Hudson Ashrafi

Chizk, T. M., Clark, J. R. R., Johns, C., Nelson, L., Ashrafi, H., Aryal, R., & Worthington, M. L. L. (2023). Genome-wide association identifies key loci controlling blackberry postharvest quality. FRONTIERS IN PLANT SCIENCE, 14. https://doi.org/10.3389/fpls.2023.1182790

Brůna, T., Aryal, R., Dudchenko, O., Sargent, D. J., Mead, D., Buti, M., … Worthington, M. (2022). A chromosome-length genome assembly and annotation of blackberry (<i>Rubus argutus</i>, cv. “Hillquist”). G3 Genes|Genomes|Genetics, 11. https://doi.org/10.1093/g3journal/jkac289

Crowl, A. A., Fritsch, P. W., Tiley, G. P., Lynch, N. P., Ranney, T. G., Ashrafi, H., & Manos, P. S. (2022, October 17). A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus). AMERICAN JOURNAL OF BOTANY, Vol. 10. https://doi.org/10.1002/ajb2.16065

Mengist, M. F., Bostan, H., De Paola, D., Teresi, S. J., Platts, A. E., Cremona, G., … Iorizzo, M. (2022, September 3). Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum). NEW PHYTOLOGIST, Vol. 9. https://doi.org/10.1111/nph.18428

Sullenberger, M. T., Jia, M., Gao, S., Ashrafi, H., & Foolad, M. R. (2022, August 12). Identification of late blight resistance quantitative trait loci in Solanum pimpinellifolium accession PI 270441. PLANT GENOME, Vol. 8. https://doi.org/10.1002/tpg2.20251

Redpath, L. E., Aryal, R., Lynch, N., Spencer, J. A., Hulse-Kemp, A. M., Ballington, J. R., … Ashrafi, H. (2022). Nuclear DNA contents and ploidy levels of North American Vaccinium species and interspecific hybrids. SCIENTIA HORTICULTURAE, 297. https://doi.org/10.1016/j.scienta.2022.110955

Adhikari, T. B., Aryal, R., Redpath, L. E., Broeck, L., Ashrafi, H., Philbrick, A. N., … Louws, F. J. (2022). RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic Colletorichum spp. in Strawberry. FRONTIERS IN GENETICS, 12. https://doi.org/10.3389/fgene.2021.805771

Edger, P. P., Iorizzo, M., Bassil, N. V., Benevenuto, J., Ferrao, L. F. V., Giongo, L., … Zalapa, J. (2022). There and back again; historical perspective and future directions for Vaccinium breeding and research studies. HORTICULTURE RESEARCH, 9. https://doi.org/10.1093/hr/uhac083

Hulse-Kemp, A. M., Bostan, H., Chen, S., Ashrafi, H., Stoffel, K., Sanseverino, W., … Van Deynze, A. (2021, June 10). An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids. PLANT GENOME, Vol. 6. https://doi.org/10.1002/tpg2.20101

Zhao, F., Maren, N. A., Kosentka, P. Z., Liao, Y.-Y., Lu, H., Duduit, J. R., … Liu, W. (2021). An optimized protocol for stepwise optimization of real-time RT-PCR analysis. HORTICULTURE RESEARCH, 8(1). https://doi.org/10.1038/s41438-021-00616-w

Kraft, L. J., Sit, T. L., Diepenbrock, L. M., Ashrafi, H., Aryal, R., Fernandez, G. E., & Burrack, H. J. (2021). Detection of Fruit Meals Within Laboratory-Raised and Field-Trapped Adult Drosophila suzukii (Diptera: Drosophilidae) Guts. Frontiers in Ecology and Evolution, 9. https://doi.org/10.3389/fevo.2021.719645

Yow, A. G., Zhang, Y., Bansal, K., Eacker, S. M., Sullivan, S., Liachko, I., … Ashrafi, H. (2021). Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type. G3-GENES GENOMES GENETICS, 11(2). https://doi.org/10.1093/g3journal/jkaa052

Redpath, L. E., Gumpertz, M., Ballington, J. R., Bassil, N., & Ashrafi, H. (2021). Genotype, Environment, Year, and Harvest Effects on Fruit Quality Traits of Five Blueberry (Vaccinium corymbosum L.) Cultivars. AGRONOMY-BASEL, 11(9). https://doi.org/10.3390/agronomy11091788

Mengist, M. F., Bostan, H., Young, E., Kay, K. L., Gillitt, N., Ballington, J., … Iorizzo, M. (2021). High-density linkage map construction and identification of loci regulating fruit quality traits in blueberry. HORTICULTURE RESEARCH, 8(1). https://doi.org/10.1038/s41438-021-00605-z

Maren, N., Zhao, F., Aryal, R., Touchell, D., Liu, W., Ranney, T., & Ashrafi, H. (2021). Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae). BMC GENOMICS, 22(1). https://doi.org/10.1186/s12864-021-07641-y

Zurn, J. D., Driskill, M., Jung, S., Main, D., Yin, M. H., Clark, M. C., … Bassil, N. (2020). A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding. G3-GENES GENOMES GENETICS, 10(10), 3729–3740. https://doi.org/10.1534/g3.120.401449

Maren, N. A., Touchell, D. H., Ranney, T. G., Ashrafi, H., Whitfield, M. B., & Chinn, M. (2020). Biomass yields, cytogenetics, fertility, and compositional analyses of novel bioenergy grass hybrids (Tripidium spp.). GLOBAL CHANGE BIOLOGY BIOENERGY, 12(5), 361–373. https://doi.org/10.1111/gcbb.12676

Jahnke, N. J., Dole, J. M., & Ashrafi, H. (2020). Simulated storage causes carbohydrate loss and rooting differences in two poinsettia cultivars. CANADIAN JOURNAL OF PLANT SCIENCE, 100(4), 459–462. https://doi.org/10.1139/cjps-2019-0232

Jiang, Y., Li, C., Takeda, F., Kramer, E. A., Ashrafi, H., & Hunter, J. (2019). 3D point cloud data to quantitatively characterize size and shape of shrub crops. HORTICULTURE RESEARCH, 6. https://doi.org/10.1038/s41438-019-0123-9

Gonda, I., Ashrafi, H., Lyon, D. A., Strickler, S. R., Hulse-Kemp, A. M., Ma, Q., … Foolad, M. R. (2019). Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection. PLANT GENOME, 12(1). https://doi.org/10.3835/plantgenome2018.02.0010

Gallardo, R. K., Zhang, Q., Dossett, M., Polashock, J. J., Rodriguez-Saona, C., Vorsa, N., … Iorizzo, M. (2018). Breeding Trait Priorities of the Blueberry Industry in the United States and Canada. HortScience, 53(7), 1021–1028. https://doi.org/10.21273/hortsci12964-18

Aryal, R., Yow, A., & Ashrafi, H. (2018, August). Developing the Genomic Resources for a Tetraploid Blueberry cv "O'Neal". Poster presented at the National Association of Plant Breeders 2018 Annual Meeting, Guelph Canada.

Aryal, R., & Ashrafi, H. (2018, July). Differential Gene Expression during Blueberry Fruits Ripening. Poster presented at the Plant Biology 2018, Montreal, Quebec, Canada.

Aryal, R., Bostan, H., Yow, A. G., Tseng, E., Iorizzo, M., & Ashrafi, H. (Januaary 13-17, 2018Januaary 13-17, 2018). Differential Gene Expression during Flower and Fruit Development of the Blueberry Cv. "O'Neal". Poster presented at the Plant and Animal Genome XXVI Conference, San Diego CA.

Redpath, L. E., Yow, A. G., Aryal, R., Hulse-Kemp, A. M., Franks, R. G., Whetten, R., & Ashrafi, H. (2018, July). Differential Gene Expression of Southern Highbush Blueberry cv. ‘O’Neal’ Floral Buds in Response to Freeze Treatment and Recovery Periods. Poster presented at the American Society for Horticultural Science, Washington D.C.

Redpath, L. E., & Ashrafi, H. (2018, April). Differential Gene Expression of ‘O’Neal’ Blueberry Floral Buds in Response to Freeze Treatment and Recovery Periods. Presented at the Genomic Science and Biomathematics Symposium, NC State University, Raleigh NC.

Redpath, L. E., Bland, T. W., Ballington, J. R., Jiang, Y., Li, C., & Ashrafi, H. (2018, July). Evaluation of Mechanically Harvested Southern Highbush Blueberries (Vaccinium corymbosum) Advanced Selections for Fresh Market. Presented at the American Society for Horticultural Science, Washington D.C.

Young, E., Redpath, L., Iorizzo, M., & Ashrafi, H. (2018, August). Fruit Quality Related Trait Evaluation in a Segregating F1 Population of Blueberry from a Cross Between "Reveille" and "Arlen" Cultivars. Poster presented at the National Association of Plant Breeders 2018 Annual Meeting, Guelph, Canada.

Ohlson, E. W., Ashrafi, H., & Foolad, M. R. (2018). Identification and Mapping of Late Blight Resistance Quantitative Trait Loci in Tomato Accession PI 163245. The Plant Genome, 0(0), 0. https://doi.org/10.3835/plantgenome2018.01.0007

Redpath, L. E., Yow, A. G., Aryal, R., Hulse-Kemp, A. M., Franks, R. G., Whetten, R., & Ashrafi, H. (2018, August). RNA-Seq Analysis of Floral Bud Response to Freeze Treatments in Southern Highbush Blueberry CV "O’Neal". Poster presented at the National Plant Breeders Association, Guelph Ontario, Canada August.

Young., E., Ballington, J. R., & Ashrafi, H. (2018, July). Single Nucleotide Polymorphic (SNP) Marker Discovery in a Diverse Panel of Blueberry (Vaccinium sp.) Species. Presented at the American Society of Horticulture Sciences, Washington, D.C.

Yow, A. G., Burchhardt, K., Rollins, J. A., Cubeta, M. A., & Ashrafi, H. (2017, September). Differential Gene Expression Analysis of Blueberry Cultivar “Arlen” in Response to Mummy Berry (Monilinia vaccinii-corymbosi) Disease Infection. Presented at the Plant Molecular Biology Consortium Retreat, Asheville, NC.

Naegele, R. P., Granke, L. L., Fry, J., Hill, T. A., Ashrafi, H., Van Deynze, A., & Hausbeck, M. K. (2017). Disease Resistance to Multiple Fungal and Oomycete Pathogens Evaluated Using a Recombinant Inbred Line Population in Pepper. PHYTOPATHOLOGY, 107(12), 1522–1531. https://doi.org/10.1094/phyto-02-17-0040-r

Yow, A. G., Burchhardt, K., Cubeta, M. A., & Ashrafi, H. (2017, March). Identification of Candidate Genes for Mummy Berry Disease Resistance in Blueberry. Poster presented at the NCSU Graduate Student Research Symposium, Raleigh, NC.

Yow, A. G., Burchhardt, K., Cubeta, M. A., & Ashrafi, H. (2017, January). Identification of Candidate Genes for Mummy Berry Disease Resistance in Blueberry. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XXV), San Diego, CA.

Hill, T. A., Chunthawodtiporn, J., Ashrafi, H., Stoffel, K., Weir, A., & Deynze, A. V. (2017). Regions Underlying Population Structure and the Genomics of Organ Size Determination in . The Plant Genome, 10(3), 0. https://doi.org/10.3835/plantgenome2017.03.0026

Hulse-Kemp, A. M., Ashrafi, H., Plieske, J., Lemm, J., Stoffel, K., Hill, T., … Van Deynze, A. (2016). A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding. HORTICULTURE RESEARCH, 3(1). https://doi.org/10.1038/hortres.2016.36

Iorizzo, M., Ellison, S., Senalik, D., Zeng, P., Satapoomin, P., Huang, J., … Simon, P. (2016). A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. NATURE GENETICS, 48(6), 657-+. https://doi.org/10.1038/ng.3565

Page, J. T., Liechty, Z. S., Alexander, R. H., Clemons, K., Hulse-Kemp, A. M., Ashrafi, H., … Udall, J. A. (2016). DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton. PLOS GENETICS, 12(5). https://doi.org/10.1371/journal.pgen.1006012

Yow, A. G., Burchhardt, K., Cubeta, M. A., & Ashrafi, H. (2016, August). Identification of Differentially Expressed Genes for Mummy Berry (Monilinia vaccinii-corymbosi) Resistance in Blueberry. Poster presented at the Conference for the American Society for Horticultural Science (ASHS), Atlanta, GA.

Santiago, L. M. D., Hulse-Kemp, A. M., Resende, M., Neves, L. G., Ashrafi, H., Gill, C. A., & Stelly, D. M. (2016, January). Major CNV Detection by Read-Depth Analysis Using Capture-Based GBS in Cotton. Poster presented at the International Conference of Plant and Animal Genome Research (PAG XXIV), San Diego, CA.

Rinaldi, R., Deynze, A. V., Portis, E., Rotino, G. L., Toppino, L., Hill, T., … Lanteri, S. (2016). New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL. Frontiers in Plant Science, 7. https://doi.org/10.3389/fpls.2016.01031

Hill, T., Afnan, K., Ray, T., Chaverri, A., Ashrafi, H., Deynze, A. V., & Bradford, K. (2016, January). QTL Underlying Androgenic Haploid Production in Pepper (Capsicum annuum). Poster presented at the International Conference of Plant and Animal Genome Research (PAG XXIV), San Diego, CA.

Fernandez, G., Carter, J. R., Yow, A. G., & Ashrafi, H. (2016, January). Toward Deciphering of Mechanisms Underlying White Drupelet and Reversion Disorders of Blackberry. Poster presented at the International Conference of Plant and Animal Genome Research (PAG XXIV), San Diego, CA.

Yow, A. G., Burchhardt, K., Cubeta, M. A., & Ashrafi, H. (2016, September). Using RNA-Seq for the Identification of Candidate Genes for Mummy Berry Disease Resistance in Blueberry. Presented at the Plant Molecular Biology Consortium Retreat, Wrightsville Beach, NC.

Ashrafi, H., Hulse-Kemp, A. M., Wang, F., Yang, S. S., Guan, X., Jones, D. C., … Van Deynze, A. (2015). A Long-Read Transcriptome Assembly of Cotton (Gossypium hirsutum L.) and Intraspecific Single Nucleotide Polymorphism Discovery. The Plant Genome, 8(2), 0. https://doi.org/10.3835/plantgenome2014.10.0068

Hulse-Kemp, A. M., Ashrafi, H., Stoffel, K., Zheng, X., Saski, C. A., Scheffler, B. E., … G3. (2015). BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping. G3#58; Genes|Genomes|Genetics, 5(6), 1095–1105. https://doi.org/10.1534/g3.115.017749

Foolad, M. R., & Ashrafi, H. (2015). Characterization of early blight resistance in a recombinant inbred line population of tomato: I. Heritability and trait correlations. Advanced Studies in Biology, 7, 131–148. https://doi.org/10.12988/asb.2015.41162

Ashrafi, H., & Foolad, M. R. (2015). Characterization of early blight resistance in a recombinant inbred line population of tomato: II. Identification of QTLs and their co-localization with candidate resistance genes. Advanced Studies in Biology, 7, 149–168. https://doi.org/10.12988/asb.2015.41163

Foolad, M. R., Sullenberger, M. T., & Ashrafi, H. (2015). Detached-Leaflet Evaluation of Tomato Germplasm for Late Blight Resistance and Its Correspondence to Field and Greenhouse Screenings. Plant Disease, 99(5), 718–722. https://doi.org/10.1094/pdis-08-14-0794-re

Hulse-Kemp, A., Lemm, J., Plieske, J., Ashrafi, H., & Buyyarapu, R. (2015). Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L). G3 Gene| Genomes| Genetics, 5, 1187–1209.

Yow, A. G., Guo, W., & Ashrafi, H. (2015, November). Full-Length Transcriptome Sequencing Using PacBio Sequencing in Blueberry. Poster presented at the NCSU CALS Stewards of the Future Conference, Raleigh, NC.

Hill, T., Ashrafi, H., Chin-Wo, S. R., Stoffel, K., Truco, M.-J., Kozik, A., … Van Deynze, A. (2015). Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species. G3-GENES GENOMES GENETICS, 5(11), 2341–2355. https://doi.org/10.1534/g3.115.020040

Ashrafi, H. (2015). Using spinach to compare technologies for whole genome assemblies. Presented at the Plant and Animal Genome XXIII Conference.

Rehrig, W. Z., Ashrafi, H., Hill, T., Prince, J., & Deynze, A. V. (2014). Cosegregates with QTL for Resistance to in Pepper (). The Plant Genome, 7(2), 0. https://doi.org/10.3835/plantgenome2014.03.0011

Deynze, A. V., Hill, T., Ashrafi, H., Kozik, A., Chin-Wo, S. R., & Rehrig, W. Z. (2014, January). Deciphering Resistance to Phytophthora capsici in Pepper. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XXI), San Diego, CA.

Hulse-Kemp, A. M., Ashrafi, H., Zheng, X., Wang, F., Hoegenauer, K. A., Maeda, A. B. V., … Stelly, D. M. (2014). Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts. BMC Genomics, 15(1), 945. https://doi.org/10.1186/1471-2164-15-945

Kim, S., Park, M., Yeom, S.-I., Kim, Y.-M., Lee, J. M., Lee, H.-A., … Choi, D. (2014). Genome sequence of the hot pepper provides insights into the evolution of pungency in <i>Capsicum</i> species. Nature Genetics, 46(3), 270–278. https://doi.org/10.1038/ng.2877

Deynze, A. V., Stelly, D., Ashrafi, H., Hulse, A. M., & Jones, D. C. (2014, January). Increasing Gossypium hirsutum Intraspecific SNPs via Genomic Sequencing. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XXI), San Diego, CA.

Naegele, R. P., Ashrafi, H., Hill, T. A., Chin-Wo, S. R., Deynze, A. E. V., & Hausbeck, M. K. (2014). QTL Mapping of Fruit Rot Resistance to the Plant Pathogen Phytophthora capsici in a Recombinant Inbred Line Capsicum annuum Population. Phytopathology, 104(5), 479–483. https://doi.org/10.1094/phyto-05-13-0143-r

Ashrafi, H., Ohlson, E. W., Sullenberger, M. T., Stoffel, K., Masoudi, M., Deynze, A. V., & Foolad, M. (2014, September). SNP marker discovery for tomato breeding using Genotyping-by-Sequencing (GBS). Presented at the Tomato Breeders Round Table, NC State University, Fletcher, NC.

Truco, M. J., Ashrafi, H., Kozik, A., Leeuwen, H., Bowers, J., Wo, S. R. C., … Michelmore, R. W. (2013). An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce. G3#58; Genes|Genomes|Genetics, 3(4), 617–631. https://doi.org/10.1534/g3.112.004929

Hill, T. A., Ashrafi, H., Reyes-Chin-Wo, S., Yao, J. Q., Stoffel, K., Truco, M.-J., … Deynze, A. V. (2013). Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip. PLoS ONE, 8(2), e56200. https://doi.org/10.1371/journal.pone.0056200

Hulse, A. M., Hoegenauer, K. A., Ashrafi, H., Wang, F., Stelly, D., Deynze, A. V., … Jones, D. C. (2013, January). Genome-wide SNP Development and Validation for Intraspecific SNPs in Upland Cotton. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XXI), San Diego, CA.

Yarnes, S. C., Ashrafi, H., Reyes-Chin-Wo, S., Hill, T. A., Stoffel, K. M., & Deynze, A. V. (2013). Identification of QTLs for capsaicinoids, fruit quality, and plant architecture-related traits in an interspecific Capsicum RIL population. Genome, 56(1), 61–74. https://doi.org/10.1139/gen-2012-0083

Page, J. T., Huynh, M. D., Liechty, Z. S., Grupp, K., Stelly, D., Hulse, A. M., … Udall, J. A. (2013). Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing. G3#58; Genes|Genomes|Genetics, 3(10), 1809–1818. https://doi.org/10.1534/g3.113.007229

Zheng, X., Wang, F., Hoegenauer, K. A., Quintana, J., Ashrafi, H., Stelly, D., … Nichols, R. L. (2013, January). Resolving Tight Linkages Around Renlon by MAS for High-resolution Recombination in Chromosome-11. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XXI), San Diego, CA.

Deynze, A. V., Hill, T., & Ashrafi, H. (2013, January). Structural Genomics. Genetics, Genomics, and Breeding of Tomato, pp. 327–344. https://doi.org/10.1201/b14578-10

Wang, F., Hulse, A. M., Hoegenauer, K., Stelly, D. M., Ashrafi, H., Deynze, A. V., & Yu, J. Z. (2012, January). Collaborative Development of SNPs for Cotton Research, Introgression, MAS and Breeding. Genome-Wide Gossypium SNP Development and Validation. Presented at the Cotton Improvement Conference, Beltwide Cotton Conferences. Retrieved from http://www.cotton.org/beltwide/index.cfm?page=beltwide_overview

Ashrafi, H. (2012, October). Comparison and evaluation of cotton SNPs developed by transcriptome, genome reduction on restriction site conservation and RAD-based sequencing. Presented at the International Cotton Genome Initiative (ICGI) Research Conference, Raleigh, North Carolina, USA.

Hill, T., Ashrafi, H., Reyes-Chin-Wo, S., Romero, M. S., Kozik, A., & Deynze, A. V. (2012, January). Comparisons of high-density EST-based maps in pepper species. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XX), San Diego, CA.

Ashrafi, H., Hill, T., Stoffel, K., Kozik, A., Yao, J. Q., Chin-Wo, S., & Deynze, A. V. (2012). De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes. BMC Genomics, 13(1), 571. https://doi.org/10.1186/1471-2164-13-571

Stoffel, K., Leeuwen, H., Kozik, A., Caldwell, D., Ashrafi, H., Cui, X., … Deynze, A. V. (2012). Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.). BMC Genomics, 13(1), 185. https://doi.org/10.1186/1471-2164-13-185

Wang, F., Hulse, A. M., Hoegenauer, K., Stelly, D. M., Ashrafi, H., Deynze, A. V., & Yu, J. (2012, January). Genome-Wide Gossypium SNP Development and Validation. Presented at the Cotton Improvement Conference, Beltwide Cotton Conferences. Retrieved from http://www.cotton.org/beltwide/index.cfm?page=beltwide_overview

Hulse, A. M., Wang, F., Hoegenauer, K., Stelly, D. M., Ashrafi, H., Deynze, A. V., … Jones, D. C. (2012, January). Genome-wide SNP development and validation for allotetraploid Gossypium. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XX), San Diego, CA.

Ashrafi, H., Yao, J., Stoffel, K., Reyes-Chin-Wo, S., Hill, T., Kozik, A., & Van Deynze, A. (2012, January). Genome-wide SNP discovery from de novo assemblies of pepper (Capsicum annuum) transcriptomes. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XX), San Diego, CA.

Paterson, A. H., Wendel, J. F., Gundlach, H., Guo, H., Jenkins, J., Jin, D., … Schmutz, J. (2012). Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 492(7429), 423–427. https://doi.org/10.1038/nature11798

Merk, H. L., Ashrafi, H., & Foolad, M. R. (2012). Selective genotyping to identify late blight resistance genes in an accession of the tomato wild species Solanum pimpinellifolium. Euphytica, 187(1), 63–75. https://doi.org/10.1007/s10681-012-0729-6

Powell, A. L. T., Nguyen, C. V., Hill, T., Cheng, K. L., Figueroa-Balderas, R., Aktas, H., … Bennett, A. B. (2012). Uniform ripening Encodes a Golden 2-like Transcription Factor Regulating Tomato Fruit Chloroplast Development. Science, 336(6089), 1711–1715. https://doi.org/10.1126/science.1222218

Deynze, A. V., Hill, T. A., Yarnes, S., Rehrig, W. Z., Chin-Wo, S. R., Ashrafi, H., … Prince, J. (2011, January). An Integrated approach to breeding resistance to Phytophthora capsici In Pepper. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XIX), San Diego, CA.

Hill, T., Ashrafi, H., Chin-Wo, S. R.-, Romero, M. S., Deynze, A. V., & Kozik, A. (Aug. 6-10, 2011Aug. 6-10, 2011). Comparisons of high-density EST-based maps in pepper species. Presented at the Plant Biology, American Society of Plant Biologists, Minneapolis, MN.

Iorizzo, M., Senalik, D. A., Grzebelus, D., Bowman, M., Cavagnaro, P. F., Matvienko, M., … Simon, P. W. (2011). De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. BMC Genomics, 12(1). https://doi.org/10.1186/1471-2164-12-389

Deynze, A. V., Hill, T., Prince, J., Yarnes, S., Chunthawodtiporn, J., Rehrig, W., … Kozik, A. (2011, January). Development and Application of Genomic Tools in Pepper. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XIX), San Diego, CA.

Ashrafi, H., Kinkade, M. P., Merk, H. L., & Foolad, M. R. (2011). Identification of novel quantitative trait loci for increased lycopene content and other fruit quality traits in a tomato recombinant inbred line population. Molecular Breeding, 30(1), 549–567. https://doi.org/10.1007/s11032-011-9643-1

Deynze, A. V., Hill, T., Prince, J., Yarnes, S., Chunthawodtiporn, J., Rehrig, W., … Kozik, A. (2011, January). The Genetic Map and Genome Sequencing of Lettuce. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XIX), San Diego, CA.

Hill, T., Ashrafi, H., Kozik, A., & Deynze, A. V. (2010, January). Ultra High Density EST-Based Maps Reveal Genome Differences Between C. frutescence And C. annuum. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XVIII), San Diego, CA.

Ashrafi, H., Kinkade, M., & Foolad, M. R. (2009). A new genetic linkage map of tomato based on a Solanum lycopersicum × S. pimpinellifolium RIL population displaying locations of candidate pathogen response genes. Genome, 52(11), 935–956. https://doi.org/10.1139/g09-065

Kozik, A., Leeuwen, H., Truco, M. J., Stoffel, K., McHale, L., Ashrafi, H., … Michelmore, R. W. (2009, January). Construction of an Ultra High Density Genetic Map of Lettuce using an Affymetrix GeneChip. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XVII), San Diego, CA.

Leeuwen, H., Stoffel, K., Truco, M. J., Ashrafi, H., Cui, X., Kozik, A., … Deynze, A. V. (2009, January). Development and Utilization of a High Density 6.6 Million Feature Affymetrix GeneChip for Marker Discovery and Genotyping in Lettuce. Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XVII), San Diego, CA.

Leeuwen, H., Stoffel, K., Kozik, A., Cui, X., Ashrafi, H., McHale, L., … Michelmore, R. W. (2009, January). High-Density Mapping of the Lettuce Genome with SFP Markers in over 15,000 Unigenes. Presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XVII), San Diego, CA.

Ashrafi, H., Hill, T., Yao, J., Leeuwen, H., Michelmore, R., Kozik, A., & Deynze, A. V. (2009, January). The Application of a Whole Genome Pepper Array to Identify SFPs in a Diversity Panel. Invited presentation in Solanaceae workshop presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XVII), San Diego, CA.

Hill, T., Ashrafi, H., Yao, J., Jong, W. D., Francis, D., Kozik, A., & Deynze, A. V. (2009, October). The Application of a Whole Genome Pepper Array to Solanaceae Crops. Presented at the Cologne, Germany.

Sharma, A., Zhang, L., Niño-Liu, D., Ashrafi, H., & Foolad, M. R. (2008). A Solanum lycopersicum × Solanum pimpinellifolium Linkage Map of Tomato Displaying Genomic Locations of R-Genes, RGAs, and Candidate Resistance/Defense-Response ESTs. International Journal of Plant Genomics, 2008, 1–18. https://doi.org/10.1155/2008/926090

Foolad, M. R., Merk, H. L., & Ashrafi, H. (2008). Genetics, Genomics and Breeding of Late Blight and Early Blight Resistance in Tomato. Critical Reviews in Plant Sciences, 27(2), 75–107. https://doi.org/10.1080/07352680802147353

Ashrafi, H., Kinkade, M. R., & Foolad, M. R. (2007, January). HPLC and spectrophotometer analyses of fruit carotenoids In a Lycopersicon esculentum X L. pimpinellifolium RIL population reveals several new QTLs for lycopene content. Presented at the The International Conference on the Status of Plant and Animal Genome Research, PAG XV, San Diego, CA.

Merk, H. L., Ashrafi, H., Kinkade, M. P., & Foolad, M. R. (2007, January). Identification and molecular mapping of a new dominant gene (Ph5) conferring broad-spectrum resistance against tomato late blight. Presented at the The International Conference on the Status of Plant and Animal Genome Research, PAG XV, San Diego, CA.

Ashrafi, H., Lin, G. Y., & Foolad, M. R. (2006, March). A molecular linkage map of tomato based on RFLP markers and candidate disease-resistance/defense-response genes in an F7 RIL population. Poster presented at the Graduate Research Exposition, College of Ag. Sciences, The Pennsylvania State University, University Park, PA.

Ashrafi, H., Lin, G. Y., & Foolad, M. R. (2006, April). Identification of QTLs for tomato early blight resistance in a RIL population of a cross between Lycopersicon esculentum and L. pimpinellifolium. Poster presented at the Pennsylvania State University Genetics Symposium, University Park, PA.

Foolad, M. R., Merk, H. L., Ashrafi, H., & Kinkade, M. P. (Nov. 9-10, 2006). Identification of new sources of late blight resistance in tomato and mapping of a new resistance gene. Proc. 21st Annual Tomato Disease Workshop. Fletcher, NC: NC State University.

Ashrafi, H., Sharma, A., Kole, C., Merk, H., Lin, G. Y., & Foolad, M. R. (2006, January). Mapping of early blight resistance QTLs and candidate resistance genes in a RIL population of tomato. Poster presented at the The XIV International Conference on the Status of Plant and Animal Genome Research (PAG XIV), San Diego, CA.

Merk, H. L., Ashrafi, H., Kole, C., Kinkade, M., Lin, G. Y., & Foolad, M. R. (2006, April). Toward identification and mapping of new late blight resistance genes in tomato. Poster presented at the 2006 Pennsylvania State University Genetics Symposium, University Park, PA.

Ashrafi, H., Sharma, A., Niño-Liu, D., Zhang, L., & Foolad, M. (2005). (13) Comparative Mapping of Early Blight Resistance QTLs and Candidate Resistance Genes in F2, F3, F4 and a RIL Population of Tomato. HortScience, 40(4), 1040.

Ashrafi, H., Sharma, A., Niño-Liu, D., Zhang, L., & Foolad, M. R. (2005). Comparative mapping of early blight resistance QTLs and candidate resistance genes in F2, F3, F4 and a RIL population of Tomato. Poster presented at the 2005 ASHS Annual International Conference, Las Vegas.

Ashrafi, H., Sharma, A., Niño-Liu, D., & Foolad, M. R. (2005, March). Genetic mapping of candidate resistance genes in tomato using an F2 and a RIL population of a Lycopersicon esculentum × L. pimpinellifolium cross. Presented at the Graduate Research Exposition, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA.

Foolad, M. R., Sharma, A., Ashrafi, H., & Lin, G. (2005). Genetics and Breeding of Early Blight Resistance in Tomato. HortScience, 40, 1114–1114.

Sharma, A., Ashrafi, H., & Foolad, M. R. (2005, January). Genetics of early blight resistance in tomato. Poster presented at the The International Conference on the Status of Plant and Animal Genome Research, PAG XIII, San Diego.

R., F. M., Sharma, A., & Ashrafi, H. (2004, June). Early blight resistance in tomato: genetics, breeding and accelerated breeding. Poster presented at the First International Symposium in Tomato Diseases (ISTD) and 19th Annual Tomato Disease Workshop (ATDW), Orlando, FL.

Samaee, S. M., Shobbar, Z. S., Ashrafi, H., Hosseini-Mazinani, M., & Sheidai, M. (2003). MOLECULAR CHARACTERIZATION OF OLIVE GERMPLASM IN IRAN BY USE OF RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) AND CORRELATION WITH PHENOTYPIC STUDIES: PRELIMINARY RESULTS. Acta Horticulturae, 7(623), 169–175. https://doi.org/10.17660/actahortic.2003.623.18