EDUCATION, ACADEMIC AND PROFESSIONAL EXPERIENCE

 

EDUCATION

1993                Bachelor of Science, Major in Biochemistry. PUC

1997                MSc, Major in Biochemistry. PUC

2003                Doctoral degree in Biochemistry and Molecular Biology, Michigan State University. Advisor: Pamela Green.

2003                Post-doctoral research. Department of Plant Biology and MSU-DOE Plant Research Laboratory. Michigan State University.

2004                Research Assistant Scientist. Department of Biology. New York University. Advisor: Gloria Coruzzi.

2006                Research Assistant Scientist. Department of Biology. New York University. Advisor: Gloria Coruzzi.

APPOINTMENTS

2021- to date   Director for Research and Planning, Faculty of Biological Sciences. PUC

2017- to date   Full Professor, Departamento de Genética Molecular y Microbiología. PUC

2012- 2018     Chair of Molecular Genetics and Microbiology at PUC

2011-2017      Associate Professor, Departamento de Genética Molecular y Microbiología. PUC

2006-2011      Assistant Professor, Departamento de Genética Molecular y Microbiología. PUC

 

PROFESSIONAL ACTIVITIES [selection]

2018-present  F1000 Faculty.
2017-present Guest Editor for The Plant Cell
2014-present Associate Editor for Molecular Plant
2020-present Associate Editor for Journal of Experimental Botany.
2009-present Associate Editor for Plant Molecular Biology (stepped down due to time constraints).
2015-2019      Handling Editor for Plant Cell Physiology (stepped down due to time constraints).
2017-2018      Vice-Chair for the Global Plant Council (stepped down due to time constraints).
2016-2018      Advisory board for Plantae, American Society of Plant Biologists.
2016-2017      Founder and first elected President for the Chilean Society of Plant Biologists.
2012-2018      Chair of Molecular Genetics and Microbiology (stepped down for sabbatical period)
2010-2018.  Chair of Molecular Genetics and Microbiology, doctoral program in Biological Sciences.
2014-2016      Chief Editor for Frontiers in Plant Physiology – Plant Systems and Synthetic Biology Section [stepped down due to other editorial commitments]
2010-2016.      Associate editor for Frontiers in Plant Physiology/Plant Systems Biology.
2011-2013       Chair of the Scientific Advisory Board for the National Center for Genomics, Proteomics and Bioinformatics – OMICS Solutions.
2010                 Arabidopsis Informatics Workshop. Nottingham, United Kingdom.
2009-2011      Review Panel, Study Group Biology 3, FONDECYT, CONICYT.
2009-2010      Board of Directors iPlant Cyberinfrastructure Collaborative (NSF-funded project).
2009-2011      Biotechnology Committee, Advanced Human Capital Program, CONICYT.
2009-2014      Co-Chair of the “Systems Biology” subcommittee of the Multinational Arabidopsis Steering Committee.
2009           Member of the Nominating Committee for the iPlant Board of Directors.
2009-2011      Member of the board of directors of the Sociedad de Bioquímica y Biología Molecular de Chile.
2008           Member of the 2020 NSF panel to discuss a strategy for the future of Arabidopsis research.  The panel worked to develop a vision for setting goals and funding priorities for Arabidopsis 2020 programs.
2007-2009      Member of the Biochemistry curriculum committee.
2007-2014      Member of the “Systems Biology” subcommittee of the Multinational Arabidopsis Steering Committee.
2005-2014      Member of the International Plant Sulfur Research Network.
2005-2014      Member of the American Society of Plant Biologists.

POSTDOCTORAL SUPERVISION (FIRST POSITION)

2022                Francisca Díaz.
2022                Grace Armijo.
2022                Tomás Moyano.
2022                Karin Rothkegel.
2022                Andrea Vega (Assistant Professor at UAI)
2022                Jonathan Maldonado (Assistant Professor,USACH)
2016                Susana Cabello (VRI, PUC)
2016                Ricardo Nilo (Researcher, UNAB)
2016                Elena Vidal (Assistant Professor, U. Mayor)
2015                Alex Slater (Assistant Professor, U. Mayor)
2015                José O’Brien (Assistant Professor, PUC)
2015                Javier Canales (Assistant Professor, U. Austral de Chile)
2013                Adriana Bastías (Researcher INIA, Rayentué)
2012                Diana Gras (Researcher CONICET,CCTA,Argentina)

PHD SUPERVISION (FIRST POSITION AFTER GRADUATION)
Current           Jonathan Morales,  (2022, Expected).
Current           Liliana Lamig (2022, Expected).
Current           Laura Delgado (2022, Expected).
Current           Thomas Dussarratt (2022, Expected).
Current           Isabel Pochet (2022, Expected).
Current           Susan Hitschfeld (2022, Expected).
Current           Valentina Zapata (2022, Expected).
Current           Francois Gaspard (2022, Expected).
Current           Valentina Núñez (2024, Expected).
Current           Jorge del Rosario (2024, Expected).
Current           Felipe Sobarzo (2025, Expected).
2021                Alejandro Fonseca (Postdoc, Sweden)
2021                Catalina Ibarra (Postdoc, UAI)
2020                Sebastián Moreno (Postdoc, United Kingdom)
2020                Isabel Fredes (School teacher)
2017                Orlando Contreras (Postdoc, Sweden).
2016                Viviana Araus (Postdoc, NYU)
2016                Tomás Puelma (Software Engineer, BEE).
2015                Eleodoro Riveras. (Postdoc, Medicine, PUC)
2013                Tatiana Kraiser (Illumina FAS)
2013                José Miguel Alvarez (Postdoc, NYU)
2012                Pamela Naulin (Postdoc, PUC)
2010                Elena Vidal (Postdoc position, PUC)
2009                 Alexander Vergara. Co-advisor. (Postdoc, U. Chile)

 

UNDERGRADUATE (FIRST POSITION AFTER GRADUATION)

2021                Paula Gacitúa, Biochemistry (Master, U de los Andes)
2018                Valentina Zapata, Biochemestry (PhD, PUC)
2018                María Medina, Biochemistry (Master, U. of Cologne)
2017                Gabriela Carrasco. Biochemistry. (Research Assistant, PUC)
2015                Enzo Viera. Bioinformatics Engineering. (Research Assistant, U Talca)
2014                Juan Simón Alamos. Agronomy. (PhD, Berkeley, CA, USA)
2013                Mabel Vidal. Bioinformatics Engineering. (Research Assistant, Iowa State University, IO, USA)
2013                Bernardo Pollack. Biochemistry. (PhD, U. of Cambridge, UK)
2012                Tomás Moyano. Biochemistry. (PhD, PUC)
2010                Eleodoro Riveras. Biochemistry. (PhD, PUC)
2009                Javiera de la Cruz. Biology. (Masters, PUCV)
2009                Pamela Naulin. Biochemistry. (PhD, PUC)
2008                Claudia Valdés. Industrial Engineering. (Lab Manager, PUC)
2008                Patricio Del Sol. Civil Engineering, Computer Sciences. (Software developer, MapCity)
2008                Beatriz Hamilton. Design. (Consulting)
2008                Manuela Garretón. Design. Best thesis award. (Masters program NYU, USA)
2008                Viviana Araus. Biology. (PhD, PUC)
2007                Karem Tamayo. Biology. (Lab Manager, PUC)

HONORS AND AWARDS [selection]

2018                Friedrich Wilhelm Bessel Research Award. Alexander von Humboldt Foundation. Germany.
2018                John A. Boezi Memorial Alumnus Award. Biochemistry and Molecular Biology. Michigan State University. USA.
2012                Howard Hughes Medical Institute International Early Career Scientist Award (2012-2016). USA.
2012                Patent preparation award. IV Intelectual Property Contest. P. Universidad Católica de Chile.
2010                Patent preparation award. II Intelectual Property Contest. P. Universidad Católica de Chile.
2009                Outstanding Young Scientist Award. Sociedad de Biología de Chile – Grupo BIOS.

 

INTELLECTUAL PROPERTY

1. Patent Application: “Regulation of nitrate uptake and nitrogen use by BTB genes”. Inventor: Gutiérrez RA, Araus, EV and Vidal EA (Serial:14/921709). Filed on 2017. LICENSE negotiation ongoing.
2. Patent Application: “Plant regulatory genes promoting association with nitrogen fixing bacteria”. Inventor: Kraiser T, Gonzalez B, Gutiérrez RA. (Serial: 14/083,193). Filed on 2013.
3. Patent Application: “Transcription factors in plants related to levels of nitrate and methods of using the same” Inventor: Álvarez JM, Gutiérrez RA. (Application Number 72195-WO-PCT). Filed on 2013. LICENSED in 2013.
4. Patent Application: «Methods of affecting nitrogen assimilation in plants» Inventors: Coruzzi G, Nero D., Gutiérrez RA. (Serial: 60/919,818; 13/371,152). Filed on 2007.
5. Patent Application: «Methods of affecting plant growth with microRNA » Inventors: Coruzzi GM, Birnbaum KD, Gifford ML, Gutiérrez R.A. (Serial: 60/918,443;14/134,624). Filed on March 16, 2007
6. Patent: «System and method for representing interactions between multiple inputs» Inventors: Shasha D, Coruzzi GM, Gutiérrez RA, Poultney C. Filed on 2004. Granted 2010: US780573 B2.

 

GRANTS as PI [selection]

2022-2025      Nitrate control of leaf growth and size in Arabidopsis thaliana, PI, FONDECYT, Chile.
2021-2025      Recuperación de papa del desierto resistente a sequía y bajo nitrógeno: Establecimiento de un método de cultivo y estrategia de comercialización para su venta. PI. FIA, Chile.
2019-2021      CONICYT-Max Planck Institute. PI. CONICYT, Chile.
2018-2021      Nitrate Regulatory Networks Controlling Early Post-Embryonic Plant Growth. PI. FONDECYT, Chile.
2011-2020      FONDAP Center for Genome Regulation. PI. CONICYT – Santiago, Chile.
2015-2020      EvoNet. A phylogenomic and systems biology approach to identify genes underlying plant survival in marginal, low-N soils. co-PI. Department of Energy, USA.
2015                Science Cloud: A platform for collaborative interdisciplinary research. FONDEQUIP, Chile.
2015-2016      International networks. PI. CONICYT, Chile.
2015-2017      ICM: Millennium Nucleus Center for Plant Systems and Synthetic Biology. Director. Chile
2014-2016      Evaluation of Plant Signaling Networks in Natural Environments. co-PI. H2020-MSCA-RISE-2014. EU.

 

FORMAL COLLABORATION NETWORKS

SIGNAT Plant Signaling Networks in Natural Environments. An international research and exchange network

 

 

PUBLICATIONS

1. Contreras-López, O., Vidal, E.A., Riveras, E., Alvarez, J.M., Moyano, T.C., Sparks, E.E., Medina, J., Pasquino, A., Benfey, P.N., Coruzzi, G.M., Gutiérrez, R.A., 2022. Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate. Proc Natl Acad Sci U S A 119. https://doi.org/10.1073/pnas.2107879119
2. Di Genova, A., Nardocci, G., Maldonado-Agurto, R., Hodar, C., Valdivieso, C., Morales, P., Gajardo, F., Marina, R., Gutiérrez, R.A., Orellana, A., Cambiazo, V., González, M., Glavic, A., Mendez, M.A., Maass, A., Allende, M.L., Montecino, M.A., 2022. Genome sequencing and transcriptomic analysis of the Andean killifish Orestias ascotanensis reveals adaptation to high-altitude aquatic life. Genomics 114, 305–315. https://doi.org/10.1016/j.ygeno.2021.12.018
3. Dussarrat, T., Prigent, S., Latorre, C., Bernillon, S., Flandin, A., Díaz, F.P., Cassan, C., Van Delft, P., Jacob, D., Varala, K., Joubes, J., Gibon, Y., Rolin, D., Gutiérrez, R.A., Pétriacq, P., 2022. Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience. New Phytol 234, 1614–1628. https://doi.org/10.1111/nph.18095
4. Lamig, L., Moreno, S., Álvarez, J.M., Gutiérrez, R.A., 2022. Molecular mechanisms underlying nitrate responses in plants. Curr Biol 32, R433–R439. https://doi.org/10.1016/j.cub.2022.03.022
5. Maldonado, J.E., Gaete, A., Mandakovic, D., Aguado-Norese, C., Aguilar, M., Gutiérrez, R.A., González, M., 2022. Partners to survive: Hoffmannseggia doellii root-associated microbiome at the Atacama Desert. New Phytol 234, 2126–2139. https://doi.org/10.1111/nph.18080
6. Cerda, A., Rivera, M., Armijo, G., Ibarra-Henriquez, C., Reyes, J., Blázquez-Sánchez, P., Avilés, J., Arce, A., Seguel, A., Brown, A.J., Vásquez, Y., Cortez-San Martín, M., Cubillos, F., García, P., Ferres, M., Ramírez-Sarmiento, C.A., Federici, F., Gutiérrez, R.A., 2021. A One-Step open RT-qPCR for SARS-CoV-2 detection. medRxiv 2021.11.29.21267000. https://doi.org/10.1101/2021.11.29.21267000
7. Eshel, G., Araus, V., Undurraga, S., Soto, D.C., Moraga, C., Montecinos, A., Moyano, T., Maldonado, J., Díaz, F.P., Varala, K., Nelson, C.W., Contreras-López, O., Pal-Gabor, H., Kraiser, T., Carrasco-Puga, G., Nilo-Poyanco, R., Zegar, C.M., Orellana, A., Montecino, M., Maass, A., Allende, M.L., DeSalle, R., Stevenson, D.W., González, M., Latorre, C., Coruzzi, G.M., Gutiérrez, R.A., 2021. Plant ecological genomics at the limits of life in the Atacama Desert. Proc Natl Acad Sci U S A 118. https://doi.org/10.1073/pnas.2101177118
8. González-Martín, A., Moyano, T., Gutiérrez, D.A., Carvajal, F.J., Cerpa, W., Hanley, J.G., Gutiérrez, R.A., Álvarez, A.R., 2021. c-Abl regulates a synaptic plasticity-related transcriptional program involved in memory and learning. Prog Neurobiol 205, 102122. https://doi.org/10.1016/j.pneurobio.2021.102122
9. Herrera-Vásquez, A., Fonseca, A., Ugalde, J.M., Lamig, L., Seguel, A., Moyano, T.C., Gutiérrez, R.A., Salinas, P., Vidal, E.A., Holuigue, L., 2021. TGA class II transcription factors are essential to restrict oxidative stress in response to UV-B stress in Arabidopsis. J Exp Bot 72, 1891–1905. https://doi.org/10.1093/jxb/eraa534
10. Moyano, T.C., Gutiérrez, R.A., Alvarez, J.M., 2021. Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks. Methods Mol Biol 2328, 25–46. https://doi.org/10.1007/978-1-0716-1534-8_3
11. Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A., Abualia, R., Antonielli, L., Montesinos, J.C., Zhang, Y., Tan, S., Cuesta, C., Artner, C., Bouguyon, E., Gojon, A., Friml, J., Gutiérrez, R.A., Wabnik, K., Benková, E., 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO J 40, e106862. https://doi.org/10.15252/embj.2020106862
12. Ruffel, S., Chaput, V., Przybyla-Toscano, J., Fayos, I., Ibarra, C., Moyano, T., Fizames, C., Tillard, P., O’Brien, J.A., Gutiérrez, R.A., Gojon, A., Lejay, L., 2021. Genome-wide analysis in response to nitrogen and carbon identifies regulators for root AtNRT2 transporters. Plant Physiol 186, 696–714. https://doi.org/10.1093/plphys/kiab047
13. Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., Benkova, E., Briggs, S.P., Gutiérrez, R.A., 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Rep 22, e51813. https://doi.org/10.15252/embr.202051813
14. Zúñiga, L.M., Andrade, J.-C., Fábrega-Guerén, F., Orihuela, P.A., Velásquez, E.V., Vidal, E.A., Gutiérrez, R.A., Morales, P., Gómez-Silva, B., Croxatto, H.B., 2021. Mating induces early transcriptional response in the rat endosalpinx: the role of TNF and RA. Reproduction 161, 43–59. https://doi.org/10.1530/REP-20-0190
15. Guajardo, L., Aguilar, R., Bustos, F.J., Nardocci, G., Gutiérrez, R.A., van Zundert, B., Montecino, M., 2020. Downregulation of the Polycomb-Associated Methyltransferase Ezh2 during Maturation of Hippocampal Neurons Is Mediated by MicroRNAs Let-7 and miR-124. Int J Mol Sci 21. https://doi.org/10.3390/ijms21228472
16. Moreno, S., Canales, J., Hong, L., Robinson, D., Roeder, A.H.K., Gutiérrez, R.A., 2020. Nitrate Defines Shoot Size through Compensatory Roles for Endoreplication and Cell Division in Arabidopsis thaliana. Curr Biol 30, 1988-2000.e3. https://doi.org/10.1016/j.cub.2020.03.036
17. Naulin, P.A., Armijo, G.I., Vega, A.S., Tamayo, K.P., Gras, D.E., de la Cruz, J., Gutiérrez, R.A., 2020. Nitrate Induction of Primary Root Growth Requires Cytokinin Signaling in Arabidopsis thaliana. Plant Cell Physiol 61, 342–352. https://doi.org/10.1093/pcp/pcz199
18. Pérez-Palma, E., Bustos, B.I., Lal, D., Buch, S., Azocar, L., Toliat, M.R., Lieb, W., Franke, A., Hinz, S., Burmeister, G., von Shönfels, W., Schafmayer, C., Ahnert, P., Völzke, H., Völker, U., Homuth, G., Lerch, M.M., Puschel, K., Gutiérrez, R.A., Hampe, J., Nürnberg, P., Miquel, J.F., De Ferrari, G.V., 2020. Copy number variants in lipid metabolism genes are associated with gallstones disease in men. Eur J Hum Genet 28, 264–273. https://doi.org/10.1038/s41431-019-0501-7
19. Riveras, E., Azocar, L., Moyano, T.C., Ocares, M., Molina, H., Romero, D., Roa, J.C., Valbuena, J.R., Gutiérrez, R.A., Miquel, J.F., 2020. Transcriptomic profiles reveal differences in zinc metabolism, inflammation, and tight junction proteins in duodenum from cholesterol gallstone subjects. Sci Rep 10, 7448. https://doi.org/10.1038/s41598-020-64137-7
20. Swift, J., Alvarez, J.M., Araus, V., Gutiérrez, R.A., Coruzzi, G.M., 2020. Nutrient dose-responsive transcriptome changes driven by Michaelis-Menten kinetics underlie plant growth rates. Proc Natl Acad Sci U S A 117, 12531–12540. https://doi.org/10.1073/pnas.1918619117
21. Vidal, E.A., Alvarez, J.M., Araus, V., Riveras, E., Brooks, M.D., Krouk, G., Ruffel, S., Lejay, L., Crawford, N.M., Coruzzi, G.M., Gutiérrez, R.A., 2020. Nitrate in 2020: Thirty Years from Transport to Signaling Networks. Plant Cell 32, 2094–2119. https://doi.org/10.1105/tpc.19.00748
22. Wozniak, A., Cerda, A., Ibarra-Henríquez, C., Sebastian, V., Armijo, G., Lamig, L., Miranda, C., Lagos, M., Solari, S., Guzmán, A.M., Quiroga, T., Hitschfeld, S., Riveras, E., Ferrés, M., Gutiérrez, R.A., García, P., 2020. A simple RNA preparation method for SARS-CoV-2 detection by RT-qPCR. Sci Rep 10, 16608. https://doi.org/10.1038/s41598-020-73616-w
23. Alvarez, J.M., Moyano, T.C., Zhang, T., Gras, D.E., Herrera, F.J., Araus, V., O’Brien, J.A., Carrillo, L., Medina, J., Vicente-Carbajosa, J., Jiang, J., Gutiérrez, R.A., 2019. Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots. Mol Plant 12, 1545–1560. https://doi.org/10.1016/j.molp.2019.09.002
24. Brooks, M.D., Cirrone, J., Pasquino, A.V., Alvarez, J.M., Swift, J., Mittal, S., Juang, C.-L., Varala, K., Gutiérrez, R.A., Krouk, G., Shasha, D., Coruzzi, G.M., 2019. Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions. Nat Commun 10, 1569. https://doi.org/10.1038/s41467-019-09522-1
25. Bustos, B.I., Pérez-Palma, E., Buch, S., Azócar, L., Riveras, E., Ugarte, G.D., Toliat, M., Nürnberg, P., Lieb, W., Franke, A., Hinz, S., Burmeister, G., von Schönfels, W., Schafmayer, C., Völzke, H., Völker, U., Homuth, G., Lerch, M.M., Santos, J.L., Puschel, K., Bambs, C., Roa, J.C., Gutiérrez, R.A., Hampe, J., De Ferrari, G.V., Miquel, J.F., 2019. Variants in ABCG8 and TRAF3 genes confer risk for gallstone disease in admixed Latinos with Mapuche Native American ancestry. Sci Rep 9, 772. https://doi.org/10.1038/s41598-018-35852-z
26. Cruz, N., Méndez, T., Ramos, P., Urbina, D., Vega, A., Gutiérrez, R.A., Moya-León, M.A., Herrera, R., 2019. Induction of PrMADS10 on the lower side of bent pine tree stems: potential role in modifying plant cell wall properties and wood anatomy. Sci Rep 9, 18981. https://doi.org/10.1038/s41598-019-55276-7
27. Díaz, F.P., Latorre, C., Carrasco-Puga, G., Wood, J.R., Wilmshurst, J.M., Soto, D.C., Cole, T.L., Gutiérrez, R.A., 2019. Multiscale climate change impacts on plant diversity in the Atacama Desert. Glob Chang Biol 25, 1733–1745. https://doi.org/10.1111/gcb.14583
28. Falter-Braun, P., Brady, S., Gutiérrez, R.A., Coruzzi, G.M., Krouk, G., 2019. iPlant Systems Biology (iPSB): An International Network Hub in the Plant Community. Mol Plant 12, 727–730. https://doi.org/10.1016/j.molp.2019.05.005
29. Fernández-Gómez, B., Maldonado, J., Mandakovic, D., Gaete, A., Gutiérrez, R.A., Maass, A., Cambiazo, V., González, M., 2019. Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils. Sci Rep 9, 1042. https://doi.org/10.1038/s41598-018-37776-0
30. Fredes, I., Moreno, S., Díaz, F.P., Gutiérrez, R.A., 2019. Nitrate signaling and the control of Arabidopsis growth and development. Curr Opin Plant Biol 47, 112–118. https://doi.org/10.1016/j.pbi.2018.10.004
31. Pollak, B., Cerda, A., Delmans, M., Álamos, S., Moyano, T., West, A., Gutiérrez, R.A., Patron, N.J., Federici, F., Haseloff, J., 2019. Loop assembly: a simple and open system for recursive fabrication of DNA circuits. New Phytol 222, 628–640.https://doi.org/10.1111/nph.15625
32. Vega, A., O’Brien, J.A., Gutiérrez, R.A., 2019. Nitrate and hormonal signaling crosstalk for plant growth and development. Curr Opin Plant Biol 52, 155–163. https://doi.org/10.1016/j.pbi.2019.10.001
33. Vidal, E.A., Moyano, T.C., Bustos, B.I., Pérez-Palma, E., Moraga, C., Riveras, E., Montecinos, A., Azócar, L., Soto, D.C., Vidal, M., Di Genova, A., Puschel, K., Nürnberg, P., Buch, S., Hampe, J., Allende, M.L., Cambiazo, V., González, M., Hodar, C., Montecino, M., Muñoz-Espinoza, C., Orellana, A., Reyes-Jara, A., Travisany, D., Vizoso, P., Moraga, M., Eyheramendy, S., Maass, A., De Ferrari, G.V., Miquel, J.F., Gutiérrez, R.A., 2019. Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans. Sci Rep 9, 2132. https://doi.org/10.1038/s41598-019-39391-z
34. Contreras-López, O., Moyano, T.C., Soto, D.C., Gutiérrez, R.A., 2018. Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data. Methods Mol Biol 1761, 275–301. https://doi.org/10.1007/978-1-4939-7747-5_21
35. Gras, D.E., Vidal, E.A., Undurraga, S.F., Riveras, E., Moreno, S., Dominguez-Figueroa, J., Alabadi, D., Blázquez, M.A., Medina, J., Gutiérrez, R.A., 2018. SMZ/SNZ and gibberellin signaling are required for nitrate-elicited delay of flowering time in Arabidopsis thaliana. J Exp Bot 69, 619–631. https://doi.org/10.1093/jxb/erx423
36. Mandakovic, D., Rojas, C., Maldonado, J., Latorre, M., Travisany, D., Delage, E., Bihouée, A., Jean, G., Díaz, F.P., Fernández-Gómez, B., Cabrera, P., Gaete, A., Latorre, C., Gutiérrez, R.A., Maass, A., Cambiazo, V., Navarrete, S.A., Eveillard, D., González, M., 2018. Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience. Sci Rep 8, 5875. https://doi.org/10.1038/s41598-018-23931-0
37. Muñoz-Llanos, M., García-Pérez, M.A., Xu, X., Tejos-Bravo, M., Vidal, E.A., Moyano, T.C., Gutiérrez, R.A., Aguayo, F.I., Pacheco, A., García-Rojo, G., Aliaga, E., Rojas, P.S., Cidlowski, J.A., Fiedler, J.L., 2018. MicroRNA Profiling and Bioinformatics Target Analysis in Dorsal Hippocampus of Chronically Stressed Rats: Relevance to Depression Pathophysiology. Front Mol Neurosci 11, 251. https://doi.org/10.3389/fnmol.2018.00251
38. Wood, J.R., Díaz, F.P., Latorre, C., Wilmshurst, J.M., Burge, O.R., Gutiérrez, R.A., 2018. Plant pathogen responses to Late Pleistocene and Holocene climate change in the central Atacama Desert, Chile. Sci Rep 8, 17208. https://doi.org/10.1038/s41598-018-35299-2
39. Armijo, G., Gutiérrez, R.A., 2017. Emerging Players in the Nitrate Signaling Pathway. Mol Plant 10, 1019–1022. https://doi.org/10.1016/j.molp.2017.07.006
40. Canales, J., Contreras-López, O., Álvarez, J.M., Gutiérrez, R.A., 2017. Nitrate induction of root hair density is mediated by TGA1/TGA4 and CPC transcription factors in Arabidopsis thaliana. Plant J 92, 305–316. https://doi.org/10.1111/tpj.13656
41. Friesner, J., Assmann, S.M., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., Buell, C.R., Bucksch, A., Busch, W., Demura, T., Dinneny, J.R., Doherty, C.J., Eveland, A.L., Falter-Braun, P., Gehan, M.A., Gonzales, M., Grotewold, E., Gutierrez, R., Kramer, U., Krouk, G., Ma, S., Markelz, R.J.C., Megraw, M., Meyers, B.C., Murray, J.A.H., Provart, N.J., Rhee, S., Smith, R., Spalding, E.P., Taylor, C., Teal, T.K., Torii, K.U., Town, C., Vaughn, M., Vierstra, R., Ware, D., Wilkins, O., Williams, C., Brady, S.M., 2017. The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiol 175, 1499–1509. https://doi.org/10.1104/pp.17.01490
42. Pastenes, L., Valdivieso, C., Di Genova, A., Travisany, D., Hart, A., Montecino, M., Orellana, A., Gonzalez, M., Gutiérrez, R.A., Allende, M.L., Maass, A., Méndez, M.A., 2017. Global gene expression analysis provides insight into local adaptation to geothermal streams in tadpoles of the Andean toad Rhinella spinulosa. Sci Rep 7, 1966. https://doi.org/10.1038/s41598-017-01982-z
43. Puelma, T., Araus, V., Canales, J., Vidal, E.A., Cabello, J.M., Soto, A., Gutiérrez, R.A., 2017. GENIUS: web server to predict local gene networks and key genes for biological functions. Bioinformatics 33, 760–761. https://doi.org/10.1093/bioinformatics/btw702
44. Undurraga, S.F., Ibarra-Henríquez, C., Fredes, I., Álvarez, J.M., Gutiérrez, R.A., 2017. Nitrate signaling and early responses in Arabidopsis roots. J Exp Bot 68, 2541–2551. https://doi.org/10.1093/jxb/erx041
45. Acuña, M., Martínez, P., Moraga, C., He, X., Moraga, M., Hunter, B., Nuernberg, P., Gutiérrez, R.A., González, M., Schuchman, E.H., Santos, J.L., Miquel, J.F., Mabe, P., Zanlungo, S., 2016. Epidemiological, clinical and biochemical characterization of the p.(Ala359Asp) SMPD1 variant causing Niemann-Pick disease type B. Eur J Hum Genet 24, 208–213. https://doi.org/10.1038/ejhg.2015.89
46. Araus, V., Vidal, E.A., Puelma, T., Alamos, S., Mieulet, D., Guiderdoni, E., Gutiérrez, R.A., 2016. Members of BTB Gene Family of Scaffold Proteins Suppress Nitrate Uptake and Nitrogen Use Efficiency. Plant Physiol 171, 1523–1532. https://doi.org/10.1104/pp.15.01731
47. Díaz, F.P., Frugone, M., Gutiérrez, R.A., Latorre, C., 2016. Nitrogen cycling in an extreme hyperarid environment inferred from ?(15)N analyses of plants, soils and herbivore diet. Sci Rep 6, 22226. https://doi.org/10.1038/srep22226
48. O’Brien, J.A., Vega, A., Bouguyon, E., Krouk, G., Gojon, A., Coruzzi, G., Gutiérrez, R.A., 2016. Nitrate Transport, Sensing, and Responses in Plants. Mol Plant 9, 837–856. https://doi.org/10.1016/j.molp.2016.05.004
49. Pérez-Delgado, C.M., Moyano, T.C., García-Calderón, M., Canales, J., Gutiérrez, R.A., Márquez, A.J., Betti, M., 2016. Use of transcriptomics and co-expression networks to analyze the interconnections between nitrogen assimilation and photorespiratory metabolism. J Exp Bot 67, 3095–3108. https://doi.org/10.1093/jxb/erw170
50. Yazaki, J., Galli, M., Kim, A.Y., Nito, K., Aleman, F., Chang, K.N., Carvunis, A.-R., Quan, R., Nguyen, H., Song, L., Alvarez, J.M., Huang, S.-S.C., Chen, H., Ramachandran, N., Altmann, S., Gutiérrez, R.A., Hill, D.E., Schroeder, J.I., Chory, J., LaBaer, J., Vidal, M., Braun, P., Ecker, J.R., 2016. Mapping transcription factor interactome networks using HaloTag protein arrays. Proc Natl Acad Sci U S A 113, E4238-4247. https://doi.org/10.1073/pnas.1603229113
51. Moyano, T.C., Vidal, E.A., Contreras-López, O., Gutiérrez, R.A., 2015. Constructing simple biological networks for understanding complex high-throughput data in plants. Methods Mol Biol 1284, 503–526. https://doi.org/10.1007/978-1-4939-2444-8_25
52. Riveras, E., Alvarez, J.M., Vidal, E.A., Oses, C., Vega, A., Gutiérrez, R.A., 2015. The Calcium Ion Is a Second Messenger in the Nitrate Signaling Pathway of Arabidopsis. Plant Physiol 169, 1397–1404. https://doi.org/10.1104/pp.15.00961
53. Vega, A., Canessa, P., Hoppe, G., Retamal, I., Moyano, T.C., Canales, J., Gutiérrez, R.A., Rubilar, J., 2015. Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in  Solanum lycopersicum. Front Plant Sci 6, 911. https://doi.org/10.3389/fpls.2015.00911
54. Vidal, E.A., Álvarez, J.M., Moyano, T.C., Gutiérrez, R.A., 2015. Transcriptional networks in the nitrate response of Arabidopsis thaliana. Curr Opin Plant Biol 27, 125–132. https://doi.org/10.1016/j.pbi.2015.06.010
55. Alvarez, J.M., Riveras, E., Vidal, E.A., Gras, D.E., Contreras-López, O., Tamayo, K.P., Aceituno, F., Gómez, I., Ruffel, S., Lejay, L., Jordana, X., Gutiérrez, R.A., 2014. Systems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response of Arabidopsis thaliana roots. Plant J 80, 1–13. https://doi.org/10.1111/tpj.12618
56. Canales, J., Moyano, T.C., Villarroel, E., Gutiérrez, R.A., 2014. Systems analysis of transcriptome data provides new hypotheses about Arabidopsis root response to nitrate treatments. Front Plant Sci 5, 22. https://doi.org/10.3389/fpls.2014.00022
57. Vidal, E.A., Álvarez, J.M., Gutiérrez, R.A., 2014a. Nitrate regulation of AFB3 and NAC4 gene expression in Arabidopsis roots depends on NRT1.1 nitrate transport function. Plant Signal Behav 9, e28501. https://doi.org/10.4161/psb.28501
58. Vidal, E.A., Moyano, T.C., Canales, J., Gutiérrez, R.A., 2014b. Nitrogen control of developmental phase transitions in Arabidopsis thaliana. J Exp Bot 65, 5611–5618. https://doi.org/10.1093/jxb/eru326
59. Federici, F., Rudge, T.J., Pollak, B., Haseloff, J., Gutiérrez, R.A., 2013. Synthetic Biology: opportunities for Chilean bioindustry and education. Biol Res 46, 383–393. https://doi.org/10.4067/S0716-97602013000400010
60. Vidal, E.A., Moyano, T.C., Krouk, G., Katari, M.S., Tanurdzic, M., McCombie, W.R., Coruzzi, G.M., Gutiérrez, R.A., 2013a. Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics 14, 701. https://doi.org/10.1186/1471-2164-14-701
61. Vidal, E.A., Moyano, T.C., Riveras, E., Contreras-López, O., Gutiérrez, R.A., 2013b. Systems approaches map regulatory networks downstream of the auxin receptor AFB3 in the nitrate response of Arabidopsis thaliana roots. Proc Natl Acad Sci U S A 110, 12840–12845. https://doi.org/10.1073/pnas.1310937110
62. Zúñiga, A., Poupin, M.J., Donoso, R., Ledger, T., Guiliani, N., Gutiérrez, R.A., González, B., 2013. Quorum sensing and indole-3-acetic acid degradation play a role in colonization and plant growth promotion of Arabidopsis thaliana by Burkholderia phytofirmans  PsJN. Mol Plant Microbe Interact 26, 546–553. https://doi.org/10.1094/MPMI-10-12-0241-R
63. Alvarez, J.M., Vidal, E.A., Gutiérrez, R.A., 2012. Integration of local and systemic signaling pathways for plant N responses. Curr Opin Plant Biol 15, 185–191. https://doi.org/10.1016/j.pbi.2012.03.009
64. Gutiérrez, R.A., 2012. Systems biology for enhanced plant nitrogen nutrition. Science 336, 1673–1675. https://doi.org/10.1126/science.1217620
65. Puelma, T., Gutiérrez, R.A., Soto, A., 2012. Discriminative local subspaces in gene expression data for effective gene function prediction. Bioinformatics 28, 2256–2264. https://doi.org/10.1093/bioinformatics/bts455
66. Fuentes, D., Meneses, M., Nunes-Nesi, A., Araújo, W.L., Tapia, R., Gómez, I., Holuigue, L., Gutiérrez, R.A., Fernie, A.R., Jordana, X., 2011. A deficiency in the flavoprotein of Arabidopsis mitochondrial complex II results in elevated photosynthesis and better growth in nitrogen-limiting conditions. Plant Physiol 157, 1114–1127. https://doi.org/10.1104/pp.111.183939
67. Kraiser, T., Gras, D.E., Gutiérrez, A.G., González, B., Gutiérrez, R.A., 2011. A holistic view of nitrogen acquisition in plants. J Exp Bot 62, 1455–1466. https://doi.org/10.1093/jxb/erq425
68. Krouk, G., Ruffel, S., Gutiérrez, R.A., Gojon, A., Crawford, N.M., Coruzzi, G.M., Lacombe, B., 2011. A framework integrating plant growth with hormones and nutrients. Trends Plant Sci 16, 178–182. https://doi.org/10.1016/j.tplants.2011.02.004
69. Vega, A., Gutiérrez, R.A., Peña-Neira, A., Cramer, G.R., Arce-Johnson, P., 2011. Compatible GLRaV-3 viral infections affect berry ripening decreasing sugar accumulation and anthocyanin biosynthesis in Vitis vinifera. Plant Mol Biol 77, 261–274. https://doi.org/10.1007/s11103-011-9807-8
70. Das, M., Reichman, J.R., Haberer, G., Welzl, G., Aceituno, F.F., Mader, M.T., Watrud, L.S., Pfleeger, T.G., Gutiérrez, R.A., Schäffner, A.R., Olszyk, D.M., 2010. A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and Brassica napus. Plant Mol Biol 72, 545–556. https://doi.org/10.1007/s11103-009-9590-y
71. Katari, M.S., Nowicki, S.D., Aceituno, F.F., Nero, D., Kelfer, J., Thompson, L.P., Cabello, J.M., Davidson, R.S., Goldberg, A.P., Shasha, D.E., Coruzzi, G.M., Gutiérrez, R.A., 2010. VirtualPlant: a software platform to support systems biology research. Plant Physiol 152, 500–515. https://doi.org/10.1104/pp.109.147025
72. McClung, C.R., Gutiérrez, R.A., 2010. Network news: prime time for systems biology of the plant circadian clock. Curr Opin Genet Dev 20, 588–598. https://doi.org/10.1016/j.gde.2010.08.010
73. Vidal, E.A., Araus, V., Lu, C., Parry, G., Green, P.J., Coruzzi, G.M., Gutiérrez, R.A., 2010a. Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proc Natl Acad Sci U S A 107, 4477–4482. https://doi.org/10.1073/pnas.0909571107
74. Vidal, E.A., Tamayo, K.P., Gutierrez, R.A., 2010b. Gene networks for nitrogen sensing, signaling, and response in Arabidopsis thaliana. Wiley Interdiscip Rev Syst Biol Med 2, 683–693. https://doi.org/10.1002/wsbm.87
75. Krouk, G., Tranchina, D., Lejay, L., Cruikshank, A.A., Shasha, D., Coruzzi, G.M., Gutiérrez, R.A., 2009. A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis. PLoS Comput Biol 5, e1000326. https://doi.org/10.1371/journal.pcbi.1000326
76. Aceituno, F.F., Moseyko, N., Rhee, S.Y., Gutiérrez, R.A., 2008. The rules of gene expression in plants: organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana. BMC Genomics 9, 438. https://doi.org/10.1186/1471-2164-9-438
77. Bender, J., Benfey, P., Bergmann, D., Borevitz, J., Coruzzi, G., Dangl, J., Dean, C., Ecker, J., Estelle, M., Glazebrook, J., Grant, S., Guerinot, M.L., Gutierrez, R., Long, J., Nordborg, M., Poethig, S., Raikhel, N., Schmitt, J., Schnittger, A., Vidal, M., 2008. 2020 vision for biology: the role of plants in addressing grand challenges in biology. Mol Plant 1, 561–563. https://doi.org/10.1093/mp/ssn040
78. Gifford, M.L., Dean, A., Gutierrez, R.A., Coruzzi, G.M., Birnbaum, K.D., 2008. Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci U S A 105, 803–808. https://doi.org/10.1073/pnas.0709559105
79. Gutiérrez, R.A., Stokes, T.L., Thum, K., Xu, X., Obertello, M., Katari, M.S., Tanurdzic, M., Dean, A., Nero, D.C., McClung, C.R., Coruzzi, G.M., 2008. Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A 105, 4939–4944. https://doi.org/10.1073/pnas.0800211105
80. Holuigue, L., Vielle-Calzada, J.-P., Gutiérrez, R.A., 2008. Crops in all shapes and sizes. Genome Biol 9, 319. https://doi.org/10.1186/gb-2008-9-9-319
81. Thum, K.E., Shin, M.J., Gutiérrez, R.A., Mukherjee, I., Katari, M.S., Nero, D., Shasha, D., Coruzzi, G.M., 2008. An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in  Arabidopsis. BMC Syst Biol 2, 31. https://doi.org/10.1186/1752-0509-2-31
82. Vidal, E.A., Gutiérrez, R.A., 2008. A systems view of nitrogen nutrient and metabolite responses in Arabidopsis. Curr Opin Plant Biol 11, 521–529. https://doi.org/10.1016/j.pbi.2008.07.003
83. Gutiérrez, R.A., Gifford, M.L., Poultney, C., Wang, R., Shasha, D.E., Coruzzi, G.M., Crawford, N.M., 2007a. Insights into the genomic nitrate response using genetics and the Sungear Software System. J Exp Bot 58, 2359–2367. https://doi.org/10.1093/jxb/erm079
84. Gutiérrez, R.A., Lejay, L.V., Dean, A., Chiaromonte, F., Shasha, D.E., Coruzzi, G.M., 2007b. Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol 8, R7. https://doi.org/10.1186/gb-2007-8-1-r7
85. Poultney, C.S., Gutiérrez, R.A., Katari, M.S., Gifford, M.L., Paley, W.B., Coruzzi, G.M., Shasha, D.E., 2007. Sungear: interactive visualization and functional analysis of genomic datasets. Bioinformatics 23, 259–261. https://doi.org/10.1093/bioinformatics/btl496
86. Gutiérrez, R.A., Shasha, D.E., Coruzzi, G.M., 2005. Systems biology for the virtual plant. Plant Physiol 138, 550–554. https://doi.org/10.1104/pp.104.900150
87. Li, C., Potuschak, T., Colón-Carmona, A., Gutiérrez, R.A., Doerner, P., 2005. Arabidopsis TCP20 links regulation of growth and cell division control pathways. Proc Natl Acad Sci U S A 102, 12978–12983. https://doi.org/10.1073/pnas.0504039102
88. Lidder, P., Gutiérrez, R.A., Salomé, P.A., McClung, C.R., Green, P.J., 2005. Circadian control of messenger RNA stability. Association with a sequence-specific messenger RNA decay pathway. Plant Physiol 138, 2374–2385. https://doi.org/10.1104/pp.105.060368
89. Gutiérrez, R.A., Green, P.J., Keegstra, K., Ohlrogge, J.B., 2004a. Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms? Genome Biol 5, R53. https://doi.org/10.1186/gb-2004-5-8-r53
90. Gutiérrez, R.A., Larson, M.D., Wilkerson, C., 2004b. The plant-specific database. Classification of Arabidopsis proteins based on their phylogenetic profile. Plant Physiol 135, 1888–1892. https://doi.org/10.1104/pp.104.043687
91. Wang, R., Tischner, R., Gutiérrez, R.A., Hoffman, M., Xing, X., Chen, M., Coruzzi, G., Crawford, N.M., 2004. Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol 136, 2512–2522. https://doi.org/10.1104/pp.104.044610
92. Gutierrez, R.A., Ewing, R.M., Cherry, J.M., Green, P.J., 2002. Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific  clock-controlled genes. Proc Natl Acad Sci U S A 99, 11513–11518. https://doi.org/10.1073/pnas.152204099
93. Gutiérrez, R.A., MacIntosh, G.C., Green, P.J., 1999. Current perspectives on mRNA stability in plants: multiple levels and mechanisms of control. Trends Plant Sci 4, 429–438. https://doi.org/10.1016/s1360-1385(99)01484-3