Iorizzo, M., Senalik, D.A., Ellison, S., Grzebelus, D., Cavagnaro, P., Allender, C., Brunet, J., Spooner, D.M., Van Deynze, A., Simon, P.W. 2013. Genetic structure and domestication of carrot. American Journal of Botany. 100(5):930-938.
Iorizzo, M., Grzebelus, D., Senalik, D.A., Szklarczyk, M., Spooner, D.M., Simon, P.W. 2012. Against the traffic: The first evidence for mitochondrial DNA transfer into the plastid genome. Mobile Genetic Elements. 2(6):261-266.
Ellison, S.L., Iorizzo, M., Senalik, D.A., Simon, P.W. 2013. Genome-wide association of the domestication syndrome in carrot (Daucus carota L.) [abstract]. Plant and Animal Genome Conference. Paper No. P0698.
Iorizzo, M., Senalik, D.A., Ellison, S.L., Grzebelus, D., Cavagnaro, P., Spooner, D.M., Van Deynze, A., Simon, P.W. 2013. Development of a high-throughput SNP resource to advance genomic, genetic and breeding research in carrot (Daucus carota L.) [abstract]. Plant and Animal Genome Conference. Paper No. P0762.
Grzebelus, D., Baranski, R., Iorizzo, M., Senalik, D.A., Ellison, S.L., Cavagnaro, P., Macko-Podgorni, A., Heller-Uszynska, K., Kilian, A., Simon, P.W. 2013. Diversity Arrays Technology (DArT) platform for genotyping and mapping in carrot (Daucus carota L.) [abstract]. Plant and Animal Genome Conference. Paper No. P0697.
Alessandro, M.S., Galamarini, C.R., Iorizzo, M., Simon, P.W. 2013. Molecular mapping of vernalization requirement and fertility restoration genes in carrot. Theoretical and Applied Genetics. 126(2):415-423.
Simon, P.W., Iorizzo, M., Senalik, D.A., Szklarczyk, M., Grzebelus, D., Spooner, D.M. 2012. De novo assembly and characterization of the carrot mitochondrial genome using next generation sequencing data from whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome. Biomed Central (BMC) Plant Biology. 12:1-17.
Baransi, R., Maksylewicz-Kaul, A., Nothnagel, T., Cavagnaro, P., Simon, P.W., Grzebelus, D. 2011. Genetic diversity of carrot (Daucus carota L.) cultivars revealed by analysis of SSR loci. Genetic Resources and Crop Evolution. 59(2):163-170.
Zalapa, J.E., Steffan, S.A., Simon, P.W., Senalik, D.A., Polashock, J.J., Vorsa, N., Fajardo, D., Harbut, R., Zhu, H., Mccown, B., Zeldin, E. 2012. In silico analysis of 454 data yields the complete American cranberry (Vaccinium macrocarpon Ait.) plastid genome [abstract]. Plant and Animal Genome Conference. Paper No. P0047.
Iorizzo, M., Simon, P.W., Senalik, D.A., Szklarczyk, M., Grzeblus, D. 2012. De novo assembly of the carrot mitochondrial genome [abstract]. Plant and Animal Genome Conference. Paper No. P0040.
Zalapa, J.E., Cuevas, H.E., Steffan, S.A., Simon, P.W., Senalik, D.A., Zhu, H., Mccown, B., Zeldin, E., Harbut, R. 2012. Using next generation sequencing approaches for the isolation of simple sequence repeats (SSR) in the plant sciences. American Journal of Botany. 99(2):193-208.
Grzebelus, D., Baranski, R., Spalik, K., Allender, C., Simon, P.W. 2011. Daucus. In: Kole, C., editor, Wild Crop Relatives: Genomic and Breeding Resources. New York, NY:Springer. p. 91-113.
Mccann, L.C., Bethke, P.C., Casler, M.D., Simon, P.W. 2011. Allocation of experimental resources to minimize the variance of genotype mean chip color and tuber composition. Crop Science. 52(4):1475-1481.
Iorizzo, M., Senalik, D.A., Grzebelus, D., Bowman, M., Cavagnaro, P.F., Matvienko, M., Ashrafi, H., Van Deynze, A., Simon, P.W. 2011. De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. Biomed Central (BMC) Genomics. 12:389.
Cavagnaro, P.F., Chung, S., Manin, S., Yildiz, M., Ali, A., Alessandro, M.S., Iorizzo, M., Senalik, D.A., Simon, P.W. 2011. Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae. Biomed Central (BMC) Genomics. 12:386.
Bo, K., Song, H., Shen, J., Qian, C., Staub, J.E., Simon, P.W., Lou, Q., Chen, J. 2011. Inheritance and mapping of the ore gene controlling the quantity of ß-carotene in cucumber (Cucumis sativus L.) endocarp. Molecular Breeding. 30(1):335-344.
Iovene, M., Cavagnaro, P.F., Simon, P.W., Senalik, D.A., Buell, C.R., Jiang, J. 2011. Comparative FISH mapping of Daucus species (Apiaceae family). Chromosome Research. 19:493-506.
Garcia Lampasona, S., Burba, J.L., Simon, P.W. 2010. Molecular markers: are they really useful to detect genetic variability in local garlic collections? The Americas Journal of Plant Science and Biotechnology. 4(SI1):104-112.
Bhasi, A., Simon, P.W., Senalik, D.A., Kumar, B., Manikandan, V., Philge, P., Senapathy, P. 2011. The Development of RoBuST: An integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae [abstract]. Plant and Animal Genome Conference. P. 811.
Iorizzo, M., Bowman, M., Simon, P.W., Cavagnaro, P., Senalik, D.A., Carputo, D., Van Deynze, A. 2011. Development of EST based markers for exploiting the carrot genome [abstract]. Plant and Animal Genome Conference. p. 175.
Bhasi, A., Simon, P.W., Senalik, D.A., Kumar, B., Manikandan, V., Philip, P., Senapathy, P. 2010. RoBuST: An Integrated Resource of Genomics Information for Plants in the Root and Bulb Crop Families Apiaceae and Alliaceae. Biomed Central (BMC) Plant Biology. 10:161.
Simon, P.W. 2010. New carrot and garlic germplasm to advance breeding and understand crop origins [abstract]. American Society of Horticulture Science Meeting. p. 11.
Mccann, L.C., Bethke, P.C., Simon, P.W. 2010. Extensive Variation in Fried Chip Color and Tuber Composition in Cold-Stored Tubers of Wild Potato (Solanum) Germplasm. Journal of Agriculture and Food Chemistry. 58(4):2368-2376.
Bowman, M.J., Willis, D.K., Simon, P.W. 2010. Quantification of the Ratio of Plastid to Chromosomal Genome in Leaf and Root Tissue of Carrot (Daucus Carota) Using Real Time Quantitative PCR [abstract]. Plant and Animal Genome Conference. p. 114.
Acharya, L., Simon, P.W. 2010. Diversity of garlic (Allium sativum L.) using SSR, EST and AFLP markers [abstract]. Plant and Animal Genome Conference. p. 124.
Bowman, M., Matvienko, M., Van Deynze, A., Simon, P.W., Senalik, D.A. 2010. Developing genomic resources for the apiaceae [abstract]. Plant and Animal Genome Conference. P. 037.
Podgorni, M., Mschichowska, A., Grzebelus, E., Grzebelus, D., Simon, P.W. 2010. DcSto, stowaway-like miniature inverted-repeat transposable elements (MITEs), are abundant and polymorphic in the carrot genome [abstract]. Plant and Animal Genome Conference. p. 205.
Cuevas, H.E., Staub, J.E., Simon, P.W. 2010. Inheritance of the Quantity of ß-carotene and Fruit Maturity of Melon (Cucumis Melon L.). Euphytica. 171(3):301-311.
Ortiz, R., Simon, P.W., Jansky, S.H., Stelly, D. 2009. Ploidy Manipulation of the Gametophyte, Endosperm, and Sporophyte in Nature and for Crop Improvement – A Tribute to Prof. Stanley J. Peloquin (1921-2008). Annals Of Botany. 104(5):795-807.
Just, B.J., Santos, C.F., Yandell, B.S., Simon, P.W. 2009. Major QTL for Carrot Color are Associated with Carotenoid Biosynthetic Genes and Interact Epistatically in a Domesticated x Wild Carrot Cross. Theoretical and Applied Genetics. 119(7):1155-1169.
Baenziger, P.S., Simon, P.W., Wehner, T.C. 2009. Educating the Next Generation of Plant Breeders: The Need and the Challenge. Society for Advancement of Breeding Researches in Asia and Oceania. 14:1-10.
Lopez, P.A., Widrlechner, M.P., Simon, P.W., Rai, S., Bailey, T.B., Gardner, C.A. 2009. Applying Molecular Markers in Coriander Populations with Diverse Geographical Origins. In: Proceedings of the XIII National Congress of Mexican Society of Horticultural Sciences, August 17-21, 2009, Torreon, Coahuila, Mexico. p. 2.
Cuevas, H.E., Staub, J.E., Simon, P.W., Zalapa, J.E. 2010. A Consensus Linkage Map that Identifies Genomic Regions Controlling Beta-Carotene Quantity and Fruit Maturity in Melon (Cucumis Melo L.). Theoretical and Applied Genetics. 119:741-756.
Sun, T., Simon, P.W., Tanumihardjo, S.A. 2009. Antioxidants and Antioxidant Capacity of Biofortified Carrots (Daucus Carota, L.) of Various Colors. Journal of Agricultural and Food Chemistry. 57(10):4142-4147.
Simon, P.W., Cavagnaro, P.F., Chung, S., Szklarczyk, M., Grzebelus, D., Senalik, D.A., Atkins, A.E. 2009. Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences. Molecular Genetics and Genomics. 281(3):273-288.
Simon, P.W., Cavagnaro, P.F., Senalik, D.A. 2009. SplinkBES - A Splinkerette-Based Method for Generating Long End Sequences From Large Insert DNA Libraries. Biotechniques. 47:681-690.
Peloquin, S.J., Simon, P.W., Jansky, S.H. 2009. The Concept of Horizontal Linkage and Its Application to Genetics and Breeding. In: Mohan, R.H., editor. Research Advances in Heredity. 1st edition. Kerala, India:Global Research Network. p. 1-7.
Simon, P.W., Roberts, P.A., Nunez, J. 2009. Progress in the Development of Nutrient-Rich Nematode Resistant Carrots [abstract]. 33rd International Carrot Conference. Paper No. BG-101.
Simon, P.W., Kane, R.T. 2009. Genetic Influences on the Seed Yielding Ability of Carrot Hybrids [abstract]. 33rd International Carrot Conference. Paper No. BG-102.
Simon, P.W., Cavagnaro, P.F., Chung, S., Ali, A., Yildiz, M., Alesandro, M.S. 2009. Development of 304 new microsatellite markers for carrot. Analysis of their potential for linkage mapping, assessment of genetic diversity and cross-taxa utilization [abstract]. 33rd International Carrot Conference. Paper No. BG-103.
Simon, P.W., Bowman, M.J., Willis, D.K. 2009. Understanding the molecular mechanism of carotenoid accumulation in carrot (Daucus carota) using real time quantitative PCR [abstract]. 33rd International Carrot Conference. Paper No. BG-104.
Simon, P.W., Bowman, M.J., Willis, D.K. 2009. Expression Analysis of Carotenoid Biosynthesis Genes in Carrot (Daucus Carota) Using Real Time Quantitative PCR. Plant and Animal Genome Conference [abstract]. Plant and Animal Genome Conference. p. 717.
Simon, P.W., Cavagnaro, P.F., Chung, S., Ali, A., Yildiz, M., Alesandro, M.S. 2009. Development and Characterization of Novel SSR Markers in Carrot (Daucus Carota L.) and Their Application for Mapping and Diversity Analysis in Apiaceae. Plant and Animal Genome Conference [abstract]. Plant and Animal Genome Conference. p. 132.
Simon, P.W., Iovene, M., Cavagnaro, P.F., Jiang, J. 2009. Association Between Pachytene Chromosomes and Linkage Groups in Carrot. Plant and Animal Genome Conference [abstract]. Plant and Animal Genome Conference. p. 201.
Iovene, M., Wielgus, S.M., Simon, P.W., Buell, C.R., Jiang, J. 2008. Chromatin structure and physical mapping of chromosome 6 of potato and comparative analyses with tomato. Genetics. 180(3):1307-1317.
Mills, J.P., Simon, P.W., Tanumihardjo, S.A. 2008. Biofortified Carrot Intake Enhances Liver Antioxidant Capacity and Vitamin A Status in Mongolian Gerbils. Journal of Nutrition. 138(9):1692-1698.
Grzebelus, D., Simon, P.W. 2008. Diversity of DcMaster-like elements of the PIF/Harbinger superfamily in the carrot genome. Genetica. Available: http://www.ncbi.nlm.nih.gov/pubmed/18535910.
Iovene, M., Grzebelus, E., Carputo, D., Jiang, J., Simon, P.W. 2008. Major Cytogenetic Landmarks and Karyotype analysis in Carrot and Other Apiaceace. American Journal of Botany. 95:793-804.
Cuevas, H.E., Staub, J.E., Simon, P.W., McCreight, J.D., Zalapa, J.E. 2008. Mapping of Genetic Loci that Regulate Accumulation of Beta-Carotene in Fruit of U.S. Western Shipping Melon (Cucumis Melo L.) and Their Association With Putative Carotenoid Biosynthesis Genes. Theoretical and Applied Genetics 117:1345-1359.
Cavagnaro, P.F., Chung, S., Simon, P.W. 2008. Construction and characterization of a deep-coverage carrot (Daucus carota L.) BAC library [abstract]. 2008 Plant and Animal Genome Meeting. p. 56.
Iovene, M., Grzebelus, E., Carputo, D., Jiang, J., Simon, P.W. 2008. Major Cytogenetic Landmarks and Karyotype Analysis in Carrot (Daucus carota L.) and Other Apiaceace [abstract]. 2008 Plant and Animal Genome Meeting. p. 201.
Behera, T., Simon, P.W., Staub, J.E. 2007. Bitter Gourd; A vegetable to Improve Human Health. Medicinal and Aromatic Plants: Production, Business and Applications. 1(2):224-227.
Ipek, M., Ipek, A., Simon, P.W. 2008. Genetic Characterization of Allium Tuncelianum: An Endemic Edible Allium Species With Garlic Odor. Scientia Horticultureae. 115(4):409-415.
Simon, P.W., Tanumihardjo, S.A., Clevidence, B.A., Novotny Dura, J. 2008. Role of Color and Pigments in Breeding, Genetics, and Nutritional Improvement of Carrots. In: Culver, C.A., Wrolstad, R.E., editors. Color Quality of Fresh and Processed Foods. Washington, D.C.: Oxford University Press. p. 151-165.
Peloquin, S.J., Boiteux, L.S., Simon, P.W., Jansky, S.H. 2008. A chromosome-specific estimate of transmission of heterozygosity by 2n gametes in potato. Journal of Heredity. 99(2):177-181.
Ipek, M., Ipek, A., Simon, P.W. 2008. Molecular Characterization of Kastamonu Garlic: An Economically Important Garlic Clone in Turkey. Scientia Horticultureae. 115(2):203-208.
Ipek, M., Ipek, A., Senalik, D.A., Simon, P.W. 2007. Characterization of an Unusual Cytoplasmic Chimera Detected in Bolting Garlic (Allium sativum L.) Clones. Journal of the American Society for Horticultural Science. 132:664-669.
Camadro, E.L., Cauhepe, M.A., Simon, P.W. 2008. Compatibility Relations Between the Edible Carrot Daucus Carota and D. Pusillus, a Related Wild Species from the Argentinian Pampas. Euphytica. 159(1-2):103-109.
Mills, J.P., Simon, P.W., Tanumihardjo, S.A. 2007. ß-Carotene from Red Carrot Maintains Vitamin A Status, but Lycopene Bioavailability Is Lower Relative to Tomato Paste in Mongolian Gerbils. Journal of Nutrition. 137:1395-1400.
Cuevas, H.E., Staub, J.E., Simon, P.W., McCreight, J.D., Zalapa, J.E. 2007. Carotenoid pathway genes and accumulation of B-carotene in Cucumis melo L [abstract]. American Society for Horticultural Science 104th Annual Conference. 42(4):1013-1014.
Lopez, P.A., Widrlechner, M.P., Simon, P.W., Rai, S., Bailey, T.B., Gardner, C.A. 2007. Screening coriander gene pool for special uses. In: Janick, J. and Whipkey, A., editors. Issues in New Crops and New Uses. 2006 AAIC Annual Meeting and Sixth New Crops Symposium, October 14-18, 2006, San Diego, California. p. 280-283.
Cavagnaro, P.F., Camargo, A., Galmarini, C.R., Simon, P.W. 2007. Effect of cooking on garlic (Allium sativum) antiplatelet activity and thiosulfinates content. Journal of Agricultural and Food Chemistry. 55:1280-1288.
Porter Dosti, M., Mills, J.P., Simon, P.W., Tanumihardjo, S.A. 2006. Bioavailability of beta-carotene (betaC) from purple carrots is the same as typical orange carrots while high-betaC carrots increase betaC stores in Mongolian gerbils (Meriones unguiculatus). British Journal of Nutrition. 96(2):260-269.
Lopez, P.A., Widrlechner, M.P., Simon, P.W., Rai, S., Bailey, T.B., Gardner, C.A. 2006. Screening the gene pool for special uses in coriander [abstract]. Association for the Advancement of Industrial Crops Conference. p. 68
Grzebelus, D., Jagosz, B., Simon, P.W. 2007. The DcMaster Transposon Display maps polymorphic insertion sites in the carrot (Daucus carota L.) genome. Gene. 390:67-74.
Camadro, E.L., Cauhepe, M.A., Simon, P.W. 2007. Geographical Distribution of Wild Daucus Species in the Natural Grasslands of the Argentinian Pampas . Genetic Resources and Crop Evolution. 54(4):855-863.
Ipek, A., Ipek, M., Simon, P.W. 2006. Association of reversible inactivation of maize transposable element, Ds, with tissue-specific processing of the 35s:TPase transcript in carrot (Daucus carota l.)[abstract]. Journal of Horticultural Science and Biotechnology. 81:819-826.
Grzebelus, D., Yau, Y., Simon, P.W. 2006. Master - a novel family of PIF/Harbinger-like transposable elements identified in carrot (Daucus carota L.). Molecular Genetics and Genomics. 275:450-459.
Baranski, R., Baranska, M., Schulz, H., Simon, P.W., Nothnagel, T. 2006. Single seed Raman measurements allow taxonomical discrimination of Apiaceae accessions collected in gene banks. Biopolymers. 81:497-505.
Ipek, A., Masson, P., Simon, P.W. 2006. Genetic transformation of an Ac/Ds - based transposon tagging system in carrot (Daucus carota). European Journal of Horticultural Science. 71:245-251.
Kurilich, A.C., Clevidence, B.A., Britz, S.J., Simon, P.W., Novotny Dura, J. 2005. Plasma and urine responses are lower for acylated vs nonacylated anthocyanins from raw and cooked purple carrot. Journal of Agricultural and Food Chemistry. 53:6537-6542.
Silva, E.M., Simon, P.W. 2006. Genetic, Physiological, and Environmental Factors Affecting Acrylamide Concentration in Fried Potato Products. In: Friedman, M., Mottram, D., editors. Advances in Experimental Medicine and Biology. New York, NY:Springer. p. 371-386.
Santos, C.A., Senalik, D.A., Simon, P.W. 2005. Path analysis suggests phytoene accumulation as the key step limiting the carotenoid pathway in roots of white carrot. Genetics and Molecular Biology. 28:287-293.
Surles, R., Weng, N., Simon, P.W., Tanumihardjo, S. 2004. Carotenoid profiles and consumer sensory evaluation of specialty carrots. Journal of Agriculture and Food Chemistry. 52:3417-3421.
Yau, Y.Y., Santos, K., Simon, P.W. 2005. Molecular tagging and selection for sugar-type in carrot roots using co-dominant, PCR-based markers. Molecular Breeding. 16:1-10
Ipek, M., Ipek, A., Almquist, S.G., Simon, P.W. 2005. Demonstration of linkage and development of the first low-density genetic map of garlic based on aflptm markers. Theoretical and Applied Genetics. 110:228-236.
Molldrem, K., Li, J., Simon, P.W., Tanumijardjo, S. 2004. Lutein and beta-carotene are bioavailable in humans from lutein-containing yellow carrots. American Journal of Clinical Nutrition. 80:131-136.
Santos, C.A., Simon, P.W. 2004. Merging carrot linkage groups based on conserved dominant AFLP markers in F2 populations. Journal of the American Society for Horticultural Science. 129:211-217.
Horvitz, M.A., Simon, P.W., Tanumihardjo, S.A. 2004. Relative bioavailability of lycopene from lycopene "red" carrots compared to tomato. American Journal of Clinical Nutrition.
Santos, C.A., Simon, P.W. 2003. Sequencing of specific AFLP amplicons reveals highly conserved DNA sequences mapping to the same linkage groups in two unrelated F2 populations of carrot. Genetics and Molecular Biology. 25:195-201.
Hyman, J., Simon, P.W., Burmeister, A. 2003. Development of co-dominant markers linked to the Mj-l locus in carrot (Daucus carota L. ssp. sativus)[abstract]. HortScience. 38:717.
Cavagnaro, P., Masuelli, R., Simon, P.W. 2003. Molecular data suggest multiple members comprising the alliinase gene family in garlic [abstract]. HortScience. 38:804-805.
Santos, C.A., Simon, P.W. 2002. QTL analyses reveal clustered loci for accumulation of major provitamin A carotenes and lycopene in carrot roots. Molecular Genetics and Genomics. 268:122-129.
Ipek, M., Ipek, A., Simon, P.W. 2003. Comparison of AFLPs, RAPD markers, and isozymes for diversity assessment of garlic and detection of putative duplicates in germplasm collections. Journal of the American Society for Horticultural Science. 128:246-252.
Bach, I.C., Olesen, A., Simon, P.W. 2002. PCR-based markers to differentiate the mitochondrial genomes of petaloid and male fertile carrot (Daucus carota L.). Euphytica. 127:353-365.
Etoh, T., Simon, P.W. 2002. Diversity, fertility and seed production of garlic. In: Rabinowitch, H.D. and Currah, L., editors. Advances in Allium Science. New York, NY: CABI Publishing. p. 101-118.