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Benfey Lab Publications Baskin TI, Peret B, Baluska F, Benfey PN, Bennett M, Forde BG, Gilroy S,
Helariutta Y, Hepler PK, Leyser O, Masson PH, Muday GK, Murphy AS, Poethig S,
Rahman A, Roberts K, Scheres B, Sharp RE, Somerville C. Shootward and rootward:
peak terminology for plant polarity. Trends Plant Sci. 2010 Sep 10. [Epub ahead
of print] Abstract Moreno-Risueno MA, Van Norman JM, Moreno A, Zhang J, Ahnert SE, Benfey PN.
Oscillating gene expression determines competence for periodic Arabidopsis root
branching. Science. 2010 Sep 10;329(5997):1306-11. Abstract pdf Iyer-Pascuzzi AS, Benfey PN. Fluorescence-activated cell sorting in plant developmental biology. Methods Mol Biol. 2010;655:313-9. Abstract Long TA, Tsukagoshi H, Busch W, Lahner B, Salt DE, Benfey PN. The bHLH Sozzani R, Cui H, Moreno-Risueno MA, Busch W, Van Norman JM, Vernoux T, Brady SM, Dewitte W, Murray JA, Benfey PN. Spatiotemporal regulation of cell-cycle
genes by SHORTROOT links patterning and growth. Nature. 2010 Jul
1;466(7302):128-32. Abstract Orlando DA, Brady SM, Fink TM, Benfey PN, Ahnert SE. Detecting separate time
scales in genetic expression data. BMC Genomics. 2010 Jun 16;11:381. Abstract Carlsbecker A, Lee JY, Roberts CJ, Dettmer J, Lehesranta S, Zhou J, Lindgren
O, Moreno-Risueno MA, Vaten A, Thitamadee S, Campilho A, Sebastian J, Bowman JL, Benfey PN, Bennett M, Schiefelbein J. Getting to the root of plant biology:
impact of the Arabidopsis genome sequence on root research. Plant J. 2010
Mar;61(6):992-1000. Review. Abstract Busch W, Benfey PN. Information processing without brains--the power of Van Norman JM, Benfey PN. Arabidopsis thaliana as a Model Organism in Systems De Smet I, Lau S, Voss U, Vanneste S, Benjamins R, Rademacher EH, Schlereth Iyer-Pascuzzi AS, Symonova O, Mileyko Y, Hao Y, Belcher H, Harer J, Weitz JS, Petricka JJ, Van Norman JM, Benfey PN. Symmetry breaking in plants: molecular Moreno-Risueno MA, Busch W, Benfey PN. Omics meet networks - using systems Cui H, Benfey PN. Cortex proliferation: simple phenotype, complex regulatory Tromas A, Braun N, Muller P, Khodus T, Paponov IA, Palme K, Ljung K, Lee JY, Benfey PN, Birnbaum KD. Primer and interviews: Gene regulation in Arabidopsis Cartwright DA, Brady SM, Orlando DA, Sturmfels B, Benfey PN. Reconstructing Petersson SV, Johansson AI, Kowalczyk M, Makoveychuk A, Wang JY, Moritz T, Grebe M, Benfey PN, Sandberg G, Ljung K. An Auxin Gradient and Maximum in the Arabidopsis Root Apex Shown by High-Resolution Cell-Specific Analysis of IAA Distribution and Synthesis.(2009) Plant Cell. [Epub ahead of print] Abstract. Cui H, Benfey PN. Interplay between SCARECROW, GA and LIKE HETEROCHROMATIN PROTEIN 1 in ground tissue patterning in the Arabidopsis root. Plant J. 2009 Mar 20. [Epub ahead of print] Abstract Colinas, J., Schmidler, S. C., Bohrer, G., Iordanov, B. and Benfey, P. N. (2008). Intergenic and genic sequence lengths have opposite relationships with respect to gene expression. PLoS One 3, e3670. Abstract Iyer-Pascuzzi A, Simpson J, Herrera-Estrella L, Benfey PN. Functional genomics of Arabidopsis root functional genomics. (2008) Curr Opin Plant Biol. [Epub ahead of print]Abstract Gallagher KL, Benfey PN. Both the conserved GRAS domain and nuclear localization are required for SHORT-ROOT movement. Plant J. 2008 Dec 4. [Epub ahead of print] Abstract Chaudhuri B, Hörmann F, Lalonde S, Brady SM, Orlando DA, Benfey P, Frommer WB. Protonophore- and pH-insensitive glucose and sucrose accumulation detected by FRET nanosensors in Arabidopsis root tips. (2008) Plant J. 56(6):948-62. Abstract De Smet I, Vassileva V, De Rybel B, Levesque MP, Grunewald W, Van Damme D, Van Noorden G, 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, Beeckman T. (2008) Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root. Science. 322(5901):594-7. Abstract Iyer-Pascuzzi AS, Benfey PN. Transcriptional networks in root cell fate specification. (2008) Biochim Biophys Acta. [Epub ahead of print] Abstract Petricka JJ, Benfey PN. Root layers: complex regulation of developmental patterning. (2008) Curr Opin Genet Dev. 18(4):354-61. Abstract Swarup K, Benková E, Swarup R, Casimiro I, Péret B, Yang Y, Parry G, Nielsen E, De Smet I, Vanneste S, Levesque MP, Carrier D, James N, Calvo V, Ljung K, Kramer E, Roberts R, Graham N, Marillonnet S, Patel K, Jones JD, Taylor CG, Schachtman DP, May S, Sandberg G, Benfey P, Friml J, Kerr I, Beeckman T, Laplaze L, Bennett MJ. The auxin influx carrier LAX3 promotes lateral root emergence. (2008) Nat Cell Biol. 10(8):946-54. Abstract 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) Roudier, F.,
G. Schindelman, R. DeSalle, and P.N. Benfey (2002) The Colinas, J.,
K. Birnbaum, P.N. Benfey (2002) Using cauliflower to find Muller, S.,
E. Fuchs, M. Ovecka, J. Wysocka-Diller, P.N. Benfey, M.T. Benfey, P.N.
(2002) Auxin Action: Slogging out of the Swamp. Current Ausubel, F.
and Benfey, P.N. (2002) Arabidopsis functional genomics. 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
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