Student Publications

Research publications from MPS students. The student's name is bolded.

2025

• Ellison EL, Zhou P, Chu YH, Hermanson P, Gomez-Cano L, Myers ZA, Abnave A, Gray J, Hirsch CN, Grotewold E, Springer NM. 2025. Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions. G3 (Bethesda) 15.
• Gomez-Cano L, Jiang N, Grotewold E. 2025. Extraction and Quantification of Phenolic Compounds in Maize. Cold Spring Harb Protoc 2025:pdb prot108576.
• Heger L, Sharma N, McCoy AG, Martin FN, Miles LA, Chilvers MI, Naegele RP, Miles TD. 2025. Multiplexed real-time and digital PCR tools to differentiate clades of Plasmopara viticola causing downy mildew in grapes. Plant Dis doi:10.1094/PDIS-01-25-0173-SR.
• Jiang N, Gomez-Cano L, Grotewold E. 2025. Extraction and Quantification of Total Anthocyanins, Determination of Anthocyanidin Core Structures, and Characterization of Specific Anthocyanins from Maize. Cold Spring Harb Protoc 2025:pdb prot108577.
• Jiang X, Koenig AM, Walker BJ, Hu J. 2025. A cytosolic glyoxylate shunt complements the canonical photorespiratory pathway in Arabidopsis. Nat Commun 16:4057.
• Palande S, Arsenault J, Basurto-Lozada P, Bleich A, Brown BNI, Buysse SF, Connors NA, Das Adhikari S, Dobson KC, Guerra-Castillo FX, Guerrero-Carrillo MF, Harlow S, Herrera-Orozco H, Hightower AT, Izquierdo P, Jacobs M, Johnson NA, Leuenberger W, Lopez-Hernandez A, Luckie-Duque A, Martinez-Avila C, Mendoza-Galindo EJ, Plancarte DC, Schuster JM, Shomer H, Sitar SC, Steensma AK, Thomson JE, Villasenor-Amador D, Waterman R, Webster BM, Whyte M, Zorilla-Azcue S, Montgomery BL, Husbands AY, Krishnan A, Percival S, Munch E, VanBuren R, Chitwood DH, Rougon-Cardoso A. 2025. Expression-based machine learning models for predicting plant tissue identity. Appl Plant Sci 13:e11621.
• Petrich J, Alvarez CE, Gomez-Cano L, Dewberry R, Grotewold E, Casati P, Falcone Ferreyra ML. 2025. Functional characterization of a maize UDP-glucosyltransferase involved in the biosynthesis of flavonoid 7-O-glucosides and di-O-glucosides. Plant Physiol Biochem 221:109583.
• Range KL, Chiang TK, Pramanik A, Landa JF, Snyder SN, Zuo X, Tiede DM, Utschig LM, Hegg EL, Sutter M, Kerfeld CA, Ralston CY. 2025. Chaotrope-Based Approach for Rapid In Vitro Assembly and Loading of Bacterial Microcompartment Shells. ACS Nano 19:11913-11923.
• Steensma AK, Kaste JAM, Heo J, Orr DJ, Sung CL, Shachar-Hill Y, Walker BJ. 2025. Modeling with uncertainty quantification reveals the essentials of a non-canonical algal carbon-concentrating mechanism. Plant Physiol 197.
• Susanto F, Jones AD, Donnelly S Lundquist PK. 2025. Cyanoglobule lipid droplets are a stress-responsive metabolic compartment of cyanobacteria and the progenitor of plant plastoglobules. The Plant Cell. Accepted.
• Xin H, Strickland LW, Hamilton JP, Trusky JK, Fang C, Butler NM, Douches DS, Buell CR, Jiang J. 2025. Jan and mini-Jan, a model system for potato functional genomics. Plant Biotechnol J 23:1243-1256.

2024

• Bibik JD, Bryson AE, Hamberger B. 2024. Compartmentalized Terpenoid Production in Plants Using Agrobacterium-Mediated Transient Expression. Methods Mol Biol 2760:21-34.
• Check JC, Harkness RJ, Heger L, Sakalidis ML, Chilvers MI, Mahaffee WF, Miles TD. 2024. It's a Trap! Part I: Exploring the Applications of Rotating-Arm Impaction Samplers in Plant Pathology. Plant Dis 108:1910-1922.
• Check JC, Harkness RJ, Heger L, Chilvers MI, Mahaffee WF, Sakalidis ML, Miles TD. 2024. It's a Trap! Part II: An Approachable Guide to Constructing and Using Rotating-Arm Air Samplers. Plant Dis 108:1923-1936.
• Chu YH, Lee YS, Gomez-Cano F, Gomez-Cano L, Zhou P, Doseff AI, Springer N, Grotewold E. 2024. Molecular mechanisms underlying gene regulatory variation of maize metabolic traits. Plant Cell 36:3709-3728.
• Kulke M, Kurtz E, Boren DM, Olson DM, Koenig AM, Hoffmann-Benning S, Vermaas JV. 2024. PLAT domain protein 1 (PLAT1/PLAFP) binds to the Arabidopsis thaliana plasma membrane and inserts a lipid. Plant Sci 338:111900.
• Lotreck S, Segura Abá K, Lehti-Shiu MD, Seeger A, Brown BNI, Ranaweera T, Schumacher A, Ghassemi M, Shiu S. 2024. Plant Science Knowledge Graph Corpus: a gold standard entity and relation corpus for the molecular plant sciences Open Access in silico Plants 6.
• Mathieu D, Bryson AE, Hamberger B, Singan V, Keymanesh K, Wang M, Barry K, Mondo S, Pangilinan J, Koriabine M, Grigoriev IV, Bonito G, Hamberger B. 2024. Multilevel analysis between Physcomitrium patens and Mortierellaceae endophytes explores potential long-standing interaction among land plants and fungi. Plant J 118:304-323.
• Park D, Al Shoffe Y, Algul BE, Engelgau P, Beaudry RM, Watkins CB. 2024. Preharvest application of 1-methylcyclopropene and 1-aminoethoxyvinylglycine affects watercore severity and volatile profiles of ‘Fuji’ apples stored in air and controlled atmospheres. Postharvest Biology and Technology 211.
• Rogers A, Jaiswal N, Roggenkamp E, Kim HS, MacCready JS, Chilvers MI, Scofield SR, Iyer-Pascuzzi AS, Helm M. 2024. Genome-Informed Trophic Classification and Functional Characterization of Virulence Proteins from the Maize Tar Spot Pathogen Phyllachora maydis. Phytopathology 114:1940-1949.
• Roggenkamp EM, Check JC, Biswal AK, Floyd CM, Miles LA, Nicolli CP, Shim S, Salgado-Salazar C, Alakonya AE, Malvick DK, Smith DK, Telenko DEP, Chilvers MI. 2024. Development of a qPCR Assay for Species-Specific Detection of the Tar Spot Pathogen Phyllachora maydis. PhytoFrontiers 4.
• Rosling A, Eshghi Sahraei S, Kalsoom Khan F, Desiro A, Bryson AE, Mondo SJ, Grigoriev IV, Bonito G, Sanchez-Garcia M. 2024. Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis. BMC Genomics 25:529.
• Smith K, Strand DD, Kramer DM, Walker BJ. 2024. The role of photorespiration in preventing feedback regulation via ATP synthase in Nicotiana tabacum. Plant Cell Environ 47:416-428.
• Tejera-Nieves M, Seong DY, Reist L, Walker BJ. 2024. The Dynamic Assimilation Technique measures photosynthetic CO2 response curves with similar fidelity to steady-state approaches in half the time. J Exp Bot 75:2819-2828.
• Thibault E, Brandizzi F. 2024. Post-translational modifications: emerging directors of cell-fate decisions during endoplasmic reticulum stress in Arabidopsis thaliana. Biochem Soc Trans 52:831-848.

2023

• Amses K, Desiro A, Bryson A, Grigoriev I, Mondo S, Lipzen A, LaButti K, Riley R, Singan V, Salazar-Hamm P, King J, Ballou E, Pawlowska T, Adeleke R, Bonito G, Uehling J. 2023. Convergent reductive evolution and host adaptation in Mycoavidus bacterial endosymbionts of Mortierellaceae fungi. Fungal Genet Biol 169:103838.
• Bryson AE, Lanier ER, Lau KH, Hamilton JP, Vaillancourt B, Mathieu D, Yocca AE, Miller GP, Edger PP, Buell CR, Hamberger B. 2023. Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory. Nat Commun 14:343.
• Chou MY, Andersen TB, Mechan Llontop ME, Beculheimer N, Sow A, Moreno N, Shade A, Hamberger B, Bonito G. 2023. Terpenes modulate bacterial and fungal growth and sorghum rhizobiome communities. Microbiol Spectr 11:e0133223.
• de Silva APG, Engelgau P, Sugimoto N, Beaudry RM. 2023. Factors affecting 1-MCP release from an α-cyclodextrin encapsulant dissolved in water. ISHS Acta Horticulturae doi:https://doi.org/10.17660/ActaHortic.2023.1364.11.
• Gregory LM, Roze LV, Walker BJ. 2023. Increased activity of core photorespiratory enzymes and CO(2) transfer conductances are associated with higher and more optimal photosynthetic rates under elevated temperatures in the extremophile Rhazya stricta. Plant Cell Environ 46:3704-3720.
• Jacobs M, Thompson S, Platts AE, Body MJA, Kelsey A, Saad A, Abeli P, Teresi SJ, Schilmiller A, Beaudry R, Feldmann MJ, Knapp SJ, Song GQ, Miles T, Edger PP. 2023. Uncovering genetic and metabolite markers associated with resistance against anthracnose fruit rot in northern highbush blueberry. Hortic Res 10:uhad169.
• Jiang X, Walker BJ, He SY, Hu J. 2023. The role of photorespiration in plant immunity. Front Plant Sci 14:1125945.
• Johnson LYD, Major IT, Chen Y, Yang C, Vanegas-Cano LJ, Howe GA. 2023. Diversification of JAZ-MYC signaling function in immune metabolism. New Phytol 239:2277-2291.
• Ko DK, Kim JY, Thibault EA, Brandizzi F. 2023. An IRE1-proteasome system signalling cohort controls cell fate determination in unresolved proteotoxic stress of the plant endoplasmic reticulum. Nat Plants 9:1333-1346.
• Kokarakis EJ, Rillema R, Ducat DC, Sakkos JK. 2023. Developing Cyanobacterial Quorum Sensing Toolkits: Toward Interspecies Coordination in Mixed Autotroph/Heterotroph Communities. ACS Synth Biol 12:265-276.
• Kumar J, Gomez-Cano F, Hunt SW, Lotreck SG, Mathieu DT, Wilson ML, Long TM. 2023. Central Dogma, Dictionaries, and Functions: Using Programming Concepts to Simulate Biological Processes. CourseSource doi:https://doi.org/10.24918/cs.2023.24.
• Lanier ER, Andersen TB, Hamberger B. 2023. Plant terpene specialized metabolism: complex networks or simple linear pathways? Plant J 114:1178-1201.
• Li P, Zhang Z, Tong Y, Foda BM, Day B. 2023. ILEE: Algorithms and toolbox for unguided and accurate quantitative analysis of cytoskeletal images. J Cell Biol 222.
• MacCready JS, Roggenkamp EM, Gdanetz K, Chilvers MI. 2023. Elucidating the Obligate Nature and Biological Capacity of an Invasive Fungal Corn Pathogen. Mol Plant Microbe Interact 36:411-424.
• Palande S, Kaste JAM, Roberts MD, Segura Aba K, Claucherty C, Dacon J, Doko R, Jayakody TB, Jeffery HR, Kelly N, Manousidaki A, Parks HM, Roggenkamp EM, Schumacher AM, Yang J, Percival S, Pardo J, Husbands AY, Krishnan A, Montgomery BL, Munch E, Thompson AM, Rougon-Cardoso A, Chitwood DH, VanBuren R. 2023. Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants. PLoS Biol 21:e3002397.
• Parks HM, Cinelli MA, Bedewitz MA, Grabar JM, Hurney SM, Walker KD, Jones AD, Barry CS. 2023. Redirecting tropane alkaloid metabolism reveals pyrrolidine alkaloid diversity in Atropa belladonna. New Phytol 237:1810-1825.
• Sharma N, Froehlich JE, Rillema R, Raba DA, Chambers T, Kerfeld CA, Kramer DM, Walker B, Brandizzi F. 2023. Arabidopsis stromal carbonic anhydrases exhibit non-overlapping roles in photosynthetic efficiency and development. Plant J 115:386-397.
• Solorzano JE, Issendorf SE, Drott MT, Check JC, Roggenkamp EM, Cruz CD, Kleczewski NM, Gongora-Canul CC, Malvick DK. 2023. A new and effective method to induce infection of Phyllachora maydis into corn for tar spot studies in controlled environments. Plant Methods 19:83.
• Steensma AK, Shachar-Hill Y, Walker BJ. 2023. The carbon-concentrating mechanism of the extremophilic red microalga Cyanidioschyzon merolae. Photosynth Res 156:247-264.
• Szymanski S, Longley R, Hatlen RJ, Heger L, Sharma N, Bonito G, Miles TD. 2023. The Blueberry Fruit Mycobiome Varies by Tissue Type and Fungicide Treatment. Phytobiomes Journal 7.

2022

• Bird KA, Jacobs M, Sebolt A, Rhoades K, Alger EI, Colle M, Alekman ML, Bies PK, Cario AJ, Chigurupati RS, Collazo DR, Finley S, Garland B, Hein KM, Hicks J, Hillenberg AR, Kado LI, Kilian VR, Longueuil PF, Mahesha V, Mervak C, Munsell K, Patel RM, Peters NML, Steffes MO, Suryadevara S, Thummalapally A, Urban G, Walia AKW, T.B., McKain MR, Iezzoni AF, Edger PP. 2022. Parental origins of the cultivated tetraploid sour cherry (Prunus cerasus L.) Plants, People, Planet 4.
• Edger PP, Iorizzo M, Bassil NV, Benevenuto J, Ferrao LFV, Giongo L, Hummer K, Lawas LMF, Leisner CP, Li C, Munoz PR, Ashrafi H, Atucha A, Babiker EM, Canales E, Chagne D, DeVetter L, Ehlenfeldt M, Espley RV, Gallardo K, Gunther CS, Hardigan M, Hulse-Kemp AM, Jacobs M, Lila MA, Luby C, Main D, Mengist MF, Owens GL, Perkins-Veazie P, Polashock J, Pottorff M, Rowland LJ, Sims CA, Song GQ, Spencer J, Vorsa N, Yocca AE, Zalapa J. 2022. There and back again; historical perspective and future directions for Vaccinium breeding and research studies. Hortic Res 9:uhac083.
• Fiesel PD, Parks HM, Last RL, Barry CS. 2022. Fruity, sticky, stinky, spicy, bitter, addictive, and deadly: evolutionary signatures of metabolic complexity in the Solanaceae. Nat Prod Rep 39:1438-1464.
• Lucker BF, Temple JA, Panchy NL, Benning UF, Bibik JD, Neofotis PG, Weissman JC, Baxter IR, Shiu S, Kramer DM. 2022. Selection-enriched genomic loci (SEGL) reveals genetic loci for environmental adaptation and photosynthetic productivity in Chlamydomonas reinhardtii. Algal Research 64.
• Schenck CA, Anthony TM, Jacobs M, Jones AD, Last RL. 2022. Natural variation meets synthetic biology: Promiscuous trichome-expressed acyltransferases from Nicotiana. Plant Physiol 190:146-164.
• Young DY, Pang N, Shachar-Hill Y. 2022. 13C-labeling reveals how membrane lipid components contribute to triacylglycerol accumulation in Chlamydomonas. Plant Physiol 189:1326-1344.

2021

• Cusack SA, Wang P, Lotreck SG, Moore BM, Meng F, Conner JK, Krysan PJ, Lehti-Shiu MD, Shiu SH. 2021. Predictive Models of Genetic Redundancy in Arabidopsis thaliana. Mol Biol Evol 38:3397-3414.
• Gregory LM, McClain AM, Kramer DM, Pardo JD, Smith KE, Tessmer OL, Walker BJ, Ziccardi LG, Sharkey TD. 2021. The triose phosphate utilization limitation of photosynthetic rate: Out of global models but important for leaf models. Plant Cell Environ 44:3223-3226.
• Li J, Peng J, Jiang X, Rea AC, Peng J, Hu J. 2021. DeepLearnMOR: a deep-learning framework for fluorescence image-based classification of organelle morphology. Plant Physiol 186:1786-1799.
• Young DY, Shachar-Hill Y. 2021. Large fluxes of fatty acids from membranes to triacylglycerol and back during N-deprivation and recovery in Chlamydomonas. Plant Physiol 185:796-814.

2020

• Bryson AE, Wilson Brown M, Mullins J, Dong W, Bahmani K, Bornowski N, Chiu C, Engelgau P, Gettings B, Gomezcano F, Gregory LM, Haber AC, Hoh D, Jennings EE, Ji Z, Kaur P, Kenchanmane Raju SK, Long Y, Lotreck SG, Mathieu DT, Ranaweera T, Ritter EJ, Sadohara R, Shrote RZ, Smith KE, Teresi SJ, Venegas J, Wang H, Wilson ML, Tarrant AR, Frank MH, Migicovsky Z, Kumar J, VanBuren R, Londo JP, Chitwood DH. 2020. Composite modeling of leaf shape along shoots discriminates Vitis species better than individual leaves. Appl Plant Sci 8:e11404.
• Gomez-Cano L, Gomez-Cano F, Dillon FM, Alers-Velazquez R, Doseff AI, Grotewold E, Gray J. 2020. Discovery of modules involved in the biosynthesis and regulation of maize phenolic compounds. Plant Sci 291:110364.
• Koenig AM, Benning C, Hoffmann-Benning S. 2020. Chapter 2 - Lipid trafficking and signaling in plants. Lipid Signaling and Metabolism doi:https://doi.org/10.1016/B978-0-12-819404-1.00002-6.
• Koenig AM, Hoffmann-Benning S. 2020. The interplay of phloem-mobile signals in plant development and stress response. Biosci Rep 40.
• Li P, Lu YJ, Chen H, Day B. 2020. The Lifecycle of the Plant Immune System. CRC Crit Rev Plant Sci 39:72-100.
• Miller GP, Bhat WW, Lanier ER, Johnson SR, Mathieu DT, Hamberger B. 2020. The biosynthesis of the anti-microbial diterpenoid leubethanol in Leucophyllum frutescens proceeds via an all-cis prenyl intermediate. Plant J 104:693-705.