Amanda M. Hulse-Kemp

Amanda M. Hulse-Kemp is a computational biologist with the United States Department of Agriculture – Agricultural Research Service. She works in the Genomics and Bioinformatics Research Unit and is stationed on the North Carolina State University campus in Raleigh, North Carolina.

Amanda M. Hulse-Kemp
Alma mater
Academic career
Institutions

Early life

Amanda Hulse-Kemp grew up in Harrisonburg, Virginia.[1] She earned her Bachelor of Science Degree in Biology and Animal Biotechnology from the University of Nevada, Reno, in 2010.[1][2] Hulse-Kemp earned her Ph.D. in 2015 from Texas A&M University's Interdisciplinary Graduate Program in Genetics, where her doctoral advisor was Dr. David Stelly.[2][3][4] In Stelly's lab, she coordinated the development of the CottonSNP63K Array, the first of its kind for cotton.[5][6] The CottonSNP63K array has already been utilized to make characterization of germplasm resources more efficient and to identify economically important genes.[1] She and Dr. Stelly also formed International Cotton SNP Chip Consortium.[6] She completed postdoctoral research at the Seed Biotechnology Center at the University of California, Davis, where she focused on bioinformatics, resource development and integration of genomics and biotechnology tools for enhancing breeding of vegetables and other crops.[3][2] At the center, she assisted in genetic analyses of pepper, cotton, tomato, coffee, and spinach.[7]

Career

Hulse-Kemp works as a computational biologist at the intersection of genomics and biotechnology and crop breeding.[3] She works with the United States Department of Agriculture – Agriculture Research Service in the Genomics and Bioinformatics Research Unit.[3] Her current research focus involves utilizing bioinformatics to enhance ARS breeding programs in both plants and animals.[3] She is a USDA assistant professor at North Carolina State University in the Department of Crop and Soil Sciences.[8] She collaborated on the Coffee Genome Project, which aims to sequence Coffea arabica and to examine inter-variety diversity.[9] She was part of the team behind the first sequencing of the C. arabica genome.[10]

Awards and Publications

As a PhD. student at Texas A&M University, she earned the Ethel Ashworth-Tsutsui Memorial Award for Research in 2014,[11] the Texas A&M University Distinguished Graduate Student award, the Dean's Outstanding Achievement Award for Graduate Research,[1][6] and the BB Singh Award for Crop Science Thesis.[12]

Hulse-Kemp has co-authored the following publications:

  • "Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus" in Evolutionary Bioinformatics, 2012[13]
  • "Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Resequencing" in Genes, Genomes, Genetics, 2013[14]
  • "Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations" in Journal of Animal Science and Biotechnology, 2013[15]
  • "Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement" in Nature Biotechnology, 2015[16]
  • "BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping" in Genes, Genomes, Genetics, 2015[17]
  • "DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton" & a Correct in PLOS Genetics, 2016[18][19]
  • "Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array" in BMC Plant Biology, 2017[20]
  • "Sub genome-anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids" in Scientific Reports, 2017[21]
  • "Comparative transcriptomics and genomic patterns of discordance in Capsiceae (Solanaceae)" in Molecular Phylogenetics and Evolution, 2018[22]
  • "Feeding high-oleic peanuts to layer hens enhances egg yolk color and oleic fatty acid content in shell eggs" in Poultry Science, 2019[23]
  • "Enhancing Upland cotton for drought resilience, productivity, and fiber quality: comparative evaluation and genetic dissection" in Molecular Genetics and Genomics, 2020[24]

She has been lead author on the following publications:

  • "Genetic Variants Contribute to Gene Expression Variability in Humans" in Genetics, 2013[25]
  • "Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts" in BMC Genomics, 2014[26]
  • "Development of 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp" in Genes, Genomes, Genetics, 2015[27]
  • "A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding" in Horticulture Research, 2016[28]
  • "Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library" in Horticulture Research, 2018[29]

References
  1. Texas A&M University (September 2015). "Texas A&M Plant Breeding Bulletin Announcement of Amanda Hulse-Kemp receiving her Ph.D." (PDF). TEXAS A&M PLANT BREEDING BULLETIN. Retrieved February 14, 2020.
  2. Kaki Carl (2017-12-01). "Meet Amanda Hulse-Kemp". NC State University. Retrieved 2020-02-14.
  3. "Amanda Hulse-Kemp". ars.usda.gov. Retrieved 2020-02-14.
  4. Bautista, Carol Vargas (8 November 2017). "Former Students". Genetics at Texas A&M University. Retrieved 2020-02-14.
  5. "The CottonSNP63K Project". cottongen.org. Retrieved 2020-02-14.
  6. Texas A&M University Department of Soil and Crop Sciences (May 2015). "Congratulations" (PDF). AGGIE Agenda. Retrieved February 14, 2020.
  7. UC Davis Seed Biotechnology Center (2017). "Annual Report of the Seed Biotechnology Center (UC Davis)" (PDF). Annual Report 2017. Retrieved February 14, 2020.
  8. "Amanda Hulse-Kemp". NC State University. Retrieved 2020-02-14.
  9. "People". coffeegenome.ucdavis.edu. Retrieved 2020-02-14.
  10. "Arabica coffee genome sequenced: Coincides with birth of California-grown specialty coffee industry". ScienceDaily. 2017-01-13. Retrieved 2020-02-14.
  11. Science, Texas A&M University-. "Science Outreach | Texas A&M University | College Station, TX". outreach.science.tamu.edu. Retrieved 2020-02-14.
  12. Beth Luedeker (2016-01-19). "2015 Soil&Crop Sciences Departmental Awards". soilcrop.tamu.edu. Retrieved 2020-02-14.
  13. Yang, Ence; Hulse, Amanda M.; Cai, James J. (2012). "Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes inAspergillus fumigatus". Evolutionary Bioinformatics. 8: 623–44. doi:10.4137/ebo.s10372. ISSN 1176-9343. PMC 3510868. PMID 23225993.
  14. Page, Justin T.; Huynh, Mark D.; Liechty, Zach S.; Grupp, Kara; Stelly, David; Hulse, Amanda M.; Ashrafi, Hamid; Deynze, Allen Van; Wendel, Jonathan F.; Udall, Joshua A. (2013-10-01). "Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing". G3: Genes, Genomes, Genetics. 3 (10): 1809–1818. doi:10.1534/g3.113.007229. ISSN 2160-1836. PMC 3789805. PMID 23979935.
  15. Gomez-Raya, Luis; Hulse, Amanda M.; Thain, David; Rauw, Wendy M. (2013-08-06). "Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations". Journal of Animal Science and Biotechnology. 4 (1): 30. doi:10.1186/2049-1891-4-30. ISSN 2049-1891. PMC 3765333. PMID 23916349.
  16. Zhang, Tianzhen; Hu, Yan; Jiang, Wenkai; Fang, Lei; Guan, Xueying; Chen, Jiedan; Zhang, Jinbo; Saski, Christopher A.; Scheffler, Brian E.; Stelly, David M.; Hulse-Kemp, Amanda M. (2015). "Sequencing of allotetraploid cotton ( Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement". Nature Biotechnology. 33 (5): 531–537. doi:10.1038/nbt.3207. ISSN 1546-1696. PMID 25893781.
  17. Hulse-Kemp, Amanda M.; Ashrafi, Hamid; Stoffel, Kevin; Zheng, Xiuting; Saski, Christopher A.; Scheffler, Brian E.; Fang, David D.; Chen, Z. Jeffrey; Deynze, Allen Van; Stelly, David M. (2015-06-01). "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. doi:10.1534/g3.115.017749. ISSN 2160-1836. PMC 4478540. PMID 25858960.
  18. Page, Justin T.; Liechty, Zach S.; Alexander, Rich H.; Clemons, Kimberly; Hulse-Kemp, Amanda M.; Ashrafi, Hamid; Deynze, Allen Van; Stelly, David M.; Udall, Joshua A. (2016-05-11). "DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton". PLOS Genetics. 12 (5): e1006012. doi:10.1371/journal.pgen.1006012. ISSN 1553-7404. PMC 4864293. PMID 27168520.
  19. Page, Justin T.; Liechty, Zach S.; Alexander, Rich H.; Clemons, Kimberly; Hulse-Kemp, Amanda M.; Ashrafi, Hamid; Deynze, Allen Van; Stelly, David M.; Udall, Joshua A. (2016-07-22). "Correction: DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton". PLOS Genetics. 12 (7): e1006206. doi:10.1371/journal.pgen.1006206. ISSN 1553-7404. PMC 4957745. PMID 27447832.
  20. Hinze, Lori L.; Hulse-Kemp, Amanda M.; Wilson, Iain W.; Zhu, Qian-Hao; Llewellyn, Danny J.; Taylor, Jen M.; Spriggs, Andrew; Fang, David D.; Ulloa, Mauricio; Burke, John J.; Giband, Marc (2017-02-03). "Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array". BMC Plant Biology. 17 (1): 37. doi:10.1186/s12870-017-0981-y. ISSN 1471-2229. PMC 5291959. PMID 28158969.
  21. Saski, Christopher A.; Scheffler, Brian E.; Hulse-Kemp, Amanda M.; Liu, Bo; Song, Qingxin; Ando, Atsumi; Stelly, David M.; Scheffler, Jodi A.; Grimwood, Jane; Jones, Don C.; Peterson, Daniel G. (2017-11-10). "Sub genome anchored physical frameworks of the allotetraploid Upland cotton ( Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids". Scientific Reports. 7 (1): 15274. Bibcode:2017NatSR...715274S. doi:10.1038/s41598-017-14885-w. ISSN 2045-2322. PMC 5681701. PMID 29127298.
  22. Spalink, Daniel; Stoffel, Kevin; Walden, Genevieve K.; Hulse-Kemp, Amanda M.; Hill, Theresa A.; Van Deynze, Allen; Bohs, Lynn (2018). "Comparative transcriptomics and genomic patterns of discordance in Capsiceae (Solanaceae)". Molecular Phylogenetics and Evolution. 126: 293–302. doi:10.1016/j.ympev.2018.04.030. ISSN 1055-7903. PMID 29702214. S2CID 13701098.
  23. Toomer, Ondulla T.; Hulse-Kemp, Amanda M.; Dean, Lisa L.; Boykin, Deborah L.; Malheiros, Ramon; Anderson, Kenneth E. (2019). "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. doi:10.3382/ps/pey531. ISSN 1525-3171. PMID 30535420.
  24. Ulloa, Mauricio; De Santiago, Luis M.; Hulse-Kemp, Amanda M.; Stelly, David M.; Burke, John J. (2020-01-01). "Enhancing Upland cotton for drought resilience, productivity, and fiber quality: comparative evaluation and genetic dissection". Molecular Genetics and Genomics. 295 (1): 155–176. doi:10.1007/s00438-019-01611-6. ISSN 1617-4623. PMID 31620883. S2CID 204707151.
  25. Hulse, Amanda M.; Cai, James J. (2013-01-01). "Genetic Variants Contribute to Gene Expression Variability in Humans". Genetics. 193 (1): 95–108. doi:10.1534/genetics.112.146779. ISSN 0016-6731. PMC 3527258. PMID 23150607.
  26. Hulse-Kemp, Amanda M.; Ashrafi, Hamid; Zheng, Xiuting; Wang, Fei; Hoegenauer, Kevin A.; Maeda, Andrea BV; Yang, S. Samuel; Stoffel, Kevin; Matvienko, Marta; Clemons, Kimberly; Udall, Joshua A. (2014-10-30). "Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts". BMC Genomics. 15 (1): 945. doi:10.1186/1471-2164-15-945. ISSN 1471-2164. PMC 4298081. PMID 25359292.
  27. Hulse-Kemp, Amanda M.; Lemm, Jana; Plieske, Joerg; Ashrafi, Hamid; Buyyarapu, Ramesh; Fang, David D.; Frelichowski, James; Giband, Marc; Hague, Steve; Hinze, Lori L.; Kochan, Kelli J. (2015-06-01). "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. doi:10.1534/g3.115.018416. ISSN 2160-1836. PMC 4478548. PMID 25908569.
  28. Hulse-Kemp, Amanda M.; Ashrafi, Hamid; Plieske, Joerg; Lemm, Jana; Stoffel, Kevin; Hill, Theresa; Luerssen, Hartmut; Pethiyagoda, Charit L.; Lawley, Cindy T.; Ganal, Martin W.; Van Deynze, Allen (2016-07-27). "A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding". Horticulture Research. 3 (1): 16036. doi:10.1038/hortres.2016.36. ISSN 2052-7276. PMC 4962762. PMID 27602231.
  29. Hulse-Kemp, Amanda M.; Maheshwari, Shamoni; Stoffel, Kevin; Hill, Theresa A.; Jaffe, David; Williams, Stephen R.; Weisenfeld, Neil; Ramakrishnan, Srividya; Kumar, Vijay; Shah, Preyas; Schatz, Michael C. (2018-01-12). "Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library". Horticulture Research. 5 (1): 4. doi:10.1038/s41438-017-0011-0. ISSN 2052-7276. PMC 5798813. PMID 29423234.
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