Research Project: Integrative Applied Agricultural Genomics and Bioinformatics Research

Location: Genomics and Bioinformatics Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Exploring the influence of seed bacteria and fungi on seed germination and seedling traits in Brachypodium hybridum accessions - (Peer Reviewed Journal)

The integration of quantitative trait locus mapping and transcriptome studies reveals candidate genes for water stress response in St. Augustinegrass - (Peer Reviewed Journal)
Rockstad, G.B., Yu, X., De Siqueira Gesteira, G., Gaire, ., Dickey, A.N., Gouveia, B.T., Schoonmaker, A.N., Hulse-Kemp, A.M., Milla-Lewis, S.R. 2025. The integration of quantitative trait locus mapping and transcriptome studies reveals candidate genes for water stress response in St. Augustinegrass. BMC Plant Biology. 25:662. https://doi.org/10.1186/s12870-025-06692-7.

Genetic marker data for sweetpotato improvement - (Peer Reviewed Journal)
Power, I., Simpson, S.A., Ballard, L.L., Liu, X.F., Scheffler, B.E., Lamb, M.C., Arias De Ares, R.S. 2025. Genetic marker data for sweetpotato improvement. Data in Brief. https://doi.org/10.1016/j.dib.2025.111630.

Structures, antioxidant, and angiotensin I-converting enzyme (ACE)-inhibitory activities of peptides derived from protein hydrosylates of three phenolics-rich legume genera - (Peer Reviewed Journal)
Chang, S.K., Zhang, Y., Pechan, T. 2025. Structures, antioxidant, and angiotensin I-converting enzyme (ACE)-inhibitory activities of peptides derived from protein hydrosylates of three phenolics-rich legume genera. Journal of Food Science. https://doi.org/10.1111/1750-3841.70069.

Evaluating UAV-captured RGB and multispectral imagery as a proxy for visual rating of leaf spot in cultivated peanut - (Peer Reviewed Journal)
Newman, C., Austin, R., Andres, R., Read, Q.D., Garrity, N., Fritz, K., Oakley, A., Hulse-Kemp, A.M., Dunne, J. 2025. Evaluating UAV-captured RGB and multispectral imagery as a proxy for visual rating of leaf spot in cultivated peanut . The Plant Phenome Journal. https://doi.org/10.1002/ppj2.70019.

Comparative transcriptomic and phenotypic analysis of monoclonal and polyclonal Populus deltoides genotypes - (Peer Reviewed Journal)
Gosselaar, M., Arick Ii, M.A., Hsu, C., Renninger, H., Siegert, C.M., Shafqat, W., Peterson, D.G., Himes, A. 2025. Comparative transcriptomic and phenotypic analysis of monoclonal and polyclonal Populus deltoides genotypes. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2024.1498535.

Overexpression of SIMK in menadione-treated alfalfa enhances antioxidant machinery and leads to oxidative stress resistance - (Peer Reviewed Journal)
Sojka, J., Takac, T., Hlavackova, K., Melicher, P., Ovecka, M., Pechan, T., Samaj, J. 2024. Overexpression of SIMK in menadione-treated alfalfa enhances antioxidant machinery and leads to oxidative stress resistance. Plant Stress. https://doi.org/10.1016/j.stress.2024.100608.

De novo whole-genome assembly and annotation of a high-quality coffee variety from the primary origin of coffee, Coffea arabica var. Geisha - (Peer Reviewed Journal)
Medrano, J.F., Cantu, D., Minio, A., Dreischer, C., Gibbons, T., Chin, J., Chen, S., Van Deynze, A., Hulse-Kemp, A.M. 2024. De novo whole-genome assembly and annotation of a high-quality coffee variety from the primary origin of coffee, Coffea arabica var. Geisha. G3: Genes, genomics, genetics. https://doi.org/10.1093/g3journal/jkae262.

Actin cytoskeleton and plasma membrane aquaporins are involved in different drought response of Arabidopsis rhd2 and der1 root hair mutants - (Peer Reviewed Journal)
Takac, T., Kubenova, L., Samajova, O., Dvorak, P., Rehak, J., Haberland, J., Pechan, T., Ovecka, M., Samaj, J. 2024. Actin cytoskeleton and plasma membrane aquaporins are involved in different drought response of Arabidopsis rhd2 and der1 root hair mutants. Plant Physiology and Biochemistry. https://doi.org/10.1016/j.plaphy.2024.109137.

Citdet: a benchmark dataset for citrus fruit detection - (Peer Reviewed Journal)
Jordan, J.A., Manching, H.K., Mattia, M.R., Bowman, K.D., Hulse-Kemp, A.M., Beksi, W.J. 2024. Citdet: a benchmark dataset for citrus fruit detection. International of Electrical and Electronics Engineers (IEEE) Robotics and Automation Letters. https://doi.org/10.1109/LRA.2024.3474473.

Complete genome sequence of lima bean endornavirus 1: a putative new member of the genus Alphaendornavirus (family Endornaviridae) - (Peer Reviewed Journal)
2024. Complete genome sequence of lima bean endornavirus 1: a putative new member of the genus Alphaendornavirus (family Endornaviridae). Archives of Virology. https://doi.org/10.1007/s00705-024-06135-y.

Complete genome sequence of an umbravirus from white snakeroot (Ageratina altissima) - (Peer Reviewed Journal)
Aboughanem-Sabanadzo, N., Sabanadzovic, S. 2024. Complete genome sequence of an umbravirus from white snakeroot (Ageratina altissima). Archives of Virology. https://doi.org/10.1007/s00705-024-06125-0.

ITSxpress Version 2: Software to rapidly trim internal transcribed spacer sequences with quality scores for amplicon sequencing - (Peer Reviewed Journal)
Einarsson, S.V., Rivers, A.R. 2024. ITSxpress Version 2: Software to rapidly trim internal transcribed spacer sequences with quality scores for amplicon sequencing. Microbiology Spectrum. https://doi.org/10.1128/spectrum.00601-24.

Genomic diversity and evolution of the Hawaiian Islands endemic Kokia (Malvaceae) - (Peer Reviewed Journal)
Kayal, E., Arick Ii, M.A., Hsu, C., Thrash, A., Yorkston, M., Morden, C.W., Wendel, J.F., Peterson, D.G., Grover, C.E. 2024. Genomic diversity and evolution of the Hawaiian Islands endemic Kokia (Malvaceae). G3: Genes, genomics, genetics. https://doi.org/10.1093/g3journal/jkae180.

Little evidence for homoeologous gene conversion and homoeologous exchange events in Gossypium allopolyploids - (Peer Reviewed Journal)
Conover, J.L., Grover, C.E., Sharbrough, J., Sloan, D.B., Peterson, D.G., Wendel, J.F. 2024. Little evidence for homoeologous gene conversion and homoeologous exchange events in Gossypium allopolyploids. American Journal of Botany. https://doi.org/10.1002/ajb2.16386.

agile genetics: single gene resolution without the fuss - (Peer Reviewed Journal)
Vaughn, J.N., Korani, W., Clevenger, J., Ozias-Akins, P. 2024. agile genetics: single gene resolution without the fuss. Bioessays. https://doi.org/10.1002/bies.202300206.

A blueberry (Vaccinium spp.) crop ontology to enable standardized phenotyping for blueberry breeding and research - (Peer Reviewed Journal)
Hilsop, L.M., Luby, C.H., Loarca, J., Humann, J., Hummer, K.E., Bassil, N.V., Zhao, D., Sheehan, M., Casa, A.M., Billings, G.T., Echeverria, D., Ashrafi, H., Babiker, E.M., Edger, P., Ehlenfeldt, M.K., Hancock, J., Finn, C.E., Iorizzo, M., Mackey, T.A., Munoz, P.R., Olmstead, J., Rowland, L.J., Sandefur, P., Spencer, J., Stringer, S.J., Vorsa, N., Wagner, A., Hulse-Kemp, A.M. 2024. A blueberry (Vaccinium spp.) crop ontology to enable standardized phenotyping for blueberry breeding and research. Journal of the American Pomological Society. 59:1433-1442. https://doi.org/10.21273/HORTSCI17676-23.

Few-shot fruit segmentation via transfer learning - (Peer Reviewed Journal)
Jordan, J.A., Manching, H.K., Hulse-Kemp, A.M., Beksi, W.J. 2024. Few-shot fruit segmentation via transfer learning. IEEE International Conference on Robotics and Automation. https://doi.org/10.1109/ICRA57147.2024.10610003.

The Glycine max abscisic acid-activated protein kinase-like kinase 1 (GmAALK1) modulates drought stress response - (Peer Reviewed Journal)
Sah, S., Popescu, G.V., Reddy, K.R., Klink, V.P., Li, J. 2024. The Glycine max abscisic acid-activated protein kinase-like kinase 1 (GmAALK1) modulates drought stress response. Journal of Plant Growth Regulation. 44:1642-1663. https://doi.org/10.1007/s00344-024-11287-x.

MicroMPN: methods and software for high-throughput screening of microbe suppression in mixed populations - (Peer Reviewed Journal)
Franco Melendez, K.P., Schuster, L., Donahey, M.C., Kairalla, E., Jansen, M.A., Reisch, C., Rivers, A.R. 2024. MicroMPN: methods and software for high-throughput screening of microbe suppression in mixed populations. Microbiology Spectrum. https://doi.org/10.1128/spectrum.03578-23.

Methyl viologen-induced changes in the Arabidopsis proteome implicate PATELLIN 4 in oxidative stress responses - (Peer Reviewed Journal)
Melicher, P., Dvorak, P., Rehak, J., Samajova, O., Pechan, T., Samaj, J., Takac, T. 2024. Methyl viologen-induced changes in the Arabidopsis proteome implicate PATELLIN 4 in oxidative stress responses. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erad363.

Genome resequencing facilitates high-resolution exploration of a maize quantitative trait locus for resistance to aflatoxin accumulation - (Peer Reviewed Journal)
Shan, X., Williams, W.P., Peterson, D.G. 2023. Genome resequencing facilitates high-resolution exploration of a maize quantitative trait locus for resistance to aflatoxin accumulation. Euphytica. https://doi.org/10.1007/s10681-023-03232-y.

Innovations in double digest restriction-site associated DNA sequencing (ddRAD-Seq) method for more efficient SNP identification - (Peer Reviewed Journal)
Magbanua, Z.V., Hsu, C., Pechanova, O., Arick Ii, M., Grover, C.E., Peterson, D.G. 2022. Innovations in double digest restriction-site associated DNA sequencing (ddRAD-Seq) method for more efficient SNP identification. Analytical Biochemistry. https://doi.org/10.1016/j.ab.2022.115001.

Transcriptome analysis of the 2,4-dichlorophenoxyacetic acid (2,4-D)-tolerant cotton chromosome substitution line CS-B15sh and its susceptible parental lines G. hirsutum L. cv. Texas Marker-1 and G. barbadense L. cv. Pima 379 - (Peer Reviewed Journal)
Perez, L.M., Mauleon, R., Arick Ii, M.A., Magbanua, Z.V., Peterson, D.G., Dean, J.F., Tseng, T. 2022. Transcriptome analysis of the 2,4-dichlorophenoxyacetic acid (2,4-D)-tolerant cotton chromosome substitution line CS-B15sh and its susceptible parental lines G. hirsutum L. cv. Texas Marker-1 and G. barbadense L. cv. Pima 379. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2022.910369.

Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels - (Peer Reviewed Journal)
Forsythe, E.S., Grover, C.E., Miller, E.R., Conover, J.L., Arick Ii, M.A., Chavarro, M.F., Leal-Bertioli, S.C., Peterson, D.G., Sharbrough, J., Wendel, J.F., Sloan, D.B. 2022. Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels. Proceedings of the National Academy of Sciences (PNAS). https://doi.org/10.1073/pnas.2204187119.