No photo of Kenneth Birnbaum

Kenneth Birnbaum

Professor of Biology

    20012020

    Research output per year

    If you made any changes in Pure these will be visible here soon.

    Research Output

    Filter
    Article
    2020

    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

    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

    2016

    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

    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

    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

    2015

    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., Jan 1 2015, In : Methods in Molecular Biology. 1284, p. 175-183 9 p.

    Research output: Contribution to journalArticle

    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., Jan 1 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., Jan 1 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 1 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., Mar 11 2013, In : Plant physiology. 161, 3, p. 1086-1096 11 p.

    Research output: Contribution to journalArticle

    2012

    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 1 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 1 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., Jun 27 2011, In : PloS one. 6, 6, e21303.

    Research output: Contribution to journalArticle

    2010

    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., Nov 22 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 1 2010, In : Developmental Cell. 19, 1, p. 103-113 11 p.

    Research output: Contribution to journalArticle

    2009

    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 1 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

    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 1 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., Dec 1 2005, In : Plant Cell. 17, 7, p. 1908-1925 18 p.

    Research output: Contribution to journalArticle

    2003

    A Gene Expression Map of the Arabidopsis Root

    Birnbaum, K., Shasha, D. E., Wang, J. Y., Jung, J. W., Lambert, G. M., Galbraith, D. W. & Benfey, P. N., Dec 12 2003, In : Science. 302, 5652, p. 1956-1960 5 p.

    Research output: Contribution to journalArticle

    Integrating Gene Flow, Crop Biology, and Farm Management in On-Farm Conservation of Avocado (Persea americana, Lauraceae)

    Birnbaum, K., DeSalle, R., Peters, C. M. & Benfey, P. N., Nov 2003, In : American Journal of Botany. 90, 11, p. 1619-1627 9 p.

    Research output: Contribution to journalArticle

    2002

    MANAGEDPOP: A computer simulation to project allelic diversity in managed populations with overlapping generations

    Birnbaum, K., Benfey, P. N., Peters, C. M. & Desalle, R., Dec 1 2002, In : Molecular Ecology Notes. 2, 4, p. 615-617 3 p.

    Research output: Contribution to journalArticle

    Using cauliflower to find conserved non-coding regions in Arabidopsis

    Colinas, J., Birnbaum, K. & Benfey, P. N., Jan 1 2002, In : Plant physiology. 129, 2, p. 451-454 4 p.

    Research output: Contribution to journalArticle

    2001

    cis element/transcription factor Analysis (cis/TF): A method for discovering transcription factor/cis element relationships

    Birnbaum, K., Benfey, P. N. & Shasha, D. E., Oct 4 2001, In : Genome Research. 11, 9, p. 1567-1573 7 p.

    Research output: Contribution to journalArticle