Search for Benfey lab publications on Pubmed.


Shahan R+, Hsu C-W+, Nolan TM#, Cole BJ#, Taylor IW, Greenstreet L, Zhang S, Afanassiev A, Vlot AHC, Schiebinger G, Benfey PN*, Ohler U* (2022) A single cell Arabidopsis root atlas reveals developmental trajectories in wild type and cell identity mutants. Developmental Cell. 57(4): 543-560. DOI: 10.1016/j.devcel.2022.01.008


Shahan R, Nolan TM, Benfey PN. Single-cell analysis of cell identity in the Arabidopsis root apical meristem: insights and opportunities. J Exp Bot. 2021 Oct 13;  72(19):6679–6686. doi:

Tzipilevich E,  Russ D, Dangl JL, Benfey PN. Plant immune system activation is necessary for efficient root colonization by auxin-secreting beneficial bacteria. Cell Host & Microbe. 2021 Oct 4;  29(10):1507-1520. doi: 10.1016/j.chom.2021.09.005


Wachsman G, Benfey PN. Lateral Root Initiation: The Emergence of New Primordia Following Cell Death. Curr Biol. 2020 Feb 3; 30(3):R121-R122. doi: 10.1016/j.cub.2019.12.032. PMID: 32017881

Shahan R, Benfey PN. A Co-opted Regulator of Lateral Root Development Controls Nodule Organogenesis in Lotus. Dev Cell. 2020 Jan 6; 52(1):6-7. doi: 10.1016/j.devcel.2019.12.009. PMID: 31951556

Yamada M, Han X, Benfey PN. RGF1 controls root meristem size through ROS signalling. Nature. 2020 Jan; 577(7788):85-88. doi: 10.1038/s41586-019-1819-6. Epub 2019 Dec 4. PMID: 31801996

Jia KP, Dickinson AJ, Mi J, Cui G, Xiao TT, Kharbatia NM, Guo X, Sugiono E, Aranda M, Blilou I, Rueping M, Benfey PN, Al-Babili S. Anchorene is a carotenoid-derived regulatory metabolite required for anchor root formation in Arabidopsis. Sci Adv. 2019 Nov 27; 5(11)  doi: 10.1126/sciadv.aaw6787. eCollection 2019 Nov. PMID: 31807696

Zhang Y, Yang M, Duncan S, Yang X, Abdelhamid MAS, Huang L, Zhang H, Benfey PN, Waller ZAE, Ding Y. G-quadruplex structures trigger RNA phase separation. Nucleic Acids Res. 2019 Dec 16;47(22):11746-11754. doi: 10.1093/nar/gkz978. PMID:31722410

Dickinson AJ, Lehner K, Mi J, Jia KP, Mijar M, Dinneny J, Al-Babili S, Benfey PN. β-Cyclocitral is a conserved root growth regulator. Proc Natl Acad Sci U S A. 2019 May 21;116(21):10563-10567. doi: 10.1073/pnas.1821445116. Epub 2019 May 8. PMID: 31068462

Di Mambro R, Svolacchia N, Dello Ioio R, Pierdonati E, Salvi E, Pedrazzini E, Vitale A, Perilli S, Sozzani R, Benfey PN, Busch W, Costantino P, Sabatini S. The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size. Curr Biol. 2019 Apr 1;29(7):1199-1205.e4. doi: 10.1016/j.cub.2019.02.022. Epub 2019 Mar 14. PMID: 30880016

Chen WQ, Drapek C, Li DX, Xu ZH, Benfey PN, Bai SN. Histone Deacetylase HDA19 Affects Root Cortical Cell Fate by Interacting with SCARECROW. Plant Physiol. 2019 May;180(1):276-288. doi: 10.1104/pp.19.00056. Epub 2019 Feb 8. PMID: 30737268


Grondin A, Dixit S, Torres R, Venkateshwarlu C, Rogers E, Mitchell-Olds T, Benfey PN, Kumar A, Henry A. Physiological mechanisms contributing to the QTL qDTY(3.2) effects on improved performance of rice Moroberekan x Swarna BC(2)F(3:4) lines under drought. Rice (N Y). 2018 Jul 31;11(1):43. doi:
10.1186/s12284-018-0234-1. PubMed PMID: 30066052; PubMed Central PMCID:

Pierre-Jerome E, Drapek C, Benfey PN. Regulation of Division and Differentiation of Plant Stem Cells. Anna Rev Cell Dev Biol. 2018 Oct 6;34:289-310. doi: 10.1146/annurev-cellbio-100617-062459. Epub 2018 Aug 22. PubMed PMID: 30134119.

Drapek C, Sparks EE, Marhavy P, Taylor I, Andersen TG, Hennacy JH, Geldner N, Benfey PN. Minimum requirements for changing and maintaining endodermis cell identity in the Arabidopsis root. Nat Plants. 2018 Aug;4(8):586-595. doi: 10.1038/s41477-018-0213-y. Epub 2018 Jul 30. PubMed PMID: 30061749.

Shibata M, Breuer C, Kawamura A, Clark NM, Rymen B, Braidwood L, Morohashi K, Busch W, Benfey PN, Sozzani R, Sugimoto K. GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis. Development. 2018 Feb 8;145(3). pii: dev159707. doi:
10.1242/dev.159707. PubMed PMID: 29439132; PubMed Central PMCID: PMC5818008.


Wendrich JR, Möller BK, Li S, Saiga S, Sozzani R, Benfey PN, De Rybel B, Weijers D. Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem. Proc Natl Acad Sci U S A. 2017 Oct 17;114(42):E8922-E8929. doi:10.1073/pnas.1707400114. Epub 2017 Oct 2. PubMed PMID: 28973915; PubMed Central PMCID: PMC5651754.

Di Mambro R, De Ruvo M, Pacifici E, Salvi E, Sozzani R, Benfey PN, Busch W, Novak O, Ljung K, Di Paola L, Marée AFM, Costantino P, Grieneisen VA, Sabatini S. Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root. Proc Natl Acad Sci U S A. 2017 Aug 22.
pii: 201705833. doi: 10.1073/pnas.1705833114. [Epub ahead of print] PubMed PMID:

Hsu PY, Benfey PN. Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants. Proteomics. 2017 Jul 31. doi: 10.1002/pmic.201700038. [Epub ahead of print] Review. PubMed PMID: 28759167.

Drapek C, Sparks EE, Benfey PN. Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation. Trends Genet. 2017 Aug;33(8):529-539. doi: 10.1016/j.tig.2017.05.002. Epub 2017 Jun 21. Review. PubMed PMID: 28647055; PubMed Central PMCID: PMC5522350.

Wachsman G, Modliszewski JL, Valdes M, Benfey PN. A SIMPLE Pipeline for Mapping Point Mutations. Plant Physiol. 2017 Jul;174(3):1307-1313. doi: 10.1104/pp.17.00415. Epub 2017 May 25. PubMed PMID: 28546435; PubMed Central PMCID: PMC5490893.

Sparks EE, Benfey PN. Tissue-Specific Transcriptome Profiling in Arabidopsis Roots. Methods Mol Biol. 2017;1610:107-122. doi: 10.1007/978-1-4939-7003-2_8.
PubMed PMID: 28439860.

Nevarez PA, Qiu Y, Inoue H, Yoo CY, Benfey PN, Schnell DJ, Chen M. Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus. Plant Physiol. 2017 Apr;173(4):1953-1966. doi:10.1104/pp.16.00116. Epub 2017 Feb 23. PubMed PMID: 28232584; PubMed Central PMCID: PMC5373053.

Li C, Sako Y, Imai A, Nishiyama T, Thompson K, Kubo M, Hiwatashi Y, Kabeya Y,
Karlson D, Wu SH, Ishikawa M, Murata T, Benfey PN, Sato Y, Tamada Y, Hasebe M. A Lin28 homologue reprograms differentiated cells to stem cells in the moss Physcomitrella patens. Nat Commun. 2017 Jan 27;8:14242. doi: 10.1038/ncomms14242. PubMed PMID: 28128346; PubMed Central PMCID: PMC5290140.


Sparks EE, Drapek C, Gaudinier A, Li S, Ansariola M, Shen N, Hennacy JH, Zhang J, Turco G, Petricka JJ, Foret J, Hartemink AJ, Gordân R, Megraw M, Brady SM, Benfey PN. Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. Dev Cell. 2016 Dec 5. PMID:27923776

Fernández-Marcos M, Desvoyes B, Manzano C, Liberman LM, Benfey PN, Del Pozo JC, Gutierrez C.
Control of Arabidopsis lateral root primordium boundaries by MYB36. New Phytol. 2017 Jan. PMID:27891649

Li S, Yamada M, Han X, Ohler U, Benfey PN. High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. Dev Cell. 2016 Nov 21. PMID:27840108

Hsu PY, Calviello L, Wu HL, Li FW, Rothfels CJ, Ohler U, Benfey PN. Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. PNAS USA. 2016 Oct 21. PMID:27791167

Clark NM, Hinde E, Winter CM, Fisher AP, Crosti G, Blilou I, Gratton E, Benfey PN, Sozzani R. Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy. Elife. 2016 Jun 11;5. PMID:27288545

Rogers ED, Monaenkova D, Mijar M, Nori A, Goldman DI, Benfey PN. X-Ray Computed Tomography Reveals the Response of Root System Architecture to Soil Texture. Plant Physiol. 2016 Jul;171(3):2028-40. Epub 2016 May 16. PMID: 27208237

Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker JR. Unique cell-type-specific patterns of DNA methylation in the root meristem. Nat Plants. 2016 Apr 29;2(5):16058. PMID:27243651

Liberman LM, Benfey PN. A Friend in Need (of Nutrients) Is a… Cell. 2016 Apr 7;165(2):269-71. PMID:27058660

Verbon EH, Liberman LM. Beneficial Microbes Affect Endogenous Mechanisms Controlling Root Development. Trends Plant Sci. 2016 Mar;21(3):218-29. Epub 2016 Feb 11.

Benfey PN. Defining the Path from Stem Cells to Differentiated Tissue. Curr Top Dev Biol. 2016;116:35-43. Epub 2016 Feb 8. PMID:26970612

Sparks EE, Benfey PN. Identifying Gene Regulatory Networks in Arabidopsis by In Silico Prediction, Yeast-1-Hybrid, and Inducible Gene Profiling Assays. Methods Mol Biol. 2016;1370:29-50. PMID:26659952


Moreno-Risueno MA, Sozzani R, Yardımcı GG, Petricka JJ, Vernoux T, Blilou I, Alonso J, Winter CM, Ohler U, Scheres B, and Benfey PN. Transcriptional control of tissue formation throughout root development Science 23 October 2015: 426-430.

Liberman LM, Sparks EE, Moreno-Risueno MA, Petricka JJ, Benfey PN. MYB36 regulates the transition from proliferation to differentiation in the Arabidopsis root. Proc Natl Acad Sci U S A. 2015 Sep 14. pii: 201515576. [Epub ahead of print]

Jackson TL , Baker GW, Wilks FR Jr, Popov VA, Mathur J, Benfey PN. Large cellular inclusions accumulate in Arabidopsis roots exposed to low sulfur conditions. Plant Physiology June 2015 pp.00465.2015 PMID: 26099270

Wachsman G, Sparks EE, Benfey PN Genes and networks regulating root anatomy and architecture. New Phytol. 2015 May 20. doi: 10.1111/nph.13469. [Epub ahead of print]. PMID: 25989832

Cederholm HM, Benfey PN. Distinct sensitivities to phosphate deprivation suggest that RGF peptides play disparate roles in Arabidopsis thaliana root development. New Phytol. 2015 Apr 9. doi: 10.1111/nph.13405. [Epub ahead of print]. PMID: 25856240

Zurek PR, Topp CN, Benfey PN. Quantitative trait locus mapping reveals regions of the maize genome controlling root system architecture. Plant Physiol. 2015 Apr;167(4):1487-96. Epub 2015 Feb 11. PMID: 25673779


Rogers ED, Benfey PN. Regulation of plant root system architecture: implications for crop advancement. Curr Opin Biotechnol. 2014 Nov 29;32C:93-98. Epub ahead of print. Review. PMID: 25448235

Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M. Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. Plant Cell. 2014 Jul;26(7):2746-60. doi: 10.1105/tpc.114.125617. Epub 2014 Jul 17. PMID: 25035402

Van Norman JM, Zhang J, Cazzonelli CI, Pogson BJ, Harrison PJ, Bugg TD, Chan KX, Thompson AJ, Benfey PN. Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative. Proc Natl Acad Sci U S A. 2014 Mar 17. [Epub ahead of print] PMID: 24639533

Sparks EE, Benfey PN. HEC of a Job Regulating Stem Cells. Dev Cell. 2014 Feb 24 PMID: 24576420

Sozzani R, Busch W, Spalding EP, Benfey PN.Advanced imaging techniques for the study of plant growth and development. Trends Plant Sci. 2014 Jan 13. [Epub ahead of print] PMID: 24434036


Van Norman JM, Xuan W, Beeckman T, Benfey PN. To branch or not to branch: the role of pre-patterning in lateral root formation. Development. 2013 Nov. PMID:24130327

Moubayidin L, Di Mambro R, Sozzani R, Pacifici E, Salvi E, Terpstra I, Bao D, van Dijken A, Dello Ioio R, Perilli S, Ljung K, Benfey PN, Heidstra R, Costantino P, Sabatini S. Spatial coordination between stem cell activity and cell differentiation in the root meristem. Dev Cell. 2013 Aug 26 PMID:23987513

Sparks E, Wachsman G, Benfey PN. Spatiotemporal signalling in plant development. Nat Rev Genet. 2013 Aug 16. PMID: 23949543

Li S*, Liberman LM*, Mukherjee N, Benfey PN, Ohler U. Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Res. 2013 Jul 1. [Epub ahead of print] PMID: 23816784

Liberman LM, Benfey PN. Polarized radicals. Cell. Preview 2013 Apr 11. PMID: 23582319

Topp CN, Iyer-Pascuzzi AS, Anderson JT, Lee CR, Zurek PR, Symonova O, Zheng Y, Bucksch A, Mileyko Y, Galkovskyi T, Moore BT, Harer J, Edelsbrunner H, Mitchell-Olds T, Weitz JS, Benfey PN. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. Proc Natl Acad Sci U S A. 2013 Apr 30. Epub 2013 Apr 11. PMID: 23580618

Moussaieff A, Rogachev I, Brodsky L, Malitsky S, Toal TW, Belcher H, Yativ M, Brady SM, Benfey PN, Aharoni A. High-resolution metabolic mapping of cell types in plant roots. Proc Natl Acad Sci U S A. 2013 Mar 26. Epub 2013 Mar 8. PMID: 23476065

Fang S, Clark RT, Zheng Y, Iyer-Pascuzzi AS, Weitz JS, Kochian LV, Edelsbrunner H, Liao H, Benfey PN. Genotypic recognition and spatial responses by rice roots. Proc Natl Acad Sci U S A. 2013 Jan 29. [Epub ahead of print] PubMed PMID: 23362379.

Iyer-Pascuzzi AS, Zurek PR, Benfey PN. High-throughput, noninvasive imaging of root systems. Methods Mol Biol. 2013;959:177-87. doi:10.1007/978-1-62703-221-6_11. PubMed PMID: 23299675.


Benfey PN. Toward a Systems Analysis of the Root. Cold Spring Harb Symp Quant Biol. 2012 Dec 12. [Epub ahead of print] PubMed PMID: 23234807.

Busch W, Moore BT, Martsberger B, Mace DL, Twigg RW, Jung J, Pruteanu-Malinici I, Kennedy SJ, Fricke GK, Clark RL, Ohler U, Benfey PN. A microfluidic device and computational platform for high-throughput live imaging of gene expression. Nat Methods. 2012 Nov;9(11):1101-6. doi: 10.1038/nmeth.2185. Epub 2012 Sep 30. PubMed PMID: 23023597; PubMed Central PMCID: PMC3492502.

Cruz-Ramírez A, Díaz-Triviño S, Blilou I, Grieneisen VA, Sozzani R, Zamioudis C, Miskolczi P, Nieuwland J, Benjamins R, Dhonukshe P, Caballero-Pérez J, Horvath B, Long Y, Mähönen AP, Zhang H, Xu J, Murray JA, Benfey PN, Bako L, Marée AF, Scheres B. A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division. Cell. 2012 Aug 31;150(5):1002-15. doi:10.1016/j.cell.2012.07.017. Epub 2012 Aug 23. PubMed PMID: 22921914.

Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price CA, Topp CN, Iyer-Pascuzzi AS, Zurek PR, Fang S, Harer J, Benfey PN, Weitz JS. GiA Roots: software for the high throughput analysis of plant root system architecture. BMC Plant Biol. 2012 Jul 26;12:116. doi: 10.1186/1471-2229-12-116. PubMed PMID: 22834569; PubMed Central PMCID: PMC3444351.

Ingram PA, Zhu J, Shariff A, Davis IW, Benfey PN, Elich T. High-throughput imaging and analysis of root system architecture in Brachypodium distachyon under differential nutrient availability. Philos Trans R Soc Lond B Biol Sci. 2012 Jun 5;367(1595):1559-69.

Rogers ED, Jackson T, Moussaieff A, Aharoni A, Benfey PN. Cell type-specific transcriptional profiling: implications for metabolite profiling. Plant J. 2012 Apr;70(1):5-17. doi: 10.1111/j.1365-313X.2012.04888.x.

Petricka JJ, Schauer MA, Megraw M, Breakfield NW, Thompson JW, Georgiev S, Soderblom EJ, Ohler U, Moseley MA, Grossniklaus U, Benfey PN. The protein expression landscape of the Arabidopsis root. Proc Natl Acad Sci U S A. 2012 May 1;109(18):6811-8. Epub 2012 Mar 23.

Heidi M. Cederholm, Anjali S. Iyer-Pascuzzi, Philip N. Benfey. Patterning the primary root in Arabidopsis. Wiley Interdisciplinary Reviews: Developmental Biology Volume 1, Issue 5, pages 675–691, September/October 2012. Epub 2012 Mar 22.

Petricka JJ, Winter CM, Benfey PN. Control of Arabidopsis root development. Annu Rev Plant Biol. 2012 Jun 2;63:563-90. Epub 2012 Feb 9.

Moreno-Risueno MA, Van Norman JM, Benfey PN. Transcriptional switches direct plant organ formation and patterning. Curr Top Dev Biol. 2012;98:229-57. Review.

Liberman LM, Sozzani R, Benfey PN. Integrative systems biology: an attempt to describe a simple weed. Curr Opin Plant Biol. 2012 Apr;15(2):162-7. Epub 2012 Jan 23.


Iyer-Pascuzzi AS, Jackson T, Cui H, Petricka JJ, Busch W, Tsukagoshi H, Benfey PN. Cell identity regulators link development and stress responses in the Arabidopsis root. Dev Cell. 2011 Oct 18;21(4):770-82.

Breakfield NW, Corcoran DL, Petricka JJ, Shen J, Sae-Seaw J, Rubio-Somoza I, Weigel D, Ohler U, Benfey PN. High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. Genome Res. 2012 Jan;22(1):163-76. Epub 2011 Sep 22.

Moreno-Risueno MA, Benfey PN. Time-based patterning in development: The role of oscillating gene expression. Transcription. 2011 May;2(3):124-129.

Benfey PN. Taking a developmental perspective on systems biology. Dev Cell. 2011 Jul 19;21(1):27-8.

Petricka JJ, Benfey PN. Reconstructing regulatory network transitions. Trends Cell Biol. 2011 Aug;21(8):442-51. doi: 10.1016/j.tcb.2011.05.001. Epub 2011 May 31. Review.

Zhu J, Ingram PA, Benfey PN, Elich T. From lab to field, new approaches to phenotyping root system architecture. Curr Opin Plant Biol. 2011 Jun;14(3):310-7. Epub 2011 Apr 27.

Sozzani R, Benfey PN. High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype. Genome Biol. 2011;12(3):219. Epub 2011 Mar 28. Review.

Van Norman JM, Breakfield NW, Benfey PN. Intercellular communication during plant development. Plant Cell. 2011 Mar;23(3):855-64. Epub 2011 Mar 8. Review.

Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, Ahnert S, Ohler U, Ware D, Walhout AJ, Benfey PN. A stele-enriched gene regulatory network in the Arabidopsis root. Mol Syst Biol. 2011 Jan 18;7:459.


Pop A, Huttenhower C, Iyer-Pascuzzi A, Benfey PN, Troyanskaya OG. Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. BMC Syst Biol. 2010 Dec 31;4:180.

To JP, Zhu J, Benfey PN, Elich T. Optimizing root system architecture in biofuel crops for sustainable energy production and soil carbon sequestration. F1000 Biol Rep. 2010 Sep 8;2:65.

Tsukagoshi H, Busch W, Benfey PN. Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root. Cell. 2010 Nov 12;143(4):606-16

Baskin TI, Peret B, Baluska F, Benfey PN, Bennett M, Forde BG, Gilroy S, Helariutta Y, Hepler PK, Leyser O, Masson PH, Muday GK, Murphy AS, Poethig S, Rahman A, Roberts K, Scheres B, Sharp RE, Somerville C. Shootward and rootward: peak terminology for plant polarity. Trends Plant Sci. 2010 Sep 10. [Epub ahead of print]

Moreno-Risueno MA, Van Norman JM, Moreno A, Zhang J, Ahnert SE, Benfey PN. Oscillating gene expression determines competence for periodic Arabidopsis root branching. Science. 2010 Sep 10;329(5997):1306-11.

Iyer-Pascuzzi AS, Benfey PN. Fluorescence-activated cell sorting in plant developmental biology. Methods Mol Biol. 2010;655:313-9.

Long TA, Tsukagoshi H, Busch W, Lahner B, Salt DE, Benfey PN. The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots. Plant Cell. 2010 Jul;22(7):2219-36. Epub 2010 Jul 30.

Sozzani R, Cui H, Moreno-Risueno MA, Busch W, Van Norman JM, Vernoux T, Brady SM, Dewitte W, Murray JA, Benfey PN. Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature. 2010 Jul 1;466(7302):128-32.

Orlando DA, Brady SM, Fink TM, Benfey PN, Ahnert SE. Detecting separate time scales in genetic expression data. BMC Genomics. 2010 Jun 16;11:381.

Carlsbecker A, Lee JY, Roberts CJ, Dettmer J, Lehesranta S, Zhou J, Lindgren O, Moreno-Risueno MA, Vaten A, Thitamadee S, Campilho A, Sebastian J, Bowman JL, Helariutta Y, Benfey PN. Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate. Nature. 2010 May 20;465(7296):316-21. Epub 2010 Apr 21.

Benfey PN, Bennett M, Schiefelbein J. Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research. Plant J. 2010 Mar;61(6):992-1000. Review.

Busch W, Benfey PN. Information processing without brains–the power of
intercellular regulators in plants.
Development. 2010 Apr;137(8):1215-26. Review.

Van Norman JM, Benfey PN. Arabidopsis thaliana as a Model Organism in Systems Biology. Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):372-9.

De Smet I, Lau S, Voss U, Vanneste S, Benjamins R, Rademacher EH, Schlereth A, De Rybel B, Vassileva V, Grunewald W, Naudts M, Levesque MP, Ehrismann JS, Inz√© D, Luschnig C, Benfey PN, Weijers D, Van Montagu MC, Bennett MJ, Jürgens G, Beeckman T. Bimodular auxin response controls organogenesis in Arabidopsis. Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2705-10. Epub 2010 Jan 25. Abstract

Iyer-Pascuzzi AS, Symonova O, Mileyko Y, Hao Y, Belcher H, Harer J, Weitz JS, Benfey PN. Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems. Plant Physiol. 2010 Mar;152(3):1148-57. Epub 2010 Jan 27. Abstract

Petricka JJ, Van Norman JM, Benfey PN. Symmetry breaking in plants: molecular mechanisms regulating asymmetric cell divisions in Arabidopsis. Cold Spring Harb Perspect Biol. 2009 Nov;1(5):a000497. Abstract

Moreno-Risueno MA, Busch W, Benfey PN. Omics meet networks – using systems approaches to infer regulatory networks in plants. Curr Opin Plant Biol. 2010 Apr;13(2):126-31. Epub 2009 Dec 28. Review. Abstract

Cui H, Benfey PN. Cortex proliferation: simple phenotype, complex regulatory mechanisms. Plant Signal Behav. 2009 Jun;4(6):551-3. doi:
10.1111/j.1365-313X.2009.03839.x. Epub 2009 Jun 15. Abstract

Tromas A, Braun N, Muller P, Khodus T, Paponov IA, Palme K, Ljung K, Lee JY, Benfey P, Murray JA, Scheres B, Perrot-Rechenmann C. The AUXIN BINDING PROTEIN 1 is required for differential auxin responses mediating root growth. PLoS One. 2009 Sep 24;4(9):e6648. Abstract

Benfey PN, Birnbaum KD. Primer and interviews: Gene regulation in Arabidopsis thaliana. Interview by Julie C. Kiefer. Dev Dyn. 2009 Sep;238(9):2449-58.

Cartwright DA, Brady SM, Orlando DA, Sturmfels B, Benfey PN. Reconstructing
spatiotemporal gene expression data from partial observations. Bioinformatics.
2009 Oct 1;25(19):2581-7. Epub 2009 Jul 16. Abstract

Petersson SV, Johansson AI, Kowalczyk M, Makoveychuk A, Wang JY, Moritz T, Grebe M, Benfey PN, Sandberg G, Ljung K. An Auxin Gradient and Maximum in the Arabidopsis Root Apex Shown by High-Resolution Cell-Specific Analysis of IAA Distribution and Synthesis.(2009) Plant Cell. [Epub ahead of print]

Cui H, Benfey PN. Interplay between SCARECROW, GA and LIKE HETEROCHROMATIN PROTEIN 1 in ground tissue patterning in the Arabidopsis root. Plant J. 2009 Mar 20. [Epub ahead of print]

Colinas, J., Schmidler, S. C., Bohrer, G., Iordanov, B. and Benfey, P. N. (2008). Intergenic and genic sequence lengths have opposite relationships with respect to gene expression. PLoS One 3, e3670. Abstract

Iyer-Pascuzzi A, Simpson J, Herrera-Estrella L, Benfey PN. Functional genomics of Arabidopsis root functional genomics. (2008) Curr Opin Plant Biol. [Epub ahead of print]Abstract

Gallagher KL, Benfey PN. Both the conserved GRAS domain and nuclear localization are required for SHORT-ROOT movement. Plant J. 2008 Dec 4. [Epub ahead of print] Abstract

Chaudhuri B, Hörmann F, Lalonde S, Brady SM, Orlando DA, Benfey P, Frommer WB. Protonophore- and pH-insensitive glucose and sucrose accumulation detected by FRET nanosensors in Arabidopsis root tips. (2008) Plant J. 56(6):948-62. Abstract

De Smet I, Vassileva V, De Rybel B, Levesque MP, Grunewald W, Van Damme D, Van Noorden G, Naudts M, Van Isterdael G, De Clercq R, Wang JY, Meuli N, Vanneste S, Friml J, Hilson P, Jürgens G, Ingram GC, Inzé D, Benfey PN, Beeckman T. (2008) Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root. Science. 322(5901):594-7. Abstract

Iyer-Pascuzzi AS, Benfey PN. Transcriptional networks in root cell fate specification. (2008) Biochim Biophys Acta. [Epub ahead of print] Abstract

Petricka JJ, Benfey PN. Root layers: complex regulation of developmental patterning. (2008) Curr Opin Genet Dev. 18(4):354-61. Abstract

Swarup K, Benková E, Swarup R, Casimiro I, Péret B, Yang Y, Parry G, Nielsen E, De Smet I, Vanneste S, Levesque MP, Carrier D, James N, Calvo V, Ljung K, Kramer E, Roberts R, Graham N, Marillonnet S, Patel K, Jones JD, Taylor CG, Schachtman DP, May S, Sandberg G, Benfey P, Friml J, Kerr I, Beeckman T, Laplaze L, Bennett MJ. The auxin influx carrier LAX3 promotes lateral root emergence. (2008) Nat Cell Biol. 10(8):946-54. Abstract

Benfey PN, Mitchell-Olds T. From genotype to phenotype: systems biology meets natural variation. (2008) Science. 320 ( 5875 ): 495-7. Abstract available for free. Science Online Full Text.

Dinneny JR, Long TA, Wang JY, Jung JW, Mace D, Pointer S, Barron C, Brady SM, Schiefelbein J, Benfey PN. Cell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress. (2008) Science. Abstract available for free. Science Online Full Text.

Dinneny JR, Benfey PN. Plant stem cell niches: standing the test of time. (2008) Cell. 132 ( 4 ): 553-7. Abstract available for free. Cell Press Full Text.

Brady SM, Orlando DA, Lee JY, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN. A high-resolution root spatiotemporal map reveals dominant expression patterns. (2007) Science. 318 ( 5851 ): 801-6 . Abstract available for free. Science Online Full Text

Cui H, Levesque MP, Vernoux T, Jung JW, Paquette AJ, Gallagher KL, Wang JY, Blilou I, Scheres B, Benfey PN. An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. (2007) Science. 316(5823), 421-5. Abstract available for free. Science Online Full Text

Brady SM, Song S, Dhugga KS, Rafalski JA, Benfey PN. (2007) Combining expression and comparative evolutionary analysis. The COBRA gene family. Plant Physiol. 143(1), 172-87. Abstract

Weitz JS, Benfey PN, Wingreen NS. (2007) Evolution, interactions, and biological networks. PLoS Biol. 5(1), e11. Full Text

Long TA, Benfey PN. (2006) Transcription factors and hormones: new insights into plant cell differentiation. Curr Opin Cell Biol. [Epub ahead of print] Abstract

Brady SM, Long TA, Benfey PN. (2006) Unraveling the dynamic transcriptome. Plant Cell 18(9), 2101-11. Abstract

Mace DL, Lee JY, Twigg RW, Colinas J, Benfey PN, Ohler U. (2006) Quantification of transcription factor expression from Arabidopsis images. Bioinformatics. 22(14), e323-31. Abstract

Levesque MP, Vernoux T, Busch W, Cui H, Wang JY, Blilou I, Hassan H, Nakajima K, Matsumoto N, Lohmann JU, Scheres B, Benfey PN. (2006) Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol. 4(5), e143. Abstract

Lee JY, Colinas J, Wang JY, Mace D, Ohler U, Benfey PN. (2006) Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proc Natl Acad Sci U S A 103(15), 6055-60. Abstract

Friml J, Benfey P, Benkova E, Bennett M, Berleth T, Geldner N, Grebe M, Heisler M, Hejatko J, Jurgens G, Laux T, Lindsey K, Lukowitz W, Luschnig C, Offringa R, Scheres B, Swarup R, Torres-Ruiz R, Weijers D, Zazimalova E. (2006) Apical-basal polarity: why plant cells don’t stand on their heads. Trends Plant Sci. 11(1), 12-4. Abstract

Dinneny JR, Benfey PN. (2005) Stem cell research goes underground: the RETINOBLASTOMA-RELATED gene in root development. Cell 123(7), 1180-2. Abstract

Lim J, Jung JW, Lim CE, Lee MH, Kim BJ, Kim M, Bruce WB, Benfey PN. (2005) Conservation and diversification of SCARECROW in maize. Plant Mol Biol. 59(4), 619-30. Abstract

Vernoux T, Benfey PN. (2005) Signals that regulate stem cell activity during plant development. Curr Opin Genet Dev. 15(4), 388-94. Abstract

Birnbaum K, Jung JW, Wang JY, Lambert GM, Hirst JA, Galbraith DW, Benfey PN. (2005) Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nat Methods 2(8), 615-9. Abstract

Nawy T, Lee JY, Colinas J, Wang JY, Thongrod SC, Malamy JE, Birnbaum K, Benfey PN. (2005) Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell 17(7), 1908-25. Abstract

Roudier F, Fernandez AG, Fujita M, Himmelspach R, Borner GH, Schindelman G, Song S, Baskin TI, Dupree P, Wasteneys GO, Benfey PN. (2005) COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation. Plant Cell 17(6), 1749-63. Abstract

Paquette AJ, Benfey PN. (2005) Maturation of the ground tissue of the root is regulated by gibberellin and SCARECROW and requires SHORT-ROOT. Plant Physiol. 138(2), 636-40. Abstract

Lee JY, Levesque M, Benfey PN. (2005) High-throughput RNA isolation technologies. New tools for high-resolution gene expression profiling in plant systems. Plant Physiol. 138(2), 585-90. Abstract

Benfey PN. (2005) Developmental networks. Plant Physiol 138(2), 548-9. Abstract

Gallagher, K.L. and P.N. Benfey (2005) Not just another hole in the wall: understanding intercellular protein trafficking. Genes and Development 19, 189-195. Abstract

Gallagher, K.L., A.J. Paquette, K. Nakajima, and Benfey P.N. (2004) Mechanisms regulating SHORT-ROOT intercellular movement. Current Biology 14, 1847-1851. Abstract

Birnbaum, K. and P.N. Benfey (2004) Network building: transcriptional circuits in the root. Current Opinion in Plant Biology 7, 582-588. Abstract

Benfey, P.N. (2004) Development and ecology in the time of systems biology. Developmental Cell. 7, 329-330. Abstract

Sena, G., J.W. Jung, and P.N. Benfey (2004) A broad competence to respond to SHORT ROOT revealed by tissue-specific ectopic expression. Development 131, 2817-26. Abstract

Irish, V.F. and P.N. Benfey (2004) Beyond Arabidopsis. Translational biology meets evolutionary developmental biology. Plant Physiology 135, 611-614. Abstract

Levesque, M.P. and P.N. Benfey (2004) Systems biology. Current Biology 14, R179-180. Abstract

Benfey P.N. (2004) A common switch used by plants and animals. Cell 116, 4-5. Abstract

Birnbaum, K., D.E. Shasha, J.Y. Wang, J. Jung, G.M. Lambert, D.W. Galbraith, and P. N. Benfey (2003) A gene expression map of the Arabidopsis root. Science 302, 1956-60. Abstract Full Text

Levesque, M., D. Shasha, W. Kim, M. Surette, and P. Benfey (2003)
Trait-to-Gene: A computational method for inferring the function of
uncharacterized genes.
Current Biology 13, 129-133. Abstract

Roudier, F., G. Schindelman, R. DeSalle, and P.N. Benfey (2002) The
COBRA Family of Putative GPI-Anchored Proteins in Arabidopsis. A New
Fellowship in Expansion.
Plant Physiology 130, 538-548. Abstract

Colinas, J., K. Birnbaum, P.N. Benfey (2002) Using cauliflower to find
conserved non-coding regions in Arabidopsis.
Plant Physiology 129, 451-4.

Muller, S., E. Fuchs, M. Ovecka, J. Wysocka-Diller, P.N. Benfey, M.T.
Hauser (2002) Two New Loci, PLEIADE and HYADE, Implicate Organ-Specific
Regulation of Cytokinesis in Arabidopsis.
Plant Physiology. 130, 312-24 Abstract

Benfey, P.N. (2002) Auxin Action: Slogging out of the Swamp. Current
Biology. 12, R389-90 Abstract

Ausubel, F. and Benfey, P.N. (2002) Arabidopsis functional genomics.
Plant Physiology. 129, 393 Abstract

Nakajima, K. and P.N. Benfey (2002). Signaling in and out: control of cell division and differentiation in the shoot and root. Plant Cell 14 Suppl:S265-76 Abstract

Nakajima, K., G. Sena, T. Nawy and P.N. Benfey (2001) Intercellular movement of the putative transcription factor SHR in root patterning. Nature 413, 307-311 Abstract

Birnbaum, K., P.N. Benfey and D.E. Shasha (2001) Cis-Element/Transcription Factor analysis (cis/TF): a method for discovering transcription factor cis-element relationships. Genome Research 11(9), 1567-1573 Abstract

Nawy, T. and P.N. Benfey (2001) Signaling the tips: Regulation of stem cell function in plants. Differentiation 68, 155-158 Abstract

Paquette, A.J. and P.N. Benfey (2001) Axis formation and polarity in plants. Current Opinion in Genetics and Development 11, 405-409 Abstract

Schindelman, G., A. Morikami, J. Jung, T.I. Baskin, N.C. Carpita, P. Derbyshire, M.C. McCann, and P.N. Benfey (2001) COBRA encodes a putative GPI-anchored protein, which is polarly localized and necessary for oriented cell expansion in Arabidopsis. Genes and Development 15, 1115-1127 Abstract

Benfey, P.N. & Weigel, D. (2001) Transcriptional networks controlling plant development. Plant Physiology 125, 109-111 Abstract

Mahonen, A.P., M. Bonke, L. Kauppinen, M. Riikonen, P.N. Benfey, and Y. Helariutta (2000) A novel two-component hybrid molecule regulates vascular morphogenesis of the Arabidopsis root. Genes and Development 14, 2938-2943 Abstract

Benfey, P.N., and B. Scheres (2000) Root development. J. Current Biology 10,R813-815 Abstract

Lim, J., Y. Helariutta, C.D. Specht, J. Jung, L. Sims, W.B. Bruce, S. Diehn, and P.N. Benfey (2000) Molecular analysis of the SCARECROW gene in maize reveals a common basis for radial patterning in diverse meristems. Plant Cell 12, 1307-1318 Abstract

Helariutta, Y., H. Fukaki, J. Wysocka-Diller, K. Nakajima, J. Jung, G. Sena, M.T. Hauser, and P.N Benfey (2000) The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell 101, 555-567 Abstract

Wysocka-Diller, J.W., Y. Helariutta, H. Fukaki, J.E. Malamy, and P.N Benfey (2000) Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot. Development 127, 595-603 Abstract

Sabatini S., D. Beis D, H. Wolkenfelt, J. Murfett, T. Guilfoyle, J.E. Malamy, P.N. Benfey, O. Leyser, N. Bechtold, P. Weisbeek & B. Scheres (1999) An auxin-dependent distal organizer of pattern and polarity in the Arabidopsis root. Cell 99, 463-472 Abstract

Scheres, B. and P.N. Benfey (1999) Asymmetric cell division in plants. Annual Review of Plant Physiology and Plant Molecular Biology 50, 505-537

Pysh, L.D., J.W. Wysocka-Diller, C. Camilleri, D. Bouchez, and P.N. Benfey (1999) The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes. Plant Journal 18, 111-9 Abstract

Benfey, P.N. (1999) Stem cells: A tale of two kingdoms. Current Biology 9,R171-2 Abstract

Benfey, P.N. (1999) Is the shoot a root with a view? Current Opinions in Plant Biology 2, 39-43 Abstract

Fukaki, H., J. Wysocka-Diller, T. Kato, H. Fujisawa, P.N. Benfey, and M. Tasaka (1998) Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana. Plant Journal 14, 425-30 Abstract

Malamy, J.E. and P.N. Benfey (1997) A rapid system for assessing transgene expression in roots of Arabidopsis. Plant Journal 12, 957-963

Wysocka-Diller, J. and P.N. Benfey (1997) Root development: signaling down and around. BioEssays 19, 959-965 Abstract

Malamy, J. E. and P.N. Benfey (1997) Organization and cell differentiation in lateral roots of Arabidopsis thaliana. Development 124, 33-44 Abstract

Malamy, J. E. and P.N. Benfey (1997) Down and out in Arabidopsis: the formation of lateral roots. Trends in Plant Science 2, 390-396

Di Laurenzio, L., Wysocka-Diller, J., Malamy, J. E., Pysh, L ., Helariutta, Y., Freshour, G., Hahn, M.G., Feldmann, K. A. and P.N. Benfey (1996) The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell 86, 423-433

Scheres,B., Di Laurenzio, L, Willemsen, V., Hauser,M.-T., Janmaat, K., Weisbeek, P. and P.N. Benfey, (1995) Mutations affecting the radial organisation of the Arabidopsis root display specific defects throughout the embryonic axis. Development 121, 53-62

Hauser, M.T., Morikami, A. and P.N. Benfey, (1995) Conditional root expansion mutants of Arabidopsis. Development 121, 1237-1252 Abstract

Aeschbacher, R.A., Hauser, M.T., Feldmann, K.A. and P.N. Benfey, (1995) The SABRE gene is required for normal cell expansion in Arabidopsis. Genes & Development 9, 330-340 Abstract

Benfey, P.N and Schiefelbein, J.W., (1994) Getting to the root of plant development: the genetics of Arabidopsis root formation. Trends in Genetics 94, 84-88 Abstract

Benfey, P.N., Linstead, P.J., Roberts, K., Schiefelbein, J.W. Hauser, M.-T., and R.A. Aeschbacher (1993) Root development in Arabidopsis: four mutants with dramatically altered root morphogenesis. Development, 119, 53-70 Abstract