Philip Benfey, PhD
Publications
De Smet I, Vassileva V, De Rybel B, Levesque MP, Grunewald W, Naudts M, Van Isterdael G, De Clercq R,Wang JY, Meuli N, Vanneste S, Friml J, Hilson P, Jürgens G, Ingram, GC, Inzé D, Benfey PN and T Beeckman (2008) Receptor-like kinase ACR4 restricts stem cell divisions in the Arabidopsis root Science in press
Long TA, Brady SM and PN Benfey, (2008) Systems Approaches to Identifying Gene Regulatory Networks in Plants. Annual Review Cell Dev Biol. in press
Petricka JJ and PN Benfey (2008) Root layers: complex regulation of developmental patterning.
Curr Opin Genet Dev. in press
Dinneny JR, Long TA, Wang JY, Jung JW, Mace D, Pointer S, Barron C, Brady SM, Schiefelbein J and PN Benfey (2008) Cell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress. Science 320:942-5.
Benfey PN and T. Mitchell-Olds (2008) From genotype to phenotype: systems biology meets natural variation. Science 320:495-7
Dinneny JR and Benfey PN (2008) Plant stem cell niches: standing the test of time. Cell 132:553-7
Brady SM, Orlando DA, Lee J-Y, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U, and PN Benfey (2007) A High-Resolution Root Spatiotemporal Map Reveals Dominant Expression Patterns. Science 318: 801-806
Cui H, Levesque MP, Vernoux T, Jung JW, Paquette AJ, Gallagher, KL, Wang JY, Blilou I, Scheres B and PN Benfey (2007) An Evolutionarily Conserved Mechanism Delimiting SHR movement defines a Single Layer of Endodermis in Plants. Science 316:421-5
Weitz, JS, Benfey, PN and NS Wingreen (2007) Evolution, Interactions, and Biological Networks. PloS Biology Jan;5(1):e11
Brady SM, Song S, Dhugga KS, Rafalski JA, Benfey PN (2007) Combining expression and comparative evolutionary analysis. The COBRA gene family. Plant Physiol. 143:172-87
Long TA and Benfey PN (2006) Transcription factors and hormones: new insights into plant cell differentiation. Curr Opin Cell Biol. 18(6):710-4.
Brady SM, Long TA and Benfey PN (2006) Unraveling the dynamic transcriptome.
Plant Cell 18:2101-11
Mace DL, Lee JY, Twigg RW, Colinas J, Benfey PN and Ohler U. (2006) Quantification of transcription factor expression from Arabidopsis images. Bioinformatics. 22:e323-31.
Levesque MP, Vernoux T, Busch W, Cui H, Wang JY, Blilou I, Hassan H, Nakajima K, Matsumoto N, Lohmann JU, Scheres B, and Benfey PN (2006) Whole-genome Analysis of the SHORT-ROOT Developmental Pathway in Arabidopsis. PloS Biology 4:e143
Lee JY, Colinas J, Wang JY, Mace D, Ohler U and Benfey PN (2006) Transcriptional and post-transcriptional regulation of transcription factor expression in Arabidopsis roots. PNAS 103:6055-60
Lim J, Jung JW, Lim CE, Lee MH, Kim BJ, Kim M, Bruce WB and Benfey PN. (2005) Conservation and diversification of SCARECROW in maize. Plant Mol Biol. 59(4):619-30
Dinneny JR and Benfey PN. (2005) Stem Cell Research Goes Underground: The RETINOBLASTOMA-RELATED Gene in Root Development. Cell 123(7):1180-2
Birnbaum K, Jung JW, Wang JY, Lambert GM, Hirst JA, Galbraith DW and Benfey PN. (2005) Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nature Methods. 2:615-9
Vernoux T and Benfey PN. (2005) Signals that regulate stem cell activity during plant development. Curr Opin Genet Dev. 15:388-94.
Paquette AJ and Benfey PN. (2005) Maturation of the ground tissue of the root is regulated by gibberellin and SCARECROW and requires SHORT-ROOT. Plant Physiol. 138:636-40.
Lee JY, Levesque M and Benfey PN. (2005) High-throughput RNA isolation technologies. New tools for high-resolution gene expression profiling in plant systems. Plant Physiol. 138:585-90
Benfey PN. (2005) Developmental networks. Plant Physiol. 138:548-9
Nawy T, Lee JY, Colinas J, Wang JY, Thongrod SC, Malamy JE, Birnbaum K and Benfey PN. (2005)Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell 17:1908-25.
Roudier F, Fernandez AG, Fujita M, Himmelspach R, Borner GH, Schindelman G, Song S, Baskin TI, Dupree P, Wasteneys GO and PN Benfey (2005) COBRA, an Arabidopsis Extracellular Glycosyl-Phosphatidyl Inositol-Anchored Protein, Specifically Controls Highly Anisotropic Expansion through Its Involvement in Cellulose Microfibril Orientation.
Plant Cell 17:1749-63.
Gallagher K.L. and P.N. Benfey (2005) Not just another hole in the wall: understanding intercellular protein trafficking. Genes & Development 19:189-95
Gallagher K.L., Paquette A.J., Nakajima K., and P.N. Benfey (2004) Mechanisms Regulating SHORT-ROOT Intercellular Movement. Curr Biol. 14, 1847-51
P.N. Benfey (2004) Development and ecology in the time of systems biology. Dev Cell. 7:329-30
Birnbaum K. and P.N. Benfey (2004) Network building: transcriptional circuits in the root. Curr Opin Plant Biol. 7,582-8
Irish V.F. and P.N. Benfey (2004) Beyond Arabidopsis. Translational biology meets evolutionary developmental biology. Plant Physiol. 135,611-4
Sena, G., Jung, J., and P.N. Benfey (2004) A broad competence to respond to SHORT-ROOT as revealed by tissue-specific ectopic expression. Development 131, 2817-26
Levesque M.P. and P.N. Benfey (2004) Systems biology. Curr Biol. 14,R179-80
Benfey, P.N. (2004) A common switch used by plants and animals. Cell 116, 4-5
Birnbaum, K., Shasha, D.E., Wang, J.Y., Jung, J., Lambert, G.M., Galbraith, D.W. and P. N. Benfey (2003) A gene expression map of the Arabidopsis root. Science 302, 1956-60
Levesque, M., Shasha, D., Kim, W., Surette, M.G. and Benfey, P.N. (2003) Trait-To-Gene: A Computational Method for Predicting the Function of Uncharacterized Genes. Current Biology 13, 129-133
Brenner E.D., Stevenson D.W, McCombie R.W., Katari M.S., Rudd S.A., Mayer K.F., Palenchar P.M., Runko S.J., Twigg R.W., Dai G., Martienssen R.A., Benfey P.N. and G.M. Coruzzi (2003) Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biol. 4,R78
Benfey, P.N. (2003) MicroRNA is here to stay. Nature 425, 244-5
Birnbaum, K., DeSalle, R., Peters, C.M. and P. N. Benfey (2003) Integrating gene flow, crop biology, and farm management in the on-farm conservation of avocado (Persea americana, Lauraceae). American Journal of Botany 90, 1619-1627
Roudier, F., Schindelman, G, DeSalle, R. 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.
Birnbaum, K., Benfey, P.N., Peters, C.M., and R. DeSalle (2002) MANAGEDPOP: a computer simulation to project allelic diversity in managed populations with overlapping generations Molecular Ecology Notes 2, 615-617
Muller S, Fuchs E, Ovecka M, Wysocka-Diller J, Benfey P.N, and MT Hauser (2002) Two New Loci, PLEIADE and HYADE, Implicate Organ-Specific Regulation of Cytokinesis in Arabidopsis. Plant Physiology 130, 312-24
Colinas J, Birnbaum K, and P.N. Benfey (2002) Using cauliflower to find conserved non-coding regions in Arabidopsis. Plant Physiology 129, 451-4
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, S265-S276
Benfey, P.N. (2002) Auxin action: slogging out of the swamp. Current Biology 12, R389-90
Nakajima, K., Sena,G., Nawy, T. and P.N. Benfey (2001) Intercellular movement of the putative transcription factor SHR in root patterning. Nature 413, 307-311
Birnbaum, K., Benfey, P.N. and D. Shasha (2001) Cis-Element/Transcription Factor Analysis (cis/TF): A Method for Discovering Transcription Factor cis-Element Relationships. Genome Research 11, 1567—1573
Paquette, A.J., and P.N. Benfey (2001) Axis formation and polarity in plants. Current Opinion in Genetics and Development 11, 405-409
Nawy, T., and P.N. Benfey (2001)Signaling the tips: regulation of stem cell function in plants. Differentiation 68, 155-158
Schindelman, G, Morikami , A., Jung, J., Baskin, T.I., Carpita, N.C., Derbyshire, P., McCann, M.C., 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 & Development 15, 1115-1127
Weigel, D. and P. N. Benfey (2001) Transcriptional Networks Controlling Plant Development, Plant Physiology 125, 109-111
Mähönen, A.P., Bonke, P., Kauppinen, L., Riikonen, M., Benfey, P. N. and Helariutta, Y. A (2000) Novel Two Component Hybrid Molecule Regulates Vascular Morphogenesis of the Arabidopsis Root Genes & Development 14, 2938-43.
Benfey, P. N. and B. Scheres (2000) Root Development Primer Current Biology 10, R813-R815.
Lim, J., Helariutta, Y., Specht, C.D., Jung, J., Sims, L., Bruce, W.B., Diehn, S. 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.
Helariutta, Y., Fukaki, H., Wysocka-Diller, J. W., Nakajima, K. Jung, J., Sena, G., Hauser, M.T. and P. N. Benfey (2000) The SHORT-ROOT Gene Controls Radial Patterning of the Arabidopsis Root through Radial Signaling. Cell 101, 555-567.
Wysocka-Diller, J. W., Helariutta, Y., Fukaki, H. Malamy, J.E. and P. N. Benfey (2000) Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot Development 127, 595-603.
Sabatini, S., Beis, D., Wolkenfelt, H., Murfett, J., Guilfoyle, T., Malamy, J., Benfey, P.N., Leyser, O., Bechtold, N., Weisbeek, P., and B. Scheres (1999) An auxin-dependent distal organizer of pattern and polarity in the Arabidopsis root Cell 99, 463-472
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., Wysocka-Diller J., Camilleri, C., Bouchez, D., 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, 111-119
Benfey, P.N. (1999) Stem Cells: A Tale of Two Kingdoms. Current Biology 9, R171-R172
Benfey, P.N. (1999) Is the Shoot a Root with a View? Current Opinion in Plant Biology 2, 39-43
Fukaki,H., Wysocka-Diller, J., Kato,T., Fujisawa,H., P.N. Benfey and M. Tasaka (1998) Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana. Plant Journal 14, 425-430
Malamy, J. E. and P.N. Benfey (1997) A rapid system for assessing transgene expression in roots of Arabidopsis. Plant Journal 12, 957-963
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
Wysocka-Diller, J. and P.N. Benfey (1997) Root development: signaling down and around. BioEssays 19, 959-965
Malamy, J. E. and P.N. Benfey (1997) Organization and Cell Differentiation in Lateral Roots of Arabidopsis thaliana. Development 124, 33-44
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
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
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
Aeschbacher,R.A., Schiefelbein,J.W. and P.N. Benfey (1994) The Molecular and Genetic Basis of Root Development, Annual Review of Plant Physiology and Plant Molecular Biology 45, 25-45.
P.N. Benfey and Schiefelbein,J.W. (1994) Insights into root development from Arabidopsis root mutants, Plant, Cell & Environment 17, 675-680
P.N. Benfey and Schiefelbein,J.W., (1994) Getting to the root of plant development: the genetics of Arabidopsis root formation, Trends in Genetics 94, 84-88
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
Schiefelbein,J.W. and P.N. Benfey (1993) Meeting Report: International Symposium on the Molecular Genetics of Root Development. Plant Molecular Biology Reporter 11 60-64
Aeschbacher,R.A. and P.N. Benfey (1992) Genes that regulate plant development. Plant
Science, 83, 115-126.
Schiefelbein, J.W. and P.N. Benfey (1991) The development of plant roots: new approaches to underground problems. Plant Cell 3, 1147-1154.
Takatsuji,J., Mori,M., Benfey,P.N., Ren,L. and N.-H. Chua (1991) Characterization of a zinc-finger DNA-binding protein expressed specifically in petunia petals and seedlings. EMBO J. 11, 241-249.
Benfey,P.N. and N.-H. Chua (1990) The cauliflower mosaic virus 35S promoter: Combinatorial regulation of transcription in plants. Science 250, 959-966.
Benfey,P.N., Ren,L. and N.-H. Chua (1990) Tissue-specific expression from CaMV 35S enhancer subdomains in early stages of plant development. EMBO J. 9, 1677-1684.
Benfey,P.N., Ren,L. and N.-H. Chua (1990) Combinatorial and synergistic properties of CaMV 35S enhancer subdomains. EMBO J. 9, 1685-1696.
Benfey,P.N., Takatsuji,H., Ren,L., Shah,D.M. and N.-H. Chua (1990) Sequence requirements of the 5-enolpyruvyl shikimate 3-phosphate synthase 5' upstream region for tissue-specific expression in petals and seedlings. Plant Cell 2, 849-856.
Benfey,P.N., Ren,L. and N.-H. Chua (1989) The CaMV enhancer contains at least two domains which can confer different developmental and tissue-specific expression patterns. EMBO J., 8, 2195-2202.
Benfey,P.N. and N.-H. Chua (1989) Regulated genes in transgenic plants. Science. 244, 174-181.
Lam,E., Benfey,P.N., Gilmartin,P., Fang,R.-X. and N.-H. Chua (1989) Site specific mutations alter factor binding in vitro and change organ specific expression in transgenic plants. Proc. Natl. Acad. Sci. 86, 7890-7894.
Sarid,J., Benfey,P.N. and P. Leder (1989) The mast cell specific expression of a protease gene, RMCP II, is regulated by an enhancer element that binds specifically to mast cell trans-acting factors. J. Biol. Chem. 264, 1022-1026.
Shimizu,A., Tepler,I., Benfey,P.N., Berenstein, E.H., Siraganian,R.P. and P. Leder (1988) Human and rat mast cell high-affinity immunoglobulin E receptors: Characterization of putative alpha-chain gene products. Proc. Natl. Acad. Sci. 85, 1907-1911.
Benfey,P.N., Yin,F.H. and P. Leder, (1987) Cloning of the mast cell protease, RMCP II. J. Biol. Chem. 262, 5377-5384.
BOOKS AND BOOK CHAPTERS
Benfey, P.N. and A. Protopapas (2005) Genomics, Pearson Education Inc.
Benfey, P.N. and A. Protopapas (2005) Essentials of Genomics, Pearson Education Inc.
Benfey, P. N. (2001) Gene Discovery Laboratory CD-ROM. Brooks/Cole Thomson Learning
P. N. Benfey. (2001) Genetics of Plant Embryogenesis In The Encyclopedia
of Genetics. Ed. Sydney Brenner.
Pysh, L.D. and P.N. Benfey (1997) Root cell extension: Genetic and molecular approaches. In Radical Biology: Advances and Perspectives in the Function of Plant Roots. Flores, H.E., Lynch, J.P., and Eisenstadt, D., eds., pp. 34-47.
Hauser, M.‑T., Benfey, P.N. (1994) Genetic Regulation of Root Expansion in Arabidopsis thaliana. in Molecular Genetic Analysis of Plant Development and Metabolism eds, Coruzzi, G. & Puigdomenech, P. Springer, Berlin. 31-40.
Schiefelbein,J.W. and P.N. Benfey, (1994) Root Development in Arabidopsis, chapter for Arabidopsis, Eds., E. Meyerowitz and C. Somerville, Cold Spring Harbor Laboratory Press, 335-354
Lam,E., Benfey,P.N. and N.-H. Chua (1989) Characterization of AS-1: a factor binding site on the 35S promoter of cauliflower mosaic virus. in Lamb,C. and Beachy,R. (eds.), Plant Gene Transfer. UCLA Symposia on Molecular and Cellular Biology, New Series. Alan R. Liss, Inc., New York, Vol. 129, 71-79
Contact Information
Philip Benfey
Phone: 919-660-7338
4101 French Family Science Center
philip.benfey@duke.edu