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Items: 1 to 50 of 169

1.

Physiological mechanisms contributing to the QTL qDTY3.2 effects on improved performance of rice Moroberekan x Swarna BC2F3:4 lines under drought.

Grondin A, Dixit S, Torres R, Venkateshwarlu C, Rogers E, Mitchell-Olds T, Benfey PN, Kumar A, Henry A.

Rice (N Y). 2018 Jul 31;11(1):43. doi: 10.1186/s12284-018-0234-1.

2.

Minimum requirements for changing and maintaining endodermis cell identity in the Arabidopsis root.

Drapek C, Sparks EE, Marhavy P, Taylor I, Andersen TG, Hennacy JH, Geldner N, Benfey PN.

Nat Plants. 2018 Aug;4(8):586-595. doi: 10.1038/s41477-018-0213-y. Epub 2018 Jul 30.

PMID:
30061749
3.

GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis.

Shibata M, Breuer C, Kawamura A, Clark NM, Rymen B, Braidwood L, Morohashi K, Busch W, Benfey PN, Sozzani R, Sugimoto K.

Development. 2018 Feb 8;145(3). pii: dev159707. doi: 10.1242/dev.159707.

4.

Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem.

Wendrich JR, Möller BK, Li S, Saiga S, Sozzani R, Benfey PN, De Rybel B, Weijers D.

Proc Natl Acad Sci U S A. 2017 Oct 17;114(42):E8922-E8929. doi: 10.1073/pnas.1707400114. Epub 2017 Oct 2.

5.

Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root.

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.

Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):E7641-E7649. doi: 10.1073/pnas.1705833114. Epub 2017 Aug 22.

6.

Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants.

Hsu PY, Benfey PN.

Proteomics. 2018 May;18(10):e1700038. doi: 10.1002/pmic.201700038. Epub 2017 Oct 12. Review.

PMID:
28759167
7.

Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation.

Drapek C, Sparks EE, Benfey PN.

Trends Genet. 2017 Aug;33(8):529-539. doi: 10.1016/j.tig.2017.05.002. Epub 2017 Jun 21. Review.

8.

A SIMPLE Pipeline for Mapping Point Mutations.

Wachsman G, Modliszewski JL, Valdes M, Benfey PN.

Plant Physiol. 2017 Jul;174(3):1307-1313. doi: 10.1104/pp.17.00415. Epub 2017 May 25.

9.

Tissue-Specific Transcriptome Profiling in Arabidopsis Roots.

Sparks EE, Benfey PN.

Methods Mol Biol. 2017;1610:107-122. doi: 10.1007/978-1-4939-7003-2_8.

PMID:
28439860
10.

Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus.

Nevarez PA, Qiu Y, Inoue H, Yoo CY, Benfey PN, Schnell DJ, Chen M.

Plant Physiol. 2017 Apr;173(4):1953-1966. doi: 10.1104/pp.16.00116. Epub 2017 Feb 23.

11.

A Lin28 homologue reprograms differentiated cells to stem cells in the moss Physcomitrella patens.

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.

Nat Commun. 2017 Jan 27;8:14242. doi: 10.1038/ncomms14242.

12.

Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.

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.

Dev Cell. 2016 Dec 5;39(5):585-596. doi: 10.1016/j.devcel.2016.09.031. Epub 2016 Oct 27.

13.

Control of Arabidopsis lateral root primordium boundaries by MYB36.

Fernández-Marcos M, Desvoyes B, Manzano C, Liberman LM, Benfey PN, Del Pozo JC, Gutierrez C.

New Phytol. 2017 Jan;213(1):105-112. doi: 10.1111/nph.14304. Epub 2016 Nov 7.

14.

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation.

Li S, Yamada M, Han X, Ohler U, Benfey PN.

Dev Cell. 2016 Nov 21;39(4):508-522. doi: 10.1016/j.devcel.2016.10.012. Epub 2016 Nov 10.

15.

Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis.

Hsu PY, Calviello L, Wu HL, Li FW, Rothfels CJ, Ohler U, Benfey PN.

Proc Natl Acad Sci U S A. 2016 Oct 21. pii: 201614788. [Epub ahead of print]

16.

Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy.

Clark NM, Hinde E, Winter CM, Fisher AP, Crosti G, Blilou I, Gratton E, Benfey PN, Sozzani R.

Elife. 2016 Jun 11;5. pii: e14770. doi: 10.7554/eLife.14770.

17.

Unique cell-type-specific patterns of DNA methylation in the root meristem.

Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker JR.

Nat Plants. 2016 Apr 29;2(5):16058. doi: 10.1038/nplants.2016.58.

18.

X-Ray Computed Tomography Reveals the Response of Root System Architecture to Soil Texture.

Rogers ED, Monaenkova D, Mijar M, Nori A, Goldman DI, Benfey PN.

Plant Physiol. 2016 Jul;171(3):2028-40. doi: 10.1104/pp.16.00397. Epub 2016 May 16.

19.

A Friend in Need (of Nutrients) Is a….

Liberman LM, Benfey PN.

Cell. 2016 Apr 7;165(2):269-71. doi: 10.1016/j.cell.2016.03.036.

20.

Defining the Path from Stem Cells to Differentiated Tissue.

Benfey PN.

Curr Top Dev Biol. 2016;116:35-43. doi: 10.1016/bs.ctdb.2015.12.002. Epub 2016 Feb 8. Review.

PMID:
26970612
21.

Identifying Gene Regulatory Networks in Arabidopsis by In Silico Prediction, Yeast-1-Hybrid, and Inducible Gene Profiling Assays.

Sparks EE, Benfey PN.

Methods Mol Biol. 2016;1370:29-50. doi: 10.1007/978-1-4939-3142-2_3.

PMID:
26659952
22.

MicroRNA miR396 Regulates the Switch between Stem Cells and Transit-Amplifying Cells in Arabidopsis Roots.

Rodriguez RE, Ercoli MF, Debernardi JM, Breakfield NW, Mecchia MA, Sabatini M, Cools T, De Veylder L, Benfey PN, Palatnik JF.

Plant Cell. 2015 Dec;27(12):3354-66. doi: 10.1105/tpc.15.00452. Epub 2015 Dec 8.

23.

Transcriptional control of tissue formation throughout root development.

Moreno-Risueno MA, Sozzani R, Yardımcı GG, Petricka JJ, Vernoux T, Blilou I, Alonso J, Winter CM, Ohler U, Scheres B, Benfey PN.

Science. 2015 Oct 23;350(6259):426-30. doi: 10.1126/science.aad1171.

24.

MYB36 regulates the transition from proliferation to differentiation in the Arabidopsis root.

Liberman LM, Sparks EE, Moreno-Risueno MA, Petricka JJ, Benfey PN.

Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):12099-104. doi: 10.1073/pnas.1515576112. Epub 2015 Sep 14.

25.

Large Cellular Inclusions Accumulate in Arabidopsis Roots Exposed to Low-Sulfur Conditions.

Jackson TL, Baker GW, Wilks FR Jr, Popov VA, Mathur J, Benfey PN.

Plant Physiol. 2015 Aug;168(4):1573-89. doi: 10.1104/pp.15.00465. Epub 2015 Jun 22.

26.

Genes and networks regulating root anatomy and architecture.

Wachsman G, Sparks EE, Benfey PN.

New Phytol. 2015 Oct;208(1):26-38. doi: 10.1111/nph.13469. Epub 2015 May 20. Review.

27.

Distinct sensitivities to phosphate deprivation suggest that RGF peptides play disparate roles in Arabidopsis thaliana root development.

Cederholm HM, Benfey PN.

New Phytol. 2015 Aug;207(3):683-91. doi: 10.1111/nph.13405. Epub 2015 Apr 9.

28.

Quantitative trait locus mapping reveals regions of the maize genome controlling root system architecture.

Zurek PR, Topp CN, Benfey PN.

Plant Physiol. 2015 Apr;167(4):1487-96. doi: 10.1104/pp.114.251751. Epub 2015 Feb 11.

29.

Regulation of plant root system architecture: implications for crop advancement.

Rogers ED, Benfey PN.

Curr Opin Biotechnol. 2015 Apr;32:93-98. doi: 10.1016/j.copbio.2014.11.015. Epub 2014 Nov 29. Review.

PMID:
25448235
30.

Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.

Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M.

Plant Cell. 2014 Jul;26(7):2746-60. doi: 10.1105/tpc.114.125617. Epub 2014 Jul 17.

31.

Regulation of plant stem cell quiescence by a brassinosteroid signaling module.

Vilarrasa-Blasi J, González-García MP, Frigola D, Fàbregas N, Alexiou KG, López-Bigas N, Rivas S, Jauneau A, Lohmann JU, Benfey PN, Ibañes M, Caño-Delgado AI.

Dev Cell. 2014 Jul 14;30(1):36-47. doi: 10.1016/j.devcel.2014.05.020. Epub 2014 Jun 26. Erratum in: Dev Cell. 2015 Apr 20;33(2):238.

32.

Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative.

Van Norman JM, Zhang J, Cazzonelli CI, Pogson BJ, Harrison PJ, Bugg TD, Chan KX, Thompson AJ, Benfey PN.

Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):E1300-9. doi: 10.1073/pnas.1403016111. Epub 2014 Mar 17.

33.

HEC of a job regulating stem cells.

Sparks EE, Benfey PN.

Dev Cell. 2014 Feb 24;28(4):349-50. doi: 10.1016/j.devcel.2014.02.006.

34.

Advanced imaging techniques for the study of plant growth and development.

Sozzani R, Busch W, Spalding EP, Benfey PN.

Trends Plant Sci. 2014 May;19(5):304-10. doi: 10.1016/j.tplants.2013.12.003. Epub 2014 Jan 13. Review.

35.

To branch or not to branch: the role of pre-patterning in lateral root formation.

Van Norman JM, Xuan W, Beeckman T, Benfey PN.

Development. 2013 Nov;140(21):4301-10. doi: 10.1242/dev.090548. Review.

36.

Spatial coordination between stem cell activity and cell differentiation in the root meristem.

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.

Dev Cell. 2013 Aug 26;26(4):405-15. doi: 10.1016/j.devcel.2013.06.025.

37.

Spatiotemporal signalling in plant development.

Sparks E, Wachsman G, Benfey PN.

Nat Rev Genet. 2013 Sep;14(9):631-44. doi: 10.1038/nrg3541. Review.

38.

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.

Li S, Liberman LM, Mukherjee N, Benfey PN, Ohler U.

Genome Res. 2013 Oct;23(10):1730-9. doi: 10.1101/gr.149310.112. Epub 2013 Jul 1.

39.

Patterning the primary root in Arabidopsis.

Cederholm HM, Iyer-Pascuzzi AS, Benfey PN.

Wiley Interdiscip Rev Dev Biol. 2012 Sep-Oct;1(5):675-91. doi: 10.1002/wdev.49. Epub 2012 Mar 22. Review.

PMID:
23799568
40.

Promoting collaborative interdisciplinary research at the Duke Center for Systems Biology.

Stone JE, Benfey PN, You L.

ACS Synth Biol. 2012 May 18;1(5):153-5. doi: 10.1021/sb300036z. No abstract available.

41.

Polarized radicals.

Liberman LM, Benfey PN.

Cell. 2013 Apr 11;153(2):285-6. doi: 10.1016/j.cell.2013.03.042.

42.

3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture.

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.

Proc Natl Acad Sci U S A. 2013 Apr 30;110(18):E1695-704. doi: 10.1073/pnas.1304354110. Epub 2013 Apr 11.

43.

High-resolution metabolic mapping of cell types in plant roots.

Moussaieff A, Rogachev I, Brodsky L, Malitsky S, Toal TW, Belcher H, Yativ M, Brady SM, Benfey PN, Aharoni A.

Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):E1232-41. doi: 10.1073/pnas.1302019110. Epub 2013 Mar 8.

44.

Genotypic recognition and spatial responses by rice roots.

Fang S, Clark RT, Zheng Y, Iyer-Pascuzzi AS, Weitz JS, Kochian LV, Edelsbrunner H, Liao H, Benfey PN.

Proc Natl Acad Sci U S A. 2013 Feb 12;110(7):2670-5. doi: 10.1073/pnas.1222821110. Epub 2013 Jan 29.

45.

High-throughput, noninvasive imaging of root systems.

Iyer-Pascuzzi AS, Zurek PR, Benfey PN.

Methods Mol Biol. 2013;959:177-87. doi: 10.1007/978-1-62703-221-6_11.

PMID:
23299675
46.

Toward a systems analysis of the root.

Benfey PN.

Cold Spring Harb Symp Quant Biol. 2012;77:91-6. doi: 10.1101/sqb.2012.77.014506. Epub 2012 Dec 12. Review.

47.

A microfluidic device and computational platform for high-throughput live imaging of gene expression.

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.

Nat Methods. 2012 Nov;9(11):1101-6. doi: 10.1038/nmeth.2185. Epub 2012 Sep 30.

48.

A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division.

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.

Cell. 2012 Aug 31;150(5):1002-15. doi: 10.1016/j.cell.2012.07.017. Epub 2012 Aug 23.

49.

GiA Roots: software for the high throughput analysis of plant root system architecture.

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.

BMC Plant Biol. 2012 Jul 26;12:116. doi: 10.1186/1471-2229-12-116.

50.

POWRS: position-sensitive motif discovery.

Davis IW, Benninger C, Benfey PN, Elich T.

PLoS One. 2012;7(7):e40373. doi: 10.1371/journal.pone.0040373. Epub 2012 Jul 5.

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