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Items: 41

1.

Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks.

Clark NM, Buckner E, Fisher AP, Nelson EC, Nguyen TT, Simmons AR, de Luis Balaguer MA, Butler-Smith T, Sheldon PJ, Bergmann DC, Williams CM, Sozzani R.

Nat Commun. 2019 Dec 6;10(1):5574. doi: 10.1038/s41467-019-13132-2.

2.

Automated Imaging, Tracking, and Analytics Pipeline for Differentiating Environmental Effects on Root Meristematic Cell Division.

Buckner E, Madison I, Chou H, Matthiadis A, Melvin CE, Sozzani R, Williams C, Long TA.

Front Plant Sci. 2019 Nov 19;10:1487. doi: 10.3389/fpls.2019.01487. eCollection 2019.

3.

tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks.

Spurney RJ, Van den Broeck L, Clark NM, Fisher AP, de Luis Balaguer MA, Sozzani R.

Plant J. 2020 Feb;101(3):716-730. doi: 10.1111/tpj.14558. Epub 2019 Nov 27.

PMID:
31571287
4.

Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development.

Vallarino JG, Merchante C, Sánchez-Sevilla JF, de Luis Balaguer MA, Pott DM, Ariza MT, Casañal A, Posé D, Vioque A, Amaya I, Willmitzer L, Solano R, Sozzani R, Fernie AR, Botella MA, Giovannoni JJ, Valpuesta V, Osorio S.

Plant Biotechnol J. 2019 Sep 18. doi: 10.1111/pbi.13257. [Epub ahead of print]

5.

Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana.

Powers SK, Holehouse AS, Korasick DA, Schreiber KH, Clark NM, Jing H, Emenecker R, Han S, Tycksen E, Hwang I, Sozzani R, Jez JM, Pappu RV, Strader LC.

Mol Cell. 2019 Oct 3;76(1):177-190.e5. doi: 10.1016/j.molcel.2019.06.044. Epub 2019 Aug 14.

PMID:
31421981
6.

The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size.

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.

Curr Biol. 2019 Apr 1;29(7):1199-1205.e4. doi: 10.1016/j.cub.2019.02.022. Epub 2019 Mar 14.

PMID:
30880016
7.

DOF2.1 Controls Cytokinin-Dependent Vascular Cell Proliferation Downstream of TMO5/LHW.

Smet W, Sevilem I, de Luis Balaguer MA, Wybouw B, Mor E, Miyashima S, Blob B, Roszak P, Jacobs TB, Boekschoten M, Hooiveld G, Sozzani R, Helariutta Y, De Rybel B.

Curr Biol. 2019 Feb 4;29(3):520-529.e6. doi: 10.1016/j.cub.2018.12.041. Epub 2019 Jan 24.

8.

Mobile PEAR transcription factors integrate positional cues to prime cambial growth.

Miyashima S, Roszak P, Sevilem I, Toyokura K, Blob B, Heo JO, Mellor N, Help-Rinta-Rahko H, Otero S, Smet W, Boekschoten M, Hooiveld G, Hashimoto K, Smetana O, Siligato R, Wallner ES, Mähönen AP, Kondo Y, Melnyk CW, Greb T, Nakajima K, Sozzani R, Bishopp A, De Rybel B, Helariutta Y.

Nature. 2019 Jan;565(7740):490-494. doi: 10.1038/s41586-018-0839-y. Epub 2019 Jan 9.

PMID:
30626969
9.

Computational prediction of gene regulatory networks in plant growth and development.

Haque S, Ahmad JS, Clark NM, Williams CM, Sozzani R.

Curr Opin Plant Biol. 2019 Feb;47:96-105. doi: 10.1016/j.pbi.2018.10.005. Epub 2018 Nov 14. Review.

PMID:
30445315
10.

Tracking Gene Expression via Light Sheet Microscopy and Computer Vision in Living Organisms.

Buckner E, Ottley C, Williams C, Luis Balaguer A, Melvin CE, Sozzani R.

Conf Proc IEEE Eng Med Biol Soc. 2018 Jul;2018:818-821. doi: 10.1109/EMBC.2018.8512416.

PMID:
30440517
11.

Identifying Differentially Expressed Genes Using Fluorescence-Activated Cell Sorting (FACS) and RNA Sequencing from Low Input Samples.

Clark NM, Fisher AP, Sozzani R.

Methods Mol Biol. 2018;1819:139-151. doi: 10.1007/978-1-4939-8618-7_6.

PMID:
30421402
12.

Exposure to heavy metal stress triggers changes in plasmodesmatal permeability via deposition and breakdown of callose.

O'Lexy R, Kasai K, Clark N, Fujiwara T, Sozzani R, Gallagher KL.

J Exp Bot. 2018 Jun 27;69(15):3715-3728. doi: 10.1093/jxb/ery171.

13.

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.

14.

Dose-Duration Reciprocity for G protein activation: Modulation of kinase to substrate ratio alters cell signaling.

Liao KL, Melvin CE, Sozzani R, Jones RD, Elston TC, Jones AM.

PLoS One. 2017 Dec 29;12(12):e0190000. doi: 10.1371/journal.pone.0190000. eCollection 2017.

15.

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.

16.

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.

17.

Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells.

de Luis Balaguer MA, Fisher AP, Clark NM, Fernandez-Espinosa MG, Möller BK, Weijers D, Lohmann JU, Williams C, Lorenzo O, Sozzani R.

Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):E7632-E7640. doi: 10.1073/pnas.1707566114. Epub 2017 Aug 21.

18.

Genetic Architecture and Molecular Networks Underlying Leaf Thickness in Desert-Adapted Tomato Solanum pennellii.

Coneva V, Frank MH, Balaguer MAL, Li M, Sozzani R, Chitwood DH.

Plant Physiol. 2017 Sep;175(1):376-391. doi: 10.1104/pp.17.00790. Epub 2017 Aug 9.

19.

Inferring Gene Regulatory Networks in the Arabidopsis Root Using a Dynamic Bayesian Network Approach.

de Luis Balaguer MA, Sozzani R.

Methods Mol Biol. 2017;1629:331-348. doi: 10.1007/978-1-4939-7125-1_21.

PMID:
28623595
20.
21.

Light sheet microscopy reveals more gradual light attenuation in light-green versus dark-green soybean leaves.

Slattery RA, Grennan AK, Sivaguru M, Sozzani R, Ort DR.

J Exp Bot. 2016 Aug;67(15):4697-709. doi: 10.1093/jxb/erw246. Epub 2016 Jun 20.

22.

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.

23.

Multi-sample Arabidopsis Growth and Imaging Chamber (MAGIC) for long term imaging in the ZEISS Lightsheet Z.1.

de Luis Balaguer MA, Ramos-Pezzotti M, Rahhal MB, Melvin CE, Johannes E, Horn TJ, Sozzani R.

Dev Biol. 2016 Nov 1;419(1):19-25. doi: 10.1016/j.ydbio.2016.05.029. Epub 2016 May 26.

24.

Uncovering the networks involved in stem cell maintenance and asymmetric cell division in the Arabidopsis root.

Fisher AP, Sozzani R.

Curr Opin Plant Biol. 2016 Feb;29:38-43. doi: 10.1016/j.pbi.2015.11.002. Epub 2015 Dec 17. Review.

PMID:
26707611
25.

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.

26.

Intercellular protein movement: deciphering the language of development.

Gallagher KL, Sozzani R, Lee CM.

Annu Rev Cell Dev Biol. 2014;30:207-33. doi: 10.1146/annurev-cellbio-100913-012915. Review.

PMID:
25288113
27.

Experimental data and computational modeling link auxin gradient and development in the Arabidopsis root.

Clark NM, de Luis Balaguer MA, Sozzani R.

Front Plant Sci. 2014 Jul 7;5:328. doi: 10.3389/fpls.2014.00328. eCollection 2014. Review.

28.

Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants.

Kajala K, Ramakrishna P, Fisher A, Bergmann DC, De Smet I, Sozzani R, Weijers D, Brady SM.

Ann Bot. 2014 Jun;113(7):1083-1105. Review.

29.

Postembryonic control of root meristem growth and development.

Sozzani R, Iyer-Pascuzzi A.

Curr Opin Plant Biol. 2014 Feb;17:7-12. doi: 10.1016/j.pbi.2013.10.005. Epub 2013 Nov 5. Review.

PMID:
24507488
30.

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.

31.

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.

32.

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.

33.

Integrative systems biology: an attempt to describe a simple weed.

Liberman LM, Sozzani R, Benfey PN.

Curr Opin Plant Biol. 2012 Apr;15(2):162-7. doi: 10.1016/j.pbi.2012.01.004. Epub 2012 Jan 23. Review.

34.

High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype.

Sozzani R, Benfey PN.

Genome Biol. 2011;12(3):219. doi: 10.1186/gb-2011-12-3-219. Epub 2011 Mar 28. Review.

35.

Arabidopsis homologs of the petunia hairy meristem gene are required for maintenance of shoot and root indeterminacy.

Engstrom EM, Andersen CM, Gumulak-Smith J, Hu J, Orlova E, Sozzani R, Bowman JL.

Plant Physiol. 2011 Feb;155(2):735-50. doi: 10.1104/pp.110.168757. Epub 2010 Dec 20.

36.

Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth.

Sozzani R, Cui H, Moreno-Risueno MA, Busch W, Van Norman JM, Vernoux T, Brady SM, Dewitte W, Murray JA, Benfey PN.

Nature. 2010 Jul 1;466(7302):128-32. doi: 10.1038/nature09143.

37.

The E2FD/DEL2 factor is a component of a regulatory network controlling cell proliferation and development in Arabidopsis.

Sozzani R, Maggio C, Giordo R, Umana E, Ascencio-Ibañez JT, Hanley-Bowdoin L, Bergounioux C, Cella R, Albani D.

Plant Mol Biol. 2010 Mar;72(4-5):381-95. doi: 10.1007/s11103-009-9577-8. Epub 2009 Nov 25.

PMID:
19937368
38.

The Arabidopsis MCM2 gene is essential to embryo development and its over-expression alters root meristem function.

Ni DA, Sozzani R, Blanchet S, Domenichini S, Reuzeau C, Cella R, Bergounioux C, Raynaud C.

New Phytol. 2009 Oct;184(2):311-22. doi: 10.1111/j.1469-8137.2009.02961.x. Epub 2009 Jul 24.

39.

Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.

Ascencio-Ibáñez JT, Sozzani R, Lee TJ, Chu TM, Wolfinger RD, Cella R, Hanley-Bowdoin L.

Plant Physiol. 2008 Sep;148(1):436-54. doi: 10.1104/pp.108.121038. Epub 2008 Jul 23.

40.

Two cell-cycle regulated SET-domain proteins interact with proliferating cell nuclear antigen (PCNA) in Arabidopsis.

Raynaud C, Sozzani R, Glab N, Domenichini S, Perennes C, Cella R, Kondorosi E, Bergounioux C.

Plant J. 2006 Aug;47(3):395-407. Epub 2006 Jun 12.

41.

Interplay between Arabidopsis activating factors E2Fb and E2Fa in cell cycle progression and development.

Sozzani R, Maggio C, Varotto S, Canova S, Bergounioux C, Albani D, Cella R.

Plant Physiol. 2006 Apr;140(4):1355-66. Epub 2006 Mar 2.

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