Benfey Lab Publications
Click on the links to access abstracts on PubMed or Web of Science.

Benfey PN, Mitchell-Olds T. From genotype to phenotype: systems biology meets natural variation. (2008) Science. 320 ( 5875 ): 495-7. Abstract available for free. Science Online Full Text.

Dinneny JR, Long TA, Wang JY, Jung JW, Mace D, Pointer S, Barron C, Brady SM, Schiefelbein J, Benfey PN. Cell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress. (2008) Science. Abstract available for free. Science Online Full Text.

Dinneny JR, Benfey PN. Plant stem cell niches: standing the test of time. (2008) Cell. 132 ( 4 ): 553-7. Abstract available for free. Cell Press Full Text.

Brady SM, Orlando DA, Lee JY, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN. A high-resolution root spatiotemporal map reveals dominant expression patterns. (2007) Science. 318 ( 5851 ): 801-6 . Abstract available for free. Science Online Full Text

Cui H, Levesque MP, Vernoux T, Jung JW, Paquette AJ, Gallagher KL, Wang JY, Blilou I, Scheres B, Benfey PN. An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. (2007) Science. 316(5823), 421-5. Abstract available for free. Science Online Full Text

Brady SM, Song S, Dhugga KS, Rafalski JA, Benfey PN. (2007) Combining expression and comparative evolutionary analysis. The COBRA gene family. Plant Physiol. 143(1), 172-87. Abstract

Weitz JS, Benfey PN, Wingreen NS. (2007) Evolution, interactions, and biological networks. PLoS Biol. 5(1), e11. Full Text

Long TA, Benfey PN. (2006) Transcription factors and hormones: new insights into plant cell differentiation. Curr Opin Cell Biol. [Epub ahead of print] Abstract

Brady SM, Long TA, Benfey PN. (2006) Unraveling the dynamic transcriptome. Plant Cell 18(9), 2101-11. Abstract

Mace DL, Lee JY, Twigg RW, Colinas J, Benfey PN, Ohler U. (2006) Quantification of transcription factor expression from Arabidopsis images. Bioinformatics. 22(14), e323-31. Abstract

Levesque MP, Vernoux T, Busch W, Cui H, Wang JY, Blilou I, Hassan H, Nakajima K, Matsumoto N, Lohmann JU, Scheres B, Benfey PN. (2006) Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol. 4(5), e143. Abstract

Lee JY, Colinas J, Wang JY, Mace D, Ohler U, Benfey PN. (2006) Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proc Natl Acad Sci U S A 103(15), 6055-60. Abstract

Friml J, Benfey P, Benkova E, Bennett M, Berleth T, Geldner N, Grebe M, Heisler M, Hejatko J, Jurgens G, Laux T, Lindsey K, Lukowitz W, Luschnig C, Offringa R, Scheres B, Swarup R, Torres-Ruiz R, Weijers D, Zazimalova E. (2006) Apical-basal polarity: why plant cells don't stand on their heads. Trends Plant Sci. 11(1), 12-4. Abstract

Dinneny JR, Benfey PN. (2005) Stem cell research goes underground: the RETINOBLASTOMA-RELATED gene in root development. Cell 123(7), 1180-2. Abstract

Lim J, Jung JW, Lim CE, Lee MH, Kim BJ, Kim M, Bruce WB, Benfey PN. (2005) Conservation and diversification of SCARECROW in maize. Plant Mol Biol. 59(4), 619-30. Abstract

Vernoux T, Benfey PN. (2005) Signals that regulate stem cell activity during plant development. Curr Opin Genet Dev. 15(4), 388-94. Abstract

Birnbaum K, Jung JW, Wang JY, Lambert GM, Hirst JA, Galbraith DW, Benfey PN. (2005) Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nat Methods 2(8), 615-9. Abstract

Nawy T, Lee JY, Colinas J, Wang JY, Thongrod SC, Malamy JE, Birnbaum K, Benfey PN. (2005) Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell 17(7), 1908-25. Abstract

Roudier F, Fernandez AG, Fujita M, Himmelspach R, Borner GH, Schindelman G, Song S, Baskin TI, Dupree P, Wasteneys GO, Benfey PN. (2005) COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation. Plant Cell 17(6), 1749-63. Abstract

Paquette AJ, Benfey PN. (2005) Maturation of the ground tissue of the root is regulated by gibberellin and SCARECROW and requires SHORT-ROOT. Plant Physiol. 138(2), 636-40. Abstract

Lee JY, Levesque M, Benfey PN. (2005) High-throughput RNA isolation technologies. New tools for high-resolution gene expression profiling in plant systems. Plant Physiol. 138(2), 585-90. Abstract

Benfey PN. (2005) Developmental networks. Plant Physiol 138(2), 548-9. Abstract

Gallagher, K.L. and P.N. Benfey (2005) Not just another hole in the wall: understanding intercellular protein trafficking. Genes and Development 19, 189-195. Abstract

Gallagher, K.L., A.J. Paquette, K. Nakajima, and Benfey P.N. (2004) Mechanisms regulating SHORT-ROOT intercellular movement. Current Biology 14, 1847-1851. Abstract

Birnbaum, K. and P.N. Benfey (2004) Network building: transcriptional circuits in the root. Current Opinion in Plant Biology 7, 582-588. Abstract

Benfey, P.N. (2004) Development and ecology in the time of systems biology. Developmental Cell. 7, 329-330. Abstract

Sena, G., J.W. Jung, and P.N. Benfey (2004) A broad competence to respond to SHORT ROOT revealed by tissue-specific ectopic expression. Development 131, 2817-26. Abstract

Irish, V.F. and P.N. Benfey (2004) Beyond Arabidopsis. Translational biology meets evolutionary developmental biology. Plant Physiology 135, 611-614. Abstract

Levesque, M.P. and P.N. Benfey (2004) Systems biology. Current Biology 14, R179-180. Abstract

Benfey P.N. (2004) A common switch used by plants and animals. Cell 116, 4-5. Abstract

Birnbaum, K., D.E. Shasha, J.Y. Wang, J. Jung, G.M. Lambert, D.W. Galbraith, and P. N. Benfey (2003) A gene expression map of the Arabidopsis root. Science 302, 1956-60. Abstract Full Text

Levesque, M., D. Shasha, W. Kim, M. Surette, and P. Benfey (2003)
Trait-to-Gene: A computational method for inferring the function of
uncharacterized genes. Current Biology 13, 129-133. Abstract

Roudier, F., G. Schindelman, R. DeSalle, and P.N. Benfey (2002) The
COBRA Family of Putative GPI-Anchored Proteins in Arabidopsis. A New
Fellowship in Expansion. Plant Physiology 130, 538-548. Abstract

Colinas, J., K. Birnbaum, P.N. Benfey (2002) Using cauliflower to find
conserved non-coding regions in Arabidopsis. Plant Physiology 129, 451-4.
Abstract

Muller, S., E. Fuchs, M. Ovecka, J. Wysocka-Diller, P.N. Benfey, M.T.
Hauser (2002) Two New Loci, PLEIADE and HYADE, Implicate Organ-Specific
Regulation of Cytokinesis in Arabidopsis. Plant Physiology. 130, 312-24 Abstract

Benfey, P.N. (2002) Auxin Action: Slogging out of the Swamp. Current
Biology. 12, R389-90 Abstract

Ausubel, F. and Benfey, P.N. (2002) Arabidopsis functional genomics.
Plant Physiology. 129, 393 Abstract

Nakajima, K. and P.N. Benfey (2002). Signaling in and out: control of cell division and differentiation in the shoot and root. Plant Cell 14 Suppl:S265-76 Abstract

Nakajima, K., G. Sena, T. Nawy and P.N. Benfey (2001) Intercellular movement of the putative transcription factor SHR in root patterning. Nature 413, 307-311 Abstract

Birnbaum, K., P.N. Benfey and D.E. Shasha (2001) Cis-Element/Transcription Factor analysis (cis/TF): a method for discovering transcription factor cis-element relationships. Genome Research 11(9), 1567-1573 Abstract

Nawy, T. and P.N. Benfey (2001) Signaling the tips: Regulation of stem cell function in plants. Differentiation 68, 155-158 Abstract

Paquette, A.J. and P.N. Benfey (2001) Axis formation and polarity in plants. Current Opinion in Genetics and Development 11, 405-409 Abstract

Schindelman, G., A. Morikami, J. Jung, T.I. Baskin, N.C. Carpita, P. Derbyshire, M.C. McCann, and P.N. Benfey (2001) COBRA encodes a putative GPI-anchored protein, which is polarly localized and necessary for oriented cell expansion in Arabidopsis. Genes and Development 15, 1115-1127

Benfey, P.N. & Weigel, D. (2001) Transcriptional networks controlling plant development. Plant Physiology 125, 109-111 Abstract

Mahonen, A.P., M. Bonke, L. Kauppinen, M. Riikonen, P.N. Benfey, and Y. Helariutta (2000) A novel two-component hybrid molecule regulates vascular morphogenesis of the Arabidopsis root. Genes and Development 14, 2938-2943 Abstract

Benfey, P.N., and B. Scheres (2000) Root development. J. Current Biology 10,R813-815 Abstract

Lim, J., Y. Helariutta, C.D. Specht, J. Jung, L. Sims, W.B. Bruce, S. Diehn, and P.N. Benfey (2000) Molecular analysis of the SCARECROW gene in maize reveals a common basis for radial patterning in diverse meristems. Plant Cell 12, 1307-1318 Abstract

Helariutta, Y., H. Fukaki, J. Wysocka-Diller, K. Nakajima, J. Jung, G. Sena, M.T. Hauser, and P.N Benfey (2000) The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell 101, 555-567 Abstract

Wysocka-Diller, J.W., Y. Helariutta, H. Fukaki, J.E. Malamy, and P.N Benfey (2000) Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot. Development 127, 595-603 Abstract

Sabatini S., D. Beis D, H. Wolkenfelt, J. Murfett, T. Guilfoyle, J.E. Malamy, P.N. Benfey, O. Leyser, N. Bechtold, P. Weisbeek & B. Scheres (1999) An auxin-dependent distal organizer of pattern and polarity in the Arabidopsis root. Cell 99, 463-472 Abstract

Scheres, B. and P.N. Benfey (1999) Asymmetric cell division in plants. Annual Review of Plant Physiology and Plant Molecular Biology 50, 505-537

Pysh, L.D., J.W. Wysocka-Diller, C. Camilleri, D. Bouchez, and P.N. Benfey (1999) The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes. Plant Journal 18, 111-9 Abstract


Benfey, P.N. (1999) Stem cells: A tale of two kingdoms. Current Biology 9,R171-2 Abstract


Benfey, P.N. (1999) Is the shoot a root with a view? Current Opinions in Plant Biology 2, 39-43 Abstract


Fukaki, H., J. Wysocka-Diller, T. Kato, H. Fujisawa, P.N. Benfey, and M. Tasaka (1998) Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana. Plant Journal 14, 425-30 Abstract


Malamy, J.E. and P.N. Benfey (1997) A rapid system for assessing transgene expression in roots of Arabidopsis. Plant Journal 12, 957-963
Abstract

Wysocka-Diller, J. and P.N. Benfey (1997) Root development: signaling down and around. BioEssays 19, 959-965 Abstract

Malamy, J. E. and P.N. Benfey (1997) Organization and cell differentiation in lateral roots of Arabidopsis thaliana. Development 124, 33-44 Abstract

Malamy, J. E. and P.N. Benfey (1997) Down and out in Arabidopsis: the formation of lateral roots. Trends in Plant Science 2, 390-396

Di Laurenzio, L., Wysocka-Diller, J., Malamy, J. E., Pysh, L ., Helariutta, Y., Freshour, G., Hahn, M.G., Feldmann, K. A. and P.N. Benfey (1996) The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell 86, 423-433
Abstract

Scheres,B., Di Laurenzio, L, Willemsen, V., Hauser,M.-T., Janmaat, K., Weisbeek, P. and P.N. Benfey, (1995) Mutations affecting the radial organisation of the Arabidopsis root display specific defects throughout the embryonic axis. Development 121, 53-62


Hauser, M.T., Morikami, A. and P.N. Benfey, (1995) Conditional root expansion mutants of Arabidopsis. Development 121, 1237-1252 Abstract


Aeschbacher, R.A., Hauser, M.T., Feldmann, K.A. and P.N. Benfey, (1995) The SABRE gene is required for normal cell expansion in Arabidopsis. Genes & Development 9, 330-340 Abstract


Benfey, P.N and Schiefelbein, J.W., (1994) Getting to the root of plant development: the genetics of Arabidopsis root formation. Trends in Genetics 94, 84-88 Abstract


Benfey, P.N., Linstead, P.J., Roberts, K., Schiefelbein, J.W. Hauser, M.-T., and R.A. Aeschbacher (1993) Root development in Arabidopsis: four mutants with dramatically altered root morphogenesis. Development, 119, 53-70 Abstract