Siobhan Brady

image of Siobhan Brady

Associate Professor


UC Davis Genome Center
Plant Biology

Offices and Labs

1302 GBSF


2005 PhD Developmental Biology University of Toronto
1999 BS Molecular Plant Biology University of Toronto

Research Contribution

The Brady lab studies the root of the model plant, Arabidopsis thaliana, which is ideally suited to understand the molecular processes that underlie how and when cells determine their identity. These features in combination with various genomic tools are used to map the network of interactions that turn on or off gene expression in individual tissues.

Research Interests

Genomics, Developmental Biology, Plant Biology, Systems Biology, Transcriptional Networks


NSERC Postdoctoral Fellow, 2005-2008

Department and Center Affiliations

Genome Center
Plant Biology


American Society of Plant Biology
Society of Developmental Biology

CBS Grad Group Affiliations

Integrated Genetics and Genomics
Plant Biology
Biochemistry, Molecular, Cellular and Developmental Biology

Specialties / Focus

Plant Biology
  • Molecular Biology, Biochemistry, and Genomics


brady lab website


2/3/2011 2:53:31 PM
  • Brady SM, McCourt P. (2003) Hormone Cross-Talk in Seed Dormancy. Journal of Plant Growth Regulation. 22:25-31.
  • 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.
  • 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.
  • Brady SM, Benfey PN. (2006). A systems approach to understanding root development. Canadian Journal of Botany. 84:1-7.
  • Brady SM, Long, TA, Benfey PN. (2006) Unravelling the Dynamic Transcriptome. Plant Cell. 18:2101-2111.
  • 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.
  • Brady SM, Provart NJ. (2007) Extreme Breeding – Leveraging Genomics for Crop Improvement. Journal of the Science of Food and Agriculture. 97:925-929
  • Brady SM, Orlando DA, Lee JY, Wang, JY, Koch D, 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.
  • 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, April 24.
  • Long TA,Brady SM, Benfey PN. (2008) Systems Approaches to Identifying Gene Regulatory Networks in Plants. Annual Review of Cell and Developmental Biology. 24:81-103.
  • 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. Plant Journal. 56:948-62.
  • Brady SM, Benfey PN. (2009) Riding the Genomics Wave: Moving Towards a Systems Understanding of Root Development.. Chapter in Plant Systems Biology (Blackwell Publishing).
  • Orlando DA, Brady SM, Koch J, Dinneny JR, Benfey PN. (2009) Manipulating Large Scale Gene Arabidopsis Expression Data: Identifying Dominant Expression Patterns and Biological Process Enrichment. Methods in Molecular Biology. 553:57-77.
  • Brady SM, Provart NJ. (2009) Large Scale Data Sets and Queryable Browsers for Hypothesis Generation in Plant Biology. Plant Cell. 21:1034-1051
  • Cartwright D, Brady SM, Orlando DA, Sturmfels B, Benfey PN. (2009). Reconstructing Spatiotemporal Gene Expression Data. Bioinformatics. 25:2581-2587.
  • Pu L, Brady SM. (2010) Systems Biology Update: Cell Type-Specific Transcriptional Regulatory Networks. Plant Physiology. 152:411-419.
  • Orlando DA, Brady SM, Fink TAM, Benfey PN, Ahnert SE. (2010) Detecting Separate Time Scales in Gene Expression Data. BMC Genomics. 11:381.
  • Sozanni R, Cui H, Moreno-Risueno MA, Busch W, VanNorman JM, Vernoux T, Brady SM, Dewitte W, Murray JAH, Benfey PN. (2010) Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature. 466:128-132.
  • 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 AJM, Benfey PN. (2011) A stele-enriched gene regulatory network in the Arabidopsis Root. Molecular Systems Biology. 7:459.