Publications of Philip N. Benfey    :chronological  alphabetical  combined  bibtex listing:

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Papers Published

  1. Dickinson, AJ; Lehner, K; Mi, J; Jia, K-P; Mijar, M; Dinneny, J; Al-Babili, S; Benfey, PN, β-Cyclocitral is a conserved root growth regulator., Proceedings of the National Academy of Sciences of the United States of America, vol. 116 no. 21 (May, 2019), pp. 10563-10567 [doi]  [abs].
  2. Chen, W-Q; Drapek, C; Li, D-X; Xu, Z-H; Benfey, PN; Bai, S-N, Histone Deacetylase HDA19 Affects Root Cortical Cell Fate by Interacting with SCARECROW., Plant Physiology, vol. 180 no. 1 (May, 2019), pp. 276-288 [doi]  [abs].
  3. Di Mambro, R; Svolacchia, N; Dello Ioio, R; Pierdonati, E; Salvi, E; Pedrazzini, E; Vitale, A; Perilli, S; Sozzani, R; Benfey, PN; Busch, W; Costantino, P; Sabatini, S, The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size., Current Biology : Cb, vol. 29 no. 7 (April, 2019), pp. 1199-1205.e4 [doi]  [abs].
  4. Pierre-Jerome, E; Drapek, C; Benfey, PN, Regulation of Division and Differentiation of Plant Stem Cells., Annual Review of Cell and Developmental Biology, vol. 34 (October, 2018), pp. 289-310 [doi]  [abs].
  5. Drapek, C; Sparks, EE; Marhavy, P; Taylor, I; Andersen, TG; Hennacy, JH; Geldner, N; Benfey, PN, Minimum requirements for changing and maintaining endodermis cell identity in the Arabidopsis root., Nature Plants, vol. 4 no. 8 (August, 2018), pp. 586-595 [doi]  [abs].
  6. Grondin, A; Dixit, S; Torres, R; Venkateshwarlu, C; Rogers, E; Mitchell-Olds, T; Benfey, PN; Kumar, A; Henry, A, Physiological mechanisms contributing to the QTL qDTY3.2 effects on improved performance of rice Moroberekan x Swarna BC2F3:4 lines under drought., Rice (New York, N.Y.), vol. 11 no. 1 (July, 2018), pp. 43 [doi]  [abs].
  7. Hsu, PY; Benfey, PN, Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants., Proteomics, vol. 18 no. 10 (May, 2018), pp. e1700038 [doi]  [abs].
  8. Shibata, M; Breuer, C; Kawamura, A; Clark, NM; Rymen, B; Braidwood, L; Morohashi, K; Busch, W; Benfey, PN; Sozzani, R; Sugimoto, K, GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis., Development (Cambridge, England), vol. 145 no. 3 (February, 2018) [doi]  [abs].
  9. Wendrich, JR; Möller, BK; Li, S; Saiga, S; Sozzani, R; Benfey, PN; De Rybel, B; Weijers, D, Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem., Proceedings of the National Academy of Sciences of the United States of America, vol. 114 no. 42 (October, 2017), pp. E8922-E8929 [doi]  [abs].
  10. Di Mambro, R; De Ruvo, M; Pacifici, E; Salvi, E; Sozzani, R; Benfey, PN; Busch, W; Novak, O; Ljung, K; Di Paola, L; Marée, AFM; Costantino, P; Grieneisen, VA; Sabatini, S, Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root., Proceedings of the National Academy of Sciences of the United States of America, vol. 114 no. 36 (September, 2017), pp. E7641-E7649 [doi]  [abs].
  11. Drapek, C; Sparks, EE; Benfey, PN, Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation., Trends in Genetics : Tig, vol. 33 no. 8 (August, 2017), pp. 529-539 [doi]  [abs].
  12. Wachsman, G; Modliszewski, JL; Valdes, M; Benfey, PN, A SIMPLE Pipeline for Mapping Point Mutations., Plant Physiology, vol. 174 no. 3 (July, 2017), pp. 1307-1313 [doi]  [abs].
  13. Nevarez, PA; Qiu, Y; Inoue, H; Yoo, CY; Benfey, PN; Schnell, DJ; Chen, M, Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus., Plant Physiology, vol. 173 no. 4 (April, 2017), pp. 1953-1966 [doi]  [abs].
  14. Li, C; Sako, Y; Imai, A; Nishiyama, T; Thompson, K; Kubo, M; Hiwatashi, Y; Kabeya, Y; Karlson, D; Wu, S-H; Ishikawa, M; Murata, T; Benfey, PN; Sato, Y; Tamada, Y; Hasebe, M, A Lin28 homologue reprograms differentiated cells to stem cells in the moss Physcomitrella patens., Nature Communications, vol. 8 (January, 2017), pp. 14242 [doi]  [abs].
  15. Fernández-Marcos, M; Desvoyes, B; Manzano, C; Liberman, LM; Benfey, PN; Del Pozo, JC; Gutierrez, C, Control of Arabidopsis lateral root primordium boundaries by MYB36., The New Phytologist, vol. 213 no. 1 (January, 2017), pp. 105-112 [doi]  [abs].
  16. Sparks, EE; Benfey, PN, Tissue-Specific Transcriptome Profiling in Arabidopsis Roots., Methods in Molecular Biology (Clifton, N.J.), vol. 1610 (January, 2017), pp. 107-122 [doi]  [abs].
  17. Sparks, EE; Drapek, C; Gaudinier, A; Li, S; Ansariola, M; Shen, N; Hennacy, JH; Zhang, J; Turco, G; Petricka, JJ; Foret, J; Hartemink, AJ; Gordân, R; Megraw, M; Brady, SM; Benfey, PN, Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors., Dev Cell, vol. 39 no. 5 (December, 2016), pp. 585-596 [doi]  [abs].
  18. Wachsman, G; Modliszewski, J; Valdés, M; Benfey, P, A SIMPLE pipeline for mapping point mutations (November, 2016) [doi]  [abs].
  19. Li, S; Yamada, M; Han, X; Ohler, U; Benfey, PN, High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation., Developmental Cell, vol. 39 no. 4 (November, 2016), pp. 508-522, CELL PRESS [doi]  [abs].
  20. Hsu, PY; Calviello, L; Wu, H-YL; Li, F-W; Rothfels, CJ; Ohler, U; Benfey, PN, Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis., Proc Natl Acad Sci U S A, vol. 113 no. 45 (November, 2016), pp. E7126-E7135 [doi]  [abs].
  21. Rogers, ED; Monaenkova, D; Mijar, M; Nori, A; Goldman, DI; Benfey, PN, X-Ray Computed Tomography Reveals the Response of Root System Architecture to Soil Texture., Plant Physiology, vol. 171 no. 3 (July, 2016), pp. 2028-2040 [doi]  [abs].
  22. Clark, NM; Hinde, E; Winter, CM; Fisher, AP; Crosti, G; Blilou, I; Gratton, E; Benfey, PN; Sozzani, R, Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy., Elife, vol. 5 (June, 2016) [doi]  [abs].
  23. Kawakatsu, T; Stuart, T; Valdes, M; Breakfield, N; Schmitz, RJ; Nery, JR; Urich, MA; Han, X; Lister, R; Benfey, PN; Ecker, JR, Unique cell-type-specific patterns of DNA methylation in the root meristem., Nature Plants, vol. 2 no. 5 (April, 2016), pp. 16058 [doi]  [abs].
  24. Liberman, LM; Benfey, PN, A Friend in Need (of Nutrients) Is a…., Cell, vol. 165 no. 2 (April, 2016), pp. 269-271 [doi]  [abs].
  25. Sparks, EE; Benfey, PN, Identifying Gene Regulatory Networks in Arabidopsis by In Silico Prediction, Yeast-1-Hybrid, and Inducible Gene Profiling Assays., Methods in Molecular Biology (Clifton, N.J.), vol. 1370 (January, 2016), pp. 29-50 [doi]  [abs].
  26. Benfey, PN, Defining the Path from Stem Cells to Differentiated Tissue., Current Topics in Developmental Biology, vol. 116 (January, 2016), pp. 35-43 [doi]  [abs].
  27. Rodriguez, RE; Ercoli, MF; Debernardi, JM; Breakfield, NW; Mecchia, MA; Sabatini, M; Cools, T; De Veylder, L; Benfey, PN; Palatnik, JF, MicroRNA miR396 Regulates the Switch between Stem Cells and Transit-Amplifying Cells in Arabidopsis Roots., The Plant Cell, vol. 27 no. 12 (December, 2015), pp. 3354-3366 [doi]  [abs].
  28. Moreno-Risueno, MA; Sozzani, R; Yardımcı, GG; Petricka, JJ; Vernoux, T; Blilou, I; Alonso, J; Winter, CM; Ohler, U; Scheres, B; Benfey, PN, Transcriptional control of tissue formation throughout root development., Science, vol. 350 no. 6259 (October, 2015), pp. 426-430 [doi]  [abs].
  29. Wachsman, G; Sparks, EE; Benfey, PN, Genes and networks regulating root anatomy and architecture., The New Phytologist, vol. 208 no. 1 (October, 2015), pp. 26-38 [doi]  [abs].
  30. Liberman, LM; Sparks, EE; Moreno-Risueno, MA; Petricka, JJ; Benfey, PN, MYB36 regulates the transition from proliferation to differentiation in the Arabidopsis root., Proceedings of the National Academy of Sciences of the United States of America, vol. 112 no. 39 (September, 2015), pp. 12099-12104 [doi]  [abs].
  31. Jackson, TL; Baker, GW; Wilks, FR; Popov, VA; Mathur, J; Benfey, PN, Large Cellular Inclusions Accumulate in Arabidopsis Roots Exposed to Low-Sulfur Conditions., Plant Physiology, vol. 168 no. 4 (August, 2015), pp. 1573-1589 [doi]  [abs].
  32. Cederholm, HM; Benfey, PN, Distinct sensitivities to phosphate deprivation suggest that RGF peptides play disparate roles in Arabidopsis thaliana root development., The New Phytologist, vol. 207 no. 3 (August, 2015), pp. 683-691 [doi]  [abs].
  33. Zurek, PR; Topp, CN; Benfey, PN, Quantitative trait locus mapping reveals regions of the maize genome controlling root system architecture., Plant Physiology, vol. 167 no. 4 (April, 2015), pp. 1487-1496 [doi]  [abs].
  34. Rogers, ED; Benfey, PN, Regulation of plant root system architecture: implications for crop advancement., Current Opinion in Biotechnology, vol. 32 (April, 2015), pp. 93-98 [doi]  [abs].
  35. Vilarrasa-Blasi, J; González-García, MP; Frigola, D; Fàbregas-Vallvé, N; Alexiou, KG; López-Bigas, N; Rivas, S; Jauneau, A; Lohmann, JU; Benfey, PN; Ibañes, M; Caño-Delgado, AI, Erratum to Regulation of Plant Stem Cell Quiescence by a Brassinosteroid Signaling Module [Developmental Cell 30 (2014) 36-47] DOI: 10.1016/j.devcel.2015.01.021, Developmental Cell, vol. 33 no. 2 (January, 2015), pp. 238, Elsevier BV [doi] .
  36. Morton, T; Petricka, J; Corcoran, DL; Li, S; Winter, CM; Carda, A; Benfey, PN; Ohler, U; Megraw, M, Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures., Plant Cell, vol. 26 no. 7 (July, 2014), pp. 2746-2760 [doi]  [abs].
  37. Vilarrasa-Blasi, J; González-García, M-P; Frigola, D; Fàbregas, N; Alexiou, KG; López-Bigas, N; Rivas, S; Jauneau, A; Lohmann, JU; Benfey, PN; Ibañes, M; Caño-Delgado, AI, Regulation of plant stem cell quiescence by a brassinosteroid signaling module., Developmental Cell, vol. 30 no. 1 (July, 2014), pp. 36-47 [doi]  [abs].
  38. Sozzani, R; Busch, W; Spalding, EP; Benfey, PN, Advanced imaging techniques for the study of plant growth and development., Trends in Plant Science, vol. 19 no. 5 (May, 2014), pp. 304-310 [doi]  [abs].
  39. Van Norman, JM; Zhang, J; Cazzonelli, CI; Pogson, BJ; Harrison, PJ; Bugg, TDH; Chan, KX; Thompson, AJ; Benfey, PN, Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative., Proceedings of the National Academy of Sciences of the United States of America, vol. 111 no. 13 (April, 2014), pp. E1300-E1309 [doi]  [abs].
  40. Sparks, EE; Benfey, PN, HEC of a job regulating stem cells., Developmental Cell, vol. 28 no. 4 (February, 2014), pp. 349-350 [doi]  [abs].
  41. Sozzani, R; Busch, W; Spalding, EP; Benfey, PN, Advanced imaging techniques for the study of plant growth and development, Trends in Plant Science, vol. 19 no. 5 (January, 2014), pp. 304-310 [doi]  [abs].
  42. Vilarrasa-Blasi, J; González-García, MP; Frigola, D; Fàbregas, N; Alexiou, KG; López-Bigas, N; Rivas, S; Jauneau, A; Lohmann, JU; Benfey, PN; Ibañes, M; Caño-Delgado, AI, Regulation of plant stem cell quiescence by a brassinosteroid signaling module, Developmental Cell, vol. 30 no. 1 (2014), pp. 36-47 [doi]  [abs].
  43. Iyer-Pascuzzi, AS; Zurek, PR; Benfey, PN, High-throughput, noninvasive imaging of root systems, Methods in Molecular Biology (Clifton, N.J.), vol. 959 (December, 2013), pp. 177-187 [doi]  [abs].
  44. Van Norman, JM; Xuan, W; Beeckman, T; Benfey, PN, To branch or not to branch: the role of pre-patterning in lateral root formation., Development (Cambridge, England), vol. 140 no. 21 (November, 2013), pp. 4301-4310 [24130327], [doi]  [abs].
  45. Benfey, P, Philip Benfey., Current Biology : Cb, vol. 23 no. 19 (October, 2013), pp. R857-R858 [doi] .
  46. Li, S; Liberman, LM; Mukherjee, N; Benfey, PN; Ohler, U, Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data., Genome Res, vol. 23 no. 10 (October, 2013), pp. 1730-1739 [23816784], [doi]  [abs].
  47. Sparks, E; Wachsman, G; Benfey, PN, Spatiotemporal signalling in plant development., Nature Reviews. Genetics, vol. 14 no. 9 (September, 2013), pp. 631-644 [23949543], [doi]  [abs].
  48. Benfey, PN; Scheres, B, Arabidopsis as a Model for Systems Biology (August, 2013), pp. 391-406, Elsevier [doi] .
  49. Moubayidin, L; Di Mambro, R; Sozzani, R; Pacifici, E; Salvi, E; Terpstra, I; Bao, D; van Dijken, A; Dello Ioio, R; Perilli, S; Ljung, K; Benfey, PN; Heidstra, R; Costantino, P; Sabatini, S, Spatial coordination between stem cell activity and cell differentiation in the root meristem., Developmental Cell, vol. 26 no. 4 (August, 2013), pp. 405-415 [23987513], [doi]  [abs].
  50. Topp, CN; Iyer-Pascuzzi, AS; Anderson, JT; Lee, C-R; Zurek, PR; Symonova, O; Zheng, Y; Bucksch, A; Mileyko, Y; Galkovskyi, T; Moore, BT; Harer, J; Edelsbrunner, H; Mitchell-Olds, T; Weitz, JS; Benfey, PN, 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture., Proceedings of the National Academy of Sciences of the United States of America, vol. 110 no. 18 (April, 2013), pp. E1695-E1704 [23580618], [doi]  [abs].
  51. Liberman, LM; Benfey, PN, Polarized radicals., Cell, vol. 153 no. 2 (April, 2013), pp. 285-286 [23582319], [doi]  [abs].
  52. Moussaieff, A; Rogachev, I; Brodsky, L; Malitsky, S; Toal, TW; Belcher, H; Yativ, M; Brady, SM; Benfey, PN; Aharoni, A, High-resolution metabolic mapping of cell types in plant roots., Proceedings of the National Academy of Sciences of the United States of America, vol. 110 no. 13 (March, 2013), pp. E1232-E1241 [23476065], [doi]  [abs].
  53. Fang, S; Clark, RT; Zheng, Y; Iyer-Pascuzzi, AS; Weitz, JS; Kochian, LV; Edelsbrunner, H; Liao, H; Benfey, PN, Genotypic recognition and spatial responses by rice roots., Proc Natl Acad Sci U S A, vol. 110 no. 7 (February, 2013), pp. 2670-2675 [23362379], [doi]  [abs].
  54. Fang, S; Clark, RT; Zheng, Y; Iyer-Pascuzzi, AS; Weitz, JS; Kochian, LV; Edelsbrunner, H; Liao, H; Benfey, PN, Genotypic recognition and spatial responses by rice roots., Proceedings of the National Academy of Sciences of the United States of America, vol. 110 no. 7 (February, 2013), pp. 2670-2675 [doi]  [abs].
  55. Iyer-Pascuzzi, AS; Zurek, PR; Benfey, PN, High-throughput, noninvasive imaging of root systems., Methods in Molecular Biology (Clifton, N.J.), vol. 959 no. 7 (January, 2013), pp. 177-187 [23299675], [doi]  [abs].
  56. Topp, CN; Benfey, PN, Growth control of root architecture (December, 2012), pp. 373-386, Elsevier [doi] .
  57. Busch, W; Moore, BT; Martsberger, B; Mace, DL; Twigg, RW; Jung, J; Pruteanu-Malinici, I; Kennedy, SJ; Fricke, GK; Clark, RL; Ohler, U; Benfey, PN, A microfluidic device and computational platform for high-throughput live imaging of gene expression., Nat Methods, vol. 9 no. 11 (November, 2012), pp. 1101-1106 [23023597], [doi]  [abs].
  58. Cederholm, HM; Iyer-Pascuzzi, AS; Benfey, PN, Patterning the primary root in Arabidopsis., Wiley Interdisciplinary Reviews. Developmental Biology, vol. 1 no. 5 (September, 2012), pp. 675-691 [23799568], [doi]  [abs].
  59. Cruz-Ramírez, A; Díaz-Triviño, S; Blilou, I; Grieneisen, VA; Sozzani, R; Zamioudis, C; Miskolczi, P; Nieuwland, J; Benjamins, R; Dhonukshe, P; Caballero-Pérez, J; Horvath, B; Long, Y; Mähönen, AP; Zhang, H; Xu, J; Murray, JAH; Benfey, PN; Bako, L; Marée, AFM; Scheres, B, A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division., Cell, vol. 150 no. 5 (August, 2012), pp. 1002-1015 [22921914], [doi]  [abs].
  60. Ingram, PA; Zhu, J; Shariff, A; Davis, IW; Benfey, PN; Elich, T, High-throughput imaging and analysis of root system architecture in Brachypodium distachyon under differential nutrient availability., Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 367 no. 1595 (June, 2012), pp. 1559-1569 [22527399], [doi]  [abs].
  61. Stone, JE; Benfey, PN; You, L, Promoting collaborative interdisciplinary research at the Duke Center for Systems Biology., Acs Synthetic Biology, vol. 1 no. 5 (May, 2012), pp. 153-155 [doi]  [abs].
  62. Petricka, JJ; Schauer, MA; Megraw, M; Breakfield, NW; Thompson, JW; Georgiev, S; Soderblom, EJ; Ohler, U; Moseley, MA; Grossniklaus, U; Benfey, PN, The protein expression landscape of the Arabidopsis root., Proc Natl Acad Sci U S A, vol. 109 no. 18 (May, 2012), pp. 6811-6818 [22447775], [doi]  [abs].
  63. Rogers, ED; Jackson, T; Moussaieff, A; Aharoni, A; Benfey, PN, Cell type-specific transcriptional profiling: implications for metabolite profiling., The Plant Journal : for Cell and Molecular Biology, vol. 70 no. 1 (April, 2012), pp. 5-17 [22449039], [doi]  [abs].
  64. Liberman, LM; Sozzani, R; Benfey, PN, Integrative systems biology: an attempt to describe a simple weed., Current Opinion in Plant Biology, vol. 15 no. 2 (April, 2012), pp. 162-167 [22277598], [doi]  [abs].
  65. Bruex, A; Kainkaryam, RM; Wieckowski, Y; Kang, YH; Bernhardt, C; Xia, Y; Zheng, X; Wang, JY; Lee, MM; Benfey, P; Woolf, PJ; Schiefelbein, J, A gene regulatory network for root epidermis cell differentiation in Arabidopsis., Plos Genetics, vol. 8 no. 1 (January, 2012), pp. e1002446 [doi]  [abs].
  66. De Smet, I; White, PJ; Bengough, AG; Dupuy, L; Parizot, B; Casimiro, I; Heidstra, R; Laskowski, M; Lepetit, M; Hochholdinger, F; Draye, X; Zhang, H; Broadley, MR; Péret, B; Hammond, JP; Fukaki, H; Mooney, S; Lynch, JP; Nacry, P; Schurr, U; Laplaze, L; Benfey, P; Beeckman, T; Bennett, M, Analyzing lateral root development: how to move forward., The Plant Cell, vol. 24 no. 1 (January, 2012), pp. 15-20 [doi]  [abs].
  67. Benfey, PN, Toward a systems analysis of the root., Cold Spring Harbor Symposia on Quantitative Biology, vol. 77 no. 7 (January, 2012), pp. 91-96 [23234807], [doi]  [abs].
  68. Petricka, JJ; Winter, CM; Benfey, PN, Control of Arabidopsis root development., Annual Review of Plant Biology, vol. 63 no. 18 (January, 2012), pp. 563-590 [22404466], [doi]  [abs].
  69. Davis, IW; Benninger, C; Benfey, PN; Elich, T, POWRS: position-sensitive motif discovery., Plos One, vol. 7 no. 7 (January, 2012), pp. e40373 [22792292], [doi]  [abs].
  70. Moreno-Risueno, MA; Van Norman, JM; Benfey, PN, Transcriptional switches direct plant organ formation and patterning., Current Topics in Developmental Biology, vol. 98 no. 18 (January, 2012), pp. 229-257 [22305165], [doi]  [abs].
  71. Breakfield, NW; Corcoran, DL; Petricka, JJ; Shen, J; Sae-Seaw, J; Rubio-Somoza, I; Weigel, D; Ohler, U; Benfey, PN, High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis., Genome Res, vol. 22 no. 1 (January, 2012), pp. 163-176 [21940835], [doi]  [abs].
  72. Galkovskyi, T; Mileyko, Y; Bucksch, A; Moore, B; Symonova, O; Price, CA; Topp, CN; Iyer-Pascuzzi, AS; Zurek, PR; Fang, S; Harer, J; Benfey, PN; Weitz, JS, GiA Roots: software for the high throughput analysis of plant root system architecture., Bmc Plant Biology, vol. 12 (January, 2012), pp. 116 [22834569], [doi]  [abs].
  73. Galkovskyi, T; Mileyko, Y; Bucksch, A; Moore, B; Symonova, O; Price, CA; Topp, CN; Iyer-Pascuzzi, AS; Zurek, PR; Fang, S; Harer, J; Benfey, PN; Weitz, JS, GiA Roots: software for the high throughput analysis of plant root system architecture, Bmc Plant Biology, vol. 12 no. 1 (2012), pp. 116-116, Springer Nature [22834569], [doi]  [abs].
  74. Zheng, Y; Gu, S; Edelsbrunner, H; Tomasi, C; Benfey, P, Detailed reconstruction of 3D plant root shape, Proceedings of the Ieee International Conference on Computer Vision (December, 2011), pp. 2026-2033, IEEE [doi]  [abs].
  75. Iyer-Pascuzzi, AS; Jackson, T; Cui, H; Petricka, JJ; Busch, W; Tsukagoshi, H; Benfey, PN, Cell identity regulators link development and stress responses in the Arabidopsis root., Developmental Cell, vol. 21 no. 4 (October, 2011), pp. 770-782 [22014526], [doi]  [abs].
  76. Petricka, JJ; Benfey, PN, Reconstructing regulatory network transitions., Trends in Cell Biology, vol. 21 no. 8 (August, 2011), pp. 442-451 [21632251], [doi]  [abs].
  77. Benfey, PN, Taking a developmental perspective on systems biology., Developmental Cell, vol. 21 no. 1 (July, 2011), pp. 27-28 [21763604], [doi]  [abs].
  78. Zhu, J; Ingram, PA; Benfey, PN; Elich, T, From lab to field, new approaches to phenotyping root system architecture., Current Opinion in Plant Biology, vol. 14 no. 3 (June, 2011), pp. 310-317 [21530367], [doi]  [abs].
  79. Moreno-Risueno, MA; Benfey, PN, Time-based patterning in development: The role of oscillating gene expression., Transcription, vol. 2 no. 3 (May, 2011), pp. 124-129 [21826283], [doi]  [abs].
  80. Van Norman, JM; Breakfield, NW; Benfey, PN, Intercellular communication during plant development., The Plant Cell, vol. 23 no. 3 (March, 2011), pp. 855-864 [21386031], [doi]  [abs].
  81. Brady, SM; Zhang, L; Megraw, M; Martinez, NJ; Jiang, E; Yi, CS; Liu, W; Zeng, A; Taylor-Teeples, M; Kim, D; Ahnert, S; Ohler, U; Ware, D; Walhout, AJM; Benfey, PN, A stele-enriched gene regulatory network in the Arabidopsis root., Molecular Systems Biology, vol. 7 no. 3 (January, 2011), pp. 459 [21245844], [doi]  [abs].
  82. Sozzani, R; Benfey, PN, High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype., Genome Biology, vol. 12 no. 3 (January, 2011), pp. 219 [21457493], [doi]  [abs].
  83. Pop, A; Huttenhower, C; Iyer-Pascuzzi, A; Benfey, PN; Troyanskaya, OG, Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana., Bmc Systems Biology, vol. 4 (December, 2010), pp. 180 [21194434], [doi]  [abs].
  84. Baskin, TI; Peret, B; Baluška, 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 in Plant Science, vol. 15 no. 11 (November, 2010), pp. 593-594 [20833574], [doi] .
  85. Tsukagoshi, H; Busch, W; Benfey, PN, Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root., Cell, vol. 143 no. 4 (November, 2010), pp. 606-616 [21074051], [doi]  [abs].
  86. 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 (New York, N.Y.), vol. 329 no. 5997 (September, 2010), pp. 1306-1311 [20829477], [doi]  [abs].
  87. Long, TA; Tsukagoshi, H; Busch, W; Lahner, B; Salt, DE; Benfey, PN, The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots., The Plant Cell, vol. 22 no. 7 (July, 2010), pp. 2219-2236 [20675571], [doi]  [abs].
  88. Sozzani, R; Cui, H; Moreno-Risueno, MA; Busch, W; Van Norman, JM; Vernoux, T; Brady, SM; Dewitte, W; Murray, JAH; Benfey, PN, Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth., Nature, vol. 466 no. 7302 (July, 2010), pp. 128-132 [20596025], [doi]  [abs].
  89. Carlsbecker, A; Lee, J-Y; Roberts, CJ; Dettmer, J; Lehesranta, S; Zhou, J; Lindgren, O; Moreno-Risueno, MA; Vatén, A; Thitamadee, S; Campilho, A; Sebastian, J; Bowman, JL; Helariutta, Y; Benfey, PN, Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate., Nature, vol. 465 no. 7296 (May, 2010), pp. 316-321 [20410882], [doi]  [abs].
  90. Moreno-Risueno, MA; Busch, W; Benfey, PN, Omics meet networks - using systems approaches to infer regulatory networks in plants., Current Opinion in Plant Biology, vol. 13 no. 2 (April, 2010), pp. 126-131 [20036612], [doi]  [abs].
  91. Busch, W; Benfey, PN, Information processing without brains--the power of intercellular regulators in plants., Development (Cambridge, England), vol. 137 no. 8 (April, 2010), pp. 1215-1226 [20332147], [doi]  [abs].
  92. Iyer-Pascuzzi, AS; Symonova, O; Mileyko, Y; Hao, Y; Belcher, H; Harer, J; Weitz, JS; Benfey, PN, Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems., Plant Physiology, vol. 152 no. 3 (March, 2010), pp. 1148-1157 [20107024], [doi]  [abs].
  93. Benfey, PN; Bennett, M; Schiefelbein, J, 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 [20409273], [doi]  [abs].
  94. De Smet, I; Lau, S; Voss, U; Vanneste, S; Benjamins, R; Rademacher, EH; Schlereth, A; De Rybel, B; Vassileva, V; Grunewald, W; Naudts, M; Levesque, MP; Ehrismann, JS; Inzé, D; Luschnig, C; Benfey, PN; Weijers, D; Van Montagu, MCE; Bennett, MJ; Jürgens, G; Beeckman, T, 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. 2705-2710 [20133796], [doi]  [abs].
  95. To, JP; Zhu, J; Benfey, PN; Elich, T, Optimizing root system architecture in biofuel crops for sustainable energy production and soil carbon sequestration., F1000 Biology Reports, vol. 2 (January, 2010), pp. 65 [21173868], [doi]  [abs].
  96. Iyer-Pascuzzi, AS; Benfey, PN, Fluorescence-activated cell sorting in plant developmental biology., Methods in Molecular Biology (Clifton, N.J.), vol. 655 (January, 2010), pp. 313-319 [20734270], [doi]  [abs].
  97. Orlando, DA; Brady, SM; Fink, TMA; Benfey, PN; Ahnert, SE, Detecting separate time scales in genetic expression data., Bmc Genomics, vol. 11 (January, 2010), pp. 381 [20565716], [doi]  [abs].
  98. Petricka, JJ; Van Norman, JM; Benfey, PN, 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 [20066115], [doi]  [abs].
  99. Van Norman, JM; Benfey, PN, Arabidopsis thaliana as a model organism in systems biology., Wiley Interdisciplinary Reviews. Systems Biology and Medicine, vol. 1 no. 3 (November, 2009), pp. 372-379, WILEY [20228888], [doi]  [abs].
  100. Cartwright, DA; Brady, SM; Orlando, DA; Sturmfels, B; Benfey, PN, Reconstructing spatiotemporal gene expression data from partial observations., Bioinformatics (Oxford, England), vol. 25 no. 19 (October, 2009), pp. 2581-2587 [19608707], [doi]  [abs].
  101. Tromas, A; Braun, N; Muller, P; Khodus, T; Paponov, IA; Palme, K; Ljung, K; Lee, J-Y; Benfey, P; Murray, JAH; Scheres, B; Perrot-Rechenmann, C, The AUXIN BINDING PROTEIN 1 is required for differential auxin responses mediating root growth., Plos One, vol. 4 no. 9 (September, 2009), pp. e6648 [doi]  [abs].
  102. Benfey, PN; Birnbaum, KD, Primer and interviews: Gene regulation in Arabidopsis thaliana. Interview by Julie C. Kiefer., Developmental Dynamics : an Official Publication of the American Association of Anatomists, vol. 238 no. 9 (September, 2009), pp. 2449-2458 [doi]  [abs].
  103. Benfey, PN; Cui, H; Twigg, R; Long, T; Iyer-Pascuzzi, A; Tsukagoshi, H; Sozzani, R; Jackson, T; Van Norman, J; Moreno-Risueno, M, Development rooted in interwoven networks, Developmental Biology, vol. 331 no. 2 (July, 2009), pp. 386-386, Elsevier BV [doi] .
  104. 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., The Plant Cell, vol. 21 no. 6 (June, 2009), pp. 1659-1668 [19491238], [doi]  [abs].
  105. Cui, H; Benfey, PN, Interplay between SCARECROW, GA and LIKE HETEROCHROMATIN PROTEIN 1 in ground tissue patterning in the Arabidopsis root., The Plant Journal : for Cell and Molecular Biology, vol. 58 no. 6 (June, 2009), pp. 1016-1027 [doi]  [abs].
  106. 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 [doi]  [abs].
  107. Iyer-Pascuzzi, A; Simpson, J; Herrera-Estrella, L; Benfey, PN, Functional genomics of root growth and development in Arabidopsis., Current Opinion in Plant Biology, vol. 12 no. 2 (April, 2009), pp. 165-171 [19117793], [doi]  [abs].
  108. Iyer-Pascuzzi, AS; Benfey, PN, Transcriptional networks in root cell fate specification., Biochimica Et Biophysica Acta, vol. 1789 no. 4 (April, 2009), pp. 315-325 [18973837], [doi]  [abs].
  109. Gallagher, KL; Benfey, PN, Both the conserved GRAS domain and nuclear localization are required for SHORT-ROOT movement., The Plant Journal : for Cell and Molecular Biology, vol. 57 no. 5 (March, 2009), pp. 785-797 [19000160], [doi]  [abs].
  110. Orlando, DA; Brady, SM; Koch, JD; Dinneny, JR; Benfey, PN, Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment., Methods in Molecular Biology (Clifton, N.J.), vol. 553 (Winter, 2009), pp. 57-77 [19588101], [doi]  [abs].
  111. Cui, H; Benfey, PN, Cortex proliferation: Simple phenotype, complex regulatory mechanisms, Plant Signaling & Behavior, vol. 4 no. 6 (2009), pp. 551-553, Informa UK Limited [19816127], [doi]  [abs].
  112. 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., The Plant Journal : for Cell and Molecular Biology, vol. 56 no. 6 (December, 2008), pp. 948-962 [doi]  [abs].
  113. 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, Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root., Science (New York, N.Y.), vol. 322 no. 5901 (October, 2008), pp. 594-597 [18948541], [doi]  [abs].
  114. Petricka, JJ; Benfey, PN, Root layers: complex regulation of developmental patterning., Current Opinion in Genetics & Development, vol. 18 no. 4 (August, 2008), pp. 354-361 [18617392], [doi]  [abs].
  115. 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, JDG; 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., Nature Cell Biology, vol. 10 no. 8 (August, 2008), pp. 946-954 [doi]  [abs].
  116. 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., Science (New York, N.Y.), vol. 320 no. 5878 (May, 2008), pp. 942-945 [18436742], [doi]  [abs].
  117. Benfey, PN; Mitchell-Olds, T, From genotype to phenotype: systems biology meets natural variation., Science (New York, N.Y.), vol. 320 no. 5875 (April, 2008), pp. 495-497 [18436781], [doi]  [abs].
  118. Dinneny, JR; Benfey, PN, Plant stem cell niches: standing the test of time., Cell, vol. 132 no. 4 (February, 2008), pp. 553-557 [18295573], [doi]  [abs].
  119. Colinas, J; Schmidler, SC; Bohrer, G; Iordanov, B; Benfey, PN, Intergenic and genic sequence lengths have opposite relationships with respect to gene expression., Plos One, vol. 3 no. 11 (January, 2008), pp. e3670 [18989364], [doi]  [abs].
  120. Long, TA; Brady, SM; Benfey, PN, Systems approaches to identifying gene regulatory networks in plants., Annual Review of Cell and Developmental Biology, vol. 24 (January, 2008), pp. 81-103 [18616425], [doi]  [abs].
  121. Brady, SM; Orlando, DA; Lee, J-Y; Wang, JY; Koch, J; Dinneny, JR; Mace, D; Ohler, U; Benfey, PN, A high-resolution root spatiotemporal map reveals dominant expression patterns., Science, vol. 318 no. 5851 (November, 2007), pp. 801-806 [17975066], [doi]  [abs].
  122. 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., Science (New York, N.Y.), vol. 316 no. 5823 (April, 2007), pp. 421-425 [17446396], [doi]  [abs].
  123. Brady, SM; Song, S; Dhugga, KS; Rafalski, JA; Benfey, PN, Combining expression and comparative evolutionary analysis. The COBRA gene family., Plant Physiology, vol. 143 no. 1 (January, 2007), pp. 172-187 [17098858], [doi]  [abs].
  124. Weitz, JS; Benfey, PN; Wingreen, NS, Evolution, interactions, and biological networks., Plos Biology, vol. 5 no. 1 (January, 2007), pp. e11 [17227140], [doi] .
  125. Long, TA; Benfey, PN, Transcription factors and hormones: new insights into plant cell differentiation., Current Opinion in Cell Biology, vol. 18 no. 6 (December, 2006), pp. 710-714 [17034999], [doi]  [abs].
  126. Brady, SM; Benfey, PN, Erratum: A systems approach to understanding root development (Canadian Journal of Botany (2006) 84, (695-701)), Canadian Journal of Botany, vol. 84 no. 9 (September, 2006), pp. 1508, Canadian Science Publishing [doi] .
  127. Brady, SM; Long, TA; Benfey, PN, Unraveling the dynamic transcriptome., The Plant Cell, vol. 18 no. 9 (September, 2006), pp. 2101-2111 [16968906], [doi] .
  128. Levesque, MP; Vernoux, T; Busch, W; Cui, H; Wang, JY; Blilou, I; Hassan, H; Nakajima, K; Matsumoto, N; Lohmann, JU; Scheres, B; Benfey, PN, Erratum: Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis (PLoS Biology 4, 5 DOI: 10.1371/journal.pbio.0040143), Plos Biology, vol. 4 no. 7 (July, 2006), pp. 1284, Public Library of Science (PLoS) [doi] .
  129. Mace, DL; Lee, J-Y; Twigg, RW; Colinas, J; Benfey, PN; Ohler, U, Quantification of transcription factor expression from Arabidopsis images., Bioinformatics, vol. 22 no. 14 (July, 2006), pp. e323-e331 [16873489], [doi]  [abs].
  130. Brady, SM; Benfey, PN, A systems approach to understanding root development, Canadian Journal of Botany, vol. 84 no. 5 (May, 2006), pp. 695-701, Canadian Science Publishing [doi]  [abs].
  131. Levesque, MP; Vernoux, T; Busch, W; Cui, H; Wang, JY; Blilou, I; Hassan, H; Nakajima, K; Matsumoto, N; Lohmann, JU; Scheres, B; Benfey, PN, Whole-genome analysis of the short-root developmental pathway in Arabidopsis, edited by Preuss, D, Plos Biology, vol. 4 no. 5 (May, 2006), pp. 739-752 [16640459], [doi]  [abs].
  132. Lee, J-Y; Colinas, J; Wang, JY; Mace, D; Ohler, U; Benfey, PN, Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots., Proceedings of the National Academy of Sciences of the United States of America, vol. 103 no. 15 (April, 2006), pp. 6055-6060 [16581911], [doi]  [abs].
  133. Friml, J; Benfey, P; Benková, E; Bennett, M; Berleth, T; Geldner, N; Grebe, M; Heisler, M; Hejátko, J; Jürgens, G; Laux, T; Lindsey, K; Lukowitz, W; Luschnig, C; Offringa, R; Scheres, B; Swarup, R; Torres-Ruiz, R; Weijers, D; Zazímalová, E, Apical-basal polarity: why plant cells don't stand on their heads., Trends in Plant Science, vol. 11 no. 1 (January, 2006), pp. 12-14 [doi] .
  134. Dinneny, JR; Benfey, PN, Stem cell research goes underground: the RETINOBLASTOMA-RELATED gene in root development., Cell, vol. 123 no. 7 (December, 2005), pp. 1180-1182 [16377557], [doi]  [abs].
  135. Lim, J; Jung, JW; Lim, CE; Lee, M-H; Kim, BJ; Kim, M; Bruce, WB; Benfey, PN, Conservation and diversification of SCARECROW in maize., Plant Molecular Biology, vol. 59 no. 4 (November, 2005), pp. 619-630 [16244911], [doi]  [abs].
  136. Vernoux, T; Benfey, PN, Signals that regulate stem cell activity during plant development., Current Opinion in Genetics & Development, vol. 15 no. 4 (August, 2005), pp. 388-394 [15967658], [doi]  [abs].
  137. Birnbaum, K; Jung, JW; Wang, JY; Lambert, GM; Hirst, JA; Galbraith, DW; Benfey, PN, Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines., Nature Methods, vol. 2 no. 8 (August, 2005), pp. 615-619 [16170893], [doi] .
  138. Nawy, T; Lee, J-Y; Colinas, J; Wang, JY; Thongrod, SC; Malamy, JE; Birnbaum, K; Benfey, PN, Transcriptional profile of the Arabidopsis root quiescent center., The Plant Cell, vol. 17 no. 7 (July, 2005), pp. 1908-1925 [15937229], [doi]  [abs].
  139. Roudier, F; Fernandez, AG; Fujita, M; Himmelspach, R; Borner, GHH; Schindelman, G; Song, S; Baskin, TI; Dupree, P; Wasteneys, GO; Benfey, PN, COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation., The Plant Cell, vol. 17 no. 6 (June, 2005), pp. 1749-1763, AMER SOC PLANT BIOLOGISTS [15849274], [doi]  [abs].
  140. Benfey, PN, Developmental networks., Plant Physiology, vol. 138 no. 2 (June, 2005), pp. 548-549 [15955911], [doi] .
  141. Lee, J-Y; Levesque, M; Benfey, PN, High-throughput RNA isolation technologies. New tools for high-resolution gene expression profiling in plant systems., Plant Physiology, vol. 138 no. 2 (June, 2005), pp. 585-590 [15955922], [doi] .
  142. Paquette, AJ; Benfey, PN, Maturation of the ground tissue of the root is regulated by gibberellin and SCARECROW and requires SHORT-ROOT., Plant Physiology, vol. 138 no. 2 (June, 2005), pp. 636-640 [15955927], [doi] .
  143. Gallagher, KL; Benfey, PN, Not just another hole in the wall: understanding intercellular protein trafficking., Genes & Development, vol. 19 no. 2 (January, 2005), pp. 189-195 [15655108], [doi]  [abs].
  144. Gallagher, KL; Paquette, AJ; Nakajima, K; Benfey, PN, Mechanisms regulating SHORT-ROOT intercellular movement., Current Biology : Cb, vol. 14 no. 20 (October, 2004), pp. 1847-1851 [15498493], [doi]  [abs].
  145. Birnbaum, K; Benfey, PN, Network building: transcriptional circuits in the root., Current Opinion in Plant Biology, vol. 7 no. 5 (October, 2004), pp. 582-588 [15337102], [doi]  [abs].
  146. Benfey, PN, Development and ecology in the time of systems biology., Developmental Cell, vol. 7 no. 3 (September, 2004), pp. 329-330 [15363408], [doi] .
  147. Irish, VF; Benfey, PN, Beyond Arabidopsis. Translational biology meets evolutionary developmental biology., Plant Physiology, vol. 135 no. 2 (June, 2004), pp. 611-614 [15208409], [doi]  [abs].
  148. Sena, G; Jung, JW; Benfey, PN, A broad competence to respond to SHORT ROOT revealed by tissue-specific ectopic expression., Development (Cambridge, England), vol. 131 no. 12 (June, 2004), pp. 2817-2826 [15142972], [doi]  [abs].
  149. Levesque, MP; Benfey, PN, Systems biology., Current Biology : Cb, vol. 14 no. 5 (March, 2004), pp. R179-R180 [15028228], [doi] .
  150. Benfey, PN, A common switch used by plants and animals., Cell, vol. 116 no. 1 (January, 2004), pp. 4-5 [14718159], [doi]  [abs].
  151. Irish, V; Benfey, P, Growth and development: Something old, something new...., Current Opinion in Plant Biology, vol. 7 no. 1 (January, 2004), pp. 1-3, Elsevier BV [doi] .
  152. Birnbaum, K; Shasha, DE; Wang, JY; Jung, JW; Lambert, GM; Galbraith, DW; Benfey, PN, A gene expression map of the Arabidopsis root., Science (New York, N.Y.), vol. 302 no. 5652 (December, 2003), pp. 1956-1960 [14671301], [doi]  [abs].
  153. Birnbaum, K; Desalle, R; Peters, CM; Benfey, PN, Integrating gene flow, crop biology, and farm management in on-farm conservation of avocado (Persea americana, Lauraceae)., American Journal of Botany, vol. 90 no. 11 (November, 2003), pp. 1619-1627 [21653337], [doi]  [abs].
  154. Benfey, PN, Molecular biology: microRNA is here to stay., Nature, vol. 425 no. 6955 (September, 2003), pp. 244-245 (Prize for one of three best News and Views in 2003.) [13679896], [doi]  [abs].
  155. Levesque, M; Shasha, D; Kim, W; Surette, MG; Benfey, PN, Trait-to-gene: a computational method for predicting the function of uncharacterized genes., Current Biology : Cb, vol. 13 no. 2 (January, 2003), pp. 129-133 [12546786], [doi]  [abs].
  156. Brenner, ED; Stevenson, DW; McCombie, RW; Katari, MS; Rudd, SA; Mayer, KFX; 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 no. 12 (January, 2003), pp. R78 [14659015], [doi]  [abs].
  157. Birnbaum, K; Benfey, PN; Peters, CM; Desalle, R, MANAGEDPOP: A computer simulation to project allelic diversity in managed populations with overlapping generations, Molecular Ecology Notes, vol. 2 no. 4 (December, 2002), pp. 615-617, WILEY [doi]  [abs].
  158. Roudier, F; Schindelman, G; DeSalle, R; Benfey, PN, The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion., Plant Physiology, vol. 130 no. 2 (October, 2002), pp. 538-548 [12376623], [doi]  [abs].
  159. Müller, S; Fuchs, E; Ovecka, M; Wysocka-Diller, J; Benfey, PN; Hauser, M-T, Two new loci, PLEIADE and HYADE, implicate organ-specific regulation of cytokinesis in Arabidopsis., Plant Physiology, vol. 130 no. 1 (September, 2002), pp. 312-324 [12226511], [doi]  [abs].
  160. Colinas, J; Birnbaum, K; Benfey, PN, Using cauliflower to find conserved non-coding regions in arabidopsis (vol 129, pg 451, 2002), Plant Physiology, vol. 129 no. 4 (August, 2002), pp. 1929-1929, AMER SOC PLANT BIOLOGISTS .
  161. Ausubel, F; Benfey, P, Arabidopsis functional genomics., Plant Physiology, vol. 129 no. 2 (June, 2002), pp. 393 [doi] .
  162. Benfey, PN, Auxin action: slogging out of the swamp., Current Biology : Cb, vol. 12 no. 11 (June, 2002), pp. R389-R390 [12062071], [doi]  [abs].
  163. Colinas, J; Birnbaum, K; Benfey, PN, Using cauliflower to find conserved non-coding regions in Arabidopsis., Plant Physiology, vol. 129 no. 2 (June, 2002), pp. 451-454 [12068091], [doi] .
  164. Nakajima, K; Benfey, PN, Signaling in and out: control of cell division and differentiation in the shoot and root., The Plant Cell, vol. 14 Suppl (January, 2002), pp. S265-S276 [12045282], [doi] .
  165. Nawy, T; Benfey, P, Signaling the tips: regulation of stem cell function in plants., Differentiation; Research in Biological Diversity, vol. 68 no. 4-5 (October, 2001), pp. 155-158 [doi] .
  166. Birnbaum, K; Benfey, PN; Shasha, DE, cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships., Genome Research, vol. 11 no. 9 (September, 2001), pp. 1567-1573 [11544201], [doi]  [abs].
  167. Nakajima, K; Sena, G; Nawy, T; Benfey, PN, Intercellular movement of the putative transcription factor SHR in root patterning., Nature, vol. 413 no. 6853 (September, 2001), pp. 307-311 [11565032], [doi]  [abs].
  168. Paquette, AJ; Benfey, PN, Axis formation and polarity in plants., Current Opinion in Genetics & Development, vol. 11 no. 4 (August, 2001), pp. 405-409 [11448626], [doi]  [abs].
  169. Schindelman, G; Morikami, A; Jung, J; Baskin, TI; Carpita, NC; Derbyshire, P; McCann, MC; Benfey, PN, COBRA encodes a putative GPI-anchored protein, which is polarly localized and necessary for oriented cell expansion in Arabidopsis., Genes & Development, vol. 15 no. 9 (May, 2001), pp. 1115-1127 [11331607], [doi]  [abs].
  170. Benfey, PN; Weigel, D, Transcriptional networks controlling plant development., Plant Physiology, vol. 125 no. 1 (January, 2001), pp. 109-111 [11154309], [doi] .
  171. Mähönen, AP; Bonke, M; Kauppinen, L; Riikonen, M; Benfey, PN; Helariutta, Y, A novel two-component hybrid molecule regulates vascular morphogenesis of the Arabidopsis root., Genes & Development, vol. 14 no. 23 (December, 2000), pp. 2938-2943 [11114883], [doi]  [abs].
  172. Benfey, PN; Scheres, B, Root development., Current Biology : Cb, vol. 10 no. 22 (November, 2000), pp. R813-R815 [11102819], [doi] .
  173. Lim, J; Helariutta, Y; Specht, CD; Jung, J; Sims, L; Bruce, WB; Diehn, S; Benfey, PN, Molecular analysis of the SCARECROW gene in maize reveals a common basis for radial patterning in diverse meristems., The Plant Cell, vol. 12 no. 8 (August, 2000), pp. 1307-1318 [10948251], [doi]  [abs].
  174. Helariutta, Y; Fukaki, H; Wysocka-Diller, J; Nakajima, K; Jung, J; Sena, G; Hauser, MT; Benfey, PN, The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling., Cell, vol. 101 no. 5 (May, 2000), pp. 555-567 [10850497], [doi]  [abs].
  175. Wysocka-Diller, JW; Helariutta, Y; Fukaki, H; Malamy, JE; Benfey, PN, Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot., Development (Cambridge, England), vol. 127 no. 3 (February, 2000), pp. 595-603 [10631180]  [abs].
  176. Sabatini, S; Beis, D; Wolkenfelt, H; Murfett, J; Guilfoyle, T; Malamy, J; Benfey, P; Leyser, O; Bechtold, N; Weisbeek, P; Scheres, B, An auxin-dependent distal organizer of pattern and polarity in the Arabidopsis root., Cell, vol. 99 no. 5 (November, 1999), pp. 463-472 [doi]  [abs].
  177. Scheres, B; Benfey, PN, ASYMMETRIC CELL DIVISION IN PLANTS., Annual Review of Plant Physiology and Plant Molecular Biology, vol. 50 (June, 1999), pp. 505-537 [15012218], [doi]  [abs].
  178. Pysh, LD; Wysocka-Diller, JW; Camilleri, C; Bouchez, D; Benfey, PN, The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes., The Plant Journal : for Cell and Molecular Biology, vol. 18 no. 1 (April, 1999), pp. 111-119 [10341448], [doi]  [abs].
  179. Benfey, PN, Stem cells: A tale of two kingdoms., Current Biology : Cb, vol. 9 no. 5 (March, 1999), pp. R171-R172 [10074441], [doi]  [abs].
  180. Benfey, PN, Is the shoot a root with a view?, Current Opinion in Plant Biology, vol. 2 no. 1 (February, 1999), pp. 39-43 [10047569], [doi]  [abs].
  181. Fukaki, H; Wysocka-Diller, J; Kato, T; Fujisawa, H; Benfey, PN; Tasaka, M, Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana., The Plant Journal : for Cell and Molecular Biology, vol. 14 no. 4 (May, 1998), pp. 425-430 [9670559], [doi]  [abs].
  182. Wysocka-Diller, JW; Benfey, PN, Root development: signaling down and around., Bioessays, vol. 19 no. 11 (November, 1997), pp. 959-965 [9394618], [doi]  [abs].
  183. Malamy, JE; Benfey, PN, Analysis of SCARECROW expression using a rapid system for assessing transgene expression in Arabidopsis roots., The Plant Journal : for Cell and Molecular Biology, vol. 12 no. 4 (October, 1997), pp. 957-963 [9375406], [doi]  [abs].
  184. Malamy, JE; Benfey, PN, Organization and cell differentiation in lateral roots of Arabidopsis thaliana., Development (Cambridge, England), vol. 124 no. 1 (January, 1997), pp. 33-44 [9006065]  [abs].
  185. Malamy, JE; Benfey, PN, Down and out in arabidopsis: The formation of lateral roots, Trends in Plant Science, vol. 2 no. 10 (January, 1997), pp. 390-396, Elsevier BV [doi]  [abs].
  186. Di Laurenzio, L; Wysocka-Diller, J; Malamy, JE; Pysh, L; Helariutta, Y; Freshour, G; Hahn, MG; Feldmann, KA; Benfey, PN, The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root., Cell, vol. 86 no. 3 (August, 1996), pp. 423-433 [8756724], [doi]  [abs].
  187. Hauser, MT; Morikami, A; Benfey, PN, Conditional root expansion mutants of Arabidopsis., Development (Cambridge, England), vol. 121 no. 4 (April, 1995), pp. 1237-1252 [7743935]  [abs].
  188. Aeschbacher, RA; Hauser, MT; Feldmann, KA; Benfey, PN, The SABRE gene is required for normal cell expansion in Arabidopsis., Genes & Development, vol. 9 no. 3 (February, 1995), pp. 330-340 [7867930], [doi]  [abs].
  189. Scheres, B; Di Laurenzio, L; Willemsen, V; Hauser, MT; Janmaat, K; Weisbeek, P; Benfey, PN, Mutations affecting the radial organisation of the Arabidopsis root display specific defects throughout the embryonic axis, Development (Cambridge, England), vol. 121 no. 1 (January, 1995), pp. 53-62  [abs].
  190. Aeschbacher, RA; Schiefelbein, JW; Benfey, PN, The genetic and molecular basis of root development, Annual Review of Plant Physiology and Plant Molecular Biology, vol. 45 no. 1 (December, 1994), pp. 25-45, ANNUAL REVIEWS [Gateway.cgi], [doi] .
  191. Benfey, PN; Schiefelbein, JW, Getting to the root of plant development: the genetics of Arabidopsis root formation., Trends in Genetics : Tig, vol. 10 no. 3 (March, 1994), pp. 84-88 [8178369], [doi]  [abs].
  192. BENFEY, PN; SCHIEFELBEIN, JW, Insights into root development from Arabidopsis root mutants, Plant, Cell & Environment, vol. 17 no. 5 (January, 1994), pp. 675-680 [doi]  [abs].
  193. Benfey, PN; Linstead, PJ; Roberts, K; Schiefelbein, JW; Hauser, MT; Aeschbacher, RA, Root development in Arabidopsis: four mutants with dramatically altered root morphogenesis., Development (Cambridge, England), vol. 119 no. 1 (September, 1993), pp. 57-70 [8275864]  [abs].
  194. Schiefelbein, JW; Benfey, PN, International Symposium on the Molecular Genetics of Root Development, Plant Molecular Biology Reporter, vol. 11 no. 1 (March, 1993), pp. 60-64, Springer Nature [doi] .
  195. Aeschbacher, RA; Benfey, PN, Genes that regulate plant development, Plant Science., vol. 83 no. 2 (January, 1992), pp. 115-126, Elsevier BV [doi]  [abs].
  196. Takatsuji, H; Mori, M; Benfey, PN; Ren, L; Chua, NH, Characterization of a zinc finger DNA-binding protein expressed specifically in Petunia petals and seedlings., The Embo Journal, vol. 11 no. 1 (January, 1992), pp. 241-249 [1740109], [doi]  [abs].
  197. Schiefelbein, JW; Benfey, PN, The development of plant roots: new approaches to underground problems., The Plant Cell, vol. 3 no. 11 (November, 1991), pp. 1147-1154 [1821762], [doi] .
  198. Benfey, PN; Chua, NH, The Cauliflower Mosaic Virus 35S Promoter: Combinatorial Regulation of Transcription in Plants., Science (New York, N.Y.), vol. 250 no. 4983 (November, 1990), pp. 959-966 [17746920], [doi]  [abs].
  199. Benfey, PN; Takatsuji, H; Ren, L; Shah, DM; Chua, NH, Sequence Requirements of the 5-Enolpyruvylshikimate-3-phosphate Synthase 5[prime]-Upstream Region for Tissue-Specific Expression in Flowers and Seedlings., The Plant Cell, vol. 2 no. 9 (September, 1990), pp. 849-856 [12354968], [doi]  [abs].
  200. Benfey, PN; Ren, L; Chua, NH, Combinatorial and synergistic properties of CaMV 35S enhancer subdomains., The Embo Journal, vol. 9 no. 6 (June, 1990), pp. 1685-1696 [2347302], [doi]  [abs].
  201. Benfey, PN; Ren, L; Chua, NH, Tissue-specific expression from CaMV 35S enhancer subdomains in early stages of plant development., The Embo Journal, vol. 9 no. 6 (June, 1990), pp. 1677-1684 [2347301], [doi]  [abs].
  202. Lam, E; Benfey, PN; Gilmartin, PM; Fang, RX; Chua, NH, Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants., Proceedings of the National Academy of Sciences of the United States of America, vol. 86 no. 20 (October, 1989), pp. 7890-7894 [2813365], [doi]  [abs].
  203. Benfey, PN; Ren, L; Chua, NH, The CaMV 35S enhancer contains at least two domains which can confer different developmental and tissue-specific expression patterns., The Embo Journal, vol. 8 no. 8 (August, 1989), pp. 2195-2202 [16453896], [doi]  [abs].
  204. BENFEY, PN; REN, L; CHUA, NH, THE CAMV S-35 ENHANCER CONTAINS AT LEAST 2 DOMAINS WHICH CAN CONFER DIFFERENT DEVELOPMENTAL AND TISSUE-SPECIFIC EXPRESSION PATTERNS, The Embo Journal, vol. 8 no. 8 (August, 1989), pp. 2195-2202 .
  205. Benfey, PN; Chua, NH, Regulated genes in transgenic plants., Science (New York, N.Y.), vol. 244 no. 4901 (April, 1989), pp. 174-181 [17835349], [doi]  [abs].
  206. Sarid, J; Benfey, PN; Leder, P, 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., The Journal of Biological Chemistry, vol. 264 no. 2 (January, 1989), pp. 1022-1026 [2642895]  [abs].
  207. Shimizu, A; Tepler, I; Benfey, PN; Berenstein, EH; Siraganian, RP; Leder, P, Human and rat mast cell high-affinity immunoglobulin E receptors: characterization of putative alpha-chain gene products., Proceedings of the National Academy of Sciences of the United States of America, vol. 85 no. 6 (March, 1988), pp. 1907-1911 [2964640], [doi]  [abs].
  208. Benfey, PN; Yin, FH; Leder, P, Cloning of the mast cell protease, RMCP II. Evidence for cell-specific expression and a multi-gene family., The Journal of Biological Chemistry, vol. 262 no. 11 (April, 1987), pp. 5377-5384 [3549719]  [abs].

Book Chapters

  1. Sparks, EE; Benfey, PN, The contribution of root systems to plant nutrient acquisition, in Plant Macronutrient Use Efficiency: Molecular and Genomic Perspectives in Crop Plants (January, 2017), pp. 83-92, Elsevier [doi]  [abs].
  2. To, JPC; Benfey, PN; Elich, TD, Root-associated stress response networks, in Plant Abiotic Stress, Second Edition (January, 2014), pp. 69-107, JOHN WILEY & SONS INC [doi]  [abs].
  3. Sparks, EE; Imai, A; Hasebe, M; Benfey, PN, Developmental regulation and de novo formation of stem cells in plants, in Stem Cells: From Basic Research to Therapy, Volume 1: Basic Stem Cell Biology, Tissue Formation during Development, and Model Organisms (January, 2014), pp. 403-432, CRC Press [doi]  [abs].
  4. Benfey, PN, Plant Development, Genetics of, in Brenner's Encyclopedia of Genetics: Second Edition (February, 2013), pp. 340-342, Elsevier [doi]  [abs].
  5. Van Norman, JM; Liberman, LM; Benfey, PN, Arabidopsis root: A model organ in plant genomics, in Plant Roots: The Hidden Half, Fourth Edition (January, 2013), pp. 17-34  [abs].
  6. Tromas, A; Braun, N; Muller, P; Khodus, T; Paponov, IA; Palme, K; Ljung, K; Lee, JY; Benfey, P; Murray, JAH; Scheres, B; Perrot-Rechenmann, C, Auxin binding protein 1 for root growth, in Plant Physiology (January, 2011), pp. 214-229  [abs].
  7. Dinneny, JR; Benfey, PN, Studying Root Development Using a Genomic Approach, in Root Development, Annual Plant Reviews, edited by Tom Beeckman, vol. 37 (October, 2009), pp. 325-351, WILEY-BLACKWELL [doi]  [abs].
  8. Brady, SM; Benfey, PN, Development and Systems Biology: Riding the Genomics Wave towards a Systems Understanding of Root Development, in Annual Plant Reviews, Annual Plant Reviews, edited by Gloria Coruzzi and Rodrigo Gutiérrez, vol. 35 (August, 2009), pp. 304-330, WILEY-BLACKWELL [doi]  [abs].
  9. 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 .

Book Chapter

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