Publications

Pereira, H. D., Nonato, J. V. A., Duarte, R. C. R. M., Gerhardt, I. R., Dante, R. A., Arruda, P., & Yassitepe, J. E. de C. T. (2025). Temporal field phenomics of transgenic maize events subjected to drought stress: Cross‐validation scenarios and machine learning models. The Plant Phenome Journal, 8(1). https://doi.org/10.1002/ppj2.70015

Braz, G. T., Riboldi, L. B., Pinto, M. S., Forni-Martins, E. R., Yassitepe, J. E. C. T., Dante, R. A., & Gerhardt, I. R. (2024). Revisiting the cytogenetics of Vellozia Vand.: immunolocalization of KNL1 elucidates the chromosome number for the genus. Brazilian Journal of Botany, 48(1), 6. https://doi.org/10.1007/s40415-024-01064-1

Souza, K. X. S. de, Bolfe, É. L., Leite, M. A. de A., Bambini, M. D., Visoli, M. C., Luchiari Júnior, A., da Silva, F. R., Esquerdo, J. C. D. M., & Yassitepe, J. E. de C. T. (2024). Quantum computing: current and potential applications in digital agriculture. Pesquisa Agropecuária Brasileira, 59. https://doi.org/10.1590/s1678-3921.pab2024.v59.03753

Temporal field phenomics of transgenic maize events subjected to drought stress: cross-validation scenarios and machine learning models. https://www.gccrc.unicamp.br/wp-content/uploads/2024/11/Data-availability-for-phenomic-prediction.zip

Koltun, A., Alves Da Silva, P., Torres, I. Y., Bonifácio-Anacleto, F., Erika De Carvalho, J., & Yassitepe, T. (n.d.). Microsatellite markers in maize: challenges and guidelines for implementing multiplex SSR analyses Microsatellite markers in maize: challenges and guidelines for implementing multiplex SSR analyses ARTICLE. Crop Breeding and Applied Biotechnology, 24(1), 2024. https://doi.org/10.1590/1984

Hernandes-Lopes, J., Pinto, M. S., Vieira, L. R., Monteiro, P. B., Gerasimova, S. V., Nonato, J. V. A., Bruno, M. H. F., Vikhorev, A., Rausch-Fernandes, F., Gerhardt, I. R., Pauwels, L., Arruda, P., Dante, R. A., & Yassitepe, J. E. de C. T. (2023). Enabling genome editing in tropical maize lines through an improved, morphogenic regulator-assisted transformation protocol. Frontiers in Genome Editing, 5. https://doi.org/10.3389/fgeed.2023.1241035

Costa, F. de F., Souza, R. S. C. de, Voidaleski, M. F., Gomes, R. R., Reis, G. F., Lima, B. J. F. de S., Candido, G. Z., Geraldo, M. R., Soares, J. M. B., Schneider, G. X., Trindade, E. da S., Bini, I. H., Moreno, L. F., Bombassaro, A., Queiroz-Telles, F., Raittz, R. T., Quan, Y., Arruda, P., Attili-Angelis, D., … Vicente, V. A. (2023). Sugarcane: an unexpected habitat for black yeasts in Chaetothyriales. IMA Fungus, 14(1), 20. https://doi.org/10.1186/s43008-023-00124-7

Fuchs, P., Feixes-Prats, E., Arruda, P., Feitosa-Araújo, E., Fernie, A. R., Grefen, C., Lichtenauer, S., Linka, N., de Godoy Maia, I., Meyer, A. J., Schilasky, S., Sweetlove, L. J., Wege, S., Weber, A. P. M., Millar, A. H., Keech, O., Florez-Sarasa, I., Barreto, P., & Schwarzländer, M. (2023). PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 2 localizes to the Golgi. Plant Physiology. https://doi.org/10.1093/plphys/kiad540

Hernandes-Lopes, J., Yassitepe, J. E. de C. T., Koltun, A., Pauwels, L., Silva, V. C. H. da, Dante, R. A., Gerhardt, I. R., & Arruda, P. (2023). Genome editing in maize: Toward improving complex traits in a global crop. Genetics and Molecular Biology, 46(1 suppl 1). https://doi.org/10.1590/1678-4685-gmb-2022-0217

Ferrocino, I., Rantsiou, K., McClure, R., Kostic, T., de Souza, R. S. C., Lange, L., FitzGerald, J., Kriaa, A., Cotter, P., Maguin, E., Schelkle, B., Schloter, M., Berg, G., Sessitsch, A., & Cocolin, L. (2023). The need for an integrated multi‐OMICs approach in microbiome science in the food system. Comprehensive Reviews in Food Science and Food Safety. https://doi.org/10.1111/1541-4337.13103

Camargo, A. P., de Souza, R. S. C., Jose, J., Gerhardt, I. R., Dante, R. A., Mukherjee, S., Huntemann, M., Kyrpides, N. C., Carazzolle, M. F., & Arruda, P. (2022). Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot. The ISME Journal. https://doi.org/10.1038/s41396-022-01345-1

Lange, L., Berg, G., Cernava, T., Champomier-Vergès, M.-C., Charles, T., Cocolin, L., Cotter, P., D’Hondt, K., Kostic, T., Maguin, E., Makhalanyane, T., Meisner, A., Ryan, M., Kiran, G. S., de Souza, R. S., Sanz, Y., Schloter, M., Smidt, H., Wakelin, S., & Sessitsch, A. (2022). Microbiome ethics, guiding principles for microbiome research, use and knowledge management. Environmental Microbiome, 17(1), 50. https://doi.org/10.1186/s40793-022-00444-y

Olmo, Rocío, Stefanie Urimare Wetzels, Jaderson Silveira Leite Armanhi, Paulo Arruda, Gabriele Berg, Tomislav Cernava, Paul D. Cotter, Solon Cordeiro Araujo, Rafael Soares Correa de Souza […], and Martin Wagner. 2022. “Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems – A Selection of Case Studies.” Frontiers in Microbiology 13. doi: 10.3389/fmicb.2022.834622.

Barreto, Pedro, Charlene Dambire, Gunjan Sharma, Jorge Vicente, Rory Osborne, Juliana Yassitepe, Daniel J. Gibbs, Ivan G. Maia, Michael J. Holdsworth, and Paulo Arruda. 2022. “Mitochondrial Retrograde Signaling through UCP1-Mediated Inhibition of the Plant Oxygen-Sensing Pathway.” Current Biology 32 (6): 1403-1411.e4. https://doi.org/10.1016/j.cub.2022.01.037.

Meisner, Annelein, Beatrix Wepner, Tanja Kostic, Leo S van Overbeek, Christine J Bunthof, Rafael Soares Correa de Souza, Marta Olivares, et al. 2022. “Calling for a Systems Approach in Microbiome Research and Innovation.” Current Opinion in Biotechnology 73 (February): 171–78. https://doi.org/10.1016/j.copbio.2021.08.003.

Armanhi, Jaderson Silveira Leite, Rafael Soares Correa de Souza, Bárbara Bort Biazotti, Juliana Erika de Carvalho Teixeira Yassitepe, and Paulo Arruda. 2021. “Modulating Drought Stress Response of Maize by a Synthetic Bacterial Community.” Frontiers in Microbiology 12 (October). https://doi.org/10.3389/fmicb.2021.747541.

Souza, Rafael Soares Correa de, Jaderson Silveira Leite Armanhi, and Paulo Arruda. 2020. “From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency.” Frontiers in Plant Science 11 (August). https://doi.org/10.3389/fpls.2020.01179.

Nayfach, Stephen, Antonio Pedro Camargo, Frederik Schulz, Emiley Eloe-Fadrosh, Simon Roux, and Nikos C. Kyrpides. 2021. “CheckV Assesses the Quality and Completeness of Metagenome-Assembled Viral Genomes.” Nature Biotechnology 39 (5): 578–85. https://doi.org/10.1038/s41587-020-00774-7.

Nayfach, Stephen, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, et al. 2021. “A Genomic Catalog of Earth’s Microbiomes.” Nature Biotechnology 39 (4): 499–509. https://doi.org/10.1038/s41587-020-0718-6.

Ryan, M.J., M. Schloter, G. Berg, T. Kostic, L.L. Kinkel, K. Eversole, J.A. Macklin, et al. 2021. “Development of Microbiome Biobanks – Challenges and Opportunities.” Trends in Microbiology 29 (2): 89–92. https://doi.org/10.1016/j.tim.2020.06.009.

Yassitepe, Juliana Erika de Carvalho Teixeira, Viviane Cristina Heinzen da Silva, José Hernandes-Lopes, Ricardo Augusto Dante, Isabel Rodrigues Gerhardt, Fernanda Rausch Fernandes, Priscila Alves da Silva, Leticia Rios Vieira, Vanessa Bonatti, and Paulo Arruda. 2021. “Maize Transformation: From Plant Material to the Release of Genetically Modified and Edited Varieties.” Frontiers in Plant Science 12 (October). https://doi.org/10.3389/fpls.2021.766702.

Zuvanov, Luíza, Ana Letycia Basso Garcia, Fernando Henrique Correr, Rodolfo Bizarria, Ailton Pereira da Costa Filho, Alisson Hayasi da Costa, Andréa T. Thomaz, et al. 2021. “The Experience of Teaching Introductory Programming Skills to Bioscientists in Brazil.” PLOS Computational Biology 17 (11): e1009534. https://doi.org/10.1371/journal.pcbi.1009534.

Barreto, Pedro, Rafael M. Couñago, and Paulo Arruda. 2020. “Mitochondrial Uncoupling Protein-Dependent Signaling in Plant Bioenergetics and Stress Response.” Mitochondrion 53 (July): 109–20. https://doi.org/10.1016/j.mito.2020.05.001.

Aquino, Bruno, Viviane C. H. da Silva, Katlin B. Massirer, and Paulo Arruda. 2020. “Crystal Structure of DRIK1, a Stress-Responsive Receptor-like Pseudokinase, Reveals the Molecular Basis for the Absence of ATP Binding.” BMC Plant Biology 20 (1): 158. https://doi.org/10.1186/s12870-020-2328-3.

Camargo, Antonio Pedro, Rafael Soares Correa de Souza, Patrícia de Britto Costa, Isabel Rodrigues Gerhardt, Ricardo Augusto Dante, Grazielle Sales Teodoro, Anna Abrahão, et al. 2019. “Microbiomes of Velloziaceae from Phosphorus-Impoverished Soils of the Campos Rupestres, a Biodiversity Hotspot.” Scientific Data 6 (1): 140. https://doi.org/10.1038/s41597-019-0141-3.

Souza, Rafael Soares Correa de, Jaderson Silveira Leite Armanhi, Natália de Brito Damasceno, Juan Imperial, and Paulo Arruda. 2019. “Genome Sequences of a Plant Beneficial Synthetic Bacterial Community Reveal Genetic Features for Successful Plant Colonization.” Frontiers in Microbiology 10 (August). https://doi.org/10.3389/fmicb.2019.01779.

Souza, Wagner Rodrigo de, Thályta Fraga Pacheco, Karoline Estefani Duarte, Bruno Leite Sampaio, Patrícia Abrão de Oliveira Molinari, Polyana Kelly Martins, Thaís Ribeiro Santiago, et al. 2019. “Silencing of a BAHD Acyltransferase in Sugarcane Increases Biomass Digestibility.” Biotechnology for Biofuels 12 (1): 111. https://doi.org/10.1186/s13068-019-1450-7.

Souza, Wagner Rodrigo, Nelson Geraldo Oliveira, Felipe Vinecky, Ana Paula Ribeiro, Marcos Fernando Basso, Raphael Augusto das Chagas Noqueli Casari, Bárbara Andrade Dias Brito Cunha, et al. 2019. “Field Evaluation of AtDREB2A CA Overexpressing Sugarcane for Drought Tolerance.” Journal of Agronomy and Crop Science 205 (6): 545–53. https://doi.org/10.1111/jac.12341.

Wisser, Randall J, Zhou Fang, James B Holland, Juliana E C Teixeira, John Dougherty, Teclemariam Weldekidan, Natalia de Leon, et al. 2019. “The Genomic Basis for Short-Term Evolution of Environmental Adaptation in Maize.” Genetics 213 (4): 1479–94. https://doi.org/10.1534/genetics.119.302780.

Aquino, Bruno, Rafael M. Couñago, Natalia Verza, Lucas M. Ferreira, Katlin B. Massirer, Opher Gileadi, and Paulo Arruda. 2017. “Structural Characterization of Maize SIRK1 Kinase Domain Reveals an Unusual Architecture of the Activation Segment.” Frontiers in Plant Science 8 (May). https://doi.org/10.3389/fpls.2017.00852.

Armanhi, Jaderson Silveira Leite, Rafael Soares Correa de Souza, Laura Migliorini de Araújo, Vagner Katsumi Okura, Piotr Mieczkowski, Juan Imperial, and Paulo Arruda. 2016. “Multiplex Amplicon Sequencing for Microbe Identification in Community-Based Culture Collections.” Scientific Reports 6 (1): 29543. https://doi.org/10.1038/srep29543.

Armanhi, Jaderson Silveira Leite, Rafael Soares Correa de Souza, Natália de Brito Damasceno, Laura M. de Araújo, Juan Imperial, and Paulo Arruda. 2018. “A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome.” Frontiers in Plant Science 8 (January). https://doi.org/10.3389/fpls.2017.02191.

Arruda, Paulo, and Pedro Barreto. 2020. “Lysine Catabolism Through the Saccharopine Pathway: Enzymes and Intermediates Involved in Plant Responses to Abiotic and Biotic Stress.” Frontiers in Plant Science 11 (May). https://doi.org/10.3389/fpls.2020.00587.

Barreto, Pedro, Juliana E. C. T. Yassitepe, Zoe A. Wilson, and Paulo Arruda. 2017. “Mitochondrial Uncoupling Protein 1 Overexpression Increases Yield in Nicotiana Tabacum under Drought Stress by Improving Source and Sink Metabolism.” Frontiers in Plant Science 8 (November). https://doi.org/10.3389/fpls.2017.01836.

Barreto, Pedro, Vagner Okura, Izabella A. Pena, Renato Maia, Ivan G. Maia, and Paulo Arruda. 2016. “Overexpression of Mitochondrial Uncoupling Protein 1 (UCP1) Induces a Hypoxic Response in Nicotiana Tabacum Leaves.” Journal of Experimental Botany 67 (1): 301–13. https://doi.org/10.1093/jxb/erv460.

Okura, Vagner Katsumi, Rafael S. C. de Souza, Susely F. de Siqueira Tada, and Paulo Arruda. 2016. “BAC-Pool Sequencing and Assembly of 19 Mb of the Complex Sugarcane Genome.” Frontiers in Plant Science 7 (March). https://doi.org/10.3389/fpls.2016.00342.

Pena, Izabella A., Lygia A. Marques, Angelo B. A. Laranjeira, José A. Yunes, Marcos N. Eberlin, and Paulo Arruda. 2016. “Simultaneous Detection of Lysine Metabolites by a Single LC–MS/MS Method: Monitoring Lysine Degradation in Mouse Plasma.” SpringerPlus 5 (1): 172. https://doi.org/10.1186/s40064-016-1809-1.

Barreto, Pedro, Vagner Katsumi Okura, Izabella Agostinho Pena Neshich, Ivan de Godoy Maia, and Paulo Arruda. 2014. “Overexpression of UCP1 in Tobacco Induces Mitochondrial Biogenesis and Amplifies a Broad Stress Response.” BMC Plant Biology 14 (1): 144. https://doi.org/10.1186/1471-2229-14-144.

Neshich, Izabella AP, Eduardo Kiyota, and Paulo Arruda. 2013. “Genome-Wide Analysis of Lysine Catabolism in Bacteria Reveals New Connections with Osmotic Stress Resistance.” The ISME Journal 7 (12): 2400–2410. https://doi.org/10.1038/ismej.2013.123.

Arruda, Paulo, and Izabella Pena Neshich. 2012. “Nutritional‐rich and Stress‐tolerant Crops by Saccharopine Pathway Manipulation.” Food and Energy Security 1 (2): 141–47. https://doi.org/10.1002/fes3.9.

Our published research