Kenneth Birnbaum, PhD

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Associate Professor, Dept. of Biology

PhD 2000 - Courant Institute

Birnbaum Lab
Developmental and evolutionary genomics of plants; The origin and genetic programming of cell types.
Plant Stem Cells, Regeneration

Contact Information


 Center for Genomics and Systems Biology

Department of Biology, NYU
12 Waverly Place

New York, N.Y. 10003

Tel.: (212) 998-8257

Fax: (212) 995-4015

The Systems Biology of Regeneration in Plants


Ken Birnbaum’s lab works on plant stem cells and regeneration using the model Arabidopsis thaliana. His work focuses on the properties that enable plant tissues to re-organize so readily after damage, centered around two major questions. What specifically regulates the plasticity of adult somatic plant cells? And, how do organizing signals re-establish themselves in cases where signaling centers like the root stem cell niche are completely removed? In two recent examples, research in the lab has shown a role for an auxin gradient in the specific regulation of pluripotency and uncovered a mechanistic link between radial and distal patterning fields that helps establish the root stem cell niche. The lab addresses these questions using high-resolution transcriptional profiling of single cell types and single cells. In addition, the lab uses high-resolution time-lapse confocal microscopy during regeneration. Current work in the lab focuses on coordinating microscopic and single-cell transcriptomic data to map the global transcriptional changes in cells according to their position in regenerating tissue. 

Selected Publications: 
  • Bargmann, B.O., Vanneste, S., Krouk, G., Nawy, T., Efroni, I., Shani, E., Choe, G., Friml, J., Bergmann, D.C., Estelle, M., Birnbaum, K.D. (2013). A map of cell type-specific auxin responses. Mol Syst Biol 9, 688. PMID: 24022006
  • Gifford, M.L., Banta, J.A., Katari, M.S., Hulsmans, J., Chen, L., Ristova, D., Tranchina, D., Purugganan, M.D., Coruzzi, G.M., and Birnbaum, K.D. (2013). Plasticity regulators modulate specific root traits in discrete nitrogen environments. PLoS Genet 9, 2013; 9(9). PMID: 24039603
  • Birnbaum, K.D., and Kussell, E. (2011). Measuring Cell Identity in Noisy Biological Systems. Nucleic Acids Research. 2011 Nov;39(21):9093-107. PMID: 21803789
  • Sena, G., Frentz, Z., Birnbaum, K.D., and Liebler, S. (2011). Quantitation of Cellular Dynamics in Growing Arabidopsis Roots with Light Sheet Microscopy. PLoS One. (6)6. PMID: 21731697
  • Bargmann, B.O., and Birnbaum, K.D. (2010). Fluorescence activated cell sorting of plant protoplasts. J Vis Exp. Feb 18(36):1673. PMID: 20168296
  • Nawy, T., Bayer, M., Mravec, J., Friml, J., Birnbaum, K.D., and Lukowitz, W. (2010). The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo. Dev Cell 19: 103-113. PMID: 20643354
  • Bargmann, B.O., and Birnbaum, K.D. (2009). Positive fluorescent selection permits precise, rapid and in depth over-expression analysis in plant protoplasts. Plant Physiol. 149(3):1231-9. PMID: 19168642
  • Sena, G., Wang, X., Liu, H.Y., Hofhuis, H., and Birnbaum, K.D. (2009). Organ regeneration does not require a functional stem cell niche in plants. Nature. 457:1150-3. PMID: 19182776
  • Gifford, M.L., Dean, A., Gutierrez, R.A., Coruzzi, G.M., and Birnbaum, K.D. (2008). Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci U S A 105: 803-808. PMID: 18180456
  • Birnbaum, K., Shasha, D.E., Wang, J.W., Jung, J., Lambert, G., Galbraith, D., and Benfey, P. N. 2003. A gene expression map of the Arabidopsis root. Science, 302, 1956-1960. PMID: 14671301
  • Birnbaum, K. Benfey, P.N. and Shasha, D.E. 2001. cis Element/Transcription Factor Analysis (cis/TF): A Method for Discovering Transcription Factor/cis Element Relationships. Genome Research, 11, 1567-1573. PMID: 11544201