Amanda Marie Hulse-Kemp

Additional file 1 of Chromosome-scale assemblies of flowering dogwood cultivars enable identification of candidate genes regulating anthocyanin biosynthesis in leaves and bracts

Hamm, T. P., Boggess, S. L., Nowicki, M., Hadziabdic, D., Shoemaker, D. W., Trigiano, R. N., … Staton, M. E. (2026, January 1). Figshare, Vol. 1.

Additional file 1 of Chromosome-scale assemblies of flowering dogwood cultivars enable identification of candidate genes regulating anthocyanin biosynthesis in leaves and bracts

Hamm, T. P., Boggess, S. L., Nowicki, M., Hadziabdic, D., Shoemaker, D. W., Trigiano, R. N., … Staton, M. E. (2026, January 1). Figshare, Vol. 1.

Additional file 2 of Chromosome-scale assemblies of flowering dogwood cultivars enable identification of candidate genes regulating anthocyanin biosynthesis in leaves and bracts

Hamm, T. P., Boggess, S. L., Nowicki, M., Hadziabdic, D., Shoemaker, D. W., Trigiano, R. N., … Staton, M. E. (2026, January 1). Figshare, Vol. 1.

Additional file 2 of Chromosome-scale assemblies of flowering dogwood cultivars enable identification of candidate genes regulating anthocyanin biosynthesis in leaves and bracts

Hamm, T. P., Boggess, S. L., Nowicki, M., Hadziabdic, D., Shoemaker, D. W., Trigiano, R. N., … Staton, M. E. (2026, January 1). Figshare, Vol. 1.

Chromosome-scale assemblies of flowering dogwood cultivars enable identification of candidate genes regulating anthocyanin biosynthesis in leaves and bracts

Hamm, T. P., Boggess, S. L., Nowicki, M., Hadziabdic, D., Shoemaker, D. W., Trigiano, R. N., … Staton, M. E. (2026, January 1). Figshare, Vol. 1.

Chromosome-scale assemblies of flowering dogwood cultivars enable identification of candidate genes regulating anthocyanin biosynthesis in leaves and bracts

Hamm, T. P., Boggess, S. L., Nowicki, M., Hadziabdic, D., Shoemaker, D. W., Trigiano, R. N., … Staton, M. E. (2026, January 1). Figshare, Vol. 1.

BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community

Selby, P., Abbeloos, R., Adam-Blondon, A.-F., Agosto-Perez, F. J., Alaux, M., Alic, I., … BrAPIConsortium. (2025, January 1). Database, Vol. 2025.

Chromosome-Scale Assemblies of Flowering Dogwood Cultivars Enable Identification of Candidate Genes Regulating Anthocyanin Biosynthesis in Leaves and Bracts

Hamm, T. P., Boggess, S. L., Nowicki, M., Hadziabdic, D., Shoemaker, D. W., Trigiano, R. N., … Staton, M. E. (2025, July 31).

Evaluating UAV captured RGB and multispectral imagery as a proxy for visual rating of leaf spot in cultivated peanut

Newman, C., Austin, R., Andres, R., Read, Q., Garrity, N., Fritz, K., … Dunne, J. (2025, May 21). The Plant Phenome Journal, Vol. 8.

TaWUS2D regulates the number of grains per spikelet by enhancing the number of fertile ovaries in Multi-Ovary Wheat

Schoen, A. W., Sharma, P. K., Mahlandt, A., Chen, A., Sheng, H., Kochian, L., … Tiwari, V. (2025, February 8). (Vol. 2). Vol. 2.

The integration of quantitative trait locus mapping and transcriptome studies reveals candidate genes for water stress response in St. Augustinegrass

BMC Plant Biology, 25(1).

Trait mapping differentiates loci influencing spike and flag leaf glaucousness in wheat

Miller, D., Rivera‐Burgos, L., Guedira, M., DeWitt, N., Ward, B., Murphy, J. P., … Brown‐Guedira, G. (2025, July 26). The Plant Genome, Vol. 18.

A Blueberry (Vaccinium L.) Crop Ontology to Enable Standardized Phenotyping for Blueberry Breeding and Research

HortScience, 59(10), 1433–1442.

CitDet: A Benchmark Dataset for Citrus Fruit Detection

James, J. A., Manching, H. K., Mattia, M. R., Bowman, K. D., Hulse-Kemp, A. M., & Beksi, W. J. (2024, October 3). IEEE Robotics and Automation Letters, Vol. 9, pp. 10788–10795.

De novo whole-genome assembly and annotation of Coffea arabica var. Geisha, a high-quality coffee variety from the primary origin of coffee

Medrano, J. F., Cantu, D., Minio, A., Dreischer, C., Gibbons, T., Chin, J., … Hulse-Kemp, A. M. (2024, November 15). (S. Pearce, Ed.). G3 Genes Genomes Genetics.

Few-Shot Fruit Segmentation via Transfer Learning

James, J. A., Manching, H. K., Hulse-Kemp, A. M., & Beksi, W. J. (2024, May 13). 2024 IEEE INTERNATIONAL CONFERENCE ON ROBOTICS AND AUTOMATION (ICRA 2024), pp. 13618–13624.

A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane

Islam, M. S., Corak, K., McCord, P., Hulse-Kemp, A. M., & Lipka, A. E. (2023, August 2). Frontiers in Plant Science, Vol. 14.

Detecting Cotton Leaf Curl Virus Resistance Quantitative Trait Loci in Gossypium hirsutum and iCottonQTL a New R/Shiny App to Streamline Genetic Mapping

Schoonmaker, A. N., Hulse-Kemp, A. M., Youngblood, R. C., Rahmat, Z., Iqbal, M. A., Rahman, M.-ur, … Scheffler, J. A. (2023, March 3). Plants, Vol. 12.

Initiation of genomics-assisted breeding in Virginia-type peanuts through the generation of a de novo reference genome and informative markers

Newman, C. S., Andres, R. J., Youngblood, R. C., Campbell, J. D., Simpson, S. A., Cannon, S. B., … Dunne, J. C. (2023, January 27). Frontiers in Plant Science, Vol. 13.

Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa

Huff, M., Hulse-Kemp, A. M., Scheffler, B. E., Youngblood, R. C., Simpson, S. A., Babiker, E., & Staton, M. (2023, July 20). BMC Genomics, Vol. 24.

Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning

Delorean, E. E., Youngblood, R. C., Simpson, S. A., Schoonmaker, A. N., Scheffler, B. E., Rutter, W. B., & Hulse-Kemp, A. M. (2023, November 16). Frontiers in Plant Science, Vol. 14.

Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea (Hydrangea macrophylla) and insights into Asterid evolution

Wu, X., Simpson, S. A., Youngblood, R. C., Liu, X. F., Scheffler, B. E., Rinehart, T. A., … Hulse-Kemp, A. M. (2023, November 9). Horticulture Research.

Two pathogen loci determine Blumeria graminis

New Phytologist, 238(4), 1546–1561.

Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication

Chang, J., Marczuk‐Rojas, J. P., Waterman, C., Garcia‐Llanos, A., Chen, S., Ma, X., … Carretero‐Paulet, L. (2022, July 27). The Plant Genome, Vol. 7.

Efficient imaging and computer vision detection of two cell shapes in young cotton fibers

Graham, B. P., Park, J., Billings, G. T., Hulse‐Kemp, A. M., Haigler, C. H., & Lobaton, E. (2022, November 1). Applications in Plant Sciences, Vol. 11.

Genetic variability and QTL mapping of winter survivability and leaf firing in African bermudagrass

Yu, S., Schoonmaker, A. N., Yan, L., Hulse‐Kemp, A. M., Fontanier, C. H., Martin, D. L., … Wu, Y. Q. (2022, September 14). Crop Science, Vol. 10.

Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon

Vaughn, J. N., Branham, S. E., Abernathy, B., Hulse-Kemp, A. M., Rivers, A. R., Levi, A., & Wechter, W. P. (2022, December 22). Nature Communications, Vol. 13.

Leveraging National Germplasm Collections to Determine Significantly Associated Categorical Traits in Crops: Upland and Pima Cotton as a Case Study

Restrepo-Montoya, D., Hulse-Kemp, A. M., Scheffler, J. A., Haigler, C. H., Hinze, L. L., Love, J., … Frelichowski, J. (2022, April 26). Frontiers in Plant Science, Vol. 4.

Nuclear DNA contents and ploidy levels of North American Vaccinium species and interspecific hybrids

Scientia Horticulturae, 297, 110955.

Outlook for Implementation of Genomics-Based Selection in Public Cotton Breeding Programs

Billings, G. T., Jones, M. A., Rustgi, S., Bridges, W. C., Holland, J. B., Hulse-Kemp, A. M., & Campbell, B. T. (2022, May 29). Plants, Vol. 6.

There and back again; historical perspective and future directions for Vaccinium breeding and research studies

Horticulture Research, 9.

An anchored chromosome‐scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids

The Plant Genome, 14(2).

Genomic Resource Development for Hydrangea (Hydrangea macrophylla (Thunb.) Ser.)—A Transcriptome Assembly and a High-Density Genetic Linkage Map

Wu, X., Hulse-Kemp, A., Wadl, P., Smith, Z., Mockaitis, K., Staton, M., … Alexander, L. (2021, February 5). Horticulturae, Vol. 7.

High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry (Vaccinium darrowii)

Yu, J., Hulse-Kemp, A. M., Babiker, E., & Staton, M. (2021, November 1). Horticulture Research, Vol. 12.

Population structure and genetic diversity of the Pee Dee cotton breeding program

Billings, G. T., Jones, M. A., Rustgi, S., Hulse-Kemp, A. M., & Campbell, B. T. (2021, April 29). G3 Genes Genomes Genetics, Vol. 7.

Capsicum—An Abbreviated Compendium

Jarret, R. L., Barboza, G. E., Costa Batista, F. R., Berke, T., Chou, Y.-Y., Hulse-Kemp, A., … Szoke, A. (2019, January 1). Journal of the American Society for Horticultural Science, Vol. 144, pp. 3–22.

Enhancing Upland cotton for drought resilience, productivity, and fiber quality: comparative evaluation and genetic dissection

Ulloa, M., Santiago, L. M. D., Hulse-Kemp, A. M., Stelly, D. M., & Burke, J. J. (2019, October 16). Molecular Genetics and Genomics, Vol. 295, pp. 155–176.

Feeding high-oleic peanuts to layer hens enhances egg yolk color and oleic fatty acid content in shell eggs

Poultry Science, 98(4), 1732–1748.

Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library

Hulse-Kemp, A. M., Maheshwari, S., Stoffel, K., Hill, T. A., Jaffe, D., Williams, S. R., … Deynze, A. V. (2018, January 12). Horticulture Research, Vol. 5.

Sequencing‐Based Bin Map Construction of a Tomato Mapping Population, Facilitating High‐Resolution Quantitative Trait Loci Detection

The Plant Genome, 12(1).

Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array

Hinze, L. L., Hulse-Kemp, A. M., Wilson, I. W., Zhu, Q.-H., Llewellyn, D. J., Taylor, J. M., … Stelly, D. M. (2017, February 3). BMC Plant Biology, Vol. 17, p. 37,

Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library

Hulse-Kemp, A. M., Maheshwari, S., Stoffel, K., Hill, T. A., Jaffe, D., Williams, S., … Deynze, A. V. (2017, June 20).

A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding

Horticulture Research, 3(1), 16036.

Correction: DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton

Page, J. T., Liechty, Z. S., Alexander, R. H., Clemons, K., Hulse-Kemp, A. M., Ashrafi, H., … Udall, J. A. (2016, July 22). PLoS Genetics, Vol. 12, p. 1006206,

DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton

PLOS Genetics, 12(5), e1006012.

BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping

G3 Genes|Genomes|Genetics, 5(6), 1095–1105.

Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

G3 Genes|Genomes|Genetics, 5(6), 1187–1209.

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

Zhang, T., Hu, Y., Jiang, W., Fang, L., Guan, X., Chen, J., … Chen, Z. J. (2015, April 20). Nature Biotechnology, Vol. 33, pp. 531–537,

Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts

BMC Genomics, 15(1), 945.

Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations

Gomez-Raya, L., Hulse, A. M., Thain, D., & Rauw, W. M. (2013, August 6). Journal of Animal Science and Biotechnology/Journal of Animal Science and Biotechnology, Vol. 4, p. 30.

Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing

G3 Genes|Genomes|Genetics, 3(10), 1809–1818.

Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus

Cai, Yang, E., Hulse, A. M., & Cai. (2012, January 1). Evolutionary Bioinformatics, Vol. 11, p. 623.

Genetic Variants Contribute to Gene Expression Variability in Humans

Hulse, A. M., & Cai, J. J. (2012, November 14). Genetics, Vol. 193, p. 95–108.