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Citing NIH T32 Training Grant Support:


Smith, K., Strand, D.D., Kramer, D.M. and Walker, B.J., 2023. The role of photorespiration in preventing feedback regulation via ATP synthase in Nicotiana tabacum. Plant, Cell & Environment, 47(2), pp. 416-428. doi: https://doi.org/10.1111/pce.14759

Palande, S., Kaste, J.A.M., Roberts, M.D., Segura Abá, K., Claucherty, C., Dacon, J., Doko, R., Jayakody, T.B., Jeffery, H.R., Kelly, N. and Manousidaki, A., 2023. Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants. PLoS biology21(12), p.e3002397. doi: https://doi.org/10.1371/journal.pbio.3002397

Santos-Merino, M., Yun, L. and Ducat, D.C., 2023. Cyanobacteria as cell factories for the photosynthetic production of sucrose. Frontiers in Microbiology, 14, p.1126032. doi:https://doi.org/10.3389/fmicb.2023.1126032

Johnson, L.Y., Major, I.T., Chen, Y., Yang, C., Vanegas‐Cano, L.J. and Howe, G.A., 2023. Diversification of JAZ-MYC signaling function in immune metabolism. New Phytologist. doi: https://doi.org/10.1111/nph.19114

Fiesel, P.D., Kerwin, R.E., Jones, A.D. and Last, R.L., 2023. Trading acyls and swapping sugars: metabolic innovations in Solanum trichomes. bioRxiv, pp.2023-06. doi: https://doi.org/10.1101/2023.06.05.542877

Roberts M., Josephs E.B., 2023. Weaker selection on genes with treatment-specific expression consistent with a limit on plasticity evolution in Arabidopsis thaliana. Genetics, 224(2). doi: https://doi.org/10.1093/genetics/iyad074

Zhang C., Johnson N., Hall N., Tian X., Yu Q., Patterson E., 2023. Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) copy number variation confers glyphosate resistance in Eleusine indica. Nature Communications, 14(1), p. 4865. doi: https://doi.org/10.21203/rs.3.rs-2587355/v1

Steensma, A. K., Shachar-Hill, Y., & Walker, B. J., 2023. The carbon-concentrating mechanism of the extremophilic red microalga Cyanidioschyzon merolae. Photosynthesis research, 156(2), pp.247-264. Advance online publication. doi: https://doi.org/10.1007/s11120-023-01000-6

Lanier E. R., Andersen T.B., Hamberger B., 2023. Plant terpene specialized metabolism: complex networks or simple linear pathways? The Plant Journal, 114(5), 1178–1201. doi: https://doi.org/10.1111/tpj.16177

McClain, A.M. and Sharkey, T.D., 2023. Rapid CO2 changes cause oscillations in photosynthesis that implicate PSI acceptor-side limitations. Journal of Experimental Botany, 74(10), pp. 3163–3173. doi: https://doi.org/10.1093/jxb/erad084

Pardo, J., Wai, C. M., Harman, M., Nguyen, A., Kremling, K. A., Romay, M. C., Lepak, N., Bauerle, T. L., Buckler, E. S., Thompson, A. M., & VanBuren, R., 2023. Cross-species predictive modeling reveals conserved drought responses between maize and sorghum. Proceedings of the National Academy of Sciences, 120(10), e2216894120. doi: https://doi.org/10.1073/pnas.2216894120

J.A.M. Kaste and Y. Shachar-Hill., 2023. Model Validation and Selection in Metabolic Flux Analysis and Flux Balance Analysis. arXiv:2303.12651. doi:

McClain, A.M., Cruz, J.A., Kramer, D.M. and Sharkey, T.D., 2023. The time course of acclimation to the stress of triose phosphate use limitation. Plant, Cell & Environment, 46(1), pp.64-75. doi: https://doi.org/10.1111/pce.14476

Hoffmann, D.Y. and Shachar-Hill, Y., 2023. Do betaine lipids replace phosphatidylcholine as fatty acid editing hubs in microalgae?. Frontiers in Plant Science14, p.33. doi: https://doi.org/10.3389/fpls.2023.1077347

Bryson, A.E., Lanier, E.R., Lau, K.H., Hamilton, J.P., Vaillancourt, B., Mathieu, D., Yocca, A.E., Miller, G.P., Edger, P.P., Buell, C.R. and Hamberger, B., 2023. Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory. Nature Communications, 14(1), p.343. doi: https://doi.org/10.1038/s41467-023-35845-1

Parks, H. M., Cinelli, M. A., Bedewitz, M. A., Grabar, J. M., Hurney, S. M., Walker, K. D., Jones, A. D., & Barry, C. S., 2023. Redirecting tropane alkaloid metabolism reveals pyrrolidine alkaloid diversity in Atropa belladonna. The New phytologist, 237(5), pp.1810–1825. doi https://doi.org/10.1111/nph.18651


Kokarakis, E.J., Rillema, R., Ducat, D.C. and Sakkos, J.K., 2022. Developing Cyanobacterial Quorum Sensing Toolkits: Toward Interspecies Coordination in Mixed Autotroph/Heterotroph Communities. ACS Synthetic Biology, 12(1), pp.265–276. doi: https://doi.org/10.1021/acssynbio.2c00527

Pardo, J., Wai, C.M., Harman, M., Nguyen, A., Kremling, K.A., Romay, C., Lepak, N., Bauerle, T.L., Buckler, E.S., Thompson, A.M. and VanBuren, R., 2022. Cross-species predictive modeling reveals conserved drought responses between maize and sorghum.  bioRxiv. doi: https://doi.org/10.1101/2022.09.26.509573

Young, D.Y. and Shachar-Hill, Y., 2021. Large fluxes of fatty acids from membranes to triacylglycerol and back during N-deprivation and recovery in Chlamydomonas. Plant Physiology, 185(3), pp.796-814. doi:https://doi.org/10.1093/plphys/kiaa071

Roberts, M.D. and Josephs, E., 2022. Weaker selection on genes with treatment-specific expression may limit plasticity evolution in Arabidopsis thaliana. bioRxiv. doi: https://doi.org/10.1101/2022.10.26.513896

Noel, Z.A., Longley, R., Benucci, G.M.N., Trail, F., Chilvers, M.I. and Bonito, G., 2022. Non-target impacts of fungicide disturbance on phyllosphere yeasts in conventional and no-till management. ISME Communications, 2(1), pp.1-10. doi: http://10.1038/s43705-022-00103-w

Kaste, J.A., Green, A. and Shachar-Hill, Y., 2022. Integrative Teaching of Metabolic Modeling and Flux Analysis with Interactive Python modules. bioRxiv. doi: https://doi.org/10.1101/2022.11.16.516820

Kaste, J.A. and Shachar-Hill, Y., 2022. Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling. bioRxiv. doi: https://doi.org/10.1101/2022.09.05.506655

Kim, J.H., Castroverde, C.D.M., Huang, S., Li, C., Hilleary, R., Seroka, A., Sohrabi, R., Medina-Yerena, D., Huot, B., Wang, J. and Nomura, K., 2022. Increasing the resilience of plant immunity to a warming climate. Nature, 607(7918), pp.339-344. doi: 10.1038/s41586-022-04902-y

McClain, A.M., Cruz, J.A., Kramer, D.M. and Sharkey, T.D., 2022. The time course of acclimation to the stress of triose phosphate use limitation. Plant, Cell & Environmentt, 46(1), pp. 64–75. doi:https://doi.org/10.1111/pce.14476

Leong, B.J., Hurney, S., Fiesel, P., Anthony, T.M., Moghe, G., Jones, A.D. and Last, R.L., 2022. Identification of BAHD acyltransferases associated with acylinositol biosynthesis in Solanum quitoense (naranjilla). Plant direct, 6(6), p.e415. doi: https://doi.org/10.1002/pld3.415

Young, D.Y., Pang, N. and Shachar-Hill, Y., 2022. 13C-labeling reveals how membrane lipid components contribute to triacylglycerol accumulation in Chlamydomonas. Plant Physiology, 189(3), pp. 1326–1344. doi: https://doi.org/10.1093/plphys/kiac154

Ford, K.C., Kaste, J.A.M., Shachar-Hill, Y. and TerAvest, M.A. 2022. Flux-Balance Analysis and Mobile CRISPRi-Guided Deletion of a Conditionally Essential Gene in Shewanella oneidensis MR-1. ACS Synthetic Biology, 11(10), 3405–3413. doi:10.1021/acssynbio.2c00323

Hoopes, G.M., Zarka, D., Feke, A., Acheson, K., Hamilton, J.P., Douches, D., Buell, C.R. and Farré, E.M., 2022. Keeping time in the dark: Potato diel and circadian rhythmic gene expression reveals tissue-specific circadian clocks. Plant Direct, 6(7), p.e425. doi: https://doi.org/10.1002/pld3.425

Liber, J.A., Minier, D.H., Stouffer-Hopkins, A., Van Wyk, J., Longley, R. and Bonito, G., 2022. Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities. PeerJ, 10, p.e12701. doi: 10.7717/peerj.12701

Rodriguez, J., Gomez-Cano, L., Grotewold, E., & de Leon, N., 2022. Normalizing and Correcting Variable and Complex LC–MS Metabolomic Data with the R Package pseudoDrift. Metabolites, 12(5), 435. doi:  https://doi.org/10.3390/metabo12050435

Fiesel, P. D., Parks, H. M., Last, R. L., & Barry, C. S., 2022. Fruity, sticky, stinky, spicy, bitter, addictive, and deadly: evolutionary signatures of metabolic complexity in the Solanaceae. Natural Product Reports, 39(7), pp.1438-1464. doi: https://doi.org/10.1039/D2NP00003B

Liber, J. A., Minier, D. H., Stouffer-Hopkins, A., Van Wyk, J., Longley, R., & Bonito, G., 2022. Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities. PeerJ, 10, p.e12701. doi: https://doi.org/10.7717/peerj.12701

Angelos, E., & Brandizzi, F., 2022. The UPR regulator IRE1 promotes balanced organ development by restricting TOR-dependent control of cellular differentiation in Arabidopsis. The Plant Journal, 109(5), 1229-1248. doi: https://doi.org/10.1111/tpj.15629

Xu, Y., Wieloch, T., Kaste, J. A. M., Shachar-Hill, Y., & Sharkey, T. D., 2022. Reimport of carbon from cytosolic and vacuolar sugar pools into the Calvin–Benson cycle explains photosynthesis labeling anomalies. Proceedings of the National Academy of Sciences, 119(11). doi: https://doi.org/10.1073/pnas.2121531119

Noel, Z. A., Longley, R., Benucci, G. M. N., Trail, F., Chilvers, M. I., & Bonito, G., 2022. Non-target impacts of fungicide disturbance on phyllosphere yeasts in conventional and no-till management. ISME Communications, 2(1), pp.1-10. doi: https://doi.org/10.1038/s43705-022-00103-w

Sugimoto, K., Zager, J. J., Aubin, B. S., Lange, B. M., & Howe, G. A., 2022. Flavonoid deficiency disrupts redox homeostasis and terpenoid biosynthesis in glandular trichomes of tomato. Plant Physiology, 188(3), 1450-1468. doi: 10.1093/plphys/kiab488


Kim, J.H., Hilleary, R., Seroka, A. and He, S.Y., 2021. Crops of the future: building a climate-resilient plant immune system. Current opinion in plant biology, 60, p.101997. doi: https://doi.org/10.1016/j.pbi.2020.101997

Pardo, J., & VanBuren, R., 2021. Evolutionary innovations driving abiotic stress tolerance in C4 grasses and cereals. The Plant Cell, 33(11), pp.3391-3401. doi: 10.1093/plcell/koab205

Lavell, A., Smith, M., Xu, Y., Froehlich, J.E., De La Mora, C. and Benning, C., 2021. Proteins associated with the Arabidopsis thaliana plastid rhomboid like protein RBL10. The Plant Journal108(5), pp.1332-1345. doi: https://doi.org/10.1111/tpj.15514

Liu, J., Cook, R., Danhof, L., Lopatto, D., Stoltzfus, J.R. and Benning, C., 2021. Connecting research and teaching introductory cell and molecular biology using an Arabidopsis mutant screen. Biochemistry and Molecular Biology Education, 49(6), pp.926-934. doi: https://doi.org/10.1002/bmb.21579

Osei-Bonsu, I., McClain, A.M., Walker, B.J., Sharkey, T.D. and Kramer, D.M., 2021. The roles of photorespiration and alternative electron acceptors in the responses of photosynthesis to elevated temperatures in cowpea. Plant, Cell & Environment44(7), pp.2290-2307. doi: https://doi.org/10.1111/pce.14026.

Cook, R., Lupette, J. and Benning, C., 2021. The Role of Chloroplast Membrane Lipid Metabolism in Plant Environmental Responses. Cells, 10(3), p.706. doi: https://doi.org/10.3390/cells10030706

Angelos, E., Ko, D.K., Zemelis-Durfee, S. and Brandizzi, F., 2021. Relevance of the Unfolded Protein Response to Spaceflight-Induced Transcriptional Reprogramming in Arabidopsis. Astrobiology, 21(3), pp.367-380. doi:https://doi.org/10.1089/ast.2020.2313

Lou, Y.R., Anthony, T.M., Fiesel, P.D., Arking, R.E., Christensen, E.M., Jones, A.D. and Last, R.L., 2021. It happened again: convergent evolution of acylglucose specialized metabolism in black nightshade and wild tomato. Science advances7(46), p.eabj8726. doi: https://science.org/doi/10.1126/sciadv.abj8726


Moore, B.M., Wang, P., Fan, P., Lee, A., Leong, B., Lou, Y.R., Schenck, C.A., Sugimoto, K., Last, R., Lehti-Shiu, M.D. and Barry, C.S., 2020. Within-and cross-species predictions of plant specialized metabolism genes using transfer learning. in silico Plants, 2(1), p.diaa005. doi: 10.1093/insilicoplants/diaa005

Longley, R., Noel, Z.A., Benucci, G.M.N., Chilvers, M.I., Trail, F. and Bonito, G., 2020. Crop management impacts the soybean (Glycine max) microbiome. Frontiers in microbiology, 11, p.1116. doi: 10.3389/fmicb.2020.01116

Takeuchi, T., Lin, Y.T., Fekaris, N., Umen, J., Sears, B.B. and Benning, C., 2020. Modulation of CHT7 Complexes during Light/Dark-and Nitrogen-Mediated Life Cycle Transitions of Chlamydomonas. Plant Physiology, 184(4), pp.1762-1774. doi: https://doi.org/10.1104/pp.20.00864

Sudhakaran, M., Parra, M.R., Stoub, H., Gallo, K.A. and Doseff, A.I., 2020. Apigenin by targeting hnRNPA2 sensitizes triple-negative breast cancer spheroids to doxorubicin-induced apoptosis and regulates expression of ABCC4 and ABCG2 drug efflux transporters. Biochemical Pharmacology, p.114259. doi: https://doi.org/10.1016/j.bcp.2020.114259

Lybrand, D.B., Anthony, T.M. Jones, A.D. and Last, R.L. 2020. An integrated analytical approach reveals trichome acylsugar metabolite diversity in the wild tomato Solanum pennellii. Metabolites 10(10), 401. doi: https://www.mdpi.com/2218-1989/10/10/401

Miller, G.P., Bhat, W.W., Lanier, E.R., Johnson, S.R., Mathieu, D.T. and Hamberger, B., 2020. The biosynthesis of the anti-microbial diterpenoid leubethanol in Leucophyllum frutescens proceeds via an all-cis prenyl intermediate.The Plant Journal , 104(3), 693–705. doi: https://doi.org/10.1111/tpj.14957

Lybrand, D.B., Xu, H., Last, R.L. and Pichersky, E., 2020. How Plants Synthesize Pyrethrins: Safe and Biodegradable Insecticides. Trends in Plant Science. doi: https://doi.org/10.1016/j.tplants.2020.06.012

Fan, P., P. Wang, Y.-R. Lou, B.J. Leong, B.J. Moore, C.A. Schenck, R. Combs, P. Cao, F. Brandizzi, S.-H. Shiu and R.L. Last. 2020. Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity. eLife. doi: https://doi.org/10.1101/2020.03.04.977231.

Medina-Cucurella, A.V., Bammert, G.F., Dunkle, W., Javens, C., Zhu, Y., Mutchler, V.T., Teel, J.T., Stein, C.A., Dunham, S.A. and Whitehead, T.A., 2020. Feline Interleukin-31 shares overlapping epitopes with Oncostatin M Receptor and IL-31RA. Biochemistry. doi: https://doi.org/10.1021/acs.biochem.0c00176

Sudhakaran, M. and Doseff, A.I., 2020. The Targeted Impact of Flavones on Obesity-Induced Inflammation and the Potential Synergistic Role in Cancer and the Gut Microbiota. Molecules, 25(11), p.2477. doi: https://doi.org/10.3390/molecules25112477

Takeuchi, T., Sears, B.B., Lindeboom, C., Lin, Y.T., Fekaris, N., Zienkiewicz, K., Zienkiewicz, A., Poliner, E. and Benning, C., 2020. Chlamydomonas CHT7 is required for an effective quiescent state by regulating nutrient-responsive cell cycle gene expression. The Plant Cell, 32(4), pp.1240-1269. doi: https://doi.org/10.1105/tpc.19.00628

García-Cerdán, J.G., Schmid, E.M., Takeuchi, T., McRae, I., McDonald, K.L., Yordduangjun, N., Hassan, A.M., Grob, P., Xu, C.S., Hess, H.F. and Fletcher, D.A., 2020. Chloroplast Sec14-like 1 (CPSFL1) is essential for normal chloroplast development and affects carotenoid accumulation in Chlamydomonas. Proceedings of the National Academy of Sciences. doi: https://doi.org/10.1073/pnas.1916948117

Li, W., Lybrand, D.B., Xu, H., Zhou, F., Last, R.L. and Pichersky, E., 2020. A Trichome-Specific, Plastid-Localized Tanacetum cinerariifolium Nudix Protein Hydrolyzes the Natural Pyrethrin Pesticide Biosynthetic Intermediate trans-Chrysanthemyl Diphosphate. Frontiers in Plant Science, 11, p.482. doi: https://doi.org/10.3389/fpls.2020.00482

Havko, N.E., Das, M.R., McClain, A.M., Kapali, G., Sharkey, T.D. and Howe, G.A., 2020. Insect herbivory antagonizes leaf cooling responses to elevated temperature in tomato. Proceedings of the National Academy of Sciences, 117(4), pp.2211-2217. doi: https://doi.org/10.1073/pnas.1913885117

Pardo, J., Wai, C.M., Chay, H., Madden, C.F., Hilhorst, H.W., Farrant, J.M. and VanBuren, R., 2020. Intertwined signatures of desiccation and drought tolerance in grasses. Proceedings of the National Academy of Sciences, 117(18), pp.10079-10088. doi: https://doi.org/10.1073/pnas.2001928117

Leong, B.J., Hurney, S.M., Fiesel, P.D., Moghe, G.D., Jones, A.D. and Last, R.L., 2020. Specialized metabolism in a nonmodel nightshade: trichome acylinositol biosynthesis. Plant physiology, 183(3), pp.915-924. doi: https://doi.org/10.1104/pp.20.00276

McClain, A.M. and Sharkey, T.D., 2020. Building a better equation for electron transport estimated from Chl fluorescence: accounting for non-photosynthetic light absorption. New Phytologist, 225(2), pp.604-608. doi: https://doi.org/10.1111/nph.16255


Takeuchi, T. and Benning, C., 2019. Nitrogen-dependent coordination of cell cycle, quiescence and TAG accumulation in Chlamydomonas. Biotechnology for Biofuels, 12(1), pp.1-20. doi: 10.1186/s13068-019-1635-0

Duhl, K.L. and TerAvest, M., 2019. Shewanella oneidensis NADH dehydrogenase mutants exhibit an amino acid synthesis defect. Frontiers in Energy Research, 7, p.116. doi: https://doi.org/10.3389/fenrg.2019.00116

Sharkey, T.D., Weise, S.E., Childs, K., Preiser, A.L., Katulski, H.M., Perrin-Porzondek, C. and Liu, T., 2019. Transcriptional regulation of the glucose-6-phosphate/Phosphate translocator 2 is related to carbon exchange across the chloroplast envelope. Frontiers in plant science, 10, p.827. doi:  https://doi.org/10.3389/fpls.2019.00827

Longley, R., Benucci, G.M.N., Mills, G. and Bonito, G., 2019. Fungal and bacterial community dynamics in substrates during the cultivation of morels (Morchella rufobrunnea) indoors. FEMS microbiology letters, 366(17), p.fnz215. doi: https://doi.org/10.1093/femsle/fnz215

Benucci, G.M.N., Longley, R., Zhang, P., Zhao, Q., Bonito, G. and Yu, F., 2019. Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses. PeerJ, 7, p.e7744. doi: https://doi.org/10.7717/peerj.7744

McCoy, A.G., Roth, M.G., Shay, R., Noel, Z.A., Jayawardana, M.A., Longley, R.W., Bonito, G. and Chilvers, M.I., 2019. Identification of Fungal Communities Within the Tar Spot Complex of Corn in Michigan via Next-Generation Sequencing. Phytobiomes Journal, 3(3), pp.235-243. doi: https://doi.org/10.1094/PBIOMES-03-19-0017-R

Li, W., Lybrand, D.B., Zhou, F., Last, R.L. and Pichersky, E., 2019. Pyrethrin biosynthesis: The cytochrome P450 oxidoreducatse CYP82Q3 converts jasmolone to pyrethrolone. Plant Physiology, 181(3), pp.934-944. doi: https://doi.org/10.1104/pp.19.00499

Preiser, A.L., Fisher, N., Banerjee, A. and Sharkey, T.D., 2019. Plastidic glucose-6-phosphate dehydrogenases are regulated to maintain activity in the light. Biochemical Journal, 476(10), pp.1539-1551. doi: https://doi.org/10.1042/BCJ20190234

McClain, A.M. and Sharkey, T.D., 2019. Triose phosphate utilization and beyond: from photosynthesis to end product synthesis. Journal of Experimental Botany, 70(6), pp.1755-1766. doi: https://doi.org/10.1093/jxb/erz058

Li, L., Lavell, A., Meng, X., Berkowitz, O., Selinski, J., van de Meene, A., Carrie, C., Benning, C., Whelan, J., De Clercq, I. and Wang, Y., 2019. Arabidopsis DGD1 SUPPRESSOR 1 is a Subunit of the Mitochondrial Contact Site and Cristae Organizing System and Affects Mitochondrial Biogenesis. The Plant Cell, 31(8), pp.1856-1878. doi: https://doi.org/10.1105/tpc.18.00885

Lavell, A., Froehlich, J.E., Baylis, O., Rotondo, A. and Benning, C., 2019. A Predicted Plastid Rhomboid Protease Affects Phosphatidic Acid Metabolism in Arabidopsis thaliana. The Plant Journal, 99(5), pp.978-987.doi: https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.14377

Fan, P., Leong, B.J. and Last, R.L., 2019. Tip of the trichome: evolution of acylsugar metabolic diversity in Solanaceae. Current Opinion in Plant Biology, 49, pp.8-16. doi: https://doi.org/10.1016/j.pbi.2019.03.005

Leong, B.J., Lybrand, D.B., Lou, Y.R., Fan, P., Schilmiller, A.L. and Last, R.L., 2019. Evolution of metabolic novelty: a trichome-expressed invertase creates specialized metabolic diversity in wild tomato. Science Advances, 5(4), p.eaaw3754. doi: https://advances.sciencemag.org/content/5/4/eaaw3754.abstract

Lavell, A.A. and Benning, C., 2019. Cellular organization and regulation of plant glycerolipid metabolism. Plant and Cell Physiology, 60(6), pp.1176-1183. doi: https://doi.org/10.1093/pcp/pcz016

Jack, C.N., Rowe, S.L., Porter, S.S. and Friesen, M.L., 2019. A high-throughput method of analyzing multiple plant defensive compounds in minimized sample mass. Applications in Plant Sciences, p.e01210. doi: https://doi.org/10.1002/aps3.1210

Moore, B.M., Wang, P., Fan, P., Leong, B., Schenck, C.A., Lloyd, J.P., Lehti-Shiu, M.D., Last, R.L., Pichersky, E. and Shiu, S.H., 2019. Robust predictions of specialized metabolism genes through machine learning. Proceedings of the National Academy of Sciences, 116(6), pp.2344-2353. doi: https://doi.org/10.1073/pnas.1817074116.

Wrenbeck, E.E., Bedewitz, M.A., Klesmith, J.R., Noshin, S.R., Barry, C. and Whitehead, T.A., 2019. An automated data-driven pipeline for improving heterologous enzyme expression. ACS Synthetic Biology 8(3), pp.474-481. doi: https://pubs.acs.org/doi/full/10.1021/acssynbio.8b00486

Clark, T.J., Friel, C.A., Grman, E., Friesen, M.L. and Shachar-Hill, Y., 2019. Unfair trade underground revealed by integrating data with Nash bargaining models. New Phytologist,222(3), pp.1325-1337. doi: https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.15703

Medina-Cucurella, A.V., Steiner, P.J., Faber, M.S., Beltrán, J., Borelli, A.N., Kirby, M.B., Cutler, S.R. and Whitehead, T.A., 2019. User-defined single pot mutagenesis using unamplified oligo pools. Protein Engineering, Design and Selection, 32(1), pp.41-45. doi: https://doi.org/10.1093/protein/gzz013


Agostoni, M., Logan-Jackson, A.R., Heinz, E.R., Severin, G.B., Bruger, E.L., Waters, C.M. and Montgomery, B.L., 2018. Homeostasis of second messenger cyclic-di-AMP is critical for cyanobacterial fitness and acclimation to abiotic stress. Frontiers in microbiology, 9. doi: https://doi.org/10.3389/fmicb.2018.01121

Angelos, E. and Brandizzi, F., 2018. NADPH oxidase activity is required for ER stress survival in plants. The Plant Journal, 96(6), pp.1106-1120. doi: https://doi.org/10.1111/tpj.14091

Xu, H., Lybrand, D., Bennewitz, S., Tissier, A., Last, R.L. and Pichersky, E., 2018. Production of trans-chrysanthemic acid, the monoterpene acid moiety of natural pyrethrin insecticides, in tomato fruit. Metabolic engineering, 47, pp.271-278. doi: https://doi.org/10.1016/j.ymben.2018.04.004

Rowe, S.L., Norman, J.S. and Friesen, M.L., 2018. Coercion in the evolution of plant–microbe communication: A perspective. Molecular Plant-Microbe Interactions, 31(8), pp.789-794.doi: https://doi.org/10.1094/MPMI-11-17-0276-CR

Duhl, K.L., Tefft, N.M. and TerAvest, M.A., 2018. Shewanella oneidensis MR-1 utilizes both sodium-and proton-pumping NADH dehydrogenases during aerobic growth. Applied and Environmental Microbiology, 84(12), pp.e00415-18. doi: https://doi.org/10.1128/AEM.00415-18

Medina‐Cucurella, A.V., Zhu, Y., Bowen, S.J., Bergeron, L.M. and Whitehead, T.A., 2018. Pro region engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of anti‐NGF monoclonal antibodies. Biotechnology and bioengineering, 115(8), pp.1925-1937. doi: https://doi.org/10.1002/bit.26706

Poliner, E., Takeuchi, T., Du, Z.Y., Benning, C. and Farré, E.M., 2018. Nontransgenic marker-free gene disruption by an episomal CRISPR system in the oleaginous microalga, Nannochloropsis oceanica CCMP1779. ACS synthetic biology7(4), pp.962-968. doi: https://doi.org/10.1021/acssynbio.7b00362

Medina-Cucurella A. and Whitehead, T.A., 2018. Characterizing Protein-Protein Interactions Using Deep Sequencing Coupled to Yeast Surface Display. Methods in molecular biology, 1764, pp.101–121. doi: https://doi.org/10.1007/978-1-4939-7759-8_7


Leong, B.J. and Last, R.L. Promiscuity, impersonation and accommodation: evolution of plant specialized metabolism. 2017. Curr. Opin. Struct. Biol., 47:105–112 https://doi.org/10.1016/j.sbi.2017.07.005.

Wrenbeck E.E., Azouz L.R., Whitehead T.A. 2017. Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded, Nature Comm. 8, Article number: 15695. doi:10.1038/ncomms15695

Moghe, G.D., Leong, B.J., Hurney, S. Jones, A.D. and Last, R.L. 2017. Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant defense related specialized metabolic pathway. eLife 2017;6:e28468 DOI: 10.7554/eLife.28468.

Clark, T.J., Friel, C.A., Grman, E., Shachar-Hill, Y. and Friesen, M.L. 2017. Modelling nutritional mutualisms: challenges and opportunities for data integration. Ecol. Letts. doi: 10.1111/ele.12810

Angelos, E., Ruberti, C., Kim, S.J., and Brandizzi, F. 2017. Maintaining the factory: the roles of the unfolded protein response in cellular homeostasis in plants. Plant J. 90:671-682. doi:10.1111.tpj.13449

Wrenbeck E. E., Faber, M. S., Whitehead, T. A. 2017. Deep sequencing methods for protein engineering and design. Curr. Opin. Struct. Biol., 45:36-44, doi: 10.1016/j.sbi.2016.11.001

Klesmith, J.R., Bacik, J.P., Wrenbeck, E.E., Michalczyk, R., Whitehead, T.A. 2017. Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning. Proc. Natl. Acad. Sci. U.S.A., 114:2265-2270, doi: 10.1073/pnas.1614437114

Panchy NL, Azodi C.B., Winship EF, O'Malley RC, Shiu SH. 2017. Asymmetric evolution of the transcription profiles and cis-regulatory sites contributes to the retention of transcription factor duplicates.bioRxiv, p.115857. doi: https://doi.org/10.1101/115857

Yang, Y., Zienkiewicz, A., Lavell, A. and Benning, C. 2017. Coevolution of Domain Interactions in the Chloroplast TGD1, 2, 3 Lipid Transfer Complex Specific to Brassicaceae and Poaceae Plants. The Plant Cell, 29(6), pp.1500-1515. doi: https://doi.org/10.1105/tpc.17.00182


Wrenbeck, E.E., Klesmith, J.R., Stapleton, J.A., Adeniran, A., Tyo, K.E.J. and Whitehead T.A. 2016. Plasmid-based one-pot saturation mutagenesis.  Nature Methods13(11), pp.928-930. doi: https://doi.org/10.1038/nmeth.4029

Ning, J., Moghe, G., Leong, B.J., Kim, J., Ofner, I., Wang, Z., Adams, C., Jones, A., Zamir, D., Last, RL. 2015.  A feedback insensitive isopropylmalate synthase affects acylsugar composition in cultivated and wild tomato. Plant Physiol. 169:1821-1835. doi:10.1104/pp.15.00474

Tsai, C.H., Warakanont, J., Takeuchi, T., Sears, B.B., Moellering, E.R., Benning, C. 2014. The protein Compromised Hydrolysis of Triacylglycerols 7 (CHT7) acts as a repressor of cellular quiescence in Chlamydomonas. Proceedings of the National Academy of Sciences111(44), pp.15833-15838. doi : https://doi.org/10.1073/pnas.1414567111.

Other Publications from our Trainees:

Palande, S., Kaste, J.A., Roberts, M.D., Segura Aba, K., Claucherty, C., Dacon, J., Doko, R., Jayakody, T.B., Jeffery, H.R., Kelly, N., Manousidaki, A., Parks H.M., Roggenkamp E.M., Schumacher, A.M., Yang J., Percival S., Pardo J., Husbands A.Y., Krishnan A., Montgomery B.L., Munch E., Thompson A.M., Rougon-Cardoso A., Chitwood, D.H. and VanBuren R. 2022. The topological shape of gene expression across the evolution of flowering plants. bioRxiv, pp.2022-09. doi:https://doi.org/10.1101/2022.09.07.506951

Azodi, C.B., Pardo, J., VanBuren, R., de Los Campos, G. and Shiu, S.H., 2020. Transcriptome-based prediction of complex traits in maize. The Plant Cell, 32(1), pp.139-151. doi: https://doi.org/10.1105/tpc.19.00332

VanBuren, R., Man Wai, C., Wang, X., Pardo, J., Yocca, A.E., Wang, H., Chaluvadi, S.R., Han, G., Bryant, D., Edger, P.P. and Messing, J., 2020. Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff. Nature communications, 11(1), pp.1-11. doi: https://doi.org/10.1038/s41467-020-14724-z

VanBuren, R., Pardo, J., Man Wai, C., Evans, S. and Bartels, D., 2019. Massive tandem proliferation of ELIPs supports convergent evolution of desiccation tolerance across land plants. Plant physiology, 179(3), pp.1040-1049. doi: https://doi.org/10.1104/pp.18.01420

Beltrán, J., Steiner, P. J., Bedewitz, M., Wei, S., Peterson, F. C., Li, Z., Hughes, B. E., Hartley, Z., Robertson, N. R., Medina-Cucurella, A. V., Baumer, Z. T., Leonard, A. C., Park, S. Y., Volkman, B. F., Nusinow, D. A., Zhong, W., Wheeldon, I., Cutler, S. R., & Whitehead, T. A., 2022. Rapid biosensor development using plant hormone receptors as reprogrammable scaffolds. Nature biotechnology, 40(12), pp.1855–1861. https://doi.org/10.1038/s41587-022-01364-5

Kirby, M.B., Medina-Cucurella, A.V., Baumer, Z.T. and Whitehead, T.A., 2021. Optimization of multi-site nicking mutagenesis for generation of large, user-defined combinatorial libraries. Protein Engineering, Design and Selection, 34. doi: https://doi.org/10.1093/protein/gzab017

Lin, Y.T., Takeuchi, T., Youk, B., Umen, J., Sears, B.B. and Benning, C., 2022. Chlamydomonas CHT7 is involved in repressing DNA replication and mitotic genes during synchronous growth. G3, 12(3), p.jkac023. doi: https://doi.org/10.1093/g3journal/jkac023

Gregory, L. M., McClain, A. M., Kramer, D. M., Pardo, J. D., Smith, K. E., Tessmer, O. L., ... & Sharkey, T. D., 2021. The triose phosphate utilization limitation of photosynthetic rate: Out of global models but important for leaf models. Plant, Cell & Environment, 44(10), pp.3223-3226. doi: https://doi.org/10.1111/pce.14153

Jiang, N., Dillon, F.M., Silva, A., Gomez-Cano, L. and Grotewold, E., 2021. Rhamnose in plants-from biosynthesis to diverse functions. Plant Science, 302, p.110687. doi: https://doi.org/10.1016/j.plantsci.2020.110687 

Sudhakaran, M., Sardesai, S. and Doseff, A.I., 2019. Flavonoids: new frontier for immuno-regulation and breast cancer control. Antioxidants, 8(4), p.103. doi: https://doi.org/10.3390/antiox8040103

Panchy, N.L., Azodi, C.B., Winship, E.F., O’Malley, R.C. and Shiu, S.H., 2019. Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication. BMC evolutionary biology, 19(1), p.77. doi: https://doi.org/10.1186/s12862-019-1398-z

Li, J., Weraduwage, S.M., Peiser, A.L., Tietz, S., Weise, S.E., Strand, D.D., Froehlich, J.E., Kramer, D.M., Hu, J. and Sharkey, T.D., 2019. A Cytosolic Bypass and G6P Shunt in Plants Lacking Peroxisomal Hydroxypyruvate Reductase. Plant physiology, 180(2), pp.783-792. doi: https://doi.org/10.1104/pp.19.00256

Johnson, S.R., Bhat, W.W., Sadre, R., Miller, G.P., Garcia, A.S. and Hamberger, B., 2019. Promiscuous terpene synthases from Prunella vulgaris highlight the importance of substrate and compartment switching in terpene synthase evolution. New Phytologist. doi: https://doi.org/10.1111/nph.15778

Lantz, A.T., Solomon, C., Gog, L., McClain, A.M., Weraduwage, S.M. and Sharkey, T.D., 2019. Isoprene suppression by CO2 is not due to triose phosphate utilization (TPU) limitation. Frontiers in Forests and Global Change, 2, p.8. doi:  https://doi.org/10.3389/ffgc.2019.00008

Zuo, Z., Weraduwage, S.M., Lantz, A.T., Sanchez, L.M., Weise, S.E., Wang, J., Childs, K.L. and Sharkey, T.D., 2019. Isoprene acts as a signaling molecule in gene networks important for stress responses and plant growth. Plant physiology, 180(1), pp.124-152. doi: https://doi.org/10.1104/pp.18.01391

Medina-Cucurella, A.V., Mizrahi, R.A., Asensio, M.A., Edgar, R.C., Leong, J., Leong, R., Lim, Y.W., Nelson, A., Niedecken, A.R., Simons, J.F., Spindler, M.J., Stadtmiller, K., Wayham, N., Adler, A.S., Johnson, D.S. 2019. Preferential Identification of Agonistic OX40 Antibodies by Using Cell Lysate to Pan Natively Paired, Humanized Mouse-Derived Yeast Surface Display libraries. Antibodies, 8(1), p.17. doi: https://www.mdpi.com/2073-4468/8/1/17/htm

Hoopes, G.M., Hamilton, J.P., Kim, J., Zhao, D., Wiegert-Rininger, K., Crisovan, E. and Buell, C.R., 2018. Genome assembly and annotation of the medicinal plant Calotropis gigantea, a producer of anticancer and antimalarial cardenolides. G3: Genes, Genomes, Genetics, 8(2), pp.385-391. doi: 10.1534/g3.117.300331

Hurlock, A.K., Wang, K., Takeuchi, T., Horn, P.J. and Benning, C., 2018. In vivo lipid ‘tag and track’approach shows acyl editing of plastid lipids and chloroplast import of phosphatidylglycerol precursors in Arabidopsis thaliana. The Plant Journal, 95(6), pp.1129-1139. doi: https://doi.org/10.1534/g3.117.300331

Dums, J.T., Murphree, C.A., Vasani, N., Young, D. and Sederoff, H., 2018. Metabolic and Transcriptional Profiles of Dunaliella viridis Supplemented with Ammonium Derived from Glutamine. Frontiers in Marine Science, 5, p.311. doi: https://doi.org/10.3389/fmars.2018.00311

Johnson, S.R., Bhat, W.W., Bibik, J., Turmo, A., Hamberger, B., Hamberger, B., Boachon, B., Buell, C.R., Crisovan, E., Dudareva, N. and Garcia, N., 2019. A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae). Journal of Biological Chemistry, 294(4), pp.1349-1362. doi: https://doi.org/10.1074/jbc.RA118.006025

Hoopes, G.M., Hamilton, J.P., Wood, J.C., Esteban, E., Pasha, A., Vaillancourt, B., Provart, N.J. and Buell, C.R., 2018. An updated gene atlas for maize reveals organ-specific and stress-induced genes. The Plant Journal The Plant journal, 97(6), pp.1154–1167.doi: https://onlinelibrary.wiley.com/doi/10.1111/tpj.14184

Li, J., Weraduwage, S.M., Preiser, A.L., Weise, S.E., Strand, D.D., Froehlich, J.E., Kramer, D.M., Hu, J. and Sharkey, T.D., 2018. Loss of Peroxisomal Hydroxypyruvate Reductase Inhibits Triose Phosphate Isomerase but Stimulates Cyclic Photosynthetic Electron Flow and the Glc-6P-Phosphate Shunt. bioRxiv, p.278580. doi: 10.1101/278580

Uygun, S., Seddon, A.E., Azodi, C.B. and Shiu, S.H., 2017. Predictive models of spatial transcriptional response to high salinity. Plant physiology, 174(1), pp.450-464. doi: 10. 1104/ pp. 16. 01828

Dowdell, A.S., Murphy, M.D., Azodi, C., Swanson, S.K., Florens, L., Chen, S. and Zückert, W.R., 2017. Comprehensive spatial analysis of the Borrelia burgdorferi lipoproteome reveals a compartmentalization bias toward the bacterial surface. Journal of bacteriology, 199(6), pp.e00658-16. doi: 10.1128/JB.00658-16

Murphree, C.A., Dums, J.T., Jain, S.K., Zhao, C., Young, D.Y., Khoshnoodi, N., Tikunov, A., Macdonald, J., Pilot, G. and Sederoff, H., 2017. Amino acids are an ineffective fertilizer for Dunaliella spp. growth. Frontiers in plant science, 8, p.847. doi: 10.3389/fpls.2017.00847

Malmstrom, C.M., Bigelow, P., Trębicki, P., Busch, A.K., Friel, C., Cole, E., Abdel-Azim, H., Phillippo, C. and Alexander, H.M., 2017. Crop-associated virus reduces the rooting depth of non-crop perennial native grass more than non-crop-associated virus with known viral suppressor of RNA silencing (VSR). Virus research, 241, pp.172-184.. doi.org/10.1016/j.virusres.2017.07.006

Banerjee A., Preiser A.L., Sharkey, T.D. Engineering of Recombinant Poplar Deoxy-D-xylulose-5-phosphate Synthase (PtDXS) by Site-directed Mutagenesis Improves Its Activity. 2016. PLoSOne, 11(8), p.e0161534. doi: https://doi.org/10.1371/journal.pone.0165028 

Yang J., Preiser A.L., Li Z, Weise S.E., Sharkey T.D., 2016. Triose phosphate use limitation of photosynthesis short-term and long-term effects. Planta, 243(3) pp.687-98. doi:10.1007/s00425-015-2436-8

Clark, T.J. and Lu, Y., 2015. Analysis of loss-of-function mutants in aspartate kinase and homoserine dehydrogenase genes points to complexity in the regulation of aspartate-derived amino acid contents. Plant physiology, 168(4), pp.1512-1526. doi: https://doi.org/10.1104/pp.15.0036 

Lantz, A.T., Cardiello, J.F., Gee, T.A., Richards, M.G., Rosenstiel, T.N. and Fisher, A.J., 2015. Biochemical characterization of an isoprene synthase from Campylopus introflexus (heath star moss). Plant Physiology and Biochemistry, 94, pp.209-215. doi: 10.1016/j.plaphy.2015.06.008

Brasher, M.I., Surmacz, L., Leong, B., Pitcher, J., Swiezewska, E., Pichersky, E. and Akhtar, T.A., 2015. A two-component enzyme complex is required for dolichol biosynthesis in tomato. The Plant Journal, 82(6), pp.903-914. doi: 10.1111/tpj.12859

Thireault, C., Shyu, C., Yoshida, Y., St. Aubin, B., Campos, M.L. and Howe, G.A., 2015. Repression of jasmonate signaling by a non‐TIFY JAZ protein in Arabidopsis. The Plant Journal, 82(4), pp.669-679. doi: 10.1111/tpj.12841, 25846245

Takeuchi, T., Newton, L., Burkhardt, A., Mason, S. and Farré, E.M., 2014. Light and the circadian clock mediate time-specific changes in sensitivity to UV-B stress under light/dark cycles. Journal of experimental botany, 65(20), pp.6003-6012. doi: https://doi.org/10.1093/jxb/eru339

Bienick, M.S., Young, K.W., Klesmith, J.R., Detwiler, E.E., Tomek, K.J. and Whitehead, T.A., 2014. The interrelationship between promoter strength, gene expression, and growth rate. PloS one, 9(10). doi: 10.1371/journal.pone.0109105.