Dr. Heather Kates, Ph.D.
Bioinformatics analyst with ten years of experience in programming (R, Python as needed), pipeline development (HPC and cluster computing), genomic data processing, and statistical analysis.
Research Expertise
About
Publications
A targeted enrichment strategy for massively parallel sequencing of angiosperm plastid genomes
Applications in Plant Sciences / Jan 31, 2013
Stull, G. W., Moore, M. J., Mandala, V. S., Douglas, N. A., Kates, H., Qi, X., Brockington, S. F., Soltis, P. S., Soltis, D. E., & Gitzendanner, M. A. (2013). A targeted enrichment strategy for massively parallel sequencing of angiosperm plastid genomes. Applications in Plant Sciences, 1(2). Portico. https://doi.org/10.3732/apps.1200497
Phylogenomic Mining of the Mints Reveals Multiple Mechanisms Contributing to the Evolution of Chemical Diversity in Lamiaceae
Molecular Plant / Aug 01, 2018
Boachon, B., Buell, C. R., Crisovan, E., Dudareva, N., Garcia, N., Godden, G., Henry, L., Kamileen, M. O., Kates, H. R., Kilgore, M. B., Lichman, B. R., Mavrodiev, E. V., Newton, L., Rodriguez-Lopez, C., O’Connor, S. E., Soltis, D., Soltis, P., Vaillancourt, B., Wiegert-Rininger, K., & Zhao, D. (2018). Phylogenomic Mining of the Mints Reveals Multiple Mechanisms Contributing to the Evolution of Chemical Diversity in Lamiaceae. Molecular Plant, 11(8), 1084–1096. https://doi.org/10.1016/j.molp.2018.06.002
A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae)
Journal of Biological Chemistry / Jan 01, 2019
Johnson, S. R., Bhat, W. W., Bibik, J., Turmo, A., Hamberger, B., Evolutionary Mint Genomics Consortium, & Hamberger, B. (2019). A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae). Journal of Biological Chemistry, 294(4), 1349–1362. https://doi.org/10.1074/jbc.ra118.006025
Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus
American Journal of Botany / Mar 01, 2018
Kates, H. R., Johnson, M. G., Gardner, E. M., Zerega, N. J. C., & Wickett, N. J. (2018). Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus. American Journal of Botany, 105(3), 404–416. Portico. https://doi.org/10.1002/ajb2.1068
High‐throughput methods for efficiently building massive phylogenies from natural history collections
Applications in Plant Sciences / Feb 01, 2021
Folk, R. A., Kates, H. R., LaFrance, R., Soltis, D. E., Soltis, P. S., & Guralnick, R. P. (2021). High‐throughput methods for efficiently building massive phylogenies from natural history collections. Applications in Plant Sciences, 9(2). Portico. https://doi.org/10.1002/aps3.11410
Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (Cucurbita L.)
PLANTS, PEOPLE, PLANET / Dec 10, 2019
Khoury, C. K., Carver, D., Kates, H. R., Achicanoy, H. A., van Zonneveld, M., Thomas, E., Heinitz, C., Jarret, R., Labate, J. A., Reitsma, K., Nabhan, G. P., & Greene, S. L. (2019). Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (Cucurbita L.). PLANTS, PEOPLE, PLANET, 2(3), 269–283. Portico. https://doi.org/10.1002/ppp3.10085
The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success
Frontiers in Plant Science / Jun 23, 2021
Kates, H. R., Doby, J. R., Siniscalchi, C. M., LaFrance, R., Soltis, D. E., Soltis, P. S., Guralnick, R. P., & Folk, R. A. (2021). The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success. Frontiers in Plant Science, 12. https://doi.org/10.3389/fpls.2021.669064
Two shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants
Aug 01, 2022
Kates, H. R., O’Meara, B. C., LaFrance, R., Stull, G. W., James, E. K., Conde, D., Liu, S., Tian, Q., Yi, T., Kirst, M., Ané, J.-M., Soltis, D. E., Guralnick, R. P., Soltis, P. S., & Folk, R. A. (2022). Two shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants. https://doi.org/10.1101/2022.07.31.502231
Phylogeny and Biogeography of Morus (Moraceae)
Agronomy / Jul 30, 2023
Yang, C.-X., Liu, S.-Y., Zerega, N. J. C., Stull, G. W., Gardner, E. M., Tian, Q., Gu, W., Lu, Q., Folk, R. A., Kates, H. R., Guralnick, R. P., Soltis, D. E., Soltis, P. S., Wang, Y.-H., & Yi, T.-S. (2023). Phylogeny and Biogeography of Morus (Moraceae). Agronomy, 13(8), 2021. https://doi.org/10.3390/agronomy13082021
Fagalean phylogeny in a nutshell: Chronicling the diversification history of Fagales
Mar 07, 2023
Siniscalchi, C. M., Correa-Narvaez, J., Kates, H. R., Soltis, D. E., Soltis, P. S., Guralnick, R. P., Manchester, S. R., & Folk, R. A. (2023). Fagalean phylogeny in a nutshell: Chronicling the diversification history of Fagales. https://doi.org/10.1101/2023.03.06.531381
Pumpkins, Squashes, and Gourds (Cucurbita L.) of North America
North American Crop Wild Relatives, Volume 2 / Jan 01, 2019
Kates, H. R. (2019). Pumpkins, Squashes, and Gourds (Cucurbita L.) of North America. In North American Crop Wild Relatives, Volume 2 (pp. 195–224). Springer International Publishing. https://doi.org/10.1007/978-3-319-97121-6_6
Phylogenomic Analyses Reveal Widespread Gene Flow During the Early Radiation of Oaks and Relatives (Fagaceae: Quercoideae)
Apr 28, 2023
Liu, S., Yang, Y., Tian, Q., Yang, Z., Li, S., Valdes, P. J., Farnsworth, A., Kates, H. R., Siniscalchi, C. M., Guralnick, R. P., Soltis, D. E., Soltis, P. S., Stull, G. W., Folk, R. A., & Yi, T. (2023). Phylogenomic Analyses Reveal Widespread Gene Flow During the Early Radiation of Oaks and Relatives (Fagaceae: Quercoideae). https://doi.org/10.1101/2023.04.25.538215
Testing the evolutionary drivers of nitrogen-fixing symbioses in challenging soil environments
Sep 28, 2022
Siniscalchi, C. M., Kates, H. R., Soltis, P. S., Soltis, D. E., Guralnick, R. P., & Folk, R. A. (2022). Testing the evolutionary drivers of nitrogen-fixing symbioses in challenging soil environments. https://doi.org/10.1101/2022.09.27.509719
Spatial phylogenetics of Fagales: Investigating the history of temperate forests
Apr 18, 2023
Folk, R. A., Siniscalchi, C. M., Doby, J., Kates, H. R., Manchester, S. R., Soltis, P. S., Soltis, D. E., Guralnick, R. P., & Belitz, M. (2023). Spatial phylogenetics of Fagales: Investigating the history of temperate forests. https://doi.org/10.1101/2023.04.17.537249
Investigating miR-9 as a mediator in laryngeal cancer health disparities
Frontiers in Oncology / Apr 04, 2023
Gobin, C., Inkabi, S., Lattimore, C. C., Gu, T., Menefee, J. N., Rodriguez, M., Kates, H., Fields, C., Bian, T., Silver, N., Xing, C., Yates, C., Renne, R., Xie, M., & Fredenburg, K. M. (2023). Investigating miR-9 as a mediator in laryngeal cancer health disparities. Frontiers in Oncology, 13. https://doi.org/10.3389/fonc.2023.1096882
Phylogenetic diversity and regionalization of root nodule symbiosis
Sep 12, 2023
Folk, R. A., Belitz, M. W., Siniscalchi, C. M., Kates, H. R., Soltis, D. E., Soltis, P. S., Guralnick, R. P., & Borges, L. M. (2023). Phylogenetic diversity and regionalization of root nodule symbiosis. https://doi.org/10.1101/2023.09.08.556918
Spatial phylogenetics of Fagales: Investigating drivers of temperate forest distributions
Journal of Biogeography / Apr 10, 2024
Folk, R. A., Siniscalchi, C. M., Doby, J., Kates, H. R., Manchester, S. R., Soltis, P. S., Soltis, D. E., Guralnick, R. P., & Belitz, M. (2024). Spatial phylogenetics of Fagales: Investigating drivers of temperate forest distributions. Journal of Biogeography. Portico. https://doi.org/10.1111/jbi.14840
Anatomy of a mega-radiation: Biogeography and niche evolution inAstragalus
Jun 29, 2023
Folk, R. A., Charboneau, J. L. M., Belitz, M., Singh, T., Kates, H. R., Soltis, D. E., Soltis, P. S., Guralnick, R. P., & Siniscalchi, C. M. (2023). Anatomy of a mega-radiation: Biogeography and niche evolution inAstragalus. https://doi.org/10.1101/2023.06.27.546767
Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales
New Phytologist / Jan 16, 2024
Tian, Q., Stull, G. W., Kellermann, J., Medan, D., Nge, F. J., Liu, S., Kates, H. R., Soltis, D. E., Soltis, P. S., Guralnick, R. P., Folk, R. A., Onstein, R. E., & Yi, T. (2024). Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales. New Phytologist, 241(4), 1851–1865. Portico. https://doi.org/10.1111/nph.19504
Phylogenetic diversity and regionalization in the temperate arid zone
Nov 04, 2023
Folk, R. A., Maassoumi, A. A., Siniscalchi, C. M., Kates, H. R., Soltis, D. E., Soltis, P. S., Belitz, M. B., & Guralnick, R. P. (2023). Phylogenetic diversity and regionalization in the temperate arid zone. https://doi.org/10.1101/2023.11.01.565216
Abstract C048: Computational pathway analysis of differentially expressed miRNAs in Black compared with White laryngeal squamous cell carcinoma
Cancer Epidemiology, Biomarkers & Prevention / Jan 01, 2023
Lattimore, C. C., Kates, H., Gu, T., Jiang, J., Schmittgen, T., & Fredenburg, K. M. (2023). Abstract C048: Computational pathway analysis of differentially expressed miRNAs in Black compared with White laryngeal squamous cell carcinoma. Cancer Epidemiology, Biomarkers & Prevention, 32(1_Supplement), C048–C048. https://doi.org/10.1158/1538-7755.disp22-c048
GeoMX Digital Spatial Profiler Whole Transcriptome Assay for Human Pancreas v1
May 13, 2022
Fu, A. (2022). GeoMX Digital Spatial Profiler Whole Transcriptome Assay for Human Pancreas v1. https://doi.org/10.17504/protocols.io.8epv59bong1b/v1
Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen-fixing clade
Jul 27, 2021
Pereira, W. J., Knaack, S., Conde, D., Chakraborty, S., Folk, R. A., Triozzi, P. M., Balmant, K. M., Dervinis, C., Schmidt, H. W., Ané, J.-M., Roy, S., & Kirst, M. (2021). Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen-fixing clade. https://doi.org/10.1101/2021.07.27.453985
Domesticated mammals and birds: Species accounts
The Process of Animal Domestication / Jan 18, 2022
Sánchez-Villagra, M. R. (2022). Domesticated mammals and birds: Species accounts. In The Process of Animal Domestication (pp. 36–66). Princeton University Press. https://doi.org/10.23943/princeton/9780691217666.003.0002
Targeted Sequencing Suggests Wild-Crop Gene Flow Is Central to Different Genetic Consequences of Two Independent Pumpkin Domestications
Frontiers in Ecology and Evolution / Jul 12, 2021
Kates, H. R., Anido, F. L., Sánchez-de la Vega, G., Eguiarte, L. E., Soltis, P. S., & Soltis, D. E. (2021). Targeted Sequencing Suggests Wild-Crop Gene Flow Is Central to Different Genetic Consequences of Two Independent Pumpkin Domestications. Frontiers in Ecology and Evolution, 9. https://doi.org/10.3389/fevo.2021.618380
Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci
Molecular Phylogenetics and Evolution / Jun 01, 2017
Kates, H. R., Soltis, P. S., & Soltis, D. E. (2017). Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci. Molecular Phylogenetics and Evolution, 111, 98–109. https://doi.org/10.1016/j.ympev.2017.03.002
Population genetic variation, geographic structure, and multiple origins of autopolyploidy in Galax urceolata
American Journal of Botany / Jun 01, 2015
Servick, S., Visger, C. J., Gitzendanner, M. A., Soltis, P. S., & Soltis, D. E. (2015). Population genetic variation, geographic structure, and multiple origins of autopolyploidy in Galax urceolata. American Journal of Botany, 102(6), 973–982. Portico. https://doi.org/10.3732/ajb.1400554
Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto‐nuclear discordance and provides new insights into generic relationships
Journal of Systematics and Evolution / Dec 19, 2022
Fu, X., Liu, S., van Velzen, R., Stull, G. W., Tian, Q., Li, Y., Folk, R. A., Guralnick, R. P., Kates, H. R., Jin, J., Li, Z., Soltis, D. E., Soltis, P. S., & Yi, T. (2022). Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto‐nuclear discordance and provides new insights into generic relationships. Journal of Systematics and Evolution, 61(5), 806–826. Portico. https://doi.org/10.1111/jse.12920
Education
University of Florida
Genomics / December, 2017
Experience
University of Florida Department of Pathology & Immunology
Bioinformatics Analyst III / October, 2023 — Present
University of Florida Department of Pathology & Immunology
Data Management Analyst III / January, 2022 — October, 2023
University of Florida
Postdoctoral Researcher / January, 2018 — December, 2021
PhD Candidate and Research Fellow / August, 2011 — December, 2017
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