Kenneth D. Birnbaum

Associate Professor of Biology; Faculty Director of the Cellular Analysis Core

Ph.D. 2000 (Biology), New York University; M.S. 1993 (Environmental Science), University of Wisconsin; B.A. 1984 (Biology/English), University of Pennsylvania.

Office Address: 

New York University
Department of Biology
Center for Genomics and Systems Biology
12 Waverly Place, Room 606
New York, NY 10003


(212) 998-8257


(212) 995-4015

Personal Homepage:

Areas of Research/Interest: 

Developmental and evolutionary genomics of plants. The origin and genetic programming of cell types.

List of Publications from Pubmed

List of citations from Google Scholar


The research in my lab focuses on two inter-related questions: How do multi-cellular organisms construct specialized cells and how do the genetic components of specialized cells change over evolutionary scales? The goal is to better understand how gene regulatory networks orchestrate cell maturation, a process that results in a set of highly specialized cell types. Thus, we focus on cellular differentiation, which is one of the key steps in organ formation and development in higher organisms. The approach of the lab combines genomics and molecular genetic tools. For example, we have pioneered a new technique to isolate cell types in plants using high-speed fluidics. From there, RNA from a specific cell type population is applied to microarrays to provide a profile of gene activity at the transcriptional level. Transcriptional profiles of cells can then be used to identify likely cell-specific regulators and infer properties of the genetic circuitry of cellular specification.

Two experimental approaches are being used to address this larger question. The first project is large-scale reverse genetics guided by a detailed map of gene expression in the root and other organs. As a case study in cellular development, we have started to analyze knockouts of genes that are highly enriched in xylem, which are the water-conducting cells of the plant's vascular system. We also use computational approaches to generate testable hypotheses on the targets of transcription factors that control xylem maturation. The second project is creating detailed maps of gene expression in the roots of other plant species, such as rice. This will help us to track changes in gene expression during evolution. We can then ask how genetic networks have changed over time to create new cellular attributes and, occasionally, new cell types.

Selected Works:

Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis.
Proc Natl Acad Sci U S A   (2014 Jun 23);   PMID: 24958886
Para A, Li Y, Marshall-Colon A, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bargmann BO, Birnbaum KD, McCombie WR, Krouk G, Coruzzi GM
An undergraduate study of two transcription factors that promote lateral root formation.
Biochem Mol Biol Educ   (2014 May-Jun);   PMID: 24615800
Bargmann BO, Birnbaum KD, Brenner ED
Plasticity regulators modulate specific root traits in discrete nitrogen environments.
PLoS Genet   (2013);  PMC3764102 free full-text archive
Gifford ML, Banta JA, Katari MS, Hulsmans J, Chen L, Ristova D, Tranchina D, Purugganan MD, Coruzzi GM, Birnbaum KD
A map of cell type-specific auxin responses.
Mol Syst Biol   (2013);  PMC3792342 free full-text archive
Bargmann BO, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml J, Bergmann DC, Estelle M, Birnbaum KD
Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture.
Proc Natl Acad Sci U S A   (2013 Sep 10);  PMC3773737 free full-text archive
Rosas U, Cibrian-Jaramillo A, Ristova D, Banta JA, Gifford ML, Fan AH, Zhou RW, Kim GJ, Krouk G, Birnbaum KD, Purugganan MD, Coruzzi GM
Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
Dev Cell   (2013 Feb 25);  PMC3994294 free full-text archive
Efroni I, Han SK, Kim HJ, Wu MF, Steiner E, Birnbaum KD, Hong JC, Eshed Y, Wagner D
TARGET: a transient transformation system for genome-wide transcription factor target discovery.
Mol Plant   (2013 May);  PMC3660954 free full-text archive
Bargmann BO, Marshall-Colon A, Efroni I, Ruffel S, Birnbaum KD, Coruzzi GM, Krouk G
RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis.
Plant Physiol   (2013 Mar);  PMC3585581 free full-text archive
Ristova D, Rosas U, Krouk G, Ruffel S, Birnbaum KD, Coruzzi GM
Fluorescence-activated cell sorting for analysis of cell type-specific responses to salinity stress in Arabidopsis and rice.
Methods Mol Biol   (2012);   PMID: 22895766
Evrard A, Bargmann BO, Birnbaum KD, Tester M, Baumann U, Johnson AA
High-throughput fluorescence-based isolation of live C. elegans larvae.
Nat Protoc   (2012 Aug);   PMID: 22814389
Fernandez AG, Bargmann BO, Mis EK, Edgley ML, Birnbaum KD, Piano F
Low-cost sequencing opens new insights into diverse plant genomes.
Genome Biol   (2012);  PMC3334579 free full-text archive
Birnbaum KD
Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand.
Proc Natl Acad Sci U S A   (2011 Nov 8);  PMC3215050 free full-text archive
Ruffel S, Krouk G, Ristova D, Shasha D, Birnbaum KD, Coruzzi GM
Measuring cell identity in noisy biological systems.
Nucleic Acids Res   (2011 Nov);  PMC3241637 free full-text archive
Birnbaum KD, Kussell E
Quantitation of cellular dynamics in growing Arabidopsis roots with light sheet microscopy.
PLoS One   (2011);  PMC3120859 free full-text archive
Sena G, Frentz Z, Birnbaum KD, Leibler S
Predicting genome-wide redundancy using machine learning.
BMC Evol Biol   (2010);  PMC2998534 free full-text archive
Chen HW, Bandyopadhyay S, Shasha DE, Birnbaum KD
The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo.
Dev Cell   (2010 Jul 20);   PMID: 20643354
Nawy T, Bayer M, Mravec J, Friml J, Birnbaum KD, Lukowitz W
Built to rebuild: in search of organizing principles in plant regeneration.
Curr Opin Genet Dev   (2010 Aug);  PMC2931316 free full-text archive
Sena G, Birnbaum KD
Automated sorting of live C. elegans using laFACS.
Nat Methods   (2010 Jun);  PMC2896029 free full-text archive
Fernandez AG, Mis EK, Bargmann BO, Birnbaum KD, Piano F
Fluorescence activated cell sorting of plant protoplasts.
J Vis Exp   (2010);  PMC2896036 free full-text archive
Bargmann BO, Birnbaum KD
Primer and interviews: Gene regulation in Arabidopsis thaliana. Interview by Julie C. Kiefer.
Dev Dyn   (2009 Sep);   PMID: 19653311
Benfey PN, Birnbaum KD
Organ regeneration does not require a functional stem cell niche in plants.
Nature   (2009 Feb 26);  PMC2649681 free full-text archive
Sena G, Wang X, Liu HY, Hofhuis H, Birnbaum KD
Positive fluorescent selection permits precise, rapid, and in-depth overexpression analysis in plant protoplasts.
Plant Physiol   (2009 Mar);  PMC2649414 free full-text archive
Bargmann BO, Birnbaum KD
Slicing across kingdoms: regeneration in plants and animals.
Cell   (2008 Feb 22);  PMC2692308 free full-text archive
Birnbaum KD, Sanchez Alvarado A
Cell-specific nitrogen responses mediate developmental plasticity.
Proc Natl Acad Sci U S A   (2008 Jan 15);  PMC2206617 free full-text archive
Gifford ML, Dean A, Gutierrez RA, Coruzzi GM, Birnbaum KD
Updated on 07/10/2014