC, Matthee CA (2007) ‘Long current to nowhere?' – genetic connectivity of Jasus tristani in the southern Atlantic Ocean. African Journal of Marine Science 29: 491-497
Matthee CA, Cockroft AC, Gopal K, von der Heyden S (2007) Mitochondrial DNA variation of the west coast rock lobster, Jasus lalandii: marked genetic diversity differences among sampling sites. Marine Freshwater Research 58: 1130-1135
Cavalier-Smith T, von der Heyden S (2007) Molecular phylogeny, scale evolution and taxonomy of centrohelid Heliozoa. Molecular Phylogenetics and Evolution 44: 1186-1203
Moreira D, von der Heyden S, Bass D, López-García P, Chao E, Cavalier-Smith T (2007) Global eukaryote phylogeny: combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata. Molecular Phylogenetics and Evolution 44: 255-266
von der Heyden S, Lipinski MR, Matthee CA (2007) Species-specific genetic markers for identification of early life history stages of Cape hakes, Merluccius capensis and M. paradoxus in the southern Benguela Current. Journal of Fish Biology 70: 262-256
von der Heyden S, Lipinski MR, Matthee CA (2007) Mitochondrial DNA analyses of the Cape hakes reveal an expanding, panmictic population for Merluccius capensis and population structuring for mature fish in Merluccius paradoxus. Molecular Phylogenetics and Evolution 42: 517-527
von der Heyden S, Cavalier-Smith T (2005) Culturing and environmental DNA sequence studies uncover hidden kinetoplastid biodiversity and distinct marine and freshwater clades in Neobodo designis. International Journal of Systematic and Evolutionary Microbiology 55: 2605-2621
Bass D, Moreira D, López-García P, Polet S, Chao E, von der Heyden S, Pawlowski J, Cavalier-Smith T (2005) Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist 56: 149-161
Stoeck T, Schwarz MVJ, Boenigk J, Schweikert M, von der Heyden S, Behnke A (2005) Cellular identity of a novel 18S rRNA sequence clade within the class Kinetoplastea: the novel genus Actuariola gen. nov. (Neobodonida) with description of the type species Actuariola framii sp. nov. International Journal of Systematic and Evolutionary Microbiology 55: 2623-2635
von der Heyden S, Chao E, Vickerman K, Cavalier-Smith T (2004) Ribosomal RNA phylogeny of bodonid and diplonemid flagellates and the evolution of Euglenozoa. Journal of Eukaryotic Microbiology 51: 402-416
von der Heyden S, Chao E, Cavalier-Smith T (2004) Genetic diversity of goniomonads: an ancient divergence between freshwater and marine species. European Journal of Phycology 39: 343-350