Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells
- aPlant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695;
- bBiomathematics Program, North Carolina State University, Raleigh, NC 27695;
- cDepartamento de Botánica y Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias, Facultad de Biología, Universidad de Salamanca, 37185 Salamanca, Spain;
- dLaboratory of Biochemistry, Wageningen University, 6703HA, Wageningen, The Netherlands;
- eDepartment of Stem Cell Biology, University of Heidelberg, Heidelberg D-69120, Germany;
- fElectrical and Computer Engineering Department, North Carolina State University, Raleigh, NC 27695
See allHide authors and affiliations
Edited by Julia Bailey-Serres, University of California, Riverside, CA, and approved July 31, 2017 (received for review May 7, 2017)

Online Impact
Article Information
- Published in issue September 5, 2017.
- Published first August 21, 2017.
Author Information
- Maria Angels de Luis Balaguera,
- Adam P. Fishera,
- Natalie M. Clarka,b,
- Maria Guadalupe Fernandez-Espinosac,
- Barbara K. Möllerd,1,
- Dolf Weijersd,
- Jan U. Lohmanne,
- Cranos Williamsf,
- Oscar Lorenzoc, and
- Rosangela Sozzania,b,2
- aPlant and Microbial Biology Department, North Carolina State University, Raleigh, NC 27695;
- bBiomathematics Program, North Carolina State University, Raleigh, NC 27695;
- cDepartamento de Botánica y Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias, Facultad de Biología, Universidad de Salamanca, 37185 Salamanca, Spain;
- dLaboratory of Biochemistry, Wageningen University, 6703HA, Wageningen, The Netherlands;
- eDepartment of Stem Cell Biology, University of Heidelberg, Heidelberg D-69120, Germany;
- fElectrical and Computer Engineering Department, North Carolina State University, Raleigh, NC 27695
Edited by Julia Bailey-Serres, University of California, Riverside, CA, and approved July 31, 2017 (received for review May 7, 2017)
Footnotes
↵1Present addresses: Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), B-9052 Ghent, Belgium; and Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium.
- ↵2To whom correspondence should be addressed. Email: ross_sozzani{at}ncsu.edu.
Author contributions: M.A.d.L.B. and R.S. designed research; M.A.d.L.B., A.P.F., N.M.C., M.G.F.-E., B.K.M., D.W., O.L., and R.S. performed research; J.U.L. and C.W. contributed new reagents/analytic tools; M.A.d.L.B., A.P.F., and N.M.C. analyzed data; and M.A.d.L.B. and R.S. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, https://www.ncbi.nlm.nih.gov/geo (accession nos. GSE76710, GSE97792, and GSE97857).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1707566114/-/DCSupplemental.
Cited By...
This article has been cited by the following articles in journals that are participating in Crossref Cited-by Linking.
- Javier Brumos, Linda M. Robles, Jeonga Yun, Thien C. Vu, Savannah Jackson, Jose M. Alonso, Anna N. StepanovaDevelopmental Cell 2018 47 3
- Michitaro Shibata, Christian Breuer, Ayako Kawamura, Natalie M. Clark, Bart Rymen, Luke Braidwood, Kengo Morohashi, Wolfgang Busch, Philip N. Benfey, Rosangela Sozzani, Keiko SugimotoDevelopment 2018 145 3
- Wouter Smet, Iris Sevilem, Maria Angels de Luis Balaguer, Brecht Wybouw, Eliana Mor, Shunsuke Miyashima, Bernhard Blob, Pawel Roszak, Thomas B. Jacobs, Mark Boekschoten, Guido Hooiveld, Rosangela Sozzani, Ykä Helariutta, Bert De RybelCurrent Biology 2019 29 3
- Inmaculada Sánchez-Vicente, María Guadalupe Fernández-Espinosa, Oscar Lorenzo, Renaud BrouquisseJournal of Experimental Botany 2019 70 17
- Samiul Haque, Jabeen S Ahmad, Natalie M Clark, Cranos M Williams, Rosangela SozzaniCurrent Opinion in Plant Biology 2019 47
- Jose Lugo-Martinez, Daniel Ruiz-Perez, Giri Narasimhan, Ziv Bar-JosephMicrobiome 2019 7 1
- Keiichi Mochida, Satoru Koda, Komaki Inoue, Ryuei NishiiFrontiers in Plant Science 2018 9
- Pablo Perez-Garcia, Miguel A. Moreno-RisuenoDevelopmental Biology 2018 442 1
- Elena R. Alvarez‐Buylla, Berenice García‐Ponce, María de la Paz Sánchez, Carlos Espinosa‐Soto, Mónica L. García‐Gómez, Alma Piñeyro‐Nelson, Adriana Garay‐ArroyoNew Phytologist 2019 223 3
- Natalie M. Clark, Eli Buckner, Adam P. Fisher, Emily C. Nelson, Thomas T. Nguyen, Abigail R. Simmons, Maria A. de Luis Balaguer, Tiara Butler-Smith, Parnell J. Sheldon, Dominique C. Bergmann, Cranos M. Williams, Rossangela SozzaniNature Communications 2019 10 1
- Amy Marshall-Colón, Daniel J. KliebensteinTrends in Plant Science 2019 24 9
- Shubhada R. Kulkarni, Klaas VandepoeleBiochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2020 1863 6
- Natalie M. Clark, Adam P. Fisher, Barbara Berckmans, Lisa Van den Broeck, Emily C. Nelson, Thomas T. Nguyen, Estefano Bustillo-Avendaño, Sophia G. Zebell, Miguel A. Moreno-Risueno, Rüdiger Simon, Kimberly L. Gallagher, Rosangela SozzaniProceedings of the National Academy of Sciences 2020 117 26
- Ryan J. Spurney, Lisa Van den Broeck, Natalie M. Clark, Adam P. Fisher, Maria A. de Luis Balaguer, Rosangela SozzaniThe Plant Journal 2020 101 3
- Lisa Van den Broeck, Max Gordon, Dirk Inzé, Cranos Williams, Rosangela SozzaniFrontiers in Genetics 2020 11
- Qi Song, Jiyoung Lee, Shamima Akter, Matthew Rogers, Ruth Grene, Song LiNucleic Acids Research 2020 48 11
- Selene L Fernandez-Valverde, Felipe Aguilera, René Alexander Ramos-DíazIntegrative and Comparative Biology 2018 58 4
- MCRiceRepGP: a framework for the identification of genes associated with sexual reproduction in riceAgnieszka A. Golicz, Prem L. Bhalla, Mohan B. SinghThe Plant Journal 2018 96 1
- Ruben Gutzat, Klaus Rembart, Thomas Nussbaumer, Falko Hofmann, Rahul Pisupati, Gabriele Bradamante, Nina Daubel, Angelika Gaidora, Nicole Lettner, Mattia Donà, Magnus Nordborg, Michael Nodine, Ortrun Mittelsten ScheidThe EMBO Journal 2020 39 20
- José G. Vallarino, Catharina Merchante, José F. Sánchez‐Sevilla, María Angels Luis Balaguer, Delphine M. Pott, María T. Ariza, Ana Casañal, David Posé, Amalia Vioque, Iraida Amaya, Lothar Willmitzer, Roberto Solano, Rosangela Sozzani, Alisdair R. Fernie, Miguel A. Botella, James J. Giovannoni, Victoriano Valpuesta, Sonia OsorioPlant Biotechnology Journal 2020 18 4
- Marta Bjornson, Kaisa Kajala, Cyril Zipfel, Pingtao DingBIO-PROTOCOL 2020 10 20
- Blanca Jazmín Reyes-Hernández, Svetlana Shishkova, Rachel Amir, Aranza Xhaly Quintana-Armas, Selene Napsucialy-Mendivil, Rocio Guadalupe Cervantes-Gamez, Héctor Hugo Torres-Martínez, Jesús Montiel, Christopher D Wood, Joseph G DubrovskyJournal of Experimental Botany 2019 70 15
- Parul Gupta, Sunil Kumar Singh2019
- Chirag Gupta, Andy PereiraF1000Research 2019 8
- Kengo Morohashi, Eugenia RussinovaJournal of Plant Research 2019 132 2
- Sandra Cortijo, Marcel Bhattarai, James C. W. Locke, Sebastian E. AhnertFrontiers in Plant Science 2020 11
- Lucia Maß, Michael Holtmannspötter, Sabine ZachgoThe Plant Journal 2020 104 5
- Giuseppe Jurman, Michele Filosi, Roberto Visintainer, Samantha Riccadonna, Cesare Furlanello2019 1883
- Ihteram Ullah, Mahmoud Magdy, Lixiang Wang, Mengyu Liu, Xia LiScientific Reports 2019 9 1
- Reza Mousavi, Sri Harsha Konuru, Daniel LoboBriefings in Bioinformatics 2021
- Mónica L García-Gómez, Aaron Castillo-Jiménez, Juan Carlos Martínez-García, Elena R Álvarez-BuyllaCurrent Opinion in Plant Biology 2020 57
- Margaret Anne Pelayo, Nobutoshi Yamaguchi, Toshiro ItoCurrent Opinion in Plant Biology 2021 61
- Alexandru M.F. TomescuBiological Reviews 2021
Article usage
Citation Manager Formats
Article Classifications
- Biological Sciences
- Plant Biology