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Kenneth Birnbaum

Professor of Biology

    20012020

    Research output per year

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    Research Output

    2020

    Just passing through: The auxin gradient of the root meristem

    Guillotin, B. & Birnbaum, K. D., 2020, Current Topics in Developmental Biology. Small, S. & Briscoe, J. (eds.). Academic Press Inc., p. 433-454 22 p. (Current Topics in Developmental Biology; vol. 137).

    Research output: Chapter in Book/Report/Conference proceedingChapter

    Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud

    Wang, L., Lu, Z., delaBastide, M., Van Buren, P., Wang, X., Ghiban, C., Regulski, M., Drenkow, J., Xu, X., Ortiz-Ramirez, C., Marco, C. F., Goodwin, S., Dobin, A., Birnbaum, K. D., Jackson, D. P., Martienssen, R. A., McCombie, W. R., Micklos, D. A., Schatz, M. C., Ware, D. H. & 1 others, Gingeras, T. R., Mar 31 2020, In : Frontiers in Plant Science. 11, 289.

    Research output: Contribution to journalArticle

    Open Access
    2019

    Directions for research and training in plant omics: Big Questions and Big Data

    Argueso, C. T., Assmann, S. M., Birnbaum, K. D., Chen, S., Dinneny, J. R., Doherty, C. J., Eveland, A. L., Friesner, J., Greenlee, V. R., Law, J. A., Marshall-Colón, A., Mason, G. A., O'Lexy, R., Peck, S. C., Schmitz, R. J., Song, L., Stern, D., Varagona, M. J., Walley, J. W. & Williams, C. M., Apr 2019, In : Plant Direct. 3, 4, e00133.

    Research output: Contribution to journalArticle

    Open Access

    The Selaginella rhizophore has a unique transcriptional identity compared with root and shoot meristems

    Mello, A., Efroni, I., Rahni, R. & Birnbaum, K. D., Apr 2019, In : New Phytologist. 222, 2, p. 882-894 13 p.

    Research output: Contribution to journalArticle

    Towards Building a Plant Cell Atlas

    Rhee, S. Y., Birnbaum, K. D. & Ehrhardt, D. W., Apr 2019, In : Trends in Plant Science. 24, 4, p. 303-310 8 p.

    Research output: Contribution to journalReview article

    Week-long imaging of cell divisions in the Arabidopsis root meristem

    Rahni, R. & Birnbaum, K. D., Mar 25 2019, In : Plant Methods. 15, 1, 30.

    Research output: Contribution to journalArticle

    Open Access
    2018

    An Efficient Cell Sorting Protocol for Maize Protoplasts

    Ortiz-Ramírez, C., Arevalo, E. D., Xu, X., Jackson, D. P. & Birnbaum, K. D., Sep 1 2018, In : Current protocols in plant biology. 3, 3, p. e20072

    Research output: Contribution to journalArticle

    Power in numbers: Single-cell RNA-seq strategies to dissect complex tissues

    Birnbaum, K. D., Nov 23 2018, In : Annual Review of Genetics. 52, p. 203-221 19 p.

    Research output: Contribution to journalReview article

    2016

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

    Rahni, R., Efroni, I. & Birnbaum, K. D., Sep 26 2016, In : Developmental Cell. 38, 6, p. 635-642 8 p.

    Research output: Contribution to journalReview article

    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, G. J., Scalia, D., Ruffel, S., Birnbaum, K. D., Lacombe, B., Busch, W., Coruzzi, G. M. & Krouk, G., Oct 25 2016, In : Science signaling. 9, 451, rs13.

    Research output: Contribution to journalArticle

    How many ways are there to make a root?

    Birnbaum, K. D., Dec 1 2016, In : Current Opinion in Plant Biology. 34, p. 61-67 7 p.

    Research output: Contribution to journalReview article

    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, A. A. T., Birnbaum, K. D., Mayo, G. M., Jha, D., Henderson, S. W., Tester, M., Gilliham, M. & Roy, S. J., Feb 2016, In : Plant physiology. 170, 2, p. 1014-1029 16 p.

    Research output: Contribution to journalArticle

    Plant Cell Shape: Trafficking Gets Edgy

    Rahni, R. & Birnbaum, K. D., Feb 22 2016, In : Developmental Cell. 36, 4, p. 353-354 2 p.

    Research output: Contribution to journalShort survey

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

    Efroni, I., Mello, A., Nawy, T., Ip, P. L., Rahni, R., Delrose, N., Powers, A., Satija, R. & Birnbaum, K. D., Jun 16 2016, In : Cell. 165, 7, p. 1721-1733 13 p.

    Research output: Contribution to journalArticle

    The potential of single-cell profiling in plants

    Efroni, I. & Birnbaum, K. D., Apr 5 2016, In : Genome biology. 17, 1, 65.

    Research output: Contribution to journalArticle

    Development: Acting your cellular age

    Birnbaum, K. D., Jul 7 2015, In : Nature Plants. 1, 15100.

    Research output: Contribution to journalShort survey

    Quantification of cell identity from single-cell gene expression profiles

    Efroni, I., Ip, P. L., Nawy, T., Mello, A. & Birnbaum, K. D., Jan 22 2015, In : Genome biology. 16, 1, 9.

    Research output: Contribution to journalArticle

    Tissue-specific gene expression profiling by cell sorting

    Ip, P. L. & Birnbaum, K. D., 2015, In : Methods in Molecular Biology. 1284, p. 175-183 9 p.

    Research output: Contribution to journalArticle

    Tissue-specific gene expression profiling by cell sorting

    Ip, P. L. & Birnbaum, K. D., Mar 11 2015, Plant Functional Genomics: Methods and Protocols: Second Edition. Springer New York, p. 175-183 9 p.

    Research output: Chapter in Book/Report/Conference proceedingChapter

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

    Adrian, J., Chang, J., Ballenger, C. E., Bargmann, B. O. R., Alassimone, J., Davies, K. A., Lau, O. S., Matos, J. L., Hachez, C., Lanctot, A., Vatén, A., Birnbaum, K. D. & Bergmann, D. C., Apr 6 2015, In : Developmental Cell. 33, 1, p. 107-118 12 p.

    Research output: Contribution to journalArticle

    2014

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

    Bargmann, B. O. R., Birnbaum, K. D. & Brenner, E. D., 2014, In : Biochemistry and Molecular Biology Education. 42, 3, p. 237-245 9 p.

    Research output: Contribution to journalArticle

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

    Para, A., Li, Y., Marshall-Coloń, A., Varala, K., Francoeur, N. J., Moran, T. M., Edwards, M. B., Hackley, C., Bargmann, B. O. R., Birnbaum, K. D., Richard McCombie, W., Krouk, G. & Coruzzi, G. M., Jul 15 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 28, p. 10371-10376 6 p.

    Research output: Contribution to journalArticle

    2013

    A map of cell type-specific auxin responses

    Bargmann, B. O. R., Vanneste, S., Krouk, G., Nawy, T., Efroni, I., Shani, E., Choe, G., Friml, J., Bergmann, D. C., Estelle, M. & Birnbaum, K. D., 2013, In : Molecular systems biology. 9, 1, 688.

    Research output: Contribution to journalArticle

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

    Rosas, U., Cibrian-Jaramillo, A., Ristova, D., Banta, J. A., Gifford, M. L., Fan, A. H., Zhou, R. W., Kim, G. J., Krouk, G., Birnbaum, K. D., Purugganan, M. D. & Coruzzi, G. M., Sep 10 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 37, p. 15133-15138 6 p.

    Research output: Contribution to journalArticle

    Plasticity Regulators Modulate Specific Root Traits in Discrete Nitrogen Environments

    Gifford, M. L., Banta, J. A., Katari, M. S., Hulsmans, J., Chen, L., Ristova, D., Tranchina, D., Purugganan, M. D., Coruzzi, G. M. & Birnbaum, K. D., Sep 2013, In : PLoS genetics. 9, 9, e1003760.

    Research output: Contribution to journalArticle

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

    Efroni, I., Han, S. K., Kim, H. J., Wu, M. F., Steiner, E., Birnbaum, K. D., Hong, J. C., Eshed, Y. & Wagner, D., Feb 25 2013, In : Developmental Cell. 24, 4, p. 438-445 8 p.

    Research output: Contribution to journalArticle

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

    Ristova, D., Rosas, U., Krouk, G., Ruffel, S., Birnbaum, K. D. & Coruzzi, G. M., 2013, In : Plant physiology. 161, 3, p. 1086-1096 11 p.

    Research output: Contribution to journalArticle

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

    Bargmann, B. O. R., Marshall-Colon, A., Efroni, I., Ruffel, S., Birnbaum, K. D., Coruzzi, G. M. & Krouk, G., May 2013, In : Molecular Plant. 6, 3, p. 978-980 3 p.

    Research output: Contribution to journalLetter

    2012

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

    Evrard, A., Bargmann, B. O. R., Birnbaum, K. D., Tester, M., Baumann, U. & Johnson, A. A. T., 2012, Plant Salt Tolerance: Methods and Protocols: Methods and Protocols. Humana Press Inc., Vol. 913. p. 265-276 12 p. (Methods in Molecular Biology; vol. 913).

    Research output: Chapter in Book/Report/Conference proceedingChapter

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

    Fernandez, A. G., Bargmann, B. O. R., Mis, E. K., Edgley, M. L., Birnbaum, K. D. & Piano, F., Aug 2012, In : Nature Protocols. 7, 8, p. 1502-1510 9 p.

    Research output: Contribution to journalArticle

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

    Birnbaum, K. D., 2012, In : Genome biology. 13, 1, 1 p.

    Research output: Contribution to journalArticle

    2011

    Measuring cell identity in noisy biological systems

    Birnbaum, K. D. & Kussell, E., Nov 2011, In : Nucleic acids research. 39, 21, p. 9093-9107 15 p.

    Research output: Contribution to journalArticle

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

    Sena, G., Frentz, Z., Birnbaum, K. D. & Leibler, S., 2011, In : PloS one. 6, 6, e21303.

    Research output: Contribution to journalArticle

    2010

    Automated sorting of live C. elegans using laFACS

    Fernandez, A. G., Mis, E. K., Bargmann, B. O. R., Birnbaum, K. D. & Piano, F., Jun 2010, In : Nature methods. 7, 6, p. 417-418 2 p.

    Research output: Contribution to journalLetter

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

    Sena, G. & Birnbaum, K. D., Aug 2010, In : Current Opinion in Genetics and Development. 20, 4, p. 460-465 6 p.

    Research output: Contribution to journalReview article

    Estimation of genome-wide redundancy in Arabidopsis thaliana

    Chen, H-W., Bandyopadhyay, S., Shasha, D. & Birnbaum, K., 2010, In : BMC Evolutionary Biology. 10, p. 357

    Research output: Contribution to journalArticle

    Fluorescence activated cell sorting of plant protoplasts

    Bargmann, B. O. R. & Birnbaum, K. D., Feb 2010, In : Journal of visualized experiments : JoVE. 36, e1673.

    Research output: Contribution to journalArticle

    Predicting genome-wide redundancy using machine learning

    Chen, H. W., Bandyopadhyay, S., Shasha, D. E. & Birnbaum, K. D., 2010, In : BMC Evolutionary Biology. 10, 1, 357.

    Research output: Contribution to journalArticle

    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, K. D. & Lukowitz, W., Jul 2010, In : Developmental Cell. 19, 1, p. 103-113 11 p.

    Research output: Contribution to journalArticle

    2009

    Erratum: The fifth sentence under "Protoplast Isolation and Transfection (Materials and Methods (2009)149: (1231-1239))

    Bargmann, B. O. R. & Birnbaum, K. D., Jun 2009, In : Plant physiology. 150, 2, 1 p.

    Research output: Contribution to journalComment/debate

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

    Sena, G., Wang, X., Liu, H. Y., Hofhuis, H. & Birnbaum, K. D., Feb 26 2009, In : Nature. 457, 7233, p. 1150-1153 4 p.

    Research output: Contribution to journalArticle

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

    Bargmann, B. O. R. & Birnbaum, K. D., Mar 2009, In : Plant physiology. 149, 3, p. 1231-1239 9 p.

    Research output: Contribution to journalArticle

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

    Benfey, P. N. & Birnbaum, K. D., 2009, In : Developmental Dynamics. 238, 9, p. 2449-58

    Research output: Contribution to journalArticle

    2008

    Cell-specific nitrogen responses mediate developmental plasticity

    Gifford, M. L., Dean, A., Gutierrez, R. A., Coruzzi, G. M. & Birnbaum, K. D., Jan 15 2008, In : Proceedings of the National Academy of Sciences of the United States of America. 105, 2, p. 803-808 6 p.

    Research output: Contribution to journalArticle

    Slicing across Kingdoms: Regeneration in Plants and Animals

    Birnbaum, K. D. & Alvarado, A. S., Feb 22 2008, In : Cell. 132, 4, p. 697-710 14 p.

    Research output: Contribution to journalReview article

    2006

    Global studies of cell type-specific gene expression in plants

    Galbraith, D. W. & Birnbaum, K., 2006, In : Annual Review of Plant Biology. 57, p. 451-475 25 p.

    Research output: Contribution to journalReview article

    2005

    Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines

    Birnbaum, K., Jung, J. W., Wang, J. Y., Lambert, G. M., Hirst, J. A., Galbraith, D. W. & Benfey, P. N., Aug 2005, In : Nature methods. 2, 8, p. 615-619 5 p.

    Research output: Contribution to journalArticle

    Transcriptional profile of the arabidopsis root quiescent center

    Nawy, T., Lee, J. Y., Colinas, J., Wang, J. Y., Thongrod, S. C., Malamy, J. E., Birnbaum, K. & Benfey, P. N., 2005, In : Plant Cell. 17, 7, p. 1908-1925 18 p.

    Research output: Contribution to journalArticle