Publications

Publications

* indicates student author
¹ indicates co-first authorship
  1. Markelz, R. J. C., R. L. Baker, D. Freund, N. An*, U. K. Devisetty, M. F. Covington, M. T. Brock, A. Hegeman, S. Welch, C. Weinig, D. Kliebenstein, and J. N. Maloof. In prep. Systems genetics in Brassica rapa reveals genotype to phenotype connections from high-throughput phenotyping data. For eLife.
  2. Baker, R. L., G. L. Brock*, E. L. Newsome*, and M. Zhao. In review. Network analysis reveals evolution of phenotypic integration and structure-function relationships in response to polyploidy.
  3. Thrash, T.*, H. Lee*, and R. L. Baker. 2022. A Low-cost high-throughput phenotyping system for automatically quantifying plant size and greenness. Applications in Plant Sciences doi: http://doi.org/10.1002/aps3.11502
  4. Pegg, T. J.*, D. Gladish, and R. L. Baker. 2021. Algae to Angiosperms: Autofluorescence for rapid visualization of plant anatomy among diverse taxa. Applications in Plant Sciences open-access full text
      • Selected for journal cover art
  5. Baker, R. L. and D. R. Wang. 2021. Working with longitudinal data: quantifying developmental processes using function-valued trait modeling. American Journal of Botany. open-access full text
  6. Liu, B.*, A. Iwata-Otsubo, D. Yang*, R. L. Baker, C. Liang, S. A. Jackson, S. Liu, J. Ma, and M. Zhao. 2021. Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of Brassica genomes. The Plant Journal doi:10.1111/tpj.15037
  7. Pegg, T*., D. Gladish, R. Edelmann, and R. L. Baker. 2020. Investigation of hemicellulose alteration in Fabaceae root cell walls during flooding-induced aerenchyma formation. Microscopy and Microanalysis, 1-5 (conference proceedings) open-access full text
  8. Newsome, E. L.¹*, G. L. Brock¹*, J. Lutz*, and R. L. Baker. 2020. Variation within laminae: semi-automated methods for quantifying leaf venation using phenoVein. Applications in Plant Sciences. open-access full text
  9. Lowry, D., J. M. Sobel, A. L. Angert, T. Ashman, R. L. Baker, et al. 2019. The case for the continued use of the genus name Mimulus for all monkeyflowers. Taxon. open-access full text
  10. Baker, R. L., W. F. Leong, M. T. Brock, M. J. Rubin, R. J. C. Markelz, S. Welch, J. N. Maloof, and C. Weinig. 2019. Integrating transcriptomic network reconstruction and QTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development.  PLoS Genetics 15(9): e1008367 open-access full text
  11. Wang, D. R.¹, C. R. Guadagno¹, X. Mao, D. S. Mackay, J. R. Pleban*, R. L. Baker, C. Weinig, J-L. Jannick, B. Ewers. 2019. A framework for genomics-informed ecophysiological modeling in plants. Journal of Experimental Botany 70(9): 2561-2574 abstract |pdf
  12. Rubin, M. J., M. T. Brock, R. L. Baker, K. Anderson*, S. Wilcox*, S. Davis, and C. Weinig. 2018. Circadian rhythms are associated with shoot architecture and plant performance. New Phytologist 219:246-258 abstract | pdf
  13. Baker, R. L., W. F. Leong, S. Welch, and C. Weinig. 2018. Mapping and predicting non-linear Brassica rapa growth phenotypes based on Bayesian and frequentist  trait estimation. G3: Genes | Genomes | Genetics  8(4): 1247-1258 abstract | pdf
  14. Baker, R. L¹., W. F. Leong¹, M. T. Brock, M. Rubin*, N. An*, S. Welch, and C. Weinig. 2018. Bayesian estimation and use of high-throughput remote sensing indices for quantitative genetic analyses of leaf growth. Theoretical and Applied Genetics 131(2):283-298 abstract | pdf
  15. An, N.*, S. Welch, R. J. Markelz, R. L. Baker, C. Palmer, J. Ta*, J. Maloof and C. Weinig. 2017. Quantifying time-series of leaf morphology using 2D and 3D photogrammetry methods for high-throughput plant phenotyping. Computers and Electronics in Agriculture 135:222–232 abstract | pdf
  16. Baker, R. L., Y. Yarkhunova*, K. Vidal*, B. Ewers, and C. Weinig. 2017. Polyploidy and the relationship between leaf structure and function: Implications for the evolution of correlations between anatomy, morphology, and physiology in Brassica. BMC Plant Biology 17(3) open access pdf
  17. An, N.*, C. M. Palmer, R. L. Baker, R. J. C. Markelz, J. Ta*, J. N. Maloof, S. M. Welch, and C. Weinig. 2016. Plant high-throughput phenotyping using photogrammetry and imaging techniques to measure leaf length and rosette area. Computers and Electronics in Agriculture 127:376-394 abstract | pdf
  18. Yarkhunova, Y.*, C., E. Edwards, R. L. Baker, B. E. Ewers, and C. Weinig. 2016. Selection during domestication affects the circadian clock and expression of ecophysiological traits. New Phytologist 210(1):133-144 abstract | pdf
  19. Baker, R. L., W. F. Leong, M. T. Brock, R. J. Cody Markelz, M. F. Covington, U. K. Devisetty, C. E. Edwards, J. Maloof, S. Welch, and C. Weinig. 2015. Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape. New Phytologist. 208(1) 257-268 abstract | pdf
      • Selected for Commentary in New Phytologist > > pdf
  20. Baker, R. L., E. Scherbatskoy*, C. Lay* and P. K. Diggle. 2014. Developmental plasticity of shoot architecture: Morphological expression and ecologically relevant onset in locally adapted populations of Mimulus guttatus. International Journal of Plant Sciences 175(1):59-69 abstract | pdf
  21. Baker, R. L., L. C. Hileman and P. K. Diggle. 2012. Patterns of shoot architecture in locally adapted populations are linked to intraspecific differences in gene regulation. New Phytologist 196(1):271-281 abstract | pdf
  22. Baker, R. L. and P. K. Diggle. 2011. Node-specific branching and heterochronic changes underlie population-level differences in Mimulus guttatus (Phrymaceae) shoot architecture. American Journal of Botany 98(12):1924-1934 abstract | pdf
  23. Diggle, P. K., N. J. Abrahamson*, R. Baker, M. G. Barnes*, T. L. Koontz*, C. Lay*, J. S. Medeiros*, J. Murgel*, M. G. M. Shaner*, H. L. Simpson*, C. C. Wu* and D. L. Marshall. 2010. Dynamics of maternal and paternal effects on embryo and seed development in wild radish (Raphanus sativus). Annals of Botany 106(2):309-313 abstract | pdf
  24. Noyes, R.D., R. Baker, and B. Mai*. 2007. Mendelian segregation for two-factor apomixis in Erigeron annuus (Asteraceae). Heredity 98:92-98 abstract | pdf

Extension/Technical/Non-indexed publications

  1. Baker, R. L., M. T. Brock, M. Rubin*, J. Maloof, S. Welch, and C. Weinig. 2015. Mapping function valued traits in Brassica rapa. Wyoming Agricultural Experiment Station pp. 19-20.
  2. Baker, R. L. 2010. Use of the Scanning Electron Microscope. In P. Diggle, Plant Eco-Evo-Devo (pp 54-56).