Publications

  1. Banan, Paul RE, Feldman M, Holmes M, Schlake H, Jiang H, et al. High fidelity detection of QTL hotspots for biomass production from rapid hemispherical imaging of a C4 grass crop in the field. Proceedings of the National Academy of Sciences.
  2. Fahlgren N, Feldman M, Gehan MA, Wilson MS, Shyu C, Bryant DW, et al. A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria. Mol Plant. Elsevier; 2015;8: 1520–1535.
  3. Gehan MA, Fahlgren N, Abbasi A, Berry JC, Callen ST, Chavez L, et al. PlantCV v2: Image analysis software for high-throughput plant phenotyping. PeerJ. PeerJ Inc.; 2017;5: e4088.
  4. Feldman MJ, Paul RE, Banan D, Barrett JF, Sebastian J, Yee M-C, et al. Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria. PLoS Genet. journals.plos.org; 2017;13: e1006841.
  5. Feldman MJ, Ellsworth PZ, Fahlgren N, Gehan MA, Cousins AB, Baxter I. Components of Water Use Efficiency Have Unique Genetic Signatures in the Model C4 Grass Setaria. Plant Physiol. Am Soc Plant Biol; 2018;178: 699–715
  6. Ellsworth P, Feldman M, Baxter I, Cousins A. A genetic link between whole-plant water use efficiency and leaf carbon isotope composition in the C4 grass Setaria [Internet]. bioRxiv. 2018. p. 285676. doi:10.1101/285676
  7. Huang P, Feldman M, Schroder S, Bahri BA, Diao X, Zhi H, et al. Population genetics of Setaria viridis, a new model system. Mol Ecol. Wiley Online Library; 2014;23: 4912–4925.
  8. Ziegler GR, Hartsock RH, Baxter I. Zbrowse: an interactive GWAS results browser. PeerJ Comput Sci. PeerJ Inc.; 2015;1: e3.
  9. Kolbe AR, Brutnell TP, Cousins AB, Studer AJ. Carbonic Anhydrase Mutants in Zea mays Have Altered Stomatal Responses to Environmental Signals. Plant Physiol. Am Soc Plant Biol; 2018;177: 980–989.
  10. Ellsworth PV, Ellsworth PZ, Koteyeva NK, Cousins AB. Cell wall properties in Oryza sativa influence mesophyll CO2 conductance. New Phytol. Wiley Online Library; 2018;219: 66–76.
  11. Kolbe AR, Cousins AB. Mesophyll conductance in Zea mays responds transiently to CO2 availability: implications for transpiration efficiency in C4 crops. New Phytol. Wiley Online Library; 2018;217: 1463–1474.
  12. Kolbe AR, Studer AJ, Cousins AB. Biochemical and transcriptomic analysis of maize diversity to elucidate drivers of leaf carbon isotope composition. Funct Plant Biol. CSIRO PUBLISHING; 2018;45: 489–500.
  13. Ellsworth PZ, Ellsworth PV, Cousins AB. Relationship of leaf oxygen and carbon isotopic composition with transpiration efficiency in the C4 grasses Setaria viridis and Setaria italica. J Exp Bot. academic.oup.com; 2017;68: 3513–3528.
  14. Ellsworth PZ, Cousins AB. Carbon isotopes and water use efficiency in C4 plants. Curr Opin Plant Biol. Elsevier; 2016;31: 155–161.
  15. Wang M, Ellsworth PZ, Zhou J, Cousins AB, Sankaran S. Evaluation of water-use efficiency in foxtail millet (Setaria italica) using visible-near infrared and thermal spectral sensing techniques. Talanta. Elsevier; 2016;152: 531–539.
  16. Rellán-Álvarez R, Lobet G, Lindner H, Pradier P-L, Sebastian J, Yee M-C, et al. GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems. Elife. cdn.elifesciences.org; 2015;4. doi:10.7554/eLife.07597
  17. Sebastian J, Yee M-C, Goudinho Viana W, Rellán-Álvarez R, Feldman M, Priest HD, et al. Grasses suppress shoot-borne roots to conserve water during drought. Proc Natl Acad Sci U S A. National Acad Sciences; 2016;113: 8861–8866.
  18. Brophy JAN, LaRue T, Dinneny JR. Understanding and engineering plant form. Semin Cell Dev Biol. Elsevier; 2018;79: 68–77.
  19. Dinneny JR. A developmental biologist’s journey to rediscover the Zen of plant physiology [version 1; referees: 3 approved]. researchgate.net; 2015; Available: https://www.researchgate.net/profile/Jose_Dinneny/publication/281926415_...
  20. Dinneny JR. Traversing organizational scales in plant salt-stress responses. Curr Opin Plant Biol. Elsevier; 2015;23: 70–75.
  21. Emami S, Yee M-C, Dinneny JR. A robust family of Golden Gate Agrobacterium vectors for plant synthetic biology. Front Plant Sci. frontiersin.org; 2013;4: 339.
  22. Rellán-Álvarez R, Lobet G, Dinneny JR. Environmental Control of Root System Biology. Annu Rev Plant Biol. annualreviews.org; 2016;67: 619–642.
  23. Sebastian J, Wong MK, Tang E, Dinneny JR. Methods to promote germination of dormant Setaria viridis seeds. PLoS One. journals.plos.org; 2014;9: e95109.
  24. Schlapfer P, Zhang P, Wang C, Kim T, Banf M, Chae L, et al. Genome-wide prediction of metabolic enzymes, pathways and gene clusters in plants. Plant Physiol. Am Soc Plant Biol; 2017; doi:10.1104/pp.16.01942
  25. Zheng Y, Jiao C, Sun H, Rosli HG, Pombo MA, Zhang P, et al. iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases. Mol Plant. Elsevier; 2016;9: 1667–1670.
  26. Chae L, Kim T, Nilo-Poyanco R, Rhee SY. Genomic signatures of specialized metabolism in plants. Science. science.sciencemag.org; 2014;344: 510–513.
  27. Gil-Humanes J, Wang Y, Liang Z, Shan Q, Ozuna CV, Sánchez-León S, et al. High efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9. Plant J. Wiley Online Library; 2016; Available: http://onlinelibrary.wiley.com/doi/10.1111/tpj.13446/full
  28. Huang P, Shyu C, Coelho CP, Cao Y, Brutnell TP. Setaria viridis as a Model System to Advance Millet Genetics and Genomics. Front Plant Sci. 2016;7: 1781.
  29. Cermak T, Curtin SJ, Gil-Humanes J, Čegan R, Kono TJY, Konečná E, et al. A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. Am Soc Plant Biol; 2017; tpc–00922.
  30. Huang P, Jiang H, Zhu C, Barry K, Jenkins J, Sandor L, et al. Sparse panicle1 is required for inflorescence development in Setaria viridis and maize. Nat Plants. 2017;3: 17054.
  31. Jiang, H., Barbier, H., & Brutnell, T. (2013). Methods for performing crosses in Setaria viridis, a new model system for the grasses. Journal of visualized experiments : JoVE, (80), 50527. doi:10.3791/50527
  32. Sankalpi N. Warnasooriya, Thomas P. Brutnell; Enhancing the productivity of grasses under high-density planting by engineering light responses: from model systems to feedstocks, Journal of Experimental Botany, Volume 65, Issue 11, 1 June 2014, Pages 2825–2834, https://doi.org/10.1093/jxb/eru221
  33. Christine Shyu, Thomas P. Brutnell; Growth–defence balance in grass biomass production: the role of jasmonates, Journal of Experimental Botany, Volume 66, Issue 14, 1 July 2015, Pages 4165–4176, https://doi.org/10.1093/jxb/erv011