Publications
  1. Gaudinier, A., Brady, S. (2016) Mapping Transcriptional Networks in Plants: Data-Driven Discovery of Novel Biological Mechanisms. Annual Review of Plant Biology. URL
  2. Carriedo, L., Maloof, J., Brady, S. (2016) Molecular control of crop shade avoidance. Current Opinion in Plant Biology. 151--158 URL
  3. Etchells, J., Smit, M., Gaudinier, A., Williams, C., Brady, S. (2016) A brief history of the TDIF-PXY signalling module: balancing meristem identity and differentiation during vascular development. New Phytologist. 474--484 URL
  4. Brady, S., Provart, N. (2015) Transcriptional networks: The next generation. Current Plant Biology. 1--2 URL
  5. Provart, N., Alonso, J., Assmann, S., Bergmann, D., Brady, S., Brkljacic, J., Browse, J., Chapple, C., Colot, V., Cutler, S., et al. (2015) 50 years of Arabidopsis research: highlights and future directions. New Phytologist. URL
  6. Spiegelman, Z., Ham, B., Zhang, Z., Toal, T., Brady, S., Zheng, Y., Fei, Z., Lucas, W., Wolf, S. (2015) A tomato phloem-mobile protein regulates the shoot-to-root ratio by mediating the auxin response in distant organs. The Plant Journal. 853--863 URL
  7. Koryachko, A., Matthiadis, A., Muhammad, D., Foret, J., Brady, S., Ducoste, J., Tuck, J., Long, T., Williams, C. (2015) Clustering and Differential Alignment Algorithm: Identification of Early Stage Regulators in the Arabidopsis thaliana Iron Deficiency Response. PloS one. e0136591 URL
  8. Brady, S., Burow, M., Busch, W., Carlborg, {., Denby, K., Glazebrook, J., Hamilton, E., Harmer, S., Haswell, E., Maloof, J., et al. (2015) Reassess the t test: interact with all your data via ANOVA. The Plant Cell. 2088--2094 URL
  9. Taylor-Teeples, M., Lin, L., de Lucas, M., Turco, G., Toal, T., Gaudinier, A., Young, N., Trabucco, G., Veling, M., Lamothe, R., et al. (2015) An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature. 571--575 URL
  10. Liu, Y., You, S., Taylor-Teeples, M., Li, W., Schuetz, M., Brady, S., Douglas, C. (2014) BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 interact and regulate secondary cell wall formation via repression of REVOLUTA. The Plant Cell. 4843--4861 URL
  11. Li, B., Gaudinier, A., Tang, M., Taylor-Teeples, M., Nham, N., Ghaffari, C., Benson, D., Steinmann, M., Gray, J., Brady, S., et al. (2014) Promoter-based integration in plant defense regulation. Plant physiology. 1803--1820 URL
  12. Kajala, K., Coil, D., Brady, S. (2014) Draft genome sequence of Rhizobium rhizogenes strain ATCC 15834. Genome announcements. e01108--14 URL
  13. Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso MA, Zumstein K, Garcha J, Winte S, Masson H, Inagaki S, Federici F, Sinha N, Deal RB, Bailey-Serres J, Brady SM. (2014) Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant physiology (pp-114).
  14. Kajala, K., Ramakrishna, P., Fisher, A., Bergmann, D. C., De Smet, I., Sozzani, R., Dolf Weijers, & Brady, SM. (2014) Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants. Annals of Botany mcu065.
  15. De Lucas M, Provart NJ, & Brady SM (2014). Bioinformatic Tools in Arabidopsis Research. Arabidopsis Protocols (pp. 97-136). Humana Press.
  16. El-Showk, S., Taylor-Teeples, M., Helariutta, Y., & Brady, SM (2013). Gene regulatory networks during Arabidopsis root vascular development. International Journal of Plant Sciences 174.7 (2013): 1090-1097.
  17. Koenig, D., Jiménez-Gómez, J. M., Kimura, S., Fulop, D., Chitwood, D. H., Headland, L. R., Ravi Kumar, Michael F. Covington, Upendra Kumar Devisetty, An V. Tat, Takayuki Tohge, Anthony Bolger, Korbinian Schneeberger, Stephan Ossowski, Christa Lanz, Guangyan Xiong, Mallorie Taylor-Teeples, Siobhan M. Brady, Markus Pauly, Detlef Weigel, Björn Usadel, Alisdair R. Fernie, Jie Peng, Neelima R. Sinha, & Maloof, J. N. (2013). Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proceedings of the National Academy of Sciences. 110(28), E2655-E2662.
  18. Lucas, W. J., Groover, A., Lichtenberger, R., Furuta, K., Yadav, S. R., Helariutta, Y., Xin-Qiang He, Hiroo Fukuda, Julie Kang, Siobhan M. Brady, John W. Patrick, John Sperry, Akiko Yoshida, Ana-Flor López-Millán, Michael A. Grusak & Kachroo, P. (2013). The Plant Vascular System: Evolution, Development and Functions. Journal of integrative plant biology 55(4), 294-388.
  19. Ron M, Dorrity MW, de Lucas M, Toal T, Hernandez RI, Little SA, Maloof JN, Kliebenstein DJ, Brady SM. (2013) Identification of Novel Loci Regulating Interspecific Variation in Root Morphology and Cellular Development in Tomato. Plant Physiol. 2013 Jun;162(2):755-68. doi: 10.1104/pp.113.217802. Epub 2013 Apr 10.
  20. Moussaieff A, Rogachev I, Brodsky L, Malitsky S, Toal TW, Belcher H, Yativ M, Brady SM, Benfey PN, Aharoni A. (2013) High Resolution Metabolic Mapping of Cell Types in Plant Roots. Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):E1232-41. doi: 10.1073/pnas.1302019110. Epub 2013 Mar 8.
  21. De Lucas M, Brady SM. (2012) Gene regulatory networks in the Arabidopsis root. Curr Opin Plant Biol. 2013 Feb;16(1):50-5. doi: 10.1016/j.pbi.2012.10.007. Epub 2012 Nov 26.
  22. Belmonte, M. F., Kirkbride, R. C., Stone, S. L., Pelletier, J. M., Bui, A. Q., Yeung, E. C., Meryl Hashimoto, Jiong Fei, Corey M. Harada, Matthew D. Munoz, Brandon H. Le, Gary N. Drews, Siobhan M. Brady, Robert B. Goldberg & Harada, J. J. (2013). Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed. Proceedings of the National Academy of Sciences 110(5), E435-E444.
  23. Bassel GW, Gaudinier A, Brady SM, Hennig L, Rhee SY, De Smet I. Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell. 2012 Oct;24(10):3859-75. doi: 10.1105/tpc.112.100776. Epub 2012 Oct 30.
  24. Gaudinier A, Zhang L, Reece-Hoyes JS, Taylor-Teeples M, Pu L, Liu Z, Breton G, Pruneda-Paz JL, Kim D, Kay SA, Walhout AJ, Ware D, Brady SM. (2011) Enhanced Y1H assays for Arabidopsis. Nat Methods. 2011 Oct 30;8(12):1053-5. doi: 10.1038/nmeth.1750.
  25. Taylor-Teeples M, Ron M, Brady SM. (2011) Novel biological insights revealed from cell type-specific expression profiling. Curr Opin Plant Biol. 2011 Oct;14(5):601-7. Epub 2011 Jun 23. Review.
  26. Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, Ahnert S, Ohler U, Ware D, Walhout AJ, Benfey PN. (2011) A stele-enriched gene regulatory network in the Arabidopsis root. Molecular Systems Biol. Jan 18;7:459.
  27. Pu L, Brady S. (2010) Systems biology update: cell type-specific transcriptional regulatory networks. Plant Physiol. 152(2):411-9
  28. Cartwright DA, Brady SM, Orlando DA, Sturmfels B, Benfey PN. (2009) Reconstructing spatiotemporal gene expression data from partial observations Bioinformatics. 25(19):2581-7
  29. Orlando DA, Brady SM, Koch JD, Dinneny JR, Benfey PN. (2009) Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment. Methods Mol Biol. 553:57-77
  30. Brady SM, Provart NJ. (2009) Web-queryable large-scale data sets for hypothesis generation in plant biology. Plant Cell. 21(4):1034-51
  31. Chaudhuri B, Hormann F, Lalonde S, Brady SM, Orlando DA, Benfey PN, Frommer WB. (2008) Protonophore- and pH-insensitive glucose and sucrose accumulation detected by FRET nanosensors in Arabidopsis root tips. Plant Journal. Aug 12.
  32. Long TA, Brady SM, Benfey PN. (2008) Systems Approaches to Identifying Gene Regulatory Networks in Plants. Annual Review of Cell and Developmental Biology. Jul 10. (co-first author)
  33. Dinneny JR, Long TA, Wang JY, Mace D, Pointer S, Barran C, Brady SM, Schiefelbein JS, Benfey PN. (2008) Cell Identity Mediates the Response of Arabidopsis Roots to Salinity and Iron Stress. Science, 320:942-945.
  34. Brady SM, Orlando DA, Lee JY, Wang, JY, Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN. (2007) Dominant Root Expression Patterns Revealed in a High-Resolution Spatiotemporal Expression Map. Science. 318:801-806.
  35. Brady SM, Benfey PN. Riding the Genomics Wave: Moving Towards a Systems Understanding of Root Development. Chapter in Plant Systems Biology (Blackwell Publishing).
  36. Brady SM, Provart NJ. (2007) Extreme Breeding – Leveraging Genomics for Crop Improvement. Journal of the Science of Food and Agriculture. 97:925-929.
  37. Brady SM, Song S, Dhugga K, Rafalski JA, Benfey PN. (2007) Combining Expression and Comparative Evolutionary Analysis: The COBRA Gene Family. Plant Physiology. 143:172-187.
  38. Brady SM, Long, TA, Benfey PN. (2006) Unravelling the Dynamic Transcriptome. Plant Cell. 18:2101-2111.
  39. Brady SM, Benfey PN. (2006) A systems approach to understanding root development. Canadian Journal of Botany. 84:1-7.
  40. Toufighi K, Brady SM, Austin R, Ly E, Provart NJ. (2005) The Botany Array Resource: e-Northerns, Expression Angling and Promoter Analysis. Plant Journal. 43:153-163.
  41. Brady SM, Sarkar SF, Bonetta D, McCourt P. (2003) The ABSCISIC ACID INSENSITIVE 3 (ABI3) gene is modulated by farnesylation and is involved in auxin signaling and lateral root development in Arabidopsis. Plant Journal. 34:67-75.
  42. Brady SM, McCourt P. (2003) Hormone Cross-Talk in Seed Dormancy. Journal of Plant Growth Regulation. 22:25-31.