Philip N. Benfey, Ph.D. - Publications

Affiliations: 
Duke University, Durham, NC 
Area:
Developmental Biology, Plant Biology
Website:
http://sites.duke.edu/benfey/

150 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 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 Research. PMID 31722410 DOI: 10.1093/nar/gkz978  0.68
2019 Di Mambro R, Svolacchia N, Dello Ioio R, Pierdonati E, Salvi E, Pedrazzini E, Vitale A, Perilli S, Sozzani R, Benfey PN, Busch W, Costantino P, Sabatini S. The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size. Current Biology : Cb. PMID 30880016 DOI: 10.1016/j.cub.2019.02.022  0.96
2019 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 Physiology. PMID 30737268 DOI: 10.1104/pp.19.00056  0.48
2018 Pierre-Jerome E, Drapek C, Benfey PN. Regulation of Division and Differentiation of Plant Stem Cells. Annual Review of Cell and Developmental Biology. PMID 30134119 DOI: 10.1146/annurev-cellbio-100617-062459  0.48
2018 Drapek C, Sparks EE, Marhavy P, Taylor I, Andersen TG, Hennacy JH, Geldner N, Benfey PN. Minimum requirements for changing and maintaining endodermis cell identity in the Arabidopsis root. Nature Plants. PMID 30061749 DOI: 10.1038/s41477-018-0213-y  0.68
2018 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 in . Development (Cambridge, England). 145. PMID 29439132 DOI: 10.1242/dev.159707  0.96
2017 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 root meristem. Proceedings of the National Academy of Sciences of the United States of America. 114: E8922-E8929. PMID 28973915 DOI: 10.1073/pnas.1707400114  0.96
2017 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 root. Proceedings of the National Academy of Sciences of the United States of America. 114: E7641-E7649. PMID 28831001 DOI: 10.1073/pnas.1705833114  0.96
2017 Hsu PY, Benfey PN. Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants. Proteomics. PMID 28759167 DOI: 10.1002/pmic.201700038  0.44
2017 Drapek C, Sparks EE, Benfey PN. Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation. Trends in Genetics : Tig. 33: 529-539. PMID 28647055 DOI: 10.1016/j.tig.2017.05.002  0.68
2017 Sparks EE, Benfey PN. Tissue-Specific Transcriptome Profiling in Arabidopsis Roots. Methods in Molecular Biology (Clifton, N.J.). 1610: 107-122. PMID 28439860 DOI: 10.1007/978-1-4939-7003-2_8  0.44
2017 Nevarez PA, Qiu Y, Inoue H, Yoo CY, Benfey PN, Schnell DJ, Chen M. Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus. Plant Physiology. 173: 1953-1966. PMID 28232584 DOI: 10.1104/pp.16.00116  0.92
2017 Fernández-Marcos M, Desvoyes B, Manzano C, Liberman LM, Benfey PN, Del Pozo JC, Gutierrez C. Control of Arabidopsis lateral root primordium boundaries by MYB36. The New Phytologist. 213: 105-112. PMID 27891649 DOI: 10.1111/nph.14304  0.52
2016 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, et al. Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. Developmental Cell. 39: 585-596. PMID 27923776 DOI: 10.1016/j.devcel.2016.09.031  0.84
2016 Li S, Yamada M, Han X, Ohler U, Benfey PN. High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. Developmental Cell. 39: 508-522. PMID 27840108 DOI: 10.1016/j.devcel.2016.10.012  0.64
2016 Hsu PY, Calviello L, Wu HL, Li FW, Rothfels CJ, Ohler U, Benfey PN. Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. PMID 27791167 DOI: 10.1073/pnas.1614788113  0.64
2016 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. 5. PMID 27288545 DOI: 10.7554/eLife.14770  0.96
2016 Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker JR. Unique cell-type-specific patterns of DNA methylation in the root meristem. Nature Plants. 2: 16058. PMID 27243651 DOI: 10.1038/nplants.2016.58  0.92
2016 Liberman LM, Benfey PN. A Friend in Need (of Nutrients) Is a…. Cell. 165: 269-71. PMID 27058660 DOI: 10.1016/j.cell.2016.03.036  0.52
2016 Sparks EE, Benfey PN. Identifying Gene Regulatory Networks in Arabidopsis by In Silico Prediction, Yeast-1-Hybrid, and Inducible Gene Profiling Assays. Methods in Molecular Biology (Clifton, N.J.). 1370: 29-50. PMID 26659952 DOI: 10.1007/978-1-4939-3142-2_3  0.44
2015 Rodriguez RE, Ercoli MF, Debernardi JM, Breakfield NW, Mecchia MA, Sabatini M, Cools T, De Veylder L, Benfey PN, Palatnik JF. MicroRNA miR396 Regulates the Switch between Stem Cells and Transit-Amplifying Cells in Arabidopsis Roots. The Plant Cell. 27: 3354-66. PMID 26645252 DOI: 10.1105/tpc.15.00452  0.68
2015 Moreno-Risueno MA, Sozzani R, Yardımcı GG, Petricka JJ, Vernoux T, Blilou I, Alonso J, Winter CM, Ohler U, Scheres B, Benfey PN. Transcriptional control of tissue formation throughout root development. Science (New York, N.Y.). 350: 426-30. PMID 26494755 DOI: 10.1126/science.aad1171  0.96
2015 Liberman LM, Sparks EE, Moreno-Risueno MA, Petricka JJ, Benfey PN. MYB36 regulates the transition from proliferation to differentiation in the Arabidopsis root. Proceedings of the National Academy of Sciences of the United States of America. 112: 12099-104. PMID 26371322 DOI: 10.1073/pnas.1515576112  0.88
2015 Wachsman G, Sparks EE, Benfey PN. Genes and networks regulating root anatomy and architecture. The New Phytologist. 208: 26-38. PMID 25989832 DOI: 10.1111/nph.13469  0.44
2015 Cederholm HM, Benfey PN. Distinct sensitivities to phosphate deprivation suggest that RGF peptides play disparate roles in Arabidopsis thaliana root development. The New Phytologist. 207: 683-91. PMID 25856240 DOI: 10.1111/nph.13405  0.68
2015 Zurek PR, Topp CN, Benfey PN. Quantitative trait locus mapping reveals regions of the maize genome controlling root system architecture. Plant Physiology. 167: 1487-96. PMID 25673779 DOI: 10.1104/pp.114.251751  1
2014 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. The Plant Cell. 26: 2746-60. PMID 25035402 DOI: 10.1105/tpc.114.125617  0.68
2014 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. Proceedings of the National Academy of Sciences of the United States of America. 111: E1300-9. PMID 24639533 DOI: 10.1073/pnas.1403016111  0.68
2014 Sparks EE, Benfey PN. HEC of a job regulating stem cells. Developmental Cell. 28: 349-50. PMID 24576420 DOI: 10.1016/j.devcel.2014.02.006  0.44
2014 Sozzani R, Busch W, Spalding EP, Benfey PN. Advanced imaging techniques for the study of plant growth and development. Trends in Plant Science. 19: 304-10. PMID 24434036 DOI: 10.1016/j.tplants.2013.12.003  0.96
2013 Benfey P. Philip benfey Current Biology. 23: R857-R858. PMID 24251331 DOI: 10.1016/j.cub.2013.08.010  1
2013 Van Norman JM, Xuan W, Beeckman T, Benfey PN. To branch or not to branch: the role of pre-patterning in lateral root formation. Development (Cambridge, England). 140: 4301-10. PMID 24130327 DOI: 10.1242/dev.090548  0.68
2013 Moubayidin L, Di Mambro R, Sozzani R, Pacifici E, Salvi E, Terpstra I, Bao D, van Dijken A, Dello Ioio R, Perilli S, Ljung K, Benfey PN, Heidstra R, Costantino P, Sabatini S. Spatial coordination between stem cell activity and cell differentiation in the root meristem. Developmental Cell. 26: 405-15. PMID 23987513 DOI: 10.1016/j.devcel.2013.06.025  0.96
2013 Li S, Liberman LM, Mukherjee N, Benfey PN, Ohler U. Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Research. 23: 1730-9. PMID 23816784 DOI: 10.1101/gr.149310.112  0.64
2013 Liberman LM, Benfey PN. Polarized radicals. Cell. 153: 285-6. PMID 23582319 DOI: 10.1016/j.cell.2013.03.042  0.52
2013 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, 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: E1695-704. PMID 23580618 DOI: 10.1073/pnas.1304354110  1
2013 Moussaieff A, Rogachev I, Brodsky L, Malitsky S, Toal TW, Belcher H, Yativ M, Brady SM, Benfey PN, Aharoni A. High-resolution metabolic mapping of cell types in plant roots. Proceedings of the National Academy of Sciences of the United States of America. 110: E1232-41. PMID 23476065 DOI: 10.1073/pnas.1302019110  0.84
2013 Fang S, Clark RT, Zheng Y, Iyer-Pascuzzi AS, Weitz JS, Kochian LV, Edelsbrunner H, Liao H, Benfey PN. Genotypic recognition and spatial responses by rice roots. Proceedings of the National Academy of Sciences of the United States of America. 110: 2670-5. PMID 23362379 DOI: 10.1073/pnas.1222821110  1
2013 Iyer-Pascuzzi AS, Zurek PR, Benfey PN. High-throughput, noninvasive imaging of root systems. Methods in Molecular Biology (Clifton, N.J.). 959: 177-87. PMID 23299675 DOI: 10.1007/978-1-62703-221-6_11  1
2012 Cederholm HM, Iyer-Pascuzzi AS, Benfey PN. Patterning the primary root in Arabidopsis. Wiley Interdisciplinary Reviews. Developmental Biology. 1: 675-91. PMID 23799568 DOI: 10.1002/wdev.49  1
2012 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. Nature Methods. 9: 1101-6. PMID 23023597 DOI: 10.1038/nmeth.2185  0.92
2012 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, ... ... Benfey PN, et al. A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division. Cell. 150: 1002-15. PMID 22921914 DOI: 10.1016/j.cell.2012.07.017  0.96
2012 Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price CA, Topp CN, Iyer-Pascuzzi AS, Zurek PR, Fang S, Harer J, Benfey PN, Weitz JS. GiA Roots: software for the high throughput analysis of plant root system architecture. Bmc Plant Biology. 12: 116. PMID 22834569 DOI: 10.1186/1471-2229-12-116  1
2012 Davis IW, Benninger C, Benfey PN, Elich T. POWRS: position-sensitive motif discovery. Plos One. 7: e40373. PMID 22792292 DOI: 10.1371/journal.pone.0040373  0.68
2012 Ingram PA, Zhu J, Shariff A, Davis IW, Benfey PN, Elich T. High-throughput imaging and analysis of root system architecture in Brachypodium distachyon under differential nutrient availability. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 367: 1559-69. PMID 22527399 DOI: 10.1098/rstb.2011.0241  0.68
2012 Rogers ED, Jackson T, Moussaieff A, Aharoni A, Benfey PN. Cell type-specific transcriptional profiling: implications for metabolite profiling. The Plant Journal : For Cell and Molecular Biology. 70: 5-17. PMID 22449039 DOI: 10.1111/j.1365-313X.2012.04888.x  0.48
2012 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. Proceedings of the National Academy of Sciences of the United States of America. 109: 6811-8. PMID 22447775 DOI: 10.1073/pnas.1202546109  0.68
2012 Petricka JJ, Winter CM, Benfey PN. Control of Arabidopsis root development. Annual Review of Plant Biology. 63: 563-90. PMID 22404466 DOI: 10.1146/annurev-arplant-042811-105501  0.64
2012 Moreno-Risueno MA, Van Norman JM, Benfey PN. Transcriptional switches direct plant organ formation and patterning. Current Topics in Developmental Biology. 98: 229-57. PMID 22305165 DOI: 10.1016/B978-0-12-386499-4.00009-4  0.88
2012 Liberman LM, Sozzani R, Benfey PN. Integrative systems biology: an attempt to describe a simple weed. Current Opinion in Plant Biology. 15: 162-7. PMID 22277598 DOI: 10.1016/j.pbi.2012.01.004  0.96
2012 Bruex A, Kainkaryam RM, Wieckowski Y, Kang YH, Bernhardt C, Xia Y, Zheng X, Wang JY, Lee MM, Benfey P, Woolf PJ, Schiefelbein J. A gene regulatory network for root epidermis cell differentiation in Arabidopsis. Plos Genetics. 8: e1002446. PMID 22253603 DOI: 10.1371/journal.pgen.1002446  1
2012 De Smet I, White PJ, Bengough AG, Dupuy L, Parizot B, Casimiro I, Heidstra R, Laskowski M, Lepetit M, Hochholdinger F, Draye X, Zhang H, Broadley MR, Péret B, Hammond JP, ... ... Benfey P, et al. Analyzing lateral root development: how to move forward. The Plant Cell. 24: 15-20. PMID 22227890 DOI: 10.1105/tpc.111.094292  1
2012 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 Research. 22: 163-76. PMID 21940835 DOI: 10.1101/gr.123547.111  0.68
2011 Iyer-Pascuzzi AS, Jackson T, Cui H, Petricka JJ, Busch W, Tsukagoshi H, Benfey PN. Cell identity regulators link development and stress responses in the Arabidopsis root. Developmental Cell. 21: 770-82. PMID 22014526 DOI: 10.1016/j.devcel.2011.09.009  1
2011 Moreno-Risueno MA, Benfey PN. Time-based patterning in development: The role of oscillating gene expression. Transcription. 2: 124-129. PMID 21826283 DOI: 10.4161/trns.2.3.15637  0.88
2011 Petricka JJ, Benfey PN. Reconstructing regulatory network transitions. Trends in Cell Biology. 21: 442-51. PMID 21632251 DOI: 10.1016/j.tcb.2011.05.001  0.64
2011 Zhu J, Ingram PA, Benfey PN, Elich T. From lab to field, new approaches to phenotyping root system architecture. Current Opinion in Plant Biology. 14: 310-7. PMID 21530367 DOI: 10.1016/j.pbi.2011.03.020  0.68
2011 Sozzani R, Benfey PN. High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype. Genome Biology. 12: 219. PMID 21457493 DOI: 10.1186/gb-2011-12-3-219  0.96
2011 Van Norman JM, Breakfield NW, Benfey PN. Intercellular communication during plant development. The Plant Cell. 23: 855-64. PMID 21386031 DOI: 10.1105/tpc.111.082982  0.68
2011 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. Molecular Systems Biology. 7: 459. PMID 21245844 DOI: 10.1038/msb.2010.114  0.84
2010 Pop A, Huttenhower C, Iyer-Pascuzzi A, Benfey PN, Troyanskaya OG. Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. Bmc Systems Biology. 4: 180. PMID 21194434 DOI: 10.1186/1752-0509-4-180  0.4
2010 To JP, Zhu J, Benfey PN, Elich T. Optimizing root system architecture in biofuel crops for sustainable energy production and soil carbon sequestration. F1000 Biology Reports. 2: 65. PMID 21173868 DOI: 10.3410/B2-65  0.68
2010 Tsukagoshi H, Busch W, Benfey PN. Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root. Cell. 143: 606-16. PMID 21074051 DOI: 10.1016/j.cell.2010.10.020  0.92
2010 Baskin TI, Peret B, Baluška F, Benfey PN, Bennett M, Forde BG, Gilroy S, Helariutta Y, Hepler PK, Leyser O, Masson PH, Muday GK, Murphy AS, Poethig S, Rahman A, et al. Shootward and rootward: peak terminology for plant polarity. Trends in Plant Science. 15: 593-4. PMID 20833574 DOI: 10.1016/j.tplants.2010.08.006  0.72
2010 Moreno-Risueno MA, Van Norman JM, Moreno A, Zhang J, Ahnert SE, Benfey PN. Oscillating gene expression determines competence for periodic Arabidopsis root branching. Science (New York, N.Y.). 329: 1306-11. PMID 20829477 DOI: 10.1126/science.1191937  0.88
2010 Iyer-Pascuzzi AS, Benfey PN. Fluorescence-activated cell sorting in plant developmental biology. Methods in Molecular Biology (Clifton, N.J.). 655: 313-9. PMID 20734270 DOI: 10.1007/978-1-60761-765-5_21  1
2010 Long TA, Tsukagoshi H, Busch W, Lahner B, Salt DE, Benfey PN. The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots. The Plant Cell. 22: 2219-36. PMID 20675571 DOI: 10.1105/tpc.110.074096  0.92
2010 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. 466: 128-32. PMID 20596025 DOI: 10.1038/nature09143  1
2010 Orlando DA, Brady SM, Fink TM, Benfey PN, Ahnert SE. Detecting separate time scales in genetic expression data. Bmc Genomics. 11: 381. PMID 20565716 DOI: 10.1186/1471-2164-11-381  0.84
2010 Carlsbecker A, Lee JY, Roberts CJ, Dettmer J, Lehesranta S, Zhou J, Lindgren O, Moreno-Risueno MA, Vatén A, Thitamadee S, Campilho A, Sebastian J, Bowman JL, Helariutta Y, Benfey PN. Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate. Nature. 465: 316-21. PMID 20410882 DOI: 10.1038/nature08977  0.92
2010 Benfey PN, Bennett M, Schiefelbein J. Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research. The Plant Journal : For Cell and Molecular Biology. 61: 992-1000. PMID 20409273 DOI: 10.1111/j.1365-313X.2010.04129.x  0.44
2010 Busch W, Benfey PN. Information processing without brains--the power of intercellular regulators in plants. Development (Cambridge, England). 137: 1215-26. PMID 20332147 DOI: 10.1242/dev.034868  0.92
2010 De Smet I, Lau S, Voss U, Vanneste S, Benjamins R, Rademacher EH, Schlereth A, De Rybel B, Vassileva V, Grunewald W, Naudts M, Levesque MP, Ehrismann JS, Inzé D, Luschnig C, ... Benfey PN, et al. Bimodular auxin response controls organogenesis in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 107: 2705-10. PMID 20133796 DOI: 10.1073/pnas.0915001107  0.6
2010 Iyer-Pascuzzi AS, Symonova O, Mileyko Y, Hao Y, Belcher H, Harer J, Weitz JS, Benfey PN. Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems. Plant Physiology. 152: 1148-57. PMID 20107024 DOI: 10.1104/pp.109.150748  1
2010 Moreno-Risueno MA, Busch W, Benfey PN. Omics meet networks - using systems approaches to infer regulatory networks in plants. Current Opinion in Plant Biology. 13: 126-31. PMID 20036612 DOI: 10.1016/j.pbi.2009.11.005  0.92
2009 Van Norman JM, Benfey PN. Arabidopsis thaliana as a model organism in systems biology. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 1: 372-379. PMID 20228888 DOI: 10.1002/wsbm.25  0.68
2009 Petricka JJ, Van Norman JM, Benfey PN. Symmetry breaking in plants: molecular mechanisms regulating asymmetric cell divisions in Arabidopsis. Cold Spring Harbor Perspectives in Biology. 1: a000497. PMID 20066115 DOI: 10.1101/cshperspect.a000497  0.68
2009 Cui H, Benfey PN. Cortex proliferation: simple phenotype, complex regulatory mechanisms. Plant Signaling & Behavior. 4: 551-3. PMID 19816127 DOI: 10.1111/j.1365-313X.2009.03839.x  1
2009 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. 4: e6648. PMID 19777056 DOI: 10.1371/journal.pone.0006648  1
2009 Benfey PN, Birnbaum KD. Primer and interviews: Gene regulation in Arabidopsis thaliana. Interview by Julie C. Kiefer. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 238: 2449-58. PMID 19653311 DOI: 10.1002/dvdy.22042  1
2009 Cartwright DA, Brady SM, Orlando DA, Sturmfels B, Benfey PN. Reconstructing spatiotemporal gene expression data from partial observations. Bioinformatics (Oxford, England). 25: 2581-7. PMID 19608707 DOI: 10.1093/bioinformatics/btp437  0.84
2009 Orlando DA, Brady SM, Koch JD, Dinneny JR, Benfey PN. Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment. Methods in Molecular Biology (Clifton, N.J.). 553: 57-77. PMID 19588101 DOI: 10.1007/978-1-60327-563-7_4  0.84
2009 Petersson SV, Johansson AI, Kowalczyk M, Makoveychuk A, Wang JY, Moritz T, Grebe M, Benfey PN, Sandberg G, Ljung K. An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis. The Plant Cell. 21: 1659-68. PMID 19491238 DOI: 10.1105/tpc.109.066480  0.84
2009 Cui H, Benfey PN. Interplay between SCARECROW, GA and LIKE HETEROCHROMATIN PROTEIN 1 in ground tissue patterning in the Arabidopsis root. The Plant Journal : For Cell and Molecular Biology. 58: 1016-27. PMID 19228333 DOI: 10.1111/j.1365-313X.2009.03839.x  1
2009 Iyer-Pascuzzi A, Simpson J, Herrera-Estrella L, Benfey PN. Functional genomics of root growth and development in Arabidopsis. Current Opinion in Plant Biology. 12: 165-71. PMID 19117793 DOI: 10.1016/j.pbi.2008.11.002  0.4
2009 Gallagher KL, Benfey PN. Both the conserved GRAS domain and nuclear localization are required for SHORT-ROOT movement. The Plant Journal : For Cell and Molecular Biology. 57: 785-97. PMID 19000160 DOI: 10.1111/j.1365-313X.2008.03735.x  1
2009 Iyer-Pascuzzi AS, Benfey PN. Transcriptional networks in root cell fate specification. Biochimica Et Biophysica Acta. 1789: 315-25. PMID 18973837 DOI: 10.1016/j.bbagrm.2008.09.006  1
2008 Bender J, Benfey P, Bergmann D, Borevitz J, Coruzzi G, Dangl J, Dean C, Ecker J, Estelle M, Glazebrook J, Grant S, Guerinot ML, Gutierrez R, Long J, Nordborg M, et al. 2020 vision for biology: the role of plants in addressing grand challenges in biology. Molecular Plant. 1: 561-3. PMID 19825561 DOI: 10.1093/mp/ssn040  0.36
2008 Colinas J, Schmidler SC, Bohrer G, Iordanov B, Benfey PN. Intergenic and genic sequence lengths have opposite relationships with respect to gene expression. Plos One. 3: e3670. PMID 18989364 DOI: 10.1371/journal.pone.0003670  1
2008 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, ... ... Benfey PN, et al. Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root. Science (New York, N.Y.). 322: 594-7. PMID 18948541 DOI: 10.1126/science.1160158  0.84
2008 Chaudhuri B, Hörmann F, Lalonde S, Brady SM, Orlando DA, Benfey P, Frommer WB. Protonophore- and pH-insensitive glucose and sucrose accumulation detected by FRET nanosensors in Arabidopsis root tips. The Plant Journal : For Cell and Molecular Biology. 56: 948-62. PMID 18702670 DOI: 10.1111/j.1365-313X.2008.03652.x  1
2008 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, ... ... Benfey P, et al. The auxin influx carrier LAX3 promotes lateral root emergence. Nature Cell Biology. 10: 946-54. PMID 18622388 DOI: 10.1038/ncb1754  1
2008 Petricka JJ, Benfey PN. Root layers: complex regulation of developmental patterning. Current Opinion in Genetics & Development. 18: 354-61. PMID 18617392 DOI: 10.1016/j.gde.2008.05.001  0.64
2008 Long TA, Brady SM, Benfey PN. Systems approaches to identifying gene regulatory networks in plants. Annual Review of Cell and Developmental Biology. 24: 81-103. PMID 18616425 DOI: 10.1146/annurev.cellbio.24.110707.175408  0.88
2008 Dinneny JR, Long TA, Wang JY, Jung JW, Mace D, Pointer S, Barron C, Brady SM, Schiefelbein J, Benfey PN. Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science (New York, N.Y.). 320: 942-5. PMID 18436742 DOI: 10.1126/science.1153795  0.88
2008 Dinneny JR, Benfey PN. Plant stem cell niches: standing the test of time. Cell. 132: 553-7. PMID 18295573 DOI: 10.1016/j.cell.2008.02.001  0.64
2007 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. Science (New York, N.Y.). 318: 801-6. PMID 17975066 DOI: 10.1126/science.1146265  0.84
2007 Cui H, Levesque MP, Vernoux T, Jung JW, Paquette AJ, Gallagher KL, Wang JY, Blilou I, Scheres B, Benfey PN. An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science (New York, N.Y.). 316: 421-5. PMID 17446396 DOI: 10.1126/science.1139531  1
2007 Weitz JS, Benfey PN, Wingreen NS. Evolution, interactions, and biological networks. Plos Biology. 5: e11. PMID 17227140 DOI: 10.1371/journal.pbio.0050011  0.96
2007 Brady SM, Song S, Dhugga KS, Rafalski JA, Benfey PN. Combining expression and comparative evolutionary analysis. The COBRA gene family. Plant Physiology. 143: 172-87. PMID 17098858 DOI: 10.1104/pp.106.087262  0.84
2006 Long TA, Benfey PN. Transcription factors and hormones: new insights into plant cell differentiation. Current Opinion in Cell Biology. 18: 710-4. PMID 17034999 DOI: 10.1016/j.ceb.2006.09.004  0.88
2006 Brady SM, Long TA, Benfey PN. Unraveling the dynamic transcriptome. The Plant Cell. 18: 2101-11. PMID 16968906 DOI: 10.1105/tpc.105.037572  0.88
2006 Mace DL, Lee JY, Twigg RW, Colinas J, Benfey PN, Ohler U. Quantification of transcription factor expression from Arabidopsis images. Bioinformatics (Oxford, England). 22: e323-31. PMID 16873489 DOI: 10.1093/bioinformatics/btl228  1
2006 Levesque MP, Vernoux T, Busch W, Cui H, Wang JY, Blilou I, Hassan H, Nakajima K, Matsumoto N, Lohmann JU, Scheres B, Benfey PN. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. Plos Biology. 4: e143. PMID 16640459 DOI: 10.1371/journal.pbio.0040143  1
2006 Lee JY, Colinas J, Wang JY, Mace D, Ohler U, Benfey PN. Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proceedings of the National Academy of Sciences of the United States of America. 103: 6055-60. PMID 16581911 DOI: 10.1073/pnas.0510607103  1
2006 Friml J, Benfey P, Benková E, Bennett M, Berleth T, Geldner N, Grebe M, Heisler M, Hejátko J, Jürgens G, Laux T, Lindsey K, Lukowitz W, Luschnig C, Offringa R, et al. Apical-basal polarity: why plant cells don't stand on their heads. Trends in Plant Science. 11: 12-4. PMID 16356758 DOI: 10.1016/j.tplants.2005.11.010  1
2005 Dinneny JR, Benfey PN. Stem cell research goes underground: the RETINOBLASTOMA-RELATED gene in root development. Cell. 123: 1180-2. PMID 16377557 DOI: 10.1016/j.cell.2005.12.005  0.64
2005 Lim J, Jung JW, Lim CE, Lee MH, Kim BJ, Kim M, Bruce WB, Benfey PN. Conservation and diversification of SCARECROW in maize. Plant Molecular Biology. 59: 619-30. PMID 16244911 DOI: 10.1007/s11103-005-0578-y  0.68
2005 Birnbaum K, Jung JW, Wang JY, Lambert GM, Hirst JA, Galbraith DW, Benfey PN. Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nature Methods. 2: 615-9. PMID 16170893 DOI: 10.1038/nmeth0805-615  1
2005 Vernoux T, Benfey PN. Signals that regulate stem cell activity during plant development. Current Opinion in Genetics & Development. 15: 388-94. PMID 15967658 DOI: 10.1016/j.gde.2005.06.008  0.44
2005 Paquette AJ, Benfey PN. Maturation of the ground tissue of the root is regulated by gibberellin and SCARECROW and requires SHORT-ROOT. Plant Physiology. 138: 636-40. PMID 15955927 DOI: 10.1104/pp.104.058362  0.6
2005 Lee JY, Levesque M, Benfey PN. High-throughput RNA isolation technologies. New tools for high-resolution gene expression profiling in plant systems. Plant Physiology. 138: 585-90. PMID 15955922 DOI: 10.1104/pp.105.061812  0.84
2005 Nawy T, Lee JY, Colinas J, Wang JY, Thongrod SC, Malamy JE, Birnbaum K, Benfey PN. Transcriptional profile of the Arabidopsis root quiescent center. The Plant Cell. 17: 1908-25. PMID 15937229 DOI: 10.1105/tpc.105.031724  1
2005 Roudier F, Fernandez AG, Fujita M, Himmelspach R, Borner GH, Schindelman G, Song S, Baskin TI, Dupree P, Wasteneys GO, Benfey PN. COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation. The Plant Cell. 17: 1749-63. PMID 15849274 DOI: 10.1105/tpc.105.031732  0.48
2005 Gallagher KL, Benfey PN. Not just another hole in the wall: understanding intercellular protein trafficking. Genes & Development. 19: 189-95. PMID 15655108 DOI: 10.1101/gad.1271005  1
2004 Gallagher KL, Paquette AJ, Nakajima K, Benfey PN. Mechanisms regulating SHORT-ROOT intercellular movement. Current Biology : Cb. 14: 1847-51. PMID 15498493 DOI: 10.1016/j.cub.2004.09.081  1
2004 Birnbaum K, Benfey PN. Network building: transcriptional circuits in the root. Current Opinion in Plant Biology. 7: 582-8. PMID 15337102 DOI: 10.1016/j.pbi.2004.07.010  1
2004 Sena G, Jung JW, Benfey PN. A broad competence to respond to SHORT ROOT revealed by tissue-specific ectopic expression. Development (Cambridge, England). 131: 2817-26. PMID 15142972 DOI: 10.1242/dev.01144  0.68
2004 Levesque MP, Benfey PN. Systems biology. Current Biology : Cb. 14: R179-80. PMID 15028228 DOI: 10.1016/j.cub.2004.02.012  0.6
2003 Birnbaum K, Desalle R, Peters CM, Benfey PN. Integrating gene flow, crop biology, and farm management in on-farm conservation of avocado (Persea americana, Lauraceae). American Journal of Botany. 90: 1619-27. PMID 21653337 DOI: 10.3732/ajb.90.11.1619  1
2003 Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, Galbraith DW, Benfey PN. A gene expression map of the Arabidopsis root. Science (New York, N.Y.). 302: 1956-60. PMID 14671301 DOI: 10.1126/science.1090022  1
2003 Brenner ED, Stevenson DW, McCombie RW, Katari MS, Rudd SA, Mayer KF, Palenchar PM, Runko SJ, Twigg RW, Dai G, Martienssen RA, Benfey PN, Coruzzi GM. Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biology. 4: R78. PMID 14659015 DOI: 10.1186/gb-2003-4-12-r78  1
2003 Levesque M, Shasha D, Kim W, Surette MG, Benfey PN. Trait-to-gene: a computational method for predicting the function of uncharacterized genes. Current Biology : Cb. 13: 129-33. PMID 12546786  0.52
2002 Scheres B, Benfey P, Dolan L. Root development. The Arabidopsis Book / American Society of Plant Biologists. 1: e0101. PMID 22303222 DOI: 10.1199/tab.0101  0.44
2002 Roudier F, Schindelman G, DeSalle R, Benfey PN. The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion. Plant Physiology. 130: 538-48. PMID 12376623 DOI: 10.1104/pp.007468  0.36
2002 Müller S, Fuchs E, Ovecka M, Wysocka-Diller J, Benfey PN, Hauser MT. Two new loci, PLEIADE and HYADE, implicate organ-specific regulation of cytokinesis in Arabidopsis. Plant Physiology. 130: 312-24. PMID 12226511 DOI: 10.1104/pp.004416  0.6
2002 Colinas J, Birnbaum K, Benfey PN. Using cauliflower to find conserved non-coding regions in Arabidopsis. Plant Physiology. 129: 451-4. PMID 12068091 DOI: 10.1104/pp.002501  1
2002 Ausubel F, Benfey P. Arabidopsis functional genomics. Plant Physiology. 129: 393. PMID 12068088 DOI: 10.1104/pp.900036  1
2002 Nakajima K, Benfey PN. Signaling in and out: control of cell division and differentiation in the shoot and root. The Plant Cell. 14: S265-76. PMID 12045282  0.6
2001 Nawy T, Benfey PN. Signaling the tips: Regulation of stem cell function in plants Differentiation. 68: 155-158. PMID 11776467  1
2001 Nakajima K, Sena G, Nawy T, Benfey PN. Intercellular movement of the putative transcription factor SHR in root patterning Nature. 413: 307-311. PMID 11565032 DOI: 10.1038/35095061  1
2001 Birnbaum K, Benfey PN, Shasha DE. cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships. Genome Research. 11: 1567-73. PMID 11544201 DOI: 10.1101/gr.158301  1
2000 Mähönen AP, Bonke M, Kauppinen L, Riikonen M, Benfey PN, Helariutta Y. A novel two-component hybrid molecule regulates vascular morphogenesis of the Arabidopsis root Genes and Development. 14: 2938-2943. PMID 11114883 DOI: 10.1101/gad.189200  1
2000 Lim J, Helariutta Y, Specht CD, Jung J, Sims L, Bruce WB, Diehn S, Benfey PN. Molecular analysis of the SCARECROW gene in maize reveals a common basis for radial patterning in diverse meristems Plant Cell. 12: 1307-1318. PMID 10948251 DOI: 10.1105/tpc.12.8.1307  1
2000 Helariutta Y, Fukaki H, Wysocka-Diller J, Nakajima K, Jung J, Sena G, Hauser MT, Benfey PN. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling Cell. 101: 555-567. PMID 10850497  1
2000 Wysocka-Diller JW, Helariutta Y, Fukaki H, Malamy JE, Benfey PN. Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot Development. 127: 595-603. PMID 10631180  1
1999 Scheres B, Benfey PN. ASYMMETRIC CELL DIVISION IN PLANTS. Annual Review of Plant Physiology and Plant Molecular Biology. 50: 505-537. PMID 15012218 DOI: 10.1146/annurev.arplant.50.1.505  0.44
1999 Sabatini S, Beis D, Wolkenfelt H, Murfett J, Guilfoyle T, Malamy J, Benfey P, Leyser O, Bechtold N, Weisbeek P, Scheres B. An auxin-dependent distal organizer of pattern and polarity in the Arabidopsis root Cell. 99: 463-472. PMID 10589675  1
1998 Fukaki H, Wysocka-Diller J, Kato T, Fujisawa H, Benfey PN, Tasaka M. Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana Plant Journal. 14: 425-430. PMID 9670559 DOI: 10.1046/j.1365-313X.1998.00137.x  1
1997 Malamy JE, Benfey PN. Analysis of SCARECROW expression using a rapid system for assessing transgene expression in Arabidopsis roots Plant Journal. 12: 957-963. PMID 9375406  1
1997 Malamy JE, Benfey PN. Organization and cell differentiation in lateral roots of Arabidopsis thaliana Development. 124: 33-44. PMID 9006065  1
1996 Di Laurenzio L, Wysocka-Diller J, Malamy JE, Pysh L, Helariutta Y, Freshour G, Hahn MG, Feldmann KA, Benfey PN. The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell. 86: 423-33. PMID 8756724 DOI: 10.1016/S0092-8674(00)80115-4  1
1992 Takatsuji H, Mori M, Benfey PN, Ren L, Chua NH. Characterization of a zinc finger DNA-binding protein expressed specifically in Petunia petals and seedlings Embo Journal. 11: 241-249. PMID 1740109  1
1990 Benfey PN, Chua NH. The Cauliflower Mosaic Virus 35S Promoter: Combinatorial Regulation of Transcription in Plants. Science (New York, N.Y.). 250: 959-66. PMID 17746920 DOI: 10.1126/science.250.4983.959  1
1990 Benfey PN, Takatsuji H, Ren L, Shah DM, Chua NH. Sequence Requirements of the 5-Enolpyruvylshikimate-3-phosphate Synthase 5[prime]-Upstream Region for Tissue-Specific Expression in Flowers and Seedlings. The Plant Cell. 2: 849-856. PMID 12354968 DOI: 10.1105/tpc.2.9.849  1
1990 Benfey PN, Ren L, Chua NH. Combinatorial and synergistic properties of CaMV 35S enhancer subdomains Embo Journal. 9: 1685-1696. PMID 2347302  1
1990 Benfey PN, Ren L, Chua NH. Tissue-specific expression from CaMV 35S enhancer subdomains in early stages of plant development Embo Journal. 9: 1677-1684. PMID 2347301  1
1989 Benfey PN, Chua NH. Regulated genes in transgenic plants. Science (New York, N.Y.). 244: 174-81. PMID 17835349 DOI: 10.1126/science.244.4901.174  1
1989 Benfey PN, Ren L, Chua NH. The CaMV 35S enhancer contains at least two domains which can confer different developmental and tissue-specific expression patterns. The Embo Journal. 8: 2195-202. PMID 16453896  1
1989 Lam E, Benfey PN, Gilmartin PM, Fang RX, Chua NH. Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants Proceedings of the National Academy of Sciences of the United States of America. 86: 7890-7894. PMID 2813365  1
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