Philip N. Benfey | Scholars@Duke

Philip N. Benfey
Paul Kramer Professor of Biology in Trinity College of Arts and Sciences

Current Appointments & Affiliations

Paul Kramer Professor of Biology in Trinity College of Arts and Sciences, Biology, Trinity College of Arts & Sciences 2003
Professor of Biology, Biology, Trinity College of Arts & Sciences 2002
Investigator, HHMI, Biology, Trinity College of Arts & Sciences 2012
Affiliate of the Regeneration Next Initiative, Regeneration Next Initiative, Institutes and Centers 2016
Core Faculty in Innovation & Entrepreneurship, Duke Innovation & Entrepreneurship, Initiatives 2018

Contact Information

130 Science Drive, Room 137, Duke Box 90338, Durham, NC 27708
Duke Box 90338, Durham, NC 27708
philip.benfey@duke.edu (919) 660-7338

Background
Education, Training, & Certifications
- Ph.D., Harvard University 1986
- B.S., University of Paris (France) 1981
Duke Appointment History
- Director of the Center for Systems Biology in the Institute for Genome Sciences and Policy, Institutes and Centers, School of Medicine 2007 - 2014
- Chair, Biology, Trinity College of Arts & Sciences 2002 - 2007
Recognition
In the News
- NOV 27, 2018
  
  Duke Faculty Plentiful On ‘Highly Cited’ List
- DEC 6, 2016
  
  Transforming Plant Cells from Generalists to Specialists
- SEP 16, 2014
  
  Faculty Research Leads to Jobs and Companies
Awards & Honors
Research
Selected Grants
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Molecular Genetic Analysis of Root Morphogenesis awarded by National Institutes of Health 2002 - 2018
- Identifying Novel Peptide Hormones In Tomato Root Development awarded by Department of Agriculture 2016 - 2017
- Monsanto's Beachell-Borlaug International Scholars Program awarded by Texas A&M AgriLife Research 2015 - 2017
- Characterizing gene regulatory network dynamics controlling asymmetric cell division awarded by Arnold and Mabel Beckman Foundation 2015 - 2017
- Determining Interaction Parameters of Roots in Soil awarded by National Science Foundation 2014 - 2017
- Dynamics of the SHR-SCR Network Controlling Asymmetric Cell Division awarded by National Institutes of Health 2013 - 2015
- Arabidopsis 2010: Regulatory Networks Controlling Root Growth and Differentiation awarded by National Science Foundation 2010 - 2015
- Elucidating the Gene Regulatory Networks that Specify Invasive Behavior awarded by National Institutes of Health 2011 - 2014
- A Multidimensional Imaging Platform to Analyze Crop Root System Dynamics in Response to Changing Environments awarded by Department of Agriculture 2011 - 2013
- Duke Center for Systems Biology awarded by National Institutes of Health 2007 - 2013
- Duke Center for Systems Biology - Core A awarded by National Institutes of Health 2007 - 2013
- Illumina Hi-Seq 2000 Sequencing System awarded by National Institutes of Health 2012 - 2013
- Functional regulatory circuits induced by transcription factors and small RNAs awarded by National Institutes of Health 2011 - 2012
- GEPR: Genome-wide analysis of root traits awarded by National Science Foundation 2008 - 2012
- Exploring Lateral Root Formation in the Context of a 'Clock and Wavefront' Model awarded by National Institutes of Health 2010 - 2012
- Unraveling transcriptional subnetworks of Arabidopsis ground tissue awarded by National Institutes of Health 2009 - 2011
- Quantitative and Qualitative Differential Expression Proteomics awarded by National Institutes of Health 2010 - 2011
- Arabidopsis 2010: Identifying Transcriptional Networks at Cellular Resolution awarded by National Science Foundation 2006 - 2010
- Cell-Specific Transcriptional Responses to Environmental Stress in Arabidopsis awarded by National Institutes of Health 2007 - 2010
- Vision 2020 for Biology Workshop awarded by National Science Foundation 2008
- Cell Identity and Differentiation in Stimulus Response awarded by National Institutes of Health 2005 - 2008
- TRPGR Genomic Approaches to Identify Genes for Root System Architecture Traits awarded by National Science Foundation 2006 - 2008
- Coordination of the Multinational Arabidopsis Thaliana Functional Genomics Project awarded by National Science Foundation 2005 - 2007
- 16th International Conference on Arabidopsis Research awarded by Department of Agriculture 2005 - 2006
- SHR Motifs Required for Movement and Activation awarded by National Science Foundation 2002 - 2006
- 16th International Conference on Arabidopsis Research awarded by National Science Foundation 2005 - 2006
- SHR Motifs required for movement and activation awarded by National Institutes of Health 2002 - 2004
- Regulation of the Orientation of Cell Expansion awarded by National Science Foundation 2002 - 2003
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Pierre-Jerome, E, Drapek, C, and Benfey, PN. "Regulation of Division and Differentiation of Plant Stem Cells." Annual Review of Cell and Developmental Biology 34 (October 2018): 289-310. Full Text
  - Drapek, C, Sparks, EE, Marhavy, P, Taylor, I, Andersen, TG, Hennacy, JH, Geldner, N, and Benfey, PN. "Minimum requirements for changing and maintaining endodermis cell identity in the Arabidopsis root." Nature Plants 4, no. 8 (August 2018): 586-595. Full Text
  - Grondin, A, Dixit, S, Torres, R, Venkateshwarlu, C, Rogers, E, Mitchell-Olds, T, Benfey, PN, Kumar, A, and 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.) 11, no. 1 (July 31, 2018): 43-null. Full Text
  - Shibata, M, Breuer, C, Kawamura, A, Clark, NM, Rymen, B, Braidwood, L, Morohashi, K, Busch, W, Benfey, PN, Sozzani, R, and Sugimoto, K. "GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis." Development (Cambridge, England) 145, no. 3 (February 8, 2018). Full Text
  - Wendrich, JR, Möller, BK, Li, S, Saiga, S, Sozzani, R, Benfey, PN, De Rybel, B, and 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 114, no. 42 (October 2, 2017): E8922-E8929. Full Text
  - 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, and 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 114, no. 36 (September 2017): E7641-E7649. Full Text
  - Drapek, C, Sparks, EE, and Benfey, PN. "Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation." Trends in Genetics : Tig 33, no. 8 (August 2017): 529-539. (Review) Full Text
  - Hsu, PY, and Benfey, PN. "Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants." Proteomics (July 31, 2017). (Review) Full Text
  - Wachsman, G, Modliszewski, JL, Valdes, M, and Benfey, PN. "A SIMPLE Pipeline for Mapping Point Mutations." Plant Physiology 174, no. 3 (July 2017): 1307-1313. Full Text
  - Nevarez, PA, Qiu, Y, Inoue, H, Yoo, CY, Benfey, PN, Schnell, DJ, and Chen, M. "Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus." Plant physiology 173, no. 4 (April 2017): 1953-1966. Full Text
  - 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, and Hasebe, M. "A Lin28 homologue reprograms differentiated cells to stem cells in the moss Physcomitrella patens." Nature Communications 8 (January 27, 2017): 14242-null. Full Text
  - Fernández-Marcos, M, Desvoyes, B, Manzano, C, Liberman, LM, Benfey, PN, Del Pozo, JC, and Gutierrez, C. "Control of Arabidopsis lateral root primordium boundaries by MYB36." The New Phytologist 213, no. 1 (January 2017): 105-112. Full Text
  - Sparks, EE, and Benfey, PN. "Tissue-Specific Transcriptome Profiling in Arabidopsis Roots." Methods in molecular biology (Clifton, N.J.) 1610 (January 2017): 107-122. Full Text
  - 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, and Benfey, PN. "Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors." Developmental Cell 39, no. 5 (December 2016): 585-596. Full Text
  - Li, S, Yamada, M, Hang, X, Ohler, U, and Benfey, PN. "High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation." DEVELOPMENTAL CELL 39, no. 4 (November 21, 2016): 508-522. Full Text Link to Item
  - Wachsman, G, Modliszewski, J, Valdés, M, and Benfey, P. "A SIMPLE pipeline for mapping point mutations." (November 18, 2016). Full Text
  - Li, S, Yamada, M, Han, X, Ohler, U, and Benfey, PN. "High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation." Developmental Cell 39, no. 4 (November 10, 2016): 508-522. Full Text
  - Hsu, PY, Calviello, L, Wu, H-YL, Li, F-W, Rothfels, CJ, Ohler, U, and Benfey, PN. "Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis." Proceedings of the National Academy of Sciences of the United States of America 113, no. 45 (November 2016): E7126-E7135. Full Text
  - Rogers, ED, Monaenkova, D, Mijar, M, Nori, A, Goldman, DI, and Benfey, PN. "X-Ray Computed Tomography Reveals the Response of Root System Architecture to Soil Texture." Plant Physiology 171, no. 3 (July 2016): 2028-2040. Full Text
  - Clark, NM, Hinde, E, Winter, CM, Fisher, AP, Crosti, G, Blilou, I, Gratton, E, Benfey, PN, and Sozzani, R. "Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy." Elife 5 (June 11, 2016). Full Text
  - Kawakatsu, T, Stuart, T, Valdes, M, Breakfield, N, Schmitz, RJ, Nery, JR, Urich, MA, Han, X, Lister, R, Benfey, PN, and Ecker, JR. "Unique cell-type-specific patterns of DNA methylation in the root meristem." Nature Plants 2, no. 5 (April 29, 2016): 16058-null. Full Text
  - Liberman, LM, and Benfey, PN. "A Friend in Need (of Nutrients) Is a…." Cell 165, no. 2 (April 2016): 269-271. Full Text
  - Benfey, PN. "Defining the Path from Stem Cells to Differentiated Tissue." Current topics in developmental biology 116 (January 2016): 35-43. (Review) Full Text
  - Sparks, EE, and 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.) 1370 (January 2016): 29-50. Full Text
  - Rodriguez, RE, Ercoli, MF, Debernardi, JM, Breakfield, NW, Mecchia, MA, Sabatini, M, Cools, T, De Veylder, L, Benfey, PN, and Palatnik, JF. "MicroRNA miR396 Regulates the Switch between Stem Cells and Transit-Amplifying Cells in Arabidopsis Roots." The Plant Cell 27, no. 12 (December 8, 2015): 3354-3366. Full Text
  - Moreno-Risueno, MA, Sozzani, R, Yardımcı, GG, Petricka, JJ, Vernoux, T, Blilou, I, Alonso, J, Winter, CM, Ohler, U, Scheres, B, and Benfey, PN. "Transcriptional control of tissue formation throughout root development." Science (New York, N.Y.) 350, no. 6259 (October 2015): 426-430. Full Text
  - Wachsman, G, Sparks, EE, and Benfey, PN. "Genes and networks regulating root anatomy and architecture." The New Phytologist 208, no. 1 (October 2015): 26-38. (Review) Full Text
  - Liberman, LM, Sparks, EE, Moreno-Risueno, MA, Petricka, JJ, and 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 112, no. 39 (September 14, 2015): 12099-12104. Full Text
  - Cederholm, HM, and Benfey, PN. "Distinct sensitivities to phosphate deprivation suggest that RGF peptides play disparate roles in Arabidopsis thaliana root development." The New Phytologist 207, no. 3 (August 2015): 683-691. Full Text
  - Jackson, TL, Baker, GW, Wilks, FR, Popov, VA, Mathur, J, and Benfey, PN. "Large Cellular Inclusions Accumulate in Arabidopsis Roots Exposed to Low-Sulfur Conditions." Plant physiology 168, no. 4 (August 2015): 1573-1589. Full Text
  - Rogers, ED, and Benfey, PN. "Regulation of plant root system architecture: implications for crop advancement." Current Opinion in Biotechnology 32 (April 2015): 93-98. (Review) Full Text
  - Zurek, PR, Topp, CN, and Benfey, PN. "Quantitative trait locus mapping reveals regions of the maize genome controlling root system architecture." Plant physiology 167, no. 4 (April 2015): 1487-1496. Full Text
  - 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, and 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 33, no. 2 (January 1, 2015): 238-null. Full Text
  - Morton, T, Petricka, J, Corcoran, DL, Li, S, Winter, CM, Carda, A, Benfey, PN, Ohler, U, and Megraw, M. "Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures." The Plant Cell 26, no. 7 (July 17, 2014): 2746-2760. Full Text
  - 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, and Caño-Delgado, AI. "Regulation of plant stem cell quiescence by a brassinosteroid signaling module." Developmental Cell 30, no. 1 (July 2014): 36-47. Full Text
  - Sozzani, R, Busch, W, Spalding, EP, and Benfey, PN. "Advanced imaging techniques for the study of plant growth and development." Trends in plant science 19, no. 5 (May 2014): 304-310. (Review) Full Text
  - Van Norman, JM, Zhang, J, Cazzonelli, CI, Pogson, BJ, Harrison, PJ, Bugg, TDH, Chan, KX, Thompson, AJ, and 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 111, no. 13 (April 2014): E1300-E1309. Full Text
  - Sparks, EE, and Benfey, PN. "HEC of a job regulating stem cells." Developmental cell 28, no. 4 (February 2014): 349-350. Full Text
  - "Advanced imaging techniques for the study of plant growth and development." Trends in Plant Science 19, no. 5 (January 1, 2014): 304-310. (Review) Full Text
  - 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, and Caño-Delgado, AI. "Regulation of plant stem cell quiescence by a brassinosteroid signaling module." Developmental Cell 30, no. 1 (2014): 36-47. Full Text
  - Iyer-Pascuzzi, AS, Zurek, PR, and Benfey, PN. "High-throughput, noninvasive imaging of root systems." Methods in Molecular Biology 959 (December 1, 2013): 177-187. Full Text
  - Van Norman, JM, Xuan, W, Beeckman, T, and Benfey, PN. "To branch or not to branch: the role of pre-patterning in lateral root formation." Development 140, no. 21 (November 2013): 4301-4310. (Review) Full Text Link to Item
  - Li, S, Liberman, LM, Mukherjee, N, Benfey, PN, and Ohler, U. "Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data." Genome Research 23, no. 10 (October 2013): 1730-1739. Full Text
  - Sparks, E, Wachsman, G, and Benfey, PN. "Spatiotemporal signalling in plant development." Nature Reviews. Genetics 14, no. 9 (September 2013): 631-644. (Review) Full Text
  - 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, and Sabatini, S. "Spatial coordination between stem cell activity and cell differentiation in the root meristem." Developmental Cell 26, no. 4 (August 2013): 405-415. Full Text
  - Liberman, LM, and Benfey, PN. "Polarized radicals." Cell 153, no. 2 (April 11, 2013): 285-286. Full Text Link to Item
  - 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, and 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 110, no. 18 (April 11, 2013): E1695-E1704. Full Text
  - Moussaieff, A, Rogachev, I, Brodsky, L, Malitsky, S, Toal, TW, Belcher, H, Yativ, M, Brady, SM, Benfey, PN, and Aharoni, A. "High-resolution metabolic mapping of cell types in plant roots." Proc Natl Acad Sci U S A 110, no. 13 (March 26, 2013): E1232-E1241. Full Text Link to Item
  - Fang, S, Clark, RT, Zheng, Y, Iyer-Pascuzzi, AS, Weitz, JS, Kochian, LV, Edelsbrunner, H, Liao, H, and Benfey, PN. "Genotypic recognition and spatial responses by rice roots." Proc Natl Acad Sci U S A 110, no. 7 (February 12, 2013): 2670-2675. Full Text Link to Item
  - Fang, S, Clark, RT, Zheng, Y, Iyer-Pascuzzi, AS, Weitz, JS, Kochian, LV, Edelsbrunner, H, Liao, H, and Benfey, PN. "Genotypic recognition and spatial responses by rice roots." Proceedings of the National Academy of Sciences of the United States of America 110, no. 7 (February 2013): 2670-2675. Full Text
  - Benfey, P. "Philip benfey." Current Biology 23, no. 19 (2013): R857-R858. Full Text
  - Benfey, PN, and Scheres, B. "Arabidopsis as a Model for Systems Biology." (2013): 391-406. Full Text
  - Iyer-Pascuzzi, AS, Zurek, PR, and Benfey, PN. "High-throughput, noninvasive imaging of root systems." Methods Mol Biol 959 (2013): 177-187. Full Text Link to Item
  - Topp, CN, and Benfey, PN. "Growth control of root architecture." (December 1, 2012): 373-386. (Chapter) Full Text
  - Busch, W, Moore, BT, Martsberger, B, Mace, DL, Twigg, RW, Jung, J, Pruteanu-Malinici, I, Kennedy, SJ, Fricke, GK, Clark, RL, Ohler, U, and Benfey, PN. "A microfluidic device and computational platform for high-throughput live imaging of gene expression." Nature Methods 9, no. 11 (November 2012): 1101-1106. Full Text
  - Cederholm, HM, Iyer-Pascuzzi, AS, and Benfey, PN. "Patterning the primary root in Arabidopsis." Wiley Interdiscip Rev Dev Biol 1, no. 5 (September 2012): 675-691. (Review) Full Text Link to Item
  - 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, and Scheres, B. "A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division." Cell 150, no. 5 (August 23, 2012): 1002-1015. Full Text
  - Ingram, PA, Zhu, J, Shariff, A, Davis, IW, Benfey, PN, and 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 367, no. 1595 (June 2012): 1559-1569. Full Text
  - Petricka, JJ, Schauer, MA, Megraw, M, Breakfield, NW, Thompson, JW, Georgiev, S, Soderblom, EJ, Ohler, U, Moseley, MA, Grossniklaus, U, and Benfey, PN. "The protein expression landscape of the Arabidopsis root." Proc Natl Acad Sci U S A 109, no. 18 (May 1, 2012): 6811-6818. Full Text Link to Item
  - Stone, JE, Benfey, PN, and You, L. "Promoting collaborative interdisciplinary research at the Duke Center for Systems Biology." Acs Synthetic Biology 1, no. 5 (May 2012): 153-155. Full Text
  - Liberman, LM, Sozzani, R, and Benfey, PN. "Integrative systems biology: an attempt to describe a simple weed." Current Opinion in Plant Biology 15, no. 2 (April 2012): 162-167. (Review) Full Text
  - Rogers, ED, Jackson, T, Moussaieff, A, Aharoni, A, and Benfey, PN. "Cell type-specific transcriptional profiling: implications for metabolite profiling." The Plant Journal : for Cell and Molecular Biology 70, no. 1 (April 2012): 5-17. (Review) Full Text
  - Bruex, A, Kainkaryam, RM, Wieckowski, Y, Kang, YH, Bernhardt, C, Xia, Y, Zheng, X, Wang, JY, Lee, MM, Benfey, P, Woolf, PJ, and Schiefelbein, J. "A gene regulatory network for root epidermis cell differentiation in Arabidopsis." Plos Genetics 8, no. 1 (January 12, 2012): e1002446-null. Full Text
  - 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, and Bennett, M. "Analyzing lateral root development: how to move forward." The Plant Cell 24, no. 1 (January 6, 2012): 15-20. Full Text
  - Benfey, PN. "Toward a systems analysis of the root." Cold Spring Harbor Symposia on Quantitative Biology 77 (January 2012): 91-96. (Review) Full Text
  - Breakfield, NW, Corcoran, DL, Petricka, JJ, Shen, J, Sae-Seaw, J, Rubio-Somoza, I, Weigel, D, Ohler, U, and Benfey, PN. "High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis." Genome Res 22, no. 1 (January 2012): 163-176. Full Text Link to Item
  - Davis, IW, Benninger, C, Benfey, PN, and Elich, T. "POWRS: position-sensitive motif discovery." PLoS One 7, no. 7 (2012): e40373-. Full Text Link to Item
  - 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, and Weitz, JS. "GiA Roots: software for the high throughput analysis of plant root system architecture." Bmc Plant Biology 12 (January 2012): 116-null. Full Text
  - 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, and Weitz, JS. "GiA Roots: software for the high throughput analysis of plant root system architecture." Bmc Plant Biology 12, no. 1 (2012): 116-116. Full Text
  - Moreno-Risueno, MA, Van Norman, JM, and Benfey, PN. "Transcriptional switches direct plant organ formation and patterning." Current Topics in Developmental Biology 98 (January 2012): 229-257. (Review) Full Text
  - Petricka, JJ, Winter, CM, and Benfey, PN. "Control of Arabidopsis root development." Annual Review of Plant Biology 63 (January 2012): 563-590. (Review) Full Text
  - Zheng, Y, Gu, S, Edelsbrunner, H, Tomasi, C, and Benfey, P. "Detailed reconstruction of 3D plant root shape." Proceedings of the Ieee International Conference on Computer Vision (December 1, 2011): 2026-2033. Full Text
  - Iyer-Pascuzzi, AS, Jackson, T, Cui, H, Petricka, JJ, Busch, W, Tsukagoshi, H, and Benfey, PN. "Cell identity regulators link development and stress responses in the Arabidopsis root." Developmental Cell 21, no. 4 (October 2011): 770-782. Full Text
  - Petricka, JJ, and Benfey, PN. "Reconstructing regulatory network transitions." Trends in Cell Biology 21, no. 8 (August 2011): 442-451. (Review) Full Text
  - Benfey, PN. "Taking a developmental perspective on systems biology." Dev Cell 21, no. 1 (July 19, 2011): 27-28. Full Text Link to Item
  - Zhu, J, Ingram, PA, Benfey, PN, and Elich, T. "From lab to field, new approaches to phenotyping root system architecture." Current Opinion in Plant Biology 14, no. 3 (June 2011): 310-317. Full Text
  - Moreno-Risueno, MA, and Benfey, PN. "Time-based patterning in development: The role of oscillating gene expression." Transcription 2, no. 3 (May 2011): 124-129. Full Text Link to Item
  - Van Norman, JM, Breakfield, NW, and Benfey, PN. "Intercellular communication during plant development." Plant Cell 23, no. 3 (March 2011): 855-864. (Review) Full Text Link to Item
  - 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, and Benfey, PN. "A stele-enriched gene regulatory network in the Arabidopsis root." Molecular Systems Biology 7 (January 2011): 459-null. Full Text
  - Sozzani, R, and Benfey, PN. "High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype." Genome Biol 12, no. 3 (2011): 219-. (Review) Full Text Link to Item
  - Pop, A, Huttenhower, C, Iyer-Pascuzzi, A, Benfey, PN, and Troyanskaya, OG. "Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. (Published online)" BMC Syst Biol 4 (December 31, 2010): 180-. Full Text Link to Item
  - 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, and Somerville, C. "Shootward and rootward: peak terminology for plant polarity." Trends Plant Sci 15, no. 11 (November 2010): 593-594. (Letter) Full Text Link to Item
  - Tsukagoshi, H, Busch, W, and Benfey, PN. "Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root." Cell 143, no. 4 (November 2010): 606-616. Full Text
  - Moreno-Risueno, MA, Van Norman, JM, Moreno, A, Zhang, J, Ahnert, SE, and Benfey, PN. "Oscillating gene expression determines competence for periodic Arabidopsis root branching." Science (New York, N.Y.) 329, no. 5997 (September 2010): 1306-1311. Full Text
  - Long, TA, Tsukagoshi, H, Busch, W, Lahner, B, Salt, DE, and Benfey, PN. "The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots." The Plant Cell 22, no. 7 (July 30, 2010): 2219-2236. Full Text
  - Sozzani, R, Cui, H, Moreno-Risueno, MA, Busch, W, Van Norman, JM, Vernoux, T, Brady, SM, Dewitte, W, Murray, JAH, and Benfey, PN. "Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth." Nature 466, no. 7302 (July 2010): 128-132. Full Text
  - Orlando, DA, Brady, SM, Fink, TMA, Benfey, PN, and Ahnert, SE. "Detecting separate time scales in genetic expression data. (Published online)" BMC Genomics 11 (June 16, 2010): 381-. Full Text Open Access Copy Link to Item
  - 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, and Benfey, PN. "Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate." Nature 465, no. 7296 (May 2010): 316-321. Full Text
  - Busch, W, and Benfey, PN. "Information processing without brains--the power of intercellular regulators in plants." Development (Cambridge, England) 137, no. 8 (April 2010): 1215-1226. (Review) Full Text Open Access Copy
  - Moreno-Risueno, MA, Busch, W, and Benfey, PN. "Omics meet networks - using systems approaches to infer regulatory networks in plants." Current Opinion in Plant Biology 13, no. 2 (April 2010): 126-131. (Review) Full Text
  - Benfey, PN, Bennett, M, and 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 61, no. 6 (March 2010): 992-1000. (Review) Full Text
  - Iyer-Pascuzzi, AS, Symonova, O, Mileyko, Y, Hao, Y, Belcher, H, Harer, J, Weitz, JS, and Benfey, PN. "Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems." Plant Physiology 152, no. 3 (March 2010): 1148-1157. Full Text
  - 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, and Beeckman, T. "Bimodular auxin response controls organogenesis in Arabidopsis." Proceedings of the National Academy of Sciences of the United States of America 107, no. 6 (February 2010): 2705-2710. Full Text
  - Iyer-Pascuzzi, AS, and Benfey, PN. "Fluorescence-activated cell sorting in plant developmental biology." Methods in Molecular Biology (Clifton, N.J.) 655 (January 2010): 313-319. Full Text
  - To, JP, Zhu, J, Benfey, PN, and Elich, T. "Optimizing root system architecture in biofuel crops for sustainable energy production and soil carbon sequestration." F1000 Biology Reports 2 (January 2010): 65-null. Full Text
  - Petricka, JJ, Van Norman, JM, and Benfey, PN. "Symmetry breaking in plants: molecular mechanisms regulating asymmetric cell divisions in Arabidopsis." Cold Spring Harb Perspect Biol 1, no. 5 (November 2009): a000497-. (Review) Full Text Link to Item
  - Van Norman, JM, and Benfey, PN. "Arabidopsis thaliana as a model organism in systems biology." Wiley Interdiscip Rev Syst Biol Med 1, no. 3 (November 2009): 372-379. (Review) Full Text Link to Item
  - Van Norman, JM, and Benfey, PN. "Arabidopsis thaliana as a model organism in systems biology." Wiley Interdisciplinary Reviews Systems Biology and Medicine 1, no. 3 (November 1, 2009): 372-379. (Academic Article) Full Text Link to Item
  - Cartwright, DA, Brady, SM, Orlando, DA, Sturmfels, B, and Benfey, PN. "Reconstructing spatiotemporal gene expression data from partial observations." Bioinformatics 25, no. 19 (October 1, 2009): 2581-2587. Full Text Link to Item
  - Benfey, PN, and Birnbaum, KD. "Primer and interviews: Gene regulation in Arabidopsis thaliana. Interview by Julie C. Kiefer." Dev Dyn 238, no. 9 (September 2009): 2449-2458. (Interview) Full Text Link to Item
  - Benfey, PN, Cui, H, Twigg, R, Long, T, Iyer-Pascuzzi, A, Tsukagoshi, H, Sozzani, R, Jackson, T, Van Norman, J, and Moreno-Risueno, M. "Development rooted in interwoven networks." DEVELOPMENTAL BIOLOGY 331, no. 2 (July 15, 2009): 386-386. Full Text Link to Item
  - Cui, H, and Benfey, PN. "Cortex proliferation: simple phenotype, complex regulatory mechanisms." Plant Signaling & Behavior 4, no. 6 (June 15, 2009): 551-553. Full Text
  - Petersson, SV, Johansson, AI, Kowalczyk, M, Makoveychuk, A, Wang, JY, Moritz, T, Grebe, M, Benfey, PN, Sandberg, G, and 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 21, no. 6 (June 2, 2009): 1659-1668. Full Text
  - Cui, H, and Benfey, PN. "Cortex proliferation." Plant Signaling & Behavior 4, no. 6 (June 2009): 551-553. Full Text
  - Cui, H, and 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 58, no. 6 (June 2009): 1016-1027. Full Text
  - Iyer-Pascuzzi, A, Simpson, J, Herrera-Estrella, L, and Benfey, PN. "Functional genomics of root growth and development in Arabidopsis." Curr Opin Plant Biol 12, no. 2 (April 2009): 165-171. (Review) Full Text Link to Item
  - Iyer-Pascuzzi, AS, and Benfey, PN. "Transcriptional networks in root cell fate specification." Biochimica Et Biophysica Acta 1789, no. 4 (April 2009): 315-325. (Review) Full Text
  - Gallagher, KL, and Benfey, PN. "Both the conserved GRAS domain and nuclear localization are required for SHORT-ROOT movement." The Plant Journal : for Cell and Molecular Biology 57, no. 5 (March 2009): 785-797. Full Text
  - Orlando, DA, Brady, SM, Koch, JD, Dinneny, JR, and Benfey, PN. "Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment." Methods in Molecular Biology (Clifton, N.J.) 553 (January 2009): 57-77. (Review) Full Text
  - Tromas, A, Braun, N, Muller, P, Khodus, T, Paponov, IA, Palme, K, Ljung, K, Lee, J-Y, Benfey, P, Murray, JAH, Scheres, B, and Perrot-Rechenmann, C. "The AUXIN BINDING PROTEIN 1 is required for differential Auxin responses mediating root growth." PLoS ONE 4, no. 9 (2009). Full Text
  - Chaudhuri, B, Hörmann, F, Lalonde, S, Brady, SM, Orlando, DA, Benfey, P, and 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 56, no. 6 (December 2008): 948-962. Full Text
  - 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, and Beeckman, T. "Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root." Science (New York, N.Y.) 322, no. 5901 (October 2008): 594-597. Full Text
  - Petricka, JJ, and Benfey, PN. "Root layers: complex regulation of developmental patterning." Curr Opin Genet Dev 18, no. 4 (August 2008): 354-361. (Review) Full Text Link to Item
  - 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, and Bennett, MJ. "The auxin influx carrier LAX3 promotes lateral root emergence." Nature Cell Biology 10, no. 8 (August 2008): 946-954. Full Text
  - Dinneny, JR, Long, TA, Wang, JY, Jung, JW, Mace, D, Pointer, S, Barron, C, Brady, SM, Schiefelbein, J, and Benfey, PN. "Cell identity mediates the response of Arabidopsis roots to abiotic stress." Science (New York, N.Y.) 320, no. 5878 (May 2008): 942-945. Full Text
  - Benfey, PN, and Mitchell-Olds, T. "From genotype to phenotype: systems biology meets natural variation." Science (New York, N.Y.) 320, no. 5875 (April 2008): 495-497. Full Text
  - Dinneny, JR, and Benfey, PN. "Plant stem cell niches: standing the test of time." Cell 132, no. 4 (February 2008): 553-557. Full Text
  - Colinas, J, Schmidler, SC, Bohrer, G, Iordanov, B, and Benfey, PN. "Intergenic and genic sequence lengths have opposite relationships with respect to gene expression." Plos One 3, no. 11 (January 2008): e3670-null. Full Text Open Access Copy
  - Long, TA, Brady, SM, and Benfey, PN. "Systems approaches to identifying gene regulatory networks in plants." Annual Review of Cell and Developmental Biology 24 (January 2008): 81-103. (Review) Full Text
  - Brady, SM, Orlando, DA, Lee, J-Y, Wang, JY, Koch, J, Dinneny, JR, Mace, D, Ohler, U, and Benfey, PN. "A high-resolution root spatiotemporal map reveals dominant expression patterns." Science (New York, N.Y.) 318, no. 5851 (November 2007): 801-806. Full Text
  - Cui, H, Levesque, MP, Vernoux, T, Jung, JW, Paquette, AJ, Gallagher, KL, Wang, JY, Blilou, I, Scheres, B, and Benfey, PN. "An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants." Science (New York, N.Y.) 316, no. 5823 (April 2007): 421-425. Full Text
  - Brady, SM, Song, S, Dhugga, KS, Rafalski, JA, and Benfey, PN. "Combining expression and comparative evolutionary analysis. The COBRA gene family." Plant Physiology 143, no. 1 (January 2007): 172-187. Full Text
  - Weitz, JS, Benfey, PN, and Wingreen, NS. "Evolution, interactions, and biological networks." PLoS Biol 5, no. 1 (January 2007): e11-. Full Text Link to Item
  - Weitz, JS, Benfey, PN, and Wingreen, NS. "Evolution, interactions, and biological networks." Plos Biology 5, no. 1 (January 1, 2007): 0010-0012. Full Text
  - Long, TA, and Benfey, PN. "Transcription factors and hormones: new insights into plant cell differentiation." Curr Opin Cell Biol 18, no. 6 (December 2006): 710-714. (Review) Full Text Link to Item
  - Brady, SM, Long, TA, and Benfey, PN. "Unraveling the dynamic transcriptome." Plant Cell 18, no. 9 (September 2006): 2101-2111. (Review) Full Text Link to Item
  - Brady, SM, and Benfey, PN. "Erratum: A systems approach to understanding root development (Canadian Journal of Botany (2006) 84, (695-701))." Canadian Journal of Botany 84, no. 9 (September 1, 2006): 1508-null. Full Text
  - 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. "Erratum: Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis (PLoS Biology 4, 5 DOI: 10.1371/journal.pbio.0040143)." Plos Biology 4, no. 7 (July 19, 2006): 1284-null. Full Text
  - Mace, DL, Lee, J-Y, Twigg, RW, Colinas, J, Benfey, PN, and Ohler, U. "Quantification of transcription factor expression from Arabidopsis images." Bioinformatics 22, no. 14 (July 15, 2006): e323-e331. Full Text Link to Item
  - 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. "Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis." Plos Biology 4, no. 5 (May 2, 2006): e143-null. Full Text
  - Brady, SM, and Benfey, PN. "A systems approach to understanding root development." Canadian Journal of Botany 84, no. 5 (May 1, 2006): 695-701. (Review) Full Text
  - 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. "Whole-genome analysis of the short-root developmental pathway in Arabidopsis." Plos Biology 4, no. 5 (May 1, 2006): 739-752. Full Text
  - Lee, J-Y, Colinas, J, Wang, JY, Mace, D, Ohler, U, and 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 103, no. 15 (April 2006): 6055-6060. Full Text
  - 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, and Zažímalová, E. "Apical-basal polarity: Why plant cells don't standon their heads." Trends in Plant Science 11, no. 1 (2006): 12-14. Full Text
  - Dinneny, JR, and Benfey, PN. "Stem cell research goes underground: the RETINOBLASTOMA-RELATED gene in root development." Cell 123, no. 7 (December 2005): 1180-1182. (Review) Full Text
  - Lim, J, Jung, JW, Lim, CE, Lee, M-H, Kim, BJ, Kim, M, Bruce, WB, and Benfey, PN. "Conservation and diversification of SCARECROW in maize." Plant Molecular Biology 59, no. 4 (November 2005): 619-630. Full Text
  - Birnbaum, K, Jung, JW, Wang, JY, Lambert, GM, Hirst, JA, Galbraith, DW, and Benfey, PN. "Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines." Nature Methods 2, no. 8 (August 2005): 615-619. Full Text
  - Vernoux, T, and Benfey, PN. "Signals that regulate stem cell activity during plant development." Curr Opin Genet Dev 15, no. 4 (August 2005): 388-394. (Review) Full Text Link to Item
  - Nawy, T, Lee, J-Y, Colinas, J, Wang, JY, Thongrod, SC, Malamy, JE, Birnbaum, K, and Benfey, PN. "Transcriptional profile of the Arabidopsis root quiescent center." The Plant Cell 17, no. 7 (July 2005): 1908-1925. Full Text
  - Benfey, PN. "Developmental networks." Plant Physiol 138, no. 2 (June 2005): 548-549. Full Text Link to Item
  - Lee, J-Y, Levesque, M, and Benfey, PN. "High-throughput RNA isolation technologies. New tools for high-resolution gene expression profiling in plant systems." Plant Physiol 138, no. 2 (June 2005): 585-590. (Review) Full Text Link to Item
  - Paquette, AJ, and Benfey, PN. "Maturation of the ground tissue of the root is regulated by gibberellin and SCARECROW and requires SHORT-ROOT." Plant Physiology 138, no. 2 (June 2005): 636-640. Full Text
  - Roudier, F, Fernandez, AG, Fujita, M, Himmelspach, R, Borner, GHH, Schindelman, G, Song, S, Baskin, TI, Dupree, P, Wasteneys, GO, and 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 17, no. 6 (June 2005): 1749-1763. Full Text
  - Roudier, F, Fernandez, AG, Fujita, M, Himmelspach, R, Borner, GHH, Schindelman, G, Song, S, Baskin, TI, Dupree, P, Wasteneys, GO, and Benfey, PN. "COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation." Plant Cell 17, no. 6 (June 1, 2005): 1749-1763. (Academic Article) Full Text Link to Item
  - Gallagher, KL, and Benfey, PN. "Not just another hole in the wall: understanding intercellular protein trafficking." Genes & Development 19, no. 2 (January 2005): 189-195. (Review) Full Text
  - Birnbaum, K, and Benfey, PN. "Network building: transcriptional circuits in the root." Curr Opin Plant Biol 7, no. 5 (October 2004): 582-588. (Review) Full Text Link to Item
  - Gallagher, KL, Paquette, AJ, Nakajima, K, and Benfey, PN. "Mechanisms regulating SHORT-ROOT intercellular movement." Current Biology : Cb 14, no. 20 (October 2004): 1847-1851. Full Text
  - Benfey, PN. "Development and ecology in the time of systems biology." Dev Cell 7, no. 3 (September 2004): 329-330. Full Text Link to Item
  - Irish, VF, and Benfey, PN. "Beyond Arabidopsis. Translational biology meets evolutionary developmental biology." Plant Physiol 135, no. 2 (June 2004): 611-614. (Review) Full Text Link to Item
  - Sena, G, Jung, JW, and Benfey, PN. "A broad competence to respond to SHORT ROOT revealed by tissue-specific ectopic expression." Development (Cambridge, England) 131, no. 12 (June 2004): 2817-2826. Full Text
  - Levesque, MP, and Benfey, PN. "Systems biology." Curr Biol 14, no. 5 (March 9, 2004): R179-R180. (Review) Full Text Link to Item
  - Irish, V, and Benfey, P. "Growth and development." Current Opinion in Plant Biology 7, no. 1 (February 2004): 1-3. Full Text
  - Benfey, PN. "A common switch used by plants and animals." Cell 116, no. 1 (January 9, 2004): 4-5. Link to Item
  - Birnbaum, K, Shasha, DE, Wang, JY, Jung, JW, Lambert, GM, Galbraith, DW, and Benfey, PN. "A gene expression map of the Arabidopsis root." Science (New York, N.Y.) 302, no. 5652 (December 2003): 1956-1960. Full Text
  - Birnbaum, K, Desalle, R, Peters, CM, and Benfey, PN. "Integrating gene flow, crop biology, and farm management in on-farm conservation of avocado (Persea americana, Lauraceae)." Am J Bot 90, no. 11 (November 2003): 1619-1627. Full Text Link to Item
  - Benfey, PN. "Molecular biology: microRNA is here to stay." Nature 425, no. 6955 (September 2003): 244-245. Full Text
  - Levesque, M, Shasha, D, Kim, W, Surette, MG, and Benfey, PN. "Trait-to-gene: a computational method for predicting the function of uncharacterized genes." Curr Biol 13, no. 2 (January 21, 2003): 129-133. Link to Item
  - Benfey, PN. "MicroRNA is here to stay." Nature 425, no. 6955 (2003): 244-245.
  - Brenner, ED, Stevenson, DW, McCombie, RW, Katari, MS, Rudd, SA, Mayer, KFX, Palenchar, PM, Runko, SJ, Twigg, RW, Dai, G, Martienssen, RA, Benfey, PN, and Coruzzi, GM. "Expressed sequence tag analysis in Cycas, the most primitive living seed plant." Genome Biology 4, no. 12 (January 2003): R78-null. Full Text
  - Birnbaum, K, Benfey, PN, Peters, CM, and Desalle, R. "MANAGEDPOP: A computer simulation to project allelic diversity in managed populations with overlapping generations." Molecular Ecology Notes 2, no. 4 (December 1, 2002): 615-617. Full Text
  - Roudier, F, Schindelman, G, DeSalle, R, and Benfey, PN. "The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion." Plant Physiol 130, no. 2 (October 2002): 538-548. Full Text Link to Item
  - Müller, S, Fuchs, E, Ovecka, M, Wysocka-Diller, J, Benfey, PN, and Hauser, M-T. "Two new loci, PLEIADE and HYADE, implicate organ-specific regulation of cytokinesis in Arabidopsis." Plant Physiol 130, no. 1 (September 2002): 312-324. Full Text Link to Item
  - Colinas, J, Birnbaum, K, and Benfey, PN. "Erratum: Using cauliflower to find conserved non-coding regions in Arabidopsis (Plant Physiology (2002) 129 (451-454))." Plant Physiology 129, no. 4 (August 2, 2002): 1929-null.
  - Colinas, J, Birnbaum, K, and Benfey, PN. "Using cauliflower to find conserved non-coding regions in arabidopsis (vol 129, pg 451, 2002)." PLANT PHYSIOLOGY 129, no. 4 (August 2002): 1929-1929. Link to Item
  - Benfey, PN. "Auxin action: slogging out of the swamp." Curr Biol 12, no. 11 (June 4, 2002): R389-R390. (Review) Link to Item
  - Colinas, J, Birnbaum, K, and Benfey, PN. "Using cauliflower to find conserved non-coding regions in Arabidopsis." Plant Physiol 129, no. 2 (June 2002): 451-454. Full Text Link to Item
  - Ausubel, F, and Benfey, P. "Arabidopsis functional genomics." Plant Physiology 129, no. 2 (2002): 393--. Full Text
  - Nakajima, K, and Benfey, PN. "Signaling in and out: control of cell division and differentiation in the shoot and root." The Plant Cell 14 Suppl (January 2002): S265-S276. (Review) Full Text
  - Birnbaum, K, Benfey, PN, and Shasha, DE. "cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships." Genome Res 11, no. 9 (September 2001): 1567-1573. Full Text Link to Item
  - Nakajima, K, Sena, G, Nawy, T, and Benfey, PN. "Intercellular movement of the putative transcription factor SHR in root patterning." Nature 413, no. 6853 (September 2001): 307-311. Full Text
  - Paquette, AJ, and Benfey, PN. "Axis formation and polarity in plants." Curr Opin Genet Dev 11, no. 4 (August 2001): 405-409. (Review) Link to Item
  - Schindelman, G, Morikami, A, Jung, J, Baskin, TI, Carpita, NC, Derbyshire, P, McCann, MC, and Benfey, PN. "COBRA encodes a putative GPI-anchored protein, which is polarly localized and necessary for oriented cell expansion in Arabidopsis." Genes & Development 15, no. 9 (May 2001): 1115-1127. Full Text
  - Benfey, PN, and Weigel, D. "Transcriptional networks controlling plant development." Plant Physiol 125, no. 1 (January 2001): 109-111. (Review) Link to Item
  - Nawy, T, and Benfey, PN. "Signaling the tips: Regulation of stem cell function in plants." Differentiation 68, no. 4-5 (2001): 155-158.
  - Mähönen, AP, Bonke, M, Kauppinen, L, Riikonen, M, Benfey, PN, and Helariutta, Y. "A novel two-component hybrid molecule regulates vascular morphogenesis of the Arabidopsis root." Genes & Development 14, no. 23 (December 2000): 2938-2943. Full Text
  - Benfey, PN, and Scheres, B. "Root development." Curr Biol 10, no. 22 (November 16, 2000): R813-R815. (Review) Link to Item
  - Lim, J, Helariutta, Y, Specht, CD, Jung, J, Sims, L, Bruce, WB, Diehn, S, and Benfey, PN. "Molecular analysis of the SCARECROW gene in maize reveals a common basis for radial patterning in diverse meristems." The Plant Cell 12, no. 8 (August 2000): 1307-1318. Full Text
  - Helariutta, Y, Fukaki, H, Wysocka-Diller, J, Nakajima, K, Jung, J, Sena, G, Hauser, MT, and Benfey, PN. "The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling." Cell 101, no. 5 (May 2000): 555-567. Full Text
  - Wysocka-Diller, JW, Helariutta, Y, Fukaki, H, Malamy, JE, and Benfey, PN. "Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot." Development (Cambridge, England) 127, no. 3 (February 2000): 595-603.
  - Sabatini, S, Beis, D, Wolkenfelt, H, Murfett, J, Guilfoyle, T, Malamy, J, Benfey, P, Leyser, O, Bechtold, N, Weisbeek, P, and Scheres, B. "An auxin-dependent distal organizer of pattern and polarity in the Arabidopsis root." Cell 99, no. 5 (November 1999): 463-472. Full Text
  - Scheres, B, and Benfey, PN. "ASYMMETRIC CELL DIVISION IN PLANTS." Annual Review of Plant Physiology and Plant Molecular Biology 50 (June 1999): 505-537. Full Text
  - Pysh, LD, Wysocka-Diller, JW, Camilleri, C, Bouchez, D, and Benfey, PN. "The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes." Plant J 18, no. 1 (April 1999): 111-119. Link to Item
  - Benfey, PN. "Stem cells: A tale of two kingdoms." Curr Biol 9, no. 5 (March 11, 1999): R171-R172. (Review) Link to Item
  - Benfey, PN. "Is the shoot a root with a view?." Curr Opin Plant Biol 2, no. 1 (February 1999): 39-43. (Review) Link to Item
  - Fukaki, H, Wysocka-Diller, J, Kato, T, Fujisawa, H, Benfey, PN, and Tasaka, M. "Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana." The Plant Journal : for Cell and Molecular Biology 14, no. 4 (May 1998): 425-430. Full Text
  - Wysocka-Diller, JW, and Benfey, PN. "Root development: signaling down and around." Bioessays 19, no. 11 (November 1997): 959-965. (Review) Full Text Link to Item
  - Malamy, JE, and Benfey, PN. "Analysis of SCARECROW expression using a rapid system for assessing transgene expression in Arabidopsis roots." Plant J 12, no. 4 (October 1997): 957-963. Link to Item
  - Malamy, JE, and Benfey, PN. "Down and out in Arabidopsis: The formation of lateral roots." TRENDS IN PLANT SCIENCE 2, no. 10 (October 1997): 390-396. Full Text Link to Item
  - Malamy, JE, and Benfey, PN. "Down and out in arabidopsis: The formation of lateral roots." Trends in Plant Science 2, no. 10 (January 1, 1997): 390-396. (Review) Full Text
  - Malamy, JE, and Benfey, PN. "Organization and cell differentiation in lateral roots of Arabidopsis thaliana." Development (Cambridge, England) 124, no. 1 (January 1997): 33-44.
  - Di Laurenzio, L, Wysocka-Diller, J, Malamy, JE, Pysh, L, Helariutta, Y, Freshour, G, Hahn, MG, Feldmann, KA, and Benfey, PN. "The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root." Cell 86, no. 3 (August 1996): 423-433. Full Text
  - Hauser, MT, Morikami, A, and Benfey, PN. "Conditional root expansion mutants of Arabidopsis." Development 121, no. 4 (April 1995): 1237-1252. Link to Item
  - Aeschbacher, RA, Hauser, MT, Feldmann, KA, and Benfey, PN. "The SABRE gene is required for normal cell expansion in Arabidopsis." Genes Dev 9, no. 3 (February 1, 1995): 330-340. Link to Item
  - Scheres, B, Di Laurenzio, L, Willemsen, V, Hauser, MT, Janmaat, K, Weisbeek, P, and Benfey, PN. "Mutations affecting the radial organisation of the Arabidopsis root display specific defects throughout the embryonic axis." Development 121, no. 1 (January 1, 1995): 53-62.
  - Aeschbacher, RA, Schiefelbein, JW, and Benfey, PN. "The genetic and molecular basis of root development." Annual Review of Plant Physiology and Plant Molecular Biology 45, no. 1 (December 1, 1994): 25-45.
  - BENFEY, PN, and SCHIEFELBEIN, JW. "INSIGHTS INTO ROOT DEVELOPMENT FROM ARABIDOPSIS ROOT MUTANTS." PLANT CELL AND ENVIRONMENT 17, no. 5 (May 1994): 675-680. Full Text Link to Item
  - Benfey, PN, and Schiefelbein, JW. "Getting to the root of plant development: the genetics of Arabidopsis root formation." Trends Genet 10, no. 3 (March 1994): 84-88. (Review) Link to Item
  - Benfey, PN, Linstead, PJ, Roberts, K, Schiefelbein, JW, Hauser, MT, and Aeschbacher, RA. "Root development in Arabidopsis: four mutants with dramatically altered root morphogenesis." Development (Cambridge, England) 119, no. 1 (September 1993): 57-70.
  - Schiefelbein, JW, and Benfey, PN. "International Symposium on the Molecular Genetics of Root Development." Plant Molecular Biology Reporter 11, no. 1 (March 1, 1993): 60-64. Full Text
  - Aeschbacher, RA, and Benfey, PN. "Genes that regulate plant development." Plant Science 83, no. 2 (January 1, 1992): 115-126. (Review) Full Text
  - Takatsuji, H, Mori, M, Benfey, PN, Ren, L, and Chua, NH. "Characterization of a zinc finger DNA-binding protein expressed specifically in Petunia petals and seedlings." The Embo Journal 11, no. 1 (January 1992): 241-249. Full Text
  - Schiefelbein, JW, and Benfey, PN. "The development of plant roots: new approaches to underground problems." The Plant Cell 3, no. 11 (November 1991): 1147-1154. (Review) Full Text
  - Benfey, PN, and Chua, NH. "The Cauliflower Mosaic Virus 35S Promoter: Combinatorial Regulation of Transcription in Plants." Science (New York, N.Y.) 250, no. 4983 (November 1990): 959-966. Full Text
  - Benfey, PN, Takatsuji, H, Ren, L, Shah, DM, and 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 2, no. 9 (September 1990): 849-856. Full Text
  - Benfey, PN, Ren, L, and Chua, NH. "Tissue-specific expression from CaMV 35S enhancer subdomains in early stages of plant development." The Embo Journal 9, no. 6 (June 1990): 1677-1684. Full Text
  - Benfey, PN, Ren, L, and Chua, NH. "Combinatorial and synergistic properties of CaMV 35S enhancer subdomains." The Embo Journal 9, no. 6 (June 1990): 1685-1696. Full Text
  - Lam, E, Benfey, PN, Gilmartin, PM, Fang, RX, and Chua, NH. "Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants." Proc Natl Acad Sci U S A 86, no. 20 (October 1989): 7890-7894. Link to Item
  - BENFEY, PN, REN, L, and CHUA, NH. "THE CAMV S-35 ENHANCER CONTAINS AT LEAST 2 DOMAINS WHICH CAN CONFER DIFFERENT DEVELOPMENTAL AND TISSUE-SPECIFIC EXPRESSION PATTERNS." EMBO JOURNAL 8, no. 8 (August 1989): 2195-2202. Link to Item
  - Benfey, PN, Ren, L, and Chua, NH. "The CaMV 35S enhancer contains at least two domains which can confer different developmental and tissue-specific expression patterns." The Embo Journal 8, no. 8 (August 1989): 2195-2202. Full Text
  - Benfey, PN, and Chua, NH. "Regulated genes in transgenic plants." Science (New York, N.Y.) 244, no. 4901 (April 1989): 174-181. Full Text
  - Sarid, J, Benfey, PN, and 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." J Biol Chem 264, no. 2 (January 15, 1989): 1022-1026. Link to Item
  - Shimizu, A, Tepler, I, Benfey, PN, Berenstein, EH, Siraganian, RP, and Leder, P. "Human and rat mast cell high-affinity immunoglobulin E receptors: characterization of putative alpha-chain gene products." Proc Natl Acad Sci U S A 85, no. 6 (March 1988): 1907-1911. Link to Item
  - Benfey, PN, Yin, FH, and Leder, P. "Cloning of the mast cell protease, RMCP II. Evidence for cell-specific expression and a multi-gene family." J Biol Chem 262, no. 11 (April 15, 1987): 5377-5384. Link to Item
- Book Sections
  - Sparks, EE, and Benfey, PN. "The contribution of root systems to plant nutrient acquisition." In Plant Macronutrient Use Efficiency: Molecular and Genomic Perspectives in Crop Plants, 83-92. January 1, 2017. Full Text
  - To, JPC, Benfey, PN, and Elich, TD. "Root-associated stress response networks." In Plant Abiotic Stress, Second Edition, 69-107. January 28, 2014. Full Text
  - Sparks, EE, Imai, A, Hasebe, M, and 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, 403-432. January 1, 2014. Full Text
  - Benfey, PN. "Plant Development, Genetics of." In Brenner's Encyclopedia of Genetics: Second Edition, 340-342. February 27, 2013. Full Text
  - Van Norman, JM, Liberman, LM, and Benfey, PN. "Arabidopsis root: A model organ in plant genomics." In Plant Roots: The Hidden Half, Fourth Edition, 17-34. January 1, 2013.
  - Tromas, A, Braun, N, Muller, P, Khodus, T, Paponov, IA, Palme, K, Ljung, K, Lee, JY, Benfey, P, Murray, JAH, Scheres, B, and Perrot-Rechenmann, C. "Auxin binding protein 1 for root growth." In Plant Physiology, 214-229. January 1, 2011.
  - Dinneny, JR, and Benfey, PN. "Studying Root Development Using a Genomic Approach." In Root Development, 325-351. October 7, 2009. Full Text
  - Brady, SM, and Benfey, PN. "Development and Systems Biology: Riding the Genomics Wave towards a Systems Understanding of Root Development." In Annual Plant Reviews, 304-330. August 18, 2009. Full Text
- Conference Papers
  - Benfey, PN. "Underground Signaling Networks." July 2017. Full Text
  - Benfey, PN. "Underground Signaling Networks." June 2017. Link to Item
  - Tsukagoshi, H, Mabuchi, K, Suzuki, T, Nomoto, M, Busch, W, Tada, Y, Higashiyama, T, and Benfey, PN. "The regulation mechanism of root development by ROS." December 2014. Link to Item
  - Benfey, PN, Lee, J-Y, Colinas, J, Cui, H, Twigg, R, Long, T, and Dinneny, I. "A systems biology approach to root development." : Elsevier BV, July 2006. Full Text
  - Benfey, PN, Birnbaum, K, and Shasha, D. "Transcriptional networks in root development." 2004. Link to Item
  - Ogawa, M, Kuwahara, A, Paquette, AJ, Benfey, PN, Kamiya, Y, and Yamaguchi, S. "Roles of the gibberellin-responsive SCL3 gene in Arabidopsis." 2004. Link to Item
  - Benfey, PN, Gallagher, K, Paquette, A, Nakajima, K, and Sena, G. "Radial patterning in arabidopsis: A moving target." July 15, 2003. Link to Item
  - Nawy, T, Malamy, JE, and Benfey, PN. "The MADS box gene AGL42 is expressed in the Arabidopsis root meristem and maintains its organization." July 15, 2003. Link to Item
  - Roudier, F, Fernandez, A, and Benfey, PN. "COBRA, a GPI-Anchored membrane protein, regulates anisotropic cell expansion during Arabidopsis development." July 15, 2003. Link to Item
  - Sena, G, Nakajima, K, Jung, J, and Benfey, PN. "Analysis of Arabidopsis root pattern formation: Tissue-specific ectopic expression of the "Moving" putative transcription factor short-root." July 15, 2002. Link to Item
  - Benfey, PN, Nakajima, K, Sena, G, and Paquette, A. "Radial patterning in Arabidopsis: Signaling inside out." July 1, 2001. Link to Item
  - Helariutta, Y, Wysocka-Diller, J, Lim, J, Malamy, JE, Fukaki, H, and Benfey, PN. "Radial pattern formation in plants." June 1, 1999. Link to Item
  - Malamy, JE, and Benfey, PN. "Analysis of lateral root formation in Arabidopsis." 1998. Link to Item
  - Pysh, LD, and Benfey, PN. "Root cell extension: Genetic and molecular approaches." 1998. Link to Item
  - Malamy, JE, and Benfey, PN. "Lateral root formation in Arabidopsis thaliana." July 1997. Link to Item
  - WysockaDiller, J, Malamy, JE, DiLaurenzio, L, Pysh, L, Helariutta, Y, and Benfey, PN. "Root radial organization." June 1996. Link to Item
  - HAUSER, MT, and BENFEY, PN. "GENETIC-ANALYSIS OF CELL EXPANSION IN ROOTS OF ARABIDOPSIS." March 10, 1995. Link to Item
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