Kenneth D. Birnbaum

Professor of Biology; Faculty Director of the Cellular Analysis Core; Director, PhD Program


Areas of Research/Interest

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


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.


Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root.
Sci Signal (2016 Oct 25) PMID: 27811143
Ristova D, Carre C, Pervent M, Medici A, Kim GJ, Scalia D, Ruffel S, Birnbaum KD, Lacombe B, Busch W, Coruzzi GM, Krouk G

How many ways are there to make a root?
Curr Opin Plant Biol (2016 Dec) PMID: 27780106
Birnbaum KD

Plant Cell Shape: Trafficking Gets Edgy.
Dev Cell (2016 Feb 22) PMID: 26906728
Rahni R, Birnbaum KD

Identification of a Stelar-Localized Transport Protein That Facilitates Root-to-Shoot Transfer of Chloride in Arabidopsis.
Plant Physiol (2016 Feb) PMC4734554 free full-text archive
Li B, Byrt C, Qiu J, Baumann U, Hrmova M, Evrard A, Johnson AA, Birnbaum KD, Mayo GM, Jha D, Henderson SW, Tester M, Gilliham M, Roy SJ

Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population.
Dev Cell (2015 Apr 06) PMC4390738 free full-text archive
Adrian J, Chang J, Ballenger CE, Bargmann BO, Alassimone J, Davies KA, Lau OS, Matos JL, Hachez C, Lanctot A, Vaten A, Birnbaum KD, Bergmann DC

Quantification of cell identity from single-cell gene expression profiles.
Genome Biol (2015 Jan 22) PMC4354993 free full-text archive
Efroni I, Ip PL, Nawy T, Mello A, Birnbaum KD

Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis.
Proc Natl Acad Sci U S A (2014 Jul 15) PMC4104873 free full-text archive
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

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) PMC4164160 free full-text archive
Evrard A, Bargmann BO, Birnbaum KD, Tester M, Baumann U, Johnson AA

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 08) 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 Nov 18) 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

Fluorescence activated cell sorting of plant protoplasts.
J Vis Exp (2010 Feb 18) 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

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

Global studies of cell type-specific gene expression in plants.
Annu Rev Plant Biol (2006) PMID: 16669770
Galbraith DW, Birnbaum K

Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines.
Nat Methods (2005 Aug) PMID: 16170893
Birnbaum K, Jung JW, Wang JY, Lambert GM, Hirst JA, Galbraith DW, Benfey PN

Transcriptional profile of the Arabidopsis root quiescent center.
Plant Cell (2005 Jul) PMC1167541 free full-text archive
Nawy T, Lee JY, Colinas J, Wang JY, Thongrod SC, Malamy JE, Birnbaum K, Benfey PN

Network building: transcriptional circuits in the root.
Curr Opin Plant Biol (2004 Oct) PMID: 15337102
Birnbaum K, Benfey PN

A gene expression map of the Arabidopsis root.
Science (2003 Dec 12) PMID: 14671301
Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, Galbraith DW, Benfey PN

Using cauliflower to find conserved non-coding regions in Arabidopsis.
Plant Physiol (2002 Jun) PMC1540231 free full-text archive
Colinas J, Birnbaum K, Benfey PN