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Natural Root Cellular Variation in Responses to Osmotic Stress in Arabidopsis thaliana Accessions.

Cajero-Sanchez W, Aceves-Garcia P, Fernández-Marcos M, Gutiérrez C, Rosas U, García-Ponce B, Álvarez-Buylla ER, Sánchez MP, Garay-Arroyo A.

Genes (Basel). 2019 Nov 29;10(12). pii: E983. doi: 10.3390/genes10120983.


ULTRAPETALA1 maintains Arabidopsis root stem cell niche independently of ARABIDOPSIS TRITHORAX1.

Ornelas-Ayala D, Vega-León R, Petrone-Mendoza E, Garay-Arroyo A, García-Ponce B, Álvarez-Buylla ER, Sanchez MP.

New Phytol. 2020 Feb;225(3):1261-1272. doi: 10.1111/nph.16213. Epub 2019 Oct 28.


MADS-Box Genes Are Key Components of Genetic Regulatory Networks Involved in Abiotic Stress and Plastic Developmental Responses in Plants.

Castelán-Muñoz N, Herrera J, Cajero-Sánchez W, Arrizubieta M, Trejo C, García-Ponce B, Sánchez MP, Álvarez-Buylla ER, Garay-Arroyo A.

Front Plant Sci. 2019 Jul 10;10:853. doi: 10.3389/fpls.2019.00853. eCollection 2019. Review.


MADS-box genes underground becoming mainstream: plant root developmental mechanisms.

Alvarez-Buylla ER, García-Ponce B, Sánchez MP, Espinosa-Soto C, García-Gómez ML, Piñeyro-Nelson A, Garay-Arroyo A.

New Phytol. 2019 Aug;223(3):1143-1158. doi: 10.1111/nph.15793. Epub 2019 Apr 12. Review.


Modeling the Epigenetic Landscape in Plant Development.

Davila-Velderrain J, Caldu-Primo JL, Martinez-Garcia JC, Alvarez-Buylla ER.

Methods Mol Biol. 2018;1819:357-383. doi: 10.1007/978-1-4939-8618-7_17.


Leptin in the Commissural Nucleus Tractus Solitarii Increases the Glucose Responses to Carotid Chemoreceptors Activation by Cyanide.

Lemus M, Mojarro C, Montero S, Melnikov V, Ramírez-Flores M, de Álvarez-Buylla ER.

Adv Exp Med Biol. 2018;1071:143-149. doi: 10.1007/978-3-319-91137-3_18.


Structural robustness of mammalian transcription factor networks reveals plasticity across development.

Caldu-Primo JL, Alvarez-Buylla ER, Davila-Velderrain J.

Sci Rep. 2018 Sep 17;8(1):13922. doi: 10.1038/s41598-018-32020-1.


Role of Cytokine Combinations on CD4+ T Cell Differentiation, Partial Polarization, and Plasticity: Continuous Network Modeling Approach.

Martinez-Sanchez ME, Huerta L, Alvarez-Buylla ER, Villarreal Luján C.

Front Physiol. 2018 Aug 2;9:877. doi: 10.3389/fphys.2018.00877. eCollection 2018.


Identifying the transition to the maturation zone in three ecotypes of Arabidopsis thaliana roots.

Cajero Sánchez W, García-Ponce B, Sánchez MP, Álvarez-Buylla ER, Garay-Arroyo A.

Commun Integr Biol. 2017 Dec 14;11(1):e1395993. doi: 10.1080/19420889.2017.1395993. eCollection 2018.


Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions.

Ceapă CD, Vázquez-Hernández M, Rodríguez-Luna SD, Cruz Vázquez AP, Jiménez Suárez V, Rodríguez-Sanoja R, Alvarez-Buylla ER, Sánchez S.

PLoS One. 2018 Feb 15;13(2):e0192618. doi: 10.1371/journal.pone.0192618. eCollection 2018.


The CD4+ T cell regulatory network mediates inflammatory responses during acute hyperinsulinemia: a simulation study.

Martinez-Sanchez ME, Hiriart M, Alvarez-Buylla ER.

BMC Syst Biol. 2017 Jun 26;11(1):64. doi: 10.1186/s12918-017-0436-y.


Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation, and Prediction.

Velderraín JD, Martínez-García JC, Álvarez-Buylla ER.

Methods Mol Biol. 2017;1629:297-315. doi: 10.1007/978-1-4939-7125-1_19.


A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana.

García-Gómez ML, Azpeitia E, Álvarez-Buylla ER.

PLoS Comput Biol. 2017 Apr 20;13(4):e1005488. doi: 10.1371/journal.pcbi.1005488. eCollection 2017 Apr. Erratum in: PLoS Comput Biol. 2019 Jun 12;15(6):e1007140.


Model of polar auxin transport coupled to mechanical forces retrieves robust morphogenesis along the Arabidopsis root.

Romero-Arias JR, Hernández-Hernández V, Benítez M, Alvarez-Buylla ER, Barrio RA.

Phys Rev E. 2017 Mar;95(3-1):032410. doi: 10.1103/PhysRevE.95.032410. Epub 2017 Mar 16.


Erratum: The combination of the functionalities of feedback circuits is determinant for the attractors' number and size in pathway-like Boolean networks.

Azpeitia E, Muñoz S, González-Tokman D, Martínez-Sánchez ME, Weinstein N, Naldi A, Álvarez-Buylla ER, Rosenblueth DA, Mendoza L.

Sci Rep. 2017 Mar 22;7:44964. doi: 10.1038/srep44964. No abstract available.


Gene regulatory network underlying the immortalization of epithelial cells.

Méndez-López LF, Davila-Velderrain J, Domínguez-Hüttinger E, Enríquez-Olguín C, Martínez-García JC, Alvarez-Buylla ER.

BMC Syst Biol. 2017 Feb 16;11(1):24. doi: 10.1186/s12918-017-0393-5.


The combination of the functionalities of feedback circuits is determinant for the attractors' number and size in pathway-like Boolean networks.

Azpeitia E, Muñoz S, González-Tokman D, Martínez-Sánchez ME, Weinstein N, Naldi A, Álvarez-Buylla ER, Rosenblueth DA, Mendoza L.

Sci Rep. 2017 Feb 10;7:42023. doi: 10.1038/srep42023. Erratum in: Sci Rep. 2017 Mar 22;7:44964.


The MADS-box XAANTAL1 increases proliferation at the Arabidopsis root stem-cell niche and participates in transition to differentiation by regulating cell-cycle components.

García-Cruz KV, García-Ponce B, Garay-Arroyo A, Sanchez MP, Ugartechea-Chirino Y, Desvoyes B, Pacheco-Escobedo MA, Tapia-López R, Ransom-Rodríguez I, Gutierrez C, Alvarez-Buylla ER.

Ann Bot. 2016 Oct 1;118(4):787-796. doi: 10.1093/aob/mcw126.


Root Architecture Diversity and Meristem Dynamics in Different Populations of Arabidopsis thaliana.

Aceves-García P, Álvarez-Buylla ER, Garay-Arroyo A, García-Ponce B, Muñoz R, Sánchez Mde L.

Front Plant Sci. 2016 Jun 16;7:858. doi: 10.3389/fpls.2016.00858. eCollection 2016.


Longitudinal zonation pattern in Arabidopsis root tip defined by a multiple structural change algorithm.

Pacheco-Escobedo MA, Ivanov VB, Ransom-Rodríguez I, Arriaga-Mejía G, Ávila H, Baklanov IA, Pimentel A, Corkidi G, Doerner P, Dubrovsky JG, Álvarez-Buylla ER, Garay-Arroyo A.

Ann Bot. 2016 Oct 1;118(4):763-776. doi: 10.1093/aob/mcw101. Erratum in: Ann Bot. 2017 Jan 7;:.


Dynamic network modelling to understand flowering transition and floral patterning.

Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER.

J Exp Bot. 2016 Apr;67(9):2565-72. doi: 10.1093/jxb/erw123. Epub 2016 Mar 28.


A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle.

Ortiz-Gutiérrez E, García-Cruz K, Azpeitia E, Castillo A, Sánchez Mde L, Álvarez-Buylla ER.

PLoS Comput Biol. 2015 Sep 4;11(9):e1004486. doi: 10.1371/journal.pcbi.1004486. eCollection 2015 Sep.


Glutamatergic Receptor Activation in the Commisural Nucleus Tractus Solitarii (cNTS) Mediates Brain Glucose Retention (BGR) Response to Anoxic Carotid Chemoreceptor (CChr) Stimulation in Rats.

Cuéllar R, Montero S, Luquín S, García-Estrada J, Dobrovinskaya O, Melnikov V, Lemus M, de Álvarez-Buylla ER.

Adv Exp Med Biol. 2015;860:301-8. doi: 10.1007/978-3-319-18440-1_34.


Effects of moderate- and high-intensity chronic exercise on brain-derived neurotrophic factor expression in fast and slow muscles.

Jiménez-Maldonado A, Cerna-Cortés J, Castro-Rodríguez EM, Montero SA, Muñiz J, Rodríguez-Hernández A, Lemus M, De Álvarez-Buylla ER.

Muscle Nerve. 2016 Mar;53(3):446-51. doi: 10.1002/mus.24757. Epub 2015 Dec 29.


A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity.

Martinez-Sanchez ME, Mendoza L, Villarreal C, Alvarez-Buylla ER.

PLoS Comput Biol. 2015 Jun 19;11(6):e1004324. doi: 10.1371/journal.pcbi.1004324. eCollection 2015 Jun.


The impact of Polycomb group (PcG) and Trithorax group (TrxG) epigenetic factors in plant plasticity.

de la Paz Sanchez M, Aceves-García P, Petrone E, Steckenborn S, Vega-León R, Álvarez-Buylla ER, Garay-Arroyo A, García-Ponce B.

New Phytol. 2015 Nov;208(3):684-94. doi: 10.1111/nph.13486. Epub 2015 Jun 2. Review.


Reshaping the epigenetic landscape during early flower development: induction of attractor transitions by relative differences in gene decay rates.

Davila-Velderrain J, Villarreal C, Alvarez-Buylla ER.

BMC Syst Biol. 2015 May 13;9:20. doi: 10.1186/s12918-015-0166-y.


Modeling the epigenetic attractors landscape: toward a post-genomic mechanistic understanding of development.

Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER.

Front Genet. 2015 Apr 23;6:160. doi: 10.3389/fgene.2015.00160. eCollection 2015. Review.


A model of the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva.

Weinstein N, Ortiz-Gutiérrez E, Muñoz S, Rosenblueth DA, Álvarez-Buylla ER, Mendoza L.

BMC Bioinformatics. 2015 Mar 13;16:81. doi: 10.1186/s12859-015-0498-z.


Descriptive vs. mechanistic network models in plant development in the post-genomic era.

Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER.

Methods Mol Biol. 2015;1284:455-79. doi: 10.1007/978-1-4939-2444-8_23.


Role of transcriptional regulation in the evolution of plant phenotype: A dynamic systems approach.

Rodríguez-Mega E, Piñeyro-Nelson A, Gutierrez C, García-Ponce B, Sánchez MP, Zluhan-Martínez E, Álvarez-Buylla ER, Garay-Arroyo A.

Dev Dyn. 2015 Sep;244(9):1074-1095. doi: 10.1002/dvdy.24268. Epub 2015 Apr 8. Review.


XAANTAL2 (AGL14) Is an Important Component of the Complex Gene Regulatory Network that Underlies Arabidopsis Shoot Apical Meristem Transitions.

Pérez-Ruiz RV, García-Ponce B, Marsch-Martínez N, Ugartechea-Chirino Y, Villajuana-Bonequi M, de Folter S, Azpeitia E, Dávila-Velderrain J, Cruz-Sánchez D, Garay-Arroyo A, Sánchez Mde L, Estévez-Palmas JM, Álvarez-Buylla ER.

Mol Plant. 2015 May;8(5):796-813. doi: 10.1016/j.molp.2015.01.017. Epub 2015 Jan 28.


Chronic exercise increases plasma brain-derived neurotrophic factor levels, pancreatic islet size, and insulin tolerance in a TrkB-dependent manner.

Jiménez-Maldonado A, de Álvarez-Buylla ER, Montero S, Melnikov V, Castro-Rodríguez E, Gamboa-Domínguez A, Rodríguez-Hernández A, Lemus M, Murguía JM.

PLoS One. 2014 Dec 22;9(12):e115177. doi: 10.1371/journal.pone.0115177. eCollection 2014. Erratum in: PLoS One. 2015;10(3):e0119047.


Co-option of the polarity gene network shapes filament morphology in angiosperms.

de Almeida AM, Yockteng R, Schnable J, Alvarez-Buylla ER, Freeling M, Specht CD.

Sci Rep. 2014 Aug 29;4:6194. doi: 10.1038/srep06194.


Mechanical forces as information: an integrated approach to plant and animal development.

Hernández-Hernández V, Rueda D, Caballero L, Alvarez-Buylla ER, Benítez M.

Front Plant Sci. 2014 Jun 10;5:265. doi: 10.3389/fpls.2014.00265. eCollection 2014. Review.


ARACNe-based inference, using curated microarray data, of Arabidopsis thaliana root transcriptional regulatory networks.

Chávez Montes RA, Coello G, González-Aguilera KL, Marsch-Martínez N, de Folter S, Alvarez-Buylla ER.

BMC Plant Biol. 2014 Apr 16;14:97. doi: 10.1186/1471-2229-14-97.


Tetramer formation in Arabidopsis MADS domain proteins: analysis of a protein-protein interaction network.

Espinosa-Soto C, Immink RG, Angenent GC, Alvarez-Buylla ER, de Folter S.

BMC Syst Biol. 2014 Jan 27;8:9. doi: 10.1186/1752-0509-8-9.


Gene regulatory network models for floral organ determination.

Azpeitia E, Davila-Velderrain J, Villarreal C, Alvarez-Buylla ER.

Methods Mol Biol. 2014;1110:441-69. doi: 10.1007/978-1-4614-9408-9_26.


Molecular evolution constraints in the floral organ specification gene regulatory network module across 18 angiosperm genomes.

Davila-Velderrain J, Servin-Marquez A, Alvarez-Buylla ER.

Mol Biol Evol. 2014 Mar;31(3):560-73. doi: 10.1093/molbev/mst223. Epub 2013 Nov 21.


The MADS transcription factor XAL2/AGL14 modulates auxin transport during Arabidopsis root development by regulating PIN expression.

Garay-Arroyo A, Ortiz-Moreno E, de la Paz Sánchez M, Murphy AS, García-Ponce B, Marsch-Martínez N, de Folter S, Corvera-Poiré A, Jaimes-Miranda F, Pacheco-Escobedo MA, Dubrovsky JG, Pelaz S, Álvarez-Buylla ER.

EMBO J. 2013 Oct 30;32(21):2884-95. doi: 10.1038/emboj.2013.216. Epub 2013 Oct 11.


Molecular evolution and patterns of duplication in the SEP/AGL6-like lineage of the Zingiberales: a proposed mechanism for floral diversification.

Yockteng R, Almeida AM, Morioka K, Alvarez-Buylla ER, Specht CD.

Mol Biol Evol. 2013 Nov;30(11):2401-22. doi: 10.1093/molbev/mst137. Epub 2013 Aug 11.


Finding Missing Interactions of the Arabidopsis thaliana Root Stem Cell Niche Gene Regulatory Network.

Azpeitia E, Weinstein N, Benítez M, Mendoza L, Alvarez-Buylla ER.

Front Plant Sci. 2013 Apr 30;4:110. doi: 10.3389/fpls.2013.00110. eCollection 2013.


Cell patterns emerge from coupled chemical and physical fields with cell proliferation dynamics: the Arabidopsis thaliana root as a study system.

Barrio RA, Romero-Arias JR, Noguez MA, Azpeitia E, Ortiz-Gutiérrez E, Hernández-Hernández V, Cortes-Poza Y, Álvarez-Buylla ER.

PLoS Comput Biol. 2013;9(5):e1003026. doi: 10.1371/journal.pcbi.1003026. Epub 2013 May 2.


An efficient flat-surface collar-free grafting method for Arabidopsis thaliana seedlings.

Marsch-Martínez N, Franken J, Gonzalez-Aguilera KL, de Folter S, Angenent G, Alvarez-Buylla ER.

Plant Methods. 2013 May 4;9(1):14. doi: 10.1186/1746-4811-9-14.


Dynamic models of epidermal patterning as an approach to plant eco-evo-devo.

Benítez M, Azpeitia E, Alvarez-Buylla ER.

Curr Opin Plant Biol. 2013 Feb;16(1):11-8. doi: 10.1016/j.pbi.2012.11.005. Epub 2012 Dec 6. Review.


Brain-derived neurotrophic factor in the nucleus tractus solitarii modulates glucose homeostasis after carotid chemoreceptor stimulation in rats.

Montero S, Cuéllar R, Lemus M, Avalos R, Ramírez G, de Álvarez-Buylla ER.

Adv Exp Med Biol. 2012;758:233-9. doi: 10.1007/978-94-007-4584-1_32.


New genes in traditional seed systems: diffusion, detectability and persistence of transgenes in a maize metapopulation.

van Heerwaarden J, Ortega Del Vecchyo D, Alvarez-Buylla ER, Bellon MR.

PLoS One. 2012;7(10):e46123. doi: 10.1371/journal.pone.0046123. Epub 2012 Oct 3.


Hormone symphony during root growth and development.

Garay-Arroyo A, De La Paz Sánchez M, García-Ponce B, Azpeitia E, Alvarez-Buylla ER.

Dev Dyn. 2012 Dec;241(12):1867-85. doi: 10.1002/dvdy.23878. Epub 2012 Oct 25. Review.


General theory of genotype to phenotype mapping: derivation of epigenetic landscapes from N-node complex gene regulatory networks.

Villarreal C, Padilla-Longoria P, Alvarez-Buylla ER.

Phys Rev Lett. 2012 Sep 14;109(11):118102. Epub 2012 Sep 12.


A complex systems approach to Arabidopsis root stem-cell niche developmental mechanisms: from molecules, to networks, to morphogenesis.

Azpeitia E, Alvarez-Buylla ER.

Plant Mol Biol. 2012 Nov;80(4-5):351-63. doi: 10.1007/s11103-012-9954-6. Epub 2012 Sep 4. Review.


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