Publications of Philip N Benfey    :chronological  combined  bibtex listing:

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Papers Published

  1. NW Breakfield, DL Corcoran, JJ Petricka, J Shen, J Sae-Seaw, I Rubio-Somoza, D Weigel, U Ohler, PN Benfey, High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis., Genome research, vol. 21 no. 4 (November, 2011), pp. 770-82 [doi]  [abs].
  2. AS Iyer-Pascuzzi, T Jackson, H Cui, JJ Petricka, W Busch, H Tsukagoshi, PN Benfey, Cell identity regulators link development and stress responses in the Arabidopsis root., Developmental cell, vol. 21 no. 4 (October, 2011), pp. 770-82 [doi]  [abs].
  3. JJ Petricka, PN Benfey, Reconstructing regulatory network transitions., Trends in cell biology, vol. 21 no. 8 (August, 2011), pp. 442-51 [doi]  [abs].
  4. PN Benfey, Taking a developmental perspective on systems biology., Developmental cell, vol. 21 no. 1 (July, 2011), pp. 27-8 [doi]  [abs].
  5. J Zhu, PA Ingram, PN Benfey, T Elich, From lab to field, new approaches to phenotyping root system architecture., Current opinion in plant biology, vol. 14 no. 3 (June, 2011), pp. 310-7 [doi]  [abs].
  6. MA Moreno-Risueno, PN Benfey, Time-based patterning in development: The role of oscillating gene expression., Transcription, vol. 2 no. 3 (May, 2011), pp. 124-129 [doi]  [abs].
  7. JM Van Norman, NW Breakfield, PN Benfey, Intercellular communication during plant development., The Plant cell, vol. 23 no. 3 (March, 2011), pp. 855-64 [doi]  [abs].
  8. SM Brady, L Zhang, M Megraw, NJ Martinez, E Jiang, CS Yi, W Liu, A Zeng, M Taylor-Teeples, D Kim, S Ahnert, U Ohler, D Ware, AJ Walhout, PN Benfey, A stele-enriched gene regulatory network in the Arabidopsis root., Molecular systems biology, vol. 7 no. 3 (January, 2011), pp. 459 [doi]  [abs].
  9. R Sozzani, PN Benfey, High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype., Genome biology, vol. 12 no. 3 (2011), pp. 219 [doi]  [abs].
  10. H Tsukagoshi, W Busch, PN Benfey, Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root., Cell, vol. 143 no. 4 (November, 2010), pp. 606-16 [doi]  [abs].
  11. MA Moreno-Risueno, JM Van Norman, A Moreno, J Zhang, SE Ahnert, PN Benfey, Oscillating gene expression determines competence for periodic Arabidopsis root branching., Science (New York, N.Y.), vol. 329 no. 5997 (September, 2010), pp. 1306-11 [doi]  [abs].
  12. R Sozzani, H Cui, MA Moreno-Risueno, W Busch, JM Van Norman, T Vernoux, SM Brady, W Dewitte, JA Murray, PN Benfey, Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth., Nature, vol. 466 no. 7302 (July, 2010), pp. 128-32 [doi]  [abs].
  13. TA Long, H Tsukagoshi, W Busch, B Lahner, DE Salt, PN Benfey, The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots., The Plant cell, vol. 22 no. 7 (July, 2010), pp. 2219-36 [doi]  [abs].
  14. A Carlsbecker, JY Lee, CJ Roberts, J Dettmer, S Lehesranta, J Zhou, O Lindgren, MA Moreno-Risueno, A Vatén, S Thitamadee, A Campilho, J Sebastian, JL Bowman, Y Helariutta, PN Benfey, Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate., Nature, vol. 465 no. 7296 (May, 2010), pp. 316-21 [doi]  [abs].
  15. W Busch, PN Benfey, Information processing without brains--the power of intercellular regulators in plants., Development (Cambridge, England), vol. 137 no. 8 (April, 2010), pp. 1215-26 [doi]  [abs].
  16. DA Orlando, SM Brady, TM Fink, PN Benfey, SE Ahnert, Detecting separate time scales in genetic expression data., BMC genomics, vol. 11 (April, 2010), pp. 381 [doi]  [abs].
  17. AS Iyer-Pascuzzi, PN Benfey, Fluorescence-activated cell sorting in plant developmental biology., Methods in molecular biology (Clifton, N.J.), vol. 655 (April, 2010), pp. 313-9 [doi]  [abs].
  18. MA Moreno-Risueno, W Busch, PN Benfey, Omics meet networks - using systems approaches to infer regulatory networks in plants., Current opinion in plant biology, vol. 13 no. 2 (April, 2010), pp. 126-31 [doi]  [abs].
  19. PN Benfey, M Bennett, J Schiefelbein, Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research., The Plant journal : for cell and molecular biology, vol. 61 no. 6 (March, 2010), pp. 992-1000 [doi]  [abs].
  20. AS Iyer-Pascuzzi, O Symonova, Y Mileyko, Y Hao, H Belcher, J Harer, JS Weitz, PN Benfey, Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems., Plant physiology, vol. 152 no. 3 (March, 2010), pp. 1148-57 [doi]  [abs].
  21. I De Smet, S Lau, U Voss, S Vanneste, R Benjamins, EH Rademacher, A Schlereth, B De Rybel, V Vassileva, W Grunewald, M Naudts, MP Levesque, JS Ehrismann, D Inzé, C Luschnig, PN Benfey, D Weijers, MC Van Montagu, MJ Bennett, G Jürgens, T Beeckman, Bimodular auxin response controls organogenesis in Arabidopsis., Proceedings of the National Academy of Sciences of the United States of America, vol. 107 no. 6 (February, 2010), pp. 2705-10 [doi]  [abs].
  22. DA Orlando, SM Brady, JD Koch, JR Dinneny, PN Benfey, Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment., Methods in molecular biology (Clifton, N.J.), United States, vol. 553 (Winter, 2009), pp. 57-77  [abs].
  23. JJ Petricka, JM Van Norman, PN Benfey, Symmetry breaking in plants: molecular mechanisms regulating asymmetric cell divisions in Arabidopsis., Cold Spring Harbor perspectives in biology, vol. 1 no. 5 (November, 2009), pp. a000497 [doi]  [abs].
  24. DA Cartwright, SM Brady, DA Orlando, B Sturmfels, PN Benfey, Reconstructing spatiotemporal gene expression data from partial observations., Bioinformatics (Oxford, England), England, vol. 25 no. 19 (October, 2009), pp. 2581-7  [abs].
  25. A Tromas, N Braun, P Muller, T Khodus, IA Paponov, K Palme, K Ljung, JY Lee, P Benfey, JA Murray, B Scheres, C Perrot-Rechenmann, The AUXIN BINDING PROTEIN 1 is required for differential auxin responses mediating root growth., PloS one, United States, vol. 4 no. 9 (September, 2009), pp. e6648  [abs].
  26. H Cui, PN Benfey, Cortex proliferation: simple phenotype, complex regulatory mechanisms., Plant signaling & behavior, United States, vol. 4 no. 6 (June, 2009), pp. 551-3 .
  27. SV Petersson, AI Johansson, M Kowalczyk, A Makoveychuk, JY Wang, T Moritz, M Grebe, PN Benfey, G Sandberg, K Ljung, An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis., The Plant Cell, vol. 21 no. 6 (June, 2009), pp. 1659-68  [abs].
  28. H Cui, PN Benfey, Interplay between SCARECROW, GA and LIKE HETEROCHROMATIN PROTEIN 1 in ground tissue patterning in the Arabidopsis root., The Plant Journal, vol. 58 no. 6 (June, 2009), pp. 1016-27  [abs].
  29. A Iyer-Pascuzzi, J Simpson, L Herrera-Estrella, PN Benfey, Functional genomics of root growth and development in Arabidopsis., Current Opinion in Plant Biology, vol. 12 no. 2 (April, 2009), pp. 165-71  [abs].
  30. AS Iyer-Pascuzzi, PN Benfey, Transcriptional networks in root cell fate specification., Biochimica et Biophysica Acta, Netherlands, vol. 1789 no. 4 (April, 2009), pp. 315-25  [abs].
  31. KL Gallagher, PN Benfey, Both the conserved GRAS domain and nuclear localization are required for SHORT-ROOT movement., The Plant Journal, vol. 57 no. 5 (March, 2009), pp. 785-97  [abs].
  32. TA Long, SM Brady, PN Benfey, Systems approaches to identifying gene regulatory networks in plants., Annual review of cell and developmental biology, United States, vol. 24 (November, 2008), pp. 81-103  [abs].
  33. J Colinas, SC Schmidler, G Bohrer, B Iordanov, PN Benfey, Intergenic and genic sequence lengths have opposite relationships with respect to gene expression., PLoS ONE, United States, vol. 3 no. 11 (November, 2008), pp. e3670  [abs].
  34. AS Iyer-Pascuzzi, PN Benfey, Transcriptional networks in root cell fate specification., Biochimica et biophysica acta (October, 2008)  [abs].
  35. I De Smet, V Vassileva, B De Rybel, MP Levesque, W Grunewald, D Van Damme, G Van Noorden, M Naudts, G Van Isterdael, R De Clercq, JY Wang, N Meuli, S Vanneste, J Friml, P Hilson, G Jürgens, GC Ingram, D Inzé, PN Benfey, T Beeckman, Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root., Science (New York, N.Y.), United States, vol. 322 no. 5901 (October, 2008), pp. 594-7  [abs].
  36. B Chaudhuri, F Hörmann, S Lalonde, SM Brady, DA Orlando, P Benfey, WB Frommer, Protonophore- and pH-insensitive glucose and sucrose accumulation detected by FRET nanosensors in Arabidopsis root tips., The Plant journal : for cell and molecular biology (September, 2008)  [abs].
  37. K Swarup, E Benková, R Swarup, I Casimiro, B Péret, Y Yang, G Parry, E Nielsen, I De Smet, S Vanneste, MP Levesque, D Carrier, N James, V Calvo, K Ljung, E Kramer, R Roberts, N Graham, S Marillonnet, K Patel, JD Jones, CG Taylor, DP Schachtman, S May, G Sandberg, P Benfey, J Friml, I Kerr, T Beeckman, L Laplaze, MJ Bennett, The auxin influx carrier LAX3 promotes lateral root emergence., Nature cell biology, England, vol. 10 no. 8 (August, 2008), pp. 946-54  [abs].
  38. JJ Petricka, PN Benfey, Root layers: complex regulation of developmental patterning., Current opinion in genetics & development, England, vol. 18 no. 4 (August, 2008), pp. 354-61  [abs].
  39. JR Dinneny, TA Long, JY Wang, JW Jung, D Mace, S Pointer, C Barron, SM Brady, J Schiefelbein, PN Benfey, Cell identity mediates the response of Arabidopsis roots to abiotic stress., Science (New York, N.Y.), United States, vol. 320 no. 5878 (May, 2008), pp. 942-5  [abs].
  40. PN Benfey, T Mitchell-Olds, From genotype to phenotype: systems biology meets natural variation., Science (New York, N.Y.), United States, vol. 320 no. 5875 (April, 2008), pp. 495-7  [abs].
  41. JR Dinneny, PN Benfey, Plant stem cell niches: standing the test of time., Cell, United States, vol. 132 no. 4 (February, 2008), pp. 553-7  [abs].
  42. SM Brady, DA Orlando, JY Lee, JY Wang, J Koch, JR Dinneny, D Mace, U Ohler, PN Benfey, A high-resolution root spatiotemporal map reveals dominant expression patterns., Science (New York, N.Y.), United States, vol. 318 no. 5851 (November, 2007), pp. 801-6  [abs].
  43. H Cui, MP Levesque, T Vernoux, JW Jung, AJ Paquette, KL Gallagher, JY Wang, I Blilou, B Scheres, PN Benfey, An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants., Science (New York, N.Y.), United States, vol. 316 no. 5823 (April, 2007), pp. 421-5  [abs].
  44. JS Weitz, PN Benfey, NS Wingreen, Evolution, interactions, and biological networks., PLoS biology, United States, vol. 5 no. 1 (January, 2007), pp. e11 .
  45. SM Brady, S Song, KS Dhugga, JA Rafalski, PN Benfey, Combining expression and comparative evolutionary analysis. The COBRA gene family., Plant physiology, United States, vol. 143 no. 1 (January, 2007), pp. 172-87  [abs].
  46. TA Long, PN Benfey, Transcription factors and hormones: new insights into plant cell differentiation., Curr Opin Cell Biol, United States, vol. 18 no. 6 (December, 2006), pp. 710-4  [abs].
  47. SM Brady, TA Long, PN Benfey, Unraveling the dynamic transcriptome., Plant Cell, United States, vol. 18 no. 9 (September, 2006), pp. 2101-11 .
  48. DL Mace, JY Lee, RW Twigg, J Colinas, PN Benfey, U Ohler, Quantification of transcription factor expression from Arabidopsis images., Bioinformatics, England, vol. 22 no. 14 (July, 2006), pp. e323-31  [abs].
  49. MP Levesque, T Vernoux, W Busch, H Cui, JY Wang, I Blilou, H Hassan, K Nakajima, N Matsumoto, JU Lohmann, B Scheres, PN Benfey, Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis., PLoS Biol, United States, vol. 4 no. 5 (May, 2006), pp. e143  [abs].
  50. JY Lee, J Colinas, JY Wang, D Mace, U Ohler, PN Benfey, Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots., Proc Natl Acad Sci U S A, United States, vol. 103 no. 15 (April, 2006), pp. 6055-60  [abs].
  51. J Friml, P Benfey, E Benková, M Bennett, T Berleth, N Geldner, M Grebe, M Heisler, J Hejátko, G Jürgens, T Laux, K Lindsey, W Lukowitz, C Luschnig, R Offringa, B Scheres, R Swarup, R Torres-Ruiz, D Weijers, E Zazímalová, Apical-basal polarity: why plant cells don't stand on their heads., Trends Plant Sci, England, vol. 11 no. 1 (December, 2005), pp. 12-4 .
  52. JR Dinneny, PN Benfey, Stem Cell Research Goes Underground: The RETINOBLASTOMA-RELATED Gene in Root Development., Cell, vol. 123 no. 7 (December, 2005), pp. 1180-2  [abs].
  53. J Lim, JW Jung, CE Lim, MH Lee, BJ Kim, M Kim, WB Bruce, PN Benfey, Conservation and diversification of SCARECROW in maize., Plant Mol Biol, Netherlands, vol. 59 no. 4 (November, 2005), pp. 619-30  [abs].
  54. K Birnbaum, JW Jung, JY Wang, GM Lambert, JA Hirst, DW Galbraith, PN Benfey, Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines., Nat Methods, United States, vol. 2 no. 8 (August, 2005), pp. 615-9 .
  55. T Vernoux, PN Benfey, Signals that regulate stem cell activity during plant development., Curr Opin Genet Dev, England, vol. 15 no. 4 (August, 2005), pp. 388-94  [abs].
  56. T Nawy, JY Lee, J Colinas, JY Wang, SC Thongrod, JE Malamy, K Birnbaum, PN Benfey, Transcriptional profile of the Arabidopsis root quiescent center., Plant Cell, United States, vol. 17 no. 7 (July, 2005), pp. 1908-25  [abs].
  57. AJ Paquette, PN Benfey, Maturation of the ground tissue of the root is regulated by gibberellin and SCARECROW and requires SHORT-ROOT., Plant Physiol, United States, vol. 138 no. 2 (June, 2005), pp. 636-40 .
  58. JY Lee, M Levesque, PN Benfey, High-throughput RNA isolation technologies. New tools for high-resolution gene expression profiling in plant systems., Plant Physiol, United States, vol. 138 no. 2 (June, 2005), pp. 585-90 .
  59. PN Benfey, Developmental networks., Plant Physiol, United States, vol. 138 no. 2 (June, 2005), pp. 548-9 .
  60. F Roudier, AG Fernandez, M Fujita, R Himmelspach, GH Borner, G Schindelman, S Song, TI Baskin, P Dupree, GO Wasteneys, PN Benfey, COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation., Plant Cell, United States, vol. 17 no. 6 (June, 2005), pp. 1749-63  [abs].
  61. KL Gallagher, PN Benfey, Not just another hole in the wall: understanding intercellular protein trafficking., Genes Dev, United States, vol. 19 no. 2 (January, 2005), pp. 189-95  [abs].
  62. Birnbaum, K., Shasha, D.E., Wang, J.Y., Jung, J., Lambert, G.M., Galbraith, D.W. and P.N. Benfey, A gene expression map of the Arabidopsis root, Science, vol. 302 (December, 2003), pp. 1956-60 .
  63. Brenner ED, Stevenson DW, McCombie RW, Katari MS, Rudd SA, Mayer KF, Palenchar PM, Runko SJ, Twigg RW, Dai G, Martienssen RA, Benfey PN, Coruzzi GM, Expressed sequence tag analysis in Cycas, the most primitive living seed plant, Genome Biology, vol. 4 (2003), pp. R78 .
  64. P.N. Benfey, Molecular biology: microRNA is here to stay, Nature, vol. 425( (2003), pp. 244-245 (Prize for one of three best News and Views in 2003.) .
  65. Levesque M, Shasha D, Kim W, Surette MG and P.N. Benfey, Trait-to-gene: a computational method for predicting the function of uncharacterized genes, Current Biology, vol. 13 (2003), pp. 129-133 .
  66. Birnbaum, K., DeSalle, R., Peters, C.M. and P.N. Benfey, Integrating gene flow, crop biology, and farm management in the on-farm conservation of avocado (Persea americana, Lauraceae)., American Journal of Botany, vol. 90 (2003), pp. 1619-1627 .
  67. Roudier, F., Schindelman, G, DeSalle, R. and P.N. Benfey, The COBRA family of putative GPI-anchored proteins in Arabidopsis: a new fellowship in expansion., Plant Physiology, vol. 130 no. 2 (December, 2002), pp. 538-48. .
  68. Muller S, Fuchs E, Ovecka M, Wysocka-Diller J, Benfey P.N, and MT Hauser, Two new loci, PLEIADE and HYADE, implicate organ-specific regulation of cytokinesis in Arabidopsis., Plant Physiol., vol. 130 no. 1 (December, 2002), pp. 312-24 .
  69. Colinas J, Birnbaum K, and P.N. Benfey, Using cauliflower to find conserved non-coding regions in Arabidopsis., Plant Physiol., vol. 129 no. 2 (December, 2002), pp. 451-4 .
  70. P.N. Benfey, Auxin action: slogging out of the swamp, Curr Biol., vol. 12 no. 11 (December, 2002), pp. R389-90 .
  71. Nakajima, K and P.N. Benfey, Signaling in and out: control of cell division and differentiation in the shoot and root., Plant Cell, vol. 14 (December, 2002), pp. S265-76 .
  72. Birnbaum, K., Benfey, P.N., Peters, C.M., and R. DeSalle, MANAGEDPOP: a computer simulation to project allelic diversity in managed populations with overlapping generations, Molecular Ecology Notes, vol. 2 (January, 2002), pp. 615-617 .
  73. JM Van Norman, PN Benfey, Arabidopsis thaliana as a model organism in systems biology., Wiley interdisciplinary reviews. Systems biology and medicine, vol. 1 no. 3 , pp. 372-9 [doi]  [abs].

Book Chapters

  1. Orlando DA, Brady SM, Koch JD, Dinneny JR and PN Benfey, Manipulating Large-Scale Arabidopsis Microarray Expression Data: Identifying Dominant Expression Patterns and Biological Process Enrichment, in Plant Systems Biology, Methods in Molecular Biology, edited by Dmitry Belostotsky, vol. 553 (2009), pp. 57-78, Humana Press .
  2. Dinneny JR and PN Benfey, Studying Root Development using a Genomic Approach, in Root Development, Annual Plant Reviews, edited by Tom Beeckman, vol. 37 (2009), pp. 325-351, Wiley-Blackwell .
  3. Brady SM and PN Benfey, Development and Systems Biology: Riding the Genomics Wave Towards a Systems Understanding of Root Development, in Plant Systems Biology, Annual Plant Reviews, edited by Gloria Coruzzi and Rodrigo Gutiérrez, vol. 35 (2009), Wiley, John & Sons .

Book Chapter

  1. Lee, J-Y and P.N. Benfey, Root Apical Meristems, in Encyclopedia of Life Sciences (2006) .

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