Philip N. Benfey | Scholars@Duke

Philip N. Benfey
Paul Kramer Distinguished Professor of Biology

Current Appointments & Affiliations

Paul Kramer Distinguished Professor of Biology, 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
Core Faculty in Innovation & Entrepreneurship, Duke Innovation & Entrepreneurship, Initiatives 2018
Affiliate of the Duke Regeneration Center, Regeneration Next Initiative, Basic Science Departments 2021

Contact Information

130 Science Drive, Room 137, Duke Box 90338, Durham, NC 27708
Duke Box 90338, Durham, NC 27708
philip.benfey@duke.edu (919) 357-1743

Background
Education, Training, & Certifications
- Ph.D., Harvard University 1986
- B.S., University of Paris (France) 1981
Previous Appointments & Affiliations
- 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
- FEB 8, 2022
  
  Check It Out! A Road Map for a Plant Root
- AUG 25, 2021
  
  Growth-Promoting, Anti-Aging Retinal at the Root of Plant Growth Too
- FEB 19, 2021
  
  Time-Lapse Reveals the Hidden Dance of Roots
- OCT 30, 2020
  
  The Secret Life of Plant Roots, and Why This Matters for Climate Change
- DEC 4, 2019
  
  The Making of a Root
- NOV 19, 2019
  
  Global List of Highly Cited Puts Duke in Top Ten
- 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
- Training Program in Developmental and Stem Cell Biology awarded by National Institutes of Health 2001 - 2027
- Cell and Molecular Biology Training Program awarded by National Institutes of Health 2021 - 2026
- Genetic and Genomics Training Grant awarded by National Institutes of Health 2020 - 2025
- A Molecular Genetic Analysis of Root Morphogenesis awarded by National Institutes of Health 2019 - 2024
- Analysis of Rice Root Circumnutation by High-throughput Phenotyping awarded by Department of Agriculture 2021 - 2023
- IRES Track 1 IRTG Engaged in Dissecting and Reengineering the Regulatory Genome awarded by National Science Foundation 2019 - 2023
- Collaborative Research: Root Dynamics and Control in Heterogeneous Soft Substrates awarded by National Science Foundation 2019 - 2022
- Architecture and Dynamics of the Gene Regulatory Network Controlling Cell Fate awarded by National Institutes of Health 2020 - 2022
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Genetics Training Grant awarded by National Institutes of Health 1979 - 2020
- Organization and Function of Cellular Structure awarded by National Institutes of Health 1975 - 2020
- 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
- Expansion of Capacity for Quantitative and Qualitative Differential Expression - Acquisition of an Integrated System for Nanoscale Capillary LC/MS/MS Analysis Using a UPLC/NanoMate/Q-Tof with On-line and Off-line Data Acquisition Capabilities 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 (K. Gallagher fellowship) awarded by National Institutes of Health 2002 - 2004
- Regulation of the Orientation of Cell Expansion awarded by National Science Foundation 2002 - 2003
External Relationships
- CEPAMS
- Geoffrey Schiebinger, University of British Columbia
- Ground Control Robotics, Inc.
- Hi Fidelity Genetics LLC
- The Salk Institute
- Uwe Ohler laboratory, Humboldt University, Berlin Germany
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Northrup, Daniel L., Bruno Basso, Michael Q. Wang, Cristine L. S. Morgan, and Philip N. Benfey. “Reply to Amundson: Time to go to work.” Proceedings of the National Academy of Sciences of the United States of America 119, no. 12 (March 18, 2022): e2122842119. https://doi.org/10.1073/pnas.2122842119.
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  - Zhu, Mingyuan, Isaiah W. Taylor, and Philip N. Benfey. “Single-cell genomics revolutionizes plant development studies across scales.” Development (Cambridge, England) 149, no. 6 (March 14, 2022): dev200179. https://doi.org/10.1242/dev.200179.
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  - Shahan, Rachel, Che-Wei Hsu, Trevor M. Nolan, Benjamin J. Cole, Isaiah W. Taylor, Laura Greenstreet, Stephen Zhang, et al. “A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.” Developmental Cell 57, no. 4 (February 7, 2022): 543-560.e9. https://doi.org/10.1016/j.devcel.2022.01.008.
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  - Contreras-López, Orlando, Elena A. Vidal, Eleodoro Riveras, José M. Alvarez, Tomás C. Moyano, Erin E. Sparks, Joaquín Medina, et al. “Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate.” Proceedings of the National Academy of Sciences of the United States of America 119, no. 4 (January 2022): e2107879119. https://doi.org/10.1073/pnas.2107879119.
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  - Aguilar, Jeffrey J., Matt Moore, Logan Johnson, Rachel F. Greenhut, Eric Rogers, Drew Walker, Fletcher O’Neil, et al. “Capturing in-field root system dynamics with RootTracker.” Plant Physiology 187, no. 3 (November 2021): 1117–30. https://doi.org/10.1093/plphys/kiab352.
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  - Tzipilevich, Elhanan, Dor Russ, Jeffery L. Dangl, and Philip N. Benfey. “Plant immune system activation is necessary for efficient root colonization by auxin-secreting beneficial bacteria.” Cell Host & Microbe 29, no. 10 (October 4, 2021): 1507-1520.e4. https://doi.org/10.1016/j.chom.2021.09.005.
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  - Shahan, Rachel, Trevor M. Nolan, and Philip N. Benfey. “Single-cell analysis of cell identity in the Arabidopsis root apical meristem: insights and opportunities.” Journal of Experimental Botany 72, no. 19 (October 2021): 6679–86. https://doi.org/10.1093/jxb/erab228.
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  - Dickinson, Alexandra J., Jingyuan Zhang, Michael Luciano, Guy Wachsman, Evan Sandoval, Martin Schnermann, José R. Dinneny, and Philip N. Benfey. “A plant lipocalin promotes retinal-mediated oscillatory lateral root initiation.” Science (New York, N.Y.) 373, no. 6562 (September 2021): 1532–36. https://doi.org/10.1126/science.abf7461.
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  - Tzipilevich, Elhanan, and Philip N. Benfey. “Phage-Resistant Bacteria Reveal a Role for Potassium in Root Colonization.” Mbio 12, no. 4 (August 17, 2021): e0140321. https://doi.org/10.1128/mbio.01403-21.
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  - Goldy, Camila, Virginia Barrera, Isaiah Taylor, Celeste Buchensky, Rodrigo Vena, Philip Benfey, Lieven De Veylder, and Ramiro Rodriguez. “SCL28 promotes cell expansion and endoreplication in Arabidopsis by activating SIAMESE-RELATED cyclin-dependent kinase inhibitors,” August 11, 2021. https://doi.org/10.1101/2021.08.10.455231.
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  - Northrup, Daniel L., Bruno Basso, Michael Q. Wang, Cristine L. S. Morgan, and Philip N. Benfey. “Novel technologies for emission reduction complement conservation agriculture to achieve negative emissions from row-crop production.” Proceedings of the National Academy of Sciences of the United States of America 118, no. 28 (July 2021): e2022666118. https://doi.org/10.1073/pnas.2022666118.
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  - Shao, Yanlin, Kevin R. Lehner, Hongzhu Zhou, Isaiah Taylor, Mingyuan Zhu, Chuanzao Mao, and Philip N. Benfey. “VAP-RELATED SUPPRESSORS OF TOO MANY MOUTHS (VST) family proteins are regulators of root system architecture.” Plant Physiology 185, no. 2 (March 2021): 457–68. https://doi.org/10.1093/plphys/kiaa036.
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  - Goldy, Camila, José-Antonio Pedroza-Garcia, Natalie Breakfield, Toon Cools, Rodrigo Vena, Philip N. Benfey, Lieven De Veylder, Javier Palatnik, and Ramiro E. Rodriguez. “The Arabidopsis GRAS-type SCL28 transcription factor controls the mitotic cell cycle and division plane orientation.” Proceedings of the National Academy of Sciences of the United States of America 118, no. 6 (February 2021): e2005256118. https://doi.org/10.1073/pnas.2005256118.
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  - Taylor, Isaiah, Kevin Lehner, Erin McCaskey, Niba Nirmal, Yasemin Ozkan-Aydin, Mason Murray-Cooper, Rashmi Jain, et al. “Mechanism and function of root circumnutation.” Proceedings of the National Academy of Sciences of the United States of America 118, no. 8 (February 2021): e2018940118. https://doi.org/10.1073/pnas.2018940118.
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  - Perianez-Rodriguez, Juan, Marcos Rodriguez, Marco Marconi, Estefano Bustillo-Avendaño, Guy Wachsman, Alvaro Sanchez-Corrionero, Hugues De Gernier, et al. “An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis.” Science Advances 7, no. 1 (January 2021): eabd4722. https://doi.org/10.1126/sciadv.abd4722.
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  - Wachsman, Guy, Jingyuan Zhang, Miguel A. Moreno-Risueno, Charles T. Anderson, and Philip N. Benfey. “Cell wall remodeling and vesicle trafficking mediate the root clock in Arabidopsis.” Science (New York, N.Y.) 370, no. 6518 (November 2020): 819–23. https://doi.org/10.1126/science.abb7250.
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  - Henkhaus, Natalie, Madelaine Bartlett, David Gang, Rebecca Grumet, Ingrid Jordon-Thaden, Argelia Lorence, Eric Lyons, et al. “Plant science decadal vision 2020-2030: Reimagining the potential of plants for a healthy and sustainable future.” Plant Direct 4, no. 8 (August 2020): e00252. https://doi.org/10.1002/pld3.252.
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  - Shahan, Rachel, Che-Wei Hsu, Trevor Nolan, Benjamin Cole, Isaiah Taylor, Anna Hendrika Cornelia Vlot, Philip Benfey, and Uwe Ohler. “A single cellArabidopsisroot atlas reveals developmental trajectories in wild type and cell identity mutants,” June 30, 2020. https://doi.org/10.1101/2020.06.29.178863.
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  - Wachsman, Guy, Jingyuan Zhang, Miguel Moreno-Risueno, Charles Anderson, and Philip Benfey. “Cell wall remodeling and vesicle trafficking mediate the root clock in Arabidopsis,” March 11, 2020. https://doi.org/10.1101/2020.03.10.985747.
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  - Wachsman, Guy, and Philip N. Benfey. “Lateral Root Initiation: The Emergence of New Primordia Following Cell Death.” Current Biology : Cb 30, no. 3 (February 2020): R121–22. https://doi.org/10.1016/j.cub.2019.12.032.
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  - Shahan, Rachel, and Philip N. Benfey. “A Co-opted Regulator of Lateral Root Development Controls Nodule Organogenesis in Lotus.” Developmental Cell 52, no. 1 (January 2020): 6–7. https://doi.org/10.1016/j.devcel.2019.12.009.
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  - Yamada, Masashi, Xinwei Han, and Philip N. Benfey. “RGF1 controls root meristem size through ROS signalling.” Nature 577, no. 7788 (January 2020): 85–88. https://doi.org/10.1038/s41586-019-1819-6.
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  - Zhang, Yueying, Minglei Yang, Susan Duncan, Xiaofei Yang, Mahmoud A. S. Abdelhamid, Lin Huang, Huakun Zhang, Philip N. Benfey, Zoë A. E. Waller, and Yiliang Ding. “G-quadruplex structures trigger RNA phase separation.” Nucleic Acids Research 47, no. 22 (December 2019): 11746–54. https://doi.org/10.1093/nar/gkz978.
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  - Jia, Kun-Peng, Alexandra J. Dickinson, Jianing Mi, Guoxin Cui, Ting Ting Xiao, Najeh M. Kharbatia, Xiujie Guo, et al. “Anchorene is a carotenoid-derived regulatory metabolite required for anchor root formation in Arabidopsis.” Science Advances 5, no. 11 (November 27, 2019): eaaw6787. https://doi.org/10.1126/sciadv.aaw6787.
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  - Dickinson, Alexandra J., Kevin Lehner, Jianing Mi, Kun-Peng Jia, Medhavinee Mijar, José Dinneny, Salim Al-Babili, and Philip N. Benfey. “β-Cyclocitral is a conserved root growth regulator.” Proceedings of the National Academy of Sciences of the United States of America 116, no. 21 (May 8, 2019): 10563–67. https://doi.org/10.1073/pnas.1821445116.
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  - Chen, Wen-Qian, Colleen Drapek, Dong-Xu Li, Zhi-Hong Xu, Philip N. Benfey, and Shu-Nong Bai. “Histone Deacetylase HDA19 Affects Root Cortical Cell Fate by Interacting with SCARECROW.” Plant Physiology 180, no. 1 (May 2019): 276–88. https://doi.org/10.1104/pp.19.00056.
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  - Di Mambro, Riccardo, Noemi Svolacchia, Raffaele Dello Ioio, Emanuela Pierdonati, Elena Salvi, Emanuela Pedrazzini, Alessandro Vitale, et al. “The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size.” Current Biology : Cb 29, no. 7 (April 2019): 1199-1205.e4. https://doi.org/10.1016/j.cub.2019.02.022.
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  - Pierre-Jerome, Edith, Colleen Drapek, and Philip N. Benfey. “Regulation of Division and Differentiation of Plant Stem Cells.” Annual Review of Cell and Developmental Biology 34 (October 2018): 289–310. https://doi.org/10.1146/annurev-cellbio-100617-062459.
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  - Drapek, Colleen, Erin E. Sparks, Peter Marhavy, Isaiah Taylor, Tonni G. Andersen, Jessica H. Hennacy, Niko Geldner, and Philip N. Benfey. “Minimum requirements for changing and maintaining endodermis cell identity in the Arabidopsis root.” Nature Plants 4, no. 8 (August 2018): 586–95. https://doi.org/10.1038/s41477-018-0213-y.
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  - Grondin, Alexandre, Shalabh Dixit, Rolando Torres, Challa Venkateshwarlu, Eric Rogers, Thomas Mitchell-Olds, Philip N. Benfey, Arvind Kumar, and Amelia Henry. “Physiological mechanisms contributing to the QTL qDTY_3.2 effects on improved performance of rice Moroberekan x Swarna BC₂F_3:4 lines under drought.” Rice (New York, N.Y.) 11, no. 1 (July 31, 2018): 43. https://doi.org/10.1186/s12284-018-0234-1.
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  - Hsu, Polly Yingshan, and Philip N. Benfey. “Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants.” Proteomics 18, no. 10 (May 2018): e1700038. https://doi.org/10.1002/pmic.201700038.
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  - Shibata, Michitaro, Christian Breuer, Ayako Kawamura, Natalie M. Clark, Bart Rymen, Luke Braidwood, Kengo Morohashi, et al. “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): dev159707. https://doi.org/10.1242/dev.159707.
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  - Wendrich, Jos R., Barbara K. Möller, Song Li, Shunsuke Saiga, Rosangela Sozzani, Philip N. Benfey, Bert De Rybel, and Dolf Weijers. “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): E8922–29. https://doi.org/10.1073/pnas.1707400114.
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  - Di Mambro, Riccardo, Micol De Ruvo, Elena Pacifici, Elena Salvi, Rosangela Sozzani, Philip N. Benfey, Wolfgang Busch, et al. “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): E7641–49. https://doi.org/10.1073/pnas.1705833114.
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  - Drapek, Colleen, Erin E. Sparks, and Philip N. Benfey. “Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation.” Trends in Genetics : Tig 33, no. 8 (August 2017): 529–39. https://doi.org/10.1016/j.tig.2017.05.002.
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  - Wachsman, Guy, Jennifer L. Modliszewski, Manuel Valdes, and Philip N. Benfey. “A SIMPLE Pipeline for Mapping Point Mutations.” Plant Physiology 174, no. 3 (July 2017): 1307–13. https://doi.org/10.1104/pp.17.00415.
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  - Nevarez, P Andrew, Yongjian Qiu, Hitoshi Inoue, Chan Yul Yoo, Philip N. Benfey, Danny J. Schnell, and Meng Chen. “Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus.” Plant Physiology 173, no. 4 (April 2017): 1953–66. https://doi.org/10.1104/pp.16.00116.
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  - Li, Chen, Yusuke Sako, Akihiro Imai, Tomoaki Nishiyama, Kari Thompson, Minoru Kubo, Yuji Hiwatashi, et al. “A Lin28 homologue reprograms differentiated cells to stem cells in the moss Physcomitrella patens.” Nature Communications 8 (January 27, 2017): 14242. https://doi.org/10.1038/ncomms14242.
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  - Fernández-Marcos, María, Bénédicte Desvoyes, Concepción Manzano, Louisa M. Liberman, Philip N. Benfey, Juan C. Del Pozo, and Crisanto Gutierrez. “Control of Arabidopsis lateral root primordium boundaries by MYB36.” The New Phytologist 213, no. 1 (January 2017): 105–12. https://doi.org/10.1111/nph.14304.
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  - Sparks, Erin E., and Philip N. Benfey. “Tissue-Specific Transcriptome Profiling in Arabidopsis Roots.” Methods in Molecular Biology (Clifton, N.J.) 1610 (January 2017): 107–22. https://doi.org/10.1007/978-1-4939-7003-2_8.
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  - Sparks, Erin E., Colleen Drapek, Allison Gaudinier, Song Li, Mitra Ansariola, Ning Shen, Jessica H. Hennacy, et al. “Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.” Dev Cell 39, no. 5 (December 5, 2016): 585–96. https://doi.org/10.1016/j.devcel.2016.09.031.
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  - Li, Song, Masashi Yamada, Xinwei Han, Uwe Ohler, and Philip N. Benfey. “High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation.” Dev Cell 39, no. 4 (November 21, 2016): 508–22. https://doi.org/10.1016/j.devcel.2016.10.012.
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  - Wachsman, Guy, Jennifer Modliszewski, Manuel Valdes, and Philip Benfey. “A SIMPLE pipeline for mapping point mutations,” November 18, 2016. https://doi.org/10.1101/088591.
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  - Hsu, Polly Yingshan, Lorenzo Calviello, Hsin-Yen Larry Wu, Fay-Wei Li, Carl J. Rothfels, Uwe Ohler, and Philip N. Benfey. “Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis.” Proc Natl Acad Sci U S A 113, no. 45 (November 8, 2016): E7126–35. https://doi.org/10.1073/pnas.1614788113.
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  - Rogers, Eric D., Daria Monaenkova, Medhavinee Mijar, Apoorva Nori, Daniel I. Goldman, and Philip N. Benfey. “X-Ray Computed Tomography Reveals the Response of Root System Architecture to Soil Texture.” Plant Physiology 171, no. 3 (July 2016): 2028–40. https://doi.org/10.1104/pp.16.00397.
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  - Clark, Natalie M., Elizabeth Hinde, Cara M. Winter, Adam P. Fisher, Giuseppe Crosti, Ikram Blilou, Enrico Gratton, Philip N. Benfey, and Rosangela Sozzani. “Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy.” Elife 5 (June 11, 2016): e14770. https://doi.org/10.7554/elife.14770.
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  - Kawakatsu, Taiji, Tim Stuart, Manuel Valdes, Natalie Breakfield, Robert J. Schmitz, Joseph R. Nery, Mark A. Urich, et al. “Unique cell-type-specific patterns of DNA methylation in the root meristem.” Nature Plants 2, no. 5 (April 29, 2016): 16058. https://doi.org/10.1038/nplants.2016.58.
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  - Liberman, Louisa M., and Philip N. Benfey. “A Friend in Need (of Nutrients) Is a….” Cell 165, no. 2 (April 2016): 269–71. https://doi.org/10.1016/j.cell.2016.03.036.
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  - Benfey, Philip N. “Defining the Path from Stem Cells to Differentiated Tissue.” Current Topics in Developmental Biology 116 (January 2016): 35–43. https://doi.org/10.1016/bs.ctdb.2015.12.002.
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  - Sparks, Erin E., and Philip N. Benfey. “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. https://doi.org/10.1007/978-1-4939-3142-2_3.
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  - Rodriguez, Ramiro E., María Florencia Ercoli, Juan Manuel Debernardi, Natalie W. Breakfield, Martin A. Mecchia, Martin Sabatini, Toon Cools, Lieven De Veylder, Philip N. Benfey, and Javier F. Palatnik. “MicroRNA miR396 Regulates the Switch between Stem Cells and Transit-Amplifying Cells in Arabidopsis Roots.” The Plant Cell 27, no. 12 (December 8, 2015): 3354–66. https://doi.org/10.1105/tpc.15.00452.
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  - Moreno-Risueno, Miguel A., Rosangela Sozzani, Galip Gürkan Yardımcı, Jalean J. Petricka, Teva Vernoux, Ikram Blilou, Jose Alonso, et al. “Transcriptional control of tissue formation throughout root development.” Science 350, no. 6259 (October 23, 2015): 426–30. https://doi.org/10.1126/science.aad1171.
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  - Wachsman, Guy, Erin E. Sparks, and Philip N. Benfey. “Genes and networks regulating root anatomy and architecture.” The New Phytologist 208, no. 1 (October 2015): 26–38. https://doi.org/10.1111/nph.13469.
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  - Liberman, Louisa M., Erin E. Sparks, Miguel A. Moreno-Risueno, Jalean J. Petricka, and Philip N. Benfey. “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): 12099–104. https://doi.org/10.1073/pnas.1515576112.
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  - Cederholm, Heidi M., and Philip N. Benfey. “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): 683–91. https://doi.org/10.1111/nph.13405.
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  - Jackson, Terry L., Ginger W. Baker, Floyd R. Wilks, Vladimir A. Popov, Jaideep Mathur, and Philip N. Benfey. “Large Cellular Inclusions Accumulate in Arabidopsis Roots Exposed to Low-Sulfur Conditions.” Plant Physiology 168, no. 4 (August 2015): 1573–89. https://doi.org/10.1104/pp.15.00465.
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  - Vilarrasa-Blasi, J., M. P. González-García, D. Frigola, N. Fàbregas-Vallvé, K. G. Alexiou, N. López-Bigas, S. Rivas, et al. “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 (April 20, 2015): 238. https://doi.org/10.1016/j.devcel.2015.01.021.
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  - Rogers, Eric D., and Philip N. Benfey. “Regulation of plant root system architecture: implications for crop advancement.” Current Opinion in Biotechnology 32 (April 2015): 93–98. https://doi.org/10.1016/j.copbio.2014.11.015.
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  - Zurek, Paul R., Christopher N. Topp, and Philip N. Benfey. “Quantitative trait locus mapping reveals regions of the maize genome controlling root system architecture.” Plant Physiology 167, no. 4 (April 2015): 1487–96. https://doi.org/10.1104/pp.114.251751.
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  - Vilarrasa-Blasi, Josep, Mary-Paz González-García, David Frigola, Norma Fàbregas, Konstantinos G. Alexiou, Nuria López-Bigas, Susana Rivas, et al. “Regulation of plant stem cell quiescence by a brassinosteroid signaling module.” Developmental Cell 30, no. 1 (July 2014): 36–47. https://doi.org/10.1016/j.devcel.2014.05.020.
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  - Morton, Taj, Jalean Petricka, David L. Corcoran, Song Li, Cara M. Winter, Alexa Carda, Philip N. Benfey, Uwe Ohler, and Molly Megraw. “Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.” Plant Cell 26, no. 7 (July 2014): 2746–60. https://doi.org/10.1105/tpc.114.125617.
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  - Sozzani, Rosangela, Wolfgang Busch, Edgar P. Spalding, and Philip N. Benfey. “Advanced imaging techniques for the study of plant growth and development.” Trends in Plant Science 19, no. 5 (May 2014): 304–10. https://doi.org/10.1016/j.tplants.2013.12.003.
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  - Van Norman, Jaimie M., Jingyuan Zhang, Christopher I. Cazzonelli, Barry J. Pogson, Peter J. Harrison, Timothy D. H. Bugg, Kai Xun Chan, Andrew J. Thompson, and Philip N. Benfey. “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): E1300–1309. https://doi.org/10.1073/pnas.1403016111.
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  - Sparks, Erin E., and Philip N. Benfey. “HEC of a job regulating stem cells.” Developmental Cell 28, no. 4 (February 2014): 349–50. https://doi.org/10.1016/j.devcel.2014.02.006.
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  - Iyer-Pascuzzi, A. S., P. R. Zurek, and P. N. Benfey. “High-throughput, noninvasive imaging of root systems.” Methods in Molecular Biology 959 (December 1, 2013): 177–87. https://doi.org/10.1007/978-1-62703-221-6-11.
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  - Van Norman, Jaimie M., Wei Xuan, Tom Beeckman, and Philip N. Benfey. “To branch or not to branch: the role of pre-patterning in lateral root formation.” Development (Cambridge, England) 140, no. 21 (November 2013): 4301–10. https://doi.org/10.1242/dev.090548.
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  - Benfey, Philip. “Philip Benfey.” Current Biology : Cb 23, no. 19 (October 2013): R857–58. https://doi.org/10.1016/j.cub.2013.08.010.
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  - Li, Song, Louisa M. Liberman, Neelanjan Mukherjee, Philip N. Benfey, and Uwe Ohler. “Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.” Genome Res 23, no. 10 (October 2013): 1730–39. https://doi.org/10.1101/gr.149310.112.
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  - Sparks, Erin, Guy Wachsman, and Philip N. Benfey. “Spatiotemporal signalling in plant development.” Nature Reviews. Genetics 14, no. 9 (September 2013): 631–44. https://doi.org/10.1038/nrg3541.
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  - Benfey, P. N., and B. Scheres. “Arabidopsis as a Model for Systems Biology,” August 29, 2013, 391–406. https://doi.org/10.1016/B978-0-12-385944-0.00020-4.
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  - Moubayidin, Laila, Riccardo Di Mambro, Rosangela Sozzani, Elena Pacifici, Elena Salvi, Inez Terpstra, Dongping Bao, et al. “Spatial coordination between stem cell activity and cell differentiation in the root meristem.” Developmental Cell 26, no. 4 (August 2013): 405–15. https://doi.org/10.1016/j.devcel.2013.06.025.
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  - Topp, Christopher N., Anjali S. Iyer-Pascuzzi, Jill T. Anderson, Cheng-Ruei Lee, Paul R. Zurek, Olga Symonova, Ying Zheng, et al. “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): E1695–1704. https://doi.org/10.1073/pnas.1304354110.
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  - Liberman, Louisa M., and Philip N. Benfey. “Polarized radicals.” Cell 153, no. 2 (April 2013): 285–86. https://doi.org/10.1016/j.cell.2013.03.042.
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  - Moussaieff, Arieh, Ilana Rogachev, Leonid Brodsky, Sergey Malitsky, Ted W. Toal, Heather Belcher, Merav Yativ, Siobhan M. Brady, Philip N. Benfey, and Asaph Aharoni. “High-resolution metabolic mapping of cell types in plant roots.” Proceedings of the National Academy of Sciences of the United States of America 110, no. 13 (March 8, 2013): E1232–41. https://doi.org/10.1073/pnas.1302019110.
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  - Fang, Suqin, Randy T. Clark, Ying Zheng, Anjali S. Iyer-Pascuzzi, Joshua S. Weitz, Leon V. Kochian, Herbert Edelsbrunner, Hong Liao, and Philip N. Benfey. “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): 2670–75. https://doi.org/10.1073/pnas.1222821110.
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  - Iyer-Pascuzzi, Anjali S., Paul R. Zurek, and Philip N. Benfey. “High-throughput, noninvasive imaging of root systems.” Methods in Molecular Biology (Clifton, N.J.) 959 (January 2013): 177–87. https://doi.org/10.1007/978-1-62703-221-6_11.
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  - Topp, C. N., and P. N. Benfey. “Growth control of root architecture,” December 1, 2012, 373–86. https://doi.org/10.1016/B978-0-12-381466-1.00024-9.
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  - Busch, Wolfgang, Brad T. Moore, Bradley Martsberger, Daniel L. Mace, Richard W. Twigg, Jee Jung, Iulian Pruteanu-Malinici, et al. “A microfluidic device and computational platform for high-throughput live imaging of gene expression.” Nat Methods 9, no. 11 (November 2012): 1101–6. https://doi.org/10.1038/nmeth.2185.
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  - Cederholm, Heidi M., Anjali S. Iyer-Pascuzzi, and Philip N. Benfey. “Patterning the primary root in Arabidopsis.” Wiley Interdisciplinary Reviews. Developmental Biology 1, no. 5 (September 2012): 675–91. https://doi.org/10.1002/wdev.49.
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  - Cruz Ramírez, A., S. Díaz Triviño, I. Blilou, V. A. Grieneisen, R. Sozzani, C. Zamioudis, P. Miskolczi, et al. “A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division.” Cell 150, no. 5 (August 2012): 1002–15. https://doi.org/10.1016/j.cell.2012.07.017.
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  - Galkovskyi, Taras, Yuriy Mileyko, Alexander Bucksch, Brad Moore, Olga Symonova, Charles A. Price, Christopher N. Topp, et al. “GiA Roots: software for the high throughput analysis of plant root system architecture.” Bmc Plant Biology 12 (July 26, 2012): 116. https://doi.org/10.1186/1471-2229-12-116.
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  - Ingram, P. A., J. Zhu, A. Shariff, I. W. Davis, P. N. Benfey, and T. Elich. “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): 1559–69. https://doi.org/10.1098/rstb.2011.0241.
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  - Petricka, Jalean J., Monica A. Schauer, Molly Megraw, Natalie W. Breakfield, J Will Thompson, Stoyan Georgiev, Erik J. Soderblom, et al. “The protein expression landscape of the Arabidopsis root.” Proc Natl Acad Sci U S A 109, no. 18 (May 1, 2012): 6811–18. https://doi.org/10.1073/pnas.1202546109.
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  - Stone, Jana E., Philip N. Benfey, and Lingchong You. “Promoting collaborative interdisciplinary research at the Duke Center for Systems Biology.” Acs Synthetic Biology 1, no. 5 (May 2012): 153–55. https://doi.org/10.1021/sb300036z.
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  - Liberman, Louisa M., Rosangela Sozzani, and Philip N. Benfey. “Integrative systems biology: an attempt to describe a simple weed.” Current Opinion in Plant Biology 15, no. 2 (April 2012): 162–67. https://doi.org/10.1016/j.pbi.2012.01.004.
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  - Rogers, Eric D., Terry Jackson, Arieh Moussaieff, Asaph Aharoni, and Philip N. Benfey. “Cell type-specific transcriptional profiling: implications for metabolite profiling.” The Plant Journal : For Cell and Molecular Biology 70, no. 1 (April 2012): 5–17. https://doi.org/10.1111/j.1365-313x.2012.04888.x.
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  - Bruex, Angela, Raghunandan M. Kainkaryam, Yana Wieckowski, Yeon Hee Kang, Christine Bernhardt, Yang Xia, Xiaohua Zheng, et al. “A gene regulatory network for root epidermis cell differentiation in Arabidopsis.” Plos Genetics 8, no. 1 (January 12, 2012): e1002446. https://doi.org/10.1371/journal.pgen.1002446.
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  - De Smet, Ive, Philip J. White, A Glyn Bengough, Lionel Dupuy, Boris Parizot, Ilda Casimiro, Renze Heidstra, et al. “Analyzing lateral root development: how to move forward.” The Plant Cell 24, no. 1 (January 6, 2012): 15–20. https://doi.org/10.1105/tpc.111.094292.
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  - Benfey, P. N. “Toward a systems analysis of the root.” Cold Spring Harbor Symposia on Quantitative Biology 77 (January 2012): 91–96. https://doi.org/10.1101/sqb.2012.77.014506.
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  - Davis, Ian W., Christopher Benninger, Philip N. Benfey, and Tedd Elich. “POWRS: position-sensitive motif discovery.” Plos One 7, no. 7 (January 2012): e40373. https://doi.org/10.1371/journal.pone.0040373.
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  - Moreno-Risueno, Miguel A., Jaimie M. Van Norman, and Philip N. Benfey. “Transcriptional switches direct plant organ formation and patterning.” Current Topics in Developmental Biology 98 (January 2012): 229–57. https://doi.org/10.1016/b978-0-12-386499-4.00009-4.
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  - Petricka, Jalean J., Cara M. Winter, and Philip N. Benfey. “Control of Arabidopsis root development.” Annual Review of Plant Biology 63 (January 2012): 563–90. https://doi.org/10.1146/annurev-arplant-042811-105501.
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  - Breakfield, Natalie W., David L. Corcoran, Jalean J. Petricka, Jeffrey Shen, Juthamas Sae-Seaw, Ignacio Rubio-Somoza, Detlef Weigel, Uwe Ohler, and Philip N. Benfey. “High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis.” Genome Res 22, no. 1 (January 2012): 163–76. https://doi.org/10.1101/gr.123547.111.
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  - Galkovskyi, T., Y. Mileyko, A. Bucksch, B. Moore, O. Symonova, C. A. Price, C. N. Topp, et al. “GiA Roots: software for the high throughput analysis of plant root system architecture.” Bmc Plant Biology 12, no. 5 (2012): 116. https://doi.org/10.1186/1471-2229-12-116.
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  - Zheng, Y., S. Gu, H. Edelsbrunner, C. Tomasi, and P. Benfey. “Detailed reconstruction of 3D plant root shape.” Proceedings of the Ieee International Conference on Computer Vision, December 1, 2011, 2026–33. https://doi.org/10.1109/ICCV.2011.6126475.
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  - Iyer-Pascuzzi, Anjali S., Terry Jackson, Hongchang Cui, Jalean J. Petricka, Wolfgang Busch, Hironaka Tsukagoshi, and Philip N. Benfey. “Cell identity regulators link development and stress responses in the Arabidopsis root.” Developmental Cell 21, no. 4 (October 2011): 770–82. https://doi.org/10.1016/j.devcel.2011.09.009.
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  - Petricka, Jalean J., and Philip N. Benfey. “Reconstructing regulatory network transitions.” Trends in Cell Biology 21, no. 8 (August 2011): 442–51. https://doi.org/10.1016/j.tcb.2011.05.001.
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  - Benfey, Philip N. “Taking a developmental perspective on systems biology.” Developmental Cell 21, no. 1 (July 2011): 27–28. https://doi.org/10.1016/j.devcel.2011.06.009.
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  - Zhu, J., P. A. Ingram, P. N. Benfey, and T. Elich. “From lab to field, new approaches to phenotyping root system architecture.” Current Opinion in Plant Biology 14, no. 3 (June 2011): 310–17. https://doi.org/10.1016/j.pbi.2011.03.020.
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  - Moreno-Risueno, Miguel A., and Philip N. Benfey. “Time-based patterning in development: The role of oscillating gene expression.” Transcription 2, no. 3 (May 2011): 124–29. https://doi.org/10.4161/trns.2.3.15637.
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  - Van Norman, Jaimie M., Natalie W. Breakfield, and Philip N. Benfey. “Intercellular communication during plant development.” The Plant Cell 23, no. 3 (March 8, 2011): 855–64. https://doi.org/10.1105/tpc.111.082982.
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  - Brady, Siobhan M., Lifang Zhang, Molly Megraw, Natalia J. Martinez, Eric Jiang, Charles S. Yi, Weilin Liu, et al. “A stele-enriched gene regulatory network in the Arabidopsis root.” Mol Syst Biol 7 (January 18, 2011): 459. https://doi.org/10.1038/msb.2010.114.
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  - Sozzani, Rosangela, and Philip N. Benfey. “High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype.” Genome Biology 12, no. 3 (January 2011): 219. https://doi.org/10.1186/gb-2011-12-3-219.
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  - Pop, Ana, Curtis Huttenhower, Anjali Iyer-Pascuzzi, Philip N. Benfey, and Olga G. Troyanskaya. “Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana.” Bmc Systems Biology 4 (December 31, 2010): 180. https://doi.org/10.1186/1752-0509-4-180.
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  - Baskin, Tobias I., Benjamin Peret, Frantisek Baluška, Philip N. Benfey, Malcolm Bennett, Brian G. Forde, Simon Gilroy, et al. “Shootward and rootward: peak terminology for plant polarity.” Trends in Plant Science 15, no. 11 (November 2010): 593–94. https://doi.org/10.1016/j.tplants.2010.08.006.
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  - Tsukagoshi, Hironaka, Wolfgang Busch, and Philip N. Benfey. “Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root.” Cell 143, no. 4 (November 2010): 606–16. https://doi.org/10.1016/j.cell.2010.10.020.
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  - To, Jennifer Pc, Jinming Zhu, Philip N. Benfey, and Tedd Elich. “Optimizing root system architecture in biofuel crops for sustainable energy production and soil carbon sequestration.” F1000 Biology Reports 2 (September 8, 2010): 65. https://doi.org/10.3410/b2-65.
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  - Moreno Risueno, M. A., J. M. Van Norman, A. Moreno, J. Zhang, S. E. Ahnert, and P. N. Benfey. “Oscillating gene expression determines competence for periodic Arabidopsis root branching.” Science (New York, N.Y.) 329, no. 5997 (September 2010): 1306–11. https://doi.org/10.1126/science.1191937.
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  - International Arabidopsis Informatics Consortium, A. “An international bioinformatics infrastructure to underpin the Arabidopsis community.” The Plant Cell 22, no. 8 (August 31, 2010): 2530–36. https://doi.org/10.1105/tpc.110.078519.
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  - Long, Terri A., Hironaka Tsukagoshi, Wolfgang Busch, Brett Lahner, David E. Salt, and Philip N. Benfey. “The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots.” The Plant Cell 22, no. 7 (July 30, 2010): 2219–36. https://doi.org/10.1105/tpc.110.074096.
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  - Sozzani, R., H. Cui, M. A. Moreno-Risueno, W. Busch, J. M. Van Norman, T. Vernoux, S. M. Brady, W. Dewitte, J. A. H. Murray, and P. N. Benfey. “Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth.” Nature 466, no. 7302 (July 2010): 128–32. https://doi.org/10.1038/nature09143.
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  - Orlando, David A., Siobhan M. Brady, Thomas M. A. Fink, Philip N. Benfey, and Sebastian E. Ahnert. “Detecting separate time scales in genetic expression data.” Bmc Genomics 11 (June 16, 2010): 381. https://doi.org/10.1186/1471-2164-11-381.
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  - Carlsbecker, A., J. Y. Lee, C. J. Roberts, J. Dettmer, S. Lehesranta, J. Zhou, O. Lindgren, et al. “Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate.” Nature 465, no. 7296 (May 2010): 316–21. https://doi.org/10.1038/nature08977.
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  - Busch, Wolfgang, and Philip N. Benfey. “Information processing without brains--the power of intercellular regulators in plants.” Development (Cambridge, England) 137, no. 8 (April 2010): 1215–26. https://doi.org/10.1242/dev.034868.
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  - Moreno-Risueno, Miguel A., Wolfgang Busch, and Philip N. Benfey. “Omics meet networks - using systems approaches to infer regulatory networks in plants.” Current Opinion in Plant Biology 13, no. 2 (April 2010): 126–31. https://doi.org/10.1016/j.pbi.2009.11.005.
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  - Benfey, Philip N., Malcolm Bennett, and John Schiefelbein. “Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research.” The Plant Journal : For Cell and Molecular Biology 61, no. 6 (March 2010): 992–1000. https://doi.org/10.1111/j.1365-313x.2010.04129.x.
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  - Iyer-Pascuzzi, Anjali S., Olga Symonova, Yuriy Mileyko, Yueling Hao, Heather Belcher, John Harer, Joshua S. Weitz, and Philip N. Benfey. “Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems.” Plant Physiology 152, no. 3 (March 2010): 1148–57. https://doi.org/10.1104/pp.109.150748.
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  - De Smet, Ive, Steffen Lau, Ute Voss, Steffen Vanneste, René Benjamins, Eike H. Rademacher, Alexandra Schlereth, et al. “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): 2705–10. https://doi.org/10.1073/pnas.0915001107.
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  - Iyer-Pascuzzi, Anjali S., and Philip N. Benfey. “Fluorescence-activated cell sorting in plant developmental biology.” Methods in Molecular Biology (Clifton, N.J.) 655 (January 2010): 313–19. https://doi.org/10.1007/978-1-60761-765-5_21.
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  - Petricka, Jalean J., Jaimie M. Van Norman, and Philip N. Benfey. “Symmetry breaking in plants: molecular mechanisms regulating asymmetric cell divisions in Arabidopsis.” Cold Spring Harbor Perspectives in Biology 1, no. 5 (November 2009): a000497. https://doi.org/10.1101/cshperspect.a000497.
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  - Van Norman, Jaimie M., and Philip N. Benfey. “Arabidopsis thaliana as a model organism in systems biology.” Wiley Interdisciplinary Reviews. Systems Biology and Medicine 1, no. 3 (November 2009): 372–79. https://doi.org/10.1002/wsbm.25.
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  - Cartwright, Dustin A., Siobhan M. Brady, David A. Orlando, Bernd Sturmfels, and Philip N. Benfey. “Reconstructing spatiotemporal gene expression data from partial observations.” Bioinformatics (Oxford, England) 25, no. 19 (October 2009): 2581–87. https://doi.org/10.1093/bioinformatics/btp437.
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  - Benfey, Philip N., and Kenneth D. Birnbaum. “Primer and interviews: Gene regulation in Arabidopsis thaliana. Interview by Julie C. Kiefer.” Developmental Dynamics : An Official Publication of the American Association of Anatomists 238, no. 9 (September 2009): 2449–58. https://doi.org/10.1002/dvdy.22042.
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  - Tromas, A., N. Braun, P. Muller, T. Khodus, I. A. Paponov, K. Palme, K. Ljung, et al. “The AUXIN BINDING PROTEIN 1 is required for differential auxin responses mediating root growth.” Plos One 4, no. 9 (September 2009): e6648. https://doi.org/10.1371/journal.pone.0006648.
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  - Benfey, Philip N., Hongchang Cui, Richard Twigg, Terri Long, Anjali Iyer-Pascuzzi, Hironaka Tsukagoshi, Rosangela Sozzani, Terry Jackson, Jaimie Van Norman, and Miguel Moreno-Risueno. “Development rooted in interwoven networks.” Developmental Biology 331, no. 2 (July 2009): 386–386. https://doi.org/10.1016/j.ydbio.2009.05.012.
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  - Petersson, Sara V., Annika I. Johansson, Mariusz Kowalczyk, Alexander Makoveychuk, Jean Y. Wang, Thomas Moritz, Markus Grebe, Philip N. Benfey, Göran Sandberg, and Karin Ljung. “An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis.” The Plant Cell 21, no. 6 (June 2, 2009): 1659–68. https://doi.org/10.1105/tpc.109.066480.
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  - Cui, Hongchang, and Philip N. Benfey. “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): 1016–27. https://doi.org/10.1111/j.1365-313x.2009.03839.x.
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  - Iyer-Pascuzzi, Anjali S., and Philip N. Benfey. “Transcriptional networks in root cell fate specification.” Biochimica Et Biophysica Acta 1789, no. 4 (April 2009): 315–25. https://doi.org/10.1016/j.bbagrm.2008.09.006.
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  - Iyer-Pascuzzi, Anjali, June Simpson, Luis Herrera-Estrella, and Philip N. Benfey. “Functional genomics of root growth and development in Arabidopsis.” Current Opinion in Plant Biology 12, no. 2 (April 2009): 165–71. https://doi.org/10.1016/j.pbi.2008.11.002.
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  - Gallagher, Kimberly L., and Philip N. Benfey. “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): 785–97. https://doi.org/10.1111/j.1365-313x.2008.03735.x.
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  - Cui, H., and P. N. Benfey. “Cortex proliferation: Simple phenotype, complex regulatory mechanisms.” Plant Signaling and Behavior 4, no. 6 (2009): 551–53. https://doi.org/10.4161/psb.4.6.8731.
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  - Orlando, David A., Siobhan M. Brady, Jeremy D. Koch, José R. Dinneny, and Philip N. Benfey. “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. https://doi.org/10.1007/978-1-60327-563-7_4.
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  - Chaudhuri, Bhavna, Friederike Hörmann, Sylvie Lalonde, Siobhan M. Brady, David A. Orlando, Philip Benfey, and Wolf B. Frommer. “Protonophore- and pH-insensitive glucose and sucrose accumulation detected by FRET nanosensors in Arabidopsis root tips.” The Plant Journal : For Cell and Molecular Biology 56, no. 6 (December 2008): 948–62. https://doi.org/10.1111/j.1365-313x.2008.03652.x.
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  - De Smet, Ive, Valya Vassileva, Bert De Rybel, Mitchell P. Levesque, Wim Grunewald, Daniël Van Damme, Giel Van Noorden, et al. “Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root.” Science (New York, N.Y.) 322, no. 5901 (October 2008): 594–97. https://doi.org/10.1126/science.1160158.
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  - Petricka, Jalean J., and Philip N. Benfey. “Root layers: complex regulation of developmental patterning.” Current Opinion in Genetics & Development 18, no. 4 (August 2008): 354–61. https://doi.org/10.1016/j.gde.2008.05.001.
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  - Swarup, Kamal, Eva Benková, Ranjan Swarup, Ilda Casimiro, Benjamin Péret, Yaodong Yang, Geraint Parry, et al. “The auxin influx carrier LAX3 promotes lateral root emergence.” Nature Cell Biology 10, no. 8 (August 2008): 946–54. https://doi.org/10.1038/ncb1754.
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  - Bender, Judith, Philip Benfey, Dominique Bergmann, Justin Borevitz, Gloria Coruzzi, Jeff Dangl, Caroline Dean, et al. “2020 vision for biology: the role of plants in addressing grand challenges in biology.” Molecular Plant 1, no. 4 (July 2008): 561–63. https://doi.org/10.1093/mp/ssn040.
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  - Dinneny, José R., Terri A. Long, Jean Y. Wang, Jee W. Jung, Daniel Mace, Solomon Pointer, Christa Barron, Siobhan M. Brady, John Schiefelbein, and Philip N. Benfey. “Cell identity mediates the response of Arabidopsis roots to abiotic stress.” Science (New York, N.Y.) 320, no. 5878 (May 2008): 942–45. https://doi.org/10.1126/science.1153795.
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  - Benfey, Philip N., and Thomas Mitchell-Olds. “From genotype to phenotype: systems biology meets natural variation.” Science (New York, N.Y.) 320, no. 5875 (April 2008): 495–97. https://doi.org/10.1126/science.1153716.
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  - Dinneny, José R., and Philip N. Benfey. “Plant stem cell niches: standing the test of time.” Cell 132, no. 4 (February 2008): 553–57. https://doi.org/10.1016/j.cell.2008.02.001.
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  - Colinas, Juliette, Scott C. Schmidler, Gil Bohrer, Borislav Iordanov, and Philip N. Benfey. “Intergenic and genic sequence lengths have opposite relationships with respect to gene expression.” Plos One 3, no. 11 (January 2008): e3670. https://doi.org/10.1371/journal.pone.0003670.
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  - Long, Terri A., Siobhan M. Brady, and Philip N. Benfey. “Systems approaches to identifying gene regulatory networks in plants.” Annual Review of Cell and Developmental Biology 24 (January 2008): 81–103. https://doi.org/10.1146/annurev.cellbio.24.110707.175408.
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  - Brady, Siobhan M., David A. Orlando, Ji-Young Lee, Jean Y. Wang, Jeremy Koch, José R. Dinneny, Daniel Mace, Uwe Ohler, and Philip N. Benfey. “A high-resolution root spatiotemporal map reveals dominant expression patterns.” Science 318, no. 5851 (November 2, 2007): 801–6. https://doi.org/10.1126/science.1146265.
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  - Cui, Hongchang, Mitchell P. Levesque, Teva Vernoux, Jee W. Jung, Alice J. Paquette, Kimberly L. Gallagher, Jean Y. Wang, Ikram Blilou, Ben Scheres, and Philip N. Benfey. “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): 421–25. https://doi.org/10.1126/science.1139531.
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  - Brady, Siobhan M., Shuang Song, Kanwarpal S. Dhugga, J Antoni Rafalski, and Philip N. Benfey. “Combining expression and comparative evolutionary analysis. The COBRA gene family.” Plant Physiology 143, no. 1 (January 2007): 172–87. https://doi.org/10.1104/pp.106.087262.
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  - Weitz, J. S., P. N. Benfey, and N. S. Wingreen. “Evolution, interactions, and biological networks.” Plos Biology 5, no. 1 (January 1, 2007): 0010–0012. https://doi.org/10.1371/journal.pbio.0050011.
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  - Weitz, Joshua S., Philip N. Benfey, and Ned S. Wingreen. “Evolution, interactions, and biological networks.” Plos Biology 5, no. 1 (January 2007): e11. https://doi.org/10.1371/journal.pbio.0050011.
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  - Long, Terri A., and Philip N. Benfey. “Transcription factors and hormones: new insights into plant cell differentiation.” Current Opinion in Cell Biology 18, no. 6 (December 2006): 710–14. https://doi.org/10.1016/j.ceb.2006.09.004.
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  - Brady, S. M., and P. N. Benfey. “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. https://doi.org/10.1139/B06-134.
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  - Brady, Siobhan M., Terri A. Long, and Philip N. Benfey. “Unraveling the dynamic transcriptome.” The Plant Cell 18, no. 9 (September 2006): 2101–11. https://doi.org/10.1105/tpc.105.037572.
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  - Levesque, M. P., T. Vernoux, W. Busch, H. Cui, J. Y. Wang, I. Blilou, H. Hassan, et al. “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. https://doi.org/10.1371/journal.pbio.0040249.
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  - Mace, Daniel L., Ji-Young Lee, Richard W. Twigg, Juliette Colinas, Philip N. Benfey, and Uwe Ohler. “Quantification of transcription factor expression from Arabidopsis images.” Bioinformatics 22, no. 14 (July 15, 2006): e323–31. https://doi.org/10.1093/bioinformatics/btl228.
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  - Levesque, Mitchell P., Teva Vernoux, Wolfgang Busch, Hongchang Cui, Jean Y. Wang, Ikram Blilou, Hala Hassan, et al. “Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.” Plos Biology 4, no. 5 (May 2, 2006): e143. https://doi.org/10.1371/journal.pbio.0040143.
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  - Brady, S. M., and P. N. Benfey. “A systems approach to understanding root development.” Canadian Journal of Botany 84, no. 5 (May 1, 2006): 695–701. https://doi.org/10.1139/B06-028.
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  - Lee, Ji-Young, Juliette Colinas, Jean Y. Wang, Daniel Mace, Uwe Ohler, and Philip N. Benfey. “Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots.” Proc Natl Acad Sci U S A 103, no. 15 (April 11, 2006): 6055–60. https://doi.org/10.1073/pnas.0510607103.
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  - Friml, Jirí, Philip Benfey, Eva Benková, Malcolm Bennett, Thomas Berleth, Niko Geldner, Markus Grebe, et al. “Apical-basal polarity: why plant cells don't stand on their heads.” Trends in Plant Science 11, no. 1 (January 2006): 12–14. https://doi.org/10.1016/j.tplants.2005.11.010.
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  - Levesque, M. P., T. Vernoux, W. Busch, H. Cui, J. Y. Wang, I. Blilou, H. Hassan, et al. “Whole-genome analysis of the short-root developmental pathway in Arabidopsis.” Plos Biology 4, no. 5 (January 1, 2006): 739–52. https://doi.org/10.1371/journal.pbio.0040143.
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  - Dinneny, José R., and Philip N. Benfey. “Stem cell research goes underground: the RETINOBLASTOMA-RELATED gene in root development.” Cell 123, no. 7 (December 2005): 1180–82. https://doi.org/10.1016/j.cell.2005.12.005.
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  - Lim, Jun, Jee W. Jung, Chae Eun Lim, Mi-Hyun Lee, Bong Jun Kim, Miran Kim, Wesley B. Bruce, and Philip N. Benfey. “Conservation and diversification of SCARECROW in maize.” Plant Molecular Biology 59, no. 4 (November 2005): 619–30. https://doi.org/10.1007/s11103-005-0578-y.
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  - Birnbaum, Kenneth, Jee W. Jung, Jean Y. Wang, Georgina M. Lambert, John A. Hirst, David W. Galbraith, and Philip N. Benfey. “Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines.” Nature Methods 2, no. 8 (August 2005): 615–19. https://doi.org/10.1038/nmeth0805-615.
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  - Vernoux, Teva, and Philip N. Benfey. “Signals that regulate stem cell activity during plant development.” Current Opinion in Genetics & Development 15, no. 4 (August 2005): 388–94. https://doi.org/10.1016/j.gde.2005.06.008.
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  - Nawy, T., J. Y. Lee, J. Colinas, J. Y. Wang, S. C. Thongrod, J. E. Malamy, K. Birnbaum, and P. N. Benfey. “Transcriptional profile of the Arabidopsis root quiescent center.” Plant Cell 17, no. 7 (July 2005): 1908–25. https://doi.org/10.1105/tpc.105.031724.
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  - Benfey, Philip N. “Developmental networks.” Plant Physiology 138, no. 2 (June 2005): 548–49. https://doi.org/10.1104/pp.104.900149.
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  - Lee, J. Y., M. Levesque, and P. N. Benfey. “High-throughput RNA isolation technologies. New tools for high-resolution gene expression profiling in plant systems.” Plant Physiol 138, no. 2 (June 2005): 585–90. https://doi.org/10.1104/pp.105.061812.
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  - Paquette, Alice J., and Philip N. Benfey. “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): 636–40. https://doi.org/10.1104/pp.104.058362.
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  - Roudier, François, Anita G. Fernandez, Miki Fujita, Regina Himmelspach, Georg H. H. Borner, Gary Schindelman, Shuang Song, et al. “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): 1749–63. https://doi.org/10.1105/tpc.105.031732.
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  - Gallagher, Kimberly L., and Philip N. Benfey. “Not just another hole in the wall: understanding intercellular protein trafficking.” Genes & Development 19, no. 2 (January 2005): 189–95. https://doi.org/10.1101/gad.1271005.
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  - Birnbaum, Kenneth, and Philip N. Benfey. “Network building: transcriptional circuits in the root.” Current Opinion in Plant Biology 7, no. 5 (October 2004): 582–88. https://doi.org/10.1016/j.pbi.2004.07.010.
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  - Gallagher, Kimberly L., Alice J. Paquette, Keiji Nakajima, and Philip N. Benfey. “Mechanisms regulating SHORT-ROOT intercellular movement.” Current Biology : Cb 14, no. 20 (October 2004): 1847–51. https://doi.org/10.1016/j.cub.2004.09.081.
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  - Benfey, Philip N. “Development and ecology in the time of systems biology.” Developmental Cell 7, no. 3 (September 2004): 329–30. https://doi.org/10.1016/j.devcel.2004.08.012.
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  - Irish, Vivian F., and Philip N. Benfey. “Beyond Arabidopsis. Translational biology meets evolutionary developmental biology.” Plant Physiology 135, no. 2 (June 2004): 611–14. https://doi.org/10.1104/pp.104.041632.
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  - Sena, Giovanni, Jee W. Jung, and Philip N. Benfey. “A broad competence to respond to SHORT ROOT revealed by tissue-specific ectopic expression.” Development (Cambridge, England) 131, no. 12 (June 2004): 2817–26. https://doi.org/10.1242/dev.01144.
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  - Levesque, Mitchell P., and Philip N. Benfey. “Systems biology.” Current Biology : Cb 14, no. 5 (March 2004): R179–80. https://doi.org/10.1016/j.cub.2004.02.012.
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  - Benfey, Philip N. “A common switch used by plants and animals.” Cell 116, no. 1 (January 2004): 4–5. https://doi.org/10.1016/s0092-8674(03)01069-9.
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  - Irish, V., and P. Benfey. “Growth and development: Something old, something new....” Current Opinion in Plant Biology 7, no. 1 (January 1, 2004): 1–3. https://doi.org/10.1016/j.pbi.2003.11.012.
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  - Birnbaum, Kenneth, Dennis E. Shasha, Jean Y. Wang, Jee W. Jung, Georgina M. Lambert, David W. Galbraith, and Philip N. Benfey. “A gene expression map of the Arabidopsis root.” Science (New York, N.Y.) 302, no. 5652 (December 2003): 1956–60. https://doi.org/10.1126/science.1090022.
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  - Birnbaum, Kenneth, Rob Desalle, Charles M. Peters, and Philip N. Benfey. “Integrating gene flow, crop biology, and farm management in on-farm conservation of avocado (Persea americana, Lauraceae).” American Journal of Botany 90, no. 11 (November 2003): 1619–27. https://doi.org/10.3732/ajb.90.11.1619.
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  - Benfey, Philip N. “Molecular biology: microRNA is here to stay.” Nature 425, no. 6955 (September 2003): 244–45. https://doi.org/10.1038/425244a.
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  - Levesque, Mitchell, Dennis Shasha, Wook Kim, Michael G. Surette, and Philip N. Benfey. “Trait-to-gene: a computational method for predicting the function of uncharacterized genes.” Current Biology : Cb 13, no. 2 (January 2003): 129–33. https://doi.org/10.1016/s0960-9822(03)00009-5.
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  - Brenner, Eric D., Dennis W. Stevenson, Richard W. McCombie, Manpreet S. Katari, Stephen A. Rudd, Klaus F. X. Mayer, Peter M. Palenchar, et al. “Expressed sequence tag analysis in Cycas, the most primitive living seed plant.” Genome Biology 4, no. 12 (January 2003): R78. https://doi.org/10.1186/gb-2003-4-12-r78.
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  - Birnbaum, K., P. N. Benfey, C. M. Peters, and R. Desalle. “MANAGEDPOP: A computer simulation to project allelic diversity in managed populations with overlapping generations.” Molecular Ecology Notes 2, no. 4 (December 1, 2002): 615–17. https://doi.org/10.1046/j.1471-8286.2002.00284.x.
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  - Roudier, François, Gary Schindelman, Rob DeSalle, and Philip N. Benfey. “The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion.” Plant Physiology 130, no. 2 (October 2002): 538–48. https://doi.org/10.1104/pp.007468.
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  - Müller, Sabine, Esther Fuchs, Miroslav Ovecka, Joanna Wysocka-Diller, Philip N. Benfey, and Marie-Theres Hauser. “Two new loci, PLEIADE and HYADE, implicate organ-specific regulation of cytokinesis in Arabidopsis.” Plant Physiology 130, no. 1 (September 2002): 312–24. https://doi.org/10.1104/pp.004416.
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  - Colinas, J., K. Birnbaum, and P. N. Benfey. “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.
  - Colinas, J., K. Birnbaum, and P. N. Benfey. “Using cauliflower to find conserved non-coding regions in arabidopsis (vol 129, pg 451, 2002).” Plant Physiology 129, no. 4 (August 1, 2002): 1929–1929.
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  - Ausubel, Fred, and Philip Benfey. “Arabidopsis functional genomics.” Plant Physiology 129, no. 2 (June 2002): 393. https://doi.org/10.1104/pp.900036.
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  - Benfey, Philip N. “Auxin action: slogging out of the swamp.” Current Biology : Cb 12, no. 11 (June 2002): R389–90. https://doi.org/10.1016/s0960-9822(02)00881-3.
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  - Colinas, Juliette, Kenneth Birnbaum, and Philip N. Benfey. “Using cauliflower to find conserved non-coding regions in Arabidopsis.” Plant Physiology 129, no. 2 (June 2002): 451–54. https://doi.org/10.1104/pp.002501.
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  - Scheres, Ben, Philip Benfey, and Liam Dolan. “Root development.” The Arabidopsis Book 1 (January 2002): e0101. https://doi.org/10.1199/tab.0101.
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  - Nakajima, Keiji, and Philip N. Benfey. “Signaling in and out: control of cell division and differentiation in the shoot and root.” The Plant Cell 14 Suppl (January 2002): S265–76. https://doi.org/10.1105/tpc.010471.
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  - Nawy, T., and P. Benfey. “Signaling the tips: regulation of stem cell function in plants.” Differentiation; Research in Biological Diversity 68, no. 4–5 (October 2001): 155–58. https://doi.org/10.1046/j.1432-0436.2001.680402.x.
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  - Birnbaum, K., P. N. Benfey, and D. E. Shasha. “cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships.” Genome Research 11, no. 9 (September 2001): 1567–73. https://doi.org/10.1101/gr.158301.
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  - Nakajima, K., G. Sena, T. Nawy, and P. N. Benfey. “Intercellular movement of the putative transcription factor SHR in root patterning.” Nature 413, no. 6853 (September 2001): 307–11. https://doi.org/10.1038/35095061.
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  - Paquette, A. J., and P. N. Benfey. “Axis formation and polarity in plants.” Current Opinion in Genetics & Development 11, no. 4 (August 2001): 405–9. https://doi.org/10.1016/s0959-437x(00)00210-0.
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  - Schindelman, G., A. Morikami, J. Jung, T. I. Baskin, N. C. Carpita, P. Derbyshire, M. C. McCann, and P. N. Benfey. “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): 1115–27. https://doi.org/10.1101/gad.879101.
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  - Benfey, P. N., and D. Weigel. “Transcriptional networks controlling plant development.” Plant Physiology 125, no. 1 (January 2001): 109–11. https://doi.org/10.1104/pp.125.1.109.
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  - Mähönen, A. P., M. Bonke, L. Kauppinen, M. Riikonen, P. N. Benfey, and Y. Helariutta. “A novel two-component hybrid molecule regulates vascular morphogenesis of the Arabidopsis root.” Genes & Development 14, no. 23 (December 2000): 2938–43. https://doi.org/10.1101/gad.189200.
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  - Benfey, P. N., and B. Scheres. “Root development.” Current Biology : Cb 10, no. 22 (November 2000): R813–15. https://doi.org/10.1016/s0960-9822(00)00814-9.
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  - Lim, J., Y. Helariutta, C. D. Specht, J. Jung, L. Sims, W. B. Bruce, S. Diehn, and P. N. Benfey. “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): 1307–18. https://doi.org/10.1105/tpc.12.8.1307.
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  - Helariutta, Y., H. Fukaki, J. Wysocka-Diller, K. Nakajima, J. Jung, G. Sena, M. T. Hauser, and P. N. Benfey. “The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling.” Cell 101, no. 5 (May 2000): 555–67. https://doi.org/10.1016/s0092-8674(00)80865-x.
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  - Wysocka-Diller, J. W., Y. Helariutta, H. Fukaki, J. E. Malamy, and P. N. Benfey. “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. https://doi.org/10.1242/dev.127.3.595.
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  - Sabatini, S., D. Beis, H. Wolkenfelt, J. Murfett, T. Guilfoyle, J. Malamy, P. Benfey, et al. “An auxin-dependent distal organizer of pattern and polarity in the Arabidopsis root.” Cell 99, no. 5 (November 1999): 463–72. https://doi.org/10.1016/s0092-8674(00)81535-4.
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  - Scheres, Ben, and Philip N. Benfey. “ASYMMETRIC CELL DIVISION IN PLANTS.” Annual Review of Plant Physiology and Plant Molecular Biology 50 (June 1999): 505–37. https://doi.org/10.1146/annurev.arplant.50.1.505.
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  - Pysh, L. D., J. W. Wysocka-Diller, C. Camilleri, D. Bouchez, and P. N. Benfey. “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 18, no. 1 (April 1999): 111–19. https://doi.org/10.1046/j.1365-313x.1999.00431.x.
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  - Benfey, P. N. “Stem cells: A tale of two kingdoms.” Current Biology : Cb 9, no. 5 (March 1999): R171–72. https://doi.org/10.1016/s0960-9822(99)80105-5.
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  - Benfey, P. N. “Is the shoot a root with a view?” Current Opinion in Plant Biology 2, no. 1 (February 1999): 39–43. https://doi.org/10.1016/s1369-5266(99)80008-9.
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  - Fukaki, H., J. Wysocka-Diller, T. Kato, H. Fujisawa, P. N. Benfey, and M. Tasaka. “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): 425–30. https://doi.org/10.1046/j.1365-313x.1998.00137.x.
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  - Wysocka-Diller, J. W., and P. N. Benfey. “Root development: signaling down and around.” Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology 19, no. 11 (November 1997): 959–65. https://doi.org/10.1002/bies.950191105.
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  - Malamy, J. E., and P. N. Benfey. “Analysis of SCARECROW expression using a rapid system for assessing transgene expression in Arabidopsis roots.” The Plant Journal : For Cell and Molecular Biology 12, no. 4 (October 1997): 957–63. https://doi.org/10.1046/j.1365-313x.1997.12040957.x.
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  - Malamy, J. E., and P. N. Benfey. “Down and out in Arabidopsis: The formation of lateral roots.” Trends in Plant Science 2, no. 10 (October 1997): 390–96. https://doi.org/10.1016/S1360-1385(97)90054-6.
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  - Malamy, J. E., and P. N. Benfey. “Down and out in arabidopsis: The formation of lateral roots.” Trends in Plant Science 2, no. 10 (January 1, 1997): 390–96. https://doi.org/10.1016/S1360-1385(97)01118-7.
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  - Malamy, J. E., and P. N. Benfey. “Organization and cell differentiation in lateral roots of Arabidopsis thaliana.” Development (Cambridge, England) 124, no. 1 (January 1997): 33–44. https://doi.org/10.1242/dev.124.1.33.
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  - Di Laurenzio, L., J. Wysocka-Diller, J. E. Malamy, L. Pysh, Y. Helariutta, G. Freshour, M. G. Hahn, K. A. Feldmann, and P. N. Benfey. “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): 423–33. https://doi.org/10.1016/s0092-8674(00)80115-4.
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  - Hauser, M. T., A. Morikami, and P. N. Benfey. “Conditional root expansion mutants of Arabidopsis.” Development (Cambridge, England) 121, no. 4 (April 1995): 1237–52. https://doi.org/10.1242/dev.121.4.1237.
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  - Aeschbacher, R. A., M. T. Hauser, K. A. Feldmann, and P. N. Benfey. “The SABRE gene is required for normal cell expansion in Arabidopsis.” Genes & Development 9, no. 3 (February 1995): 330–40. https://doi.org/10.1101/gad.9.3.330.
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  - Scheres, B., L. Di Laurenzio, V. Willemsen, M. T. Hauser, K. Janmaat, P. Weisbeek, and P. N. Benfey. “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.
  - Benfey, P. N., and J. W. Schiefelbein. “Getting to the root of plant development: the genetics of Arabidopsis root formation.” Trends in Genetics : Tig 10, no. 3 (March 1994): 84–88. https://doi.org/10.1016/0168-9525(94)90230-5.
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  - Aeschbacher, R. A., J. W. Schiefelbein, and P. N. Benfrey. “The genetic and molecular basis of root development.” Annu.Rev.Plant Physiol.Plant Mol.Biol. 45 (January 1, 1994): 25–45. https://doi.org/10.1146/annurev.pp.45.060194.000325.
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  - BENFEY, P. N., and J. W. SCHIEFELBEIN. “Insights into root development from Arabidopsis root mutants.” Plant, Cell &Amp; Environment 17, no. 5 (January 1, 1994): 675–80. https://doi.org/10.1111/j.1365-3040.1994.tb00159.x.
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  - Benfey, P. N., P. J. Linstead, K. Roberts, J. W. Schiefelbein, M. T. Hauser, and R. A. Aeschbacher. “Root development in Arabidopsis: four mutants with dramatically altered root morphogenesis.” Development (Cambridge, England) 119, no. 1 (September 1993): 57–70. https://doi.org/10.1242/dev.119.supplement.57.
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  - Schiefelbein, J. W., and P. N. Benfey. “International Symposium on the Molecular Genetics of Root Development.” Plant Molecular Biology Reporter 11, no. 1 (March 1, 1993): 60–64. https://doi.org/10.1007/BF02670561.
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  - Benfey, P. “Wolfgang Barz [formula omitted] Coństitutive and Elicitation Induced Metabolism of Isoflavones and Pterocarpans in Chickpea (Cicer arietinum) Cell Suspension Cultures.” Nippon Nogeikagaku Kaishi 67, no. 12 (January 1, 1993): 1784–85. https://doi.org/10.1271/nogeikagaku1924.67.1784.
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  - Aeschbacher, R. A., and P. N. Benfey. “Genes that regulate plant development.” Plant Science 83, no. 2 (January 1, 1992): 115–26. https://doi.org/10.1016/0168-9452(92)90069-X.
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  - Takatsuji, H., M. Mori, P. N. Benfey, L. Ren, and N. H. Chua. “Characterization of a zinc finger DNA-binding protein expressed specifically in Petunia petals and seedlings.” The Embo Journal 11, no. 1 (January 1992): 241–49. https://doi.org/10.1002/j.1460-2075.1992.tb05047.x.
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  - Schiefelbein, J. W., and P. N. Benfey. “The development of plant roots: new approaches to underground problems.” The Plant Cell 3, no. 11 (November 1991): 1147–54. https://doi.org/10.1105/tpc.3.11.1147.
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  - Benfey, P. N., and N. H. Chua. “The Cauliflower Mosaic Virus 35S Promoter: Combinatorial Regulation of Transcription in Plants.” Science (New York, N.Y.) 250, no. 4983 (November 1990): 959–66. https://doi.org/10.1126/science.250.4983.959.
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  - Benfey, P. N., H. Takatsuji, L. Ren, D. M. Shah, and N. H. Chua. “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): 849–56. https://doi.org/10.1105/tpc.2.9.849.
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  - Benfey, P. N., L. Ren, and N. H. Chua. “Tissue-specific expression from CaMV 35S enhancer subdomains in early stages of plant development.” The Embo Journal 9, no. 6 (June 1990): 1677–84. https://doi.org/10.1002/j.1460-2075.1990.tb08291.x.
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  - Benfey, P. N., L. Ren, and N. H. Chua. “Combinatorial and synergistic properties of CaMV 35S enhancer subdomains.” The Embo Journal 9, no. 6 (June 1990): 1685–96. https://doi.org/10.1002/j.1460-2075.1990.tb08292.x.
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  - Lam, E., P. N. Benfey, P. M. Gilmartin, R. X. Fang, and N. H. Chua. “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 86, no. 20 (October 1989): 7890–94. https://doi.org/10.1073/pnas.86.20.7890.
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  - Benfey, P. N., L. Ren, and N. H. Chua. “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. https://doi.org/10.1002/j.1460-2075.1989.tb08342.x.
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  - Benfey, P. N., and N. H. Chua. “Regulated genes in transgenic plants.” Science (New York, N.Y.) 244, no. 4901 (April 1989): 174–81. https://doi.org/10.1126/science.244.4901.174.
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  - Sarid, J., P. N. Benfey, and P. Leder. “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 264, no. 2 (January 1989): 1022–26. https://doi.org/10.1016/s0021-9258(19)85047-0.
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  - Shimizu, A., I. Tepler, P. N. Benfey, E. H. Berenstein, R. P. Siraganian, and P. Leder. “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 85, no. 6 (March 1988): 1907–11. https://doi.org/10.1073/pnas.85.6.1907.
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  - Benfey, P. N., F. H. Yin, and P. Leder. “Cloning of the mast cell protease, RMCP II. Evidence for cell-specific expression and a multi-gene family.” The Journal of Biological Chemistry 262, no. 11 (April 1987): 5377–84. https://doi.org/10.1016/s0021-9258(18)61198-6.
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- Book Sections
  - Sparks, E. E., and P. N. Benfey. “The contribution of root systems to plant nutrient acquisition.” In Plant Macronutrient Use Efficiency: Molecular and Genomic Perspectives in Crop Plants, 83–92, 2017. https://doi.org/10.1016/B978-0-12-811308-0.00005-3.
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  - To, J. P. C., P. N. Benfey, and T. D. Elich. “Root-associated stress response networks.” In Plant Abiotic Stress, Second Edition, 69–107, 2014. https://doi.org/10.1002/9781118764374.ch4.
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  - Sparks, E. E., A. Imai, M. Hasebe, and P. N. Benfey. “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, 403–32, 2014. https://doi.org/10.1201/b16487.
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  - Benfey, P. N. “Plant Development, Genetics of.” In Brenner’s Encyclopedia of Genetics: Second Edition, 340–42, 2013. https://doi.org/10.1016/B978-0-12-374984-0.01167-0.
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  - Van Norman, J. M., L. M. Liberman, and P. N. Benfey. “Arabidopsis root: A model organ in plant genomics.” In Plant Roots: The Hidden Half, Fourth Edition, 17–34, 2013.
  - Tromas, A., N. Braun, P. Muller, T. Khodus, I. A. Paponov, K. Palme, K. Ljung, et al. “Auxin binding protein 1 for root growth.” In Plant Physiology, 214–29, 2011.
  - Dinneny, J. R., and P. N. Benfey. “Studying Root Development Using a Genomic Approach.” In Root Development, 37:325–51, 2009. https://doi.org/10.1002/9781444310023.ch12.
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  - Brady, S. M., and P. N. Benfey. “Development and Systems Biology: Riding the Genomics Wave towards a Systems Understanding of Root Development.” In Annual Plant Reviews, 35:304–30, 2009. https://doi.org/10.1002/9781444312249.ch11.
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- Conference Papers
  - Mccaskey, E. N., K. Lehner, I. Taylor, P. N. Benfey, and D. I. Goldman. “Rice Root Tip Circumnutation Facilitates Exploratory Behavior.” In Integrative and Comparative Biology, 60:E156–E156, 2020.
    Link to Item
  - Mccaskey, E. N., K. Lehner, M. Murray-Cooper, Y. Ozkan-Aydin, E. W. Hawkes, P. N. Benfey, and D. Goldman. “Circumnutation Facilitates Effective Root-Surface Exploration of Rice Roots.” In Integrative and Comparative Biology, 59:E151–E151. OXFORD UNIV PRESS INC, 2019.
    Link to Item
  - Benfey, Philip N. “Underground Signaling Networks.” In Mechanisms of Development, 145:S12–S12. Elsevier BV, 2017. https://doi.org/10.1016/j.mod.2017.04.556.
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  - Benfey, Philip N. “Underground Signaling Networks.” In In Vitro Cellular & Developmental Biology Animal, 53:S22–S22. SPRINGER, 2017.
    Link to Item
  - Tsukagoshi, Hironaka, Kaho Mabuchi, Takamasa Suzuki, Mika Nomoto, Wolfgang Busch, Yasuomi Tada, Tetsuya Higashiyama, and Philip N. Benfey. “The regulation mechanism of root development by ROS.” In Genes & Genetic Systems, 89:295–295. GENETICS SOC JAPAN, 2014.
    Link to Item
  - Cederholm, Heidi, and Philip Benfey. “Transcriptional Networks of Phosphate Acquisition.” In In Vitro Cellular & Developmental Biology Animal, 46:S103–S103, 2010.
    Link to Item
  - Benfey, Philip N., Ji-Young Lee, Juliette Colinas, Hongchang Cui, Richard Twigg, Terri Long, and I. Dinneny. “A systems biology approach to root development.” In Developmental Biology, 295:345–345. Elsevier BV, 2006. https://doi.org/10.1016/j.ydbio.2006.04.066.
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  - Lee, J., J. Colinas, J. Wang, S. Brady, D. Mace, U. Ohler, and P. Benfey. “Genome to network: An integrative approach to understanding gene regulatory networks in Arabidopsis roots.” In Comparative Biochemistry and Physiology a Molecular & Integrative Physiology, 143:S138–S138. ELSEVIER SCIENCE INC, 2006.
    Link to Item
  - Galbraith, D. W., K. D. Birnbaum, P. Benfey, G. M. Lambert, D. E. Shasha, J. Wang, and J. Jung. “A high resolution gene expression map of the arabidopsis root.” In Cytometry Part A, 59A:90–90. WILEY-LISS, 2004.
    Link to Item
  - Benfey, P. N., K. Birnbaum, and D. Shasha. “Transcriptional networks in root development.” In In Vitro Cellular & Developmental Biology Animal, 40:20A-20A. SPRINGER, 2004.
    Link to Item
  - Ogawa, M., A. Kuwahara, A. J. Paquette, P. N. Benfey, Y. Kamiya, and S. Yamaguchi. “Roles of the gibberellin-responsive SCL3 gene in Arabidopsis.” In Plant and Cell Physiology, 45:S213–S213. OXFORD UNIV PRESS, 2004.
    Link to Item
  - Benfey, P. N., K. Gallagher, A. Paquette, K. Nakajima, and G. Sena. “Radial patterning in arabidopsis: A moving target.” In Developmental Biology, 259:523–523. ACADEMIC PRESS INC ELSEVIER SCIENCE, 2003.
    Link to Item
  - Gallagher, K., A. Paquette, and P. Benfey. “Structure/function analysis of SHORTROOT (SHR) identifies a domain required for SHR movement.” In Developmental Biology, 259:573–573, 2003.
    Link to Item
  - Matsumoto, N., J. Colinas, and P. Benfey. “Promoter analyses of SHORTROOT (SHR) and SCARECROW (SCR).” In Developmental Biology, 259:474–474, 2003.
    Link to Item
  - Nawy, T., J. E. Malamy, and P. N. Benfey. “The MADS box gene AGL42 is expressed in the Arabidopsis root meristem and maintains its organization.” In Developmental Biology, 259:573–573. ACADEMIC PRESS INC ELSEVIER SCIENCE, 2003.
    Link to Item
  - Roudier, F., A. Fernandez, and P. N. Benfey. “COBRA, a GPI-Anchored membrane protein, regulates anisotropic cell expansion during Arabidopsis development.” In Developmental Biology, 259:586–586. ACADEMIC PRESS INC ELSEVIER SCIENCE, 2003.
    Link to Item
  - Sena, G., K. Nakajima, J. Jung, and P. N. Benfey. “Analysis of Arabidopsis root pattern formation: Tissue-specific ectopic expression of the "Moving" putative transcription factor short-root.” In Developmental Biology, 247:486–87. ACADEMIC PRESS INC ELSEVIER SCIENCE, 2002.
    Link to Item
  - Benfey, P. N., K. Nakajima, G. Sena, and A. Paquette. “Radial patterning in Arabidopsis: Signaling inside out.” In Developmental Biology, 235:288–288. ACADEMIC PRESS INC, 2001.
    Link to Item
  - Helariutta, Y., J. Wysocka-Diller, J. Lim, J. E. Malamy, H. Fukaki, and P. N. Benfey. “Radial pattern formation in plants.” In Developmental Biology, 210:205–205. ACADEMIC PRESS INC, 1999.
    Link to Item
  - Malamy, J. E., and P. N. Benfey. “Analysis of lateral root formation in Arabidopsis.” In Radical Biology: Advances and Perspectives on the Function of Plant Roots, edited by H. E. Flores, J. P. Lynch, and D. Eissenstat, 18:428–29. AMER SOC PLANT BIOLOGISTS, 1998.
    Link to Item
  - Pysh, L. D., and P. N. Benfey. “Root cell extension: Genetic and molecular approaches.” In Radical Biology: Advances and Perspectives on the Function of Plant Roots, edited by H. E. Flores, J. P. Lynch, and D. Eissenstat, 18:34–47. AMER SOC PLANT BIOLOGISTS, 1998.
    Link to Item
  - Schindelman, G., A. Morikami, M. T. Hauser, and P. Benfey. “Molecular genetic characterization of cobra, a cell expansion mutant of Arabidopsis thaliana.” In Radical Biology: Advances and Perspectives on the Function of Plant Roots, 18:426–27, 1998.
    Link to Item
  - Malamy, J. E., and P. N. Benfey. “Lateral root formation in Arabidopsis thaliana.” In Plant Physiology, 114:277–277. AMER SOC PLANT PHYSIOLOGISTS, 1997.
    Link to Item
  - WysockaDiller, J., J. E. Malamy, L. DiLaurenzio, L. Pysh, Y. Helariutta, and P. N. Benfey. “Root radial organization.” In Plant Physiology, 111:40001–40001. AMER SOC PLANT PHYSIOLOGISTS, 1996.
    Link to Item
  - HAUSER, M. T., and P. N. BENFEY. “GENETIC-ANALYSIS OF CELL EXPANSION IN ROOTS OF ARABIDOPSIS.” In Journal of Cellular Biochemistry, 467–467. WILEY-LISS, 1995.
    Link to Item
  - MALAMY, J. E., and P. BENFEY. “GENETIC-ANALYSIS OF LATERAL ROOT-FORMATION.” In Journal of Cellular Biochemistry, 452–452, 1995.
    Link to Item
  - LAM, E., P. BENFEY, and N. H. CHUA. “CHARACTERIZATION OF AS-1 - A FACTOR BINDING-SITE ON THE 35S PROMOTER OF CAULIFLOWER MOSAIC-VIRUS.” In Plant Gene Transfer, 129:71–79, 1990.
    Link to Item
- Datasets
  - Taylor, Isaiah, Mason Murray-Cooper, Niba Nirmal, Erin McCaskey, Philip N. Benfey, Yasemin Ozkan-Aydin, Elliot W. Hawkes, et al. “Data and scripts from: Mechanism and function of root circumnutation,” December 16, 2020. https://doi.org/10.7924/r4b27x11m.
    Data Access
- Preprints
  - Verbon, Eline, Louisa Liberman, Jiayu Zhou, Jie Yin, Corné M. J. Pieterse, Philip Benfey, Ioannis Stringlis, and Ronnie de Jonge. “Cell-type specific transcriptomics reveals roles for root hairs and endodermal barriers in interaction with beneficial rhizobacterium.” BioRxiv, May 10, 2022. https://doi.org/10.1101/2022.05.09.491085.
    Full Text
  - McCaskey, Erin, Isaiah Taylor, Christopher Pierce, Jason Ligon, Enes Aydin, Carrie Hunner, Amanda Carmichael, et al. “The rhizodynamics robot: Automated imaging system for studying long-term dynamic root growth.” BioRxiv, April 16, 2022. https://doi.org/10.1101/2022.04.15.488424.
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