The Birnbaum Lab


Plant Development and Regeneration

What gives plants their remarkable capacity to regenerate whole organs? Plants grow indeterminately in adulthood through the activity of their meristems, which contain initials, or stem cells, that constantly replenish cells for continual organogenesis. We employ a regeneration system in which we completely excise most of the root meristem, including stem cells. The root then regenerates the entire meristem and resumes normal growth. We use this system to ask basic questions about the establishment of tissue organization long after embryogenesis is complete. We combine live imaging of regenerating roots with single-cell RNA-Seq analysis to coordinate the timing of events at the microscopic and molecular level, at the resolution of the single cell.

Algal Evolution Using Fluorescent Properties

Algal cultivation is a promising system for biofuels but, unlike agricultural cultivars, algae have not been adapted for human production systems. We use Fluorescence Activated Cell Sorting (FACS) to apply selective forces on algal populations to target very specific traits for biofuel improvement. We have adapted protocols that make use of fluorescent dyes or fluorescent properties of algae and can be used as readouts for specific traits. We select traits over multiple generations, similar to the domestication of crops in which repeated selection over many generations led to highly specialized agricultural crops. Here we optimize biofuel traits such as growth and oil accumulation using the algae/FACS system.

Evolution of Plant Roots

How did plant roots and the special cell types they contain evolve? The seedless vascular plant Selaginella is in a plant lineage whose ancestors appear to have branched off early in the evolution of land plants. This group of plants, the lycophytes, is the first to display a true root. It’s not clear that the Selaginella root is homologous to the roots of flowering plants. However, they share a remarkably similar structure, with a root cap, root hairs, endodermis, and auxin-triggered development. One striking difference is that most Selaginella roots in the mature organism arise from shoot structures, leading to a long-standing debate over whether the early outgrowth – called a rhizophore – is root- or shoot-like. We have employed transcriptional analysis of all Selaginella meristems in a global comparison of the similarity between the rhizophore transcriptome the embryonic root or the early shoot structure.


Principal Investigator

Ken Birnbaum


Bruno Guillotin

Ramin Rahni

Sunil Kenchanmane Raju

PhD Students

Dylan Fitzmaurice
Graeme Vissers


Pui-Leng Ip


A pan-grass transcriptome reveals patterns of cellular divergence in crops [PDF]
Nature (2023)
Bruno Guillotin, Ramin Rahni, Michael Passalacqua, Mohammed Ateequr Mohammed, Xiaosa Xu, Sunil Kenchanmane Raju, Carlos Ortiz Ramírez, David Jackson, Simon C. Groen, Jesse Gillis, Kenneth D. Birnbaum

Plant glutamate receptors mediate a bet-hedging strategy between regeneration and defense
Developmental Cell (2022)
Marcela Hernández-Coronado, Poliana Coqueiro, Dias Araujo, Pui-Leng Ip, Custódio O. Nunes, Ramin Rahni, Michael M. Wudick, Michael A. Lizzio, José A. Feijó, Kenneth D. Birnbaum

Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization
Science (2021)
Pawel Roszak, Jung-Ok Heo, Bernhard Blob, Koichi Toyokura, Yuki Sugiyama, Maria Angels De Luis Balaguer, Winnie W. Y. Lau, Fiona Hamey, Jacopo Cirrone, Ewelina Madej, Alida M. Bouatta, Xin Wang, Marjorie Guichard, Robertas Ursache, Hugo Tavares, Kevin Verstaen, Jos Wendrich, Charles W. Melnyk, Yoshihisa Oda, Dennis Shasha, Sebastian E. Ahnert, Yvan Saeys, Bert De Rybel, Renze Heidstra, Ben Scheres, Guido Grossman, Ari Pekka Mähönen, Philipp Denninger, Berthold Göttgens, Rosangela Sozzani, Kenneth D. Birnbaum, Yrjö Helariutta

Ground tissue circuitry regulates organ complexity in maize and Setaria
Science (2021)
Carlos Ortiz-Ramírez, Bruno Guillotin, Xiaosa Xu, Ramin Rahni, Sanqiang Zhang, Zhe Yan, Poliana Coqueiro Dias Araujo, Edgar Demesa-Arevalo, Laura Lee, Joyce Van Eck, Thomas R. Gingeras, David Jackson, Kimberly L. Gallagher, & Kenneth D. Birnbaum

Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud [PDF]
Frontiers in Plant Science (2020)
Liya Wang, Zhenyuan Lu, Melissa delaBastide, Peter Van Buren, Xiaofei Wang, Cornel Ghiban, Michael Regulski, Jorg Drenkow, Xiaosa Xu, Carlos Ortiz-Ramirez, Crisitina F. Marco, Sara Goodwin, Alexander Dobin, Kenneth D. Birnbaum, David P. Jackson, Robert A. Martienssen, William R. McCombie, David A. Micklos, Michael C. Schatz, Doreen H. Ware, & Thomas R. Gingeras

Just passing through: The auxin gradient of the root meristem [PDF]
Current Topics in Developmental Biology (2020)
Bruno Guillotin & Kenneth D. Birnbaum

Directions for research and training in plant omics: Big Questions and Big Data [PDF]
Plant Direct (2020)
Cristiana T. Argueso, Sarah M. Assmann, Kenneth D. Birnbaum, Sixue Chen, José R. Dinneny, Colleen J. Doherty, Andrea L. Eveland, Joanna Friesner, Vanessa R. Greenlee, Julie A. Law, Amy Marshall-Colón, Grace Alex Mason, Ruby O'Lexy, Scott C. Peck, Robert J. Schmitz, Liang Song, David Stern, Marguerite J. Varagona, Justin W. Walley, & Cranos M. Williams

Towards Building a Plant Cell Atlas [PDF]
Trends in Plant Science (2020)
Seung Y. Rhee, Kenneth D. Birnbaum, & David W. Ehrhardt

The Selaginella rhizophore has a unique transcriptional identity compared with root and shoot meristems [PDF]
New Phytologist (2019)
Alison Mello, Idan Efroni, Ramin Rahni, & Kenneth D. Birnbaum

Week-long imaging of cell divisions in the Arabidopsis root meristem [PDF]
Plant Methods (2019)
Ramin Rahni & Kenneth D. Birnbaum

Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues [PDF]
Annual Review of Genetics (2018)
Kenneth D. Birnbaum

An Efficient Cell Sorting Protocol for Maize Protoplasts [PDF]
Current Protocols (2018)
Carlos Ortiz-Ramírez, Edgar Demesa Arevalo, Xiaosa Xu, David P. Jackson, & Kenneth D. Birnbaum

Epigenetic memory and cell fate reprogramming in plants [PDF]
Regeneration (2017)
Kenneth D. Birnbaum & François Roudier

Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root [PDF]
Science Signaling (2016)
Daniela Ristova, Clément Carré, Marjorie Pervent, Anna Medici, Grace Jaeyoon Kim, Domenica Scalia, Sandrine Ruffel, Kenneth D. Birnbaum, Benoît Lacombe, Wolfgang Busch, Gloria M. Coruzzi, & Gabriel Krouk

How many ways are there to make a root? [PDF]
Current Opinions in Plant Biology (2016)
Kenneth D. Birnbaum

A Case for Distributed Control of Local Stem Cell Behavior in Plants [PDF]
Developmental Cell (2016)
Ramin Rahni, Idan Efroni, & Kenneth D. Birnbaum

Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions [PDF]
Cell (2016)
Idan Efroni, Alison Mello, Tal Nawy, Pui-Leng Ip, Ramin Rahni, Nicholas DelRose, Ashley Powers, Rahul Satija & Kenneth D. Birnbaum

The potential of single-cell profiling in plants [PDF]
Genome Biol (2016)
Idan Efroni & Kenneth D. Birnbaum

Plant Cell Shape: Trafficking Gets Edgy [PDF]
Dev Cell (2016)
Ramin Rahni & Kenneth D. Birnbaum

Quantification of cell identity from single-cell gene expression profiles. [PDF]
Genome Biol (2015)
Idan Efroni, Pui-Leng Ip, Tal Nawy, Alison Mello & Kenneth D. Birnbaum

Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. [PDF]
Proc Natl Acad Sci USA (2014)
Para A, Li Y, Amy Marshall-Colon, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bastiaan O. R. Bargmann, Kenneth D. Birnbaum, McCombie WR, Gabriel Krouk & Gloria M. Coruzzi

An undergraduate study of two transcription factors that promote lateral root formation. [PDF]
Biochem Mol Biol Educ (2014)
Bastiaan O. R. Bargmann, Kenneth D. Birnbaum & Eric D. Brenner

Plasticity regulators modulate specific root traits in discrete nitrogen environments. [PDF]
PLoS Genet (2013)
Miriam L. Gifford, Joshua A. Banta, Manpreet S. Katari, Jo Hulsmans, Lisa Chen, Daniela Ristova, Daniel Tranchina, Michael D. Purugganan, Gloria M. Coruzzi & Kenneth D. Birnbaum

A map of cell type-specific auxin responses. [PDF]
Mol Syst Biol (2013)
Bastiaan O. R. Bargmann, Steffen Vanneste, Gabriel Krouk, Tal Nawy, Idan Efroni, Eilon Shani, Goh Choe, Jiri Friml, Dominique C. Bergmann, Mark Estelle & Kenneth D. Birnbaum

Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture. [PDF]
Proc Natl Acad Sci USA (2013)
Ulises Rosas, Angelica Cibrian-Jaramillo, Daniela Ristova, Joshua A. Banta, Miriam L. Gifford, Angela Huihui Fan, Royce W. Zhou, Grace Yaeyoon Kim, Gabriel Krouk, Kenneth D. Birnbaum, Michael D. Purugganan & Gloria M. Coruzzi

Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. [PDF]
Dev Cell (2013)
Idan Efroni, Soon-Ki Han, Hye Jin Kim, Miin-Feng Wu, Evyatar Steiner, Kenneth D. Birnbaum, Jong Chan Hong, Yuval Eshed & Doris Wagner

TARGET: a transient transformation system for genome-wide transcription factor target discovery. [PDF]
Mol Plant (2013)
Bastiaan O. R. Bargmann, Marshall-Colon A, Idan Efroni, Ruffel S, Kenneth D. Birnbaum, Gloria M. Coruzzi & Gabriel Krouk

RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis. [PDF]
Plant Physiol (2013)
Daniela Ristova, Ulises Rosas, Gabriel Krouk, Sandrine Ruffel, Kenneth D. Birnbaum & Gloria M. Coruzzi

Fluorescence-activated cell sorting for analysis of cell type-specific responses to salinity stress in Arabidopsis and rice. [PDF]
Methods Mol Biol (2012)
Evrard A, Bastiaan O. R. Bargmann, Kenneth D. Birnbaum, Mark Tester, Ute Baumann & Alexander A.T. Johnson

High-throughput fluorescence-based isolation of live C. elegans larvae. [PDF]
Nat Protoc (2012)
Anita G. Fernandez, Bastiaan O. R. Bargmann, Emily K. Mis, Mark L. Edgley, Kenneth D. Birnbaum & Fabio Piano

Low-cost sequencing opens new insights into diverse plant genomes. [PDF]
Genome Biol (2012)
Kenneth D. Birnbaum

Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand. [PDF]
Proc Natl Acad Sci USA (2011)
Sandrine Ruffel, Gabriel Krouk, Daniela Ristova, Dennis E. Shasha, Kenneth D. Birnbaum & Gloria M. Coruzzi

Measuring cell identity in noisy biological systems. [PDF]
Nucleic Acids Res (2011)
Kenneth D. Birnbaum & Edo Kussell

Quantitation of cellular dynamics in growing Arabidopsis roots with light sheet microscopy. [PDF]
PLoS One (2011)
Giovanni Sena, Zak Frentz, Kenneth D. Birnbaum & Stanislas Leibler

Predicting genome-wide redundancy using machine learning. [PDF]
BMC Evol Biol (2010)
Huang-Wen Chen, Sunayan Bandyopadhyay, Dennis E. Shasha & Kenneth D. Birnbaum

The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo. [PDF]
Dev Cell (2010)
Tal Nawy, Martin Bayer, Jozef Mravec, Jiri Friml, Kenneth D. Birnbaum & Wolfgang Lukowitz

Built to rebuild: in search of organizing principles in plant regeneration. [PDF]
Curr Opin Genet Dev (2010)
Giovanni Sena & Kenneth D. Birnbaum

Automated sorting of live C. elegans using laFACS. [PDF]
Nat Methods (2010)
Amita G. Fernandez, Emily K. Mis, Bastiaan O. R. Bargmann, Kenneth D. Birnbaum & Fabio Piano

Fluorescence activated cell sorting of plant protoplasts. [PDF]
J Vis Exp (2010)
Bastiaan O. R. Bargmann & Kenneth D. Birnbaum

Organ regeneration does not require a functional stem cell niche in plants. [PDF]
Nature (2009)
Giovanni Sena, Xiaoning Wang, Hsiao-Yun Liu, Hugo Hofhuis & Kenneth D. Birnbaum

Positive fluorescent selection permits precise, rapid, and in-depth overexpression analysis in plant protoplasts. [PDF]
Plant Physiol (2009)
Bastiaan O. R. Bargmann & Kenneth D. Birnbaum

Slicing across kingdoms: regeneration in plants and animals. [PDF]
Cell (2008)
Kenneth D. Birnbaum & Alejandro Sanchez Alvarado

Cell-specific nitrogen responses mediate developmental plasticity. [PDF]
Proc Natl Acad Sci USA (2008)
Miriam L. Gifford, Alexis Dean, Rodrigo A. Gutierrez, Gloria M. Coruzzi & Kenneth D. Birnbaum


Congratulations to Carlos Ortiz Ramirez!

Birnbaum lab postdoc will start his lab at Cinvestav, UGA-Langebio Mexico in January, 2020.

Keep an eye out for the Plant Cell Atlas meeting in March 28-30, 2020 at the Carnegie Institute for Science at Stanford. Ken is one of the organizers, contact him if you are interested in applying for attendance. See 2019 initiative paper in TIPS.

Birnbaum Lab Alum Wins Prestigious Intel ISEF 2016 Award for Plant Science

High school student Charlotte Keeley won First Award in the Plant Science category at the Intel ISEF 2016 competition, for her work on regeneration during her time in the Birnbaum lab. Charlotte's project, Plant Tissues that Fail to Regenerate Undergo Early Steps of Remodeling but Fail to Induce a Cytokinin Hormone Response was among 1,700 entries into the contest. Read the full press release and winner list here.

Lab Microscopy Footage Featured in the Imagine Science Film Festival

Excerpts from confocal timelapse movies of regeneration made in the lab were recently featured in the 7th Annual Imagine Science Film Festival, airing in NYC and in a satellite festival in Berlin.


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