Cabrera, A., Kozik, A., Howad, W., Arus, P., Iezzoni, A.F., van der Knaap, E. (2009). Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers. BMC Genomics 10, 562.
Jiang, N., Gao, D., Xiao, H., and van der Knaap, E. (2009). Genome organization of the tomato sun locus and characterization of the unusual retrotransposon Rider. Plant Journal 60, 181-193.
Xiao, H., Radovich, C., Welty, N., Hsu, J., Li, D., Meulia, T., and van der Knaap, E. (2009) Integration of tomato reproductive developmental landmarks and expression profiles, and the effect of SUN on fruit shape. BMC Plant Biology 9, 49.
Gonzalo, M.J., Brewer, M.T., Anderson, C., Sullivan, D., Gray, S., and van der Knaap, E. (2009) Tomato Fruit Shape Analysis Using Morphometric and Morphology Attributes Implemented in Tomato Analyzer Software Program. J. Am. Soc. of Hort. Sci. 134, 77-87.
Darrigues, A., Hall, J., van der Knaap, E. and Francis, D.M. (2008) Tomato Analyzer-Color Test: a new tool for efficient digital phenotyping. J. Am. Soc. of Hort. Sci. 133, 579-586.
Xiao, H., Jiang, N., Schaffner, E., Stockinger, E.J., and van der Knaap, E. (2008) A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit. Science 319 no. 5869, 1527-1530.
Gonzalo, M.J., and van der Knaap, E. (2008) A comparative analysis into the genetic bases of morphology in tomato varieties exhibiting elongated fruit shape. Theor. Appl. Genet. 116, 647-656.
Olmstead ,J.W., Sebolt, A.M., Cabrera, A., Sooriyapathirana, S.S., Hammar, S., Iriarte, G., Wang, D., Chen, C.Y., van der Knaap, E. and Iezzoni, A.F. (2008)Construction of an intra-specific sweet cherry (Prunus avium L.) genetic linkage map and synteny analysis with the Prunus reference map. Tree Genetics & Genomes 4, 897-910.
Paran, I. and van der Knaap, E. (2007) Genetic and molecular regulation of fruit and plant domestication traits in tomato and pepper. J. Exp. Bot. 58, 3841-3852.
Van Deynze, A., Stoffel, K., Buell, C.R., Kozik, A., Liu, J., van der Knaap, E., and Francis D. (2007) Diversity in conserved genes in tomato. BMC Genomics 8, 465.
Welty, N., C. Radovich, T. Meulia, and E. van der Knaap. (2007) Inflorescence development in two tomato species. Can. J. Bot. 85, 111-118.
Labate J.A., M.J. Gonzalo, D.M. Francis, W.Yang, E. van der Knaap et al. (2007) Tomato. In: Kole C (ed) Genome Mapping and Molecular Breeding in Plants. Springer, Berlin, Heidelberg, New York.
Tian, M., J. Win, J. Song, R. van der Hoorn, E. van der Knaap and S. Kamoun. (2007) A Phytophthora infestans cystatin-like protein targets a novel tomato papain-like apoplastic protease. Plant Physiol. 143, 364-377.
Eduardo, I., J Obando, J.A. Martínez, A. Alarcón, P. Arús, J.M. Álvarez, E. van der Knaap, J.P Fernández-Trujillo, and A.J. Monforte. (2007) Estimating the Genetic Architecture of Fruit Quality Traits in Melon Using a Genomic Library of Near Isogenic Lines. J. Am. Soc. of Hort. Sci. 132, 80-89.
Brewer, M.T., J.B. Moyseenko, A.J. Monforte, and E. van der Knaap. (2007) Morphological Variation in Tomato: A Comprehensive Study of Quantitative Trait Loci Controlling Fruit Shape and Development. J. Exp. Bot. 58, 1339-1349.
Brewer, M.T., Lang, L., Fujimura, K., Dujmovic, N., Gray, S., and van der Knaap, E. (2006) Development of a controlled vocabulary and software application to analyze fruit shape variation in tomato and other plant species. Plant Physiol. 141, 15-25.
Van der Knaap, E., Sanyal, A., Jackson, S.A. and Tanksley, S.D. (2004) High-resolution fine mapping and fluorescence in situ hybridization analysis of sun, a locus controlling tomato fruit shape, reveals a region of the tomato genome prone to DNA rearrangements. Genetics, 168, 2127-2140.
Van der Knaap, E. and Tanksley, S.D. (2003) The making of a bell pepper-shaped tomato fruit: identification of loci controlling fruit morphology in Yellow Stuffer tomato. Theor. Appl. Genet. 107, 139-147.
Van der Knaap, E., Lippman, Z.B. and Tanksley, S.D. (2002) Extremely elongated tomato fruit controlled by four quantitative trait loci with epistatic interactions. Theor. Appl. Genet. 104, 241-247.
Van der Knaap, E. and Tanksley, S.D. (2001) Identification and characterization of a novel locus controlling early fruit development in tomato. Theor. Appl. Genet. 103, 353-358.
Yang, W., Bai, X., Kabelka, E., Eaton, C., Kamoun, S., van der Knaap, E. and Francis, D. (2004). Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags. Mol. Breeding, 14, 21-34.