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Items: 36


Epigenetic memory and cell fate reprogramming in plants.

Birnbaum KD, Roudier F.

Regeneration (Oxf). 2017 Feb 1;4(1):15-20. doi: 10.1002/reg2.73. eCollection 2017 Feb. Review.


Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root.

Ristova D, Carré C, Pervent M, Medici A, Kim GJ, Scalia D, Ruffel S, Birnbaum KD, Lacombe B, Busch W, Coruzzi GM, Krouk G.

Sci Signal. 2016 Oct 25;9(451):rs13.


How many ways are there to make a root?

Birnbaum KD.

Curr Opin Plant Biol. 2016 Dec;34:61-67. doi: 10.1016/j.pbi.2016.10.001. Epub 2016 Oct 22. Review.


A Case for Distributed Control of Local Stem Cell Behavior in Plants.

Rahni R, Efroni I, Birnbaum KD.

Dev Cell. 2016 Sep 26;38(6):635-42. doi: 10.1016/j.devcel.2016.08.015. Review.


Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions.

Efroni I, Mello A, Nawy T, Ip PL, Rahni R, DelRose N, Powers A, Satija R, Birnbaum KD.

Cell. 2016 Jun 16;165(7):1721-1733. doi: 10.1016/j.cell.2016.04.046. Epub 2016 May 19.


The potential of single-cell profiling in plants.

Efroni I, Birnbaum KD.

Genome Biol. 2016 Apr 5;17:65. doi: 10.1186/s13059-016-0931-2.


Plant Cell Shape: Trafficking Gets Edgy.

Rahni R, Birnbaum KD.

Dev Cell. 2016 Feb 22;36(4):353-4. doi: 10.1016/j.devcel.2016.02.005.


Identification of a Stelar-Localized Transport Protein That Facilitates Root-to-Shoot Transfer of Chloride in Arabidopsis.

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.

Plant Physiol. 2016 Feb;170(2):1014-29. doi: 10.1104/pp.15.01163. Epub 2015 Dec 11.


Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population.

Adrian J, Chang J, Ballenger CE, Bargmann BO, Alassimone J, Davies KA, Lau OS, Matos JL, Hachez C, Lanctot A, Vatén A, Birnbaum KD, Bergmann DC.

Dev Cell. 2015 Apr 6;33(1):107-18. doi: 10.1016/j.devcel.2015.01.025.


Tissue-specific gene expression profiling by cell sorting.

Ip PL, Birnbaum KD.

Methods Mol Biol. 2015;1284:175-83. doi: 10.1007/978-1-4939-2444-8_8.


Quantification of cell identity from single-cell gene expression profiles.

Efroni I, Ip PL, Nawy T, Mello A, Birnbaum KD.

Genome Biol. 2015 Jan 22;16:9. doi: 10.1186/s13059-015-0580-x.


Development: Acting your cellular age.

Birnbaum KD.

Nat Plants. 2015 Jul 7;1:15100. doi: 10.1038/nplants.2015.100. No abstract available.


Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis.

Para A, Li Y, Marshall-Colón A, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bargmann BO, Birnbaum KD, McCombie WR, Krouk G, Coruzzi GM.

Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10371-6. doi: 10.1073/pnas.1404657111. Epub 2014 Jun 23.


An undergraduate study of two transcription factors that promote lateral root formation.

Bargmann BO, Birnbaum KD, Brenner ED.

Biochem Mol Biol Educ. 2014 May-Jun;42(3):237-45. doi: 10.1002/bmb.20780. Epub 2014 Feb 24.


Plasticity regulators modulate specific root traits in discrete nitrogen environments.

Gifford ML, Banta JA, Katari MS, Hulsmans J, Chen L, Ristova D, Tranchina D, Purugganan MD, Coruzzi GM, Birnbaum KD.

PLoS Genet. 2013;9(9):e1003760. doi: 10.1371/journal.pgen.1003760. Epub 2013 Sep 5.


A map of cell type-specific auxin responses.

Bargmann BO, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml J, Bergmann DC, Estelle M, Birnbaum KD.

Mol Syst Biol. 2013;9:688. doi: 10.1038/msb.2013.40.


Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture.

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.

Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):15133-8. doi: 10.1073/pnas.1305883110. Epub 2013 Aug 26. Erratum in: Proc Natl Acad Sci U S A. 2015 May 12;112(19):E2555.


Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.

Efroni I, Han SK, Kim HJ, Wu MF, Steiner E, Birnbaum KD, Hong JC, Eshed Y, Wagner D.

Dev Cell. 2013 Feb 25;24(4):438-45. doi: 10.1016/j.devcel.2013.01.019.


TARGET: a transient transformation system for genome-wide transcription factor target discovery.

Bargmann BO, Marshall-Colon A, Efroni I, Ruffel S, Birnbaum KD, Coruzzi GM, Krouk G.

Mol Plant. 2013 May;6(3):978-80. doi: 10.1093/mp/sst010. Epub 2013 Jan 18. No abstract available.


RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis.

Ristova D, Rosas U, Krouk G, Ruffel S, Birnbaum KD, Coruzzi GM.

Plant Physiol. 2013 Mar;161(3):1086-96. doi: 10.1104/pp.112.210872. Epub 2013 Jan 18.


Fluorescence-activated cell sorting for analysis of cell type-specific responses to salinity stress in Arabidopsis and rice.

Evrard A, Bargmann BO, Birnbaum KD, Tester M, Baumann U, Johnson AA.

Methods Mol Biol. 2012;913:265-76. doi: 10.1007/978-1-61779-986-0_18.


High-throughput fluorescence-based isolation of live C. elegans larvae.

Fernandez AG, Bargmann BO, Mis EK, Edgley ML, Birnbaum KD, Piano F.

Nat Protoc. 2012 Jul 19;7(8):1502-10. doi: 10.1038/nprot.2012.084.


Low-cost sequencing opens new insights into diverse plant genomes.

Birnbaum KD.

Genome Biol. 2012 Jan 30;13(1):311. doi: 10.1186/gb-2012-13-1-311.


Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand.

Ruffel S, Krouk G, Ristova D, Shasha D, Birnbaum KD, Coruzzi GM.

Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18524-9. doi: 10.1073/pnas.1108684108. Epub 2011 Oct 24.


Measuring cell identity in noisy biological systems.

Birnbaum KD, Kussell E.

Nucleic Acids Res. 2011 Nov;39(21):9093-107. doi: 10.1093/nar/gkr591. Epub 2011 Jul 29.


Quantitation of cellular dynamics in growing Arabidopsis roots with light sheet microscopy.

Sena G, Frentz Z, Birnbaum KD, Leibler S.

PLoS One. 2011;6(6):e21303. doi: 10.1371/journal.pone.0021303. Epub 2011 Jun 22.


Predicting genome-wide redundancy using machine learning.

Chen HW, Bandyopadhyay S, Shasha DE, Birnbaum KD.

BMC Evol Biol. 2010 Nov 18;10:357. doi: 10.1186/1471-2148-10-357.


The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo.

Nawy T, Bayer M, Mravec J, Friml J, Birnbaum KD, Lukowitz W.

Dev Cell. 2010 Jul 20;19(1):103-13. doi: 10.1016/j.devcel.2010.06.004.


Built to rebuild: in search of organizing principles in plant regeneration.

Sena G, Birnbaum KD.

Curr Opin Genet Dev. 2010 Aug;20(4):460-5. doi: 10.1016/j.gde.2010.04.011. Epub 2010 May 27. Review.


Automated sorting of live C. elegans using laFACS.

Fernandez AG, Mis EK, Bargmann BO, Birnbaum KD, Piano F.

Nat Methods. 2010 Jun;7(6):417-8. doi: 10.1038/nmeth.f.304. Epub 2010 May 2. No abstract available.


Fluorescence activated cell sorting of plant protoplasts.

Bargmann BO, Birnbaum KD.

J Vis Exp. 2010 Feb 18;(36). pii: 1673. doi: 10.3791/1673.


Primer and interviews: Gene regulation in Arabidopsis thaliana. Interview by Julie C. Kiefer.

Benfey PN, Birnbaum KD.

Dev Dyn. 2009 Sep;238(9):2449-58. doi: 10.1002/dvdy.22042.


Organ regeneration does not require a functional stem cell niche in plants.

Sena G, Wang X, Liu HY, Hofhuis H, Birnbaum KD.

Nature. 2009 Feb 26;457(7233):1150-3. doi: 10.1038/nature07597. Epub 2009 Jan 28.


Positive fluorescent selection permits precise, rapid, and in-depth overexpression analysis in plant protoplasts.

Bargmann BO, Birnbaum KD.

Plant Physiol. 2009 Mar;149(3):1231-9. doi: 10.1104/pp.108.133975. Epub 2009 Jan 23. Erratum in: Plant Physiol. 2009 Jun;150(2):1105.


Slicing across kingdoms: regeneration in plants and animals.

Birnbaum KD, Sánchez Alvarado A.

Cell. 2008 Feb 22;132(4):697-710. doi: 10.1016/j.cell.2008.01.040. Review.


Cell-specific nitrogen responses mediate developmental plasticity.

Gifford ML, Dean A, Gutierrez RA, Coruzzi GM, Birnbaum KD.

Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):803-8. doi: 10.1073/pnas.0709559105. Epub 2008 Jan 7.

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