Synthetic Biology

In our program we address diverse biological questions through the scales (molecules, cells, communities) using different disciplines such as systems biology, bioinformatics, functional genomics, biochemistry, ecology, molecular biology among others. We aim to study how biological systems evolve and how we can modify them to generate synthetic biology applications.

One of our current topics is to study bacterial populations’ ecological and evolutionary dynamics and their response to different environmental conditions. In particular, we are interested in studying the effect of antimicrobial substances on the complex dynamics of bacterial populations. We build synthetic communities and study their interactions using experimental evolution techniques and mathematical, computational models, and individual cell microfluidics.

Current research shows that proteins can start to fold and become functional while still being synthesized by the ribosome. In our lab we apply state of the art methods of homology detection, algorithms to detect rare codons and folding predictions to uncover the impact of the ribosome in the structure of the proteome. In our experimental strategies we use one of the most successful developments of synthetic biology: a cell free protein expression system. With this system we produce proteins in carefully determined environments without the restrictions that living cells impose; this allows us to precisely control the elements that influence protein folding during translation.

Another of our research topics include the use of functional genomics to understand and design microbial production strains. We are interested in the generation of genome scale computational tools to aid in the design of synthetic production phenotypes through the modification of the genotype-phenotype relationship ( i.e. through the regulatory network). We aim to engineer the transcriptional and translational machineries of model and non model bacteria, such as Escherichia coli and pseudomonas chlororaphis, to improve the allocation of cellular resources to synthetic functions.

We are a mix of young bioinformaticians and experimentalists, this setup provides the perfect blend for successful projects. In our lab we encourage creativity, innovation and critical thinking in a relaxed environment to promote the development of young bachelor, master, doctoral students and postdocs.

Group Staff

María de Lourdes Girard CuesyResearcherAssociate 3291686
Diego Cortez QuezadaResearcherAssociate 3291686
Ayari Fuentes HernándezResearcherAssociate 3291686
Marisa Rodríguez PadillaLaboratory TechnicianLaboratory 3291686
José Utrilla CarreriResearcherAssociate 3291686
Eria Rebollar CaudilloResearcherAssistant 622 7777, Red-UNAM 38489
David Salvador Zamorano SánchezResearcherAssistant 329 1777
María de la Paz Elizabeth Salas OcampoLaboratory TechnicianLaboratory 3291686
Rafael Peña MillerResearcherAssociate 3291686
Julio Augusto Freyre GonzálezResearcherAssociate 3133881
José Arcadio Farías RicoResearcherAssistant 3291686
María Magdalena Banda HernándezPostdoctoral 3291686
Omar Alejandro Aguilar VeraLaboratory TechnicianLaboratory 3139944
María Soledad Juárez RamírezSupport 3133881

Group Publications

2022Suárez-Varón, G., Mendoza-Cruz, E., Acosta, A., Villagrán-Santa Cruz, M., Cortez D, Hernández-Gallegos, O.. (2022). "A study of thermally-induced sex reversal in casque-headed lizards". bioRxiv. ():-. [doi:]
2021Camacho-Hernández, D.A., Nieto-Caballero, V.E., León-Burguete, J.E., Freyre-González, J.A.. (2021). "Partition Quantitative Assessment (PQA): A Quantitative Methodology to Assess the Embedded Noise in Clustered Omics and Systems Biology Data". Applied Sciences. 11(13):-. [doi:10.3390/app11135999]
2021Hidalgo, D., Martínez-Ortiz, C.A., O. Palsson, B., Jiménez, J.I., Utrilla, J.. (2021). "Regulatory perturbations of ribosome allocation reshape the growth proteome with a trade-off in adaptation capacity". bioRxiv. ():-. [doi:]
2021Orta, A.H., Bush, S.J., Gutiérrez-Mariscal, M., Castro-Obregón, S., Jaimes-Hoy, L., Grande, R., Vázquez, G., Gorostieta-Salas, E., Martínez-Pacheco, M., Díaz-Barba, K., Cornejo-Páramo, P., Sanchez-Flores, A., Székely, T., Urrutia, A.O., Cortez, D.. (2021). "Rats exhibit age-related mosaic loss of chromosome Y.". Communications Biology. 4(1):-. [doi:10.1038/s42003-021-02936-y]34934158
2021Suárez-Varón, G., Cortez, D., Cruz, M.V.S., Rojas-Hernández, U., Hernández-Gallegos, O.. (2021). "Variation of the embryonic stage of Basiliscus vittatus (Squamata: Corytophanidae) at oviposition". REVISTA MEXICANA DE BIODIVERSIDAD. 92():-. [doi:10.22201/IB.20078706E.2021.92.3795]
2021Zorro-Aranda, A., Escorcia-Rodríguez, González-Kise, J.K., Freyre-González, J.A.. (2021). "Reconstruction of a global gene regulatory network for Streptomyces coelicolor: Curation, inference, and assessment". bioRxiv. ():-. [doi:]
2021Hernández-Beltrán, J.C.R., San Millán, A., Fuentes-Hernández, A., Peña-Miller, R.. (2021). "Mathematical Models of Plasmid Population Dynamics.". Frontiers in Microbiology. 12():-. [doi:10.3389/fmicb.2021.606396]34803935
2021Sierra Cacho, D., Zamorano Sánchez, D.S., Xiqui-Vázquez, M.L., Viruega Góngora, V.I., Ramírez-Mata, A., Baca, B.E.. (2021). "CdgC, a Cyclic-di-GMP Diguanylate Cyclase of Azospirillum baldaniorum Is Involved in Internalization to Wheat Roots.". Frontiers In Plant Science. 12():-. [doi:10.3389/fpls.2021.748393]34745182
2021Basanta, M.D., Rebollar, E.A., García-Castillo, M.G., Parra Olea, G.. (2021). "Comparative Analysis of Skin Bacterial Diversity and Its Potential Antifungal Function Between Desert and Pine Forest Populations of Boreal Toads Anaxyrus boreas.". Microbial Ecology. ():-. [doi:10.1007/s00248-021-01845-1]34427721
2021Merchant-Larios, H., Diáz-Hernández, V., Cortez, D.. (2021). "Molecular and Cellular Mechanisms Underlying Temperature-Dependent Sex Determination in Turtles.". SEX DEV. 15(1-3):38-46. [doi:10.1159/000515296]34167126
2021Escorcia-Rodríguez, J.M., Tauch, A., Freyre-González, J.A.. (2021). "Corynebacterium glutamicum Regulation beyond Transcription: Organizing Principles and Reconstruction of an Extended Regulatory Network Incorporating Regulations Mediated by Small RNA and Protein-Protein Interactions.". Microorganisms. 9(7):-. [doi:10.3390/microorganisms9071395]34203422
2021Martínez-Méndez, R., Camacho-Hernández, D.A., Sulvarán-Guel, E., Zamorano-Sánchez, D.. (2021). "A Trigger Phosphodiesterase Modulates the Global c-di-GMP Pool, Motility, and Biofilm Formation in Vibrio parahaemolyticus.". Journal Of Bacteriology. 203(13):-. [doi:10.1128/JB.00046-21]33846117
2021Basanta, M.D., Betancourt-León, O., Chávez, O.L., Pérez-Torres, A., Rebollar, E.A., Martínez-Ugalde, E., Ávila-Akerberg, V.D., Martínez, T.M.G., Trejo, M.V., Parra-Olea, G.. (2021). "Batrachochytrium dendrobatidis occurrence in dead amphibians of central mexico: A report of ambystoma altamirani and lithobates montezumae". Revista Latinoamericana De Herpetologia. 4(1):173-177.
2021Suárez-Varón, G, Cortez D, Villagrán-Santa Cruz, M, Rojas-Hernández, U, Hernández-Gallegos, O. (2021). "Variación del estadio embrionario de Basiliscus vittatus (Squamata: Corytophanidae) en la oviposición". REVISTA MEXICANA DE BIODIVERSIDAD. 92():923795-. [doi:]
2021Hernandez-Beltran, J.C.R., Rodríguez-Beltrán, J., Millán, A.S., Peña-Miller, R., Fuentes-Hernández, A.. (2021). "Quantifying plasmid dynamics using single-cell microfluidics and image bioinformatics.". Plasmid. 113():-. [doi:10.1016/j.plasmid.2020.102517]32535165
2021Alonso-del Valle, A., León-Sampedro, R., Rodríguez-Beltrán, J., DelaFuente, J., Hernández-García, M., Ruiz-Garbajosa, P., Cantón, R., Peña-Miller, R., San Millán, A.. (2021). "Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities.". Nature Communications. 12(1):-. [doi:10.1038/s41467-021-22849-y]33976161
2021Ayra, L., Reyero-Saavedra, M.d.R., Isidra-Arellano, M.C., Lozano, L., Ramírez, M., Leija, A., Fuentes, S.I., Girard, L., Valdés-López, O., Hernández, G.. (2021). "Control of the Rhizobia Nitrogen-Fixing Symbiosis by Common Bean MADS-Domain/AGL Transcription Factors.". Frontiers In Plant Science. 12():-. [doi:10.3389/fpls.2021.679463]34163511
2021Vences-Guzmán, M.Á., Peña-Miller, R., Hidalgo-Aguilar, N.A., Vences-Guzmán, M.L., Guan, Z., Sohlenkamp, C.. (2021). "Identification of the Flavobacterium johnsoniae cysteate-fatty acyl transferase required for capnine synthesis and for efficient gliding motility.". Environmental Microbiology. 23(5):2448-2460. [doi:10.1111/1462-2920.15445]33626217
2021Alvear, V.M.H., Mateos, M., Cortez, D., Tamborindeguy, C., Martinez-Romero, E.. (2021). "Differential gene expression in a tripartite interaction: Drosophila , spiroplasma and parasitic wasps.". Peerj. 9():-. [doi:10.7717/peerj.11020]33717711
2021León-Buitimea, A., Morones-Ramírez, J.R., Yang, J.H., Peña-Miller, R.. (2021). "Editorial: Facing the Upcoming of Multidrug-Resistant and Extensively Drug-Resistant Bacteria: Novel Antimicrobial Therapies (NATs).". Frontiers in bioengineering and biotechnology. 9():-. [doi:10.3389/fbioe.2021.636278]33732690
2020Rebollar, E.A., Martínez-Ugalde, E., Orta, A.H.. (2020). "The Amphibian Skin Microbiome and Its Protective Role Against Chytridiomycosis". Herpetologica. 76(2):167-177. [doi:10.1655/0018-0831-76.2.167]
2020Lastiri-Pancardo, G., Mercado-Hernández, J.S., Kim, J., Jiménez, J.I., Utrilla, J.. (2020). "A quantitative method for proteome reallocation using minimal regulatory interventions.". NATURE CHEMICAL BIOLOGY. 16(9):1026-1033. [doi:10.1038/s41589-020-0593-y]32661378
2020Rodriguez, Susana, Correa-Galeote, David, Sanchez-Perez, Mishael, Ramirez, Mario, Isidra-Arellano, Mariel C., Reyero-Saavedra, Maria del Rocio, Zamorano-Sanchez, David, Hernandez, Georgina, Valdes-Lopez, Oswaldo, Girard, Lourdes. (2020). "A Novel OmpR-Type Response Regulator Controls Multiple Stages of the Rhizobium etliPhaseolus vulgaris N2-Fixing Symbiosis". Frontiers in Microbiology. 11():-. [doi:10.3389/fmicb.2020.615775]33384681
2020Martínez-Ortiz, I.C., Ahumada-Manuel, C.L., Hsueh, B.Y., Guzmán, J., Moreno, S., Cocotl-Yañez, M., Waters, C.M., Zamorano-Sánchez, D., Espín, G., Núñeza, C.. (2020). "Cyclic di-GMP-Mediated Regulation of Extracellular Mannuronan C-5 Epimerases Is Essential for Cyst Formation in Azotobacter Vinelandii.". Journal Of Bacteriology. 202(24):-. [doi:10.1128/JB.00135-20]32989089
2020Martínez-Pacheco, M., Tenorio, M., Almonte, L., Fajardo, V., Godínez, A., Fernández, D., Cornejo-Páramo, P., Díaz-Barba, K., Halbert, J., Liechti, A., Székely, T., Urrutia, A.O., Cortez, D.. (2020). "Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals.". Genome Biology And Evolution. 12(11):2015-2028. [doi:10.1093/gbe/evaa173]32790864
2020Moreno-Avitia, Fabian, Utrilla, Jose, Bolivar, Francisco, Nogales, Juan, Escalante, Adelfo. (2020). "Metabolic reconstruction ofPseudomonas chlororaphisATCC 9446 to understand its metabolic potential as a phenazine-1-carboxamide-producing strain". Applied Microbiology And Biotechnology. 104(23):10119-10132. [doi:10.1007/s00253-020-10913-4]32984920
2020de la Cruz, M., Ramírez, E.A., Sigala, J.C., Utrilla, J., Lara, A.R.. (2020). "Plasmid DNA Production in Proteome-Reduced Escherichia coli .". Microorganisms. 8(9):1-8. [doi:10.3390/microorganisms8091444]32967123
2020Cornejo-Páramo, P., Lira-Noriega, A., Ramírez-Suástegui, C., Méndez-De-La-Cruz, F.R., Székely, T., Urrutia, A.O., Cortez, D.. (2020). "Sex determination systems in reptiles are related to ambient temperature but not to the level of climatic fluctuation.". Bmc Evolutionary Biology. 20(1):-. [doi:10.1186/s12862-020-01671-y]32807071
2020Sanjuan, J., Delgado, M.J., Girard, L.. (2020). "Editorial: Microbial Control of the Nitrogen Cycle.". Frontiers in Microbiology. 11():-. [doi:10.3389/fmicb.2020.00950]32477318
2020Rodríguez-Beltrán, J., Sørum, V., Toll-Riera, M., de la Vega, C., Peña-Miller, R., Millán, Á.S.. (2020). "Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria.". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 117(27):15755-15762. [doi:10.1073/pnas.2001240117]32571917
2020Gutiérrez-Guerrero, Y.T., Ibarra-Laclette, E., Martínez Del Río, C., Barrera-Redondo, J., Rebollar, E.A., Ortega, J., León-Paniagua, L., Urrutia, A., Aguirre-Planter, E., Eguiarte, L.E.. (2020). "Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats.". GigaScience. 9(6):-. [doi:10.1093/gigascience/giaa059]32510151
2020Ahumada-Manuel, C.L., Martínez-Ortiz, I.C., Hsueh, B.Y., Guzmán, J., Waters, C.M., Zamorano-Sánchez, D., Espín, G., Núñez, C.. (2020). "Increased c-di-GMP Levels Lead to the Production of Alginates of High Molecular Mass in Azotobacter Vinelandii.". Journal Of Bacteriology. 202(24):-. [doi:10.1128/JB.00134-20]32989088
2020Escorcia-Rodríguez, J.M., Tauch, A., Freyre-González, J.A.. (2020). "Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization.". Computational and Structural Biotechnology Journal. 18():1228-1237. [doi:10.1016/j.csbj.2020.05.015]32542109
2020Ide, A.A., Hernández, V.M., Medina-Aparicio, L., Carcamo-Noriega, E., Girard, L., Hernández-Lucas, I., Dunn, M.F.. (2020). "Genetic regulation, biochemical properties and physiological importance of arginase from Sinorhizobium meliloti". MICROBIOLOGY-SGM. 166(5):484-497. [doi:10.1099/mic.0.000909]32216867
2020Rojas, E., Martinez-Pacheco, M., Rodriguez-Sastre, M.A., Ramos-Espinosa, P., Valverde, M.. (2020). "Post-transcriptional regulation of Rad51c by miR-222 contributes cellular transformation.". Plos One. 15(1):-. [doi:10.1371/journal.pone.0221681]31923208
2020Wu, D.C., Zamorano-Sánchez, D., Pagliai, F.A., Park, J.H., Floyd, K.A., Lee, C.K., Kitts, G., Rose, C.B., Bilotta, E.M., Wong, G.C.L., Yildiz, F.H.. (2020). "Reciprocal c-di-GMP signaling: Incomplete flagellum biogenesis triggers c-di-GMP signaling pathways that promote biofilm formation.". Plos Genetics. 16(3):-. [doi:10.1371/journal.pgen.1008703]32176702
2020Cornejo-Páramo, P., Dissanayake, D.S.B., Lira-Noriega, A., Martínez-Pacheco, M.L., Acosta, A., Ramírez-Suástegui, C., Méndez-de-la-Cruz, F.R., Székely, T., Urrutia, A.O., Georges, A., Cortez, D.. (2020). "Viviparous Reptile Regarded to Have Temperature-Dependent Sex Determination Has Old XY Chromosomes.". Genome Biology And Evolution. 12(6):924-930. [doi:10.1093/gbe/evaa104]32433751
2020Ferruz N, Lobos F, Lemm D, Toledo-Patino S, Farías-Rico JA, Schmidt S, Höcker B. (2020). "Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design.". Journal Of Molecular Biology. 432(13):3898-3914. [doi:10.1016/j.jmb.2020.04.013]32330481
2020Kim, J., Darlington, A., Salvador, M., Utrilla, J., Jiménez, J.I.. (2020). "Trade-offs between gene expression, growth and phenotypic diversity in microbial populations". CURRENT OPINION IN BIOTECHNOLOGY. 62():29-37. [doi:10.1016/j.copbio.2019.08.004]31580950
2019Campos, A.I., Freyre-González, J.A.. (2019). "Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions.". SCIENTIFIC REPORTS. 9(1):-. [doi:10.1038/s41598-019-39866-z]30842463
2019Bañuelos-Vazquez, L.A., Torres Tejerizo, G., Cervantes-De La Luz, L., Girard, L., Romero, D., Brom, S.. (2019). "Conjugative transfer between Rhizobium etli endosymbionts inside the root nodule". Environmental Microbiology. 21(9):3430-3441. [doi:10.1111/1462-2920.14645]31037804
2019Acosta, A., Martínez-Pacheco, M.L., Díaz-Barba, K., Porras, N., Gutiérrez-Mariscal, M., Cortez, D.. (2019). "Deciphering Ancestral Sex Chromosome Turnovers Based on Analysis of Male Mutation Bias.". Genome Biology And Evolution. 11(11):3054-3067. [doi:10.1093/gbe/evz221]31605487
2019Santos-Zavaleta, A., Salgado, H., Gama-Castro, S., Sánchez-Pérez, M., Gómez-Romero, L., Ledezma-Tejeida, D., García-Sotelo, J.S., Alquicira-Hernández, K., Muñiz-Rascado, L.J., Peña-Loredo, P., Ishida-Gutiérrez, C., Velázquez-Ramírez, D.A., Del Moral-Chávez, V., Bonavides-Martínez, C., Méndez-Cruz, C.F., Galagan, J., Collado-Vides, J.. (2019). "RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12". Nucleic Acids Research. 47(D1):212-220. [doi:10.1093/nar/gky1077]30395280
2019Delia Basanta, M., Rebollar, Eria A., Parra-Olea, Gabriela. (2019). "Potential risk of Batrachochytrium salamandrivorans in Mexico". Plos One. 14(2):-. [doi:10.1371/journal.pone.0211960]30753218
2019Kueneman, J.G., Bletz, M.C., McKenzie, V.J., Becker, C.G., Joseph, M.B., Abarca, J.G., Archer, H., Arellano, A.L., Bataille, A., Becker, M., Belden, L.K., Crottini, A., Geffers, R., Haddad, C.F.B., Harris, R.N., Holden, W.M., Hughey, M., Jarek, M., Kearns, P.J., Kerby, J.L., Kielgast, J., Kurabayashi, A., Longo, A.V., Loudon, A., Medina, D., Nuñez, J.J., Perl, R.G.B., Pinto-Tomás, A., Rabemananjara, F.C.E., Rebollar, E.A., Rodríguez, A., Rollins-Smith, L., Stevenson, R., Tebbe, C.C., Vargas Asensio, G., Waldman, B., Walke, J.B., Whitfield, S.M., Zamudio, K.R., Zúñiga Chaves, I., Woodhams, D.C., Vences, M.. (2019). "Community richness of amphibian skin bacteria correlates with bioclimate at the global scale". Nature Ecology & Evolution. 3(3):381-389. [doi:10.1038/s41559-019-0798-1]30778181
2019Astudillo-Melgar, Fernando, Ochoa-Leyva, Adrian, Utrilla, Jose, Huerta-Beristain, Gerardo. (2019). "Bacterial Diversity and Population Dynamics During the Fermentation of Palm Wine From Guerrero Mexico.". Frontiers in Microbiology. 10():-. [doi:10.3389/fmicb.2019.00531]30967846
2019Hernández-Rodríguez, D., Vásquez-Aguilar, A.A., Serio-Silva, J.C., Rebollar, E.A., Azaola-Espinosa, A.. (2019). "Molecular detection of Bifidobacterium spp. in faeces of black howler monkeys (Alouatta pigra)". JOURNAL OF MEDICAL PRIMATOLOGY. 48(2):99-105. [doi:10.1111/jmp.12395]30520095
2019Santos-Zavaleta, A., Pérez-Rueda, E., Sánchez-Pérez, M., Velázquez-Ramírez, D.A., Collado-Vides, J.. (2019). "Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.". Bmc Genomics. 20(1):-. [doi:10.1186/s12864-019-5619-z]30991941
2019Alaide Rebollar, Eria, Harris, Reid N.. (2019). "Editorial: Ecology of Amphibian-Microbial Symbioses.". Frontiers in Microbiology. 10():-. [doi:10.3389/fmicb.2019.00766]31057502
2019Hidalgo-Garcia, Alba, Torres, Maria J., Sales, Ana, Bedmar, Eulogio J., Girard, Lourdes, Delgado, Maria J.. (2019). "Rhizobium etli Produces Nitrous Oxide by Coupling the Assimilatory and Denitrification Pathways". Frontiers in Microbiology. 10():980-980. [doi:10.3389/fmicb.2019.00980]31134023
2019Estrada, Angie, Hughey, Myra C., Medina, Daniel, Rebollar, Eria A., Walke, Jenifer B., Harris, Reid N., Belden, Lisa K.. (2019). "Skin bacterial communities of neotropical treefrogs vary with local environmental conditions at the time of sampling.". Peerj. 7():-. [doi:10.7717/peerj.7044]31275740
2019Rebollar, Eria A., Bridges, Tiffany, Hughey, Myra C., Medina, Daniel, Belden, Lisa K., Harris, Reid N.. (2019). "Integrating the role of antifungal bacteria into skin symbiotic communities of three Neotropical frog species". ISME JOURNAL. 13(7):1763-1775. [doi:10.1038/s41396-019-0388-x]30867545
2019Acosta, A., Suárez-Varón, G., Rodríguez-Miranda, L.A., Lira-Noriega, A., Aguilar-Gómez, D., Gutiérrez-Mariscal, M., Hernández-Gallegos, O., Méndez-de-la-Cruz, F., Cortez, D.. (2019). "Corytophanids Replaced the Pleurodont XY System with a New Pair of XY Chromosomes.". Genome Biology And Evolution. 11(9):2666-2677. [doi:10.1093/gbe/evz196]31557287
2019Keiser, Carl N., Wantman, Trina, Rebollar, Eria A., Harris, Reid N.. (2019). "Tadpole body size and behaviour alter the social acquisition of a defensive bacterial symbiont". Royal Society open science. 6(9):191080-191080. [doi:10.1098/rsos.191080]31598324
2019Gabriel Suárez-Varón, Orlando Suárez-Rodríguez, Gisela Granados-González, Maricela Villagrán-Santa Cruz, Kevin M. Gribbins, Diego Cortez-Quezada, Oswaldo Hernández-Gallegos. (2019). "Relative clutch mass of Basiliscus vittatus Wiegmann, 1828 (Squamata, Corytophanidae): female morphological constraints". Herpetozoa. 32(3):211-219. [doi:10.3897/herpetozoa.32.e35910]
2018Isidra-Arellano, M.C., Reyero-Saavedra, M.D.R., Sánchez-Correa, M.D.S., Pingault, L., Sen, S., Joshi, T., Girard, L., Castro-Guerrero, N.A., Mendoza-Cozatl, D.G., Libault, M., Valdés-López, O.. (2018). "Phosphate deficiency negatively affects early steps of the symbiosis between common bean and Rhizobia". Genes. 9(10):-. [doi:10.3390/genes9100498]30326664
2018Aguilar A, Mora Y, Dávalos A, Girard L, Mora J, Peralta H. (2018). "Analysis of genome sequence and symbiotic ability of rhizobial strains isolated from seeds of common bean (Phaseolus vulgaris).". Bmc Genomics. 19(1):645-645. [doi:10.1186/s12864-018-5023-0]30165827
2018Latif, H., Federowicz, S., Ebrahim, A., Tarasova, J., Szubin, R., Utrilla, J., Zengler, K., Palsson, B.O.. (2018). "ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions". Plos One. 13(5):-. [doi:10.1371/journal.pone.0197272]29771928
2018Chiozzotto, Remo, Ramirez, Mario, Talbi, Chouhra, Cominelli, Eleonora, Girard, Lourdes, Sparvoli, Francesca, Hernandez, Georgina. (2018). "Characterization of the symbiotic nitrogen-fixing common bean Low Phytic Acid (lpa1) mutant response to water stress". Genes. 9(2):-. [doi:10.3390/genes9020099]29462877
2018Rodriguez-Beltran, J., Hernandez-Beltran, J.C.R., Delafuente, J., Escudero, J.A., Fuentes-Hernandez, A., MacLean, R.C., Peña-Miller, R., San Millan, A.. (2018). "Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation". Nature Ecology & Evolution. 2(5):873-881. [doi:10.1038/s41559-018-0529-z]29632354
2017Utrilla, Jose. (2017). "Evolutionary Engineering of Microorganisms to Overcome Toxicity During Lignocellulose Hydrolysates Utilization". Engineering of Microorganisms for the Production of Chemicals and Biofuels from Renewable Resources. ():181-200. [doi:]
2017Moreno-Avitia, F., Lozano, L., Utrilla, J., Bolívar, F., Escalante, A.. (2017). "Draft genome sequence of pseudomonas chlororaphis ATCC 9446, a nonpathogenic bacterium with bioremediation and industrial potential". Microbiology Resource Announcements. 5(23):-. [doi:10.1128/genomeA.00474-17]28596401
2017Steffani-Vallejo, J.L., Zuñiga, C., Cruz-Morales, P., Lozano, L., Morales, M., Licona-Cassani, C., Revah, S., Utrilla, J.. (2017). "Draft genome sequence of Sphingobacterium sp. CZ-UAM, isolated from a methanotrophic consortium". Microbiology Resource Announcements. 5(33):-. [doi:10.1128/genomeA.00792-17]28818899
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2014Mora, Yolanda, Diaz, Rafael, Vargas-Lagunas, Carmen, Peralta, Humberto, Guerrero, Gabriela, Aguilar, Alejandro, Encarnacion, Sergio, Girard, Lourdes, Mora, Jaime. (2014). "Nitrogen-fixing rhizobial strains isolated from common bean seeds: Phylogeny, physiology, and genome analysis". Applied And Environmental Microbiology. 80(18):5644-5654. [doi:10.1128/AEM.01491-14]25002426
2013Ramírez Yáñez, Mario, Guillén, G., Fuentes Membreño, Sara Isabel, Iñiguez Rabago, Luis Pedro, Aparicio Fabre, Rosaura, Zamorano Sánchez, David Salvador, Encarnación Guevara, Sergio Manuel, Panzeri, D., Castiglioni, B., Cremonesi, P., Strozzi, F., Stella, A., Girard Cuesy, María de Lourdes, Sparvoli, F., Hernández Delgado, Georgina. (2013). "Transcript profiling of common bean nodules subjected to oxidative stress". Physiologia Plantarum. 149(3):389-407. [doi:10.1111/ppl.12040]23432573
2013Reyes González, Alma Ruth, Zamorano Sánchez, David Salvador, Rivera Rosas, Patricia, Girard Cuesy, María de Lourdes. (2013). "hFixL-FxkR are the key regulators for fixKf-related gene expression". Mexican Journal of Scientific Research. ():-.
2013Ramírez Yáñez, Mario, Flores-Pacheco, G., Reyes, J.L., Álvarez, A.L., Drevon, J.J., Girard Cuesy, María de Lourdes, Hernández Delgado, Georgina. (2013). "Two Common Bean Genotypes with Contrasting Response to Phosphorus Deficiency Show Variations in the microRNA 399-Mediated PvPHO2 Regulation within the PvPHR1 Signaling Pathway". International Journal Of Molecular Sciences. 14(4):8328-8344. [doi:10.3390/ijms14048328]23591845
2013Aparicio Fabre, Rosaura, Guillén, G., Loredo, M., Arellano García, José de Jesús, Valdes López, Oswaldo, Ramírez Yáñez, Mario, Iñiguez Rabago, Luis Pedro, Panzeri, D., Castiglioni, B., Cremonesi, P., Strozzi, F., Stella, A., Girard Cuesy, María de Lourdes, Sparvoli, F., Hernández Delgado, Georgina. (2013). "Common bean (Phaseolus vulgaris L.) PvTIFY orchestrates global changes in transcript profile response to jasmonate and phosphorus deficiency". Bmc Plant Biology. 13():26-26. [doi:10.1186/1471-2229-13-26]23402340
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2011Cervantes de la Luz, Laura, Bustos Arcos, Virginia Patricia, Girard Cuesy, María de Lourdes, Santamaria Gutiérrez, Rosa Isela, Dávila Ramos, José Guillermo, Vinuesa Fleischmann, Pablo, Romero Camarena, David René, Brom Klanner, Susana. (2011). "The conjugative plasmid of a bean-nodulating Sinorhizobium fredii strain is assembled from sequences of two Rhizobium plasmids and the chromosome of a Sinorhizobium strain". Bmc Microbiology. 11(1):1-11. [doi:10.1186/1471-2180-11-149]21702991
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2005Vargas Lagunas, María del Carmen, Encarnación Guevara, Sergio Manuel, Girard Cuesy, María de Lourdes, Reyes Pérez, Agustín, Pérez-Tejada Domínguez, Yolanda, Mora Celis, Jaime. (2005). "Characterization of the alternative protection programs against oxidative-stress in free life and simbiosis from Rhizobium etli". Current Plant Science and Biotechnology. Agriculture Biological Nitrogen Fixation, Sustainable Agriculture and the Environment. 41():331-.
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2004Brom Klanner, Susana, Girard Cuesy, María de Lourdes, Tun Garrido, Cristina Soleda, García de los Santos, Alejandro, Bustos Arcos, Virginia Patricia, González Zúñiga, Víctor Manuel, Romero Camarena, David René. (2004). "Transfer of the symbiotic plasmid of Rhizobium etli CFN42 requires cointegration with p42a, which may be mediated by site-specific recombination". Journal Of Bacteriology. 186(22):7538-7548. [doi:10.1128/JB.186.22.7538-7548.2004]15516565
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