P. Universidad Católica de Chile

Facultad de Ciencias Biológicas
Departamento de Genética Molecular y Microbiología

Plant Systems Biology Lab

Publications



1.- Brooks MD, Cirrone J, Pasquino AV, Alvarez JM, Swift J, Mittal S, Juang CL, Varala K, Gutiérrez RA, Krouk G, Shasha D, Coruzzi GM (2019). Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions. Nat Commun 10, 1569. PubMed
2.- Vidal EA, Moyano TC, Bustos BI, Perez-Palma E, Moraga C, Riveras E, Montecinos A, Azocar L, Soto DC, Vidal M, Di Genova A, Puschel K, Nurnberg P, Buch S, Hampe J, Allende ML, Cambiazo V, Gonzalez M, Hodar C, Montecino M, Munoz-Espinoza C, Orellana A, Reyes-Jara A, Travisany D, Vizoso P, Moraga M, Eyheramendy S, Maass A, De Ferrari GV, Miquel JF, Gutiérrez RA (2019). Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans. Sci Rep 9, 2132. PubMed
3.- Diaz FP, Latorre C, Carrasco-Puga G, Wood JR, Wilmshurst JM, Soto DC, Cole TL, Gutiérrez RA (2019). Multiscale climate change impacts on plant diversity in the Atacama Desert. Glob Chang Biol 25, 1733-1745. PubMed
4.- Fernandez-Gomez B, Maldonado J, Mandakovic D, Gaete A, Gutiérrez RA, Maass A, Cambiazo V, Gonzalez M (2019). Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils. Sci Rep 9, 1042. PubMed
5.- Bustos BI, Perez-Palma E, Buch S, Azocar L, Riveras E, Ugarte GD, Toliat M, Nurnberg P, Lieb W, Franke A, Hinz S, Burmeister G, von Schonfels W, Schafmayer C, Volzke H, Volker U, Homuth G, Lerch MM, Santos JL, Puschel K, Bambs C, Roa JC, Gutiérrez RA, Hampe J, De Ferrari GV, Miquel JF (2019). Variants in ABCG8 and TRAF3 genes confer risk for gallstone disease in admixed Latinos with Mapuche Native American ancestry. Sci Rep 9, 772. PubMed
6.- Pollak B, Cerda A, Delmans M, Alamos S, Moyano T, West A, Gutiérrez RA, Patron NJ, Federici F, Haseloff J (2019). Loop assembly: a simple and open system for recursive fabrication of DNA circuits. New Phytol 222, 628-640. PubMed
7.- Fredes I, Moreno S, Diaz FP, Gutiérrez RA (2019). Nitrate signaling and the control of Arabidopsis growth and development. Curr Opin Plant Biol 47, 112-118. PubMed
8.- Wood JR, Diaz FP, Latorre C, Wilmshurst JM, Burge OR, Gutiérrez RA (2018). Plant pathogen responses to Late Pleistocene and Holocene climate change in the central Atacama Desert, Chile. Sci Rep 8, 17208. PubMed
9.- Mandakovic D, Rojas C, Maldonado J, Latorre M, Travisany D, Delage E, Bihouee A, Jean G, Diaz FP, Fernandez-Gomez B, Cabrera P, Gaete A, Latorre C, Gutiérrez RA, Maass A, Cambiazo V, Navarrete SA, Eveillard D, Gonzalez M (2018). Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience. Sci Rep 8, 5875. PubMed
10.- Contreras-Lopez O, Moyano TC, Soto DC, Gutiérrez RA (2018). Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data. Methods Mol Biol 1761, 275-301. PubMed
11.- Gras DE, Vidal EA, Undurraga SF, Riveras E, Moreno S, Dominguez-Figueroa J, Alabadi D, Blazquez M, Medina J, Gutiérrez RA (2017). SMZ/SNZ and gibberellin signaling are required for nitrate-elicited delay of flowering time in Arabidopsis thaliana. J Exp Bot . PubMed
12.- Canales J, Contreras-Lopez O, Alvarez JM, Gutiérrez RA (2017). Nitrate induction of root hair density is mediated by TGA1/TGA4 and CPC transcription factors in Arabidopsis thaliana. Plant J 92, 305-316. PubMed
13.- Armijo G, Gutiérrez RA (2017). Emerging Players in the Nitrate Signaling Pathway. Mol Plant 10, 1019-1022. PubMed
14.- Undurraga SF, Ibarra-Henriquez C, Fredes I, Alvarez JM, Gutiérrez RA (2017). Nitrate signaling and early responses in Arabidopsis roots. J Exp Bot 68, 2541-2551. PubMed
15.- Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutiérrez RA, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM (2017). The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiol 175, 1499-1509. PubMed
16.- Yazaki J, Galli M, Kim AY, Nito K, Aleman F, Chang KN, Carvunis AR, Quan R, Nguyen H, Song L, Alvarez JM, Huang SS, Chen H, Ramachandran N, Altmann S, Gutiérrez RA, Hill DE, Schroeder JI, Chory J, LaBaer J, Vidal M, Braun P, Ecker JR (2016). Mapping transcription factor interactome networks using HaloTag protein arrays. Proc Natl Acad Sci U S A 113, E4238-47. PubMed
17.- Puelma T, Araus V, Canales J, Vidal EA, Cabello JM, Soto A, Gutiérrez RA (2017). GENIUS: web server to predict local gene networks and key genes for biological functions. Bioinformatics 33, 760-761. PubMed
18.- O'Brien JA, Vega A, Bouguyon E, Krouk G, Gojon A, Coruzzi G, Gutiérrez RA (2016). Nitrate Transport, Sensing, and Responses in Plants. Mol Plant 9, 837-56. PubMed
19.- Araus V, Vidal EA, Puelma T, Alamos S, Mieulet D, Guiderdoni E, Gutiérrez RA (2016). Members of BTB Gene Family of Scaffold Proteins Suppress Nitrate Uptake and Nitrogen Use Efficiency. Plant Physiol 171, 1523-32. PubMed
20.- Perez-Delgado CM, Moyano TC, Garcia-Calderon M, Canales J, Gutiérrez RA, Marquez AJ, Betti M (2016). Use of transcriptomics and co-expression networks to analyze the interconnections between nitrogen assimilation and photorespiratory metabolism. J Exp Bot 67, 3095-108. PubMed
21.- Diaz FP, Frugone M, Gutiérrez RA, Latorre C (2016). Nitrogen cycling in an extreme hyperarid environment inferred from delta(15)N analyses of plants, soils and herbivore diet. Sci Rep 6, 22226. PubMed
22.- Vega A, Canessa P, Hoppe G, Retamal I, Moyano TC, Canales J, Gutiérrez RA, 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. PubMed
23.- Riveras E, Alvarez JM, Vidal EA, Oses C, Vega A, Gutiérrez RA (2015). The Calcium Ion Is a Second Messenger in the Nitrate Signaling Pathway of Arabidopsis. Plant Physiol 169, 1397-404. PubMed
24.- Vidal EA, Alvarez JM, Moyano TC, Gutiérrez RA (2015). Transcriptional networks in the nitrate response of Arabidopsis thaliana. Curr Opin Plant Biol 27, 125-32. PubMed
25.- Acuna M, Martinez P, Moraga C, He X, Moraga M, Hunter B, Nuernberg P, Gutiérrez RA, Gonzalez M, Schuchman EH, Luis Santos J, Miquel JF, Mabe P, Zanlungo S (2015). Epidemiological, clinical and biochemical characterization of the p.(Ala359Asp) SMPD1 variant causing Niemann-Pick disease type B. Eur J Hum Genet . PubMed
26.- Moyano TC, Vidal EA, Contreras-Lopez O, Gutiérrez RA (2015). Constructing simple biological networks for understanding complex high-throughput data in plants. Methods Mol Biol 1284, 503-26. PubMed
27.- Vidal EA, Moyano TC, Canales J, Gutiérrez RA (2014). Nitrogen control of developmental phase transitions in Arabidopsis thaliana. J Exp Bot . PubMed
28.- Alvarez JM, Riveras E, Vidal EA, Gras DE, Contreras-Lopez O, Tamayo KP, Aceituno F, Gomez I, Ruffel S, Lejay L, Jordana X, Gutiérrez RA (2014). Systems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response of Arabidopsis thaliana roots. Plant J . PubMed
29.- Vidal EA, Alvarez JM, Gutiérrez RA (2014). Nitrate regulation of AFB3 and NAC4 gene expression in Arabidopsis roots depends on NRT1.1 nitrate transport function. Plant Signal Behav 9. PubMed
30.- Canales J, Moyano TC, Villarroel E, Gutiérrez RA (2014). Systems analysis of transcriptome data provides new hypotheses about Arabidopsis root response to nitrate treatments. Front Plant Sci 5, 22. PubMed Download
31.- Federici F, Rudge TJ, Pollak B, Haseloff J, Gutiérrez RA (2013). Synthetic Biology: opportunities for Chilean bioindustry and education. Biol Res 46, 383-93. PubMed
32.- Vidal EA, Moyano TC, Riveras E, Contreras-Lopez O, Gutiérrez RA (2013). 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, 12840-5. PubMed Download
33.- Vidal EA, Moyano TC, Krouk G, Katari MS, Tanurdzic M, McCombie WR, Coruzzi GM, Gutiérrez RA (2013). Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics 14, 701. PubMed
34.- Zuniga A, Poupin MJ, Donoso R, Ledger T, Guiliani N, Gutiérrez RA, Gonzalez 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, 546-53. PubMed Download
35.- Puelma T, Gutiérrez RA, Soto A (2012). Discriminative local subspaces in gene expression data for effective gene function prediction. Bioinformatics 28, 2256-64. PubMed Download
36.- Gutiérrez RA (2012). Systems biology for enhanced plant nitrogen nutrition. Science 336, 1673-5. PubMed [Reprint]
37.- Alvarez JM, Vidal EA, Gutiérrez RA (2012). Integration of local and systemic signaling pathways for plant N responses. Curr Opin Plant Biol 15, 185-91. PubMed Download
38.- Fuentes D, Meneses M, Nunes-Nesi A, Araujo WL, Tapia R, Gomez I, Holuigue L, Gutiérrez RA, Fernie AR, 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, 1114-27. PubMed Download
39.- Vega A, Gutiérrez RA, Pena-Neira A, Cramer GR, 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, 261-74. PubMed Download
40.- Krouk G, Ruffel S, Gutiérrez RA, Gojon A, Crawford NM, Coruzzi GM, Lacombe B (2011). A framework integrating plant growth with hormones and nutrients. Trends Plant Sci 16, 178-82. PubMed Download
41.- Kraiser T, Gras DE, Gutierrez AG, Gonzalez B, Gutiérrez RA (2011). A holistic view of nitrogen acquisition in plants. J Exp Bot 62, 1455-66. PubMed Download
42.- International Arabidopsis Informatics Consortium (2010). An international bioinformatics infrastructure to underpin the Arabidopsis community. Plant Cell 22, 2530-6. PubMed Download
43.- Vidal EA, Araus V, Lu C, Parry G, Green PJ, Coruzzi GM, Gutiérrez RA (2010). Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proc Natl Acad Sci U S A . PubMed Download
44.- McClung CR, Gutiérrez RA (2010). Network news: prime time for systems biology of the plant circadian clock. Curr Opin Genet Dev . PubMed Download
45.- Vidal EA, Tamayo KP, Gutiérrez RA (2010). Gene networks for nitrogen sensing, signaling, and response in Arabidopsis thaliana. Wiley Interdiscip Rev Syst Biol Med 2, 683-93. PubMed Download
46.- Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, Gutiérrez RA (2010). VirtualPlant: a software platform to support systems biology research. Plant Physiol 152, 500-15. PubMed Download
47.- Das M, Reichman JR, Haberer G, Welzl G, Aceituno FF, Mader MT, Watrud LS, Pfleeger TG, Gutiérrez RA, Schaffner AR, Olszyk DM (2010). A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and Brassica napus. Plant Mol Biol 72, 545-56. PubMed Download
48.- Krouk G , Tranchina D , Lejay L , Cruikshank AA , Shasha D , Coruzzi GM , Gutiérrez RA (2009). A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis. PLoS Comput Biol 5, e1000326. PubMed Download
49.- Reforgiato D, Gutiérrez RA, Shasha D (2008). GraphClust: A Method for Clustering Database of Graphs. J Information & Knowledge Management. 7, 231-241.
50.- 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, 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, 561-3. PubMed
51.- Aceituno FF, Moseyko N, Rhee SY, Gutiérrez RA (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. PubMed Download [Supplemental Material]
52.- Holuigue L, Vielle-Calzada JP, Gutiérrez RA (2008). Crops in all shapes and sizes. Genome Biol 9, 319. PubMed
53.- Vidal EA, Gutiérrez RA (2008). A systems view of nitrogen nutrient and metabolite responses in Arabidopsis. Curr Opin Plant Biol 11, 521-9. PubMed Download
54.- Thum KE, Shin MJ, Gutiérrez RA, Mukherjee I, Katari MS, Nero D, Shasha D, Coruzzi GM (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. PubMed Download
55.- Gutiérrez RA , Stokes TL , Thum K , Xu X , Obertello M , Katari MS , Tanurdzic M , Dean A , Nero DC , McClung CR , Coruzzi GM (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 , 4939-44. PubMed Download
56.- Gifford ML , Dean A , Gutiérrez RA , Coruzzi GM , Birnbaum KD (2008). Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci U S A 105 , 803-8. PubMed Download
57.- Gutiérrez RA, Gifford ML, Poultney C, Wang R, Shasha DE, Coruzzi GM, Crawford NM (2007). Insights into the genomic nitrate response using genetics and the Sungear Software System. J Exp Bot 58, 2359-67. PubMed Download
58.- Gutiérrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM (2007). Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol 8, R7. PubMed Download
59.- Poultney CS, Gutiérrez RA, Katari MS, Gifford ML, Paley WB, Coruzzi GM, Shasha DE (2007). Sungear: interactive visualization and functional analysis of genomic datasets. Bioinformatics 23, 259-61. PubMed Download
60.- Li C, Potuschak T, Colon-Carmona A, Gutiérrez RA, Doerner P (2005). Arabidopsis TCP20 links regulation of growth and cell division control pathways. Proc Natl Acad Sci U S A 102, 12978-83. PubMed Download
61.- Lidder P*, Gutiérrez RA*, Salome PA, McClung CR, Green PJ (2005). Circadian control of messenger RNA stability. Association with a sequence-specific messenger RNA decay pathway. *Both authors contributed equally. Plant Physiol 138, 2374-85. PubMed Download
62.- Gutiérrez RA, Shasha DE, Coruzzi GM (2005). Systems biology for the virtual plant. Plant Physiol 138, 550-4. PubMed Download
63.- Wang R, Tischner R, Gutiérrez RA, Hoffman M, Xing X, Chen M, Coruzzi G, Crawford NM (2004). Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol 136, 2512-22. PubMed Download
64.- Gutiérrez RA*, Larson MD, Wilkerson C (2004). The plant-specific database. Classification of Arabidopsis proteins based on their phylogenetic profile. *Corresponding author. Plant Physiol 135, 1888-92. PubMed Download
65.- Gutiérrez RA*, Green PJ, Keegstra K, Ohlrogge JB (2004). Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms? *Corresponding author. Genome Biol 5, R53. PubMed Download
66.- Gutiérrez RA, Ewing RM, Cherry JM, Green PJ (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, 11513-8. PubMed Download
67.- Ghosh D, Sawicki M, Lala P, Erman M, Pangborn W, Eyzaguirre J, Gutierrez R, Jornvall H, Thiel DJ (2001). Multiple conformations of catalytic serine and histidine in acetylxylan esterase at 0.90 A. J Biol Chem 276, 11159-66. PubMed Download
68.- Gutiérrez RA, MacIntosh GC, Green PJ (1999). Current perspectives on mRNA stability in plants: multiple levels and mechanisms of control. Trends Plant Sci 4, 429-438. PubMed Download
69.- Ghosh D, Erman M, Sawicki M, Lala P, Weeks DR, Li N, Pangborn W, Thiel DJ, Jornvall H, Gutierrez R, Eyzaguirre J (1999). Determination of a protein structure by iodination: the structure of iodinated acetylxylan esterase. Acta Crystallogr D Biol Crystallogr 55 ( Pt 4), 779-84. PubMed Download
70.- Gutierrez R, Cederlund E, Hjelmqvist L, Peirano A, Herrera F, Ghosh D, Duax W, Jornvall H, Eyzaguirre J (1998). Acetyl xylan esterase II from Penicillium purpurogenum is similar to an esterase from Trichoderma reesei but lacks a cellulose binding domain. FEBS Lett 423, 35-8. PubMed Download
71.- Egana L, Gutierrez R, Caputo V, Peirano A, Steiner J, Eyzaguirre J (1996). Purification and characterization of two acetyl xylan esterases from Penicillium purpurogenum. Biotechnol Appl Biochem 24 ( Pt 1), 33-9. PubMed
72.- Pangborn W, Erman M, Li N, Burkhart BM, Pletnev VZ, Duax WL, Gutierrez R, Peirano A, Eyzaguirre J, Thiel DJ, Ghosh D (1996). Characterization of crystals of Penicillium purpurogenum acetyl xylan esterase from high-resolution x-ray diffraction. Proteins 24, 523-4. PubMed Download