@article{brůna_aryal_dudchenko_sargent_mead_buti_cavallini_hytönen_andrés_pham_et al._2022, title={A chromosome-length genome assembly and annotation of blackberry (<i>Rubus argutus</i>, cv. “Hillquist”)}, volume={11}, ISSN={2160-1836}, url={http://dx.doi.org/10.1093/g3journal/jkac289}, DOI={10.1093/g3journal/jkac289}, abstractNote={Abstract
               <jats:p>Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession “Hillquist” (R. argutus). “Hillquist” is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The “Hillquist” assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2 Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the “Hillquist” genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.}, journal={G3 Genes|Genomes|Genetics}, publisher={Oxford University Press (OUP)}, author={Brůna, Tomáš and Aryal, Rishi and Dudchenko, Olga and Sargent, Daniel James and Mead, Daniel and Buti, Matteo and Cavallini, Andrea and Hytönen, Timo and Andrés, Javier and Pham, Melanie and et al.}, editor={Pyhäjärvi, TEditor}, year={2022}, month={Nov} }
 @article{crowl_fritsch_tiley_lynch_ranney_ashrafi_manos_2022, title={A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus)}, volume={10}, ISSN={["1537-2197"]}, DOI={10.1002/ajb2.16065}, journal={AMERICAN JOURNAL OF BOTANY}, author={Crowl, Andrew A. and Fritsch, Peter W. and Tiley, George P. and Lynch, Nathan P. and Ranney, Thomas G. and Ashrafi, Hamid and Manos, Paul S.}, year={2022}, month={Oct} }
 @article{mengist_bostan_de paola_teresi_platts_cremona_qi_mackey_bassil_ashrafi_et al._2022, title={Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum)}, volume={9}, ISSN={["1469-8137"]}, url={https://doi.org/10.1111/nph.18428}, DOI={10.1111/nph.18428}, journal={NEW PHYTOLOGIST}, author={Mengist, Molla F. and Bostan, Hamed and De Paola, Domenico and Teresi, Scott J. and Platts, Adrian E. and Cremona, Gaetana and Qi, Xinpeng and Mackey, Ted and Bassil, Nahla V and Ashrafi, Hamid and et al.}, year={2022}, month={Sep} }
 @article{sullenberger_jia_gao_ashrafi_foolad_2022, title={Identification of late blight resistance quantitative trait loci in Solanum pimpinellifolium accession PI 270441}, volume={8}, ISSN={["1940-3372"]}, DOI={10.1002/tpg2.20251}, journal={PLANT GENOME}, author={Sullenberger, Matthew T. and Jia, Mengyuan and Gao, Sihui and Ashrafi, Hamid and Foolad, Majid R.}, year={2022}, month={Aug} }
 @article{redpath_aryal_lynch_spencer_hulse-kemp_ballington_green_bassil_hummer_ranney_et al._2022, title={Nuclear DNA contents and ploidy levels of North American Vaccinium species and interspecific hybrids}, volume={297}, ISSN={["1879-1018"]}, DOI={10.1016/j.scienta.2022.110955}, journal={SCIENTIA HORTICULTURAE}, author={Redpath, Lauren E. and Aryal, Rishi and Lynch, Nathan and Spencer, Jessica A. and Hulse-Kemp, Amanda M. and Ballington, James R. and Green, Jaimie and Bassil, Nahla and Hummer, Kim and Ranney, Thomas and et al.}, year={2022}, month={Apr} }
 @article{adhikari_aryal_redpath_broeck_ashrafi_philbrick_jacobs_sozzani_louws_2022, title={RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic Colletorichum spp. in Strawberry}, volume={12}, ISSN={["1664-8021"]}, DOI={10.3389/fgene.2021.805771}, journal={FRONTIERS IN GENETICS}, author={Adhikari, Tika B. and Aryal, Rishi and Redpath, Lauren E. and Broeck, Lisa and Ashrafi, Hamid and Philbrick, Ashley N. and Jacobs, Raymond L. and Sozzani, Rosangela and Louws, Frank J.}, year={2022}, month={Mar} }
 @article{edger_iorizzo_bassil_benevenuto_ferrao_giongo_hummer_lawas_leisner_li_et al._2022, title={There and back again; historical perspective and future directions for Vaccinium breeding and research studies}, volume={9}, ISSN={["2052-7276"]}, DOI={10.1093/hr/uhac083}, journal={HORTICULTURE RESEARCH}, author={Edger, Patrick P. and Iorizzo, Massimo and Bassil, Nahla V and Benevenuto, Juliana and Ferrao, Luis Felipe V and Giongo, Lara and Hummer, Kim and Lawas, Lovely Mae F. and Leisner, Courtney P. and Li, Changying and et al.}, year={2022}, month={Jan} }
 @article{hulse-kemp_bostan_chen_ashrafi_stoffel_sanseverino_li_cheng_schatz_garvin_et al._2021, title={An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids}, volume={6}, ISSN={["1940-3372"]}, DOI={10.1002/tpg2.20101}, journal={PLANT GENOME}, author={Hulse-Kemp, Amanda M. and Bostan, Hamed and Chen, Shiyu and Ashrafi, Hamid and Stoffel, Kevin and Sanseverino, Walter and Li, Linzhou and Cheng, Shifeng and Schatz, Michael C. and Garvin, Tyler and et al.}, year={2021}, month={Jun} }
 @article{zhao_maren_kosentka_liao_lu_duduit_huang_ashrafi_zhao_huerta_et al._2021, title={An optimized protocol for stepwise optimization of real-time RT-PCR analysis}, volume={8}, ISSN={["2052-7276"]}, url={https://doi.org/10.1038/s41438-021-00616-w}, DOI={10.1038/s41438-021-00616-w}, number={1}, journal={HORTICULTURE RESEARCH}, author={Zhao, Fangzhou and Maren, Nathan A. and Kosentka, Pawel Z. and Liao, Ying-Yu and Lu, Hongyan and Duduit, James R. and Huang, Debao and Ashrafi, Hamid and Zhao, Tuanjie and Huerta, Alejandra I and et al.}, year={2021}, month={Dec} }
 @article{kraft_sit_diepenbrock_ashrafi_aryal_fernandez_burrack_2021, title={Detection of Fruit Meals Within Laboratory-Raised and Field-Trapped Adult Drosophila suzukii (Diptera: Drosophilidae) Guts}, volume={9}, ISSN={2296-701X}, url={http://dx.doi.org/10.3389/fevo.2021.719645}, DOI={10.3389/fevo.2021.719645}, abstractNote={The feeding habits of adult Brachycera are understudied and may provide important context for understanding invasive pest biology, as with the polyphagous small fruit pest <jats:italic>Drosophila suzukii}, journal={Frontiers in Ecology and Evolution}, publisher={Frontiers Media SA}, author={Kraft, Laura J. and Sit, Tim L. and Diepenbrock, Lauren M. and Ashrafi, Hamid and Aryal, Rishi and Fernandez, Gina E. and Burrack, Hannah J.}, year={2021}, month={Aug} }
 @article{yow_zhang_bansal_eacker_sullivan_liachko_cubeta_rollins_ashrafi_2021, title={Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type}, volume={11}, ISSN={["2160-1836"]}, url={https://doi.org/10.1093/g3journal/jkaa052}, DOI={10.1093/g3journal/jkaa052}, number={2}, journal={G3-GENES GENOMES GENETICS}, publisher={Oxford University Press (OUP)}, author={Yow, Ashley G. and Zhang, Yucheng and Bansal, Kamaldeep and Eacker, Stephen M. and Sullivan, Shawn and Liachko, Ivan and Cubeta, Marc A. and Rollins, Jeffrey A. and Ashrafi, Hamid}, editor={Baltrus, DEditor}, year={2021}, month={Feb} }
 @article{redpath_gumpertz_ballington_bassil_ashrafi_2021, title={Genotype, Environment, Year, and Harvest Effects on Fruit Quality Traits of Five Blueberry (Vaccinium corymbosum L.) Cultivars}, volume={11}, ISSN={["2073-4395"]}, url={https://doi.org/10.3390/agronomy11091788}, DOI={10.3390/agronomy11091788}, number={9}, journal={AGRONOMY-BASEL}, author={Redpath, Lauren E. and Gumpertz, Marcia and Ballington, James R. and Bassil, Nahla and Ashrafi, Hamid}, year={2021}, month={Sep} }
 @article{mengist_bostan_young_kay_gillitt_ballington_kay_ferruzzi_ashrafi_lila_et al._2021, title={High-density linkage map construction and identification of loci regulating fruit quality traits in blueberry}, volume={8}, ISSN={["2052-7276"]}, url={https://doi.org/10.1038/s41438-021-00605-z}, DOI={10.1038/s41438-021-00605-z}, number={1}, journal={HORTICULTURE RESEARCH}, author={Mengist, Molla F. and Bostan, Hamed and Young, Elisheba and Kay, Kristine L. and Gillitt, Nicholas and Ballington, James and Kay, Colin D. and Ferruzzi, Mario G. and Ashrafi, Hamid and Lila, Mary Ann and et al.}, year={2021}, month={Dec} }
 @article{maren_zhao_aryal_touchell_liu_ranney_ashrafi_2021, title={Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae)}, volume={22}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-021-07641-y}, number={1}, journal={BMC GENOMICS}, author={Maren, Nathan and Zhao, Fangzhou and Aryal, Rishi and Touchell, Darren and Liu, Wusheng and Ranney, Thomas and Ashrafi, Hamid}, year={2021}, month={Jun} }
 @article{zurn_driskill_jung_main_yin_clark_cheng_ashrafi_aryal_clark_et al._2020, title={A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding}, volume={10}, ISBN={2160-1836}, DOI={10.1534/g3.120.401449}, number={10}, journal={G3-GENES GENOMES GENETICS}, author={Zurn, Jason D. and Driskill, Mandie and Jung, Sook and Main, Dorrie and Yin, Melinda H. and Clark, Melissa C. and Cheng, Lailiang and Ashrafi, Hamid and Aryal, Rishi and Clark, John R. and et al.}, year={2020}, month={Oct}, pages={3729–3740} }
 @article{maren_touchell_ranney_ashrafi_whitfield_chinn_2020, title={Biomass yields, cytogenetics, fertility, and compositional analyses of novel bioenergy grass hybrids (Tripidium spp.)}, volume={12}, ISBN={1757-1707}, url={https://doi.org/10.1111/gcbb.12676}, DOI={10.1111/gcbb.12676}, number={5}, journal={GLOBAL CHANGE BIOLOGY BIOENERGY}, publisher={Wiley}, author={Maren, Nathan A. and Touchell, Darren H. and Ranney, Thomas G. and Ashrafi, Hamid and Whitfield, Matthew B. and Chinn, Mari}, year={2020}, pages={361–373} }
 @article{jahnke_dole_ashrafi_2020, title={Simulated storage causes carbohydrate loss and rooting differences in two poinsettia cultivars}, volume={100}, ISBN={1918-1833}, DOI={10.1139/cjps-2019-0232}, number={4}, journal={CANADIAN JOURNAL OF PLANT SCIENCE}, author={Jahnke, Nathan J. and Dole, John M. and Ashrafi, Hamid}, year={2020}, month={Aug}, pages={459–462} }
 @article{jiang_li_takeda_kramer_ashrafi_hunter_2019, title={3D point cloud data to quantitatively characterize size and shape of shrub crops}, volume={6}, ISBN={2052-7276}, DOI={10.1038/s41438-019-0123-9}, journal={HORTICULTURE RESEARCH}, author={Jiang, Yu and Li, Changying and Takeda, Fumiomi and Kramer, Elizabeth A. and Ashrafi, Hamid and Hunter, Jamal}, year={2019} }
 @article{gonda_ashrafi_lyon_strickler_hulse-kemp_ma_sun_stoffel_powell_futrell_et al._2019, title={Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection}, volume={12}, ISBN={1940-3372}, DOI={10.3835/plantgenome2018.02.0010}, number={1}, journal={PLANT GENOME}, author={Gonda, Itay and Ashrafi, Hamid and Lyon, David A. and Strickler, Susan R. and Hulse-Kemp, Amanda M. and Ma, Qiyue and Sun, Honghe and Stoffel, Kevin and Powell, Adrian F. and Futrell, Stephanie and et al.}, year={2019}, month={Mar} }
 @article{gallardo_zhang_dossett_polashock_rodriguez-saona_vorsa_edger_ashrafi_babiker_finn_et al._2018, title={Breeding Trait Priorities of the Blueberry Industry in the United States and Canada}, volume={53}, DOI={10.21273/hortsci12964-18}, number={7}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Gallardo, R. Karina and Zhang, Qi and Dossett, Michael and Polashock, James J. and Rodriguez-Saona, Cesar and Vorsa, Nicholi and Edger, Patrick P. and Ashrafi, Hamid and Babiker, Ebrahiem and Finn, Chad E. and et al.}, year={2018}, month={Jul}, pages={1021–1028} }
 @misc{aryal_yow_ashrafi_2018, title={Developing the Genomic Resources for a Tetraploid Blueberry cv "O'Neal"}, note={Poster #6}, author={Aryal, Rishi and Yow, Ashley and Ashrafi, Hamid}, year={2018}, month={Aug} }
 @misc{aryal_ashrafi_2018, title={Differential Gene Expression during Blueberry Fruits Ripening}, note={Poster 300-011}, author={Aryal, Rishi and Ashrafi, Hamid}, year={2018}, month={Jul} }
 @misc{aryal_bostan_yow_tseng_iorizzo_ashrafi_Januaary 13-17, 2018, title={Differential Gene Expression during Flower and Fruit Development of the Blueberry Cv. "O'Neal"}, note={Poster P0203}, author={Aryal, Rishi and Bostan, Hamed and Yow, Ashley G. and Tseng, Elizabeth and Iorizzo, Massimo and Ashrafi, Hamid}, year={Januaary 13-17, 2018}, month={Januaary 13-17, 2018} }
 @misc{redpath_yow_aryal_hulse-kemp_franks_whetten_ashrafi_2018, title={Differential Gene Expression of Southern Highbush Blueberry cv. ‘O’Neal’ Floral Buds in Response to Freeze Treatment and Recovery Periods}, note={Poster 279}, author={Redpath, Lauren E. and Yow, Ashley G. and Aryal, Rishi and Hulse-Kemp, Amanda M. and Franks, Robert G. and Whetten, Ross and Ashrafi, Hamid}, year={2018}, month={Jul} }
 @misc{redpath_ashrafi_2018, title={Differential Gene Expression of ‘O’Neal’ Blueberry Floral Buds in Response to Freeze Treatment and Recovery Periods}, author={Redpath, Lauren E. and Ashrafi, Hamid}, year={2018}, month={Apr} }
 @misc{redpath_bland_ballington_jiang_li_ashrafi_2018, title={Evaluation of Mechanically Harvested Southern Highbush Blueberries (Vaccinium corymbosum) Advanced Selections for Fresh Market}, author={Redpath, Lauren E. and Bland, Terry W. and Ballington, James R. and Jiang, Yu and Li, Changying and Ashrafi, Hamid}, year={2018}, month={Jul} }
 @misc{young_redpath_iorizzo_ashrafi_2018, title={Fruit Quality Related Trait Evaluation in a Segregating F1 Population of Blueberry from a Cross Between "Reveille" and "Arlen" Cultivars}, note={Poster 117-SII}, author={Young, Elisheba and Redpath, Lauren and Iorizzo, Massimo and Ashrafi, Hamid}, year={2018}, month={Aug} }
 @article{ohlson_ashrafi_foolad_2018, title={Identification and Mapping of Late Blight Resistance Quantitative Trait Loci in Tomato Accession PI 163245}, volume={0}, DOI={10.3835/plantgenome2018.01.0007}, number={0}, journal={The Plant Genome}, publisher={Crop Science Society of America}, author={Ohlson, Erik W. and Ashrafi, Hamid and Foolad, Majid R.}, year={2018}, pages={0} }
 @misc{redpath_yow_aryal_hulse-kemp_franks_whetten_ashrafi_2018, title={RNA-Seq Analysis of Floral Bud Response to Freeze Treatments in Southern Highbush Blueberry CV "O’Neal"}, note={Poster 81}, author={Redpath, Lauren E. and Yow, Ashley G. and Aryal, Rishi and Hulse-Kemp, Amanda M. and Franks, Robert G. and Whetten, Ross and Ashrafi, Hamid}, year={2018}, month={Aug} }
 @misc{young._ballington_ashrafi_2018, title={Single Nucleotide Polymorphic (SNP) Marker Discovery in a Diverse Panel of Blueberry (Vaccinium sp.) Species}, note={Abstract pp. 42}, author={Young., Elisheba and Ballington, James R. and Ashrafi, Hamid}, year={2018}, month={Jul} }
 @misc{yow_burchhardt_rollins_cubeta_ashrafi_2017, title={Differential Gene Expression Analysis of Blueberry Cultivar “Arlen” in Response to Mummy Berry (Monilinia vaccinii-corymbosi) Disease Infection}, author={Yow, Ashley G. and Burchhardt, Kathleen and Rollins, Jeffrey A. and Cubeta, Marc A. and Ashrafi, Hamid}, year={2017}, month={Sep} }
 @article{naegele_granke_fry_hill_ashrafi_deynze_hausbeck_2017, title={Disease Resistance to Multiple Fungal and Oomycete Pathogens Evaluated Using a Recombinant Inbred Line Population in Pepper}, volume={107}, DOI={10.1094/phyto-02-17-0040-r}, number={12}, journal={Phytopathology}, publisher={Scientific Societies}, author={Naegele, R. P. and Granke, L. L. and Fry, J. and Hill, T. A. and Ashrafi, H. and Deynze, A. Van and Hausbeck, M. K.}, year={2017}, pages={1522–1531} }
 @misc{yow_burchhardt_cubeta_ashrafi_2017, title={Identification of Candidate Genes for Mummy Berry Disease Resistance in Blueberry}, note={Poster 205}, author={Yow, Ashley G. and Burchhardt, Kathleen and Cubeta, Marc A. and Ashrafi, Hamid}, year={2017}, month={Mar} }
 @misc{yow_burchhardt_cubeta_ashrafi_2017, title={Identification of Candidate Genes for Mummy Berry Disease Resistance in Blueberry}, note={Poster P0244}, author={Yow, Ashley G. and Burchhardt, Kathleen and Cubeta, Marc A. and Ashrafi, Hamid}, year={2017}, month={Jan} }
 @article{hill_chunthawodtiporn_ashrafi_stoffel_weir_deynze_2017, title={Regions Underlying Population Structure and the Genomics of Organ Size Determination in }, volume={10}, DOI={10.3835/plantgenome2017.03.0026}, number={3}, journal={The Plant Genome}, publisher={Crop Science Society of America}, author={Hill, Theresa A. and Chunthawodtiporn, Jareerat and Ashrafi, Hamid and Stoffel, Kevin and Weir, Allyson and Deynze, Allen Van}, year={2017}, pages={0} }
 @article{hulse-kemp_ashrafi_plieske_lemm_stoffel_hill_luerssen_pethiyagoda_lawley_ganal_et al._2016, title={A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding}, volume={3}, url={https://doi.org/10.1038/hortres.2016.36}, DOI={10.1038/hortres.2016.36}, number={1}, journal={Horticulture Research}, publisher={Springer Science and Business Media LLC}, author={Hulse-Kemp, Amanda M and Ashrafi, Hamid and Plieske, Joerg and Lemm, Jana and Stoffel, Kevin and Hill, Theresa and Luerssen, Hartmut and Pethiyagoda, Charit L and Lawley, Cindy T and Ganal, Martin W and et al.}, year={2016}, month={Dec}, pages={16036} }
 @article{iorizzo_ellison_senalik_zeng_satapoomin_huang_bowman_iovene_sanseverino_cavagnaro_et al._2016, title={A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution}, volume={48}, DOI={10.1038/ng.3565}, number={6}, journal={Nature Genetics}, publisher={Springer Nature}, author={Iorizzo, Massimo and Ellison, Shelby and Senalik, Douglas and Zeng, Peng and Satapoomin, Pimchanok and Huang, Jiaying and Bowman, Megan and Iovene, Marina and Sanseverino, Walter and Cavagnaro, Pablo and et al.}, year={2016}, month={May}, pages={657–666} }
 @article{page_liechty_alexander_clemons_hulse-kemp_ashrafi_deynze_stelly_udall_2016, title={DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton}, volume={12}, url={http://europepmc.org/abstract/med/27168520}, DOI={10.1371/journal.pgen.1006012}, number={5}, journal={PLOS Genetics}, publisher={Public Library of Science (PLoS)}, author={Page, Justin T. and Liechty, Zach S. and Alexander, Rich H. and Clemons, Kimberly and Hulse-Kemp, Amanda M. and Ashrafi, Hamid and Deynze, Allen Van and Stelly, David M. and Udall, Joshua A.}, editor={Bomblies, KirstenEditor}, year={2016}, month={May}, pages={e1006012} }
 @misc{yow_burchhardt_cubeta_ashrafi_2016, title={Identification of Differentially Expressed Genes for Mummy Berry (Monilinia vaccinii-corymbosi) Resistance in Blueberry}, note={Poster 120}, author={Yow, Ashley G. and Burchhardt, Kathleen and Cubeta, Marc A. and Ashrafi, Hamid}, year={2016}, month={Aug} }
 @misc{santiago_hulse-kemp_resende_neves_ashrafi_gill_stelly_2016, title={Major CNV Detection by Read-Depth Analysis Using Capture-Based GBS in Cotton}, note={Poster 0563}, author={Santiago, Luis M.De and Hulse-Kemp, Amanda M. and Resende, Marcio and Neves, Leandro G. and Ashrafi, Hamid and Gill, Clare A. and Stelly, David M.}, year={2016}, month={Jan} }
 @article{rinaldi_deynze_portis_rotino_toppino_hill_ashrafi_barchi_lanteri_2016, title={New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL}, volume={7}, DOI={10.3389/fpls.2016.01031}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Rinaldi, Riccardo and Deynze, Allen Van and Portis, Ezio and Rotino, Giuseppe L. and Toppino, Laura and Hill, Theresa and Ashrafi, Hamid and Barchi, Lorenzo and Lanteri, Sergio}, year={2016}, month={Jul} }
 @misc{hill_afnan_ray_chaverri_ashrafi_deynze_bradford_2016, title={QTL Underlying Androgenic Haploid Production in Pepper (Capsicum annuum)}, note={Poster 0819}, author={Hill, Theresa and Afnan, Khalis and Ray, Tui and Chaverri, Alddo and Ashrafi, Hamid and Deynze, Allen Van and Bradford, Kent}, year={2016}, month={Jan} }
 @misc{fernandez_carter_yow_ashrafi_2016, title={Toward Deciphering of Mechanisms Underlying White Drupelet and Reversion Disorders of Blackberry}, note={Poster 0245}, author={Fernandez, Gina and Carter, Johanna R. and Yow, Ashley G. and Ashrafi, Hamid}, year={2016}, month={Jan} }
 @misc{yow_burchhardt_cubeta_ashrafi_2016, title={Using RNA-Seq for the Identification of Candidate Genes for Mummy Berry Disease Resistance in Blueberry}, author={Yow, Ashley G. and Burchhardt, Kathleen and Cubeta, Marc A. and Ashrafi, Hamid}, year={2016}, month={Sep} }
 @article{ashrafi_hulse-kemp_wang_yang_guan_jones_matvienko_mockaitis_chen_stelly_et al._2015, title={A Long-Read Transcriptome Assembly of Cotton (Gossypium hirsutum L.) and Intraspecific Single Nucleotide Polymorphism Discovery}, volume={8}, DOI={10.3835/plantgenome2014.10.0068}, number={2}, journal={The Plant Genome}, publisher={Crop Science Society of America}, author={Ashrafi, H. and Hulse-Kemp, A.M. and Wang, F. and Yang, S.S. and Guan, X. and Jones, Don C. and Matvienko, Marta and Mockaitis, Keithanne and Chen, Z. Jeffrey and Stelly, David M. and et al.}, year={2015}, pages={0} }
 @article{hulse-kemp_ashrafi_stoffel_zheng_saski_scheffler_fang_chen_van deynze_stelly_et al._2015, title={BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping}, volume={5}, url={http://europepmc.org/abstract/med/25858960}, DOI={10.1534/g3.115.017749}, number={6}, journal={G3&#58; Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Hulse-Kemp, A.M. and Ashrafi, H. and Stoffel, K. and Zheng, X. and Saski, C.A. and Scheffler, B.E. and Fang, D.D. and Chen, Z.J. and Van Deynze, A. and Stelly, D.M. and et al.}, year={2015}, month={Apr}, pages={1095–1105} }
 @article{foolad_ashrafi_2015, title={Characterization of early blight resistance in a recombinant inbred line population of tomato: I. Heritability and trait correlations}, volume={7}, ISSN={13147668}, url={http://www.m-hikari.com/asb/asb2015/asb1-4-2015/41162.html}, DOI={10.12988/asb.2015.41162}, journal={Advanced Studies in Biology}, publisher={Hikari, Ltd.}, author={Foolad, Majid R. and Ashrafi, Hamid}, year={2015}, pages={131–148} }
 @article{ashrafi_foolad_2015, title={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}, volume={7}, DOI={10.12988/asb.2015.41163}, journal={Advanced Studies in Biology}, publisher={Hikari, Ltd.}, author={Ashrafi, Hamid and Foolad, Majid R.}, year={2015}, pages={149–168} }
 @article{foolad_sullenberger_ashrafi_2015, title={Detached-Leaflet Evaluation of Tomato Germplasm for Late Blight Resistance and Its Correspondence to Field and Greenhouse Screenings}, volume={99}, DOI={10.1094/pdis-08-14-0794-re}, number={5}, journal={Plant Disease}, publisher={Scientific Societies}, author={Foolad, Majid R. and Sullenberger, Matthew T. and Ashrafi, Hamid}, year={2015}, month={May}, pages={718–722} }
 @article{hulse-kemp_lemm_plieske_ashrafi_buyyarapu_2015, title={Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L)}, volume={5}, journal={G3 Gene| Genomes| Genetics}, author={Hulse-Kemp, A. and Lemm, J. and Plieske, J. and Ashrafi, H. and Buyyarapu, R.}, year={2015}, pages={1187–1209} }
 @misc{yow_guo_ashrafi_2015, title={Full-Length Transcriptome Sequencing Using PacBio Sequencing in Blueberry}, author={Yow, Ashley G. and Guo, Weiwen and Ashrafi, Hamid}, year={2015}, month={Nov} }
 @article{hill_ashrafi_chin-wo_stoffel_truco_kozik_michelmore_deynze_2015, title={Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species}, volume={5}, DOI={10.1534/g3.115.020040}, number={11}, journal={G3&#58; Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Hill, Theresa and Ashrafi, Hamid and Chin-Wo, Sebastian Reyes and Stoffel, Kevin and Truco, Maria-Jose and Kozik, Alexander and Michelmore, Richard and Deynze, Allen Van}, year={2015}, month={Sep}, pages={2341–2355} }
 @misc{ashrafi_2015, title={Using spinach to compare technologies for whole genome assemblies}, author={Ashrafi, H}, year={2015} }
 @article{rehrig_ashrafi_hill_prince_deynze_2014, title={Cosegregates with QTL for Resistance to in Pepper ()}, volume={7}, DOI={10.3835/plantgenome2014.03.0011}, number={2}, journal={The Plant Genome}, publisher={Crop Science Society of America}, author={Rehrig, William Z. and Ashrafi, Hamid and Hill, Theresa and Prince, James and Deynze, Allen Van}, year={2014}, pages={0} }
 @misc{deynze_hill_ashrafi_kozik_chin-wo_rehrig_2014, title={Deciphering Resistance to Phytophthora capsici in Pepper}, note={Poster P0413}, author={Deynze, Allen Van and Hill, Theresa and Ashrafi, Hamid and Kozik, Alexander and Chin-Wo, Sebastian Reyes and Rehrig, William Zebulun}, year={2014}, month={Jan} }
 @article{hulse-kemp_ashrafi_zheng_wang_hoegenauer_maeda_yang_stoffel_matvienko_clemons_et al._2014, title={Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts}, volume={15}, url={http://europepmc.org/abstract/med/25359292}, DOI={10.1186/1471-2164-15-945}, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Hulse-Kemp, Amanda M and Ashrafi, Hamid and Zheng, Xiuting and Wang, Fei and Hoegenauer, Kevin A and Maeda, Andrea BV and Yang, S Samuel and Stoffel, Kevin and Matvienko, Marta and Clemons, Kimberly and et al.}, year={2014}, pages={945} }
 @article{kim_park_yeom_kim_lee_lee_seo_choi_cheong_kim_et al._2014, title={Genome sequence of the hot pepper provides insights into the evolution of pungency in <i>Capsicum</i> species}, volume={46}, ISSN={1546-1718}, url={https://www.nature.com/articles/ng.2877}, DOI={10.1038/ng.2877}, abstractNote={Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.}, number={3}, journal={Nature Genetics}, publisher={Springer Nature}, author={Kim, Seungill and Park, Minkyu and Yeom, Seon-In and Kim, Yong-Min and Lee, Je Min and Lee, Hyun-Ah and Seo, Eunyoung and Choi, Jaeyoung and Cheong, Kyeongchae and Kim, Ki-Tae and et al.}, year={2014}, month={Mar}, pages={270–278} }
 @misc{deynze_stelly_ashrafi_hulse_jones_2014, title={Increasing Gossypium hirsutum Intraspecific SNPs via Genomic Sequencing}, note={Poster P0413}, author={Deynze, Allen Van and Stelly, David and Ashrafi, Hamid and Hulse, Amanda M. and Jones, Don C.}, year={2014}, month={Jan} }
 @article{naegele_ashrafi_hill_chin-wo_deynze_hausbeck_2014, title={QTL Mapping of Fruit Rot Resistance to the Plant Pathogen Phytophthora capsici in a Recombinant Inbred Line Capsicum annuum Population}, volume={104}, DOI={10.1094/phyto-05-13-0143-r}, number={5}, journal={Phytopathology}, publisher={Scientific Societies}, author={Naegele, R. P. and Ashrafi, H. and Hill, T. A. and Chin-Wo, S. Reyes and Deynze, A. E. Van and Hausbeck, M. K.}, year={2014}, month={May}, pages={479–483} }
 @misc{ashrafi_ohlson_sullenberger_stoffel_masoudi_deynze_foolad_2014, title={SNP marker discovery for tomato breeding using Genotyping-by-Sequencing (GBS)}, note={Abstract pp. 12-13}, author={Ashrafi, Hamid and Ohlson, Erik W. and Sullenberger, Matthew T. and Stoffel, Kevin and Masoudi, Mark and Deynze, Allen Van and Foolad, Majid}, year={2014}, month={Sep} }
 @article{truco_ashrafi_kozik_leeuwen_bowers_wo_stoffel_xu_hill_deynze_et al._2013, title={An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce}, volume={3}, DOI={10.1534/g3.112.004929}, number={4}, journal={G3&#58; Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Truco, Maria José and Ashrafi, Hamid and Kozik, Alexander and Leeuwen, Hans and Bowers, John and Wo, Sebastian Reyes Chin and Stoffel, Kevin and Xu, Huaqin and Hill, Theresa and Deynze, Allen Van and et al.}, year={2013}, month={Mar}, pages={617–631} }
 @article{hill_ashrafi_reyes-chin-wo_yao_stoffel_truco_kozik_michelmore_deynze_2013, title={Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip}, volume={8}, DOI={10.1371/journal.pone.0056200}, number={2}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Hill, Theresa A. and Ashrafi, Hamid and Reyes-Chin-Wo, Sebastian and Yao, JiQiang and Stoffel, Kevin and Truco, Maria-Jose and Kozik, Alexander and Michelmore, Richard W. and Deynze, Allen Van}, editor={Zhang, JianweiEditor}, year={2013}, month={Feb}, pages={e56200} }
 @misc{hulse_hoegenauer_ashrafi_wang_stelly_deynze_hinze_yu_fang_pepper_et al._2013, title={Genome-wide SNP Development and Validation for Intraspecific SNPs in Upland Cotton}, note={Poster P0761}, author={Hulse, Amanda M. and Hoegenauer, Kevin A. and Ashrafi, Hamid and Wang, Fei and Stelly, David and Deynze, Allen Van and Hinze, Lori and Yu, John Z. and Fang, David and Pepper, Alan E. and et al.}, year={2013}, month={Jan} }
 @article{yarnes_ashrafi_reyes-chin-wo_hill_stoffel_deynze_2013, title={Identification of QTLs for capsaicinoids, fruit quality, and plant architecture-related traits in an interspecific Capsicum RIL population}, volume={56}, DOI={10.1139/gen-2012-0083}, number={1}, journal={Genome}, publisher={Canadian Science Publishing}, author={Yarnes, Shawn C. and Ashrafi, Hamid and Reyes-Chin-Wo, Sebastian and Hill, Theresa A. and Stoffel, Kevin M. and Deynze, Allen Van}, editor={Gulick, P.Editor}, year={2013}, month={Jan}, pages={61–74} }
 @article{page_huynh_liechty_grupp_stelly_hulse_ashrafi_deynze_wendel_udall_2013, title={Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing}, volume={3}, DOI={10.1534/g3.113.007229}, number={10}, journal={G3&#58; Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Page, Justin T. and Huynh, Mark D. and Liechty, Zach S. and Grupp, Kara and Stelly, David and Hulse, Amanda M. and Ashrafi, Hamid and Deynze, Allen Van and Wendel, Jonathan F. and Udall, Joshua A.}, year={2013}, month={Aug}, pages={1809–1818} }
 @misc{zheng_wang_hoegenauer_quintana_ashrafi_stelly_bell_deynze_jones_nichols_2013, title={Resolving Tight Linkages Around Renlon by MAS for High-resolution Recombination in Chromosome-11}, note={Poster P4053}, author={Zheng, Xiuting and Wang, Fei and Hoegenauer, Kevin A. and Quintana, Jose and Ashrafi, Hamid and Stelly, David and Bell, Alois A. and Deynze, Allen Van and Jones, Don C. and Nichols, Robert L.}, year={2013}, month={Jan} }
 @article{deynze_hill_ashrafi_2013, title={Structural Genomics}, DOI={10.1201/b14578-10}, journal={Genetics, Genomics, and Breeding of Tomato}, publisher={Science Publishers}, author={Deynze, Allen Van and Hill, Theresa and Ashrafi, Hamid}, year={2013}, month={Jan}, pages={327–344} }
 @misc{wang_hulse_hoegenauer_stelly_ashrafi_deynze_yu_2012, title={Collaborative Development of SNPs for Cotton Research, Introgression, MAS and Breeding. Genome-Wide Gossypium SNP Development and Validation}, url={http://www.cotton.org/beltwide/index.cfm?page=beltwide_overview}, author={Wang, Fei and Hulse, Amanda M. and Hoegenauer, Kevin and Stelly, David M. and Ashrafi, Hamid and Deynze, Allen Van and Yu, John Z.}, year={2012}, month={Jan} }
 @misc{ashrafi_2012, title={Comparison and evaluation of cotton SNPs developed by transcriptome, genome reduction on restriction site conservation and RAD-based sequencing}, author={Ashrafi, H.}, year={2012}, month={Oct} }
 @misc{hill_ashrafi_reyes-chin-wo_romero_kozik_deynze_2012, title={Comparisons of high-density EST-based maps in pepper species}, note={Poster P0479}, author={Hill, Theresa and Ashrafi, Hamid and Reyes-Chin-Wo, Sebastian and Romero, Marcelo Solano and Kozik, Alexander and Deynze, Allen Van}, year={2012}, month={Jan} }
 @article{ashrafi_hill_stoffel_kozik_yao_chin-wo_deynze_2012, title={De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes}, volume={13}, DOI={10.1186/1471-2164-13-571}, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Ashrafi, Hamid and Hill, Theresa and Stoffel, Kevin and Kozik, Alexander and Yao, JiQiang and Chin-Wo, Sebastian and Deynze, Allen Van}, year={2012}, pages={571} }
 @article{stoffel_leeuwen_kozik_caldwell_ashrafi_cui_tan_hill_reyes-chin-wo_truco_et al._2012, title={Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)}, volume={13}, DOI={10.1186/1471-2164-13-185}, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Stoffel, Kevin and Leeuwen, Hans and Kozik, Alexander and Caldwell, David and Ashrafi, Hamid and Cui, Xinping and Tan, Xiaoping and Hill, Theresa and Reyes-Chin-Wo, Sebastian and Truco, Maria-Jose and et al.}, year={2012}, pages={185} }
 @misc{wang_hulse_hoegenauer_stelly_ashrafi_deynze_yu_2012, title={Genome-Wide Gossypium SNP Development and Validation}, url={http://www.cotton.org/beltwide/index.cfm?page=beltwide_overview}, author={Wang, Fei and Hulse, Amanda M. and Hoegenauer, Kevin and Stelly, David M. and Ashrafi, Hamid and Deynze, Allen Van and Yu, John}, year={2012}, month={Jan} }
 @misc{hulse_wang_hoegenauer_stelly_ashrafi_deynze_yu_chen_udall_jones_2012, title={Genome-wide SNP development and validation for allotetraploid Gossypium}, note={Poster P0199}, author={Hulse, Amanda M. and Wang, Fei and Hoegenauer, Kevin and Stelly, David M. and Ashrafi, Hamid and Deynze, Allen Van and Yu, John Z. and Chen, Jeffrey Z. and Udall, Joshua A. and Jones, Dan C.}, year={2012}, month={Jan} }
 @misc{ashrafi_yao_stoffel_reyes-chin-wo_hill_kozik_van deynze_2012, title={Genome-wide SNP discovery from de novo assemblies of pepper (Capsicum annuum) transcriptomes}, note={Poster P0480}, author={Ashrafi, Hamid and Yao, Jiqiang and Stoffel, Kevin and Reyes-Chin-Wo, Sebastian and Hill, Theresa and Kozik, Alexander and Van Deynze, Allen}, year={2012}, month={Jan} }
 @article{paterson_wendel_gundlach_guo_jenkins_jin_llewellyn_showmaker_shu_udall_et al._2012, title={Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres}, volume={492}, ISSN={0028-0836 1476-4687}, url={http://dx.doi.org/10.1038/nature11798}, DOI={10.1038/nature11798}, number={7429}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Paterson, Andrew H. and Wendel, Jonathan F. and Gundlach, Heidrun and Guo, Hui and Jenkins, Jerry and Jin, Dianchuan and Llewellyn, Danny and Showmaker, Kurtis C. and Shu, Shengqiang and Udall, Joshua and et al.}, year={2012}, month={Dec}, pages={423–427} }
 @article{merk_ashrafi_foolad_2012, title={Selective genotyping to identify late blight resistance genes in an accession of the tomato wild species Solanum pimpinellifolium}, volume={187}, DOI={10.1007/s10681-012-0729-6}, number={1}, journal={Euphytica}, publisher={Springer Nature}, author={Merk, Heather L. and Ashrafi, Hamid and Foolad, Majid R.}, year={2012}, month={Jun}, pages={63–75} }
 @article{powell_nguyen_hill_cheng_figueroa-balderas_aktas_ashrafi_pons_fernandez-munoz_vicente_et al._2012, title={Uniform ripening Encodes a Golden 2-like Transcription Factor Regulating Tomato Fruit Chloroplast Development}, volume={336}, DOI={10.1126/science.1222218}, number={6089}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Powell, A. L. T. and Nguyen, C. V. and Hill, T. and Cheng, K. L. and Figueroa-Balderas, R. and Aktas, H. and Ashrafi, H. and Pons, C. and Fernandez-Munoz, R. and Vicente, A. and et al.}, year={2012}, month={Jun}, pages={1711–1715} }
 @misc{deynze_hill_yarnes_rehrig_chin-wo_ashrafi_adamchak_kozik_prince_2011, title={An Integrated approach to breeding resistance to Phytophthora capsici In Pepper}, note={Poster 450}, author={Deynze, Allen Van and Hill, Theresa A. and Yarnes, Shawn and Rehrig, William Z. and Chin-Wo, Sebastian Reyes and Ashrafi, Hamid and Adamchak, Raoul and Kozik, Alex and Prince, Jim}, year={2011}, month={Jan} }
 @misc{hill_ashrafi_chin-wo_romero_deynze_kozik_Aug. 6-10, 2011, title={Comparisons of high-density EST-based maps in pepper species}, author={Hill, Theresa and Ashrafi, Hamid and Chin-Wo, Sebastian Reyes- and Romero, Marcelo Solano and Deynze, Allen Van and Kozik, Alexander}, year={Aug. 6-10, 2011}, month={Aug. 6-10, 2011} }
 @article{iorizzo_senalik_grzebelus_bowman_cavagnaro_matvienko_ashrafi_deynze_simon_2011, title={De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity}, volume={12}, DOI={10.1186/1471-2164-12-389}, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Iorizzo, Massimo and Senalik, Douglas A and Grzebelus, Dariusz and Bowman, Megan and Cavagnaro, Pablo F and Matvienko, Marta and Ashrafi, Hamid and Deynze, Allen Van and Simon, Philipp W}, year={2011}, month={Aug} }
 @misc{deynze_hill_prince_yarnes_chunthawodtiporn_rehrig_reyes-chin-wo_ashrafi_kozik_2011, title={Development and Application of Genomic Tools in Pepper}, note={Workshop 531}, author={Deynze, Allen Van and Hill, Theresa and Prince, Jim and Yarnes, Shawn and Chunthawodtiporn, Jareerat and Rehrig, William and Reyes-Chin-wo, Sebastian and Ashrafi, Hamid and Kozik, Alexander}, year={2011}, month={Jan} }
 @article{ashrafi_kinkade_merk_foolad_2011, title={Identification of novel quantitative trait loci for increased lycopene content and other fruit quality traits in a tomato recombinant inbred line population}, volume={30}, DOI={10.1007/s11032-011-9643-1}, number={1}, journal={Molecular Breeding}, publisher={Springer Nature}, author={Ashrafi, Hamid and Kinkade, Matthew P. and Merk, Heather L. and Foolad, Majid R.}, year={2011}, month={Oct}, pages={549–567} }
 @misc{deynze_hill_prince_yarnes_chunthawodtiporn_rehrig_reyes-chin-wo_ashrafi_kozik_2011, title={The Genetic Map and Genome Sequencing of Lettuce}, note={Workshop 531}, author={Deynze, Allen Van and Hill, Theresa and Prince, Jim and Yarnes, Shawn and Chunthawodtiporn, Jareerat and Rehrig, William and Reyes-Chin-wo, Sebastian and Ashrafi, Hamid and Kozik, Alexander}, year={2011}, month={Jan} }
 @misc{hill_ashrafi_kozik_deynze_2010, title={Ultra High Density EST-Based Maps Reveal Genome Differences Between C. frutescence And C. annuum}, author={Hill, Theresa and Ashrafi, Hamid and Kozik, Alex and Deynze, Allen Van}, year={2010}, month={Jan} }
 @article{ashrafi_kinkade_foolad_2009, title={A new genetic linkage map of tomato based on a Solanum lycopersicum × S. pimpinellifolium RIL population displaying locations of candidate pathogen response genes}, volume={52}, DOI={10.1139/g09-065}, number={11}, journal={Genome}, publisher={Canadian Science Publishing}, author={Ashrafi, Hamid and Kinkade, Matthew and Foolad, Majid R.}, editor={Gulick, PatrickEditor}, year={2009}, month={Nov}, pages={935–956} }
 @misc{kozik_leeuwen_truco_stoffel_mchale_ashrafi_lavelle_cui_deynze_michelmore_2009, title={Construction of an Ultra High Density Genetic Map of Lettuce using an Affymetrix GeneChip}, note={Poster 68}, author={Kozik, Alexander and Leeuwen, Hans and Truco, Maria Jose and Stoffel, Kevin and McHale, Leah and Ashrafi, Hamid and Lavelle, Dean and Cui, Xinping and Deynze, Allen Van and Michelmore, Richard W.}, year={2009}, month={Jan} }
 @misc{leeuwen_stoffel_truco_ashrafi_cui_kozik_michelmore_deynze_2009, title={Development and Utilization of a High Density 6.6 Million Feature Affymetrix GeneChip for Marker Discovery and Genotyping in Lettuce}, note={Poster 69}, author={Leeuwen, Hans and Stoffel, Kevin and Truco, María José and Ashrafi, Hamid and Cui, Xinping and Kozik, Alexander and Michelmore, Richard W. and Deynze, Allen Van}, year={2009}, month={Jan} }
 @misc{leeuwen_stoffel_kozik_cui_ashrafi_mchale_lavelle_wong_chen_truco_et al._2009, title={High-Density Mapping of the Lettuce Genome with SFP Markers in over 15,000 Unigenes}, note={Workshop 126}, author={Leeuwen, Hans and Stoffel, Kevin and Kozik, Alexander and Cui, Xinping and Ashrafi, Hamid and McHale, Leah and Lavelle, Dean and Wong, Gene and Chen, Fallon and Truco, María José and et al.}, year={2009}, month={Jan} }
 @misc{ashrafi_hill_yao_leeuwen_michelmore_kozik_deynze_2009, title={The Application of a Whole Genome Pepper Array to Identify SFPs in a Diversity Panel}, note={Workshop 459}, author={Ashrafi, Hamid and Hill, Theresa and Yao, Jiqiang and Leeuwen, Hans and Michelmore, Richard and Kozik, Alexander and Deynze, Allen Van}, year={2009}, month={Jan} }
 @misc{hill_ashrafi_yao_jong_francis_kozik_deynze_2009, title={The Application of a Whole Genome Pepper Array to Solanaceae Crops}, author={Hill, Theresa and Ashrafi, Hamid and Yao, Jiqiang and Jong, Walter De and Francis, David and Kozik, Alex and Deynze, Allen Van}, year={2009}, month={Oct} }
 @article{sharma_zhang_niño-liu_ashrafi_foolad_2008, title={A Solanum lycopersicum × Solanum pimpinellifolium Linkage Map of Tomato Displaying Genomic Locations of R-Genes, RGAs, and Candidate Resistance/Defense-Response ESTs}, volume={2008}, DOI={10.1155/2008/926090}, journal={International Journal of Plant Genomics}, publisher={Hindawi Limited}, author={Sharma, Arun and Zhang, Liping and Niño-Liu, David and Ashrafi, Hamid and Foolad, Majid R.}, year={2008}, pages={1–18} }
 @article{foolad_merk_ashrafi_2008, title={Genetics, Genomics and Breeding of Late Blight and Early Blight Resistance in Tomato}, volume={27}, DOI={10.1080/07352680802147353}, number={2}, journal={Critical Reviews in Plant Sciences}, publisher={Informa UK Limited}, author={Foolad, Majid R. and Merk, Heather L. and Ashrafi, Hamid}, year={2008}, month={Jun}, pages={75–107} }
 @misc{ashrafi_kinkade_foolad_2007, title={HPLC and spectrophotometer analyses of fruit carotenoids In a Lycopersicon esculentum X L. pimpinellifolium RIL population reveals several new QTLs for lycopene content}, note={Abstract published in the Proceedings for the meeting, p. 210}, author={Ashrafi, H. and Kinkade, M.R. and Foolad, M.R.}, year={2007}, month={Jan} }
 @misc{merk_ashrafi_kinkade_foolad_2007, title={Identification and molecular mapping of a new dominant gene (Ph5) conferring broad-spectrum resistance against tomato late blight}, note={Abstract published in the Proceedings for the meeting, p. 210}, author={Merk, H.L. and Ashrafi, H. and Kinkade, M.P. and Foolad, M.R.}, year={2007}, month={Jan} }
 @misc{ashrafi_lin_foolad_2006, title={A molecular linkage map of tomato based on RFLP markers and candidate disease-resistance/defense-response genes in an F7 RIL population}, author={Ashrafi, H. and Lin, G.Y. and Foolad, M.R.}, year={2006}, month={Mar} }
 @misc{ashrafi_lin_foolad_2006, title={Identification of QTLs for tomato early blight resistance in a RIL population of a cross between Lycopersicon esculentum and L. pimpinellifolium}, author={Ashrafi, H. and Lin, G.Y. and Foolad, M.R.}, year={2006}, month={Apr} }
 @inproceedings{foolad_merk_ashrafi_kinkade_Nov. 9-10, 2006, place={Fletcher, NC}, title={Identification of new sources of late blight resistance in tomato and mapping of a new resistance gene}, booktitle={Proc. 21st Annual Tomato Disease Workshop}, publisher={NC State University}, author={Foolad, M.R. and Merk, H.L. and Ashrafi, H. and Kinkade, M.P.}, year={Nov. 9-10, 2006}, month={Nov. 9-10, 2006} }
 @misc{ashrafi_sharma_kole_merk_lin_foolad_2006, title={Mapping of early blight resistance QTLs and candidate resistance genes in a RIL population of tomato}, note={Abstract published in the Proceedings for the meeting, p. 218}, author={Ashrafi, H. and Sharma, A. and Kole, C. and Merk, H. and Lin, G.Y. and Foolad, M.R.}, year={2006}, month={Jan} }
 @misc{merk_ashrafi_kole_kinkade_lin_foolad_2006, title={Toward identification and mapping of new late blight resistance genes in tomato}, note={Poster 0245}, author={Merk, H.L. and Ashrafi, H. and Kole, C. and Kinkade, M. and Lin, G.Y. and Foolad, M.R.}, year={2006}, month={Apr} }
 @article{ashrafi_sharma_niño-liu_zhang_foolad_2005, title={(13) Comparative Mapping of Early Blight Resistance QTLs and Candidate Resistance Genes in F2, F3, F4 and a RIL Population of Tomato}, volume={40}, number={4}, journal={HortScience}, author={Ashrafi, H. and Sharma, A. and Niño-Liu, D. and Zhang, L. and Foolad, M.}, year={2005}, pages={1040} }
 @misc{ashrafi_sharma_niño-liu_zhang_foolad_2005, title={Comparative mapping of early blight resistance QTLs and candidate resistance genes in F2, F3, F4 and a RIL population of Tomato}, author={Ashrafi, H. and Sharma, A. and Niño-Liu, D. and Zhang, L. and Foolad, M.R.}, year={2005} }
 @misc{ashrafi_sharma_niño-liu_foolad_2005, title={Genetic mapping of candidate resistance genes in tomato using an F2 and a RIL population of a Lycopersicon esculentum × L. pimpinellifolium cross}, author={Ashrafi, H. and Sharma, A. and Niño-Liu, D. and Foolad, M.R.}, year={2005}, month={Mar} }
 @article{foolad_sharma_ashrafi_lin_2005, title={Genetics and Breeding of Early Blight Resistance in Tomato}, volume={40}, journal={HortScience}, author={Foolad, M.R. and Sharma, A. and Ashrafi, H. and Lin, G.}, year={2005}, pages={1114–1114} }
 @misc{sharma_ashrafi_foolad_2005, title={Genetics of early blight resistance in tomato}, note={Abstract published in the Proceedings for the meeting, p. 191}, author={Sharma, A. and Ashrafi, H. and Foolad, M.R.}, year={2005}, month={Jan} }
 @misc{r._sharma_ashrafi_2004, title={Early blight resistance in tomato: genetics, breeding and accelerated breeding}, author={R., Foolad M. and Sharma, A. and Ashrafi, H.}, year={2004}, month={Jun} }
 @article{samaee_shobbar_ashrafi_hosseini-mazinani_sheidai_2003, title={MOLECULAR CHARACTERIZATION OF OLIVE GERMPLASM IN IRAN BY USE OF RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) AND CORRELATION WITH PHENOTYPIC STUDIES: PRELIMINARY RESULTS}, volume={7}, DOI={10.17660/actahortic.2003.623.18}, number={623}, journal={Acta Horticulturae}, publisher={International Society for Horticultural Science (ISHS)}, author={Samaee, S.M. and Shobbar, Z.S. and Ashrafi, H. and Hosseini-Mazinani, M. and Sheidai, M.}, year={2003}, month={Jul}, pages={169–175} }