General Lab Information

Publications

2025

  1. Sharma, R. & Xie, M. (2025). Plant genotype and rhizobia strain combinations strongly influence the transcriptome under heavy metal stress conditions in Medicago truncatula. Plant Stress https://dx.doi.org/10.1016/j.stress.2025.100854
  2. Yi, G. & Liu, Q. (2025). Structure and mechanism of human vesicular polyamine transporter. Nature Communications https://dx.doi.org/10.1038/s41467-025-59549-w
  3. Hu, J. & Liu, C. (2025). Continuity of Mitochondrial Budding: Insights from BS-C-1 Cells by In Situ Cryo-electron Tomography. Microscopy and Microanalysis https://dx.doi.org/10.1093/mam/ozae122
  4. Dai, X. & Liu, Q. (2025). Predicting metal-binding proteins and structures through integration of evolutionary-scale and physics-based modeling. Journal of Molecular Biology https://dx.doi.org/10.1016/j.jmb.2025.168962

2024

  1. Park, K. & Schwender, J. (2024). Development of Vegetative Oil Sorghum: From Lab-to-Field. Plant Biotechnology Journal https://dx.doi.org/10.1111/pbi.14527
  2. Xie, M. (2024). AtDGCR14L contributes to salt-stress tolerance via regulating pre-mRNA splicing in Arabidopsis. Plant Journal https://www.osti.gov/biblio/2478428
  3. Liu, H. (2024). Target of 1 Rapamycin kinase is a positive regulator of plant fatty acid 2 and lipid synthesis. Plant Physiology https://dx.doi.org/10.1093/plphys/kiae639
  4. Grosjean, N. & Xie, M. (2024). Functional diversification within the heme-binding split-barrel family. Journal of Biological Chemistry, 300(11), 107888 https://dx.doi.org/10.1016/j.jbc.2024.107888
  5. Jilian, F. (2024). Phosphatidylcholine remodeling is critical to lipid homeostasis in Arabidopsis trigalactosyldiacylglycerol1 mutants. Plant Journal https://www.osti.gov/biblio/2440523
  6. Zhao, J. & Liu, C. (2024). Spatially distributed cytokinins: Metabolism, signaling, and transport. Plant Communications, 5(7), 100936 https://dx.doi.org/10.1016/j.xplc.2024.100936
  7. Rolletschek, H. & Schwender, J. (2024). Mechanical forces orchestrate the metabolism of the developing oilseed rape embryo. New Phytologist https://www.osti.gov/biblio/2382637
  8. Cai, Y. & Shanklin, J. (2024). Creating yellow-seed Camelina sativa with enhanced oil accumulation by CRISPR-mediated disruption of Transparent Testa 8. Plant Biotechnology Journal https://dx.doi.org/10.1111/pbi.14403
  9. Zhao, X. (2024). Cytochrome b5 diversity in green lineages preceded the evolution of syringyl lignin biosynthesis. Plant Cell https://dx.doi.org/10.1093/plcell/koae120
  10. Muthan, B. & Xu, C. (2024). Mechanisms of Spirodela polyrhiza tolerance to FGD wastewater-induced heavy-metal stress: Lipidomics, transcriptomics, and functional validation. Journal of Hazardous Materials https://dx.doi.org/10.1016/j.jhazmat.2024.133951
  11. Jantana, B. (2024). Molecular mechanism of trehalose 6-phosphate inhibition of the plant metabolic sensor kinase SnRK1. Science Advances https://www.osti.gov/biblio/2341825
  12. Sun, J., Liu, H., Blanford, J., Cai, Y., Zhai, Z., & Shanklin, J. (2024). GRIK phosphorylates and activates KIN10 which also promotes its degradation. Frontiers in Plant Science, 15 https://dx.doi.org/10.3389/fpls.2024.1375471
  13. Maitra, S. & Shanklin, J. (2024). Sustainable co-production of plant lipids and cellulosic sugars from transgenic energycane at an industrially relevant scale: A proof of concept for alternative feedstocks. Chemical Engineering Journal https://dx.doi.org/10.1016/j.cej.2024.150450
  14. Lin, L, Zhang, X, Nandi, P, Lin, Y, Wang, L, Chu, Y, Paape, T, Yang, Y, Xiao, X, Liu, Q (2024). Correlative single-cell hard X-ray computed tomography and X-ray fluorescence imaging. Communications Biology, 7, Article 280 https://dx.doi.org/10.1038/s42003-024-05950-y
  15. Tadesse, D. (2024). Sorghum SbGhd7 is a major regulator of floral transition and directly represses genes crucial for flowering activation. New Phytologist https://dx.doi.org/10.1111/nph.19591
  16. Grojean, N. & Kumaran, D. (2024). A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Nature Communications https://www.osti.gov/biblio/2331231
  17. Anaokar, S., Liang, Y., Yu, X., Cai, Y., Cai, Y., & Shanklin, J. (2024). The expression of genes encoding novel Sesame oleosin variants facilitates enhanced triacylglycerol accumulation in Arabidopsis leaves and seeds. New Phytologist https://dx.doi.org/10.1111/nph.19548

2023

  1. Dai, X., Wu, L., Yoo, S., & Liu, Q. (2023). Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps. Briefings in Bioinformatics https://dx.doi.org/10.1093/bib/bbad405
  2. Cao, V. D., Kannan, B., Luo, G., Liu, H., Shanklin, J., & Altpeter, F. (2023). Triacylglycerol, total fatty acid, and biomass accumulation of metabolically engineered energycane grown under field conditions confirms its potential as feedstock for drop‐in fuel production. GCB Bioenergy, 15(12), 1450-1464 https://dx.doi.org/10.1111/gcbb.13107
  3. Zhang, L., Braynen, J., Fahey, A., Chopra, K., Cifani, P., Tadesse, D., Regulski, M., Hu, F., Van Dam, H. J. J., Xie, M., Ware, D., & Blaby-Haas, C. E. (2023). Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis. Frontiers in Plant Science, 14 https://dx.doi.org/10.3389/fpls.2023.1237722
  4. Cao, V. D., Luo, G., Korynta, S., Liu, H., Liang, Y., Shanklin, J., & Altpeter, F. (2023). Intron-mediated enhancement of DIACYLGLYCEROL ACYLTRANSFERASE1 expression in energycane promotes a step change for lipid accumulation in vegetative tissues. Biotechnology for Biofuels and Bioproducts, 16(1), Article 153 https://dx.doi.org/10.1186/s13068-023-02393-1
  5. Shi, H. N., Ernst, E., Heinzel, N., McCorkle, S., Rolletschek, H., Borisjuk, L., Ortleb, S., Martienssen, R. A., Shanklin, J., & Schwender, J. (2023). Mechanisms of metabolic adaptation in the duckweed Lemna gibba: an integrated metabolic, transcriptomic and flux analysis. BMC Plant Biology, 23, Article 458 https://dx.doi.org/10.1186/s12870-023-04480-9
  6. Dwivedi, N., Yamamoto, S., Zhao, Y., Hou, G., Bowling, F. Z., Tobimatsu, Y., & Liu, C. (2023). Simultaneous suppression of lignin, tricin and wall-bound phenolic biosynthesis via expression of monolignol 4-O-methyltransferases in rice. Plant Biotechnology Journal, 1-17 https://dx.doi.org/10.1111/pbi.14186
  7. Sah, S. (2023). Physiological Functions of Phospholipid:Diacylglycerol Acyltransferases. Plant And Cell Physiology https://dx.doi.org/10.1093/pcp/pcad106
  8. Banerjee, A., Liu, Q., Shanklin, J., & Ertem, M. Z. (2023). Predicting Mössbauer Parameters of Nonheme Diiron Complexes with Density Functional Theory. Inorganic Chemistry, 62(29), 11402-11413 https://dx.doi.org/10.1021/acs.inorgchem.3c00969
  9. Zhang, J., Wang, X., Wang, H., Qiao, Z., Yao, T., Xie, M., Urbanowicz, B. R., Zeng, W., Jawdy, S., Gunter, L. E., Yang, X., Czarnecki, O., Regan, S., Séguin, A., Rottmann, W. H., Winkeler, K. A., Sykes, R., Lipzen, A., Daum, C., Barry, K., Lu, M., Tuskan, G.A., Muchero, W., & Chen, J. (2023). Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus. Plant Physiology https://dx.doi.org/10.1093/plphys/kiad377
  10. Schwender, J. (2023). Walking the 'design-build-test-learn' cycle: Flux analysis and genetic engineering reveal the pliability of plant central metabolism. New Phytologist, 239(5), 1539-1541 https://dx.doi.org/10.1111/nph.18967
  11. Pang, C., Chai, J., Zhu, P., Shanklin, J., & Liu, Q. (2023). Structural Mechanism of Intracellular Autoregulation of Zinc Uptake in ZIP transporters. Nature Communications, 14, Article 3404 https://dx.doi.org/10.1038/s41467-023-39010-6
  12. Pasaribu, B., Acosta, K., Aylward, A., Liang, Y., Abramson, B. W., Colt, K., Hartwick, N., Shanklin, J., Michael, T. P., & Lam, E. (2023). Genomics of turions from the Greater Duckweed reveal its pathways for dormancy and re-emergence strategy. New Phytologist, 239(1), 116-131 https://dx.doi.org/10.1111/nph.18941
  13. Díaz, J. F., Kuhlman, B. M., Edenhoffer, N., Evans, A. C., Martin, K. A., Guida, P., Rusek, A., Atala, A., Coleman, M. A., Wilson, P. F., Almeida-Porada, G., & Porada, C. D. (2023). Immediate effects of acute Mars mission equivalent doses of SEP and GCR radiation on the murine gastrointestinal system-protective effects of curcumin-loaded nanolipoprotein particles (cNLPs). Frontiers in Astronomy and Space Sciences, 10 https://dx.doi.org/10.3389/fspas.2023.1117811
  14. Yang, J. Y., Sooksa-Nguan, T., Kannan, B., Cano-Alfanar, S., Liu, H., Kent, A. D., Shanklin, J., Altpeter, F., & Howe, A. (2023). Microbiome differences in sugarcane and metabolically engineered oilcane accessions and their implications for bioenergy production. Biotechnol Biofuels, 16, Article 56 https://dx.doi.org/10.1186/s13068-023-02302-6
  15. Blanc-Betes, E., Gomez-Casanovas, N., Yang, W. H., Chandrasoma, J., Clark, T. J., DeLucia, E. H., Hyde, C. A., Kent, A. D., Pett-Ridge, J., Rabinowitz, J. D., Raglin, S. S., Schwender, J., Shen, Y., Van Allen, R., & Von Haden, A. C. (2023). Accelerating the development of a sustainable bioenergy portfolio through stable isotopes. GCB-Bioenergy, 15(7), 840-866 https://dx.doi.org/10.1111/gcbb.13056
  16. Yu, L., Shen, W., Fan, J., Sah, S. K., Mavraganis, I., Wang, L., Gao, P., Gao, J., Zheng, Q., Meesapyodsuk, D., Yang, H., Li, Q., Zou, J., & Xu, C. (2023). A chloroplast diacylglycerol lipase modulates glycerolipid pathway balance in Arabidopsis. The Plant Journal, 115(2), 335-350 https://dx.doi.org/10.1111/tpj.16228
  17. Chai, J., Guo, G., McSweeney, S., Shanklin, J., & Liu, Q. (2023). Structural Basis for Enzymatic Terminal C-H Bond Functionalization of Alkanes. Nature Structural & Molecular Biology, 30, 521-526 https://dx.doi.org/10.1038/s41594-023-00958-0
  18. Sanders, B. C., Pokhrel, S., Labbe, A., Mathews, I., Cooper, C. J., Davidson, R. B., Phillips, G., Weiss, K. L., Zhang, Q., O’Neill, H., Kaur, M., Schmidt, J., Reichard, W., Surendranathan, S., Parvathareddy, J., Phillips, L., Rainville, C., Sterner, D. E., Kumaran, D., et al. (2023). Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nature Communications, 14(1), Article 1733 https://dx.doi.org/10.1038/s41467-023-37254-w
  19. Zhao, J., Deng, X., Qian, J., Liu, T., Ju, M., Li, J., Yang, Q., Zhu, X., Li, W., Liu, C., Jin, Z., & Zhang, K. (2023). Arabidopsis ABCG14 forms a homodimeric transporter for multiple cytokinins and mediates long-distance transport of isopentenyladenine- type cytokinins. Plant Communications, 4(2), Article 100468 https://dx.doi.org/10.1016/j.xplc.2022.100468
  20. Karasawa, A., Liu, H., Quick, M., Hendrickson, W. A., & Liu, Q. (2023). Crystallographic Characterization of Sodium Ions in a Bacterial Leucine/Sodium Symporter. Crystals, 13(2), 183 https://dx.doi.org/10.3390/cryst13020183
  21. Zhai, Z., Blanford, J., Cai, Y., Sun, J., Liu, H., Shi, H. N., Schwender, J., & Shanklin, J. (2023). CYCLIN-DEPENDENT KINASE 8 positively regulates oil synthesis by activating WRINKLED1 transcription. New Phytologist, 238(2), 724-736 https://dx.doi.org/10.1111/nph.18764
  22. Zhao, X., Zhao, Y., Gou, M., & Liu, C (2023). Tissue-preferential recruitment of electron transfer chains for cytochrome P450-catalyzed phenolic biosynthesis. Science Advances, 9(2) https://dx.doi.org/10.1126/sciadv.ade4389
  23. Liu, D., Tang, D., Xie, M., Zhang, J., Zhai, L., Mao, J., Luo, C., Lipzen, A., Zhang, Y., Savage, E., Yuan, G., Guo, H., Tadesse, D., Hu, R., Jawdy, S., Cheng, H., Li, L., Yer, H., Clark, M. M., Sun, H., Shi, J., Budhathoki, R., Kumar, R., Kamuda,T., Li, Y., et al. (2023). Agave REVEILLE1 regulates the onset and release of seasonal dormancy in Populus. Plant Physiology, 191(3) https://dx.doi.org/10.1093/plphys/kiac588

2022

  1. Cai, Y., Yu, X., & Shanklin, J. (2022). A toolkit for plant lipid engineering: surveying the efficacies of lipogenic factors for accumulating specialty lipids. Frontiers In Plant Science, 13 https://dx.doi.org/10.3389/fpls.2022.1064176
  2. Liang, Y., Yu, X., Anaokar, S., Shi, H. N., Dahl, W., Cai, Y., Luo, G., Chai, J., Cai, Y., Mollá-Morales, A., Altpeter, F., Ernst, E., Schwender, J., Martienssen, R. A., & Shanklin, J. (2022). Engineering Triacylglycerol Accumulation in Duckweed (Lemna japonica). Plant Biotechnology Journal, 21(2), 317-330 https://dx.doi.org/10.1111/pbi.13943
  3. Karasawa, A., Andi, B., Fuchs, M. R., Shi, W., McSweeney, S., Hendrickson, W. A., & Liu, Q. (2022). Multi-crystal native-SAD phasing at 5 keV with a helium environment. Iucrj, 9(6), 768-777 https://dx.doi.org/10.1107/S205225252200971X
  4. Liu, C. (2022). Cytochrome b5: A versatile electron carrier and regulator for plant metabolism. Frontiers In Plant Science, 13 https://dx.doi.org/10.3389/fpls.2022.984174
  5. Liu, H., Zhu, P., Zhang, Q., Lam, E., & Liu, Q. (2022). Plant metacaspase: a case study of microcrystal structure determination and analysis. Methods in Enzymology, 676, 103-131 https://dx.doi.org/10.1016/bs.mie.2022.07.026
  6. Ebrahim, A., Riley, B. T., Kumaran, D., Andi, B., Fuchs, M. R., McSweeney, S., & Keedy, D. (2022). The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M-pro). Iucrj, 9(5), 682-694 https://dx.doi.org/10.1107/S2052252522007497
  7. Luo, G., Cao, V. D., Kannan, B., Liu, H., Shanklin, J., & Altpeter, F. (2022). Metabolic engineering of energycane to hyperaccumulate lipids in vegetative biomass. BMC Biotechnology, 22(1), Article 24 https://dx.doi.org/10.1186/s12896-022-00753-7
  8. Kaunitz, J. D., Mandelkern, M., & Fowler, J. S. (2022). It's Not What You Take Up, It's What You Keep: How Discoveries from Diverse Disciplines Directed the Development of the FDG PET/CT Scan. Digestive Diseases and Sciences, 67(10), 4620-4632 https://dx.doi.org/10.1007/s10620-022-07615-4
  9. Kuczynski, C., McCorkle, S., Keereetaweep, J., Shanklin, J., & Schwender, J. (2022). An Expanded Role for the Transcription Factor WRINKLED1 in the Biosynthesis of Triacylglycerols during Seed Development. Frontiers In Plant Science, 13 https://dx.doi.org/10.3389/fpls.2022.955589
  10. Gan, L., Park, K., Chai, J., Updike, E., Kim, H., Voshall, A., Behera, S., Yu, X., Cai, Y., Zhang, C., Wilson, M. A., Mower, J. P., Moriyama, E. N., Zhang, C., Kaewsuwan, S., Liu, Q., Shanklin, J., & Cahoon, E. B. (2022). Primary Classification: Biological Sciences Secondary Classification: Plant Biology Divergent Evolution of Extreme Production of Variant Plant Monounsaturated Fatty Acids. Proceedings of the National Academy of Sciences of the United States of America, 119(30) https://dx.doi.org/10.1073/pnas.2201160119
  11. Cai, Y., Zhai, Z., Blanford, J., Liu, H., Shi, H. N., Schwender, J., Xu, C., & Shanklin, J. (2022). Purple acid phosphatase2 stimulates a futile cycle of lipid synthesis and degradation and mitigates the negative growth effects of triacylglycerol accumulation in vegetative tissues. New Phytologist , 236(3), 1128-1139 https://dx.doi.org/10.1111/nph.18392
  12. Pasquini, M., Grosjean, N., Hixson, K., Nicora, C., Yee, E. F., Lipton, M., Blaby, I. K., Haley, J. D., & Blaby-Haas, C. E. (2022). Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase. Cells Reports, 39(7), Article 110834 https://dx.doi.org/10.1016/j.celrep.2022.110834
  13. Cesarino, I., Eudes, A., Urbanowicz, B. R., & Xie, M. (2022). Editorial: Phenylpropanoid Systems Biology and Biotechnology. Frontiers In Plant Science, 13 https://dx.doi.org/10.3389/fpls.2022.866164
  14. Brawley, S. (2022). Polar algae flaunt their zinc assets. Nature Ecology and Evolution, 6(7), 851-852 https://dx.doi.org/10.1038/s41559-022-01721-2
  15. Brawley, S. (2022). The Mosaic Landscape of Algal Metal Transport and Usage. Microbial Metabolism of Metals and Metalloids https://dx.doi.org/10.1007/978-3-030-97185-4
  16. Liu, W., Schoonen, M., Wang, T., McSweeney, S., & Liu, Q (2022). Cryo-EM Structure of Transmembrane AAA+ Protease FtsH in the ADP State. Communications Biology, 5(1) https://dx.doi.org/10.1038/s42003-022-03213-2
  17. Lian, R., Huang, B., Wang, L., Liu, Q., Lin, Y., & Ling, H. (2022). End-to-end orientation estimation from 2D cryo-EM 2 images. Acta Crystallographica Section D: Structural Biology, 78(2), 174-186 https://dx.doi.org/10.1107/s2059798321011761
  18. Schwechheimer, C., Schröder, P., & Blaby-Haas, C. E. (2022). Plant GATA factors: their biology, phylogeny, and phylogenomics. Annual Reviews in Plant Biology, 73(1), 123-148 https://dx.doi.org/10.1146/annurev-arplant-072221-092913
  19. Clark, T. J., & Schwender, J. (2022). Elucidation of triacylglycerol overproduction in the C4 bioenergy crop Sorghum bicolor by constraint-based analysis. Frontiers In Plant Science, 13, Article 787265 https://dx.doi.org/10.3389/fpls.2022.787265
  20. Paape, T., Heiniger, B., Domingo, M. S., Clear, M. R., Lucas, M. M., & Pueyo, J. J. (2022). Genome-Wide Association Study Reveals Complex Genetic Architecture of Cadmium and Mercury Accumulation and Tolerance Traits in Medicago truncatula. Frontiers in Plant Science , 12 https://dx.doi.org/10.3389/fpls.2021.806949
  21. Xu, C., Fan, J., & Suh, E. (2022). Links between autophagy and lipid droplet dynamics. Journal of Experimental Botany, 73(9), 2848-2858 https://dx.doi.org/10.1093/jxb/erac003

2021

  1. Bennett, P. V., Johnson, A. M., Ackerman, S. E., Chaudhary, P., Keszenman, D. J., & Wilson, P. F. (2021). Dose-Rate Effects of Protons and Light Ions for DNA Damage Induction, Survival and Transformation in Apparently Normal Primary Human Fibroblasts. Radiation Research, 197(3), 298-313 https://dx.doi.org/10.1667/rade-21-00138.1
  2. Zhao, Y., Yu, X., & Liu, C (2021). The inducible accumulation of cell wall-bound p-hydroxybenzoates is involved in the regulation of gravitropic response of poplar. Frontiers In Plant Science, 12, Article 755576 https://dx.doi.org/10.3389/fpls.2021.755576
  3. Bruni, R., Laguerre, A., Kaminska, A., McSweeney, S., Hendrickson, W. A., & Liu, Q. (2021). High-throughput Cell-free Screening of Eukaryotic Membrane Protein Expression. Protein Science, 31(3), 639-651 https://dx.doi.org/10.1002/pro.4259
  4. Guy, J. E., Cai, Y., Cai, Y., Whittle, E., Chai, J., Chai, J., Lindqvist, Y., Raugei, S., & Shanklin, J. (2021). Regioselectivity mechanism of the Thunbergia alata Δ6 2 -16:0-acyl carrier protein desaturase. Plant Physiology, 188(3), 1537-1549 https://dx.doi.org/10.1093/plphys/kiab577
  5. Lian, R., Huang, B., Wang, L., Liu, Q., Lin, Y., & Ling, H. (2021). End-to-end orientation estimation from 2D cryo-EM1images. Acta Crystallographica Section D: Structural Biology, 78(2), 174-186 https://dx.doi.org/10.1107/S2059798321011761
  6. Cai, Y. (2021). Sugar traffic jam: Impaired cellulose deposition in the phloem retards long-distance sucrose transport. Plant Cell, 33(10), 3187-3188 https://dx.doi.org/10.1093/plcell/koab195
  7. Chai, L., Zhu, P., Chai, J., Pang, C., Andi, B., McSweeney, S., Shanklin, J., & Liu, Q. (2021). AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement. Crystals, 11(10), 1227 https://dx.doi.org/10.3390/cryst11101227
  8. Ng, K. K. S., Kobayashi, M. J., Fawcett, J. A., Hatakeyama, M., Paape, T., Ng, C. H., Ang, C. C., Tnah, L. H., Lee, C. T., Nishiyama, T., Sese, J., O’Brien, M. J., Copetti, D., Isa, M. N. M., Ong, R. C., Putra, M. S. K., Siregar, I. Z., Indrioko, S., Kosugi, Y. et al. (2021). The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests. Communications Biology, 4(1), Article 1166 https://dx.doi.org/10.1038/s42003-021-02682-1
  9. Öztürk, Y., Blaby-Haas, C. E., Daum, N., Andrei, A., Rauch, J., Daldal, F., & Koch, H. (2021). Maturation of Rhodobacter capsulatus Multicopper Oxidase CutO Depends on the CopA Copper Efflux Pathway and Requires the cutF Product. Frontiers in Microbiology, 12 https://dx.doi.org/10.3389/fmicb.2021.720644
  10. Yu, L., Fan, J., Zhou, C., & Xu, C. (2021). Sterols are required for the coordinated assembly of lipid droplets in developing seeds. Nature Communications , 12(1) https://dx.doi.org/10.1038/s41467-021-25908-6
  11. Halstead-Nussloch, G., Tanaka, T., Copetti, D., Paape, T., Kobayashi, F., Hatakeyama, M., Kanamori, H., Wu, J., Mascher, M., Kawaura, K., Shimizu, K., & Handa, H. (2021). Multiple Wheat Genomes Reveal Novel Gli-2 Sublocus Location and Variation of Celiac Disease Epitopes in Duplicated α-Gliadin Genes. Frontiers in Plant Science, 12 https://dx.doi.org/10.3389/fpls.2021.715985
  12. Wang, W., Liu, Q., Li, Q., & Hendrickson, W. A. (2021). Conformational Equilibria in Allosteric Control of Hsp70 Chaperones. Molecular Cell, 81(19), 3919-3933 https://dx.doi.org/10.1016/j.molcel.2021.07.039
  13. Johnson, A. M., Bennett, P. V., Sanidad, K. Z., Hoang, A. N., Jardine, J., Keszenman, D. J., & Wilson, P. F. (2021). Evaluation of Histone Deacetylase Inhibitors as Radiosensitizers for Proton and Light Ion Radiotherapy. Frontiers in Oncology, 11, Article 735940 https://dx.doi.org/10.3389/fonc.2021.735940
  14. Singh, R., Liu, H., Shanklin, J., & Singh, V. (2021). Hydrothermal Pretreatment for Valorization of Genetically Engineered Bioenergy Crop for Lipid and Cellulosic Sugar Recovery. Bioresource Technology, 341, Article 125817 https://dx.doi.org/10.1016/j.biortech.2021.125817
  15. Zhao, Y., Yu, X., Lam, P. Y., Zhang, K., Tobimatsu, Y., & Liu, C. (2021). Monolignol acyltransferase for lignin p-hydroxybenzoylation in Populus. Nature Plants, 7(9), 1288-1300 https://dx.doi.org/10.1038/s41477-021-00975-1
  16. Zhao, J., Ding, B., Zhu, E., Deng, X., Zhang, M., Zhang, P., Wang, L., Dai, Y., Xiao, S., Zhang, C., Liu, C., & Zhang, K. (2021). Phloem unloading via the apoplastic pathway is essential for shoot distribution of root-synthesized cytokinins. Plant Physiology, 186(4), 2111-2123 https://dx.doi.org/10.1093/plphys/kiab188
  17. Yao, T., Feng, K., Xie, M., Barros, J., Tschaplinski, T. J., Tuskan, G. A., Muchero, W., & Chen, J. (2021). Phylogenetic occurrence of the phenylpropanoid pathway and lignin biosynthesis in plants. Frontiers in Plant Science, 12 https://dx.doi.org/10.3389/fpls.2021.704697
  18. Anaokar, S., Liu, H., Keereetaweep, J., Zhai, Z., & Shanklin, J. (2021). Mobilizing vacuolar sugar increases vegetative triacylglycerol accumulation. Frontiers in Plant Science, 12 https://dx.doi.org/10.3389/fpls.2021.708902
  19. Cai, Y. (2021). Leading the way out: How a plant myosin facilitates vesicle tethering during exocytosis. Plant Cell, 33(7), 2104-2105 https://dx.doi.org/10.1093/plcell/koab111
  20. Wang, S., Minevich, B., Liu, J., Zhang, H., Nykypanchuk, D., Byrnes, J., Liu, W., Bershadsky, L., Liu, Q., Wang, T., Ren, G., & Gang, O. (2021). Designed and biologically active protein lattices. Nature Communications, 12(1), Article 3702 https://dx.doi.org/10.1038/s41467-021-23966-4
  21. Chai, J., Cai, Y., Pang, C., Wang, L., McSweeney, S., Shanklin, J., & Liu, Q. (2021). Structural Basis for SARS-CoV-2 Envelope Protein Recognition of Human Cell Junction Protein PALS1. Nature Communications, 12(1) https://dx.doi.org/10.1038/s41467-021-23533-x
  22. Voshall, A., Behera, S., Li, X., Yu, X., Kapil, K., Deogun, J. S., Shanklin, J., Cahoon, E. B., & Moriyama, E. N. (2021). A consensus-based ensemble approach to improve transcriptome assembly. BioRxiv https://dx.doi.org/10.1101/2020.06.08.139964
  23. Joshi, A., Datta, S., Mertz, J., Soni, N., Sivertz, M., Rusek, A., Pearson, C. F., & Jardine, J. (2021). In-situ Proton Radiation Testing of 2.4 Micron Wavelength Extended InGaAs Photodiodes at Dry Ice and Room Temperatures. Proceedings of SPIE, 11744, Article 11740C https://dx.doi.org/10.1117/12.2587103
  24. Yu, L., Zhou, C., Fan, J., Shanklin, J., & Xu, C. (2021). Mechanisms and functions of membrane lipid remodeling in plants. The Plant Journal, 107(1), 37-53 https://dx.doi.org/10.1111/tpj.15273
  25. Cai, Y. (2021). Knocksideways in Plants: An Inducible System for In Planta Visualization of Protein Interactions. Plant Cell, 33(4), 1085-1086 https://dx.doi.org/10.1093/plcell/koab002
  26. Zhai, Z., Keereetaweep, J., Liu, H., Feil, R., Lunn, J. E., & Shanklin, J. (2021). Expression of a Bacterial Trehalose-6-phosphate Synthase otsA Increases Oil Accumulation in Plant Seeds and Vegetative Tissues. Frontiers In Plant Science, 12, Article 656962 https://dx.doi.org/10.3389/fpls.2021.656962
  27. Zhai, Z., Liu, H., & Shanklin, J. (2021). Ectopic expression of OLEOSIN 1 and inactivation of GBSS1 have a synergistic effect on oil accumulation in plant leaves. Plants, 10(3), 513 https://dx.doi.org/10.3390/plants10030513
  28. Zhai, Z., Keereetaweep, J., Liu, H., Xu, C., & Shanklin, J. (2021). The role of sugar signaling in regulating plant fatty acid synthesis. Frontiers in Plant Science, 12 https://dx.doi.org/10.3389/fpls.2021.643843
  29. Yu, L., Zhou, C., Fan, J., & Xu, C. (2021). Using 14C-acetate Pulse-chase Labeling to Study Fatty Acid and Glycerolipid Metabolism in Plant Leaves. Bio-Protocol, 11(3) https://dx.doi.org/10.21769/bioprotoc.3900
  30. Brawley, S. (2021). Cyanobacteria provide a new paradigm in the regulation of cofactor dependence. Proceedings of the National Academy of Sciences of the United States of America, 118(7) https://dx.doi.org/10.1073/pnas.2100281118
  31. Arregui, G., Hipólito, P., Pallol, B., Lara-Dampier, V., García-Rodríguez, D., Varela, H. P., Zaniani, P. T., Balomenos, D., Paape, T., De La Peña, T. C., Lucas, M. M., & Pueyo, J. J. (2021). Mercury-Tolerant Ensifer medicae Strains Display High Mercuric Reductase Activity and a Protective Effect on Nitrogen Fixation in Medicago truncatula Nodules Under Mercury Stress. Frontiers in Plant Science, 11 https://dx.doi.org/10.3389/fpls.2020.560768
  32. Gallaher, S. D., Craig, R. J., Ganesan, I., Purvine, S. O., McCorkle, S., Grimwood, J., Strenkert, D., Davidi, L., Roth, M., Jeffers, T. L., Lipton, M., Niyogi, K., Schmutz, J., Theg, S. M., Blaby-Haas, C. E., & Merchant, S. (2021). Widespread polycistronic gene expression in green algae. Pnas, 118(7) https://dx.doi.org/10.1073/pnas.2017714118

2020

  1. Douglas, G. L., Cooper, M., Wu, H., Gaza, R., Guida, P., & Young, M. (2020). Impact of Galactic Cosmic Ray Simulation on Nutritional Content of Foods. Life Sciences in Space Research, 28, 22-25 https://dx.doi.org/10.1016/j.lssr.2020.12.001
  2. Takemaru, L., Guo, G., Zhu, P., Hendrickson, W. A., McSweeney, S., & Liu, Q. (2020). PyMDA: microcrystal data assembly using Python. Journal of Applied Crystallography, 53(1), 277-281 https://dx.doi.org/10.1107/S160057671901673X
  3. Wang, B., Zhao, X., Zhao, Y., Shanklin, J., Zhao, Q., & Liu, C. (2020). Arabidopsis SnRK1 negatively regulates phenylpropanoid metabolism via Kelch domain-containing F-box proteins. New Phytologist, 229(6), 3345-3359 https://dx.doi.org/10.1111/nph.17121
  4. Li, D., Ni, R., Wang, P., Zhang, X., Wang, P., Zhu, T., Sun, C., Liu, C., Lou, H., & Cheng, A. (2020). Molecular basis for chemical 13 evolution of flavones to flavonols and anthocyanins. Plant Physiology, 184(4), 1731-1743 https://dx.doi.org/10.1104/pp.20.01185
  5. Yu, X., Cai, Y., Keereetaweep, J., Wei, K., Chai, J., Deng, E., Liu, H., & Shanklin, J. (2020). Biotin Attachment Domain-Containing Proteins mediate hydroxy fatty acid-dependent inhibition of Acetyl CoA Carboxylase. Plant Physiology, 185(3), 892-901 https://dx.doi.org/10.1093/plphys/kiaa109
  6. Yu, L., Fan, J., Zhou, C., & Xu, C. (2020). Effect of Light Intensity on Chloroplast Lipid Biosynthesis in Arabidopsis. Plant Physiology, 185(1) https://dx.doi.org/10.1093/plphys/kiaa013
  7. Xu, C., Fan, J., & Shanklin, J. (2020). Metabolic and Functional Connections between Cytoplasmic and Chloroplast Triacylglycerol Storage. Progress in Lipid Research, 80, Article 101069 https://dx.doi.org/10.1016/j.plipres.2020.101069
  8. Foflonker, F., & Blaby-Haas, C. E. (2020). Co-locality to co-functionality: Eukaryotic gene neighborhoods as a resource for function. Molecular Biology and Evolution, 38(2), 650-662 https://dx.doi.org/10.1093/molbev/msaa221
  9. Yan, C., Cannon, A. E., Watkins, J. M., Keereetaweep, J., Khan, B. R., Jones, A. M., Blancaflor, E. B., Azad, R. K., & Chapman, K. D. (2020). An Intact G-Protein Complex is Required for the N-Linolenoylethanolamine Require Intact G-Protein Complexes. Plant Physiology, 184(1), 459-477 https://dx.doi.org/10.1104/pp.19.01552
  10. Yan, C., Cannon, A. E., Watkins, J. M., Keereetaweep, J., Khan, B. R., Jones, A. M., Blancaflor, E. B., Azad, R. K., & Chapman, K. D. (2020). Seedling Chloroplast Responses Induced by N-Linolenoylethanolamine Require Intact G-Protein Complexes. Plant Physiology, 184(1), 459-477 https://dx.doi.org/10.1104/pp.19.01552
  11. Xie, M., Zhang, J., Yao, T., Bryan, A. C., Pu, Y., Labbé, J., Pelletier, D. A., Engle, N. L., Morrell-Falvey, J. L., Schmutz, J., Ragauskas, A. J., Tschaplinski, T. J., Chen, F., Tuskan, G. A., Muchero, W., & Chen, J. (2020). Arabidopsis C-terminal binding protein ANGUSTIFOLIA. New Phytologist, 228(5), 1627-1639 https://dx.doi.org/10.1111/nph.16826
  12. Merchant, S., Schmollinger, S., Strenkert, D., Moseley, J. L., & Blaby-Haas, C. E. (2020). From economy to luxury copper homeostasis in Chlamydomonas and other algae. Biochimica et Biophysica Acta - Molecular Cell Research, 1867(11) https://dx.doi.org/10.1016/j.bbamcr.2020.118822
  13. Grosjean, N., & Blaby-Haas, C. E. (2020). Leveraging computational genomics to understand the molecular basis of metal homeostasis. New Phytologist, 228(5), 1472-1489 https://dx.doi.org/10.1111/nph.16820
  14. Yu, X., & Shanklin, J. (2020). Solving a furan fatty acid biosynthesis puzzle. Journal of Biological Chemistry, 295(29), 9802-9803 https://dx.doi.org/10.1074/jbc.h120.014701
  15. McSweeney, D. M., McSweeney, S., & Liu, Q. (2020). A Self-Supervised Workflow for Particle Picking in Cryo-EM. IUCrJ, 7(4), 719-727 https://dx.doi.org/10.1107/S2052252520007241
  16. Zhu, P., Yu, X., Wang, C., Zhang, Q., Liu, W., McSweeney, S., Shanklin, J., Lam, E., & Liu, Q. (2020). Structural Basis for Ca2+-Dependent Activation of a Plant Metacaspase. Nature Communications, 11(1) https://dx.doi.org/10.1038/s41467-020-15830-8
  17. Cai, Y., Yu, X., Chai, J., Liu, C., & Shanklin, J. (2020). A conserved evolutionary mechanism permits Δ9 desaturation of very long chain fatty acyl lipids. Journal of Biological Chemistry, 295(32), 11337-11345 https://dx.doi.org/10.1074/jbc.RA120.014258
  18. Simonsen, L. C., Slaba, T. C., Guida, P., & Rusek, A. (2020). NASA's first ground-based Galactic Cosmic Ray Simulator: Enabling a new era in space radiobiology research. PLOS Biology, 18(5) https://dx.doi.org/10.1371/journal.pbio.3000669
  19. Parajuli, S., Kannan, B., Karan, R., Sanahuja, G., Liu, H., Garcia-Ruiz, E., Kumar, D., Singh, V., Zhao, H., Long, S. P., Shanklin, J., & Altpeter, F. (2020). Towards oilcane: engineering hyperaccumulation of triacylglycerol into sugarcane stems. Global Change Biology, 12(7), 476-490 https://dx.doi.org/10.1111/gcbb.12684
  20. Rolletschek, H., Schwender, J., König, C., Chapman, K. D., Romsdahl, T. B., Lorenz, C., Braun, H., Denolf, P., Van Audenhove, K., Munz, E., Heinzel, N., Ortleb, S., Rutten, T., McCorkle, S., Borysyuk, T., Guendel, A., Shi, H. N., Auwermeulen, M. V., Bourot, S., & Borisjuk, L. (2020). Cellular Plasticity in Response to Suppression of Storage Proteins in the Brassica napus Embryo. Plant Cell, 32(7), 2383-2401 https://dx.doi.org/10.1105/tpc.19.00879
  21. Royer, J. C., Shanklin, J., Balch-Kenney, N., Mayorga, M. E., Houston, P., De Jong, R. M., McMahon, J., Laprade, L., Blomquist, P. A., Berry, T. D., Cai, Y., LoBuglio, K. F., Trueheart, J., & Chevreux, B. (2020). Rhodoxanthin synthase from honeysuckle; a membrane diiron enzyme catalyzes the 1 multi-step conversation of β-carotene to rhodoxanthin. Science Advances, 6(17) https://dx.doi.org/10.1126/sciadv.aay9226
  22. Selamoglu, N., Onder, O., Ozturk, Y., Khalfaoui-Hassani, B., Blaby-Haas, C. E., Garcia, B. A., Koch, H. G., & Daldal, F. (2020). Comparative Differential Cuproproteomes of Rhodobacter capsulatus Reveal Novel Copper. Metallomics, 12(4), 572-591 https://dx.doi.org/10.1039/C9MT00314B
  23. Clark, T. J., Guo, L., Morgan, J. A., & Schwender, J. (2020). Modeling Plant Metabolism: From Network Reconstruction to Mechanistic Models. Annual Review of Plant Biology, 71(1), 303-326 https://dx.doi.org/10.1146/annurev-arplant-050718-100221

2019

  1. Nguyen, N. D., Blaby, I. K., & Wang, D. (2019). ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks. BMC Genomics, 20, Article 1003 https://dx.doi.org/10.1186/s12864-019-6329-2
  2. Takemaru, L., Guo, G., Zhu, P., Hendrickson, W. A., McSweeney, S., & Liu, Q. (2019). PyMDA: Microcrystal Data Assembly Using Python. Journal of Applied Crystallography, 53(1), 277-281 https://dx.doi.org/10.1107/S160057671901673X
  3. Whittle, E., Cai, Y., Keereetaweep, J., Chai, J., Buist, P. H., & Shanklin, J. (2019). Castor Stearoyl-ACP Desaturase Can Synthesize a Vicinal Diol by Dioxygenase Chemistry. Plant Physiology, 182(2), 730-738 https://dx.doi.org/10.1104/pp.19.01111
  4. Marckmann, D., Trasnea, P., Schimpf, J., Winterstein, C., Andrei, A., Schmollinger, S., Blaby-Haas, C. E., Friedrich, T., Daldal, F., & Koch, H. (2019). The cbb3-type cytochrome oxidase assembly factor CcoG is a widely-distributed novel cupric reductase. Pnas, 116(42), 21166-21175 https://dx.doi.org/10.1073/pnas.1913803116
  5. Andi, B., Soares, A. S., Shi, W., Fuchs, M. R., McSweeney, S., & Liu, Q. (2019). Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant. Acta Crystallographica Section F, 75(9), 616-624 https://dx.doi.org/10.1107/s2053230x19011488
  6. Blaby-Haas, C. E., & Merchant, S. (2019). Comparative and Functional Algal Genomics. Annual Review of Plant Biology, 70(1), 605-638 https://dx.doi.org/10.1146/annurev-arplant-050718-095841
  7. Fan, J., Zhou, C., Yu, L., Li, P., Shanklin, J., & Xu, C. (2019). Diversion of Carbon Flux from Sugars to Lipids Improves the Growth of an Arabidopsis Starchless Mutant. Plants, 8(7), 229 https://dx.doi.org/10.3390/plants8070229
  8. Fan, J., Yu, L., & Xu, C. (2019). Dual Role for Autophagy in Lipid Metabolism in Arabidopsis. Plant Cell, 31(7), 1598-1613 https://dx.doi.org/10.1105/tpc.19.00170
  9. Liu, H., Zhai, Z., Kuczynski, C. A., Keereetaweep, J., Schwender, J., & Shanklin, J. (2019). BIOTIN ATTACHMENT DOMAIN-CONTAINING proteins, inhibitors of ACCase, are regulated by WRINKLED1. Plant Physiology, 181(1), 55-62 https://dx.doi.org/10.1104/pp.19.00587
  10. Liu, C., Zhao, Y., & Zhang, K. (2019). Cytokinin Transporters: Multisite players in cytokinin homeostasis and signal distribution. Frontiers In Plant Science , 10, Article 693 https://dx.doi.org/10.3389/fpls.2019.00693
  11. Hughes, S., Wang, F., Wang, S., Kreutzberger, M. A., Osinski, T., Orlova, A., Wall, J. S., Zuo, X., Egelman, E. H., & Conticello, V. P. (2019). Ambidextrous Helical Nanotubes from Self-Assembly of Designed Helical Hairpin Motifs. Proceedings of the National Academy of Sciences, 116(29), 14456-14464 https://dx.doi.org/10.1073/pnas.1903910116
  12. Gou, M., Yang, X., Zhao, Y., Ran, X., Song, Y., & Liu, C. (2019). Cytochrome b5 is an Obligate Electron Shuttle Protein for Syringyl Lignin Biosynthesis in Arabidopsis. The Plant Cell, 31(6), 1344-1366 https://dx.doi.org/10.1105/tpc.18.00778
  13. Tsui, H. S., Pham, N. V., Amer, B. R., Bradley, M. C., Gosschalk, J. E., Gallagher-Jones, M., Ibarra, H., Clubb, R. T., Blaby-Haas, C. E., & Clarke, C. F. (2019). Human COQ10A and COQ10B are distinct lipid-binding START domain proteins required for coenzyme Q function. Journal of Lipid Research, 60(7), 1293-1310 https://dx.doi.org/10.1194/jlr.M093534
  14. Yu, X., Cai, Y., Chai, J., Schwender, J., & Shanklin, J. (2019). Expression of a Lychee PDCT with E. coli CPS Enhances Cyclopropane Fatty Acid in Camelina Seeds. Plant Physiology, 180(3), 1351-1361 https://dx.doi.org/10.1104/pp.19.00396
  15. Guo, G., Zhu, P., Fuchs, M. R., Shi, W., Andi, B., Gao, Y., Hendrickson, W. A., McSweeney, S., & Liu, Q. (2019). Synchrotron Microcrystal Native-SAD Phasing at a Low Energy. IUCrJ, 6(4), 532-542 https://dx.doi.org/10.1107/s2052252519004536
  16. Guo, G., Xu, M., Chang, Y., Luyten, T., Seitaj, B., Liu, W., Zhu, P., Bultynck, G., Shi, L., Quick, M., & Liu, Q. (2019). Ion and pH Sensitivity of a TMBIM Ca2+ Channel. Structure, 27(6), 1013-1021 https://dx.doi.org/10.1016/j.str.2019.03.003
  17. Wang, X. H., Su, M., Gao, F., Xie, W., Zeng, Y., Li, D. L., Liu, X. L., Zhao, H., Li, Q., Li, F., Li, Q., Clarke, O. B., Lam, S. M., Shui, G., Hendrickson, W. A., & Chen, Y. H. (2019). Structural basis for activity of TRIC counter-ion channels in calcium release. Pnas, 116(10), 4238-4243 https://dx.doi.org/10.1073/pnas.1817271116
  18. Roth, M., Gallaher, S. D., Westcott, D. J., Iwai, M., Louie, K., Mueller, M., Walter, A., Foflonker, F., Bowen, B. P., Ataii, N. N., Song, J., Chen, J., Blaby-Haas, C. E., Larabell, C. A., Auer, M., Northen, T. R., Merchant, S., & Niyogi, K. (2019). Regulation of Oxygenic Photosynthesis during Trophic Transitions in the Green Alga Chromochloris zonfingiensis. Plant Cell, 31(3), 579-601 https://dx.doi.org/10.1105/tpc.18.00742
  19. Zhang, Y., Blaby-Haas, C. E., Steimle, S., Verissimo, A. F., García-Angulo, V. A., Koch, H., Daldal, F., & Khalfaoui-Hassani, B. (2019). Cu Transport by the Extended Family of CcoA-like Transporters (CalT) in Proteobacteria. Scientific Reports, 9(1), Article 1208 https://dx.doi.org/10.1038/s41598-018-37988-4
  20. Yu, L., Fan, J., & Xu, C. (2019). Peroxisomal Fatty Acid β-oxidation negatively impacts plant survival under salt stress. Plant Signaling & Behavior, 14(2), Article 1561121 https://dx.doi.org/10.1080/15592324.2018.1561121
  21. Sturtevant, D., Romsdahl, T. B., Yu, X., Burks, D., Azad, R. K., Shanklin, J., & Chapman, K. D. (2019). Tissue-specific differences in metabolites and transcripts contribute to the heterogeneity of ricinoleic acid accumulation in Ricinus communis L. (castor) seeds. Metabolomics, 15(1), Article 6 https://dx.doi.org/10.1007/s11306-018-1464-3

2018

  1. Cai, Y., Yu, X., Li, Q., Liu, C., & Shanklin, J. (2018). Two Clusters of Residues Contribute to the Activity and Substrate Specificity of Fm1, a Bifunctional Oleate and Linoleate Desaturase of Fungal Origin. Journal of Biological Chemistry, 293(51), 19844-19853 https://dx.doi.org/10.1074/jbc.RA118.005972
  2. Luxmi, R., Blaby-Haas, C. E., Kumar, D., Rauniyar, N., King, S. M., Mains, R. E., & Eipper, B. A. (2018). Proteases Shape the Chlamydomonas Secretome: Comparison to Classical Neuropeptide Processing Machinery. Proteomes, 64(4), 36 https://dx.doi.org/10.3390/proteomes6040036
  3. Zhai, Z., Keereetaweep, J., Liu, H., Feil, R., Lunn, J. E., & Shanklin, J. (2018). Trehalose 6-phosphate positively regulates fatty acid synthesis by stabilizing WRINKLED1. Plant Cell, 30(10), 2616-2627 https://dx.doi.org/10.1105/tpc.18.00521
  4. Schluter, U. & Schwender, J. (2018). The role of alanine and aspartate aminotransferases in C4 photosynthesis. Plant Biology https://dx.doi.org/10.1111/plb.12904
  5. Yu, L., Fan, J., Yan, C., & Xu, C. (2018). Starch Deficiency Enhances Lipid Synthesis and Turnover in Arabidopsis Leaves. Plant Physiology, 178(1), 118-129 https://dx.doi.org/10.1104/pp.18.00539
  6. Studier, W. (2018). T7 Expression Systems for Inducible Production of Proteins from Cloned Genes in E. coli. Current Protocols in Molecular Biology, 124(1) https://dx.doi.org/10.1002/cpmb.63
  7. Schlüter, U., Bräutigam, A., Droz, J., Schwender, J., & Weber, A. P. (2018). The role of alanine and aspartate aminotransferases in C4 photosynthesis. Plant Biology, 21(S1), 64-76 https://dx.doi.org/10.1111/plb.12904
  8. Samanovic, M. I., Hsu, H., Jones, M. B., Jones, V., McNeil, M., Becker, S. H., Jordan, A., Strnad, M., Xu, C., Jackson, M., H, L., & Darwin, K. H. (2018). Cytokinin Signaling in Mycobacterium Tuberculosis. Mbio, 9(3), Article e00989-18 https://dx.doi.org/10.1128/mBio.00989-18
  9. Sanghai, Z. A., Liu, Q., Clarke, O. B., Dufrisne, M. B., Wiriyasermkul, P., Giese, M., Leal-Pinto, E., Kloss, B., Tabuso, S., Love, J., Punta, M., Banerjee, S., Rajashankar, K. R., Rost, B., Logothetis, D. E., Quick, M., Hendrickson, W. A., & Mancia, F. (2018). Structure-based analysis of CysZ-mediated 1 cellular uptake of sulfate. eLIFE, 7 https://dx.doi.org/10.7554/eLife.27829
  10. Xu, Y., Cankaya, A. S., Hoque, R., Lee, S. J., Shea, C., Kersting, L., Schueller, M., Fowler, J. S., Szalda, D. J., Alexoff, D., Riehl, B., Gleede, T., Ferrieri, R. A., & Qu, W. (2018). Synthesis of L-[4-C-11]Asparagine by Ring-Opening Nucleophilic C-11-Cyanation Reaction of a Chiral Cyclic Sulfamidate Precursor. Chemistry - A European Journal, 24(26) https://dx.doi.org/10.1002/chem.201801029
  11. Gou, M., Xiu-Zhi, R., Martin, D. W., & Liu, C. (2018). The scaffold proteins of lignin biosynthetic cytochrome P450 enzymes. Natural Plants, 4(5), 299-310 https://dx.doi.org/10.1038/s41477-018-0142-9
  12. Guo, G., Fuchs, M. R., Shi, W., Skinner, J. M., Berman, E., Ogata, C. M., Hendrickson, W. A., McSweeney, S., & Liu, Q. (2018). Sample Manipulation and Data Assembly for Robust Microcrystal Synchrotron Crystallography. IUCrJ, 5(3), 238-243 https://dx.doi.org/10.1107/S2052252518005389
  13. Keereetaweep, J., Liu, H., Zhai, Z., & Shanklin, J. (2018). Biotin Attachment Domain-Containing Proteins Irreversibly Inhibit Acetyl CoA Carboxylase. Plant Physiology, 177(1), 208-215 https://dx.doi.org/10.1104/pp.18.00216
  14. Almeida-Porada, G., Rodman, C., Kuhlman, B. M., Brudvik, E., Moon, J. H., George, S., Guida, P., Sajuthi, S., Langefeld, C. D., Walker, S. J., Wilson, P. F., & Porada, C. D. (2018). Exposure of the Bone Marrow Microenvironment to Simulated Solar and Galactic Cosmic Radiation Induces Biological Bystander Effects on Human Hematopoiesis. Stem Cells and Development, 27(18), 1237-1256 https://dx.doi.org/10.1089/scd.2018.0005
  15. Vieni, C., McGillick, B. E., Kumaran, D., Eswaramoorthy, S., Kandavelu, P., & Swaminathan, S. (2018). Structure Based Discovery of Pan Active Botulinum Neurotoxin Inhibitors. Journal of Infectious Diseases and Therapy, 06(01) https://dx.doi.org/10.4172/2332-0877.1000351
  16. Khalfaoui-Hassani, B., Wu, H., Blaby-Haas, C. E., Zhang, Y., Sandri, F., Verissimo, A. F., Koch, H., & Daldal, F. (2018). Widespread Distribution and Functional Specificity of the Copper Importer CcoA: Distinct Cu Uptake Routes for Bacterial Cytochrome c Oxidases. mBio, 9(1) https://dx.doi.org/10.1128/mBio.00065-18
  17. Brownstein, J., Wisdom, A. J., Castle, K. D., Mowery, Y. M., Guida, P., Lee, C., Tommasino, F., La Tessa, C., Scifoni, E., Gao, J., Luo, L., Da Silva Campos, L., Ma, Y., Williams, N., Jung, S., Durante, M., & Kirsch, D. G. (2018). Characterizing The Potency and Impact Of Carbon Ion Therapy in a Primary Mouse Model of Soft Tissue Sarcoma. Molecular Cancer Therapeutics, 17(4), 858-868 https://dx.doi.org/10.1158/1535-7163.MCT-17-0965

2017

  1. Cheng, A., Zhang, X., Han, X., Zhang, Y., Gao, S., Liu, C., & Lou, H. (2017). Identification of Chalcone Isomerase in the Basal Land Plants Reveals an Ancient Evolution of Enzymatic Cyclization Activity for Synthesis of Flavonoids. New Phytologist, 217(2), 909-924 https://dx.doi.org/10.1111/nph.14852
  2. Zhang, Y., Zhao, L., Zhao, J., Li, Y., Wang, J., Guo, R., Gan, S., Liu, C., & Zhang, K. (2017). S5H/DMR6 Encodes a Salicylic Acid 5-Hydroxylase That Fine-Tunes Salicylic Acid Homeostasis. The Plant Physiology, 175(3), 1082-1093 https://dx.doi.org/10.1104/pp.17.00695
  3. Blaby-Haas, C. E., & Merchant, S. (2017). Regulating Cellular Trace Metal Economy in Algae. Current Opinion in Plant Biology, 39, 88-96 https://dx.doi.org/10.1016/j.pbi.2017.06.005
  4. Yu, X., Cahoon, R. E., Horn, P. J., Shi, H. N., Prakash, R. R., Cai, Y., Hearney, M., Chapman, K. D., Cahoon, E. B., Schwender, J., & Shanklin, J. (2017). Identification of bottlenecks in the accumulation of cyclic fatty acids in camelina seed oil. Plant Biotechnology Journal, 16(4), 926-938 https://dx.doi.org/10.1111/pbi.12839
  5. Sutherland, J. (2017). Measuring Fluorescence Polarization with a Dichrometer. Anal Biochem, 532, 9-11 https://dx.doi.org/10.1016/j.ab.2017.04.001
  6. Zhai, Z., Liu, H., Xu, C., & Shanklin, J. (2017). Sugar Potentiation of Fatty Acid and Triacylglycerol Accumulation. Plant Physiology, 175(2), 696-707 https://dx.doi.org/10.1104/pp.17.00828
  7. Brawley, S. H., Blouin, N. A., Ficko-Blean, E., Wheeler, G., Lohr, M., Goodson, H. V., Jenkins, J., Blaby-Haas, C. E., Helliwell, K. E., Chan, C. X., Marriage, T. N., Bhattacharya, D., Klein, A. S., Badis, Y., Brodie, J., Cao, Y., Collén, J., Dittami, S. M., Gachon, C. M. M., . et al. (2017). Thriving in a tough environment: Insights into the red algae from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Pnas, 114(31) https://dx.doi.org/10.1073/pnas.170308811
  8. Zinke, M., Fricke, P., Samson, C., Hwang, S., Wall, J. S., Lange, A., Zinn-Justin, S., & Lange, A. (2017). Bacteriophage Tail Tube Assembly Studied by Proton-Detected 4D Solid-State NMR. Angewandte Chemie International Edition, 56(32), 9497-9501 https://dx.doi.org/10.1002/anie.201706060
  9. Fan, J., Yu, L., & Xu, C. (2017). A Central Role for Triacylglycerol in Membrane Lipid Breakdown, Fatty Acid ?-Oxidation and Plant Survival under Extended Darkness. Plant Physiology, 174(3), 1517-1530 https://dx.doi.org/10.1104/pp.17.00653
  10. Liu, Q. & Liu, Q. (2017). TMBIM-Mediated Ca2+ Homeostasis and Cell Death. Biochimica Et Biophysica Acta-Molecular Cell Research, 1864(6), 850-857 https://dx.doi.org/10.1016/j.bbamcr.2016.12.023
  11. Zhang, X., Abrahan, C. E., Colquhoun, T. A., & Liu, C. (2017). A Proteolytic Regulator Controlling Chalcone Synthase Stability and Flavonoid Biosynthesis in Arabidopsis. The Plant Cell, 29(5), 1157-1174 https://dx.doi.org/10.1105/tpc.16.00855
  12. Sutherland, J. (2017). Linear dichroism of DNA: characterization of the orientation distribution function caused by hydrodynamic shear. Anal Biochem, 523, 24-31 https://dx.doi.org/10.1016/j.ab.2017.01.016
  13. Blaby, I. K., & Blaby-Haas, C. E. (2017). Genomics and functional genomics in Chlamydomonas reinhardtii. Microbiology Monographs, 1-26 https://dx.doi.org/10.1007/978-3-319-66365-4_1
  14. Zhai, Z., Liu, H., & Shanklin, J. (2017). Phosphorylation of WRINKLED1 by KIN10 Results in its Proteasomal Degradation; Providing a Link Between Energy Homeostasis and Lipid Synthesis. Plant Cell, 29(4), 871-889 https://dx.doi.org/10.1105/tpc.17.00019
  15. Blaby, I. K., & Blaby-Haas, C. E. (2017). Gene expression analysis by arylsulfatase assays in the green alga Chlamydomonas reinhardtii. Molecular Biology, 149-161 https://dx.doi.org/10.1007/978-1-4939-7724-6_11

2016

  1. Magnotti, E. L., Hughes, S., Dillard, R. S., Wang, S., Hough, L., Karumbamkandathil, A., Lian, T., Wall, J. S., Zuo, X., Wright, E., & Conticello, V. P. (2016). Self-Assembly of an a-Helical Peptide into a Crystalline Two-Dimensional Nanoporous Framework.. Journal of American Chemical Society, 138(50), 16274-16282 https://dx.doi.org/10.1021/jacs.6b06592
  2. Hu, M., Zhang, H., Li, Q., & Hao, Q. (2016). Structural basis for human PECAM-1-mediated trans-homophilic cell adhesion. Scientific Reports, 6(1) https://dx.doi.org/10.1038/srep38655
  3. Gou, M., Hou, G., Yang, H., Zhang, X., Cai, Y., Kai, G., & Liu, C. (2016). The MYB107 Transcription Factor Positively Regulates Suberin Biosynthesis. Plant Physiology, 173(2), 1045-1058 https://dx.doi.org/10.1104/pp.16.01614
  4. Templin, T., Sharma, P., Guida, P., & Grabham, P. (2016). Short-Term Effects of Low-LET Radiation on the Endothelial Barrier: Uncoupling of PECAM-1 and the Production of Endothelial Microparticles. Radiation Research, 186(6), 602 https://dx.doi.org/10.1667/RR14510.1
  5. Rodman, C. & Guida, P. (2016). In vitro and in vivo assessment of direct effects of simulated solar and galactic cosmic radiation on human hematopoietic stem/progenitor cells. https://www.osti.gov/biblio/1389216
  6. Zhou, Y., McGillick, B. E., Teng, Y. G., Haranahalli, K., Ojima, I., Swaminathan, S., & Rizzo, R. C. (2016). Identification of small molecule inhibitors of botulinum neurotoxin serotype E via footprint similarity. Bioorganic & Medicinal Chemistry https://dx.doi.org/10.1016/j.bmc.2016.07.031
  7. Xu, Y., Kim, S. W., Kim, D., Alexoff, D., Schueller, M., & Fowler, J. S. (2016). A mild, rapid synthesis of freebase [11C]nicotine from [11C]methyl triflate. Applied Radiation and Isotopes https://dx.doi.org/10.1016/j.apradiso.2016.08.020
  8. Wälti, M. A., Ravotti, F., Arai, H., Glabe, C. G., Wall, J. S., Böckmann, A., Güntert, P., Meier, B. H., & Riek, R. (2016). Atomic-resolution structure of a disease-relevant Aβ(1-42) amyloid fibril. Proceedings of the National Academy of Sciences of the United States of America, 113(34) https://dx.doi.org/10.1073/pnas.1600749113
  9. Huang, L., Khusnutdinova, A. N., Nocek, B., Brown, G., Xu, X., Cui, H., Petit, P., Flick, R., Zallot, R., Balmant, K. M., Ziemak, M. J., Shanklin, J., De Crécy-Lagard, V., Fiehn, O., Gregory, J. F., Joachimiak, A., Savchenko, A., Yakunin, A. F., & Hanson, A. D. (2016). A family of metal-dependent phosphatases implicated in metabolite damage-control. Nature Chemical Biology, 12(8) https://dx.doi.org/10.1038/NCHEMBIO.2108
  10. Sutherland, J. & Sutherland, J. (2016). Calibration of Photoelastic Modulator Based Dichrometers: Maintaining Constant Phase Across the Spectrum. https://www.osti.gov/biblio/1349559
  11. Yu, H. & Liu, Q. (2016). Structural Analysis of Notch-Regulating Rumi reveals basis for pathogenic mutations. https://www.osti.gov/biblio/1347286
  12. Cai, Y. & Cai, Y. (2016). Enhancing digestibility and ethanol yield of Populus wood via expression of an engineered monolignol 4-O-methyltransferase. https://www.osti.gov/biblio/1341631
  13. Kumar, G. (2016). Small molecule non-peptide inhibitors of botulinum neurotoxin serotype E: structure-activity relationship and a pharmacophore model. Bioorganic & Medical Chemistry https://dx.doi.org/10.1016/j.bmc.2016.06.036
  14. He, F. (2016). Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis. Plant Journal https://dx.doi.org/10.1111/tpj.13175
  15. Brawley, S. (2016). Ni induces the CRR1-dependent regulon revealing overlap and distinction between hypoxia and Cudeficiency responses in Chlamydomonas reinhardtii. Metallomics, 679-691 https://dx.doi.org/10.1039/C6MT00063K
  16. Sedeek, K. (2016). Amino acid change in an orchid desaturase enables mimicry of the pollinator"s sex pheromone. Current Biology https://www.osti.gov/biblio/1335436
  17. Xu, C. (2016). Triacylglycerol Metabolism, Function and Accumulation in Plant Vegetative Tissues. Annual Reviews https://dx.doi.org/10.1146/annurev-arplant-043015-111641
  18. Bai, L. (2016). Structural analysis of the dodecameric proteasome activator PafE in Mycobacterium tuberculosis. https://www.osti.gov/biblio/1257964
  19. Turkin, A. (2016). Speeding up Standard PCR Reactions with a Molecular Peptide Sled. PMC US National Library of Medicine National Institutes of Health https://www.osti.gov/biblio/1260167
  20. Yuan, Z. (2016). Structure of the Eukaryotic Replicative CMG Helicase and Pumpjack Motion. Nature Structural & Molecular Biology, 217-224 https://dx.doi.org/10.1038/nsmb.3170
  21. Shi, H. & Shi, H. (2016). Mathematical models of plant metabolism. https://www.osti.gov/biblio/1239795
  22. McGillick, B. (2016). beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Francisella tularensis and Yersinia pestis: Structure Determination, Enzymatic Characterization, and Cross Inhibition Studies. Biochemistry https://www.osti.gov/biblio/1335393

2015

  1. Blaby, I. & Blaby, I. (2015). Genome-wide analysis on Chlamydomonas reinhardtii reveals impact of hydrogen peroxide on protein stress responses and overlap with other stress transcriptomes. Plant Journal https://dx.doi.org/10.1111/tpj.13053
  2. Eswaramoorthy, S. (2015). Molecular Assembly of Clostridium botulinum progenitor M complex of type E. https://www.osti.gov/biblio/1235881
  3. Dearborn, A. (2015). Alpha-Synuclein Amyloid Fibrils with Two Entwined, Asymmetrically Associated, Protofibrils and Axially Stacked Metal Binding Sites.. The Journal of Biological Chemistry, 2310-2318 https://dx.doi.org/10.1074/jbc.M115.698787
  4. Yu, H. & Yu, H. (2015). Notch-modifying xylosyltransferase-substrate complexes support an SNi-like retaining mechanism. https://www.osti.gov/biblio/1234375
  5. Kumaran, D. & Swaminathan, S. (2015). Interactions of a potent cyclic peptide inhibitor with the light chain of botulinum neurotoxin A: insights from x-ray crystallography. https://www.osti.gov/biblio/1232693
  6. Sun, J. (2015). The Architecture of a Eukaryotic Replisome. Nature Structural & Molecular Biology , 976-982 https://dx.doi.org/10.1038/nsmb.3113
  7. Wang, H. & Fowler, J. (2015). Radiolabelling and positron emission tomography of PT70, a time-dependent inhibitor of InhA, the Mycobacterium tuberculosis enoyl-ACP reductase. https://www.osti.gov/biblio/1239783
  8. Volkow, N. & Fowler, J. (2015). Recovery of Dopamine transporters with methamphetamine detoxification is not linked to changes in dopamine release. https://www.osti.gov/biblio/1239786
  9. Provart, N. (2015). 50 Years of Arabidopsis Research: Highlights and Future Directions. https://www.osti.gov/biblio/1335407
  10. Fan, J. & Jilian, F. (2015). The Arabidopsis TriGalactosylDiacylglycerol 5 Interacts with TGD1, TGD2 and TGD4 to Facilitate Lipid Transfer from the Endoplasmic Reticulum to the Plastid. https://www.osti.gov/biblio/1341526
  11. Lee, S. & Fowler, J. (2015). An efficient and practical synthesis of [2-11C]indole via superfast nucleophilic [11C]cyanation and RANEY? Nickel catalyzed reductive cyclization. https://www.osti.gov/biblio/1239796
  12. Cai, Y. & Cai, Y. (2015). Engineering a monolignol 4-O-methyltransferase with high selectivity for the condensed lignin precursor coniferyl alchohol. Journal of Biological Chemistry https://dx.doi.org/10.1074/jbc.M115.684217
  13. Keereetaweep, J. & Jantana, B. (2015). Lipidomic Analysis of Endocannabinoid Signaling: Targeted Metabolite Identification and Quantification. https://www.osti.gov/biblio/1335430
  14. Teng, Y. (2015). Computer-aided identification, synthesis, and biological evaluation of novel inhibitors for botulinum neurotoxin serotype A. https://www.osti.gov/biblio/1232690
  15. Zhang, M. & Yu, H. (2015). A novel approach to make homogeneous protease-stable monovalent streptavidin. https://www.osti.gov/biblio/1232691
  16. Volkow, N. (2015). Caffeine Increases Striatal Dophamine D2/D3 Receptor Availability in the Human Brain.. Translational Psychiatry https://dx.doi.org/10.1038/tp.2015.46