Jose Miguel Alvarez, Ph.D. - Publications

Affiliations: 
2020 Center for Genomics and Bioinformatics Universidad Mayor 

32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Shanks CM, Rothkegel K, Brooks MD, Cheng CY, Alvarez JM, Ruffel S, Krouk G, Gutiérrez RA, Coruzzi GM. Nitrogen sensing and regulatory networks: It's about time and space. The Plant Cell. PMID 38366121 DOI: 10.1093/plcell/koae038  0.789
2023 Cerda A, Alvarez JM. Insights into molecular links and transcription networks integrating drought stress and nitrogen signaling. The New Phytologist. PMID 37974513 DOI: 10.1111/nph.19403  0.501
2023 Alvarez JM, Hinckley WE, Leonelli L, Brooks MD, Coruzzi GM. DamID-seq: A Genome-Wide DNA Methylation Method that Captures Both Transient and Stable TF-DNA Interactions in Plant Cells. Methods in Molecular Biology (Clifton, N.J.). 2698: 87-107. PMID 37682471 DOI: 10.1007/978-1-0716-3354-0_7  0.804
2023 Pacheco JM, Song L, Kuběnová L, Ovečka M, Berdion Gabarain V, Peralta JM, Lehuedé TU, Ibeas MA, Ricardi MM, Zhu S, Shen Y, Schepetilnikov M, Ryabova LA, Alvarez JM, Gutierrez RA, et al. Cell surface receptor kinase FERONIA linked to nutrient sensor TORC signaling controls root hair growth at low temperature linked to low nitrate in Arabidopsis thaliana. The New Phytologist. PMID 36716782 DOI: 10.1111/nph.18723  0.73
2022 Núñez-Lillo G, Pérez-Reyes W, Riveros A, Lillo-Carmona V, Rothkegel K, Álvarez JM, Blanco-Herrera F, Pedreschi R, Campos-Vargas R, Meneses C. Transcriptome and Gene Regulatory Network Analyses Reveal New Transcription Factors in Mature Fruit Associated with Harvest Date in . Plants (Basel, Switzerland). 11. PMID 36559585 DOI: 10.3390/plants11243473  0.406
2022 Shanks CM, Huang J, Cheng CY, Shih HS, Brooks MD, Alvarez JM, Araus V, Swift J, Henry A, Coruzzi GM. Validation of a high-confidence regulatory network for gene-to-NUE phenotype in field-grown rice. Frontiers in Plant Science. 13: 1006044. PMID 36507422 DOI: 10.3389/fpls.2022.1006044  0.791
2022 Johnson NR, Larrondo LF, Álvarez JM, Vidal EA. Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links. Elife. 11. PMID 36484778 DOI: 10.7554/eLife.83691  0.677
2022 Lamig L, Moreno S, Álvarez JM, Gutiérrez RA. Molecular mechanisms underlying nitrate responses in plants. Current Biology : Cb. 32: R433-R439. PMID 35537398 DOI: 10.1016/j.cub.2022.03.022  0.788
2022 Contreras-López O, Vidal EA, Riveras E, Alvarez JM, Moyano TC, Sparks EE, Medina J, Pasquino A, Benfey PN, Coruzzi GM, Gutiérrez RA. Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35046022 DOI: 10.1073/pnas.2107879119  0.849
2021 Moyano TC, Gutiérrez RA, Alvarez JM. Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks. Methods in Molecular Biology (Clifton, N.J.). 2328: 25-46. PMID 34251618 DOI: 10.1007/978-1-0716-1534-8_3  0.762
2021 Bueno N, Cuesta C, Centeno ML, Ordás RJ, Alvarez JM. In Vitro Plant Regeneration in Conifers: The Role of and Gene Families. Genes. 12. PMID 33808690 DOI: 10.3390/genes12030438  0.354
2021 Alvarez JM, Brooks MD, Swift J, Coruzzi GM. Time-Based Systems Biology Approaches to Capture and Model Dynamic Gene Regulatory Networks. Annual Review of Plant Biology. PMID 33667112 DOI: 10.1146/annurev-arplant-081320-090914  0.826
2021 Brooks MD, Juang CL, Katari MS, Alvarez JM, Pasquino A, Shih HJ, Huang J, Shanks C, Cirrone J, Coruzzi GM. ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks. Plant Physiology. 185: 49-66. PMID 33631799 DOI: 10.1093/plphys/kiaa012  0.814
2020 Swift J, Alvarez JM, Araus V, Gutiérrez RA, Coruzzi GM. Nutrient dose-responsive transcriptome changes driven by Michaelis-Menten kinetics underlie plant growth rates. Proceedings of the National Academy of Sciences of the United States of America. PMID 32414922 DOI: 10.1073/Pnas.1918619117  0.8
2020 Vidal EA, Alvarez JM, Araus V, Riveras E, Brooks M, Krouk G, Ruffel S, Lejay L, Crawford N, Coruzzi GM, Gutiérrez RA. Nitrate 2020: Thirty years from transport to signaling networks. The Plant Cell. PMID 32169959 DOI: 10.1105/Tpc.19.00748  0.768
2020 Alvarez JM, Schinke AL, Brooks MD, Pasquino A, Leonelli L, Varala K, Safi A, Krouk G, Krapp A, Coruzzi GM. Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade. Nature Communications. 11: 1157. PMID 32123177 DOI: 10.1038/S41467-020-14979-6  0.787
2020 Alvarez JM, Bueno N, Cuesta C, Feito I, Ordás RJ. Hormonal and gene dynamics in de novo shoot meristem formation during adventitious caulogenesis in cotyledons of Pinus pinea. Plant Cell Reports. PMID 31993729 DOI: 10.1007/s00299-020-02508-0  0.371
2020 Araus V, Swift J, Alvarez JM, Henry A, Coruzzi GM. A balancing act: how plants integrate nitrogen and water signals. Journal of Experimental Botany. PMID 31990028 DOI: 10.1093/Jxb/Eraa054  0.824
2019 Alvarez JM, Moyano TC, Zhang T, Gras DE, Herrera FJ, Araus V, O'Brien JA, Carrillo L, Medina J, Vicente-Carbajosa J, Jiang J, Gutiérrez RA. Local changes in chromatin accessibility and transcriptional networks underlying the nitrate response in Arabidopsis roots. Molecular Plant. PMID 31526863 DOI: 10.1016/J.Molp.2019.09.002  0.818
2019 Brooks MD, Cirrone J, Pasquino AV, Alvarez JM, Swift J, Mittal S, Juang CL, Varala K, Gutiérrez RA, Krouk G, Shasha D, Coruzzi GM. Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions. Nature Communications. 10: 1569. PMID 30952851 DOI: 10.1038/S41467-019-09522-1  0.811
2017 Alvarez JM, Bueno N, Cañas RA, Avila C, Cánovas FM, Ordás RJ. Analysis of the WUSCHEL-RELATED HOMEOBOX gene family in Pinus pinaster: New insights into the gene family evolution. Plant Physiology and Biochemistry : Ppb. 123: 304-318. PMID 29278847 DOI: 10.1016/j.plaphy.2017.12.031  0.353
2017 Canales J, Contreras-López O, Álvarez JM, Gutiérrez RA. Nitrate induction of root hair density is mediated by TGA1/TGA4 and CPC transcription factors in Arabidopsis thaliana. The Plant Journal : For Cell and Molecular Biology. PMID 28771873 DOI: 10.1111/Tpj.13656  0.82
2017 Undurraga SF, Ibarra-Henríquez C, Fredes I, Álvarez JM, Gutiérrez RA. Nitrate signaling and early responses in Arabidopsis roots. Journal of Experimental Botany. PMID 28369507 DOI: 10.1093/Jxb/Erx041  0.787
2016 Yazaki J, Galli M, Kim AY, Nito K, Aleman F, Chang KN, Carvunis AR, Quan R, Nguyen H, Song L, Alvarez JM, Huang SC, Chen H, Ramachandran N, Altmann S, et al. Mapping transcription factor interactome networks using HaloTag protein arrays. Proceedings of the National Academy of Sciences of the United States of America. PMID 27357687 DOI: 10.1073/Pnas.1603229113  0.777
2015 Riveras E, Alvarez JM, Vidal EA, Oses C, Vega A, Gutiérrez RA. The Calcium Ion Is a Second Messenger in the Nitrate Signaling Pathway of Arabidopsis. Plant Physiology. 169: 1397-404. PMID 26304850 DOI: 10.1104/Pp.15.00961  0.806
2015 Vidal EA, Álvarez JM, Moyano TC, Gutiérrez RA. Transcriptional networks in the nitrate response of Arabidopsis thaliana. Current Opinion in Plant Biology. 27: 125-32. PMID 26247122 DOI: 10.1016/J.Pbi.2015.06.010  0.866
2014 Alvarez JM, Riveras E, Vidal EA, Gras DE, Contreras-López O, Tamayo KP, Aceituno F, Gómez I, Ruffel S, Lejay L, Jordana X, Gutiérrez RA. Systems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response of Arabidopsis thaliana roots. The Plant Journal : For Cell and Molecular Biology. 80: 1-13. PMID 25039575 DOI: 10.1111/Tpj.12618  0.81
2014 Vidal EA, Álvarez JM, Gutiérrez RA. Nitrate regulation of AFB3 and NAC4 gene expression in Arabidopsis roots depends on NRT1.1 nitrate transport function. Plant Signaling & Behavior. 9: e28501. PMID 24642706 DOI: 10.4161/Psb.28501  0.813
2012 Alvarez JM, Cortizo M, Ordás RJ. Characterization of a type-A response regulator differentially expressed during adventitious caulogenesis in Pinus pinaster. Journal of Plant Physiology. 169: 1807-14. PMID 22959674 DOI: 10.1016/j.jplph.2012.07.014  0.338
2012 Alvarez JM, Vidal EA, Gutiérrez RA. Integration of local and systemic signaling pathways for plant N responses. Current Opinion in Plant Biology. 15: 185-91. PMID 22480431 DOI: 10.1016/J.Pbi.2012.03.009  0.797
2009 Alvarez JM, Canessa P, Mancilla RA, Polanco R, Santibáñez PA, Vicuña R. Expression of genes encoding laccase and manganese-dependent peroxidase in the fungus Ceriporiopsis subvermispora is mediated by an ACE1-like copper-fist transcription factor. Fungal Genetics and Biology : Fg & B. 46: 104-11. PMID 18955150 DOI: 10.1016/J.Fgb.2008.10.002  0.43
2008 Canessa P, Alvarez JM, Polanco R, Bull P, Vicuña R. The copper-dependent ACE1 transcription factor activates the transcription of the mco1 gene from the basidiomycete Phanerochaete chrysosporium. Microbiology (Reading, England). 154: 491-9. PMID 18227253 DOI: 10.1099/Mic.0.2007/013128-0  0.43
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